title: embryo damage sample rep3 by RNA-seq

value: embryo damage


title: TS3-iPSC

status: Public on Aug 06 2023

type: RNA

city: Guangzhou

first: Detu

last: Zhu

state: Guangdong

country: China

institute: The Third Affiliated Hospital of Guangzhou Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

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

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

molecule: total RNA

organism: Homo sapiens

source_name: TS patient-derived iPSC

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

growth_protocol: Both the WT and TS-iPSC lines were maintained in mTeSR medium (StemCell Technologies), and the CM lines were maintained in the PSC Cardiomyocyte Maintenance Medium (Gibco) following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted and purified using miRNA Extraction Kit #TR205-200 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease

value: Turner syndrome (TS)

tag: cell type

value: iPSC


title: R49pom

type: SRA

city: Liege

first: Brett

middle: C

last: Mommer

state: Wallonia

address: Tour Pharmacie (Bat. B36) Quartier Hôpital, Avenue Hippocrate 15

department: GIGA-Neurosciences

country: Belgium

institute: University of Liege

library_source: transcriptomic

data_processing:
To enable chromosome mapping of predicted transcripts on a reference sequence, scaffolds from the NODAII quail genome (Kawahara-Miki et al. 2013) were mapped to the chicken genome assembly Galgal5.0 using BWA.  Galgal5.0 FASTA sequence was combined with the resulting variant calls from the quail genome to create a chicken genome backbone with the allelic variation of the quail using FastaAlternateReferenceMaker (McKenna et al. 2010).  We will refer to this assembly as `qGG5` assembly.  Lastly, predicted transcripts were mapped to qGG5 using BLAST, top best hit was considered as the chromosomal location of the transcript.
A total of 36 RNA-seq libraries were sequenced on a NEXT-Seq 500 to produce 1.2 billion reads.  Reads from all libraries were concatenated into a single forward and reverse read file and analyzed with Trinity to generate a brain specific transcriptome of the Japanese quail (Haas et al. 2013).
All reads were screened with Trimmomatic ({Bolger:2014ek}), Our assembly yielded a total of <800K> predicted transcripts, of which <100K> yielded predicted ORF and <80K> were predicted as protein peptides using TransDecoder.
Following transcriptome assembly, predicted transcript isoforms were annotated using the Trinnotate suite, where each transcript is cross referenced to sequence similarity to various online databases (online at : trinotate.github.io).  All steps, both required and optional were carried out.  To start, coding genes were predicted using transdecoder using the chicken transcriptome Galgal5.0 Ensembl 69 assembly as the training set.  Translated transcripts were compared to SwissProt, UNIPROT, and TrEMBL using BLASTTX , the top hit was kept.  Ribosomal RNA species were predicted based using RNAmer v1.2 (Lagesen et al. 2007).  Predicted peptides from TransDecoder were additionally compared to SwissProt,  and TrEMBL using BLASTP, top hit was kept.  Protein domains were predicted by comparing peptide sequences to Pfam domains using HMMER.  Signaling peptides and trans-membrane domains were predicted using SignalP, and TmHMM, respectively.  Lastly, gene ontology categories were obtained from eggNOG, both through mapping and assessment of predicted protein.  Final annotation was summarized using a DNC cutoff of 0.05.
Differential expression of genes/transcripts was done for each of the three brain regions (POM, TnA, VMN) in a pairwise fashion for the comparisons M vs F, M vs TM, F vs TF, TM vs TF, and M vs TF. The analysis was carried out using four different publicly-available algorithms (DESeq2, EdgeR, ROTS, voom) and the genes/transcripts found to be differentially expressed by at least two algorithms at FDR<0.01 were combined into gene lists. We employed the 0.01 FDR threshold as opposed to 0.05 so as to control the experiment-wise error rate for the five selected pairwise comparisons. Additionally the top 10% of genes/transcripts remaining below FDR<0.01 by a single algorithm and all falling within the FDR<0.01 threshold for DESeq2 were added to the lists. Each algorithm produced a read count for each gene/transcript adjusted for library size, resulting in normalized read counts.
Genome_build: qGG5 reference sequence
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

organism: Coturnix japonica

source_name: adult brain

extract_protocol:
Brains were sliced in 200um-thick coronal sections in a 2800 Frigocut E cryostat (Reichert-Jung) and the sections kept on Superfrost Plus (Thermo Scientific,) microscope slides previously cooled to the temperature of the cryostat. Brain nuclei were punched using a specialized 1.25mm diameter brain punch apparatus (Leica Biosystems) using the previously observed neuroanatomical distribution of quail aromatase-positive cell populations as a guide. RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands), DNA digested on-column using the RNase-free DNase Set (Qiagen), RNA quantity measured on a NanoDrop 2000 spectrophotometer (Thermo Scientific), concentrated by vacuum centrifuge, resuspended in 10ul RNase-free water (Ambion), and quantified again on Nanodrop.
RNA samples underwent ribosomal depletion using Ribozero (Illumina, San Diego, CA), cDNA synthesis, barcoding, pooling by brain region (3 pools, each with n=12 samples/pool), and each pool was divided and run across all 4 lanes of a NextSeq500 chip (Illumina) for a total of three chips at the GIGA-Genotranscriptomics platform (ULg, Liege Belgium). The cDNA were read in paired-end, 75nt read length format, and adapter and barcode sequences trimmed prior to assembly.

treatment_protocol: At 2.5 weeks of age birds were anesthetized with isoflurane, an incision was made in the abdomen, and gonads were either inspected (sham) or removed. Following gonadectomy or inspection the incision was closed and animals were left to recover at least two weeks before additional treatments.  Individuals were assigned into one of four treatment groups according to the type of gonads observed (testes vs. Ovary) and whether they underwent gonadectomy or inspection: sham males (M), sham females (F), castrated males chronically treated with testosterone (Cx + T) and ovariectomized females chronically treated with testosterone (Ovx + T).  At 6 weeks of age, gonadectomized quail received two 20mm silastic implants filled with crystalline testosterone to mimic the elevation of circulating testosterone concentration and subsequent activation of behavior and adult features such as the development of the cloacal gland occurring between 4 and 7 weeks of age in gonadally intact males. Sham quail received two empty silastic implants. One week after the final test of sexual behavior (12 weeks of age) all individuals were sacrificed by rapid decapitation and brains were quickly dissected from the head, flash frozen on dry ice and stored at -80C for later analysis.

tag: genotype

value: wild type

tag: tissue

value: pre-optic medial nucleus

tag: treatment

value: Ovx+T female


title: sgNC#3

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

country: USA

institute: UT MD Anderson Cancer Center

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgNC3

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l hct116.sgrna.library --control-sgrna hct116.sgrna.library.negctrl --norm-method control -n hct116.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome, using STAR v.2.6.1b with the parameters: “--outSAMunmapped Within --outFilterType BySJout --twopassMode Basic --outSAMtype BAM SortedByCoordinate”. The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2). The filters of basemean >= 1, |log2Fold-Change| >= log2(1.5) and FDR <= 0.05 were used to define differentially expressed genes for downstream analysis.
For the ChIP-seq data: The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5, and were then mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4). The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”. BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between −40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: read count and differential expression result in Excel file, ChIP-seq: narrowpeak file for peaks, CRISPR screen: read count in text files and MAGECK call result in Excel files.

source_name: Colon carcinoma

growth_protocol: HCT-116 cells were cultured in McCoy's 5a medium (Coring #10-050-CV). DLD-1 cells were cultured in RPMI- 1640 (Hyclone #SH30027.1). All culture medium were supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C. SMC1A (#32363)

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I(QIAGEN #79254). Immunoprecipitated DNA purified using QIAquik PCR purification kit (QIAGEN, #28106).
RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer’s instructions. ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer’s instructions. Sample preparation for ribosome profiling was conducted according to the manufacturer’s specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina).

treatment_protocol: Cells(2×107) were first crosslinked with 1% formaldehyde (methanol-free, 16% Thermo Scientific, #28908) at room temperature for 10 minutes and then quenched with 0.125M Glycine (final concentration) for 5 minutes. After washing with cold PBS for three times, the cells were harvested using a silicon scraper. Cell pellets were resuspended in 5mL lysis buffer 1(50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rocked at 4 degree for 5 minutes, followed by centrifugation at 2000 g for 4 minutes at 4°C. The cell pellets were then incubated with 5 mL LB2 buffer (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at 4°C for 5 minutes with gently rocking. Nuclei were pelleted down by centrifugation of the cells at 2000 g for 5 min and were resuspended in 1 mL LB3 buffer (10 mM Tris-HCl, pH=8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). All lysis buffer contained protease inhibitors (Roche #04693112001). Chromatin was sonicated to around 200 bp DNA fragments, using a Diagenode Bioruptor (three rounds of 5 cycles, 30” on 30” off). Lysates were cleared by addition of Triton X-100 to a final concentration of 1% and centrifugation at 2000 g for 10 minutes at 4°C. A total of 50 μl lysates were saved from each sample for input and stored at – 80°C until use. To prepare antibody-bound beads, 30 μl of magnetic beads (Invitrogen, Dynabeads) were washed three times with blocking buffer (1× PBS, 0.5% BSA) and incubated overnight with 5 μg of the anti-SMC1A antibodies at 4°C. For each ChIP, 900 uL sonicated lysate from 2×107 cells was incubated with the antibody-bound beads overnight at 4°C. Beads were washed 6 times with RIPA wash buffer (50 mM Hepes-KOH, pH= 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and 1 time with TBS (20 Mm Tris-HCL, PH 7.6, 150Mm NaCl) for 5 minutes each time at room temperature with gently rocking. All washing buffers contain the protease inhibitors. The beads were eluted twice with 50 ul elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes at 65°C with rocking. Crosslinking was reversed by adding 6 uL 5M NaCl to the eluates and incubated at 65°C overnight. RNAs were degraded by incubation with 1μl of 10 mg/ml RNase at 37°C for 30 minutes and proteins were digested by incubation with 2 μl of 20 mg/ml of Proteinase K(Thermo Fisher) at 56°C for 2 hours. DNAs were then purified using QIAquik PCR purification kit (QIAGEN, #28106). For shRNA, sgRNA mediated knockdown and knokout experiments, lentiviruses were collected 48 hours after transfection and were then used to infect indicated cell lines. The infected cells were then treated with puromycin to select the ones with stable shRNA/sgRNA transduction.

tag: cell line


title: bone-marrow-derived macrophage siNC rep2

city: Hangzhou

first: Ning

last: Zhang

state: Zhejiang

address: 88 Jiefang Rd, Hangzhou, Zhejiang Province

institute: Second Affiliated Hospital, Zhejiang University College of Medicine

data_processing:
Basecalling was performed by Illumina NovaSeq 6000.
Sequenced reads were trimmed to remove adaptor sequences and masked to remove low-complexity or low-quality sequences.
Transcription levels are log2 read counts per kilobase of exon per million library reads (RPKM). All overlapping exons of a gene were merged to create one meta-transcript. Gene expression was quantified by the number of reads falling into annotated exons.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: bone-marrow-derived macrophages

extract_protocol:
Total RNA from MΦsiCXCR4 or MΦsiNC was extracted from cells with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bone-marrow-derived macrophages

tag: strain

tag: sirna

value: siNC

value: LPS for 12 hours


title: R15pom

value: intact male


title: sgNC#2

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgNC2


title: M191pom


title: embryo damage sample rep1 by RNA-seq

city: Shenzhen

first: Jiajie

last: She

address: huafu street

institute: Shenzhen Second people's hospital

data_processing:
Trimmomatic (v.0.27) was used for quality control of paired-end sequencing data.
Reads obtained by sequencing that mapped to rRNA and tRNA sequences from the UCSC gene annotation (hg38) using bowtie2 (v.2.3.4) were discarded, and the remaining reads were aligned to the GRCh38 using hisat2-align (v.2.1.0).
MACS2 (v.2.1.1) was used to identify m6A peaks with the parameter ‘--nomodel’ and ‘-q 0.05’. ExomePeak2 package (v.1.2.0) was used for the identification of differentially methylated peaks.
The findMotifsGenome.pl Perl script from the Homer software suite was used for motif search with the ‘-mask -rna -len 6’ parameters.
Differentially expressed genes were identified using the RNA-seq data (the corresponding MeRIP-seq input library data) by the R package DEseq2 (v.1.32.0).
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using macs2
Supplementary_files_format_and_content: peak text files

source_name: villous tissues

growth_protocol: Villous tissue was at 7 to 8 weeks in the first trimester of pregnancy

extract_protocol:
Total RNA from each sample was isolated using TRIzol reagent (Invitrogen) and fragmented into ~100-nucleotide-long fragments by zinc acetate.
bound RNA was eluted by competition with 1 mg ml−1 N6-methyladenosine (Selleckchem) and used for library construction using the NEBNext Ultra RNA Library Prep Kit v2 for Illumina. After removal of ribosomal RNA using the Epicentre Ribo-zero rRNA Removal Kit (Epicentre), total RNA from each tissue was fragmented and a library was constructed using the NEBNext Ultra RNA Library Prep Kit v2 for Illumina (New England Biolabs) as input RNA.

tag: sample

tag: chip antibody

value: untreated


title: bone-marrow-derived macrophage siNC rep1


title: sgNC#1

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgNC1


title: M157pom

value: intact female


title: embryo damage sample rep3 by meRIP-seq

value: abcam ab151230


title: WT1-iPSC

source_name: Healthy donor-derived iPSC

value: WT


title: sgSMIMP#3

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgEL3


title: bone-marrow-derived macrophage siCXCR4 rep1


title: M42pom


title: KitW/Wv mice 3 days after busulfan treatment (W3)

city: Beijing

first: Cheng

last: Jin

state: State...

address: dongdansantiao num5

institute: Chinese Academy of Medical Sciences

data_processing:
Raw sequencing reads were processed using the Cell Ranger v.3.0.1 pipeline from 10X Genomics. In brief, reads from each sample were demultiplexed, aligned to the mouse mm10 genome and unique molecular identifier (UMI) counts were quantified per gene per cell to generate a gene-barcode matrix.
Then data from multiple samples (WT, W, W3, and W5 analyses) were aggregated and normalized to the same sequencing depth, resulting in a combined gene-barcode matrix of all samples. Default parameters were used.
The UMI counts were analyzed using the Seurat R Package (v.3.0.1) following the Seurat pipline
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrix generated using the Cell Ranger v.3.0.1 pipeline from 10X Genomics
Supplementary_files_format_and_content: agg* processed data files includes the integrated analysis of 4 samples.

extract_protocol:
The testis from WT, W, W3 and W5 mice were minced and digested in collagenase type IV (1 mg/ml) at 37C for 15 min. During the process of digestion, the tissues were pipetted up and down once every five minutes. The digestion process was stopped with DMEM (containing 10% FBS). The cell suspension was filtered through 40-μm nylon mesh. After centrifugation, the cells were suspended in 0.04% BSA in PBS for loading on the 10x Chromium chip.
Cell capturing and library preparation were carried as kit instructions (Chromium Single Cell Kit [v2 chemistry]). In brief, 10,000 cells were targeted for capture per sample, after cDNA synthesis,10-12 cycles were used for library amplification. The resultant libraries were size selected, pooled, and sequenced on an Illumina Novaseq 6000 instrument.

treatment_protocol: busulfan treatment for W3 and W5

value: testis

value: 3 days after busulfan treatment

value: KitW/Wv


title: embryo damage sample rep2 by meRIP-seq

value: embryo damage


title: embryo damage sample rep2 by RNA-seq


title: M172pom


title: sgSMIMP#2

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgEL2


title: KitW/Wv mice (W)

source_name: WT


title: R18pom


title: embryo damage sample rep1 by meRIP-seq


title: sgSMIMP#1

description:
DLD1_sgNC_sgSMIMP_diffexpr-results.csv
sgEL1


title: Wildtype C57BL/6 mice (WT)

value: Wildtype


title: KitW/Wv mice 5 days after busulfan treatment (W5)

value: 5 days after busulfan treatment


title: Ras_gut_rep1

status: Public on Aug 05 2023

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center)
We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference Drosophila genome (flybase genome annotation version r5.51) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings.
We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Assembly: Drosophila genome (flybase genome annotation version r5.51)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Drosophila melanogaster

source_name: Adult midgut

extract_protocol:
After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down from total RNA samples (200ng - 1ug per sample, RIN > 7 required).
Sequencing libraries were constructed with Illumina TruSeq RNA prep kit

value: Adult midgut

value: 29 degree induction for 8 days


title: Ras_gut_rep2


title: Δlinda mutant, UV-C treatment 4, 3h

city: Gent

first: Josephine

last: Herbst

address: Technologiepark 71

institute: VIB-UGent Center for Plant Systems Biology

data_processing:
The received results were analyzed with the Galaxy platform (Galaxy @ Belgium), following the workflow provided by Dr. Lieven Sterck (RNA-seq Paired End Reads, Salmon v20211020, The Galaxy Community, 2022). In short: the sequences were trimmed by using the Trimmomatic tool (Galaxy Version 0.38.0),  quality control was performed on the raw and trimmed data by using FastQC (Galaxy Version 0.72+g alaxy1), transcript abundance was quantified using Salmon quant (Galaxy Version 0.14.1.2)  and the transcript-level estimates were summarized by tximport (Galaxy Version 0.1).
Two samples (Zeo_Col-0_4 and mock_linda_4) did not pass the quality control requirements and were omitted during further analysis.
Assembly: Arabidopsis thaliana COL-0 Araport11
Supplementary files format and content: tab-delimited file contains raw counts for every sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Plants were grown for 14 days on half-strength MS agar plates (0.8 % agar) under short-day conditions (10 h light / 14 h darkness, 100 µmoles photons m-2 s-1, 20 °C, 60 % humidity)

extract_protocol:
RNA was isolated using the Quick-RNA Plant Kit (Zymo research).
One µg of RNA was used for library preparation by macrogen. Here, the library was prepared by random fragmentation, followed by 3' and 5' adapter ligation. The adapter-ligated fragments were amplified by PCR, with primers which anneal to the end of the used adapters.

treatment_protocol: For the Zeocin treatment, plants were incubated for 3 h in half-strength liquid MS with (mock) or without 80 µg/ml Zeocin (Zeo). For the UV-C treatment, plants were irradiated with 2 kJ UV-C (UV-C) or left under and  control conditions (NL) and harvested 3 h after treatment.

value: whole seedling

value: 2 kJ UV-C


title: Δlinda mutant, UV-C treatment 3, 3h


title: Δlinda mutant, UV-C treatment 2, 3h


title: Col-0, UV-C treatment 4, 3h


title: Col-0, UV-C treatment 1, 3h


title: Col-0, UV-C treatment 3, 3h


title: Col-0, UV-C treatment 2, 3h


title: Δlinda mutant, UV-C treatment 1, 3h


title: Δlinda mutant, normal light conditions 4

value: normal light


title: Δlinda mutant, normal light conditions 3


title: Δlinda mutant, normal light conditions 1


title: Δlinda mutant, normal light conditions 2


title: Col-0, normal light conditions 2


title: Col-0, normal light conditions 3


title: Col-0, normal light conditions 4


title: Col-0, normal light conditions 1


title: Δlinda mutant, Zeocin treatment 4, 3h

value: 80 microg/ml Zeocin


title: Δlinda mutant, Zeocin treatment 3, 3h


title: Δlinda mutant, Zeocin treatment 2, 3h


title: 22Rv1NCOA6KO #4-91_untreated_rep1

first: Yonghong

last: Liu

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicne

description: NCOA6 knockout

hyb_protocol: The samples were fragmented. 0.6 μg of the fragmented sample and hybridization mix was loaded onto each of the Agilent G3 Human Gene Expression v3 8x60K Expression arrays (G4851C). The slides were hybridized in Agilent Hybridization Chamber at 65°C at a rotation rate of 10 rpm for 17 hours. The hybridized slides were washed with the Agilent Expression Wash Buffer Set 1 and 2 as per the Agilent protocol.

scan_protocol: Once dry, the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software (version A.8.5.1). Data extraction and quality assessment of the microarray data were performed using Agilent Feature Extraction Software (Version 11.0.1.1).

data_processing: The Bioconductor “limma” package (http://bioconductor.org) was used to analyze the microarray data. The data background was corrected using the “normexp” method with an offset of 16 added to the intensities. The background-corrected data were then log2-transformed and quantile-normalized.

source_name: Prostate carcinoma epithelial cell line derived from a xenograft that was serially propagated in mice after castration-induced regression and relapse of the parental, androgen-dependent CWR22 xenograft

label_protocol: 50 ng of total RNA sample that had passed the quality check was mixed with Agilent's RNA Spike-Ins. The samples were amplified and labeled with Cy3 by using the Agilent Quick Amp Labeling Kit (Agilent p/n 5190-2331) according to the protocol (version 6.7). As a result, the Cy3-labeled cRNA was generated. The cRNA samples were purified using Qiagen RNeasy mini spin columns. Yield and dye incorporation of the samples were measured on Nanodrop.

growth_protocol: The 22Rv1-derived cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (10437028; Thermo Fisher) and 1% penicillin (10000 IU)/streptomycin (10000 µg/ml) solution (30-002-CI; Corning). Cells were maintained at 37°C in a 5% CO2 cell culture incubator.

extract_protocol: Total RNA samples were extracted from the 22Rv1-derived cell lines using the TRIzol reagent (15596018; Thermo Fisher) followed by purification with the RNeasy Mini Kit (74106; Qiagen) according to the manufacturer's instructions. Quality of the samples was checked by using the Nanodrop ND-1000 and Agilent Bioanalyzer Nano Chip.

treatment_protocol: The 22Rv1Ctrl cell line was established by transfecting 22Rv1Par. cells with PX459 plasmids to transiently express Cas9. The 22Rv1NCOA6KO #2-74, #2-96, #4-91 and #4-105 cell lines were established by transfecting 22Rv1Par. cells with constructed PX459 plasmids to transiently co-express Cas9 and sgRNA targeting the exon 5 or 6 of the NCOA6 gene. The transfected cells were cultured in RPMI 1640 complete medium containing 5 µg/ml puromycin (P8833; Sigma) for 2 days. Selected cells were seeded into 150 mm dishes at a density of 200 cells per dish to grow clones. Individual clones were picked up and expanded. Positive clones including the 22Rv1NCOA6KO #2-74, #2-96, #4-91 and #4-105 cell lines were identified by PCR-based genotyping, DNA sequencing, and Western blot analysis.

value: Prostate cancer cells

value: NCOA6 knockout

value: Untreated


title: 22Rv1Ctrl_untreated_rep2

description: NCOA6 wild type

value: NCOA6 wild type


title: 22Rv1NCOA6KO #2-74_untreated_rep1

description: NCOA6 knockout


title: 22Rv1NCOA6KO #2-96_untreated_rep1

description: NCOA6 knockout


title: 22Rv1Par._untreated_rep2

description: NCOA6 wild type


title: 22Rv1NCOA6KO #4-105_untreated_rep1

description: NCOA6 knockout


title: Δlinda mutant, Zeocin treatment 1, 3h


title: 22Rv1Par._untreated_rep1

description: NCOA6 wild type


title: Col-0, Zeocin treatment 2, 3h


title: Δlinda mutant, mock treatment 3, 3h

value: mock (1/2 MS)


title: Col-0, Zeocin treatment 3, 3h


title: Col-0, Zeocin treatment 1, 3h


title: Δlinda mutant, mock treatment 1, 3h


title: D35 iTSLC rep3 [Day35_PAX4_TRUNC_iTSL_C_RHP7860]

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Paired-end FASTQ reads were aligned to human genome build GRCh38 using hisat2 with defaut parameters
SAM files were processed and sorted to BAM format using sambamba v 0.63
Transcript counts were generated with htseq-count (v0.5.4p3)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file that includes count for each sample
Supplementary files format and content: tab-delimited text file that includes TPM for each sample

source_name: donor-derived hiPSC

extract_protocol:
RNA was harvested using MN NucleoSpin RNA Kit.
Libraries were prepared using the TruSEQ Stranded Total RNA Prep with Ribo-Zero Human Cat. No. RS-122-2201 as per manufacturer's protocol. Libraries sequenced using 150bp paired-end on HiSeq 4000 Platform.

tag: time

value: donor-derived hiPSC

value: iTSL C

value: Pancreatic beta-like cells

value: beta cell differentiation


title: D35 iTSLB rep3 [Day35_PAX4_TRUNC_iTSL_B_RHP7857]

value: iTSL B


title: 22Rv1Ctrl_untreated_rep1

description: NCOA6 wild type


title: D35 iTSLC rep1 [Day35_PAX4_TRUNC_iTSL_C_RHP7858]


title: Col-0, mock treatment 3, 3h


title: Col-0, mock treatment 1, 3h


title: D35 iTSLC rep2 [Day35_PAX4_TRUNC_iTSL_C_RHP7859]


title: Col-0, mock treatment 4, 3h


title: Col-0, mock treatment 2, 3h


title: D35 iTSLA rep3 [Day35_PAX4_TRUNC_iTSL_A_RHP7854]

value: iTSL A


title: D35 iTSLB rep2 [Day35_PAX4_TRUNC_iTSL_B_RHP7856]


title: D35 iTSLB rep1 [Day35_PAX4_TRUNC_iTSL_B_RHP7855]


title: D35 iTSLA rep2 [Day35_PAX4_TRUNC_iTSL_A_RHP7853]


title: D35 iTSLA rep1 [Day35_PAX4_TRUNC_iTSL_A_RHP7852]


title: D35 is181C rep3 [Day35_R192H_HOMO_is0181_C_RHP7851]


title: Δlinda mutant, mock treatment 2, 3h


title: D35 is181C rep2 [Day35_R192H_HOMO_is0181_C_RHP7850]


title: D35 is181B rep1 [Day35_R192H_HOMO_is0181_B_RHP7847]


title: D35 is181A rep2 [Day35_R192H_HOMO_is0181_A_RHP7845]


title: D35 is181A rep3 [Day35_R192H_HOMO_is0181_A_RHP7846]


title: D35 i043B rep2 [Day35_R192H_HOMO_is043_B_RHP7843]

value: is043 B


title: D35 is043A rep3 [Day35_R192H_HOMO_is043_A_RHP7841]

value: is043 A


title: D35 is181C rep1 [Day35_R192H_HOMO_is0181_C_RHP7849]


title: D35 is040B rep2 [Day35_R192H_HET_is040_B_RHP7837]

value: is040 B


title: D35 is043A rep1 [Day35_R192H_HOMO_is043_A_RHP7839]


title: D35 is043A rep2 [Day35_R192H_HOMO_is043_A_RHP7840]


title: D35 is040A rep2 [Day35_R192H_HET_is040_A_RHP7835]

value: is040 A


title: D35 is040A rep1 [Day35_R192H_HET_is040_A_RHP7834]


title: D35 is040B rep1 [Day35_R192H_HET_is040_B_RHP7836]


title: D35 is039C rep3 [Day35_R192H_HET_is039_C_RHP7833]

value: is039 C


title: D35 is039C rep1 [Day35_R192H_HET_is039_C_RHP7831]


title: D35 i173B rep3 [Day35_WT_is073_B_RHP7827]

value: is173 B

value: WT


title: D35 is039B rep1 [Day35_R192H_HET_is039_B_RHP7828]

value: is039 B


title: D35 is039B rep2 [Day35_R192H_HET_is039_B_RHP7829]


title: D35 i173B rep1 [Day35_WT_is073_B_RHP7825]


title: D35 is039C rep2 [Day35_R192H_HET_is039_C_RHP7832]


title: D35 is039B rep3 [Day35_R192H_HET_is039_B_RHP7830]


title: D35 i070B rep3 [Day35_WT_is070_B_RHP7824]

value: is070 B


title: D35 i070B rep2 [Day35_WT_is070_B_RHP7823]


title: D35 is181B rep2 [Day35_R192H_HOMO_is0181_B_RHP7848]


title: D35 i070B rep1 [Day35_WT_is070_B_RHP7822]


title: D35 is181A rep1 [Day35_R192H_HOMO_is0181_A_RHP7844]


title: D35 is070A rep3 [Day35_WT_is070_A_RHP7821]

value: is070 A


title: D35 i043B rep1 [Day35_R192H_HOMO_is043_B_RHP7842]


title: D35 is070A rep2 [Day35_WT_is070_A_RHP7820]


title: D20 iTSLC rep3 [Day20_PAX4_TRUNC_iTSL_C_RHP7818]

value: Endocrine progenitor cells


title: D35 is070A rep1 [Day35_WT_is070_A_RHP7819]

value: donor-derived hiPSC


title: D20 iTSLC rep1 [Day20_PAX4_TRUNC_iTSL_C_RHP7816]

value: iTSL C


title: D35 is040B rep3 [Day35_R192H_HET_is040_B_RHP7838]

value: Pancreatic beta-like cells


title: D20 iTSLA rep3 [Day20_PAX4_TRUNC_iTSL_A_RHP7815]

value: beta cell differentiation


title: D20 iTSLC rep2 [Day20_PAX4_TRUNC_iTSL_C_RHP7817]


title: D20 iTSLA rep1 [Day20_PAX4_TRUNC_iTSL_A_RHP7813]


title: D20 is181C rep2 [Day20_R192H_HOMO_is0181_C_RHP7811]


title: D20 iTSLA rep2 [Day20_PAX4_TRUNC_iTSL_A_RHP7814]


title: D20 is181C rep1 [Day20_R192H_HOMO_is0181_C_RHP7810]


title: D20 is181B rep3 [Day20_R192H_HOMO_is0181_B_RHP7809]


title: D20 is181A rep2 [Day20_R192H_HOMO_is0181_A_RHP7805]


title: D20 is181B rep1 [Day20_R192H_HOMO_is0181_B_RHP7807]


title: D20 i043B rep3 [Day20_R192H_HOMO_is043_B_RHP7803]


title: D20 is181A rep1 [Day20_R192H_HOMO_is0181_A_RHP7804]


title: D35 i173B rep2 [Day35_WT_is073_B_RHP7826]


title: D20 i043B rep1 [Day20_R192H_HOMO_is043_B_RHP7801]


title: D20 is181A rep3 [Day20_R192H_HOMO_is0181_A_RHP7806]


title: D20 is181C rep3 [Day20_R192H_HOMO_is0181_C_RHP7812]


title: D20 is181B rep2 [Day20_R192H_HOMO_is0181_B_RHP7808]


title: D20 is043A rep3 [Day20_R192H_HOMO_is043_A_RHP7800]


title: D20 is043A rep2 [Day20_R192H_HOMO_is043_A_RHP7799]


title: D20 is040B rep3 [Day20_R192H_HET_is040_B_RHP7797]


title: D20 is040B rep2 [Day20_R192H_HET_is040_B_RHP7796]


title: D20 is040A rep2 [Day20_R192H_HET_is040_A_RHP7793]


title: D20 is040A rep3 [Day20_R192H_HET_is040_A_RHP7794]


title: D20 is040A rep1 [Day20_R192H_HET_is040_A_RHP7792]


title: D20 is039C rep3 [Day20_R192H_HET_is039_C_RHP7426]


title: D20 is039C rep1 [Day20_R192H_HET_is039_C_RHP7424]


title: D20 is039B rep2 [Day20_R192H_HET_is039_B_RHP7422]


title: D20 is039B rep1 [Day20_R192H_HET_is039_B_RHP7421]


title: D20 is039B rep3 [Day20_R192H_HET_is039_B_RHP7423]


title: D20 i173B rep1 [Day20_WT_is073_B_RHP7418]


title: D20 i173B rep3 [Day20_WT_is073_B_RHP7420]


title: D20 i043B rep2 [Day20_R192H_HOMO_is043_B_RHP7802]


title: D20 i173B rep2 [Day20_WT_is073_B_RHP7419]


title: D20 i070B rep2 [Day20_WT_is070_B_RHP7416]


title: D20 i070B rep3 [Day20_WT_is070_B_RHP7417]


title: D20 is070A rep2 [Day20_WT_is070_A_RHP7414]


title: D20 is070A rep1 [Day20_WT_is070_A_RHP7413]


title: D13 is181B rep2 [Day13_R192H_HOMO_is0181_B_RHP7408]

value: Pancreatic progenitor cells


title: D13 is181C rep1 [Day13_R192H_HOMO_is0181_C_RHP7410]


title: D13 is181C rep2 [Day13_R192H_HOMO_is0181_C_RHP7411]


title: D13 is181B rep3 [Day13_R192H_HOMO_is0181_B_RHP7409]


title: D20 i070B rep1 [Day20_WT_is070_B_RHP7415]


title: D13 is181A rep2 [Day13_R192H_HOMO_is0181_A_RHP7405]


title: D13 is181A rep3 [Day13_R192H_HOMO_is0181_A_RHP7406]


title: D20 is043A rep1 [Day20_R192H_HOMO_is043_A_RHP7798]


title: D13 is181A rep1 [Day13_R192H_HOMO_is0181_A_RHP7404]


title: D13 i043B rep3 [Day13_R192H_HOMO_is043_B_RHP7403]


title: D13 is043A rep3 [Day13_R192H_HOMO_is043_A_RHP7400]


title: D13 i043B rep2 [Day13_R192H_HOMO_is043_B_RHP7402]


title: D20 is039C rep2 [Day20_R192H_HET_is039_C_RHP7425]


title: D13 i043B rep1 [Day13_R192H_HOMO_is043_B_RHP7401]


title: D13 is043A rep1 [Day13_R192H_HOMO_is043_A_RHP7398]


title: D13 is040B rep1 [Day13_R192H_HET_is040_B_RHP7395]


title: D13 is040B rep2 [Day13_R192H_HET_is040_B_RHP7396]


title: D13 is040A rep3 [Day13_R192H_HET_is040_A_RHP7394]


title: D20 is040B rep1 [Day20_R192H_HET_is040_B_RHP7795]


title: D13 is040A rep1 [Day13_R192H_HET_is040_A_RHP7392]


title: D13 is181C rep3 [Day13_R192H_HOMO_is0181_C_RHP7412]


title: D13 is181B rep1 [Day13_R192H_HOMO_is0181_B_RHP7407]


title: D13 is039C rep3 [Day13_R192H_HET_is039_C_RHP7391]


title: D13 is039C rep2 [Day13_R192H_HET_is039_C_RHP7390]


title: D13 is039B rep3 [Day13_R192H_HET_is039_B_RHP7388]


title: D13 is039B rep2 [Day13_R192H_HET_is039_B_RHP7387]


title: D13 is039B rep1 [Day13_R192H_HET_is039_B_RHP7386]


title: D13 i173B rep3 [Day13_WT_is073_B_RHP7385]


title: D13 i173B rep2 [Day13_WT_is073_B_RHP7384]


title: D13 i070B rep3 [Day13_WT_is070_B_RHP7382]


title: D13 i070B rep2 [Day13_WT_is070_B_RHP7381]


title: D13 i070B rep1 [Day13_WT_is070_B_RHP7380]


title: D13 is070A rep3 [Day13_WT_is070_A_RHP7379]


title: D13 is070A rep1 [Day13_WT_is070_A_RHP7377]


title: D13 is070A rep2 [Day13_WT_is070_A_RHP7378]


title: D0 iTSLC rep2 [Day0_PAX4_TRUNC_iTSL_C_RHP7375]

value: Undifferentiated pluripotent stem cells


title: D0 iTSLC rep1 [Day0_PAX4_TRUNC_iTSL_C_RHP7374]


title: D0 iTSLB rep3 [Day0_PAX4_TRUNC_iTSL_B_RHP7373]

value: iTSL B


title: D13 is043A rep2 [Day13_R192H_HOMO_is043_A_RHP7399]

value: is043 A


title: D13 is040B rep3 [Day13_R192H_HET_is040_B_RHP7397]


title: D0 iTSLB rep1 [Day0_PAX4_TRUNC_iTSL_B_RHP7371]


title: D0 iTSLA rep3 [Day0_PAX4_TRUNC_iTSL_A_RHP7370]

value: iTSL A


title: D0 iTSLB rep2 [Day0_PAX4_TRUNC_iTSL_B_RHP7372]


title: D13 is040A rep2 [Day13_R192H_HET_is040_A_RHP7393]

value: is040 A


title: D13 is039C rep1 [Day13_R192H_HET_is039_C_RHP7389]

value: is039 C


title: D0 iTSLA rep2 [Day0_PAX4_TRUNC_iTSL_A_RHP7369]


title: D0 is181C rep1 [Day0_R192H_HOMO_is0181_C_RHP7365]


title: D0 iTSLA rep1 [Day0_PAX4_TRUNC_iTSL_A_RHP7368]


title: D0 is181C rep2 [Day0_R192H_HOMO_is0181_C_RHP7366]


title: D0 is181B rep2 [Day0_R192H_HOMO_is0181_B_RHP7363]


title: D0 is181C rep3 [Day0_R192H_HOMO_is0181_C_RHP7367]


title: D0 is181A rep3 [Day0_R192H_HOMO_is0181_A_RHP7361]


title: D0 is181B rep1 [Day0_R192H_HOMO_is0181_B_RHP7362]


title: D0 i043B rep2 [Day0_R192H_HOMO_is043_B_RHP7357]

value: is043 B


title: D0 is181A rep1 [Day0_R192H_HOMO_is0181_A_RHP7359]


title: D13 i173B rep1 [Day13_WT_is073_B_RHP7383]

value: is173 B

value: WT


title: D0 i043B rep3 [Day0_R192H_HOMO_is043_B_RHP7358]


title: D0 is181A rep2 [Day0_R192H_HOMO_is0181_A_RHP7360]


title: D0 is043A rep2 [Day0_R192H_HOMO_is043_A_RHP7354]


title: D0 is043A rep1 [Day0_R192H_HOMO_is043_A_RHP7353]


title: D0 iTSLC rep3 [Day0_PAX4_TRUNC_iTSL_C_RHP7376]


title: D0 is040B rep3 [Day0_R192H_HET_is040_B_RHP7352]

value: is040 B


title: D0 is040B rep1 [Day0_R192H_HET_is040_B_RHP7350]


title: D0 is040B rep2 [Day0_R192H_HET_is040_B_RHP7351]


title: D0 is040A rep3 [Day0_R192H_HET_is040_A_RHP7349]


title: D0 is040A rep1 [Day0_R192H_HET_is040_A_RHP7347]


title: D0 is040A rep2 [Day0_R192H_HET_is040_A_RHP7348]


title: D0 is039C rep3 [Day0_R192H_HET_is039_C_RHP7346]


title: D0 is039C rep1 [Day0_R192H_HET_is039_C_RHP7344]


title: D0 is039C rep2 [Day0_R192H_HET_is039_C_RHP7345]


title: D0 is181B rep3 [Day0_R192H_HOMO_is0181_B_RHP7364]


title: D0 is039B rep3 [Day0_R192H_HET_is039_B_RHP7343]

value: is039 B


title: D0 is039B rep2 [Day0_R192H_HET_is039_B_RHP7342]


title: D0 i070B rep3 [Day0_WT_is070_B_RHP7337]

value: is070 B


title: D0 i173B rep2 [Day0_WT_is073_B_RHP7339]

value: donor-derived hiPSC


title: D0 i173B rep3 [Day0_WT_is073_B_RHP7340]


title: D0 i173B rep1 [Day0_WT_is073_B_RHP7338]


title: D0 i043B rep1 [Day0_R192H_HOMO_is043_B_RHP7356]


title: D0 i070B rep1 [Day0_WT_is070_B_RHP7335]


title: D0 is070A rep3 [Day0_WT_is070_A_RHP7334]

value: is070 A


title: D0 is043A rep3 [Day0_R192H_HOMO_is043_A_RHP7355]


title: D0 is070A rep2 [Day0_WT_is070_A_RHP7333]


title: 22Rv1NCOA6-3xFLAG #67

library_source: genomic

data_processing:
The sequence reads were mapped to the reference genome hg19 using software BWA
Duplicate reads were removed using Picard tools (http://broadinstitute.github.io/picard/).
Software MACS and iSeq were used for peak calling. Since the peaks are highly overlapped, the results generated by iSeq were used. For the iSeq method, a region with the posterior probability > 0.9 was claimed to be a binding region.
Genome_build: hg19
Supplementary_files_format_and_content: wig files include NCOA6-3xFLAG peaks

molecule: genomic DNA

growth_protocol: The 22Rv1Par., 22Rv1NCOA6-3xFLAG #67 and 22Rv1NCOA6-3xFLAG #100 cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (10437028; Thermo Fisher) and 1% penicillin (10000 IU)/streptomycin (10000 µg/ml) solution (30-002-CI; Corning). Cells were maintained at 37°C in a 5% CO2 cell culture incubator.

extract_protocol:
ChIP assays were performed using the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (9005S; Cell Signaling Technology) according to the manufacturer’s instructions. Sample quality checks were performed by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 DNA quantitation assay and Agilent Bioanalyzer.
The Rubicon ThruPlex DNA-Seq library preparation system (p/n R400523, protocol QAM-328-001) was used to prepare ChIP-Seq libraries for sequencing on the Illumina NGS sequencing instruments. 1 ng of ChIP’d DNA was used for generating a double-stranded DNA library. The genomic DNA fragments were blunt ended and then the 5' end of the fragments were ligated with stem-loop adapters with blocked 5' end, leaving a nick at the 3' end. Then, the 3' end was extened during library synthesis and Illumina-compatible indexes were incorporated with 11 amplification cycles. The fragments were purified by using the AMPure XP Bead Purification System. Fragments with a size smaller than 200 bp as well as unincorporated PCR reagents and nucleotides were removed. The resulting libraries were quantitated by using the NanoDrop ND-1000 spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter ligated fragments, the libraries were quantitated by qPCR by using the Applied Biosystems ViiA7 TM Real-Time PCR System and a KAPA Library Quant Kit.

treatment_protocol: For inserting the 3xFLAG coding sequence between the last a.a. code and the STOP code of NCOA6, single-stranded DNA (ssDNA) donor template with short homologous arms and the plasmid for co-expressing Cas9 and sgRNA targeting a site near the STOP code of NCOA6 were co-introduced into 22Rv1 cells by using Lipofectamine 3000. The transfected cells were cultured in RPMI 1640 complete medium containing 5 µg/ml puromycin (P8833; Sigma) for 2 days. Selected cells were seeded into 150 mm dishes at a density of 200 cells per dish to grow clones. Individual clones were picked up and expanded. Positive clones including the 22Rv1NCOA6-3XFLAG #67 and #100 cell lines were identified by PCR-based genotyping, DNA sequencing, and Western blot analysis.

value: Prostate carcinoma epithelial cell line

value: anti-FLAG (Sigma-Aldrich; Cat# F1804; RRID:AB_262044)

value: Untreated

value: NCOA6-3xFLAG knock-in


title: D0 is039B rep1 [Day0_R192H_HET_is039_B_RHP7341]

value: Undifferentiated pluripotent stem cells

value: beta cell differentiation


title: 22Rv1Par.

value: NCOA6 wild type


title: 22Rv1NCOA6-3xFLAG #100


title: D0 i070B rep2 [Day0_WT_is070_B_RHP7336]


title: D0 is070A rep1 [Day0_WT_is070_A_RHP7332]


title: 205854170025_R05C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: We followed standard protocols from Illumina regarding Infinium arrays.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting at Epigenetic Clock Development Foundation, Los Angeles. https://clockfoundation.org/

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

label: Cy3 and Cy5

organism: Phoca groenlandica

label_protocol: Zymo EZ DNA Methylation Kit

extract_protocol: DNA extraction: DNA Easy Blood and Tissue Kit from Qiagen

tag: age

tag: confidenceinageestimate

tag: specieslatinname

value: Pagophilus groenlandicus

value: Blood

tag: female

tag: tissuedetailed

value: whole blood EDTA

tag: tissuecolor

value: blue

tag: tissues

value: Blood / Skin


title: 205854170005_R05C01

organism: Zalophus californianus

value: Zalophus californianus

value: Skin

value: skin

value: cyan


title: 205854170025_R04C01


title: 205854170025_R02C01


title: 205854170025_R03C01

organism: Phoca vitulina

value: Phoca vitulina


title: 205854170025_R02C02


title: 205854170005_R05C02


title: 205854170025_R01C01


title: 205854170005_R01C02


title: 205854170005_R02C01


title: 205854170025_R04C02


title: 205854170005_R04C02


title: 205854170005_R03C02


title: 205854170005_R03C01


title: 205854170005_R06C01


title: 205854170027_R05C01


title: 205854170027_R05C02


title: 205854170027_R01C02


title: 205854170027_R06C01


title: 205854170027_R02C02


title: 205854170005_R04C01


title: 205854170027_R04C01


title: 205854170005_R02C02


title: 205854170027_R06C02


title: 205854170027_R01C01


title: 205854170019_R02C01


title: 205854170027_R02C01


title: 205854170005_R01C01


title: 205854170027_R03C01


title: 205863120005_R05C02


title: 205128010020_R02C02

tag: predictedspecieslatinname

tag: predictedtissue

tag: predictedfemale

tag: errortissue

tag: errorfemale


title: 205128010020_R03C02

tag: tissue


title: 205128010021_R04C01


title: 205128010039_R06C01


title: 205128010039_R05C01


title: 205128010021_R05C02


title: 205128010021_R04C02


title: 205128010020_R06C02


title: 205128010021_R03C01


title: 205128010032_R01C01


title: 205128010020_R06C01


title: 205128010020_R04C01


title: 205128010020_R05C01


title: 205128010038_R05C01


title: 205128010021_R05C01


title: 205128010020_R04C02


title: 205128010020_R01C02


title: 205128010038_R06C01


title: 204529320113_R06C01

organism: Odobenus rosmarus divergens

value: Odobenus rosmarus divergens

value: Odobenus rosmarus

value: Blood / Fibroblast / iPSC / Skin


title: 205128010039_R01C02


title: 204529320105_R01C01


title: 205128010026_R02C02


title: 205128010021_R01C02


title: 205128010021_R06C01


title: 204529320054_R01C02

organism: Eumetopias jubatus

value: Eumetopias jubatus


title: 204529320054_R02C02

organism: Neophoca cinerea

value: Neophoca cinerea


title: 204529320054_R03C02


title: 204529320103_R06C02


title: 204529320040_R01C01


title: 204529320054_R06C01


title: 205128010041_R02C02


title: 204529320059_R06C02


title: 204529320051_R06C02


title: 204529320059_R01C01


title: 204529320051_R05C02


title: 204529320059_R01C02


title: 204529320051_R04C01


title: 204529320059_R04C01


title: 204529320051_R04C02


title: 204529320051_R05C01


title: 204529320051_R03C02


title: 204529320038_R01C02


title: 204529320051_R03C01


title: 204529320038_R06C01


title: 204529320051_R06C01


title: 204529320038_R05C02


title: 204529320059_R05C01


title: 204529320059_R05C02


title: 204529320038_R02C02


title: 204529320038_R06C02


title: 204529320038_R05C01


title: 204551090057_R02C02


title: 204529320038_R04C02


title: 204529320038_R03C01


title: 204529320038_R03C02


title: 204551090057_R03C02


title: 204551090057_R01C02


title: 204551090057_R01C01


title: 204551090016_R06C02


title: 204529320038_R04C01


title: 204551090057_R06C01


title: 204551090016_R04C02


title: 203877620024_R04C01


title: 204551090016_R05C02


title: 203877620076_R03C02


title: 204551090016_R03C02


title: 203877620076_R01C02


title: 203877620079_R03C02


title: 203877620076_R06C01


title: 203877620079_R06C01


title: 203877620079_R01C02


title: 204551090016_R02C02


title: 203877620076_R05C01


title: 203877620002_R02C01


title: 203877620080_R06C01


title: 203867110005_R06C02


title: 203877620002_R01C01


title: 203867110005_R04C02


title: 203877620043_R04C01


title: 203867110005_R05C02


title: 203877620076_R01C01


title: 203877620076_R03C01


title: 203877620080_R03C02


title: 203877620043_R02C02


title: 203877620079_R06C02


title: 203877620076_R04C01


title: 203877620043_R06C01


title: 203877620002_R05C01


title: 203867110005_R02C02


title: 203867110005_R01C02


title: 203877620002_R04C01


title: 203867110005_R01C01


title: 203877620001_R06C02


title: 203867110005_R06C01


title: 203877620071_R01C01


title: 203877620075_R06C02


title: 203877620001_R03C02


title: 203877620001_R04C02


title: 203877620075_R04C01


title: 203877620075_R01C02


title: 203877620075_R04C02


title: 203877620001_R02C02


title: 203531420041_R04C02


title: 203877620075_R03C01


title: 203867110005_R02C01


title: 203877620001_R02C01


title: 203531420054_R01C01


title: 203877620001_R05C02


title: 203531420021_R06C02


title: 203877620075_R06C01


title: 203531420054_R02C01


title: 203531420041_R02C02


title: 203531420008_R04C01


title: 203531420008_R06C02


title: 203531420041_R03C02


title: 203531420008_R01C01


title: 203531420008_R05C01


title: 203877620075_R05C01


title: 203531420019_R05C02


title: 203877620075_R05C02


title: 204529320059_R03C01


title: 203524370004_R06C02


title: 203531420072_R06C01


title: 203531420072_R05C01


title: 203531420027_R01C02


title: 203531420027_R03C02


title: 203531420015_R04C02


title: 202897220096_R06C02

hyb_protocol: standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.
normalized (Sesame) Beta values

organism: Orcinus orca

label_protocol: standard Illumina protocol

extract_protocol: none provided

value: Orcinus orca

tag: ageyears


title: 202897220096_R04C02


title: 203531420063_R01C01


title: 202897220152_R06C01

value: WholeBlood


title: 203531420018_R04C02


title: 202897220152_R04C01


title: 202897220096_R02C02


title: 202897220152_R05C01


title: 203531420027_R02C02


title: 202897220096_R04C01


title: 202897220070_R06C01


title: 202897220070_R04C01


title: 202897220070_R05C01


title: 202897220159_R05C01


title: 202894750035_R06C01


title: 202897220070_R03C01


title: 202897220096_R05C02


title: 202897220096_R03C02


title: 202897220096_R06C01


title: 202897220096_R01C02


title: 202897220096_R05C01


title: 202897220152_R03C01


title: 202897220096_R01C01


title: 202894750002_R06C02


title: 202894750002_R04C02


title: 202894750002_R05C01


title: 202894750002_R01C01


title: 202894750002_R02C02


title: 202897220096_R02C01


title: 202894750002_R03C01


title: 202894750002_R01C02


title: 202894750003_R06C02


title: 202894750002_R02C01


title: 202894750002_R03C02


title: 202894750003_R03C02


title: 202894750003_R02C02


title: 202894750003_R06C01


title: 202894750003_R05C02


title: 202894750003_R01C02


title: 202894750003_R04C02


title: 202894750003_R04C01


title: 202894750003_R02C01


title: 202894750002_R04C01


title: 202894750003_R05C01


title: 202894750003_R01C01


title: 202894750002_R05C02


title: 202897220049_R06C02


title: 202894750003_R03C01


title: 202897220149_R02C02


title: 202897220049_R04C02


title: 202897220049_R05C02


title: 202897220049_R03C02


title: 202897220049_R02C02


title: 202897220049_R06C01


title: 202897220049_R05C01


title: 202897220049_R04C01


title: 202897220049_R02C01


title: 202897220049_R03C01


title: 202894750022_R05C02


title: 202897220049_R01C01


title: 202897220096_R03C01


title: 202894750022_R06C02


title: 202894750022_R03C02


title: 202894750022_R04C02


title: 202894750022_R01C02


title: 202894750022_R05C01


title: 202894750022_R02C01


title: 202894750022_R06C01


title: 202894750022_R01C01


title: 202894750022_R04C01


title: 202894750023_R04C02


title: 202894750023_R05C02


title: 202894750023_R03C02


title: 202894750023_R02C02


title: 202894750023_R05C01


title: 202894750023_R04C01


title: 202894750023_R03C01


title: 202897220049_R01C02


title: 202894750023_R01C02


title: 202894750023_R02C01


title: 202894750023_R01C01


title: 202894750038_R04C02


title: 202894750038_R05C02


title: 202894750038_R03C02


title: 202894750038_R01C02


title: 202894750038_R02C02


title: 202894750038_R06C02


title: 202894750038_R04C01


title: 202894750023_R06C02


title: 202894750038_R02C01


title: 202897220012_R06C02


title: 202897220012_R05C02


title: 202894750038_R03C01


title: 202897220012_R02C02


title: 202897220012_R04C02


title: 202897220012_R03C02


title: 202894750023_R06C01


title: 202897220012_R01C02


title: 202897220012_R05C01


title: 202897220012_R03C01


title: 202897220012_R02C01


title: 202897220012_R04C01


title: 202897220012_R01C01


title: 202897220100_R06C02


title: 202897220100_R05C02


title: 202897220100_R03C02


title: 202894750038_R06C01


title: 202894750038_R05C01


title: 202897220100_R01C02


title: 202897220100_R06C01


title: 202894750038_R01C01


title: 202897220100_R04C01


title: 202897220100_R02C01


title: 202897220100_R01C01


title: 202897220112_R05C02


title: 202897220112_R06C02


title: 202897220012_R06C01


title: 202897220112_R04C02


title: 202897220112_R01C02


title: 202897220112_R02C02


title: 202897220112_R06C01


title: 202897220112_R04C01


title: 202897220112_R03C01


title: 202897220112_R03C02


title: 202897220112_R05C01


title: 202897220112_R02C01


title: 202897220102_R06C02


title: 202897220112_R01C01


title: 202897220102_R04C02


title: 202897220100_R04C02


title: 202897220102_R03C02


title: 202897220100_R02C02


title: 202897220100_R05C01


title: 202897220100_R03C01


title: 202897220102_R01C02


title: 202897220102_R05C01


title: 202897220102_R02C01


title: 202897220102_R06C01


title: 202897220102_R04C01


title: 202897220102_R03C01


title: 202897220101_R05C02


title: 202897220101_R06C02


title: 202897220101_R02C02


title: 202897220101_R03C02


title: 202897220101_R01C02


title: 202897220101_R04C02


title: 202897220101_R03C01


title: 202897220101_R02C01


title: 202897220101_R05C01


title: 205619060100_R06C02

organism: Balaena mysticetus

value: Liver

value: Balaena mysticetus

value: Kidney

tag: agebillkoski

tag: agebyeyelens

tag: agemeasurement

value: Eye lens


title: 205619060100_R03C02

tag: age

tag: ageestimatedusingcetaceanskinclock

value: yes


title: 205619060100_R02C02

tag: confidenceinageestimate

tag: specieslatinname


title: 205619060100_R01C02

tag: female


title: 202897220102_R05C02


title: 202897220102_R02C02


title: 205619060100_R05C01

value: Muscle


title: 205619060100_R06C01


title: 205619060100_R03C01


title: 205619060100_R01C01


title: 205619060100_R02C01


title: 205619060097_R06C02

value: Heart

value: Skin


title: 205619060097_R06C01


title: 205619060097_R03C01


title: 205619060097_R03C02

value: Cortex


title: 205619060097_R02C01


title: 205619060097_R01C01


title: 205619060097_R05C01


title: 202897220101_R04C01


title: 202897220101_R06C01


title: 202897220101_R01C01


title: 205619060089_R02C02


title: 205619060089_R01C02


title: 205619060089_R03C02


title: 205619060089_R04C02


title: 205619060089_R05C01


title: 205619060097_R04C01


title: 204551090085_R05C02


title: 205619060089_R06C02


title: 204551090085_R04C02


title: 205619060089_R05C02


title: 204551090085_R06C02


title: 204551090085_R02C02


title: 204551090085_R01C02


title: 204551090085_R03C02


title: 205619060100_R04C01


title: 204551090085_R06C01


title: 204551090085_R04C01


title: 204551090085_R05C01


title: 204551090085_R03C01


title: 204551090085_R02C01


title: 204551090040_R05C02


title: 204551090085_R01C01


title: 204551090040_R06C02


title: 204551090040_R03C02


title: 204551090040_R02C02


title: 204551090040_R01C02


title: 204551090040_R04C02


title: 204551090040_R06C01


title: 204551090040_R04C01


title: 205619060089_R06C01


title: 204551090040_R02C01


title: 204551090040_R05C01


title: 204551090040_R03C01


title: 204551090069_R06C02


title: 204551090069_R04C02


title: 204551090069_R03C02


title: 204551090069_R02C02


title: 204551090069_R06C01


title: 204551090069_R01C01


title: 204551090069_R05C01


title: 204551090069_R02C01


title: 204551090029_R06C02


title: 204551090069_R03C01


title: 204551090029_R04C02


title: 204551090029_R05C02


title: 204551090029_R03C02


title: 204551090029_R02C02


title: 204551090029_R06C01


title: 204551090029_R01C02

value: 1 - now 8


title: 204551090029_R05C01


title: 204551090029_R01C01


title: 204529320049_R03C01


title: 204551090029_R02C01


title: 204529320049_R02C01


title: 204551090069_R05C02


title: 204529320049_R01C01


title: 204551090040_R01C01


title: 204529320087_R06C02


title: 204529320087_R04C02


title: 204551090069_R01C02


title: 204529320087_R05C02


title: 204529320087_R05C01


title: 204529320087_R06C01


title: 204529320087_R02C02


title: 204529320087_R01C02


title: 204529320087_R03C01


title: 204529320087_R04C01


title: 204529320087_R02C01


title: 204529320087_R01C01


title: 204529320093_R06C02


title: 204529320093_R04C02


title: 204529320093_R05C02


title: 204529320093_R03C02


title: 204529320093_R02C02


title: 204529320093_R01C02


title: 204551090029_R04C01


title: 204529320093_R03C01


title: 204529320093_R04C01


title: 204529320093_R06C01


title: 204529320093_R02C01


title: 204529320093_R01C01


title: 204529320087_R03C02


title: 204529320113_R06C02


title: 204529320113_R03C02


title: 204529320113_R05C02


title: 204529320113_R01C02


title: 204529320113_R02C02


title: 204529320093_R05C01


title: 204529320113_R04C02


title: 205483080016_R04C02

label: Cy5 and Cy3

extract_protocol: genomic DNA was extracted

value: Mus musculus

value: Blood

tag: ageinweeks

tag: predictfemalebasedonall

tag: predicttissuebasedonall

tag: tissuecolor

value: turquoise


title: 205483080016_R01C02

tag: predictedfemale

tag: predictedtissue


title: 205483080016_R01C01


title: 205483080001_R06C02


title: 205483080016_R05C01


title: 205483080001_R06C01

value: blue


title: 205483080016_R02C01


title: 205483080016_R02C02


title: 205483080016_R03C01


title: 205483080016_R05C02


title: 205483080001_R04C02


title: 205483080001_R03C01


title: 205483080001_R03C02


title: 205483080020_R05C02


title: 205483080001_R02C01


title: 205483080001_R01C02


title: 205483080020_R06C02


title: 205483080001_R04C01


title: 205483080001_R02C02


title: 205483080016_R03C02


title: 205483080016_R06C02


title: 205483080020_R04C02


title: 205483080016_R06C01


title: 205483080016_R04C01


title: 205483080001_R01C01


title: 205483080001_R05C01


title: 205483080020_R02C02


title: 205483080020_R03C02


title: 205483080001_R05C02


title: 205483080020_R01C02


title: 205483080020_R06C01


title: 205483080020_R05C01


title: 205483080020_R04C01

value: yellow


title: 205483080020_R03C01


title: 205483080020_R02C01


title: 205483080042_R05C02


title: 205483080042_R04C02


title: 205483080042_R01C02


title: 205477000002_R06C02

value: green


title: 205483080042_R03C01


title: 205483080042_R04C01


title: 205483080042_R02C02


title: 205483080042_R06C02


title: 205483080020_R01C01


title: 205483080042_R01C01


title: 205477000002_R03C02


title: 205477000002_R02C02


title: 205477000002_R01C01


title: 205483080042_R05C01


title: 205477000002_R01C02


title: 205477000002_R04C01


title: 205477000002_R03C01


title: 205477000002_R04C02


title: 205483080042_R06C01


title: 205477000002_R06C01


title: 205477000002_R02C01


title: 205477000002_R05C02


title: 205483080042_R03C02


title: 205483080042_R02C01


title: 205477000002_R05C01


title: 205477000001_R05C02


title: 205477000001_R04C02


title: 205477000001_R03C02


title: 205477000001_R05C01

value: brown


title: 205477000001_R02C02

value: Liver


title: 205477000001_R06C02


title: 205477000001_R06C01


title: 205477000001_R04C01


title: 205307780030_R04C02


title: 205477000001_R03C01


title: 205307780030_R02C02


title: 205477000001_R02C01


title: 205477000001_R01C02


title: 205307780030_R05C02


title: 205483080026_R05C02


title: 205307780030_R02C01


title: 205477000001_R01C01


title: 205307780030_R03C01


title: 205307780030_R01C01


title: 205307780030_R01C02


title: 205483080026_R02C02


title: 205307780030_R06C02


title: 205307780030_R05C01


title: 205483080026_R06C02


title: 205307780030_R03C02


title: 205307780030_R06C01


title: 205307780030_R04C01


title: 205483080026_R04C02


title: 205483080026_R03C02


title: 205483080026_R01C02


title: 205483080026_R05C01


title: 205483080025_R04C02


title: 205483080026_R01C01


title: 205483080025_R06C02


title: 205483080025_R05C02


title: 205483080025_R03C02


title: 205483080025_R02C02


title: 205483080025_R06C01


title: 205483080026_R03C01


title: 205483080025_R01C02


title: 205483080026_R04C01


title: 205483080026_R06C01


title: 205483080026_R02C01


title: 205483080009_R05C02


title: 205483080025_R04C01


title: 205483080009_R04C02


title: 205483080009_R06C01


title: 205483080009_R04C01


title: 205483080009_R03C02


title: 205483080009_R05C01


title: 205483080009_R01C01


title: 205483080025_R03C01


title: 205483080009_R02C02


title: 205483080025_R01C01


title: 205483080009_R03C01


title: 205483080009_R01C02


title: 205483080009_R06C02


title: 205483080025_R02C01


title: 205483080009_R02C01


title: 205483080025_R05C01


title: 205483080027_R04C01


title: 205483080027_R03C01


title: 205483080027_R05C02


title: 205483080027_R02C02


title: 205483080027_R06C01


title: 205483080027_R01C02


title: 205307780043_R06C02


title: 205483080027_R04C02


title: 205483080027_R06C02


title: 205483080027_R03C02


title: 205483080027_R02C01


title: 205483080027_R05C01


title: 205307780043_R04C02


title: 205483080027_R01C01


title: 205307780043_R05C02


title: 205307780038_R04C02


title: 205307780038_R05C02


title: 205307780038_R06C02


title: 205307780038_R03C02


title: 205307780043_R01C02


title: 205307780043_R03C01


title: 205307780043_R02C02


title: 205307780043_R03C02


title: 205307780038_R01C02


title: 205307780038_R02C02


title: 205307780043_R02C01


title: 205307780043_R01C01


title: 205307780043_R05C01


title: 205307780043_R04C01


title: 205307780038_R05C01


title: 205307780038_R04C01


title: 205307780038_R02C01


title: 205307780038_R03C01


title: 205307780052_R05C02


title: 205307780052_R03C02


title: 205307780038_R01C01


title: 205307780052_R06C02


title: 205307780052_R04C02


title: 205307780052_R05C01


title: 205307780038_R06C01


title: 205307780052_R02C02


title: 205307780043_R06C01


title: 205307780052_R02C01


title: 205307780052_R06C01


title: 205307780052_R04C01


title: 205307780048_R05C02


title: 205307780048_R04C01


title: 205307780048_R04C02


title: 205307780048_R06C02


title: 205307780048_R03C01


title: 205307780048_R05C01


title: 205307780052_R01C02


title: 205307780048_R03C02


title: 205307780048_R06C01


title: 205307780048_R02C01


title: 205307780048_R01C01


title: 205307780048_R02C02


title: 205307780046_R06C02


title: 205307780046_R01C02


title: 205307780046_R02C02


title: 205307780052_R01C01


title: 205307780046_R05C02


title: 205307780052_R03C01


title: 205307780046_R03C02


title: 205307780046_R06C01


title: 205307780046_R04C02


title: 205307780046_R03C01


title: 205307780046_R04C01


title: 205307780048_R01C02


title: 205307780046_R01C01


title: 205307780041_R03C02


title: 205307780041_R02C02


title: 205307780041_R01C02


title: 205307780046_R05C01


title: 205307780041_R06C02


title: 205307780041_R04C02


title: 205307780041_R05C01


title: 205307780041_R04C01


title: 205307780050_R03C02


title: 205307780041_R01C01


title: 205307780041_R02C01


title: 205307780041_R03C01


title: 205307780046_R02C01


title: 205307780050_R05C02


title: 205307780041_R06C01


title: 205307780050_R04C02


title: 205307780041_R05C02


title: 205307780050_R04C01


title: 205307780050_R06C02


title: 205307780050_R01C01


title: 205307780050_R05C01


title: 205307780031_R05C02


title: 205307780050_R02C01


title: 205307780050_R01C02


title: 205307780050_R03C01


title: 205307780050_R02C02


title: 205307780031_R03C02


title: 205307780031_R04C02


title: 205307780031_R06C01


title: 205307780031_R01C02


title: 205307780031_R05C01


title: 205307780031_R06C02


title: 205307780033_R06C02


title: 205307780031_R02C01


title: 205307780033_R05C02


title: 205307780033_R01C02


title: 205307780033_R06C01


title: 205307780033_R02C02


title: 205307780033_R03C02


title: 205307780033_R05C01


title: 205307780033_R04C01


title: 205307780033_R03C01


title: 205307780031_R04C01


title: genomic DNA from Marmoset Brain 206139140104_R03C01

description: genomic DNA from Marmoset Brain

hyb_protocol: standard Affymetrix protocol

organism: Callithrix jacchus

source_name: Brain

label_protocol: standard Affymetrix protocol

tag: speciescommonname

value: Marmoset

tag: maximumlifespanyears

tag: ageatsexualmaturityyears

tag: networktrainingset

value: no

tag: panmammalianclocktrainingset


title: genomic DNA from Marmoset Brain 206139140104_R04C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R06C02

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R05C02

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140104_R01C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140104_R02C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R04C02

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R03C02

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R01C02

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R06C01

description: genomic DNA from Marmoset Brain


title: 205307780033_R02C01

tag: tissue


title: 205307780031_R01C01

tag: age


title: 205307780033_R01C01


title: 205307780033_R04C02


title: genomic DNA from Marmoset Brain 206139140103_R05C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140104_R05C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R02C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Tate's shrew opossum Liver 206139140104_R06C02

organism: Caenolestes fuliginosus

source_name: Liver

value: Tate's shrew opossum


title: genomic DNA from Marmoset Brain 206139140103_R04C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Marmoset Brain 206139140103_R03C01

description: genomic DNA from Marmoset Brain


title: genomic DNA from Tate's shrew opossum Liver 206139140104_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R01C02

organism: Tursiops aduncus

source_name: Skin

value: Indo-Pacific bottlenose dolphin


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R05C02


title: genomic DNA from Coarse-haired wombat Blood 206139140104_R02C02

organism: Vombatus ursinus

source_name: Blood

value: Coarse-haired wombat


title: genomic DNA from Tate's shrew opossum Liver 206139140104_R04C02


title: genomic DNA from Tate's shrew opossum Liver 206139140104_R03C02


title: genomic DNA from Coarse-haired wombat Blood 206139140104_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140103_R01C01


title: genomic DNA from Marmoset Brain 206139140103_R02C02

description: genomic DNA from Marmoset Brain


title: 205307780031_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R03C01


title: genomic DNA from Coarse-haired wombat Blood 206139140104_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140074_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140061_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140030_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820045_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206139140006_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820051_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820049_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820044_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820064_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R01C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R04C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R03C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R02C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R02C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R05C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R06C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R01C02


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R06C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R05C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R04C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R03C01


title: 205307780031_R03C01


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R01C01


title: genomic DNA from Mouse Brain 206139140063_R06C02

description: genomic DNA from Mouse Brain

value: Mouse


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820065_R03C01


title: genomic DNA from Mouse Kidney 206139140063_R05C02

description: genomic DNA from Mouse Kidney

source_name: Kidney


title: genomic DNA from Mouse Liver 206139140063_R01C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206139140063_R02C02

description: genomic DNA from Mouse Spleen

source_name: Spleen


title: genomic DNA from Mouse Spleen 206139140063_R03C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Adipose 206139140063_R02C01

description: genomic DNA from Mouse Adipose

source_name: Adipose


title: genomic DNA from Mouse Kidney 206139140063_R03C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206139140063_R05C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140063_R04C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Adipose 206139140092_R06C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820054_R01C01


title: genomic DNA from Mouse Kidney 206139140063_R01C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Indo-Pacific bottlenose dolphin Skin 206116820066_R04C02


title: genomic DNA from Mouse Liver 206139140092_R03C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Liver 206139140092_R05C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140092_R01C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206139140092_R06C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Adipose 206139140092_R02C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Kidney 206139140092_R05C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse ES 206139140092_R03C01

description: genomic DNA from Mouse ES

source_name: ES


title: genomic DNA from Mouse Kidney 206139140092_R04C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Kidney 206139140092_R02C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206139140092_R01C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206139140057_R05C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Spleen 206139140057_R04C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206139140057_R06C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Adipose 206139140057_R03C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Liver 206139140063_R04C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206139140063_R06C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206139140057_R02C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140057_R01C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Brain 206139140057_R05C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206139140057_R06C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206139140092_R04C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206116820056_R05C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Liver 206139140057_R01C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140057_R03C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Adipose 206139140057_R04C01

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Spleen 206139140057_R02C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206116820056_R06C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206116820056_R04C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206116820056_R03C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206116820056_R02C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206116820056_R06C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Kidney 206116820056_R05C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206116820056_R01C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Adipose 206116820056_R04C01

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse ES 206116820056_R03C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Brain 206116820056_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Kidney 206116820056_R02C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206139140055_R02C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206139140055_R01C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140055_R04C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206139140055_R05C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206139140055_R06C02

description: genomic DNA from Mouse Spleen


title: 205307780050_R06C01

value: Skin


title: genomic DNA from Mouse Spleen 206139140055_R04C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206139140055_R03C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse ES 206139140055_R06C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Brain 206139140055_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Kidney 206139140055_R03C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206116820035_R05C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206116820035_R03C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse ES 206116820035_R02C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206116820035_R06C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206116820035_R04C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Liver 206116820035_R01C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206116820035_R04C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Kidney 206116820035_R02C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206116820035_R05C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Spleen 206116820035_R03C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206116820072_R05C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206116820072_R04C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206116820072_R06C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206116820072_R02C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140055_R05C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Kidney 206116820072_R06C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Brain 206116820072_R04C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206116820035_R06C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206116820072_R02C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206116820072_R03C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206116820072_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206116820071_R04C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Liver 206116820071_R06C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206116820071_R06C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Adipose 206116820071_R03C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Kidney 206116820071_R02C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Kidney 206116820010_R06C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse ES 206116820071_R02C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Brain 206116820071_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206116820071_R03C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Liver 206116820010_R04C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206116820010_R03C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206116820010_R02C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Liver 206116820071_R04C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse ES 206116820010_R01C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Adipose 206116820010_R04C01

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Adipose 206116820010_R05C01

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Spleen 206116820072_R01C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse ES 206116820072_R03C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206116820010_R03C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse ES 206116820072_R05C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse ES 206116820010_R02C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206116820071_R05C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206116820010_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Kidney 206116820020_R06C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206116820020_R05C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206116820071_R01C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Liver 206116820020_R02C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse ES 206116820071_R05C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206116820020_R01C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Spleen 206116820020_R05C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206116820020_R06C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206116820010_R05C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206116820010_R06C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206116820020_R02C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Brain 206116820020_R03C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Spleen 206116820020_R01C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206116820067_R04C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Kidney 206116820067_R05C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse ES 206116820067_R06C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206116820020_R04C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse ES 206116820067_R01C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206116820067_R06C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206116820067_R02C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206116820067_R03C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206116820067_R04C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Liver 206116820067_R05C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Spleen 206116820067_R03C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Kidney 206116820067_R02C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Spleen 206116820067_R01C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206116820020_R04C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Adipose 206116820020_R03C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Adipose 206139140106_R05C02

description: genomic DNA from Mouse Adipose


title: genomic DNA from Mouse Liver 206139140106_R06C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140106_R04C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206139140106_R03C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206139140106_R03C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140106_R05C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206139140106_R06C01

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206139140106_R01C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140106_R02C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206139140106_R04C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Liver 206139140106_R02C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Liver 206139140072_R03C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Brain 206139140072_R02C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Liver 206139140072_R03C01

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140072_R04C01

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Liver 206139140079_R05C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140072_R02C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Brain 206139140072_R06C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140072_R05C01

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Spleen 206139140079_R06C02

description: genomic DNA from Mouse Spleen


title: genomic DNA from Mouse Brain 206139140079_R03C02

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse ES 206139140079_R02C02

description: genomic DNA from Mouse ES


title: genomic DNA from Mouse Liver 206139140079_R01C02

description: genomic DNA from Mouse Liver


title: genomic DNA from Mouse Kidney 206139140072_R04C02

description: genomic DNA from Mouse Kidney


title: genomic DNA from Mouse Brain 206139140079_R02C01

description: genomic DNA from Mouse Brain


title: genomic DNA from Mouse Kidney 206139140072_R06C02

description: genomic DNA from Mouse Kidney