title: sgRB1+sgP130_350nM Dox-2

data_processing:
Reads were mapped to the Hg19 genome by STAR.
HTseq was used to generate count file with gene names(53).
R package DESeq2 was used to normalize counts (mean-ratio method), calculate total reads, and determine differential gene expression(54).
MA plots were generated to display differentially expressed genes.
Principal component analysis showed sufficient clustering of biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized reads

source_name: sgRB1+sgP130_350nM Dox, HFFs

tag: crispr-cas9 targets

value: 350 nM Doxorubicin

tag: bio repeat


title: sgRB1+sgP130_siCTL_0_B

status: Public on Oct 10 2019

type: SRA

city: Boston

first: Amy

middle: E

last: Schade

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
Reads were mapped to the Hg19 genome by STAR.
HTseq was used to generate count file with gene names(53).
R package DESeq2 was used to normalize counts (mean-ratio method), calculate total reads, and determine differential gene expression(54).
MA plots were generated to display differentially expressed genes.
Principal component analysis showed sufficient clustering of biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized reads.

molecule: total RNA

organism: Homo sapiens

source_name: Human Foreskin Fibroblasts (HFF)

extract_protocol:
Total RNA was isolated from HFFs using Qiagen RNeasy plus kit, treated with DNAse (Turbo DNA-free, Life Technologies), and quality control checked using Qubit, TapeStation, and qPCR.
Libraries were prepared using Kappa stranded mRNA Hyper Prep

tag: cell type

value: Human Foreskin Fibroblasts (HFF)

tag: crispr-cas9 target

tag: sirna target

value: siControl

tag: doxorubicin treatment

value: 0 nM

tag: biological replicate

value: bio repeat B


title: sgRB1+sgP130_siP107_0_A

value: bio repeat A


title: sgRB1+sgP130_siCTL_350_B


title: sgRB1+sgP130_siP107_0_B


title: sgP130_siP107_0_A


title: sgP130_siP107_0_B


title: sgP130_siP107_350_B


title: sgRB1+sgP130_0nM Dox-2

source_name: sgRB1+sgP130_0nM Dox, HFFs

tag: treatment

value: 0 nM Doxorubicin


title: sgRB1+sgP130_siP107_350_A


title: YCC16_shL_NTC-2, Biological Replicate 2

type: RNA

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-NTC - Replicate 2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene level normalized expression signal intensity data of the HTA 2.0 arrays were calculated from CEL files using Gene Level-SST-RMA method which performs GCCN and SST prior to RMA in Affymetrix Expression Console (v1.4.1.46) .

label: biotin

source_name: shL-NTC transduced YCC16 gastric cancer cells - Replicate 2

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: YCC16 gastric cancer cell line were seeded in 6 well culture plates and maintained in MEM media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: The total RNA was isolated from the cells using RNeasy mini kit (Qiagen) following manufacture's standard protocol. All RNA samples had both 18S and 28S bands with RIN (RNA integrity number) value as 10 and free of DNA and protein contamination.

treatment_protocol: Upon reaching 60-70% confluency, the cells were transduced with shL-NTC, shL-OCT4 and shL-RXRalpha lentiviral particles with 8µg/ml hexadimethirine bromide. Puromycin at the concentration of 2µg/ml  was used to select the positive cells after 48Hrs of transduction.

tag: cell line

tag: tissue

value: gastric adenocarcinoma cell line


title: sgRB1+sgP130_siCTL_0_A


title: sgRB1+sgP130_350nM Dox-1


title: sgP130_siCTL_0_B


title: sgP130_siP107_350_A


title: YCC16_shL_NTC-1, Biological Replicate 1

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-NTC - Replicate 1

source_name: shL-NTC transduced YCC16 gastric cancer cells - Replicate 1


title: sgRB1+sgP130_siP107_350_B


title: sgRB1+sgP130_0nM Dox-1


title: sgP130_siCTL_0_A


title: sgRB1_350nM Dox-2

source_name: sgRB1_350nM Dox, HFFs


title: sgRB1_350nM Dox-1


title: sgP130_350nM Dox-1

source_name: sgP130_350nM Dox, HFFs


title: sgRB1_0nM Dox-2

source_name: sgRB1_0nM Dox, HFFs


title: sgP130_350nM Dox-2


title: sgRB1+sgP130_siCTL_350_A


title: sgRB1_0nM Dox-1


title: Control_350nM Dox-2

source_name: Control_350nM Dox, HFFs

value: sgControl+sgControl


title: Control_0nM Dox-2

source_name: Control_0nM Dox, HFFs


title: Control_350nM Dox-1


title: sgP130_0nM Dox-2

source_name: sgP130_0nM Dox, HFFs


title: OVACR3-COL11A1

city: Albany

first: Dong-Joo

last: Cheon

address: 47 New Scotland Ave

institute: Albany Medical COllege

data_processing:
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0)/RSEM version 1.2.25 with default parameters, using a custom human GRCh38 transcriptome refernce downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 23 annotation. Expression counts for each gene (TPM: transcripts per million) in all samples were normalized by sequence depth.
Genome_build: Custom human GRCh38 transcriptome refernce downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding genes based on human GENCODE version 23 annotation.
Supplementary_files_format_and_content: "processed data.xlsx" contains information about tracking ID of the RNA, locus and FKPM values for all smaples

source_name: OVCAR3 cells were transfected with COL11A1 gene

growth_protocol: Cells were cultured in RPMI containing 10% FBS and 1% penstrep. Cells were trypsinized, washed with PBS, and used for RNA extraction

extract_protocol:
Total RNA was extracted by Qiagen RNA extraction kit. Quality and concentration was measured using 2100 Bioanalyzer (Aglient) and  Nanodrop 8000 (Thermo Scientific) respectively. One microgram of total RNA per sample was used for poly-A mRNA selection suing streptavidin-coated magnetic beads. cDNA was synthesized from enriched and fragemented RNA using Super-Script II (Invitrogen) reverse transcriptase and random primers.
Library construction was performed using the Illumina TruSeq Stranded mRNA library preparation kit. Briefly, the cDNA was converted into double-stranded DNA, and the resulting dsDNA was enriched with PCR for libary preparation. The PCR-amplied library was purified using Agencourt AMPure XP beads (Beckman Coulter). The concentration of the amplifed library was measured with a NanoDrop spectrophotometer and an aliquot of the library is resolved on an Agilent 2100 Bioanalyzer.  Sample libraries were multiplexed and sequenced on a NextSeq 500 platform (Illumina) using 75bp single-end sequencing. On average, about 20 milion reads were generated from each sample.

value: ovarian cancer cells

tag: genotype/variation

value: COL11A1 overexpression


title: A2780-COL11A1

source_name: A2780 cells were transfected with COL11A1 gene


title: Control_0nM Dox-1


title: A2780-shCOL11A1

source_name: A2780 cells transfected with shCOL11A1


title: A2780CIS

source_name: A2780CIS is a cisplatin resistant cell line generated by chronic exposure to cisplatin and enrichment of resistant populations

value: high endogenous levels of COL11A1


title: A2780-scrambled shRNA

source_name: A2780 cells transfected with scrambled sh RNA

value: scrambled shRNA


title: NEK_START_RNA_REPLICATE_2

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Reads were downloaded using ftp from BGI, saved in compressed fastq format.
FASTQC analysis indicated high quality read pairs, and no futher processing (e.g. trimming) was required prior to alignment
Alignments to the reference genome were obtained using bowtie2 (v 2.2.7), with parameters --very-sensitive -p 12 --no-unal --no-discordant.
Reads aligning to predicted CDS regions were counted using bedtools (v2.23.0) with parameters multicov -D -bams
Genome_build: Tbb v5.2, Jan 2015
Supplementary_files_format_and_content: Excel file giving gene identities, map locations, and raw sequence counts for each gene

organism: Trypanosoma brucei brucei

source_name: In vitro culture

growth_protocol: The cells were seeded at 2x103 cells/ml in 50ml HMI-9 medium (except for the selected monomorphs which were seeded at 1x103 cells/ml due to their shorter doubling time) and incubated at 37oC for 48 hours. The density of the cultures never exceeded 6.8x105 cells/ml

extract_protocol:
Qiagen RNeasyâMini Kit as per the manufacturer’s instructions. The isolated RNA was TURBOTMDNase treated according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was prepared from triplicate populations of the parental ‘Start’ GFPESproAnTat1.1ES NEK RNAi cells, the monomorphic ‘End’ GFPESproAnTat1.1ES NEK RNAi cells

tag: strain

value: Trypanosoma brucei brucei AnTaT 90.13


title: NEK_END_RNA_REPLICATE_1


title: NEK_END_RNA_REPLICATE_3


title: NEK_END_RNA_REPLICATE_2


title: 33_YAK_-dox_post-MACS_rep3

data_processing:
Reads were obtained in compressed fastq format from the local service provider.
Processing of the VSGseq data was performed using the pipeline provided at https://github.com/mugnierlab/VSGSeqPipeline/blob/master/VSGSeqPipeline.py
Alignments to the reference dataset were obtained using bowtie (v1.1.1), with parameters -v 2 -m 1 -p 24
Reads aligning to the VSG regions were counted using MULTo1.0  (v Feb 2014)
Genome_build: VSG reference set provided
Supplementary_files_format_and_content: Excel file containing RPKM values of sample reads against VSG reference set

growth_protocol: Triplicate populations of -/+ DOX GFPESproAnTat1.1ES HYP2, NEK and DYRK RNAi cells were expanded from a single cell

extract_protocol:
RNA was extracted from 25ml of each of the pre-MACS populations and from the entirety of the MACS flow-throughs using a Qiagen RNeasy Mini Kit  with DNase treatment  performed using the TURBO DNA-freeTM Kit (Ambion) . The final elution was performed with 30µl of RNase-free dH2O. To puriify and concentrate the pre-MACS RNA samples, the RNA was ethanol precipitated and resuspended in 10µl RNase-free dH2O
First strand cDNA was produced using the SuperScript III First-Strand Synthesis System (Invitrogen) and processed as detailed in Mugnier et al, 2015  (PMID: 25814582) using NextEra XT Library Preparation system (Illumina)

treatment_protocol: Magnetic-activated cell sorting (MACS) was performed to enrich populations of GFPESproANTat1.1ES cells for cells that did not express VSG AnTat1.1 according to Schulz et al., 2016 (PMID: 27805593)

tag: enrichment for vsg antat1.1 negative cells by macs

value: After enrichment


title: 35_YAK_+dox_post-MACS_rep2


title: NEK_START_RNA_REPLICATE_3


title: 36_YAK_+dox_post-MACS_rep3


title: 34_YAK_+dox_post-MACS_rep1


title: NEK_START_RNA_REPLICATE_1


title: 31_YAK_-dox_post-MACS_rep1


title: 28_YAK_+dox_pre-MACS_rep1

value: Before enrichment


title: 30_YAK_+dox_pre-MACS_rep3


title: 29_YAK_+dox_pre-MACS_rep2


title: 27_YAK_-dox_pre-MACS_rep3


title: sgP130_0nM Dox-1


title: hindgut_Ednrb-FLEX_6

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Ednrb mutant in NCC cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse MOE430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor.

organism: Mus musculus

source_name: E14 hindgut cells

label_protocol: Biotinylated cRNA was prepared from 150 ng total RNA using the Ambion MessageAmpIII RNA Amplification kit, Catalog #1793.

extract_protocol: Total RNA was extracted using TRIzol, processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.

treatment_protocol: The terminal colon was dissected from the terminal colon of E14 wild type (WT), EdnrBNCC-/- (FLEX-EdnrB) and EdnrB(lacZ/lacZ) (EdnrB-/-) embryos.

value: hindgut cells

tag: genotype

value: Ednrb-FLEX(NCC-/-)

tag: developmental stage


title: OVCAR3-GFP

source_name: OVCAR3 cells were transfected with GFP gene

value: GFP overexpression


title: 25_YAK_-dox_pre-MACS_rep1


title: 23_NEK_+dox_post-MACS_rep2


title: 24_NEK_+dox_post-MACS_rep3


title: 26_YAK_-dox_pre-MACS_rep2


title: YCC16_shL_NTC-3, Biological Replicate 3

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-NTC - Replicate 3

source_name: shL-NTC transduced YCC16 gastric cancer cells - Replicate 3


title: 22_NEK_+dox_post-MACS_rep1


title: 21_NEK_-dox_post-MACS_rep3


title: 18_NEK_+dox_pre-MACS_rep3


title: 20_NEK_-dox_post-MACS_rep2


title: 17_NEK_+dox_pre-MACS_rep2


title: 19_NEK_-dox_post-MACS_rep1


title: 32_YAK_-dox_post-MACS_rep2


title: 16_NEK_+dox_pre-MACS_rep1


title: 15_NEK_-dox_pre-MACS_rep3


title: 10_HYP2_+dox_post-MACS_rep1


title: 11_HYP2_+dox_post-MACS_rep2


title: 9_HYP2_-dox_post-MACS_rep3


title: 12_HYP2_+dox_post-MACS_rep3


title: 6_HYP2_+dox_pre-MACS_rep3


title: 4_HYP2_+dox_pre-MACS_rep1


title: 14_NEK_-dox_pre-MACS_rep2


title: 5_HYP2_+dox_pre-MACS_rep2


title: 8_HYP2_-dox_post-MACS_rep2


title: scRNA-seq from C57BL/6 mouse 4

city: Epalinges

first: Santiago

last: Carmona

address: Ch. des Boveresses 155

country: Switzerland

institute: UNIL

data_processing:
The Cell Ranger Single Cell Software Suite 2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq) was used to perform sample demultiplexing, barcode processing, reads downsampling per sample (down to 118,806 mean reads per cell) and single cell 5’ gene counting using default parameters
High-quality CD8 TIL filtering: cells having less than 1,500 or more than 30,000 UMIs,  cells having less than 1,500 or more than 5,000 detected genes, cells in which ribosomal protein coding genes represented more than 50% of UMI content and cells in which mitochondrial protein coding genes represented more than 5% of UMI content were filtered out. The 5542 quality-passed cells were further filtered based on expression of CD8 T cells markers: 3574 cells expressing Cd8a, Cd8b1 and Cd2 but not Cd4 were kept for further analysis (aggregated_filtered_matrix.tar.gz)
Genome_build: mm10
Supplementary_files_format_and_content: aggregated_matrix.tar.gz contains UMI counts matrix (Market Exchange Format for sparse matrices) and TSV files with genes and barcode sequences (corresponding to row and column indices respectively. Sample code: 1=PMEL1, 2=WT1, 3=WT3, 4=PMEL3, *5=PMEL2, 6=WT2, 7=WT4*). aggregated_filtered_matrix.tar.gz contains the same information only for filtered high-quality CD8 T-cells. VDJ_annotations.csv.tar.gz Samples VDJ annotations files link cell barcodes ID with T-cell receptor sequences and annotated VDJ segments (plese refer to The Cell Ranger Single Cell Software Suite 2.2.0 VDJ for more information on the output)

molecule: polyA RNA

source_name: scRNA-seq from C57BL/6 mouse

extract_protocol:
The right flank of mice (C57BL/6 or PMEL) was shaved and B16-F10 cells (2.5x10^5) were injected subcutaneously. Tumors were excised 15 days post tumor engraftment, manually dissociated and digested enzymatically with Tumor Dissociation Kit (Miltenyi Biotec). Digested tumors were mashed through 70 µm filters. Hematopoietic cells were further purified using a discontinuous Percoll gradient (GE Healthcare). Cells at the interface were harvested and washed twice before further use. Tumor infiltrating CD8 T cells were sorted by flow cytometry and were used for single-cell RNA-seq.
Cellular suspensions were loaded on a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 5’ Library & Gel Bead Kit (PN-1000006) following the manufacturer's instruction (protocol CG000086 Rev E), and the 10x mouse V(D)J Enrichment Kit (PN-1000071) was used to enrich for TCR sequences, after which V(D)J-enriched libraries were constructed with the Chromium Single Cell 5’ Library Construction Kit (PN-1000020). The sequencing libraries were loaded on Illumina NextSeq High Output Flow Cells using read lengths of 26 nt for read1 and 132 nt for read2.

value: C57BL/6 mouse

value: sorted CD8 T cells infiltrating B16 tumors


title: 3_HYP2_-dox_pre-MACS_rep3


title: 13_NEK_-dox_pre-MACS_rep1


title: 1_HYP2_-dox_pre-MACS_rep1


title: 2_HYP2_-dox_pre-MACS_rep2


title: 7_HYP2_-dox_post-MACS_rep1


title: scRNA-seq from C57BL/6 mouse 3


title: scRNA-seq from PMEL mouse 2

source_name: scRNA-seq from PMEL mouse

value: PMEL mouse (Jackson Laboratory, Cat#005023)


title: scRNA-seq from C57BL/6 mouse 2


title: scRNA-seq from PMEL mouse 1


title: scRNA-seq from PMEL mouse 3


title: T1_right-cortex_homozygous_1/5

city: Auckland

first: Tina

last: Nie

address: 3 Symonds St

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

scan_protocol: Results were obtained form the nCounter Digital Analyzer using 280 field-of-view counts.

data_processing: Data was processed using the nSolver analysis software version 3.0 (NanoString Technologies). Background subtraction was performed by subtracting the geometric mean of the negative controls. The geometric mean of the positive controls was used to calculate the normalisation factor. Normalisation to reference genes was completed using the reference (housekeeping) genes B2m, Hprt and Ubc. Gene counts obtained by the nCounter can be analysed by a variety of methods depending on user preference and R packages designed specifically for the analysis of Nanostring data may perform their own normalisation on the raw counts.

source_name: right cortex, homozygous, 100 days

extract_protocol: RNA was extracted using the RNeasy Mini or Midi Lipid Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: Homozygous

tag: time point

value: brain

tag: brain region

value: right cortex

tag: gender

value: male

tag: collection time

value: PM

tag: previously diabetic? (t3 only)

tag: age (days)


title: T1_right-cortex_nontransgenic_6

source_name: right cortex, nontransgenic, 100 days

value: Nontransgenic


title: T1_right-cortex_nontransgenic_8/9

value: AM


title: T1_right-cortex_homozygous_8/9


title: T1_right-cortex_homozygous_6/7


title: T1_right-cortex_nontransgenic_4/5


title: scRNA-seq from C57BL/6 mouse 1

tag: cell type


title: T1_right-cortex_nontransgenic_1/3


title: T1_right-cortex_nontransgenic_2/7


title: T1_right-cortex_hemizygous_9/10

source_name: right cortex, hemizygous, 100 days

value: Hemizygous


title: T1_left-cortex_homozygous_8/9

source_name: left cortex, homozygous, 100 days

value: left cortex


title: T1_left-cortex_nontransgenic_8/9

source_name: left cortex, nontransgenic, 100 days


title: T1_left-cortex_homozygous_1/5


title: T1_left-cortex_homozygous_6/7


title: T1_left-cortex_nontransgenic_6


title: T1_left-cortex_homozygous_3/4


title: T1_right-cortex_homozygous_3/4


title: T1_left-cortex_nontransgenic_1/3


title: T1_left-cortex_hemizygous_5/6

source_name: left cortex, hemizygous, 100 days


title: T1_left-cortex_hemizygous_9/10


title: T1_left-cortex_nontransgenic_2/7


title: T2_right-cortex_homozygous_4/8

source_name: right cortex, hemizygous, diabetes onset


title: T1_left-cortex_nontransgenic_4/5


title: T2_right-cortex_nontransgenic_6/9

source_name: right cortex, nontransgenic, diabetes onset control


title: T2_right-cortex_homozygous_1/3


title: T2_right-cortex_nontransgenic_11/14


title: T1_right-cortex_hemizygous_5/6


title: T1_right-cortex_hemizygous_8


title: T1_right-cortex_hemizygous_3/4


title: T1_right-cortex_hemizygous_1/2


title: T2_right-cortex_nontransgenic_5/10


title: T2_right-cortex_homozygous_5


title: T2_right-cortex_homozygous_6/9


title: T2_right-cortex_homozygous_7/10


title: T1_left-cortex_hemizygous_3/4


title: T1_left-cortex_hemizygous_1/2


title: T2_right-cortex_nontransgenic_2/15


title: T2_right-cortex_nontransgenic_4/13


title: T2_right-cortex_hemizygous_9


title: T2_right-cortex_hemizygous_5/10


title: T2_right-cortex_hemizygous_7/12


title: T2_right-cortex_nontransgenic_1/3


title: T2_right-cortex_hemizygous_8/14


title: T2_right-cortex_hemizygous_4/6


title: T2_left-cortex_homozygous_7/10

source_name: left cortex, homozygous, diabetes onset


title: T2_right-cortex_nontransgenic_7/8


title: T2_left-cortex_homozygous_6/9


title: EIIa_Lung_ECTRAP_R3

city: Ann Arbor

first: Santhi

last: Ganesh

state: Michigan

address: 1150 W Medical Center Drive

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment raw sequences using Bowtie2 (version 2.2.3)
Quantification and transcript length normalization with rSeq
Genome_build: mouse Gencode reference GRCm38.p2
Supplementary_files_format_and_content: CSV file contains read counts after rSeq processing; includes all genes in transcriptome and values represent read counts adjusted for transcript length

source_name: Lung ECs

extract_protocol:
RNA (before/after TRAP) was isolated using the Qiagen RNeasy kit. SMARTer Ultra Low Input kit (Clontech) was used for RNA conversion (5 ng for tissue lysate, 10 ng for EC-TRAP samples).
cDNA was bead-purified and mechanically sheared to a 200-250 base pair range. End repair with T4 DNA polymerase was followed by dA-tailing using Klenow 3’ to 5’ exonuclease and adenosine triphosphate to create a 3’ adenosine overhang to promote adapter ligation. After purification, samples were linearized by PCR before being size-selected in a range of 300-350 bp using Invitrogen’s E-Gel system. Final enrichment of the adapter-modified cDNA fragments was performed by PCR using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: Tissues were snap frozen after cycloheximide perfusion and mechanically dissociated, unless otherwise indicated

value: Lung

value: EIIa-Cre

value: Control

tag: isolation method

value: mechanic tissue dissociation

tag: molecule subtype

value: polysome-associated mRNA


title: EIIa_Lung_lysate_R3

source_name: Lung

tag: treatment

value: total mRNA


title: EIIa_Lung_lysate_R2


title: T2_left-cortex_homozygous_5


title: EIIa_Lung_ECTRAP_R2


title: T2_left-cortex_homozygous_4/8


title: T2_left-cortex_homozygous_1/3


title: EIIa_Lung_ECTRAP_R1


title: EIIa_Lung_lysate_R1


title: EIIa_Liver_ECTRAP_R3

source_name: Liver ECs

value: Liver


title: EIIa_Liver_lysate_R3

source_name: Liver


title: T2_left-cortex_nontransgenic_6/9

source_name: left cortex, nontransgenic, diabetes onset control


title: T2_left-cortex_nontransgenic_7/8


title: T2_left-cortex_nontransgenic_1/3


title: T2_left-cortex_nontransgenic_2/15


title: EIIa_Kidney_ECTRAP_R3

source_name: Kidney ECs

value: Kidney


title: T2_left-cortex_hemizygous_9

source_name: left cortex, hemizygous, diabetes onset


title: T2_left-cortex_nontransgenic_4/13


title: EIIa_Liver_lysate_R1


title: T2_left-cortex_hemizygous_8/14


title: EIIa_Kidney_lysate_R3

source_name: Kidney


title: EIIa_Liver_ECTRAP_R1


title: T2_left-cortex_hemizygous_5/10


title: T2_left-cortex_nontransgenic_5/10


title: EIIa_Kidney_ECTRAP_R2


title: T2_left-cortex_nontransgenic_11/14


title: EIIa_Liver_ECTRAP_R2


title: T2_left-cortex_hemizygous_7/12


title: T2_left-cortex_hemizygous_4/6


title: T2_midbrain_homozygous_7/10

source_name: midbrain, homozygous, diabetes onset

value: Homozygous

value: midbrain


title: EIIa_Kidney_lysate_R2


title: EIIa_Kidney_ECTRAP_R1


title: T2_midbrain_homozygous_6/9

value: brain


title: EIIa_Kidney_lysate_R1


title: EIIa_Heart_ECTRAP_R3

source_name: Heart ECs

value: Heart


title: EIIa_Liver_lysate_R2


title: T2_midbrain_homozygous_5

value: male


title: T2_midbrain_homozygous_4/8

value: PM


title: EIIa_Heart_lysate_R3

source_name: Heart


title: T2_midbrain_homozygous_1/3

value: AM


title: EIIa_Heart_ECTRAP_R2


title: T2_midbrain_nontransgenic_11/14

source_name: midbrain, nontransgenic, diabetes onset control

value: Nontransgenic


title: T2_midbrain_nontransgenic_7/8


title: T2_midbrain_nontransgenic_6/9


title: EIIa_Heart_ECTRAP_R1


title: EIIa_Brain_lysate_R3

source_name: Brain

value: Brain


title: EIIa_Brain_ECTRAP_R3

source_name: Brain ECs


title: EIIa_Brain_ECTRAP_R2


title: T2_midbrain_nontransgenic_4/13


title: T2_midbrain_nontransgenic_5/10


title: EIIa_Brain_lysate_R2


title: T2_midbrain_nontransgenic_2/15


title: EIIa_Brain_ECTRAP_R1


title: T2_midbrain_nontransgenic_1/3


title: T2_midbrain_hemizygous_9

source_name: midbrain, hemizygous, diabetes onset

value: Hemizygous


title: T2_midbrain_hemizygous_8/14


title: T2_midbrain_hemizygous_4/6


title: T2_midbrain_hemizygous_5/10


title: Blood_lysate_R2

source_name: RBC lysed blood

value: Blood

value: Tek-Cre

value: fresh cells


title: Blood_TRAP_R1

source_name: RBC lysed blood after TRAP

value: Control

value: polysome-associated mRNA


title: Blood_TRAP_R2


title: Lung_ECTRAP_R3

source_name: Lung ECs

value: Lung

value: mechanic tissue dissociation


title: T2_midbrain_hemizygous_7/12


title: EIIa_Heart_lysate_R2

value: EIIa-Cre

value: total mRNA


title: T3_right-cortex_homozygous_10

source_name: right cortex, homozygous, 400 days

value: Homozygous

value: brain

value: right cortex

value: Y


title: T3_right-cortex_homozygous_8/9

value: male

value: AM


title: T3_right-cortex_homozygous_3/4


title: T3_right-cortex_homozygous_6

value: N


title: EIIa_Heart_lysate_R1

value: Heart


title: Blood_lysate_R1

value: Blood


title: Lung_lysate_R3

source_name: Lung

value: Tek-Cre


title: Lung_lysate_R2


title: Lung_ECTRAP_R1


title: EIIa_Brain_lysate_R1

value: Brain


title: Lung_ECTRAP_R2

value: Control


title: T3_right-cortex_nontransgenic_8/9

source_name: right cortex, nontransgenic, 400 days

value: Nontransgenic

value: PM


title: T3_right-cortex_nontransgenic_7


title: T3_right-cortex_nontransgenic_10


title: Lung_lysate_R1

value: Lung

value: mechanic tissue dissociation


title: Liver_ECTRAP_R3

source_name: Liver ECs

value: Liver

value: polysome-associated mRNA


title: Liver_ECTRAP_R2


title: Liver_lysate_R2

source_name: Liver

value: total mRNA


title: T3_right-cortex_hemizygous_8/10

source_name: right cortex, hemizygous, 400 days

value: Hemizygous

value: brain

value: right cortex


title: Liver_ECTRAP_R1


title: Kidney_ECTRAP_R3

source_name: Kidney ECs

value: Kidney


title: T3_right-cortex_nontransgenic_3/4

value: male

value: AM

value: N


title: T3_right-cortex_nontransgenic_5/6


title: Kidney_lysate_R3

source_name: Kidney

value: Tek-Cre


title: T3_right-cortex_nontransgenic_1

value: Y


title: T3_right-cortex_homozygous_1

value: Homozygous


title: T3_right-cortex_homozygous_2/7


title: Kidney_ECTRAP_R2

value: Control


title: T3_right-cortex_hemizygous_9

value: PM


title: T3_right-cortex_hemizygous_2/3


title: T3_right-cortex_hemizygous_4/5


title: Kidney_lysate_R2


title: Kidney_ECTRAP_R1


title: T3_right-cortex_hemizygous_1


title: T3_midbrain_homozygous_10

source_name: midbrain, homozygous, 400 days

value: midbrain


title: Kidney_lysate_R1

value: mechanic tissue dissociation


title: T3_midbrain_homozygous_6


title: Heart_lysate_R3

source_name: Heart

value: Heart


title: T3_midbrain_homozygous_8/9


title: Liver_lysate_R3

value: Liver


title: T3_midbrain_homozygous_3/4


title: Heart_ECTRAP_R2

source_name: Heart ECs

value: polysome-associated mRNA


title: T3_right-cortex_hemizygous_6

value: Hemizygous


title: T3_midbrain_homozygous_1/5

value: brain


title: Heart_lysate_R2

value: total mRNA


title: T3_midbrain_nontransgenic_10

source_name: midbrain, nontransgenic, 400 days

value: Nontransgenic


title: Heart_ECTRAP_R1


title: T3_midbrain_nontransgenic_8/9

value: male


title: Brain_ECTRAP_R3

source_name: Brain ECs

value: Brain


title: Brain_lysate_R3

source_name: Brain


title: T3_midbrain_nontransgenic_3/4

value: AM

value: N


title: Brain_lysate_R2

value: Tek-Cre


title: Heart_ECTRAP_R3


title: Brain_ECTRAP_R1


title: T3_midbrain_nontransgenic_5/6


title: T3_midbrain_nontransgenic_1/2

value: Y


title: Brain_lysate_R1

value: Control


title: T3_midbrain_homozygous_2/7

value: Homozygous


title: T3_midbrain_hemizygous_6

source_name: midbrain, hemizygous, 400 days

value: midbrain


title: T3_midbrain_hemizygous_8/10

value: PM


title: PCL

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 400 N Broadway

institute: Johns Hopkins Univeristy

data_processing:
Alignment and counting was performed using CellRanger
Normalization was performed using Seurat v2’s NormalizeData
Scaling was performed using Seurat v2’s ScaleData
Identification of principle components was performed using Seurat v2’s RunPCA
Clustering was performed using Seurat v2’s FindClusters
Genome_build: hg38
bam files were generated using CellRanger.
Supplementary_files_format_and_content: Both counts and cell metadata are provided in csv format.

source_name: PCL

extract_protocol:
Macrophages were sorted from mice quadriceps 1 week after undergoing volumetric muscle loss surgery with treatment of urinary bladder matrix, polycaprolactone, or saline.
After sorting, cells were encapsulated using the 10x Chromium single cell RNA sequencing platform. Library prep followed the 10x 3’ v2 protocol and were sequenced using an Illumina HiSeq 2000.

value: polycaprolactone

value: macrophage


title: T3_midbrain_hemizygous_4/5


title: T3_midbrain_hemizygous_7/9


title: saline

source_name: saline

value: saline


title: T3_midbrain_hemizygous_2/3

value: Hemizygous


title: ECM

source_name: ECM

value: urinary bladder matrix


title: Heart_lysate_R1

value: Heart

value: mechanic tissue dissociation

value: total mRNA


title: DCAV endo CD8 LN rep2 (ATAC-seq)

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

library_source: genomic

data_processing:
For analysis of sequences, first, adapters were trimmed using AdapterRemoval (v. 2.2.1a). Second, the paired-end ATAC-seq were aligned to the mouse reference genome (mm10) using Bowtie2 (2.3.4.1) with the following parameters --no-discordant --no-unal --no-mixed -X 2000. Third, the reads were shifted (Tn5 insertion) after removing the reads from mitochondrial DNA and duplicated reads.
ATAC-seq peak regions of the pooled sample were called using HOMER (v4.9.1) with the following parameters -region -size 500 -minDist 50 -o auto -tbp 0. Then, the fragment counts for each peak region for each sample were obtained using bedtools (v2.24.0). Differentially accessible peak regions between conditions using the two replicates per condition (adjusted p- value ≤ 1e-5) were called using DESeq (v1.30.0) using the “pooled” dispersion estimation with the “local” fit. Then, overlapping differentially accessible peak regions (adjusted p-value ≤ 1e-5) per condition were merged using bedtools (v.2.24.0).
ATAC-seq coverage tracks were generated using deepTools (v.3.0.2). The size factors estimated by DESeq (v1.30.0) were used to normalize ATAC-seq coverage tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Unnormalized chromatin accessibility tracks (bigWig). These tracks can be normalized using the the sample-specific size factors estimated using DESeq: 1.0323702 for WT_BR.bw, 1.2470387 for WT_BR2.bw, 0.7297277 for DCAV_BR.bw, and 0.8030310 for DCAV_BR2.bw .

molecule: genomic DNA

source_name: CD44low naïve CD8+ T cells

extract_protocol:
Approximately 30,000 CD44low naïve CD8+ T cells per replicate from LNs were sorted by FACS into PBS containing 10% FBS in DNA loBind Eppendorf tubes. Pelleted cells were lysed in 50 μl of reaction mix (25 μl of 2 x TD, 2.5 μl of Tn5 enzyme, 0.25 μl of 2% digitonin, 22.25 μl of nuclease-free water).
The mix was incubated at 37°C for 30 minutes with agitation at 300 rpm. DNA was purified using a QIAgen MinElute Reaction Cleanup kit and Nextera sequencing primers ligated using PCR amplification. Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) was used post-PCR and library quality was verified using a Tapestation machine.

value: lymph nodes

value: CD44low naive CD8+ T cells

tag: age

value: 10 weeks

value: CD11cCre x Itgavflox/flox


title: DCAV endo CD8 LN rep1 (ATAC-seq)

tag: tissue


title: T3_hindbrain_homozygous_12

source_name: hindbrain, homozygous, 400 days

value: brain

value: hindbrain

value: male

value: AM

value: N


title: T3_midbrain_hemizygous_1

value: midbrain


title: T3_midbrain_nontransgenic_7

value: Nontransgenic

value: Y


title: Brain_ECTRAP_R2

value: Brain

value: Tek-Cre

value: Control

value: polysome-associated mRNA


title: WT endo CD8 LN rep2 (ATAC-seq)

value: CD11cCre x Itgavwt/wt


title: T3_hindbrain_homozygous_3/4

value: Homozygous


title: T3_hindbrain_homozygous_9


title: WT endo CD8 LN rep1 (ATAC-seq)

value: lymph nodes

value: CD44low naive CD8+ T cells


title: PauparKD_rep2

first: Ruth

middle: A

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped to a reference genome (Mouse: UCSC/mm9) using Hisat2 (Kim et al., 2015) with default settings
Relative abundance (aka expression level) of genes and splice isoforms was determined using htseq-count (Anders et al., 2015) with default settings
Differentially expressed genes were calculated using DESeq2 (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-file includes read counts for all genes as determine by htseq-count for Control KD and Paupar KD samples

source_name: MIN6 cells

extract_protocol:
Qiagen RNeasy Mini kit
Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina). RNA libraries were prepared for sequencing using standard Illumina protocols  RNA prep kit (Illumina).

value: MIN6 cells

value: Paupar ASO


title: ControlKD_rep3

value: Control ASO


title: PauparKD_rep3


title: Adult islets_rep3

description: Adult islets_rep3

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
To reconstruct the transcriptomes, we first mapped all reads of total RNAs to the mouse reference genome (mm10) with TopHat v1.3.2 (Trapnell et al., 2012).
Cufflinks (v1.2.1) was subsequently applied to assemble the whole transcriptome and to identify all possible transcripts.
Differentially expressed genes were calculated using DESeq2 (Anders S et al 2010 Genome Biology).
Genome_build: mm10
Supplementary_files_format_and_content: csv-file includes DESeq2 output showing differentially expressed genes between cohorts

source_name: pancreatic islets

extract_protocol:
Whole embryonic pancreas was dissected out and total RNA was isolated using QIAGEN RNeasy Micro kit. Pancreatic islets were isolated through collagenase treatment and total RNA was isolated using QIAGEN RNeasy Micro kit.
Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina). RNA libraries were prepared for sequencing using standard Illumina protocols  RNA prep kit (Illumina).

value: isolated pancreatic islets

value: 12 weeks

value: Wildtype


title: ControlKD_rep2


title: ControlKD_rep1


title: Adult islets_rep2

description: Adult islets_rep2


title: T3_hindbrain_hemizygous_12

source_name: hindbrain, hemizygous, 400 days

value: Hemizygous

value: brain

value: hindbrain

value: male

value: AM


title: Adult islets_rep1

description: Adult islets_rep1


title: T3_hindbrain_hemizygous_11/13

value: PM

value: Y


title: Embryonic pancreas_rep3

description: Embryonic pancreas_rep3

source_name: e15.5 embryonic pancreas

value: embryonic pancreas


title: T3_hindbrain_nontransgenic_12

source_name: hindbrain, nontransgenic, 400 days

value: Nontransgenic

value: N


title: T3_hindbrain_nontransgenic_1/2


title: T3_hindbrain_nontransgenic_7


title: T3_hindbrain_nontransgenic_4/11


title: T3_hindbrain_nontransgenic_8


title: T3_hindbrain_nontransgenic_5/6


title: Embryonic pancreas_rep1

description: Embryonic pancreas_rep1


title: PauparKD_rep1


title: T3_hindbrain_hemizygous_7/9


title: KO_rep3

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were aligned to the mouse genome (mm9) using HISAT2 v2.1.0 (Kim et al., 2013)
Relative abundance (aka expression level) of genes and splice isoforms was determined using htseq-count (Anders et al., 2015) with default settings
Differentially expressed genes were calculated using DESeq2 (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-file includes read counts for all genes as determine by htseq-count for Paupar WT and KO samples

extract_protocol:
Pancreatic islets were isolated through collagenase treatment and total RNA was isolated using QIAGEN RNeasy Micro kit.
Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina). RNA libraries were prepared for sequencing using standard Illumina protocols  RNA prep kit (Illumina).

value: isolated islets

tag: mouse age

value: 6 weeks

value: Paupar -/-


title: T3_hindbrain_homozygous_1/11

value: Homozygous


title: T3_hindbrain_hemizygous_2/3


title: T3_left-cortex_homozygous_10

source_name: left cortex, homozygous, 400 days

value: left cortex


title: KO_rep2


title: T3_left-cortex_homozygous_8/9


title: KO_rep1


title: T3_left-cortex_homozygous_6


title: WT_rep3

value: Paupar +/+


title: T3_left-cortex_homozygous_2/7


title: T3_left-cortex_homozygous_3/4


title: WT_rep2


title: T3_left-cortex_homozygous_1/5


title: Embryonic pancreas_rep2

description: Embryonic pancreas_rep2

value: Wildtype


title: HUVEC_HHT_p10_R4

data_processing:
Fastq generation was performed using Illumina’s bcl2fastq2 software
Alignment raw sequences using Bowtie2 (version 2.2.3)
Quantification and transcript length normalization with rSeq
Genome_build: human Gencode reference GRCh38.p12
Supplementary_files_format_and_content: CSV file contains read counts after rSeq processing; includes all genes in transcriptome and values represent read counts adjusted for transcript length

source_name: HUVECs (passage 10)

growth_protocol: HUVECs were freshly isolated/pooled from 3 umbilical cords, or commercially obtained (Lonza) and treated at passage 1 or passage 10, respectively.

extract_protocol:
RNA from cells was isolated using the Qiagen RNeasy kit and converted into cDNA using the SmartSeq V4 kit from Clontech.
Subsequent cDNA was bead purified and sheared to a ~300bp range; libraries were made using the Kapa HyperPrep kit for Illumina according to the manufacturer's protocol (Kapa BioSystems) using Nextflex barcodes. Size selection after linearization and amplification was performed using the E-gel system (Invitrogen)

treatment_protocol: Cells were expanded to ~80% confluence before incubation with 100µg/ml cycloheximide or 2µg/ml homoharringtonine for 5 minutes.

value: HUVECs

value: wildtype

value: homoharringtonine

value: fresh cells

value: total mRNA


title: T3_hindbrain_hemizygous_8/10

value: Hemizygous

value: brain

value: hindbrain

value: male

value: PM


title: T3_left-cortex_nontransgenic_11

source_name: left cortex, nontransgenic, 400 days

value: Nontransgenic

value: AM

value: N


title: T3_left-cortex_nontransgenic_7

value: Y


title: T3_left-cortex_nontransgenic_8/9

value: left cortex


title: T3_left-cortex_nontransgenic_1


title: T3_left-cortex_nontransgenic_3/4


title: HUVEC_HHT_p10_R3


title: HUVEC_HHT_p10_R2


title: HUVEC_HHT_p1_R2

source_name: HUVECs (passage 1)


title: HUVEC_HHT_p10_R1


title: HUVEC_HHT_p1_R4


title: T3_left-cortex_hemizygous_8/10

source_name: left cortex, hemizygous, 400 days


title: T3_left-cortex_hemizygous_7/9


title: T3_left-cortex_hemizygous_6


title: HUVEC_CHX_p10_R4

value: cycloheximide


title: HUVEC_HHT_p1_R3


title: T3_left-cortex_nontransgenic_5/6


title: HUVEC_HHT_p1_R1


title: HUVEC_CHX_p10_R1


title: HUVEC_CHX_p10_R2


title: T3_left-cortex_hemizygous_4/5


title: WT_rep1

value: isolated islets

value: 6 weeks

value: Paupar +/+


title: HUVEC_CHX_p1_R4

value: HUVECs

value: wildtype


title: 10339543

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

data_processing:
NextSeq data were analysed using the 10x Genomics suite Cell Ranger 2.0.1 and specifically the function mkfastq.
Mapping with STAR against drosophila reference genome, detecting the number of cells and genes per cell and finally quantifying gene expression
Genome_build: dm6
Supplementary_files_format_and_content: 3 tab-delimited file containing genes Flybase id/Name association (genes.tsv), cell/barcode association (barcodes.tsv), gene/cell/expression association (matrix.mtx)

organism: Drosophila melanogaster

source_name: FACS sorted tumor neuroblasts

growth_protocol: Animals were grown in a standart food medium.

extract_protocol:
Single cells were processed using the Single cell 3’ Library, Gel beads & multiplex kit (10X Genomics, Pleasanton) as per the manufacter’s protocol.
Cells, were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller (10X  genomics, Pleasanton),  where  all  generated  cDNA  share  a  common  10x  Barcode.  Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions.

value: Tumors were induced during larval stages by the inactivation of prospero. The genotype was the following:poxn-Gal4, UAS-GFP UAS-prosRNAi2, UAS-dicer2

value: prospero (pros) gene knock down

tag: strains

value: Vienna Drosophila RNAi Center #101477; Bloomington Stock Centre #24650 ; Bloomington Stock Centre  #32185


title: T3_left-cortex_hemizygous_1

value: Hemizygous

value: brain


title: T2_hindbrain_homozygous_5

source_name: hindbrain, homozygous, diabetes onset

value: Homozygous

value: hindbrain

value: male


title: T2_hindbrain_homozygous_4/8

value: PM


title: HUVEC_CHX_p1_R3

value: fresh cells

value: total mRNA


title: HUVEC_CHX_p1_R1

value: cycloheximide


title: T2_hindbrain_homozygous_1/3

value: AM


title: T2_hindbrain_nontransgenic_6/9

source_name: hindbrain, nontransgenic, diabetes onset control

value: Nontransgenic


title: T3_left-cortex_hemizygous_2/3

value: left cortex

value: Y


title: T2_hindbrain_nontransgenic_7/8


title: HUVEC_CHX_p10_R3

value: HUVECs

value: wildtype


title: T2_hindbrain_nontransgenic_5/10


title: HUVEC_CHX_p1_R2


title: T2_hindbrain_nontransgenic_2/15


title: T2_hindbrain_nontransgenic_11/14


title: Liver_lysate_R1

source_name: Liver

value: Liver

value: Tek-Cre

value: Control

value: mechanic tissue dissociation


title: T2_hindbrain_nontransgenic_1/3

value: brain


title: T2_hindbrain_homozygous_6/9

value: Homozygous

value: hindbrain


title: HUVEC_Ctrl_p10_R2


title: HUVEC_Ctrl_p10_R3


title: T2_hindbrain_hemizygous_8/14

source_name: hindbrain, hemizygous, diabetes onset

value: Hemizygous

value: male

value: PM


title: T2_hindbrain_homozygous_7/10


title: T2_hindbrain_hemizygous_7/12


title: T2_hindbrain_hemizygous_9


title: HUVEC_Ctrl_p10_R4

value: fresh cells

value: total mRNA


title: T2_hindbrain_hemizygous_5/10


title: HUVEC_Ctrl_p1_R4


title: HUVEC_Ctrl_p1_R3


title: HUVEC_Ctrl_p10_R1


title: T1_midbrain_homozygous_8/9

source_name: midbrain, homozygous, 100 days

value: midbrain


title: T1_midbrain_homozygous_3/4

value: AM


title: T1_midbrain_homozygous_6/7


title: T1_midbrain_homozygous_1/5


title: T1_midbrain_nontransgenic_8/9

source_name: midbrain, nontransgenic, 100 days

value: Nontransgenic


title: T2_hindbrain_hemizygous_4/6


title: HUVEC_Ctrl_p1_R2

value: HUVECs


title: T1_midbrain_nontransgenic_6


title: HUVEC_Ctrl_p1_R1

value: wildtype


title: T1_midbrain_nontransgenic_4/5


title: f.19.sb.sk

city: Columbus

first: Zhaojun

last: Qiu

state: Ohio

address: 460 West 12th Ave

institute: The Ohio State University

description: the skin of a female 19 week human fetus with  spina bifida

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.2.1). It was vst transformed and quantile normalized.

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (Ambion, TX).

extract_protocol: RNA was extracted with Trizol reagent. The concentration and purity of RNA were examined by NanoDrop®ND-1000, and its quality was veriﬁed by arose electrophoresis.

tag: diagnosis

value: spina bifida

value: 19 week

value: Female

tag: organ

value: Skin

tag: array id


title: T1_midbrain_nontransgenic_2/7

tag: genotype

tag: time point

value: brain


title: T1_midbrain_nontransgenic_1/3

tag: brain region

tag: gender


title: m.22.c.sp

description: the spinal cord of a male 22 week normal control human fetus

value: control

value: 22 week

value: Male

value: Spinal cord


title: m.22.c.br

description: the brain of a male 22 week normal control human fetus

value: Brain


title: m.19.cr.sp

description: the spinal cord residual of a male 19 week human fetus with craniorachischisis

value: craniorachischisis

value: Spinal cord Residual


title: m.22.c.sk

description: the skin of a male 22 week normal control human fetus


title: m.16.c.sp

description: the spinal cord of a male 16 week normal control human fetus

value: 16 week


title: m.19.cr.b

description: the brain residual of a male 19 week human fetus with craniorachischisis

value: Brain Residual


title: spr-4;spr-3 rep 3 [day 10]

first: Derek

last: Drake

institute: Harvard Medical School

description:
day10_s3s4_3.1
processed data file: spr-day10-gene-counts.txt

data_processing:
Reads were aligned to the Caenorhabditis elegans WBcel235 genome with Ensembl WBcel235.86 gene models using STAR with options --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 15 --alignIntronMax 1000000 --alignMatesGapMax 1000000. Expression levels of genes were quantified as gene counts using FeatureCounts v1.5.1 with options -C -p -B -s 0 -t exon -g gene_id.
Genome_build: WBcel235
Supplementary_files_format_and_content: spr-day10-gene-counts.txt: Tab-delimited text file indicates gene counts for each sample.

organism: Caenorhabditis elegans

source_name: Whole C. elegans

growth_protocol: C. elegans strains were cultured at 20°C under standard conditions as described in Brenner.

extract_protocol:
To analyze RNA from transgenic lines, 100 worms of each strain (including controls) were placed into 1.5 ml M9 buffer. Worms were washed once in M9, pelleted by centrifugation, resuspended in 200 µl Trizol, vortexed for 2 minutes and flash frozen in liquid nitrogen. Worms were then freeze-cracked by thawing in a 37°C water bath and re-freezing in liquid nitrogen. This was repeated 2 more times. After the final thaw, 100 µl of Trizol was added and the tubes were maintained at room temperature for 5 minutes. RNA was then extracted with 140 µl of chloroform, precipitated with an equal volume of 70% ethanol and transferred to an RNeasy spin column (Qiagen) and purified.
cDNA was synthesized using Clontech SmartSeq v4 reagents from 2ng RNA, due to low yields from aged worms. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2ng of sheared cDNA using Rubicon Genomics Thruplex DNAseq reagents according to manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq500 run with paired-end 75 bp reads at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: strain/background

tag: genotype/variation

value: day 10

value: whole body


title: T1_midbrain_hemizygous_9/10

source_name: midbrain, hemizygous, 100 days

value: Hemizygous

value: midbrain

value: male

tag: collection time

value: PM

tag: previously diabetic? (t3 only)

tag: age (days)


title: m.16.c.br

description: the brain of a male 16 week normal control human fetus


title: f.20.c.sk

description: the skin of a female 20 week normal control human fetus

value: 20 week

value: Female

value: Skin


title: m.19.cr.sk

description: the skin of a male 19 week human fetus with craniorachischisis

value: 19 week


title: f.16.a.sk

description: the skin of a female 16 week human fetus with anencephaly

value: anencephaly and spina bifida


title: spr-4;spr-3 rep 2 [day 10]

description:
day10_s3s4_2.1
processed data file: spr-day10-gene-counts.txt


title: T1_midbrain_hemizygous_8

value: brain


title: N2 rep 3 [day 10]

description:
day10_n2_3.1
processed data file: spr-day10-gene-counts.txt

value: WT


title: spr-4;spr-3 rep 1 [day 10]

description:
day10_s3s4_1.2
processed data file: spr-day10-gene-counts.txt


title: f.20.c.sp

description: the spinal cord of a female 20 week normal control human fetus

value: control

value: Spinal cord


title: T1_midbrain_hemizygous_3/4


title: BAG3_KO_rep2

city: Philadelphia

first: Christopher

last: McDermott-Roe

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Reads clipped to remove 3’ adapter sequences, aligned to genome (hg19) and counted in STAR v2.5.2a with the following settings: --outSAMtype BAM SortedByCoordinate; --clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; --quantMode GeneCounts; --outSAMattributes NH HI AS NM MD.
Count files imported into edgeR and analyzed via QLF test.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files, 'Ensembl_ID' and 'cpm' values for each sample.

source_name: Human iPSC-cardiomyocytes

growth_protocol: Cells maintained in RPMI containing B27 plus insulin

extract_protocol:
RNA isolated using Qiagen Rneasy system
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Human iPSC-derived cardiomyocytes


title: T1_midbrain_hemizygous_5/6


title: T1_hindbrain_homozygous_8/9

source_name: hindbrain, homozygous, 100 days

value: Homozygous

value: hindbrain


title: N2 rep 2 [day 10]

description:
day10_n2_2.1
processed data file: spr-day10-gene-counts.txt

tag: age

value: day 10

value: whole body


title: BAG3_RH_rep3


title: N2 rep 1 [day 10]

description:
day10_n2_1.2
processed data file: spr-day10-gene-counts.txt

tag: tissue


title: BAG3_KO_rep1


title: BAG3_RH_rep2


title: T1_midbrain_hemizygous_1/2

value: Hemizygous

value: midbrain


title: T1_hindbrain_homozygous_3/4

value: male

value: AM


title: T1_hindbrain_homozygous_6/7


title: f.20.sb.sk

description: the skin of a female 20 week human fetus with  spina bifida

value: spina bifida

value: 20 week

value: Female


title: f.20.sb.sp

description: the spinal cord of a female 20 week human fetus with  spina bifida


title: BAG3_RH_rep1


title: spr-4;spr-3;daf-2 rep 2 [day 10]

description:
day10_d2s3s4_2.2
processed data file: spr-day10-gene-counts.txt


title: f.20.c.br

description: the brain of a female 20 week normal control human fetus

value: Brain


title: T1_hindbrain_homozygous_1/5

value: brain

value: PM


title: f.20.sb.br

description: the brain of a female 20 week human fetus with  spina bifida


title: T2_hindbrain_nontransgenic_4/13

value: Nontransgenic


title: m.18.c.sk

description: the skin of a male 18 week normal control human fetus

value: control

value: 18 week

value: Male

value: Skin


title: T1_hindbrain_nontransgenic_8/9

source_name: hindbrain, nontransgenic, 100 days

value: hindbrain


title: spr-4;spr-3;daf-2 rep 1 [day 10]

description:
day10_d2s3s4_1.2
processed data file: spr-day10-gene-counts.txt

value: day 10

value: whole body


title: BAG3_WT_rep3

value: Human iPSC-derived cardiomyocytes


title: BAG3_WT_rep2


title: daf-2 rep 3 [day 10]

description:
day10_d2_3.2
processed data file: spr-day10-gene-counts.txt


title: m.18.a.sk

description: the skin of a male 18 week human fetus with anencephaly and spina bifida

value: anencephaly and spina bifida


title: spr-4;spr-3;daf-2 rep 3 [day 10]

description:
day10_d2s3s4_3.1
processed data file: spr-day10-gene-counts.txt


title: f.18.c.sp

description: the spinal cord of a female 18 week normal control human fetus

value: Spinal cord


title: daf-2 rep 2 [day 10]

description:
day10_d2_2.2
processed data file: spr-day10-gene-counts.txt


title: T1_hindbrain_nontransgenic_4/5

value: male


title: daf-2 rep 1 [day 10]

description:
day10_d2_1.2
processed data file: spr-day10-gene-counts.txt


title: T1_hindbrain_nontransgenic_2/7

value: AM


title: BAG3_WT_rep1


title: f.18.c.br

description: the brain of a female 18 week normal control human fetus

value: Female


title: spr-4;spr-3 rep 3 [day 2]

data_processing:
Reads were aligned to the Caenorhabditis elegans WBcel235 genome with Ensembl WBcel235.86 gene models using STAR with options --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 15 --alignIntronMax 1000000 --alignMatesGapMax 1000000. Expression levels of genes were quantified as gene counts using FeatureCounts v1.5.1 with options -C -p -B -s 2 -t exon -g gene_id.
Genome_build: WBcel235
Supplementary_files_format_and_content: Tab-delimited text file indicates gene counts for each sample

source_name: whole C. elegans

growth_protocol: C. elegans strains were cultured at 20°C under standard conditions as described in Brenner

extract_protocol:
To analyze RNA from transgenic lines, 100 worms (24 hours post-L4) of each strain (including controls) were placed into 1.5 ml M9 buffer. Worms were washed once in M9, pelleted by centrifugation, resuspended in 200 µl Trizol, vortexed for 2 minutes and flash frozen in liquid nitrogen. Worms were then freeze-cracked by thawing in a 37°C water bath and re-freezing in liquid nitrogen. This was repeated 2 more times. After the final thaw, 100 µl of Trizol was added and the tubes were maintained at room temperature for 5 minutes. RNA was then extracted with 140 µl of chloroform, precipitated with an equal volume of 70% ethanol and transferred to an RNeasy spin column (Qiagen) and purified.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75 bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: day 2


title: spr-4;spr-3 rep 2 [day 2]


title: SaOS2-p21_ON_3

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Reads were mapped to the Hg19 genome by STAR
HTseq was used to generate count file with gene names
R package DESeq2 was used to normalize counts (mean-ratio method), calculate total reads, and determine differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts generated through DESeq2

growth_protocol: DMEM, 10% FBS

extract_protocol:
Qiagen RNAeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated or 24h 1µg/ml doxycycline

value: Tet-inducible p21 (ON)

tag: cell line


title: SaOS2-p21_ON_1


title: T1_hindbrain_nontransgenic_1/3

value: brain

value: PM


title: m.20.a.sk

description: the skin of a male 20 week human fetus with anencephaly and spina bifida

value: 20 week


title: SaOS2-p21_ON_2


title: T1_hindbrain_nontransgenic_6

value: Nontransgenic


title: T1_hindbrain_hemizygous_8

source_name: hindbrain, hemizygous, 100 days

value: Hemizygous


title: SaOS2-p21_OFF_3

value: Tet-inducible p21 (OFF)


title: T1_hindbrain_hemizygous_9/10

value: hindbrain


title: SaOS2-p21_OFF_2


title: N2 rep 3 [day 2]


title: N2 rep 2 [day 2]


title: m.20.c.sk

description: the skin of a male 20 week normal control human fetus

value: control

value: Male

value: Skin


title: SaOS2-p21_OFF_1


title: T1_hindbrain_hemizygous_3/4


title: TCQA 2

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from treated skin at day 30 after treatment

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array (430 2.0 ). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
RMA

source_name: skin treated with TCQA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: The dorsal skin of mice were treated daily with TCQA or milliQ water for a month. Upon sacrfice, skin from the treated area was collected and total RNA was extracted.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80°C until use.

value: skin


title: m.20.a.br

description: the brain residual of a male 20 week human fetus with anencephaly and spina bifida

value: anencephaly and spina bifida

value: Brain residual


title: m.20.a.sp

description: the spinal cord of a male 20 week human fetus with anencephaly and spina bifida

value: Spinal cord


title: Control 2

source_name: skin treated with MilliQ

treatment_protocol: The dorsal skin of mice were treated daily with TCQA or milliQ water for a month. Upon sacrfice, skin from the treated area was collected and total RNA was extracted.


title: TCQA 1


title: spr-4;spr-3 rep 1 [day 2]


title: Control 1


title: N2 rep 1 [day 2]


title: spr-4;spr-3;daf-2 rep 2 [day 2]


title: spr-4;spr-3;daf-2 rep 3 [day 2]


title: IR12-2

city: Dalian City

first: xue

last: li

state: Liaoning Province

address: No. 1 Light Industry Court, Ganjingzi District

department: School of food science and technology

country: China

institute: Dalian Polytechnic University

data_processing:
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: NCBI accession number SDAR00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Hafnia alvei

source_name: △luxI/R_aquatic products

growth_protocol: the wild-type and ΔluxIR were routinely cultured in Luria-Bertani (LB) broth (10 g tryptone per liter, 5 g yeast extract, 5 g NaCl per liter) with pH adjustment of 7 and were grown at 30°C with shaking at 150 rpm

extract_protocol:
The culture solution under different conditions was centrifuged and the supernatant was discarded. After freezing in liquid nitrogen, it was stored in a -80 degree refrigerator to prepare for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: {delta}luxI/R

tag: isolation source

value: Instant sea cucumber


title: IR12-3


title: T1_hindbrain_hemizygous_1/2

value: male


title: IR12-1


title: T1_hindbrain_hemizygous_5/6

value: brain


title: W12-3

source_name: wild type_aquatic products

value: wild type


title: spr-4;spr-3;daf-2 rep 1 [day 2]

value: day 2


title: ZC-3

city: Qingdao

first: Rongjian

last: Xu

address: No.38 Dengzhou Road

institute: The Affiliated Hospital of Qingdao University

description: The assay started from 4 to 8 μg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, ttp://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. After RNA hybridization, tag-conjugating Cy3 dye were circulated through the microfluidic chip for dye staining. Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device)

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) and a spacer segment of polyethylene glycol toextend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

data_processing: Images were digitized using Array-Pro image analysis software (Media Cybernetics). Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression)

source_name: noncalcified aortic valve

label_protocol: The assay started from 4 to 8μg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted by Total RNA Purification Kit（LC Sciences, Cat. TRK-1001）following the manufacturer's instructions.

value: 70 years

value: noncalcified aortic valve


title: GH-1

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device)

source_name: calcified aortic valve

value: 56 years

value: calcified aortic valve


title: GH-2

value: female

value: 62 years


title: daf-2 rep 3 [day 2]

city: Boston

address: 77 Avenue Louis Pasteur


title: W12-1


title: W12-2


title: Experimental/Mutant mouse embryo at E17.5, biological replicate 3

city: St-Hyacinthe

last: Boerboom

state: Québec

address: 3200 rue sicotte

department: Biomédecine Vétérinaire

country: Canada

institute: Faculté de Médecine Vétérinaire (University of Montreal)

hyb_protocol: Performed as per Génome Québec protocole. For more information, contact Génome Québec LAB http://gqinnovationcenter.com/index.aspx?l=e

data_processing: Results were analyzed using Transcriptome Analysis Console software (4.0). Thresholds used for p-value and fold change were 0.05 and +/-2 respectively.

source_name: E17.5=Müllerian duct fully elongated Mut=mutant

extract_protocol: Total RNA was extracted using QIAGEN Rneasy mini kit according to manufacturer's instructions

treatment_protocol: E17.5 mice embryos were collected and genotyped. Selected embryos were dissected. The Müllerian duct was isolated, collected in an eppendorf tube and flash frozen in liquide nitrogen. Samples were kept at -80 celcius for eventual extraction.

value: Müllerian duct


title: ZC-2


title: ZC-1


title: daf-2 rep 1 [day 2]


title: Mutant rep 3

status: Public on Oct 09 2019

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

data_processing:
Trimmed, clean reads were mapped to the pig reference genome (Sscrofa 10.2) using the SOAP2 software and allowing five mismatches(Li et al., 2009).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol (Mortazavi et al., 2008). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
A FDR of no more than 0.001 (FDR ≤ 0.001) and a difference ratio of the RPKM between the wild-type and mutant samples of no less than 1 (|log2 ratio| ≥ 1) were adopted as the significance thresholds to identify DEGs.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: txt files include RPKM values for each Sample.

organism: Sus scrofa

source_name: pig embryo at 17.5-18.0 dpc

extract_protocol:
Embryos were harvested from the uterus and stored in liquid nitrogen for RNA extraction. The extra-embryonic tissues of each embryo were collected for DNA extraction and genotyping of the VRTN QTNs. Total RNA was isolated from three wild-type (qq) and three mutant (QQ) pig embryos using Trizol reagent, which was then used to construct cDNA libraries using the TruSeq RNA Sample Preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Large White

value: homozygous for the two QTNs (QQ)

value: embryo

tag: developmental stage


title: Mutant rep 2

tag: genotype


title: WT rep3


title: WT rep2


title: Experimental/Mutant mouse embryo at E17.5, biological replicate 2

scan_protocol: Performed as per Génome Québec protocole. For more information, contact Génome Québec LAB http://gqinnovationcenter.com/index.aspx?l=e


title: WT rep1


title: Experimental/Mutant mouse embryo at E17.5, biological replicate 1

label_protocol: Performed as per Génome Québec protocole. For more information, contact Génome Québec LAB http://gqinnovationcenter.com/index.aspx?l=e


title: L3-Eye_input_2

city: Paris

first: Radoslaw

middle: Kamil

last: Ejsmont

address: 8-10 rue Charles V

institute: CRI

data_processing:
Basecalls performed with BaseSpace FastQ Version: 1.0.0
Raw reads adapter and low quality trimmed using fastq-mcf version 1.04.807
Read mapped using Bowtie version 2.2.1 to the Drosophila Melanogaster genome DM3 build
Peaks called with Macs 2.1.0
Genome_build: DM3
Supplementary_files_format_and_content: BED files containing the “narrowPeak” peaks called with Mac2 (default parameters) using the IP samples as treatment and input samples as control

source_name: L3 eye disc

growth_protocol: The Drosophila knock in IMAGO line ato:GFP was keept at 25 degrees at standard conditions

extract_protocol:
400 L3 larvae of the ato:GFP genotype were dissected to isolate 800 eye discs that were later fixed and sonicated. A 10% of the sonicated volume was used as the input. The rest was used to isolate the DNA bound to the transcription factor Atonal using anti GFP antibodies.
TruSeqLT

treatment_protocol: The sample was keept under normal growing contions and was not treated before dissection

value: eye disc

tag: chip antibody

tag: replicates

value: knock in IMAGO line ato:GFP


title: L3-Eye_input_1


title: L3-Eye_atoIP_2

value: anti-GFP


title: L3-Eye_atoIP_1


title: Chick_H5_smartseq2_scRNA-seq

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

description: chicken-single-cell.counts.txt

data_processing:
Reads were mapped using RNA-STAR (2.4.2a) (Dobin, Davis et al. 2013) to the chicken genome Galgal4 assembly and the ERCC spike-in controls using the default parameters. Gene expression levels were quantified as read counts using the featureCounts function from the Subread package with default parameters. Reads that aligned to more than one locus as well as ambiguous fragments were excluded from all further analysis. To remove cells with low quality sequencing, cells with a) less than 100,000 sequenced reads or b) less than 50% uniquely mapped reads were excluded from any further analysis. Further filtering was done based on the distributions of a) the number of expressed genes per cell, b) the proportion of reads on mitochondrial genes or c) the proportion of reads on ERCC spike-ins, requiring that the cells are within 3 MADs (Median Absolute Deviation) for each distribution (McCarthy, Campbell et al. 2017). In the remaining 124 cells, 10,291 genes were detected using the following criteria: a) they had any reads in more than 5 cells and b) had an average number of counts above 1. The cell-based factors from the deconvolved pool-based size factors were used for the normalisation of the gene counts, as described in (Lun, Bach et al. 2016), using pool sizes of 10, 20, 40 and 60 cells. The clustering was done with the pagoda2 package (https://github.com/hms-dbmi/pagoda2) using the infomap and the walktrap community methods. There was a 96% concordance between the two methods and the infomap method was used to obtain the final clusters. An analysis for differentially expressed genes was performed using the SCDE package (Kharchenko, Silberstein et al. 2014) to find cluster specific gene markers. For each cluster a one-versus-one approach was applied between all pairs of clusters using the default parameters.
Genome_build: galGal4
Supplementary_files_format_and_content: chicken-7-8ss-counts.txt
Supplementary_files_format_and_content: chicken-single-cell.counts.txt

organism: Gallus gallus

source_name: FoxD3_Nc1_Citrine+ neural crest isolated by FACS

growth_protocol: Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.

extract_protocol:
Individual NC cells were collected by FACS, cDNA was generated and sequencing libraries were prepared as previously described (Picelli, Faridani et al. 2014). Libraries were sequenced using 50bp single-end reads for 96 cells on the Illumina NextSeq500 platform. A 4x107 dilution of ERCC spike in control was used.
SMARTseq2

treatment_protocol: Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37oC for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37oC for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion. We collected ~300 and ~600 NC cells per embryo at 5-6ss and 8-10ss respectively.

tag: development

value: stage 5-8ss

value: neural crest

value: FAC sorted for FoxD3_NC1_Citrine+ cells

tag: amplification


title: Chick_H6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_H9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: scATAC

data_processing:
Sequenced files were demultiplexed and features counted using CellRanger (v3.0.0)
Seurat (v3.0.1) R package was used for data processing for scRNA samples and the Loupe Cell Browser for the scATAC samples
Genome_build: galGal5. Custom genomes were build using CellRanger to allow proper mapping of reads/fragments.

source_name: scATAC

extract_protocol:
Isolated cells were then loaded onto the 10X Chromium machine and libraries prepared as per manufacturer's protocol
As per manufacturer's protocol

treatment_protocol: Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion.

tag: genotype/variation

value: Wild-type

value: Embryo

value: Neural crest (NC1+ cells)

value: Dissociation and FACS

tag: treatment

value: NC1:citrine electroporation at HH4

value: 10X Chromium v2

tag: assay

value: scATAC-seq


title: Control mouse embryo at E17.5, biological replicate 3

source_name: E17.5=Müllerian duct fully elongated Ctrl=control

value: Müllerian duct


title: Control mouse embryo at E17.5, biological replicate 2


title: Chick_H4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Control mouse embryo at E17.5, biological replicate 1


title: h-PBMC: Zol. (-)

city: Shinagawa

first: Reiko

last: Takimoto

state: Tokyo

department: Department of Biochemistry

institute: Showa University, School of Dentistry

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hrs at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

source_name: h-PBMC

label_protocol: Biotinylated cDNA was prepared from 100 ng of total RNA using GeneChip WT PLUS Reagent Kit（Thermo Fisher Scientific).

growth_protocol: h-PBMC were cultured in the presence of 10% FBS.

extract_protocol: Extraction of total RNA was performed by Rneasy mini kit (Qiagen).

treatment_protocol: h-PBMC were incuvated  for 8 hours with 5 mM of Zoledronate (Zol. (+)) or without (Zol. (-)).

value: human peripheral blood mononuclear cells


title: Chick_H3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_H12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: h-PBMC: Zol. (+)


title: Chick_H2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Mutant rep 1

value: Large White

value: homozygous for the two QTNs (QQ)


title: Chick_H10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_H1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G7_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: scRNA

source_name: scRNA

value: scRNA-seq


title: Chick_G1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_H11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_G3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E7_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_F1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: BAG3_KO_rep3

source_name: Human iPSC-cardiomyocytes

value: Human iPSC-derived cardiomyocytes


title: Chick_E5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C7_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_E6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_D2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_C11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B4_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A7_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A9_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A6_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A3_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A5_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A2_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A12_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A11_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_B7_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: 9_S26_smartseq2_scRNA-seq


title: 91_S15_smartseq2_scRNA-seq


title: 8_S53_smartseq2_scRNA-seq


title: 88_S1_smartseq2_scRNA-seq


title: 89_S54_smartseq2_scRNA-seq


title: 86_S60_smartseq2_scRNA-seq


title: 87_S55_smartseq2_scRNA-seq


title: Chick_B10_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: 84_S62_smartseq2_scRNA-seq


title: 85_S61_smartseq2_scRNA-seq


title: 83_S63_smartseq2_scRNA-seq


title: 80_S38_smartseq2_scRNA-seq


title: 82_S64_smartseq2_scRNA-seq


title: 81_S37_smartseq2_scRNA-seq


title: Chick_A8_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: Chick_A1_smartseq2_scRNA-seq

description: chicken-single-cell.counts.txt


title: 77_S3_smartseq2_scRNA-seq


title: 7_S45_smartseq2_scRNA-seq


title: 75_S40_smartseq2_scRNA-seq


title: 78_S39_smartseq2_scRNA-seq


title: 76_S49_smartseq2_scRNA-seq


title: 93_S30_smartseq2_scRNA-seq


title: 92_S2_smartseq2_scRNA-seq


title: 73_S16_smartseq2_scRNA-seq


title: 6_S27_smartseq2_scRNA-seq


title: 74_S4_smartseq2_scRNA-seq


title: 90_S31_smartseq2_scRNA-seq


title: 60_S17_smartseq2_scRNA-seq


title: 59_S50_smartseq2_scRNA-seq


title: 58_S18_smartseq2_scRNA-seq


title: 57_S41_smartseq2_scRNA-seq


title: 55_S51_smartseq2_scRNA-seq


title: 56_S19_smartseq2_scRNA-seq


title: 54_S66_smartseq2_scRNA-seq


title: 53_S67_smartseq2_scRNA-seq


title: 52_S56_smartseq2_scRNA-seq


title: 51_S68_smartseq2_scRNA-seq


title: 4_S28_smartseq2_scRNA-seq


title: 50_S69_smartseq2_scRNA-seq


title: 48_S20_smartseq2_scRNA-seq


title: 47_S57_smartseq2_scRNA-seq


title: 46_S47_smartseq2_scRNA-seq


title: 45_S11_smartseq2_scRNA-seq


title: 44_S70_smartseq2_scRNA-seq


title: 40_S12_smartseq2_scRNA-seq


title: 42_S21_smartseq2_scRNA-seq


title: 41_S5_smartseq2_scRNA-seq


title: 5_S10_smartseq2_scRNA-seq


title: 3_S35_smartseq2_scRNA-seq


title: 38_S42_smartseq2_scRNA-seq


title: 36_S73_smartseq2_scRNA-seq


title: 39_S72_smartseq2_scRNA-seq


title: 37_S6_smartseq2_scRNA-seq


title: 35_S43_smartseq2_scRNA-seq


title: 33_S13_smartseq2_scRNA-seq


title: 34_S58_smartseq2_scRNA-seq


title: 32_S22_smartseq2_scRNA-seq


title: daf-2 rep 2 [day 2]

source_name: whole C. elegans

value: day 2


title: 49_S46_smartseq2_scRNA-seq

value: stage 5-8ss


title: 30_S7_smartseq2_scRNA-seq

value: neural crest


title: 31_S32_smartseq2_scRNA-seq

value: FAC sorted for FoxD3_NC1_Citrine+ cells


title: 28_S74_smartseq2_scRNA-seq


title: 23_S8_smartseq2_scRNA-seq


title: 26_S23_smartseq2_scRNA-seq


title: 25_S24_smartseq2_scRNA-seq


title: 24_S52_smartseq2_scRNA-seq


title: 43_S71_smartseq2_scRNA-seq


title: 2_S36_smartseq2_scRNA-seq


title: 22_S48_smartseq2_scRNA-seq


title: 20_S75_smartseq2_scRNA-seq


title: 19_S76_smartseq2_scRNA-seq


title: 18_S77_smartseq2_scRNA-seq


title: 17_S78_smartseq2_scRNA-seq


title: 16_S14_smartseq2_scRNA-seq


title: 15_S79_smartseq2_scRNA-seq


title: 14_S80_smartseq2_scRNA-seq


title: 13_S81_smartseq2_scRNA-seq


title: 27_S44_smartseq2_scRNA-seq


title: 12_S9_smartseq2_scRNA-seq


title: 11_S59_smartseq2_scRNA-seq


title: non-neural crest_8-10ss rep4 ATAC-seq

data_processing:
Reads were mapped using  Bowtie -m 2 (v.1.0.0) to galGal4. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Peak calling was performed using MACS2, de novo motif search was performed using Homer (v.4.7)
Genome_build: galGal4
Supplementary_files_format_and_content: read counts (txt file)

source_name: FoxD3_Nc1_Citrine NEGATIVE neural crest isolated by FACS

extract_protocol:
FAC-sorted cells were lysed (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and tagmented using Illumina Nextera DNA kit (FC-121-1030) for 30mins at 37°C. Tagmented DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix for 11 cycles. Tagmentation efficiency was assessed using Agilent Tapestation. Three biological replicates were obtained for each stage.
Libraries were prepared using Illumina Nextera DNA kit and sequenced on Illumina Illumina NextSeq 500 using 40bp paired end reads

treatment_protocol: Dissected cranial regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion. We collected ~300 and ~600 NC cells per embryo at 5-6ss and 8-10ss respectively.

value: stage 8-10ss

value: FAC sorted for FoxD3_NC1_Citrine NEGATIVE cells

value: Illumina Nextera DNA kit


title: neural crest bulk TF_KD rep2 RNA-seq

data_processing:
Reads were mapped using STAR (v.2.4.2a) for RNA-seq to galGal5. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Differential Expression analysis was performed using DESeq2 R package.
Genome_build: galGal5
Supplementary_files_format_and_content: read counts (txt file)

source_name: dorsal neural tube microdissection

extract_protocol:
RNA was extracted from dissected half dorsal neural tubes using Ambion RNAqueous Micro Total RNA isolation kit (Cat.#AM1931, ThermoFisher Scientific), the integrity was checked using Bioanalyser, and only samples with RIN>7 were used for analysis. 6 individual embryos and associated RNA-seq libraries were analysed.
RNA-seq libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Cat.#634889, Takara Bio Clontech) and sequenced using 40bp paired-end reads on Illumina NextSeq500.

value: stage 5-10ss

value: embryo microdissection

value: TF knockdown


title: neural crest bulk control rep2 RNA-seq

value: control


title: 10_S34_smartseq2_scRNA-seq


title: neural crest bulk control rep3 RNA-seq


title: 21_S25_smartseq2_scRNA-seq


title: neural crest bulk TF_KD rep3 RNA-seq


title: neural crest bulk control rep1 RNA-seq


title: neural crest bulk TF_KD rep1 RNA-seq


title: non-neural crest_8-10ss rep3 ATAC-seq


title: non-neural crest_8-10ss rep2 ATAC-seq


title: non-neural crest_8-10ss rep1 ATAC-seq


title: non-neural crest_5-6ss rep1 ATAC-seq

value: stage 5-6ss


title: non-neural crest_5-6ss rep3 ATAC-seq


title: neural crest-8-10ss_FoxD3 rep3 ATAC-seq


title: neural crest-8-10ss_FoxD3 rep1 ATAC-seq


title: whole epiblast rep2 ATAC-seq

source_name: microdissection of the whole epiblast

value: whole epiblast


title: neural crest-8-10ss_FoxD3 rep2 ATAC-seq


title: HH10 somites ATAC-seq

source_name: microdissection of HH10 somites

value: somites


title: whole epiblast rep1 ATAC-seq


title: neural crest-5-6ss_Pax7 ATAC-seq

source_name: Pax7_enhancer195_Citrine+ neural crest isolated by FACS

value: FAC sorted for Pax7_enh195_Citrine+ cells


title: neural crest-5-6ss_FoxD3 rep2 ATAC-seq


title: neural crest-5-6ss_FoxD3 rep1 ATAC-seq


title: Regressed_40

city: Edinburgh

first: Jana

last: Travnickova

address: Crewe Road South

department: MRC Institute of Genetics and Molecular Medicine

institute: MRC Human Genetics Unit & Cancer Research UK EC

description: NexteraXT library preparation

data_processing:
Sequence quality was checked using FastQC (version 0.11.3), Reads were aligned to the zebrafish genome (GRCz11) using STAR (STAR_2.5.1b) with the default parameters, Raw counts of reads covering the transcriptome (Ensembl annotation version GRCz11) was obtained using htseq-count (0.6.1)
Illumina  software used for basecalling.
Sequence quality was checked using FastQC (version 0.11.3)
Reads were aligned to the zebrafish genome (GRCz11) using STAR (STAR_2.5.1b) with the default parameters or using Salmon in the alignment-based mode
The quality of the resulting alignment to the transcriptome (Ensembl annotation version GRCz11) has been checked using RNASeqQC (v1.1.8.1)
Raw counts of reads covering the transcriptome (Ensembl annotation version GRCz11) was obtained using htseq-count (0.6.1) with the “-s reverse” option.
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: tab-delimited filed of raw counts at gene level for each sample

organism: Danio rerio

source_name: mitfa:GFP cells from regressed triple melanoma

extract_protocol:
FACS sorting of 11 GFP+ living cells from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cells from regressed triple melanoma


title: Regressed_37

description: NexteraXT library preparation

extract_protocol:
FACS sorting of 50 GFP+ living cells from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads


title: Regressed_68

description: NexteraXT library preparation


title: Primary_45

description: NexteraXT library preparation

source_name: mitfa:GFP cells from triple melanoma

extract_protocol:
FACS sorting of 50 GFP+ living cells from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: GFP+ cells from primary triple melanoma


title: Regressed_69

description: NexteraXT library preparation

extract_protocol:
FACS sorting of 10 GFP+ living cells from regression site, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads


title: Primary_34

description: NexteraXT library preparation


title: Primary_46

description: NexteraXT library preparation


title: Primary_33

description: NexteraXT library preparation


title: non-neural crest_5-6ss rep4 ATAC-seq


title: Primary_35

description: NexteraXT library preparation


title: Primary_31

description: NexteraXT library preparation


title: Primary_30

description: NexteraXT library preparation


title: non-neural crest_5-6ss rep2 ATAC-seq


title: Primary_5

description: NexteraXT library preparation


title: Primary_28

description: NexteraXT library preparation


title: Primary_29

description: NexteraXT library preparation


title: Primary_7

description: NexteraXT library preparation


title: Primary_9

description: NexteraXT library preparation


title: Primary_3

description: NexteraXT library preparation


title: Amel3

description: Truseq library preparation

source_name: Triple Nodular Melanoma

extract_protocol:
Whole tumour was dissected, dissociated and RNA extracted using Trizol with column cleanup
polyA selection
cDNA - TruSeq or Nextera XT
RNA-Seq, Paired end reads

value: Primary melanoma - triple nodular amelanotic


title: Amel2

description: Truseq library preparation


title: triple_6

description: Truseq library preparation

value: Primary melanoma - triple nodular pigmented


title: Amel6

description: Truseq library preparation


title: Amel4

description: Truseq library preparation


title: Amel5

description: Truseq library preparation


title: Amel1

description: Truseq library preparation


title: triple_5

description: Truseq library preparation

source_name: Triple Superficial Melanoma

value: Primary melanoma- triple superficial


title: triple_4

description: Truseq library preparation


title: triple_3

description: Truseq library preparation


title: triple_2

description: Truseq library preparation


title: triple_1

description: Truseq library preparation


title: p53_5

description: Truseq library preparation

source_name: Double Superficial Melanoma

value: Primary melanoma - double


title: Primary_4

description: NexteraXT library preparation


title: p53_3

description: Truseq library preparation


title: p53_2

description: Truseq library preparation


title: GC077042_TGCAGCTA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

data_processing: Sequence quality was checked using FastQC (version 0.11.4). Raw reads were trimmed, using Cutadapt to remove Smart-Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 (Ensembl V92, 20178) including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment-based mode.

source_name: mitfa:GFP cell from recurring_nodular triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from recurring tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077042_TGCAGCTA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT

value: GFP+ cell from primary_nodular triple melanoma


title: p53_4

description: Truseq library preparation


title: GC077042_TGCAGCTA-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_nodular triple melanoma

extract_protocol:
FACS sorting of a single GFP+ living cell from regressed tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA -  Nextera XT

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077042_TGCAGCTA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: p53_1

description: Truseq library preparation