title: ATACseq_13

description: Transposed DNA


title: ATACseq_18

status: Public on Feb 02 2021

type: SRA

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

country: USA

institute: St. Jude Children's Research Hospital

description: Transposed DNA

library_source: genomic

data_processing:
Peaks were called using MACS2 peak caller
ATACseq an RNAseq reads were aligned to the hg19 human genome using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bw; RNA-seq: raw counts

molecule: genomic DNA

organism: Homo sapiens

source_name: Human ALL Clinical Sample

growth_protocol: Cryopreserved patient samples were thawed using RPMI + 20% FBS and flow sorted for viable cells

extract_protocol:
DNA was transposed using the FAST-ATAC protocol and mini-elute reaction cleanup kit was used to isolate the transposed  DNA and RNA was collected using the Norgen RNA Isolation Kit
Library was constructed using illumina barcodes and SPRI bead size selection

tag: cancer type

value: Human ALL Clinical Sample

tag: cell type

value: primary acute lymphoblastic leukemia cells


title: ATACseq_10

description: Transposed DNA


title: ATACseq_1

description: Transposed DNA


title: ATACseq_16

description: Transposed DNA


title: ATACseq_6

description: Transposed DNA


title: ATACseq_2

description: Transposed DNA


title: ATACseq_8

description: Transposed DNA


title: ATRT, INI267

status: Public on Jun 02 2021

type: genomic

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using Illumina protocol

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

data_processing:
RnBeads Bioconductor R package (version 1.6.1)
matrix processed value definition: beta-value

label: cy3, cy5

source_name: Fresh frozen sample

label_protocol: Illumina Protocol

extract_protocol: Illumina Protocol

tag: gender

value: Male

tag: sample type

value: ATRT

tag: disease state

value: tumour


title: ATACseq_5

description: Transposed DNA


title: ATACseq_22

description: Transposed DNA


title: 26695 Triple pH 7.0 replicate 1

status: Public on Jan 19 2021

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
Libraries were sequenced on a NovaSeq 6000 with paired reads of 150-bp length, according to the manufacturer’s protocol.  Bcl2fastq2 conversion software (Illumina) was used to generate de-multiplexed Fastq files. A total of four independent RNA-seq libraries from four sets of H. pylori cultures grown under pH 5.3 or pH 7.0 conditions were sequenced.
RNA-seq data were trimmed to remove all bases below a quality of Q3, and adapter sequences were removed using FastQ quality control software (FaQCs).
Kallisto pseudocounting was applied to all annotated genes in the H. pylori 26695 reference genome
The EdgeR package for R was used to analyze count files. Data from individual samples were normalized within EdgeR and analyzed using the generalized linear model (GLM).
Fold change values were calculated by comparing the means of normalized pseudocounts for samples from each group (calculated by edgeR).
Genome_build: H. pylori 26695 reference genome (GenBank accession number GCA_000008525.1).
Supplementary_files_format_and_content: counts, tpm, normalized counts

molecule: total RNA

organism: Helicobacter pylori

source_name: 26695 Triple pH 7.0

growth_protocol: H. pylori cells were cultured in either pH 5.3 or pH 7.0 medium for 1 h.

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

tag: arsrs tcs

value: Triple mutant (ΔArsS, ΔCrdS, ΔFlgS)

tag: ph condition


title: 26695 Triple pH 5.3 replicate 3

source_name: 26695 Triple pH 5.3


title: 26695 Triple pH 7.0 replicate 3


title: 26695 Triple pH 7.0 replicate 2


title: 26695 Triple pH 5.3 replicate 4


title: ATACseq_7

description: Transposed DNA


title: 26695 Triple pH 7.0 replicate 4


title: 26695 Triple pH 5.3 replicate 2


title: ATACseq_17

description: Transposed DNA


title: 26695 Triple pH 5.3 replicate 1

value: ΔArsS


title: 26695 ΔArsS pH 7.0 replicate 4


title: 26695 ΔArsS pH 5.3 replicate 4


title: 26695 ΔArsS pH 7.0 replicate 1


title: 26695 ΔArsS pH 5.3 replicate 2


title: 26695 ΔArsS pH 5.3 replicate 3


title: 26695 ΔArsS pH 7.0 replicate 2


title: 26695 ΔArsS pH 7.0 replicate 3


title: 26695 ΔArsS pH 5.3 replicate 1


title: 26695 DrdxA pH 7.0 replicate 3

value: WT


title: 26695 DrdxA pH 7.0 replicate 1


title: 26695 DrdxA pH 7.0 replicate 4


title: 26695 DrdxA pH 5.3 replicate 2


title: 26695 DrdxA pH 5.3 replicate 1


title: 26695 D52N pH 7.0 replicate 3


title: 26695 DrdxA pH 5.3 replicate 3


title: 26695 DrdxA pH 7.0 replicate 2


title: 26695 D52N pH 7.0 replicate 4


title: 26695 D52N pH 7.0 replicate 2


title: 26695 D52N pH 5.3 replicate 1


title: 26695 D52N pH 5.3 replicate 2


title: 26695 D52N pH 7.0 replicate 1


title: 26695 D52N pH 5.3 replicate 4


title: 26695 D52E pH 7.0 replicate 3


title: 26695 D52E pH 7.0 replicate 2


title: 26695 D52E pH 7.0 replicate 4


title: 26695 D52E pH 7.0 replicate 1


title: 26695 D52E pH 5.3 replicate 3


title: 26695 D52E pH 5.3 replicate 4


title: 26695 DrdxA pH 5.3 replicate 4


title: 26695 D52E pH 5.3 replicate 2


title: 26695 D52D pH 7.0 replicate 3


title: 26695 D52D pH 7.0 replicate 2


title: 26695 D52D pH 7.0 replicate 4


title: 26695 D52D pH 7.0 replicate 1


title: ceh-28, dat-1, mec-3, gcy-35, unc-4 expressing neurons

status: Public on Dec 17 2020

first: David

last: Miller

address: 465 21st Ave South

department: Cell and Developmental Biology

data_processing:
Base calling was done with Illumina Real-Time Analysis Software (version 2.4.11). Data were processed using the 10x Genomics Cell Ranger (version 3.1.0) pipeline, mapping to a modified version of the WormBase reference transcriptome WS273. The modification consisted of extending the 3' UTRs from 0-400 base pairs (see Methods of the paper for details).
Genome_build: WBcel235
Supplementary_files_format_and_content: The gene_by_cell_count_matrix.txt file contains a sparse matrix where rows are genes, cells are columns and values are UMI counts for each gene in each cell. This is the filtered matrix with only the detected genes and cells that passed quality control. The gene_annotation file is a csv file containing gene ids and gene symbols. The cell annotation file is a csv file with the barcode, experiment id, tissue type and neuron type annotations for each cell. c_elegans.PRJNA13758.WS273.canonical_geneset.extend3UTR_optimized.gtf.gz contains the modified reference genome gene annotations.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: ceh-28::GFP and dat-1::GFP and mec-3::RFP and gcy-35::GFP and unc-4::GFP cells

growth_protocol: Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22. To obtain synchronized cultures of L4 worms, embryos obtained by hypochlorite treatment of adult hermaphrodites were allowed to hatch in M9 buffer overnight (16-23 hours) and then grown on NA22-seeded plates for 45-48 hours. The developmental age of each culture was determined by scoring vulval morphology (>75 worms). Single cell suspensions were obtained as described, with some modifications. Worms were collected and separated from bacteria by washing twice with ice-cold M9 and centrifuging at 150 rcf for 2.5 minutes. Worms were transferred to a 1.6 mL centrifuge tube and pelleted at 16,000 rcf for 1 minute. 250 uL pellets of packed worms were treated with 500 uL of SDS-DTT solution (20 mM HEPES, 0.25% SDS, 200 mM DTT, 3% sucrose, pH 8.0) for 2-4 minutes. In initial experiments, we noted that SDS-DTT treatment for 2 minutes was sufficient to dissociate neurons from the head and tail, but longer times were required for effective dissociation of neurons in the mid-body and ventral nerve cord. The duration of SDS-DTT was therefore selected based on the cells targeted in each experiment. For example, NC3582, OH11746, and juIs14L4 larvae were treated for 4 minutes to ensure dissociation and release of ventral cord motor neurons. NC3579 and NC3580 L4 larvae were treated with SDS-DTT for 3 minutes. All other strains were incubated in SDS-DTT for 2 minutes. Following SDS-DTT treatment, worms were washed five times by diluting with 1 mL egg buffer and pelleting at 16,000 rcf for 30 seconds. Worms were then incubated in pronase (15 mg/mL, Sigma-Aldrich P8811) in egg buffer for 23 minutes. During the pronase incubation, the solution was triturated by pipetting through a P1000 pipette tip for four sets of 80 repetitions. The status of dissociation was monitored under a fluorescence dissecting microscope at 5-minute intervals. The pronase digestion was stopped by adding 750 µL L-15 media supplemented with 10% fetal bovine serum (L-15-10), and cells were pelleted by centrifuging at 530 rcf for 5 minutes at 4 C. The pellet was resuspended in L-15-10, and single-cells were separated from whole worms and debris by centrifuging at 100 rcf for 2 minutes at 4 C. The supernatant was then passed through a 35-micron filter into the collection tube. The pellet was resuspended a second time in L-15-10, spun at 100 rcf for 2 minutes at 4 C, and the resulting supernatant was added to the collection tube. Sorting was performed on a BD FACSAria™III equipped with a 70-micron diameter nozzle. DAPI was added to the sample (final concentration of 1 µg/mL) to label dead and dying cells. Our general strategy used fluorescent reporter strains to target subgroups of neurons. For example, we used an eat-4::mCherry reporter (OH9625) to target glutamatergic neurons, and an ift-20::NLS-TagRFPreporter (OH11157) to label ciliated sensory neurons. We used an intersectional labeling strategy with a nuclear-localized pan-neural marker (otIs355 [rab-3(prom1)::2xNLS-TagRFP] IV) to exclude cell fragments labeled with cytosolic GFP markers (NC3582). In other cases, we used an intersectional strategy to exclude non-neuronal cells. For example, ceh-34p::HIS-24::mCherry is expressed in pharyngeal muscles, pharyngeal neurons, and coelomocytes. To target pharyngeal neurons, we generated strain NC3583 by crossing stIs10447 [ceh-34p::HIS-24::mCherry] with the pan-neural GFP marker evIs111 to isolate the cells that were positive for both mCherry and GFP. Non-fluorescent N2 standards and single-color controls (in the case of intersectional labeling approaches) were used to set gates to exclude auto-fluorescent cells and to compensate for bleed-through between fluorescent channels. In some cases, we set FACS gates to encompass a wide range of fluorescent intensities above background to ensure capture of targeted cell types. This less stringent approach may contribute to the presence of non-neuronal cells in our dataset (see Results). Cells were sorted under the “4-way Purity” mask. Sorted cells were collected into L-15-33 (L-15 medium containing 33% fetal bovine serum), concentrated by centrifugation at 500 rcf for 12 minutes at 4°C, and counted on a hemocytometer. Single-cell suspensions used for 10x Genomics single-cell sequencing ranged from 300-900 cells/µL.

extract_protocol:
Single-cell capture and library preparation followed published 10x Genomics protocols.
5000 or 10000 cells were targeted per sample, and library preparation was completed using either v2 or v3 chemistry kits (see individual Samples for details).

tag: strain

tag: developmental stage

tag: cells targeted

tag: 10x genomics library kit


title: nlp-13, ceh-2 expressing neurons

source_name: nlp-13::GFP+ and ceh-2::GFP cells

value: nlp-13::GFP - 63.5% L4, 22.6% early adult. ceh-2::GFP 46.6% L4, 50% early adult


title: 26695 D52D pH 5.3 replicate 4


title: unc-53 expressing neurons

source_name: unc-53::GFP+ neurons

value: NC3636; hdIs1 [unc-53p::GFP + rol-6(su1006)]; otIs355 [rab-3prom1::2xNLS-tagRFP] IV


title: 26695 D52D pH 5.3 replicate 3


title: unc-86 expressing neurons

source_name: unc-86::myr-GFP+ neurons

value: CX5974; unc-86::myr-GFP + odr-1::RFP] IV

value: 72% L4; 28% early adult


title: WES 5 b_Day232 recipient

status: Public on Jul 22 2020

city: st louis

first: andrew

last: malone

state: MO

address: 4525 laclede ave

institute: Washington University

description: Whole-exome sequence

data_processing:
Library strategy: whole exome sequencing
scRNA-Seq: The Illumina HiSeq platform was used to generate paired end read sequence (2x150) on the S4 flow cell to a depth of 50,000 reads per cell for gene expression and 5,000 reads per cell for VDJ sequence. The Cellranger 3.0 pipeline was used to generate BAM files and gene expression matrices for each biopsy. Matrices were used to generate Seurat objects using Seurat v3
The unnormalized counts data (*rawcounts.csv) are from the output of the Cellranger pipeline and embedded within the Seurat single cell object.
Whole-exome-seq: libraries were pooled and hybridized with the xGen Exome Research Panel v1.0 reagent (IDT Technologies) that spans 39 Mb target region (19,396 genes) of the human genome.The Illumina NovaSeq6000 instrument was used to generate approximately 5Gb of paired end sequence data (2x150) on the S4 flow cell was generated targeting 50x coverage per sample.

source_name: PBMC

extract_protocol:
18G needle core biopsy tissues
Core tissue was dissociated into singel cell suspension
cells were dissociated using Trypsin and DNaseI at 37C
cDNA libraries were prepared per 10X Chromium standard protocol usig 5-prime kits

tag: tissue

value: PBMC

tag: protocol

tag: platform

value: Illumina NovaSeq6000

tag: time point


title: 26695 D52N pH 5.3 replicate 3


title: 26695 D52D pH 5.3 replicate 1


title: WES 5 a_Day232 donor

description: Whole-exome sequence

value: xGen Exome Research Panel v1.0 reagent (IDT Technologies)


title: 26695 D52D pH 5.3 replicate 2


title: WES 4 a_Day5 donor

description: Whole-exome sequence


title: WES 4 b_Day5 recipient

description: Whole-exome sequence


title: WES 3 a_Day11 donor

description: Whole-exome sequence


title: WES 2 b_Day2542 recipient

description: Whole-exome sequence


title: WES 1 a_Day28 donor

description: Whole-exome sequence


title: WES 1 b_Day28 recipient

description: Whole-exome sequence


title: WES 3 b_Day11 recipient

description: Whole-exome sequence


title: 26695 D52E pH 5.3 replicate 1


title: Biopsy6_Pre-treatment

description: single cell RNA-seq

data_processing:
scRNA-Seq: The Illumina HiSeq platform was used to generate paired end read sequence (2x150) on the S4 flow cell to a depth of 50,000 reads per cell for gene expression and 5,000 reads per cell for VDJ sequence. The Cellranger 3.0 pipeline was used to generate BAM files and gene expression matrices for each biopsy. Matrices were used to generate Seurat objects using Seurat v3
The unnormalized counts data (*rawcounts.csv) are from the output of the Cellranger pipeline and embedded within the Seurat single cell object.
Whole-exome-seq: libraries were pooled and hybridized with the xGen Exome Research Panel v1.0 reagent (IDT Technologies) that spans 39 Mb target region (19,396 genes) of the human genome.The Illumina NovaSeq6000 instrument was used to generate approximately 5Gb of paired end sequence data (2x150) on the S4 flow cell was generated targeting 50x coverage per sample.

source_name: Needle Biopsy (kidney)

value: Needle Biopsy (kidney)

value: 10X Chromium


title: Biopsy5_Day232

description:
single cell RNA-seq
MGI.count.matrix.csv


title: Biopsy1_Day28


title: Biopsy3_Day11


title: Biopsy2_Day2542


title: WT, 24 h, rep2

status: Public on May 21 2020

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

country: Germany

institute: Ruhr University Bochum

description:
gene_expression_DUF1127.FPKM.xls
d3_24h_vs_WT_24h.genes.DEA.xls

data_processing:
Adapter sequences and raw reads of low quality were removed through in-house scripts by Novogene.
Clean paired-end reads were mapped via HISAT2 software.
Novel genes were using the Cufflinks Reference Annotation Based Transcript (RABT) assembly method.
The read numbers that were mapped for each gene were counted via HTSeq. FPKM (Fragments Per Kilobase of exon model per Million reads mapped) values were calculated.
A differential expression analysis was performed between two groups (three biological replicates each) using the DESeq2 R package. P values were adjusted via Banjamini.Hochberg procedure for determination of the False Discovery Rate. An adjusted p value below 0.05 was cosidered to describe a significantly differentially expressed gene.
Genome_build: ASM9202v1; small RNA genes were added from Wilms et al. (2012, DOI: 10.4161/rna.17212), Lee et al. (2013, DOI: 10.1371/journal.pone.0070720) and from Möller et al. (2014, DOI: 10.1371/journal.pone.0110427)
Supplementary_files_format_and_content: Files include FPKM values calculated from the three biological replicates, the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Agrobacterium fabrum str. C58

source_name: Agrobacterium fabrum C58 total RNA

growth_protocol: Cells were grown at 30 °C in YEB medium. Samples were taken at an optical density (600 nm) of 0.5, of 1.5 and after 24 h.

extract_protocol:
RNA was extracted via hot-phenol method as described in Wilms et al. (2012, DOI: 10.4161/rna.17212). Samples were treated with RNase-free DNase.
RNA libraries were prepared by Novogene. 1 µg of RNA was used. Sequencing libraries were generated with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer's instructions. Index codes were added to attribute sequences to each sample. Fragmentation was done with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. First strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand was synthesized with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activites. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system (Backman Cooulter, USA). The cDNA was incubated at 37 °C for 15 min with 3 µl USER Enzyme (NEB, USA) and then at 95 °C for 5 min.The subsequent PCR was done with Phusion High-Fidelity DNA polymerase, Universail PCR primers and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.

tag: genotype

value: wild type

tag: od

value: at 24 hours


title: WT, 24 h, rep3


title: 0-8h unsexed vas-GFP germ cells

status: Public on Sep 10 2020

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

description: Sex: unsexed

data_processing:
Alignment and generation of feature-barcode matrices was performed with Cell Ranger (unsexed: version 3.0.1, sexed: version 3.1.0)
Data was preprocessed using PCA (number of dimensions=100) with Monocle3
Dimension reduction using the UMAP method (maximum components=2) was performed with Monocle3
Clustering analysis with the leiden algorithm was done with Monocle3
Genome_build: Drosophila BDGP6.28
Supplementary_files_format_and_content: The features, barcode, and matrix files were generated by Cell Ranger
Supplementary_files_format_and_content: exprs_*.csv: Count matrix

organism: Drosophila melanogaster

source_name: germ cells

growth_protocol: Eggs were laid on 0.8% grape juice plates for the designated periods at 25°C or for double the time at 18°C

extract_protocol:
Embryos were dechorinated and homogenized with the loose pestle in a Dounce homogenizer for 6-7 strokes, filtered twice through 70mm mesh and collected at 850 g for 2 min, and FACS sorted for GFP expression.
Unsexed sample: 10X Genomics Chromium Single Cell 3' v2 kit; sexed samples: 10X Genomics Chromium Single Cell 3' v3 kit

value: vas-GFP

value: 0-8h embryos

tag: Sex

value: not applicable


title: Paired Adjacent Normal sample from Z2084_N patient

status: Public on May 10 2020

city: L'Hospitalet de Llobregat

first: Victor

last: Moreno

state: Barcelona

address: Granvia 199

department: Oncology Data Analytics Program

country: Spain

institute: Catalan Institute of Oncology

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2084_N

hyb_protocol: Bisulfite conversion of DNA (200-500 ng) was performed according to the manufacturer’s recommendations for the Illumina Infinium Assay (EZ DNA methylation kit. Zymo Research. Cat. No. D5004).

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Methylation level at each locus was measured using β values calculated based on Illumina’s standard, using the average probe intensity for the methylated and unmethylated alleles
matrix processed value definition: Average Beta

label: Cy3, Cy5

source_name: colon

label_protocol: Cy3 and Cy5;   Standard Illumina labelling protocol

extract_protocol: Genomic DNA was extracted from colon tissue by the phenol-chloroform procedure, quantified using a Nano Drop ND 2000c spectrophotometer (NanoDrop Thermo scientific, Wilmington, DE) and stored at 4ºC.

value: Normal

tag: Stage

value: IIA

value: Male

tag: age

tag: location

value: Left


title: Tumor sample from Z2015_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2015_T_0

value: Tumor

tag: gender

value: Right


title: Paired Adjacent Normal sample from Z2038_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2038_N

value: Female


title: Tumor sample from Z2038_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2038_T


title: Mucosa sample from Z2107_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2107_M

value: Mucosa


title: Tumor sample from Y2099_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2099_T


title: Tumor sample from Z2084_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2084_T


title: Paired Adjacent Normal sample from Z2061_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2061_N


title: Paired Adjacent Normal sample from Y2099_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2099_N


title: Tumor sample from Y2076_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2076_T


title: Tumor sample from Z2061_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2061_T


title: Biopsy7_Post-treatment

description: single cell RNA-seq


title: Paired Adjacent Normal sample from Y2076_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2076_N


title: Tumor sample from Y2053_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2053_T


title: Tumor sample from Y2030_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2030_T


title: WES 2 a_Day2542 donor

description: Whole-exome sequence

value: PBMC

value: Illumina NovaSeq6000


title: Paired Adjacent Normal sample from Y2030_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2030_N


title: Biopsy4_Day5

description:
single cell RNA-seq
MGI.count.matrix.csv

value: Needle Biopsy (kidney)


title: Tumor sample from Y2007_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2007_T


title: Paired Adjacent Normal sample from Y2007_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2007_N


title: Tumor sample from X2080_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2080_T


title: WT, 24 h, rep1

description:
gene_expression_DUF1127.FPKM.xls
d3_24h_vs_WT_24h.genes.DEA.xls


title: Paired Adjacent Normal sample from X2057_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2057_N


title: scRNA-seq of notum-1-treatment embryo replicate 1

status: Public on Aug 18 2021

city: New Haven

first: Scott

middle: A.

last: Holley

state: CT

address: 219 Prospect St

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

description: No other description

data_processing:
We aligned the scRNA-seq data to Grcz11 and demultiplexed using Cell Ranger (10X Genomics, version 3.0).
Genome_build: Grcz11
Supplementary_files_format_and_content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes (column labels for MTX file) and gene names (row labels for MTX file).

organism: Danio rerio

source_name: tail

extract_protocol:
Cells were dissociated by incubation in 20 U/mL papain solution (Worthing Biochemical) for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required.
Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard Illumina BCL data output folder. The BCL data includes the paired-end Read 1 (containing the 16 bp 10x Barcode and 10 bp UMI) and Read 2 and the sample index in the i7 index read.

treatment_protocol: Embryos were incubated until the 10-12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild-type, FGF, or BMP inhibition or twelve tails for Wnt inhibition were pooled together.

tag: treatment


title: Tumor sample from X2057_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2057_T


title: Paired Adjacent Normal sample from Z2015_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Z2015_N_0


title: Tumor sample from X2034_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2034_T


title: Mucosa sample from W6143_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W6143_M


title: Paired Adjacent Normal sample from W2072_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2072_N


title: Mucosa sample from W2141_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2141_M


title: Paired Adjacent Normal sample from W2095_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2095_N


title: Tumor sample from W2072_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2072_T


title: Mucosa sample from W2118_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2118_M


title: Paired Adjacent Normal sample from X2034_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2034_N


title: Tumor sample from W2003_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2003_T


title: Tumor sample from W2049_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2049_T


title: Tumor sample from X2011_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2011_T


title: Paired Adjacent Normal sample from W2049_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2049_N


title: Mucosa sample from V6135_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V6135_M


title: Mucosa sample from V2133_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2133_M


title: Paired Adjacent Normal sample from W2026_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2026_N


title: Tumor sample from V2087_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2087_T


title: Mucosa sample from V2110_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2110_M


title: Mucosa sample from X2126_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2126_M


title: Paired Adjacent Normal sample from Y2053_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Y2053_N


title: Paired Adjacent Normal sample from V2087_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2087_N


title: Paired Adjacent Normal sample from V2064_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2064_N


title: Tumor sample from V2064_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2064_T


title: Paired Adjacent Normal sample from X2080_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2080_N


title: Tumor sample from V2041_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2041_T


title: Paired Adjacent Normal sample from V2018_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2018_N


title: Paired Adjacent Normal sample from V2041_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
V2041_N


title: Tumor sample from W2095_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2095_T


title: Mucosa sample from T6141_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T6141_M


title: Paired Adjacent Normal sample from X2011_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
X2011_N


title: Paired Adjacent Normal sample from T2047_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2047_N


title: Tumor sample from T2024_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2024_T


title: Paired Adjacent Normal sample from T2093_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2093_N

value: IIB


title: Mucosa sample from S2131_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2131_M


title: Tumor sample from T2001_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2001_T


title: Tumor sample from T2093_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2093_T


title: Mucosa sample from S2108_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2108_M


title: Tumor sample from S2062_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2062_T


title: Tumor sample from S2085_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2085_T


title: Paired Adjacent Normal sample from S2062_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2062_N


title: Paired Adjacent Normal sample from S2039_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2039_N


title: Mucosa sample from T2116_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2116_M


title: Tumor sample from W2026_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
W2026_T


title: Tumor sample from S2039_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2039_T


title: Mucosa sample from R6142_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R6142_M


title: Paired Adjacent Normal sample from S2016_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2016_N


title: Mucosa sample from R2140_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2140_M


title: Tumor sample from T2047_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2047_T


title: Paired Adjacent Normal sample from S2085_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2085_N


title: Tumor sample from S2016_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
S2016_T


title: Tumor sample from R2094_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2094_T


title: Paired Adjacent Normal sample from R2094_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2094_N


title: Tumor sample from R2071_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2071_T


title: Paired Adjacent Normal sample from R2071_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2071_N


title: Tumor sample from R2048_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2048_T


title: Tumor sample from R2025_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2025_T


title: Paired Adjacent Normal sample from T2070_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2070_N


title: Paired Adjacent Normal sample from T2024_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
T2024_N


title: Paired Adjacent Normal sample from R2048_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2048_N


title: Tumor sample from R2002_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2002_T


title: Paired Adjacent Normal sample from R2025_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2025_N


title: Paired Adjacent Normal sample from R2002_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2002_N


title: Mucosa sample from Q2132_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2132_M


title: Tumor sample from Q2086_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2086_T


title: Mucosa sample from Q2109_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2109_M


title: Paired Adjacent Normal sample from Q2063_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2063_N


title: Paired Adjacent Normal sample from Q2040_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2040_N


title: Tumor sample from Q2017_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2017_T


title: Paired Adjacent Normal sample from Q2086_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2086_N


title: Tumor sample from Q2063_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2063_T


title: Paired Adjacent Normal sample from Q2017_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2017_N


title: Tumor sample from Q2040_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q2040_T


title: Mucosa sample from P2124_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2124_M


title: Mucosa sample from P2101_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2101_M


title: Tumor sample from P2078_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2078_T


title: Paired Adjacent Normal sample from P2078_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2078_N


title: Tumor sample from P2055_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2055_T


title: Paired Adjacent Normal sample from P2055_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2055_N


title: Tumor sample from P2009_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2009_T


title: Tumor sample from P2032_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2032_T


title: Paired Adjacent Normal sample from P2032_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2032_N


title: Paired Adjacent Normal sample from P2009_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
P2009_N


title: Mucosa sample from N2128_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2128_M


title: Tumor sample from N2082_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2082_T


title: Mucosa sample from N2105_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2105_M


title: Tumor sample from N2059_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2059_T


title: Paired Adjacent Normal sample from N2059_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2059_N


title: Mucosa sample from Q6134_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
Q6134_M


title: Tumor sample from N2036_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2036_T


title: Paired Adjacent Normal sample from N2013_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2013_N


title: Tumor sample from N2013_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2013_T


title: Mucosa sample from M2121_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2121_M


title: Tumor sample from M2098_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2098_T


title: Paired Adjacent Normal sample from M2075_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2075_N


title: Tumor sample from M2075_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2075_T


title: Tumor sample from M2029_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2029_T


title: Tumor sample from M2052_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2052_T


title: Paired Adjacent Normal sample from M2029_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2029_N


title: Paired Adjacent Normal sample from M2098_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2098_N


title: Paired Adjacent Normal sample from M2052_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2052_N


title: Mucosa sample from L2135_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2135_M


title: Paired Adjacent Normal sample from M2006_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2006_N


title: Mucosa sample from L2112_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2112_M


title: Tumor sample from M2006_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2006_T


title: Tumor sample from L2066_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2066_T


title: Paired Adjacent Normal sample from L2089_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2089_N


title: Paired Adjacent Normal sample from L2066_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2066_N


title: Paired Adjacent Normal sample from L2020_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2020_N


title: Tumor sample from L2043_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2043_T


title: Paired Adjacent Normal sample from N2036_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
N2036_N


title: Paired Adjacent Normal sample from L2043_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2043_N


title: Tumor sample from L2020_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2020_T


title: Mucosa sample from M2144_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
M2144_M


title: Mucosa sample from K6139_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K6139_M


title: Tumor sample from K2091_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2091_T


title: Mucosa sample from K2137_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2137_M


title: Paired Adjacent Normal sample from K2091_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2091_N


title: Tumor sample from K2068_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2068_T


title: Paired Adjacent Normal sample from K2068_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2068_N


title: Mucosa sample from L6137_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L6137_M


title: Paired Adjacent Normal sample from K2045_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2045_N


title: Tumor sample from K2022_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2022_T


title: Paired Adjacent Normal sample from J2083_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2083_N


title: Paired Adjacent Normal sample from K2022_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2022_N


title: Tumor sample from J2060_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2060_T


title: Tumor sample from K2045_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2045_T


title: Paired Adjacent Normal sample from J2037_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2037_N


title: Paired Adjacent Normal sample from J2060_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2060_N


title: Tumor sample from L2089_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
L2089_T


title: Tumor sample from J2037_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2037_T


title: Mucosa sample from K2114_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
K2114_M


title: Mucosa sample from J2106_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2106_M


title: Paired Adjacent Normal sample from J2014_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2014_N


title: Tumor sample from J2014_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
J2014_T


title: Mucosa sample from H6136_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H6136_M


title: Mucosa sample from H2134_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2134_M


title: Tumor sample from H2088_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2088_T


title: Mucosa sample from H2111_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2111_M


title: Tumor sample from H2065_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2065_T


title: Paired Adjacent Normal sample from H2088_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2088_N


title: Paired Adjacent Normal sample from H2065_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2065_N


title: Paired Adjacent Normal sample from H2042_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2042_N


title: Paired Adjacent Normal sample from H2019_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2019_N


title: Tumor sample from H2042_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2042_T


title: Mucosa sample from G2120_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2120_M


title: Paired Adjacent Normal sample from G2074_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2074_N


title: Tumor sample from F2077_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2077_T


title: Paired Adjacent Normal sample from G2005_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2005_N


title: Tumor sample from G2005_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2005_T


title: Tumor sample from G2097_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2097_T


title: Tumor sample from G2051_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2051_T


title: Paired Adjacent Normal sample from G2097_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2097_N


title: Paired Adjacent Normal sample from F2054_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2054_N


title: Paired Adjacent Normal sample from F2031_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2031_N


title: Tumor sample from F2054_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2054_T


title: Paired Adjacent Normal sample from G2051_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2051_N


title: Tumor sample from F2008_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2008_T


title: Paired Adjacent Normal sample from G2028_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2028_N


title: Paired Adjacent Normal sample from F2100_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2100_N


title: Tumor sample from F2031_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2031_T


title: Tumor sample from F2100_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2100_T


title: Tumor sample from G2028_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2028_T


title: Mucosa sample from E6140_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E6140_M


title: Paired Adjacent Normal sample from F2008_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2008_N


title: Paired Adjacent Normal sample from E2092_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2092_N


title: Mucosa sample from E2115_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2115_M


title: Tumor sample from H2019_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
H2019_T


title: Tumor sample from E2046_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2046_T


title: Tumor sample from E2069_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2069_T


title: Paired Adjacent Normal sample from E2069_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2069_N


title: Tumor sample from E2092_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2092_T


title: Mucosa sample from G2143_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
G2143_M


title: Paired Adjacent Normal sample from F2077_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
F2077_N


title: Paired Adjacent Normal sample from E2046_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2046_N


title: Tumor sample from D2010_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2010_T


title: Mucosa sample from D2125_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2125_M


title: Paired Adjacent Normal sample from D2010_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2010_N


title: Tumor sample from E2023_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2023_T


title: Tumor sample from C2067_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2067_T


title: Paired Adjacent Normal sample from E2023_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
E2023_N


title: Paired Adjacent Normal sample from D2079_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2079_N


title: Paired Adjacent Normal sample from C2044_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2044_N


title: Paired Adjacent Normal sample from D2033_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2033_N


title: Tumor sample from D2079_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2079_T


title: Tumor sample from D2033_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2033_T


title: Mucosa sample from D2102_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2102_M


title: Paired Adjacent Normal sample from C2067_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2067_N


title: Paired Adjacent Normal sample from C2021_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2021_N


title: Paired Adjacent Normal sample from C2090_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2090_N


title: Mucosa sample from D2148_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2148_M


title: Mucosa sample from C2113_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2113_M


title: Mucosa sample from C2136_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2136_M


title: Tumor sample from C2044_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2044_T


title: Tumor sample from C2090_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2090_T


title: Mucosa sample from B2150_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2150_M


title: Mucosa sample from B2104_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2104_M


title: Paired Adjacent Normal sample from B2081_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2081_N


title: Tumor sample from B2081_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2081_T


title: Tumor sample from C2021_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C2021_T


title: Mucosa sample from B2127_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2127_M


title: Tumor sample from B2058_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2058_T


title: Tumor sample from D2056_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
D2056_T


title: Mucosa sample from C6138_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
C6138_M


title: Tumor sample from B2012_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2012_T


title: Tumor sample from B2035_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2035_T


title: Paired Adjacent Normal sample from B2012_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2012_N


title: Paired Adjacent Normal sample from B2035_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2035_N


title: Paired Adjacent Normal sample from B2058_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
B2058_N


title: Mucosa sample from A6144_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A6144_M


title: Paired Adjacent Normal sample from A2096_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2096_N


title: Tumor sample from A2027_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2027_T


title: Tumor sample from A2096_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2096_T


title: Paired Adjacent Normal sample from A2073_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2073_N


title: Paired Adjacent Normal sample from A2027_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2027_N


title: Tumor sample from A2073_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2073_T


title: Tumor sample from A2050_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2050_T


title: Paired Adjacent Normal sample from A2004_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2004_N


title: Tumor sample from A2004_T patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2004_T


title: ZFX_ZF_11_13_FLAG_DKO_clone1_rep2

status: Public on Apr 30 2020

city: Los Angeles

first: Weiya

middle: Stephanie

last: Ni

state: California

address: 1450 Biggy Street

institute: University of Southern California

description: USC_RNA397_ZFX_ZF_11_13_FLAG_DKO_clone1_rep2

data_processing:
RNA-seq results were aligned to Gencode v19 and reads were counted using STAR.
Read count table is generated using STAR as well.
Genome_build: hg19
Supplementary_files_format_and_content: text files include read count for each gene.

growth_protocol: HEK293T cells were grown according to ATCC protocol

extract_protocol:
Total RNA were extracted following the trizol protocol.
Libraries were prepared using Kapa Stranded mRNA kit with beads (Kapa #KK8421) according to provided protocol.

tag: cell line

tag: clone name

value: DKO clone1

value: DKO

tag: grna

value: ZFX KO:g1, g2; ZNF711 KO:g1,g2


title: ZFX_ZF_11_13_FLAG_DKO_clone1_rep1

description: USC_RNA396_ZFX_ZF_11_13_FLAG_DKO_clone1_rep1


title: Mucosa sample from R2117_M healthy donor

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
R2117_M


title: ZFX_ZF_11_13_FLAG_DKO_clone1_rep3

description: USC_RNA398_ZFX_ZF_11_13_FLAG_DKO_clone1_rep3


title: HEK293T, ZFX ChIP in HEK293T - rep1

data_processing:
Sequencing results were aligned to hg19 using bwa
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak files with quantitative data

extract_protocol:
Chromatins were prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Librarys were prepared using KAPA Hyper Prep Kit (Kapa #KK8505) according to provided protocol

value: kidney cell line HEK293T

tag: factor

value: ZFX

tag: chip antibody

value: CST, L28B6, lot 1


title: ChIP-chip repeat 1

status: Public on Dec 08 2019

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

country: China

institute: Hunan Normal University

description:
Sample1
ChIP-chip MDA-MB-468

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4μg of Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA). For array hybridization, Roche Nimblegen's HG18 Deluxe HX1 Promoter array was used, which is a single array design containing all known well-characterized RefSeq genes. The promoter regions (from about -7250bp to +3250bp of the TSSs) on this array are covered by ~2100, 000 50-75mer probes with approximately 100bp spacing, dependent on the sequence composition of the region.

scan_protocol: Microarrays were scanned using an Axon 4000B microarray scanner with GenePix 6.0.

data_processing:
Data Normalization: Median-centering, quantile normalization, and linear smoothing is performed by Bioconductor packages Ringo, limma, and MEDME. ChIP Enrichment Peak-Finding: A permutation-based peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) is applied to analysis the ChIP-on-chip data.
Supplementary files format and content: *_635_ratio_peaks.gff: Identified peaks which represent regions of significant positive enrichment.
Supplementary files format and content: Enriched peaks.csv: Enriched peaks data of the 3 samples which contains all identified peaks overlapping the promoter region of the relevant transcript (-7250bp ~ +3250bp).
Supplementary files format and content: Summary of enriched peaks.csv: The summary list of peaks overlapping the promoter region of the transcripts for the 3 samples.

source_name: p53 ChIP DNA from MDA-MB-468 cells

label_protocol: The purified DNA was quantified using a nanodrop ND-1000. For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen ChIP-on-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer (IP sample) or Cy5-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Cell samples were cross-linked in 1% formaldehyde for 10 min at room temperature. Cross-linking was stopped by addition of 1 M glycine to a final concentration of 125 mM for 5 min. Cells were washed twice with PBS, scraped and collected by centrifugation. The cell pellet was dissolved in nuclei lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCl, pH 8.0). Extracts were sonicated using the Bioruptor (Diagenode) at high power until DNA fragments of ∼200–1000 bp were formed. Sonicated chromatin was diluted in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 16.7 mM Tris–HCl, pH 8.0). The immuno-complexes were precipitated using antibodies against p53 (Milli pore), or IgG (Santa Cruz Biotechnologies). Precipitated complexes were reverse cross-linked and proteins digested with proteinase K (Fermentas) overnight at 65°C. DNA fragments were purified using Qiagen MinElute columns (Qiagen).The Immunoaffinity-enriched DNA was amplified using a WGA kit from Sigma-Aldrich (GenomePlex® Complete Whole Genome Amplification (WGA2) kit). The amplified DNA samples were then purified with QIAquick PCR purification kit (Qiagen).

tag: cell type

source_name: Input DNA from MDA-MB-468 cells

value: none, input DNA


title: ChIP-chip repeat 3

description:
Sample3
ChIP-chip MDA-MB-468


title: ChIP-chip repeat 2

description:
Sample2
ChIP-chip MDA-MB-468


title: Tumor_WT_w2222

status: Public on Oct 09 2019

city: Pittsburgh

first: Edward

middle: V

last: Prochownik

state: PA

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
CLC Genomics Workbench v12.0
Genome_build: Reference sequence = Mus_musculus_ensembl_v80_Sequence Gene track = mus_musculus_refseq_GRCm38.p6_Genes  mRNA track = mus_musculus_refseq_GRCm38.p6_mRNA
Supplementary_files_format_and_content: CPMs

organism: Mus musculus

source_name: Tumor

extract_protocol:
RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: hdtvi plasmid

value: SB_WT+xloc+SB_YAP S127A

tag: strain

value: FVB

tag: tissue


title: Tumor_WT_w2223

value: Tumor


title: Paired Adjacent Normal sample from A2050_N patient

description:
Extraction by phenol-chloroform procedure, quantified with Nano Drop ND 2000c
A2050_N

value: Normal

value: IIA

value: Male

value: Left


title: Tumor_WT_w2210


title: Tumor_WT_w2204


title: Tumor_S45A_s1786

value: SB_S45A+xloc+SB_YAP S127A


title: Tumor_S45A_s1776

value: Female


title: Tumor_S45A_s1764


title: Tumor_WT_w2217


title: Tumor_S33Y_s2172

value: SB_S33Y+xloc+SB_YAP S127A


title: Tumor_S45A_s1760


title: Tumor_S33Y_s2173


title: Tumor_S33Y_s2160


title: Tumor_S33Y_s2157


title: Tumor_S45A_s1762


title: Tumor_S33A_s2146

value: SB_S33A+xloc+SB_YAP S127A


title: Tumor_S33Y_s2155


title: Tumor_S33A_s2132


title: Tumor_S33A_s2140


title: Tumor_S33A_s1797


title: Normal Liver_c1

source_name: Liver

value: no injection

value: Liver


title: Normal Liver_c7


title: Normal Liver_c4


title: Tumor_N387K_n2293

value: SB_N387K+xloc+SB_YAP S127A


title: Tumor_N387K_n2279


title: Normal Liver_c12


title: Tumor_N387K_n2284


title: Tumor_N387K_n2272


title: Tumor_N387K_n2275


title: Normal Liver_c17


title: Tumor_K335I_k2261

value: SB_K335I+xloc+SB_YAP S127A


title: Tumor_K335I_k2266


title: Tumor_Del90_s2139

value: SB_Del90+xloc+SB_YAP S127A


title: Tumor_K335I_k2250


title: Tumor_K335I_k2253


title: Tumor_S33A_s2144


title: Tumor_Del90_s1800


title: Tumor_Del36-53_d2135

value: SB_Del36-53+xloc+SB_YAP S127A


title: Tumor_Del90_s1758


title: Tumor_Del36-53_d2136


title: Tumor_Del90_s1799


title: Tumor_Del36-53_d2130


title: Tumor_Del36-53_d2147


title: Tumor_Del20-32_s1770

value: SB_Del20-32+xloc+SB_YAP S127A


title: Tumor_Del20-32_s1779

value: FVB


title: Tumor_Del36-53_d2123

value: Tumor


title: Tumor_Del20-32_s1769


title: Tumor_Del20-32_s1766


title: Tumor_Del20-32_s1780


title: HEK293T, ZFX ChIP in HEK293T - rep2

value: kidney cell line HEK293T

value: ZFX

value: CST, L28B6, lot 1


title: Tumor_K335I_k2242

value: Male


title: Tumor_Del90_s2138


title: JLKD066

status: Public on Sep 17 2019

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: WGBS

data_processing:
Filter using Illumina flag
trim and filter reads using TrimGalore
Align to hg38 using Bismark
Remove PCR duplicates
Extract DNA methylation using Bismark
Genome_build: Hg38
Supplementary_files_format_and_content: Bismark cytosine reports

extract_protocol:
genomic DNA extracted and purified using the Qiagen Puregene kit
Five (5) μg of DNA was fragmented to ~300 bp using 28 cycles of 15 seconds on/15 seconds off on a Diagenode Bioruptor. DNA was end-repaired using 1× T4 DNA ligase buffer, 400 μM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 min at 20°C. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1× NEB 2 buffer, 200 μM dATP, and 15 U Klenow Fragment (3′ to 5′ exo-, NEB) for 30 min at 37°C. After another DNA purification using the PCR MinElute kit (Qiagen), 3 μL of Illumina's methylated sequencing adapters were ligated on using 1× ligase buffer and 5 μL Quick T4 DNA Ligase (NEB) for 30 min at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.
Bisulfite-Seq 100 bp single end on Illumina HiSeq 2000

tag: subject status

value: Control

tag: age (years)

value: dorsal lateral prefrontal cortex

tag: brain area

value: brodmann area 9


title: JLKD069

description: WGBS

tag: Sex

value: Female


title: JLKD059

description: WGBS

value: Autism Spectrum Disorder


title: JLKD060

description: WGBS


title: JLKD057

description: WGBS


title: JLKD055

description: WGBS


title: JLKD058

description: WGBS


title: JLKD063

description: WGBS


title: JLKD061

description: WGBS


title: JLKD054

description: WGBS


title: JLKD065

description: WGBS


title: JLKD067

description: WGBS


title: JLKD062

description: WGBS


title: JLKD056

description:
WGBS
NOTE: The NICHD Brain Bank labelled this sample as male, but subsequent analysis of its methylation patterns suggests this sample is from a female.

value: not determined


title: JLKD052

description: WGBS


title: BSC_5214: RTT_2

description: WGBS

source_name: post-mortem brain

extract_protocol:
genomic DNA extracted and purified using the Zymo Duet Kit
DNA was extracted from BA9 cortex from RTT and Control samples using the Zymo Duet Kit (Zymo). 200ng of total DNA was bisulfite converting using the Zymo Lighting kit (Zymo) and 50ng of converted DNA was used as input for library construction using the Illumina TruSeq DNA Methylation Kit (Illumina).  Each sample was given a unique barcode and 14 cycles of PCR amplification.  Final libraries were size selected with two rounds of KAPA Pure Beads: 0.7X Left and 0.65X Left/0.55X Right for a final library size centered around 370-470 base pairs. Final libraries were assessed with Bioanalyzer (Agilent), quantified, pooled and run for 150 bp paired end sequencing on two lanes of the HiSeqX (Illumina).
Bisulfite-Seq 150 bp paired end on Illumina HiSeqX

value: Rett Syndrome

tag: mutation

value: MECP2 p.R270X


title: BSC_1815: RTT_3

description: WGBS


title: BSC_4687: RTT_1

description: WGBS

value: MECP2 p.R255X


title: BSC_5075: RTT_5

description: WGBS

value: RTT MECP2 mutation negative


title: BSC_754: Control_6

description: WGBS


title: BSC_738: Control_4

description: WGBS


title: 10X 2673 retinal single-cells batch E2

status: Public on Aug 23 2019

city: Genève 4

first: Quentin

last: Lo Giudice

state: switzerland

address: 1 rue Michel Servet

department: Department of Basic Neurosciences

country: Switzerland

institute: University of Geneva

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star.
After the CellRanger 2.1.1 processing, Seurat package version 2.3 (Butler et al., 2018) was used to import in R version 3.4.4 (R Core Team) 2 batches of 2673 and 2675 cells to perform downstream analysis. The merge of batches was performed by aggregation with the inbuilt Seurat function MergeSeurat while batch effect correction was made possible by linear regression of the transcriptomic expression of the 2 batches during the scaling and centering of the dataset by the ScaleData function.
Cells considered during the creation of the Seurat object expressed at least 200 genes, and genes kept are expressed in a minimum of 3 cells. Mitochondrial gene effect was regressed out for the whole data. 1648 variable gene were defined on variability plot as mean expression above 0.1 and dispersion above 1.
Genome_build: mm10
Supplementary_files_format_and_content: Merged5347cells_RAW.csv : comma-delimited text files (csv) including counts values of the merged datasets.
Supplementary_files_format_and_content: Merged5347cellsLogNormalized.csv : comma-delimited text files (csv) including log-normalized counts values of the merged datasets.
Supplementary_files_format_and_content: Merged5347cellsLogNormalizedScaled.csv : comma-delimited text files (csv) including the scaled and log-normalized counts values of the merged datasets.

source_name: Retinal E15.5 cells

extract_protocol:
Coordinated pregnant mice of 12 to 30 weeks were ethically sacrificed to extract E15.5 embryos eyes. Thirty retinas were extracted in ice-cold L15, micro-dissected under a stereomicroscope and incubated in 200µl single cell dissociation solution consisting in a papain (1mg/ml) enriched HBSS at 37°C for 12 minutes with trituration every 2 minutes. At the end of the incubation time, cells were further dissociated via gentle up-and-down pipetting. Reaction was stopped with the addition of 400µl of ovalbumin enriched cold HBSS and the cell suspension was then passed on a 40µm cell strainer to remove cellular aggregates.  Cells were then centrifuged 5 min at 500 G at 4°C. After removal of the liquid, the pellet was suspended in 250µl of cold HBSS and the resulting solution was finally FAC-sorted on a MoFloAstrios device (Beckman) to reach a concentration of 410 cells /µl.
The libraries of single-cells were prepared using the Chromium 3’ v2 (chimistry SC3pv2) platform following the manufacturer’s protocol (10X Genomics, Pleasanton, CA). Briefly, single cells were partitioned into Gel beads in EMulsion (GEMs) in the GemCode instrument followed by cell lysis and barcoded reverse transcription of RNA, amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 7,000 single cells were loaded on each channel with 2675 cells recovered for the first replicate (index F2), and 2673 cells recovered in the second (index E2). Libraries were sequenced on the Illumina HiSeq 4000 (Paired end reads: Read 1, 26bp, Read 2, 98bp).

value: Progenitors, neuroblasts and nascent neurons cells

value: retina

tag: developmental stage

value: embryonic E15.5

tag: genotype

value: wild type


title: 10X 2675 retinal single-cells batch F2


title: Cholinergic neurons 2

status: Public on Aug 21 2019

source_name: cho-1::SL2::YFP+ neurons

value: NC3579; otIs354 [cho-1(fosmid)::SL2::YFP::H2B]; otIs355 [rab-3(prom1)::2xNLS-tagRFP] IV

tag: cells targeted

tag: 10x genomics library kit


title: Ciliated sensory neurons

source_name: ift-20::TagRFP+ neurons

value: 74% L4, 18% early adult


title: BSC_5020: RTT_6

description: WGBS


title: Glutamatergic neurons

source_name: eat-4::mCherry+ neurons


title: GABAergic neurons 2

source_name: unc-47::GFP+ neurons

value: NC3582; oxIs12 [unc-47p::GFP + lin-15(+)] X; otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV


title: Serotonergic and ceh-10 + neurons

source_name: tph-1::GFP and ceh-10::GFP+ neurons


title: JLKD051

description: WGBS

value: Male


title: Pan-neural 1

source_name: All C. elegans neurons (rab-3::tagRFP+ neurons)

value: OH10689; otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV


title: Pharyngeal neurons

source_name: ceh-34::mCherry+ neurons


title: Pan-neural 2


title: unc-3 expressing neurons

source_name: unc-3::mCherry+ neurons


title: Cholinergic neurons 1


title: BSC_812: Control_5

description: WGBS

value: Control

value: brodmann area 9


title: nmr-1 expressing neurons

source_name: nmr-1-GFP+ neurons

value: NC3572; akIs3 [nmr-1::GFP + lin-15(+)] V; otIs355 [rab-3p(prom1)::2x-NLS::tagRFP] IV


title: BSC_1711: Control_3

description: WGBS

value: Female


title: EV Rep 2

status: Public on Apr 18 2019

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

institute: Duke University School of Medicine

data_processing:
Fastq files were adapter trimmed using Trimmomatic v0.32 using Illumina primers and MINLEN:20, aligned to the human genome, build GRCh38/h38, using HISAT2.0.5 options -U, -S, -p 8.  Aligned read files were then counted using htseq-count v0.5.4p3 using options --stranded no, -m intersection-strict, -a 1 and ‘exon’ as the feature to be counted using a UCSC hg38 GTF annotation file.  Counted files were analyzed for differential expression using DESeq2v1.18.1
Genome_build: h38
Supplementary_files_format_and_content: htseq-count files for all reads

source_name: 293T Cells

growth_protocol: Each cell line is split into 6-15cm plates at about 5-7 million cells per plate in 20 mL of DMEM media supplemented with 10% tetracycline-free FBS.  Grown at 37C and 5% CO2

extract_protocol:
Cytosol is removed using a low salt buffer containing 0.03% digitonin.  Cells are washed with the same buffer containing 0.004% digitonin before the remaining membrane fraction is lysed with a 1% NP-40 high-salt buffer.  Polysomes are enriched by collecting the void of an Sephacryl-400 column and biotin labeled polysomes isolated by incubating on streptavidin beads.  The final bead-bound polysomes are extracted using an RNeasy Kit from Qiagen.
Bioanalyzer is used to calculate the concentration of total RNA and 10 ng per sample is collected and libraries made using Ultra II RNA Library Kit (NEB, E7645S)

treatment_protocol: Cells are treated with doxycycline for 16 hours before 50 uM of biotin is added to the media and cells incubated for 3 hours.  After three hours, cells are washed with PBS containing 50 ug/mL cycloheximide for 10 minutes, scraped up into a tube and cells pelleted.

tag: cell line

value: Stable, inducible HEK293 cell line

tag: genotype/variation

tag: treatment

value: 10 ng/mL doxycycline


title: SEC61B Rep 1

value: 5 ng/mL doxycycline


title: EV Rep 3


title: SEC61B Rep 3


title: BSC_1136: Control_1

description: WGBS


title: BSC_4852: RTT_4

description: WGBS

value: Rett Syndrome

value: heterozygous G451T missense mutation in Exon 4 of the MeCP2 gene


title: BSC_1406: Control_2

description: WGBS


title: LRRC59 Rep 2


title: acr-2 expressing neurons

source_name: acr-2::GFP+ neurons


title: LRRC59 Rep 1


title: LRRC59 Rep 3


title: GABAergic neurons 1

value: 68% L4, 28% early adult


title: SEC61B Rep 2


title: EV Rep 1


title: GOYA RNASeq Sample 544

status: Public on Feb 01 2019

city: SOUTH SAN FRANCISCO

middle: Ryan

last: Bolen

state: CA

address: One DNA way

institute: Genentech

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501163_20160901

data_processing:
Alignment of reads performed using gsnap to GRCh38
Uniquely mapped reads were summarized to feature counts using the summarizeOverlaps function in BioC, & based on Gencode gene models. Only reads on the same strand as the feature were counted.
Genome_build: GRCh38
Supplementary_files_format_and_content: GOYA_stranded_counts.csv - generated by counting genomic features using the summarizeOverlaps function in BioC, & based on Gencode models.
Supplementary_files_format_and_content: GOYA_stranded_log2CPM.csv - Library sizes were calculated via DESeq2, and normalized log2 RPM values were calculated with limma-voom

source_name: DLBCL

extract_protocol:
RNA was isolated and purified from pre-treatment formalin fixed paraffin embedded (FFPE) biopsies using Qiagen’s FFPE RNAEasy preparation kits.
cDNA libraries were generated using TruSeq (Illumina) RNAseq

value: Rituximab

tag: chemotherapy cycles

tag: cell of origin

value: ABC

tag: ipi

value: Low

tag: region

value: Western Europe

tag: pfstt

tag: pfscs

tag: ostt

tag: oscs


title: GOYA RNASeq Sample 543

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501162_20160901

value: GCB

value: High-Intermediate

value: Eastern Europe

tag: Sex


title: GOYA RNASeq Sample 539

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501148_20160901

value: High

value: Asia

value: Male


title: GOYA RNASeq Sample 546

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501165_20160901

value: UNCLASSIFIED

value: Female


title: GOYA RNASeq Sample 548

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501172_20160906

value: Low-Intermediate


title: GOYA RNASeq Sample 551

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501177_20160901


title: GOYA RNASeq Sample 553

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501182_20160901


title: GOYA RNASeq Sample 533

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501096_20160913


title: GOYA RNASeq Sample 538

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501146_20160911


title: GOYA RNASeq Sample 550

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501176_20160906


title: GOYA RNASeq Sample 545

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501164_20160901


title: GOYA RNASeq Sample 542

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501161_20160904


title: GOYA RNASeq Sample 540

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501156_20160901


title: GOYA RNASeq Sample 549

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501175_20160911


title: GOYA RNASeq Sample 536

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501143_20160901


title: GOYA RNASeq Sample 547

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501166_20160901

value: Other


title: GOYA RNASeq Sample 534

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501097_20160901


title: GOYA RNASeq Sample 531

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501094_20160901


title: GOYA RNASeq Sample 532

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501095_20160904


title: GOYA RNASeq Sample 530

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501093_20160901


title: GOYA RNASeq Sample 552

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501181_20160904


title: GOYA RNASeq Sample 541

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501157_20160904


title: GOYA RNASeq Sample 529

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501089_20160901


title: GOYA RNASeq Sample 528

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501088_20160913


title: GOYA RNASeq Sample 537

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501145_20160901


title: GOYA RNASeq Sample 527

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501084_20160901


title: GOYA RNASeq Sample 535

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501105_20160827


title: GOYA RNASeq Sample 524

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501081_20160827


title: GOYA RNASeq Sample 525

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501082_20160827


title: GOYA RNASeq Sample 523

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501079_20160901


title: GOYA RNASeq Sample 518

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501074_20160827


title: GOYA RNASeq Sample 519

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501075_20160911


title: GOYA RNASeq Sample 516

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501071_20160901


title: GOYA RNASeq Sample 521

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501077_20160827


title: GOYA RNASeq Sample 520

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501076_20160827


title: GOYA RNASeq Sample 513

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501068_20160901


title: GOYA RNASeq Sample 514

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501069_20160901


title: GOYA RNASeq Sample 510

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501065_20160901

value: North America


title: GOYA RNASeq Sample 504

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501059_20160901


title: GOYA RNASeq Sample 511

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501066_20160901


title: GOYA RNASeq Sample 508

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501063_20160905


title: GOYA RNASeq Sample 522

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501078_20160901


title: GOYA RNASeq Sample 517

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501073_20160901


title: GOYA RNASeq Sample 505

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501060_20160901


title: GOYA RNASeq Sample 515

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501070_20160911


title: GOYA RNASeq Sample 509

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501064_20160904


title: GOYA RNASeq Sample 507

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501062_20160901


title: GOYA RNASeq Sample 512

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501067_20160827


title: GOYA RNASeq Sample 526

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501083_20160901


title: GOYA RNASeq Sample 506

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501061_20160913


title: GOYA RNASeq Sample 503

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501058_20160901


title: GOYA RNASeq Sample 502

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501057_20160904


title: GOYA RNASeq Sample 500

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501052_20160827


title: GOYA RNASeq Sample 501

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501056_20160901


title: GOYA RNASeq Sample 499

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501049_20160911


title: GOYA RNASeq Sample 497

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501045_20160904


title: GOYA RNASeq Sample 498

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501048_20160901


title: GOYA RNASeq Sample 492

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501033_20160910


title: GOYA RNASeq Sample 490

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501031_20160901


title: GOYA RNASeq Sample 494

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501036_20160906


title: GOYA RNASeq Sample 489

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501030_20160905


title: GOYA RNASeq Sample 493

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501034_20160910


title: GOYA RNASeq Sample 495

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501042_20160906


title: GOYA RNASeq Sample 491

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501032_20160910


title: GOYA RNASeq Sample 487

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501028_20160905


title: GOYA RNASeq Sample 484

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501021_20160913


title: GOYA RNASeq Sample 485

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501025_20160905


title: GOYA RNASeq Sample 496

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501044_20160906


title: GOYA RNASeq Sample 481

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501015_20160910


title: GOYA RNASeq Sample 488

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501029_20160905


title: GOYA RNASeq Sample 478

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501011_20160910


title: GOYA RNASeq Sample 480

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501014_20160910


title: GOYA RNASeq Sample 479

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501013_20160827


title: GOYA RNASeq Sample 473

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501003_20160901


title: GOYA RNASeq Sample 474

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501004_20160904


title: GOYA RNASeq Sample 475

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501005_20160905


title: GOYA RNASeq Sample 483

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501019_20160906


title: GOYA RNASeq Sample 482

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501017_20160906


title: GOYA RNASeq Sample 472

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501001_20160906


title: GOYA RNASeq Sample 470

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500827_20160901


title: GOYA RNASeq Sample 471

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500829_20160827


title: GOYA RNASeq Sample 476

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501007_20160905


title: GOYA RNASeq Sample 469

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500826_20160904


title: GOYA RNASeq Sample 468

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500825_20160901


title: GOYA RNASeq Sample 467

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500824_20160827


title: GOYA RNASeq Sample 486

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501027_20160911


title: GOYA RNASeq Sample 477

description: bo21005_ngs_rna_wts_rnaaccess_bo2100501009_20160905


title: GOYA RNASeq Sample 465

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500821_20160829


title: GOYA RNASeq Sample 463

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500819_20160827


title: GOYA RNASeq Sample 464

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500820_20160827


title: GOYA RNASeq Sample 460

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500816_20160827


title: GOYA RNASeq Sample 462

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500818_20160827


title: GOYA RNASeq Sample 461

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500817_20160828


title: GOYA RNASeq Sample 459

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500814_20160901


title: GOYA RNASeq Sample 454

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500807_20160827


title: GOYA RNASeq Sample 458

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500813_20160901


title: GOYA RNASeq Sample 456

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500811_20160827


title: GOYA RNASeq Sample 455

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500809_20160828


title: GOYA RNASeq Sample 450

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500799_20160827


title: GOYA RNASeq Sample 452

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500803_20160901


title: GOYA RNASeq Sample 448

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500795_20160829


title: GOYA RNASeq Sample 451

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500801_20160901


title: GOYA RNASeq Sample 449

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500796_20160827


title: GOYA RNASeq Sample 446

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500791_20160901


title: GOYA RNASeq Sample 445

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500789_20160901


title: GOYA RNASeq Sample 444

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500788_20160901


title: GOYA RNASeq Sample 441

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500783_20160828


title: GOYA RNASeq Sample 447

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500792_20160827


title: GOYA RNASeq Sample 442

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500784_20160827


title: GOYA RNASeq Sample 443

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500785_20160827


title: GOYA RNASeq Sample 440

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500782_20160827


title: GOYA RNASeq Sample 439

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500781_20160828


title: GOYA RNASeq Sample 438

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500772_20160827


title: GOYA RNASeq Sample 466

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500822_20160827


title: GOYA RNASeq Sample 437

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500771_20160827


title: GOYA RNASeq Sample 457

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500812_20160827


title: GOYA RNASeq Sample 436

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500770_20160827


title: GOYA RNASeq Sample 435

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500769_20160827


title: GOYA RNASeq Sample 432

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500766_20160901


title: GOYA RNASeq Sample 434

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500768_20160827


title: GOYA RNASeq Sample 431

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500765_20160901


title: GOYA RNASeq Sample 453

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500805_20160827


title: GOYA RNASeq Sample 433

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500767_20160901


title: GOYA RNASeq Sample 430

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500763_20160828


title: GOYA RNASeq Sample 429

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500760_20160901


title: GOYA RNASeq Sample 427

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500752_20160901


title: GOYA RNASeq Sample 426

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500740_20160901


title: GOYA RNASeq Sample 428

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500759_20160827


title: GOYA RNASeq Sample 425

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500738_20160901


title: GOYA RNASeq Sample 423

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500736_20160911


title: GOYA RNASeq Sample 424

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500737_20160901


title: GOYA RNASeq Sample 420

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500728_20160901


title: GOYA RNASeq Sample 421

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500729_20160901


title: GOYA RNASeq Sample 418

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500721_20160901


title: GOYA RNASeq Sample 414

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500710_20160906


title: GOYA RNASeq Sample 416

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500712_20160911


title: GOYA RNASeq Sample 422

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500734_20160901


title: GOYA RNASeq Sample 415

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500711_20160901


title: GOYA RNASeq Sample 413

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500709_20160901


title: GOYA RNASeq Sample 417

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500713_20160901


title: GOYA RNASeq Sample 419

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500725_20160901


title: GOYA RNASeq Sample 412

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500708_20160901


title: GOYA RNASeq Sample 411

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500706_20160901


title: GOYA RNASeq Sample 410

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500702_20160827


title: GOYA RNASeq Sample 409

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500696_20160901


title: GOYA RNASeq Sample 408

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500695_20160901


title: GOYA RNASeq Sample 407

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500694_20160901


title: GOYA RNASeq Sample 405

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500691_20160827


title: GOYA RNASeq Sample 406

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500692_20160901


title: GOYA RNASeq Sample 401

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500679_20160911


title: GOYA RNASeq Sample 403

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500687_20160901


title: GOYA RNASeq Sample 402

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500681_20160901


title: GOYA RNASeq Sample 400

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500677_20160901


title: GOYA RNASeq Sample 397

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500674_20160904


title: GOYA RNASeq Sample 398

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500675_20160911


title: GOYA RNASeq Sample 395

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500672_20160901


title: GOYA RNASeq Sample 394

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500671_20160901


title: GOYA RNASeq Sample 396

description: bo21005_ngs_rna_wts_rnaaccess_bo2100500673_20160901