title: w9_thymus_10x

city: Beijing

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing data from 10x was aligned and quantified using the CellRanger software package with default parameters.  For modified STRT-seq data, raw reads of each cell were first split by specific barcode sequence attached in Read 2. The template switch oligo (TSO) sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Subsequently, reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Next, the stripped Read1 sequences were aligned to hg19 human transcriptome (UCSC) using TopHat (version 2.0.12) (Trapnell et al., 2009). Uniquely mapped reads were counted by HTSeq package(Anders et al., 2015) and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

extract_protocol: Single cells in good condition were picked into lysis buffer by mouth pipetting, and the scRNA-seq preparation procedure was based on STRT with some modifications (Li et al., 2017; Picelli et al., 2013; Picelli et al., 2014). Then, cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode whereas N standing for unique molecular identifiers (UMI), shown in Table S2) and TSO primer for template switching (Hashimshony et al., 2012; Islam et al., 2014; Macosko et al., 2015). After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 17 cycles of PCR using ISPCR primer and 3' Anchor primer (see Table S2). Samples were pooled and purified using Agencourt AMPure XP beads (Beckman). 4 cycles of PCR were performed to introduce index sequence (shown in Table S2). After this step, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. The cDNA was incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher) for 1 hour at room temperature. Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems). After adaptor ligation, the libraries were amplified by 7 cycles of PCR using QP2 primer and short universal primer (shown in Table S2). The libraries were sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner (sequenced by Novogene).

value: Thymus

tag: development stage


title: CS15_and_CS17_Blood_Liver

status: Public on Oct 09 2019

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

value: Blood and Liver

value: CS15 and CS17


title: GC077042_TGCAGCTA-CTATTAAG_primary_superficial_sc

city: Edinburgh

first: Jana

last: Travnickova

address: Crewe Road South

department: MRC Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: MRC Human Genetics Unit & Cancer Research UK EC

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.

organism: Danio rerio

source_name: mitfa:GFP cell from primary_superficial 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

tag: genotype

value: GFP+ cell from primary_superficial triple melanoma


title: w10_thymus_10x


title: w8_thymus_10x


title: GC077042_TGCAGCTA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation

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-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077042_TCGACGTC-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_TCGACGTC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_TCGACGTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: CS23_Liver_10x

value: Liver


title: CS14_CS15_AGM

value: AGM

value: CS14 and CS15


title: CS20_Liver_10x


title: GC077042_TCGACGTC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_TCGACGTC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: thymic_TEC of _w9

source_name: human embryonic cells


title: GC077042_TCCTGAGC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_superficial triple melanoma

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077042_TCCTGAGC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_TCCTGAGC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma

value: GFP+ cell from primary_nodular triple melanoma


title: S19 [delta]per_rep_2

city: Bareilly

first: Khushal

middle: Singh

last: Solanki

state: Uttar Pradesh

address: Izatnagar

country: India

institute: ICAR-Indian Veterinary Research Institute

data_processing:
Base calling was done on the instrument (Illumina,  NextSeq 500) by Real Time Analysis (RTA) 2.4.6 (a NextSeq software)
In-house perl scripts were used for the removal of adapters adapters and trimming of low quality bases from the end of the raw reads
These processed reads were further filtered / trimmed using PRINSEQ (prinseq-lite.pl) for quality >= Q25 and minumum length of 50 bp
Transcriptome analysis was carried out using RSEM (RNA-Seq by Expectation Maximization) (Li and Dewey, 2011)
Differential gene expression analyis was carried out using DE package tools, such as DESeq2 (Love, Huber, and Anders, 2014), edgeR (Robinson et al., 2010) and EBSeq (Lenget al., 2013)
Genome_build: Mouse (GrCm38.83)
Supplementary_files_format_and_content: Tab-delimited text files include differential gene expression results of DESeq2 (Love, Huber, and Anders, 2014), edgeR (Robinson et al., 2010) and EBSeq (Lenget)

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
At day 15th post immunization (p.i.), all mice were euthanized humanely, spleen was harvested aseptically. Total RNA was extracted from each spleen sample usingTRIzol reagent (QIAzolRLysis reagent, Qiagen, USA) and then purified using RNeasy mini kit (Qiagen, USA). cDNA library preperation was carried out using low sample (LS) protocol of ‘Truseq RNA library prep kit v2 (#15026495 Rev. F, ILLUMINA proprietary, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice of treatment group was intraperitoneally (i.p.)  inoculated with 5 x 105 CFU of  Brucella abortus S19∆per in 200µl PBS and control group with 200µl PBS alone respectively

tag: treatment

value: Brucella abortus S19 [delta]per

tag: time

value: 15th day post immunization


title: thymic_TEC of _w8-early


title: S19 [delta]per_rep_1


title: GC077042_TCCTGAGC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: PBS_rep_2

value: phosphate buffered saline


title: Control

type: RNA

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlasTM imaging station.

data_processing: The robust multichip average (RMA) method was used background correction and normalization with GeneSpring GX 14.9.1 software

label: Biotin

source_name: Tongue

label_protocol: 10 ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: GFP-SAS cells were incubated in a humidified atomosphere of 95% air and 5% CO2 at 37℃

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

treatment_protocol: GFP-SAS cells were treated with 25 nM of LNA/DNA antisense oligonucleotide against miR-361-3p or non-target (NT) for 24 h.

tag: cell type

value: Squamous cell carcinoma cell line

tag: cell line

value: GFP-SAS


title: GC077042_TCCTGAGC-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: Inhibition of miR-361-3p


title: PBS_rep_1


title: GC077042_TCCTGAGC-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_TCGACGTC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGGCATG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_TAGGCATG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGGCATG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: thymic_TEC_of_w8_w10

value: w8 and w10


title: GC077042_TAGGCATG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_TAGGCATG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGCGCTC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: w7_thymus

value: Thymus


title: GC077042_TAGCGCTC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGCGCTC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGCGCTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: GC077042_TACGCTGC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_TAGCGCTC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: ECAPS 1081

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Gene expression from bronchial epithelial cells collected from former and e-cig smoker.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene10sthsentrezg R package (version 17.0.0).

label: biotin

source_name: bronchial epithelial cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA).  RNA integrity was assessed by Agilent BioAnalyzer, and RNA purity confirmed using a NanoDrop spectrophotometer.

tag: site

value: BU

tag: smoking status

value: Former and E-Cig Smoker

tag: age

tag: Sex

value: Female

tag: race

value: White

tag: pack years

tag: last tcig (months)

tag: first ecig (months)

tag: nicalert level

value: 3 (100-200 ng/mL cotinine)

tag: rin

tag: batch

value: batch 3

value: bronchial epithelial cells


title: GC077042_TACGCTGC-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation

tag: tissue

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077042_TACGCTGC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

tag: genotype

value: GFP+ cell from primary_superficial triple melanoma


title: GC077042_TAAGGCGA-GAGCCTTA_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077042_TAAGGCGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: ECAPS 1078

description: Gene expression from bronchial epithelial cells collected from current smoker.

value: Current Smoker

value: Male

value: 6 (1000+ ng/mL cotinine)

value: batch 4


title: ECAPS 1070


title: ECAPS 1059

value: Black or African American


title: ECAPS 0034

value: UCLA


title: ECAPS 1042

value: BU

value: 4 (200-500 ng/mL cotinine)


title: ECAPS 1075

value: Former and E-Cig Smoker


title: GC077042_TAAGGCGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: ECAPS 1032

value: White


title: ECAPS 1068

description: Gene expression from bronchial epithelial cells collected from former smoker.

value: Former Smoker

value: 1 (10-30 ng/mL cotinine)


title: ECAPS 0029

value: batch 3

value: bronchial epithelial cells


title: ECAPS 1071

value: Female

value: Multiple


title: ECAPS 1064


title: GC077042_TACGCTGC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: ECAPS 1060


title: GC077042_GTAGAGGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077042_TAAGGCGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GTAGAGGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: ECAPS 1031


title: ECAPS 1030


title: GC077042_GTAGAGGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GTAGAGGA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: ECAPS 1027

value: Current Smoker

value: 6 (1000+ ng/mL cotinine)


title: GC077042_GGAGCTAC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GGAGCTAC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_GGAGCTAC-GAGCCTTA_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: GC077042_GGAGCTAC-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GGAGCTAC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: ECAPS 1017

value: Male

value: Black or African American


title: ECAPS 1018

value: BU

value: batch 1


title: GC077042_GGACTCCT-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: ECAPS 0018

value: UCLA

value: Former and E-Cig Smoker

value: White


title: ECAPS 1011


title: ECAPS 0021


title: ECAPS 0003

value: Former Smoker


title: ECAPS 1015

value: 5 (500-1000 ng/mL cotinine)

value: batch 3

value: bronchial epithelial cells


title: GC077042_GTAGAGGA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: ECAPS 0027


title: GC077042_GGACTCCT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_GGACTCCT-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_GTAGAGGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: ECAPS 0020


title: GC077042_GGACTCCT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077042_GGACTCCT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: ECAPS 0007

value: Female


title: ECAPS 1006

value: Current Smoker

value: 6 (1000+ ng/mL cotinine)


title: ECAPS 0006

value: Male


title: GC077042_GGACTCCT-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: ECAPS 1009

value: American Indian or Alaska Native


title: GC077042_GGACTCCT-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: ECAPS 1033

value: BU


title: ECAPS 1012

value: batch 1


title: GC077042_GCTCATGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: ECAPS 0024

value: UCLA

value: Black or African American


title: ECAPS 0026

value: Former Smoker

value: White


title: GC077042_GCTCATGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCTCATGA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCGTAGTA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: ECAPS L007

value: batch 4


title: GC077042_GCGTAGTA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCGTAGTA-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCGTAGTA-CCTAGAGT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCGTAGTA-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: ECAPS 0002

value: bronchial epithelial cells


title: ECAPS 1028

value: 1 (10-30 ng/mL cotinine)


title: GC077042_CTCTCTAC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_CTCTCTAC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: GC077042_CTCTCTAC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: ECAPS 1026

value: Female

value: 3 (100-200 ng/mL cotinine)


title: GC077042_GCTCATGA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: ECAPS 1037


title: GC077042_CTCTCTAC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077042_CTCTCTAC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_GCTCATGA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGTACTAG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: TNRC_si_total_RNA_rep2

city: Glasgow

first: Ania

last: Wilczynska

address: Switchback Road

institute: Beatson Insistute for Cancer Research

description: total RNA from TNRC6A and TNRC6B siRNA transfected HEK293 cell replicate 2

data_processing:
Base calling bcl2fastq 2.0
Alignment using TopHat2 on Gencode_v19
Raw counts were obtained using htseq-count on gene_id
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts for each gene ID

extract_protocol:
RNA was extracted with TRIzol using the standard protocol
Illumina Truseq stranded library kit

tag: ip antibody

tag: sirna

value: TNRC6A TNRC6B

tag: sucrose gradient fraction


title: ECAPS 1005

value: Male

value: 2 (30-100 ng/mL cotinine)

tag: cell type


title: ctrl_si_total_RNA_rep2

description: total RNA from ctrl siRNA transfected HEK293 cell replicate 2

tag: cell line

value: control


title: ctrl_si_total_RNA_rep1

description: total RNA from ctrl siRNA transfected HEK293 cell replicate 1


title: GC077042_CGTACTAG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGTACTAG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: ECAPS 1047

tag: site

value: BU

tag: smoking status

value: Multiple

value: batch 3


title: ECAPS 0008

value: UCLA

value: Former Smoker

tag: age

tag: Sex

value: batch 1


title: GC077042_CGTACTAG-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077042_CGTACTAG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: CNOT_si_POLY_RNA_rep4

description: RNA of polysomal fraction 6-11 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 4

value: polysomal (fractions 6-11)


title: CNOT_si_POLY_RNA_rep2

description: RNA of polysomal fraction 6-11 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 2


title: CNOT_si_POLY_RNA_rep3

description: RNA of polysomal fraction 6-11 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 3


title: GC077042_CGGAGCCT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGGAGCCT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: GC077042_TACGCTGC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_POLY_RNA_rep1

description: RNA of polysomal fraction 6-11 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 1


title: GC077042_CGGAGCCT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_POLY_RNA_rep3

description: RNA of polysomal fraction 6-11 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 3


title: ECAPS 1036

value: Current Smoker

value: Female

tag: race

value: White

tag: pack years

value: 6 (1000+ ng/mL cotinine)

value: batch 4

value: bronchial epithelial cells


title: ctrl_si_POLY_RNA_rep4

description: RNA of polysomal fraction 6-11 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 4

value: control


title: ctrl_si_POLY_RNA_rep2

description: RNA of polysomal fraction 6-11 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 2


title: GC077042_CGGAGCCT-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: TNRC_si_total_RNA_rep1

description: total RNA from TNRC6A and TNRC6B siRNA transfected HEK293 cell replicate 1

value: TNRC6A TNRC6B


title: GC077042_CGATCAGT-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_POLY_RNA_rep1

description: RNA of polysomal fraction 6-11 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 1


title: GC077042_CGGAGCCT-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: GC077042_CGATCAGT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_SUB_RNA_rep4

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 4

value: subpolysomal (fractions 1-5)


title: GC077042_CGATCAGT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGATCAGT-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_SUB_RNA_rep1

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 1


title: CNOT_si_SUB_RNA_rep3

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 3


title: ctrl_si_SUB_RNA_rep4

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 4


title: GC077042_CGATCAGT-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: GC077042_CGATCAGT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_SUB_RNA_rep3

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 3


title: GC077042_CGAGGCTG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_SUB_RNA_rep1

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 1


title: ECAPS 0015

description: Gene expression from bronchial epithelial cells collected from former smoker.

value: UCLA

value: Former Smoker

value: Male

tag: last tcig (months)

tag: first ecig (months)


title: GC077042_CGAGGCTG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGAGGCTG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: ctrl_si_SUB_RNA_rep2

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from ctrl siRNA transfected HEK293 cells replicate 2


title: GC077042_CGAGGCTG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_gradient_total_RNA_rep4

description: total RNA from CNOT1 siRNA transfected HEK293 cells  inputs for sucrose density gradients replicate 4


title: CNOT_si_gradient_total_RNA_rep3

description: total RNA from CNOT1 siRNA transfected HEK293 cells  inputs for sucrose density gradients replicate 3


title: GC077042_CGAGGCTG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_gradient_total_RNA_rep1

description: total RNA from CNOT1 siRNA transfected HEK293 cells  inputs for sucrose density gradients replicate 1


title: ctrl_si_gradient_total_RNA_rep4

description: total RNA from ctrl siRNA transfected HEK293 cell inputs for sucrose density gradients  replicate 4


title: GC077042_CCTAAGAC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_CCTAAGAC-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: CNOT_si_SUB_RNA_rep2

description: RNA of subpolysomal fraction 1-5 of sucrose density gradients from CNOT1 siRNA transfected HEK293 cells replicate 2


title: GC077042_CCTAAGAC-TCGACTAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGAGGCTG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: ctrl_si_gradient_total_RNA_rep2

description: total RNA from ctrl siRNA transfected HEK293 cell inputs for sucrose density gradients  replicate 2


title: GC077042_CCTAAGAC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_gradient_total_RNA_rep1

description: total RNA from ctrl siRNA transfected HEK293 cell inputs for sucrose density gradients  replicate 1


title: GC077042_CCTAAGAC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: DDX6_IP_rep3

description: replicate 3 of RNA IP of endogenous DDX6 from HEK293 cells


title: DDX6_IP_rep2

description: replicate 2 of RNA IP of endogenous DDX6 from HEK293 cells


title: GC077042_CCTAAGAC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: DDX6_IP_rep1

description: replicate 1 of RNA IP of endogenous DDX6 from HEK293 cells


title: CNOT_si_gradient_total_RNA_rep2

description: total RNA from CNOT1 siRNA transfected HEK293 cells  inputs for sucrose density gradients replicate 2


title: eIF4A2_IP_rep3

description: replicate 3 of RNA IP of endogenous eIF4A2 from HEK293 cells


title: GC077042_CCTAAGAC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_CCTAAGAC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077042_ATGCGCAG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_CGAGGCTG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: eIF4A2_IP_rep2

description: replicate 2 of RNA IP of endogenous eIF4A2 from HEK293 cells


title: eIF4A2_IP_rep1

description: replicate 1 of RNA IP of endogenous eIF4A2 from HEK293 cells


title: GC077042_ATGCGCAG-CCTAGAGT_regressed_nodular_sc

description: NexteraXT library preparation


title: ctrl_si_gradient_total_RNA_rep3

description: total RNA from ctrl siRNA transfected HEK293 cell inputs for sucrose density gradients  replicate 3


title: eIF4A1_IP_rep3

description: replicate 3 of RNA IP of endogenous eIF4A1 from HEK293 cells


title: Total_RNA_RIPseq_rep3

description: replicate 2 of total mRNA input from RNA IP


title: GC077042_ATCTCAGG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: eIF4A1_IP_rep2

description: replicate 2 of RNA IP of endogenous eIF4A1 from HEK293 cells


title: GC077042_ATCTCAGG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: Total_RNA_RIPseq_rep2


title: GC077042_ATCTCAGG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: Total_RNA_RIPseq_rep1

description: replicate 1 of total mRNA input from RNA IP


title: GC077042_ATCTCAGG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077042_ATCTCAGG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_ATGCGCAG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_ATCTCAGG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_AGGCAGAA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_AGGCAGAA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_AGGCAGAA-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077042_ATGCGCAG-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: eIF4A1_IP_rep1

description: replicate 1 of RNA IP of endogenous eIF4A1 from HEK293 cells


title: GC077042_AGGCAGAA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077042_ACTGAGCG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077042_ACTGAGCG-TCGACTAG_regressed_nodular_sc

description: NexteraXT library preparation


title: P1_MBD

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using bowtie2 v2.1.0
Raw counts, Reads Per Kilobase Million(RPKM) and relative methylation scorewere(rms) were calculated by R package MEDIPS v3.5.1
Genome_build: hg38
Supplementary_files_format_and_content: MBD.xlsx

molecule: genomic DNA

source_name: PCOS_ovarian granulosa cells

extract_protocol:
After collected, the ovarian granulosa cells were put in liquid nitrogen quickly, and preserved in low temperature environment. AxyPrep genome DNA extraction kit (Corning, NY, USA) was used to isolate genome DNA from granulosa cells following a manufacturer’s protocol. Genome DNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and fragmentated with M220 Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA).
MBD-seq libraries were prepared using the MethylMiner™ Methylated DNA Enrichment Kit from Invitrogen and NEBNext® Ultra™ IDNA Library Prep Kit from NEB.

tag: subject status

value: Polycystic ovary syndrome

value: ovarian granulosa cells


title: P2_Input


title: P2_MBD


title: N3_MBD

source_name: normal_ovarian granulosa cells

value: Normal control


title: P1_Input


title: P3_Input


title: ECAPS 0004

description: Gene expression from bronchial epithelial cells collected from former smoker.

value: White

tag: nicalert level

tag: rin

tag: batch

value: batch 1


title: GC077042_ACTGAGCG-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation

tag: genotype

tag: tissue


title: PF sutures of Runx2+/– at P7

city: Nagasaki

first: Toshihisa

last: Komori

address: 1-7-1 Sakamoto

department: Cell Biology

institute: Nagasaki University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (mouse Gene Expression Microarray 8x60k; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: PF suture, Runx2+/–at P7

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from sutures of P5 Runx2+/+, P7 Runx2+/+, and P7 Runx2+/-mice using ISOGEN following the manufacturer's recommendations.

tag: strain

value: Posterior Frontal sutures


title: PF sutures of Runx2+/+ at P7

source_name: PF suture, Runx2+/+ at P7


title: GC077042_ACTCGCTA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: PF sutures of Runx2+/+ at P5

source_name: PF suture,  Runx2+/+ at P5


title: ECAPS 1077

value: BU

value: Female

value: 1 (10-30 ng/mL cotinine)

value: batch 3

tag: cell type

value: bronchial epithelial cells


title: N3_Input


title: GC077042_ACTGAGCG-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077042_ACTCGCTA-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: N1_MBD


title: GC077042_ACTCGCTA-GAGCCTTA_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: N2_MBD


title: GC077042_AAGAGGCA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: P3 [miRNA-seq]

description: R18069516-libmix-BBS-4-P3-miRNA-seq_combined

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to known miRNA in miRBase v22.1 using bowtie2 v2.1.0
Raw counts and Reads Per Million(RPM) were calculated by customized script
Genome_build: miRBase
Supplementary_files_format_and_content: xlsx files include raw counts and RPM values for each Sample ...

extract_protocol:
After collected, the ovarian granulosa cells were put in liquid nitrogen quickly, and preserved in low temperature environment. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from granulosa cells following a manufacturer’s protocol. Total RNA quantity was determined with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA) and quality was assessed by running an 1% agarose gel electrophoresis, stained with 4S Red Plus Nucleic Acid Stain (Sango, Shanghai, China).
miRNA-seq libraries were prepared using the TruSeq® Small RNA Library Preparation kit from Illumina® and sequenced using a 150 bp single-end reads Illumina Illumina HiSeq 2000 Sequencer (Illumina Inc., San Diego, CA, USA). After sequencing, adapters and low-quality sequences were removed from obtained raw reads and clean data was counted by Fastqc program. 15-30nt fragments were reserved for subsequent analysis and mapped to the reference genome using Bowtie2 program.

tag: molecule subtype

value: miRNA


title: P4 [miRNA-seq]

description: R19006355-libmix-20190219-P4-miRNA-seq_combined


title: N1_Input


title: P5 [miRNA-seq]

description: R19006355-libmix-20190219-P5-miRNA-seq_combined


title: P3_MBD


title: GC077042_AAGAGGCA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077042_AAGAGGCA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: N2_Input


title: N5 [miRNA-seq]

description: R19006355-libmix-20190219-N5-miRNA-seq_combined


title: GC077042_AAGAGGCA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: P1 [miRNA-seq]

description: R18069516-libmix-BBS-4-P1-miRNA-seq_combined


title: GC077042_AAGAGGCA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: P2 [miRNA-seq]

description: R18069516-libmix-BBS-4-P2-miRNA-seq_combined


title: GC077042_AAGAGGCA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077042_ACTCGCTA-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_TGCAGCTA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: N3 [miRNA-seq]

description: R18069516-libmix-BBS-4-N3-miRNA-seq_combined


title: N1 [miRNA-seq]

description: R18069516-libmix-BBS-4-N1-miRNA-seq_combined


title: N2 [miRNA-seq]

description: R18069516-libmix-BBS-4-N2-miRNA-seq_combined


title: N4 [miRNA-seq]

description: R19006355-libmix-20190219-N4-miRNA-seq_combined


title: neural crest bulk_non_NC  rep2 RNA-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:
RNA-seq
counts_RNA-seq.txt

data_processing:
Reads were mapped using STAR (v.2.4.2a) for RNA-seq to galGal4. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Differential Expression analysis was performed using DESeq2 R package.
Genome_build: galGal4
Supplementary_files_format_and_content: read counts (txt file)

organism: Gallus gallus

source_name: FoxD3_Nc1_Citrine NEGATIVE, non-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:
FAC-sorted cells were washed with PBS and stored at 80°C in lysis buffer. RNA was extracted 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.  At least three biological replicas for each stage were used for analysis.
Sequencing libraries were prepared using Takara SMARTer low input RNA kit and sequenced using 100bp paired-end reads on the Illumina Hiseq2000 platform.

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.

tag: developmental stage

value: stage 5-10ss

value: neural crest

value: FAC sorted for FoxD3_NC1_Citrine+ cells

tag: amplification

value: Takara SMARTer


title: GC077041_TGCAGCTA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: GC077041_TCGACGTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_TCGACGTC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_TGCAGCTA-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_TGCAGCTA-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: neural crest bulk_non_NC  rep1 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: neural crest bulk_non_NC  rep3 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: GC077041_TCGACGTC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_TCGACGTC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_TCCTGAGC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077041_TCCTGAGC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: neural crest bulk_8-10ss  rep2 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt

source_name: FoxD3_Nc1_Citrine+ neural crest isolated by FACS

value: stage 8-10ss


title: neural crest bulk_8-10ss  rep3 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: neural crest bulk_8-10ss  rep1 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: GC077041_TCCTGAGC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: neural crest bulk_5-6ss rep4 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt

value: stage 5-6ss


title: GC077041_TCCTGAGC-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_TCCTGAGC-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: neural crest bulk_5-6ss rep3 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: GC077041_TGCAGCTA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_TAGGCATG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: neural crest bulk_5-6ss rep1 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: GC077041_TAGGCATG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: neural crest bulk_8-10ss  rep4 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: PFC_Setd1a_ChIPSeq_rep2

city: New York

first: Joseph

last: Gogos

state: NY

address: 3227 Broadway, JGL Science Bldg, Quad 4A, Room L4-005

institute: Columbia University

data_processing:
Reads were aligned to the Mus musculus genome version mm10 using bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Poor quality and duplicated reads were removed using respectively samtools v1.3.1(Li et al., 2009) and Picard (http://broadinstitute.github.io/picard). To measure the reproducibility between biological replicates and to avoid arbitrary thresholding biases for both Setd1a and Mef2, we perform IDR following the ENCODE framework (Landt et al., 2012) using MACS v2.1.1 as peak caller (DOI: 10.1186/gb-2008-9-9-r137) and IDR 2.0.2 (Li et al., 2011). We defined good biological replicates when the ratio N1/N2 and Np/Nt was below 2. For all subsequent analysis, biological replicates were merged into single alignment files for each antibody using samtools v1.3.1 (Li et al., 2009) and difference in sequencing depth between the libraries was corrected by normalization for library size using HOMER v4.8.2 (Heinz et al., 2010).
Genome_build: mm10

source_name: Prefrontal cortex

extract_protocol: Whole prefrontal cortex was dissected from 6-week old wild-type (WT) mice. Dissected tissue was thoroughly minced on ice using razor blades, then fixed with EGS for 30 min and/or for 5 min at room temperature with methanol-free formaldehyde (Pierce, Thermo Fisher Scientific) diluted to 1% in PBS. Fixation was quenched by adding 1/10th volume of 1.25 M glycine. Fixed tissue was collected by centrifugation at 200 g for 5 min at 4ºC, then washed twice with cold PBS. Washed tissue was flash-frozen with liquid nitrogen then cryofractured using a Covaris CryoPrep Impactor on power setting 6. Nuclei and chromatin immunoprecipitation were performed as in Markenscoff-Papadimitriou et al.(Markenscoff-Papadimitriou et al., 2014): briefly, the cryofractured tissue was lysed in ChIP Lysis Buffer (50 mM Tris-HCl pH 7.5, 150 nM NaCl, 0.5% NP-40, 0.25% Sodium Deoxychoalate, 0.1% SDS) in rotation for 40 min at 4ºC. Nuclei were centrifuged (1700x g, 5 min, 4ºC), and the pellet was resuspended in shearing buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8, 0.25% SDS), then sheared on a Covaris S2 sonicator (12 or 16  min, 2% Duty Cycle, Intensity 3, 200 cycles per burst, frequency sweeping). Sheared chromatin was centrifuged (10,000 g for 10 min at 4ºC) to remove insoluble material. Sheared chromatin was diluted 5-fold with ChIP Dilution Buffer (CDB: 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS) and pre-cleared for two hours at 4ºC with protein G dynabeads (Thermo Fisher Scientific). Each ChIP was set up with the appropriate antibody (10 mg of anti-Setd1a, 1 mg of anti-H3K27ac, -H3K4me2 and -H3K4me3, 3 mg of anti-H3K4me1, 5 mg of Mef2) and 10-20 mg of cleared chromatin, incubating then overnight at 4ºC. Protein G dynabeads were blocked overnight with 2 mg/ml yeast tRNA (Thermo Fisher Scientific), then added to antibody bound chromatin and rotated for 3 hr at 4ºC. Bead-bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate) and once with TE (pH7.5). DNA was eluted from beads by incubating at 65ºC for 30 min with 25 mL ChIP Elution Buffer (1% SDS, 0.1 M Sodium Bicarbonate). This elution was repeated and the combined elution fractions were incubated overnight at 65ºC with proteinase K (Thermo Fisher Scientific) and RNaseA (Thermo Fisher Scientific). ChIP DNA was purified 1.8X of AMPure XP beads and eluted in 30 ml of nuclease free water. Libraries were prepared with Ovation Ultralow System V2 1-16 (NuGEN technologies) according to manufacturers’ recommendation.

value: Prefrontal cortex

tag: age

value: 6 weeks old

value: male

tag: chip antibody


title: PFC_Setd1a_ChIPSeq_rep1

tag: Sex


title: GC077041_TAGCGCTC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: neural crest bulk_5-6ss rep2 RNA-seq

description:
RNA-seq
counts_RNA-seq.txt


title: GC077041_TAGCGCTC-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_TAGCGCTC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_superficial triple melanoma


title: GC077041_TAGGCATG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: Kmt2d-/- 96-9 Chondrocytes D7 rep2

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

institute: Johns Hopkins University

data_processing:
reads were pseudoaligned to the mouse reference transcriptome (GRCm38)
Transcript abundances were subsequently quantified using Salmon (Patro et al., 2017). We then used the tximport R package(Soneson et al., 2015) to convert the transcript abundances into normalized gene-level counts, by setting the “countsFromAbundance” parameter equal to “lengthScaledTPM”. Next, we used the edgeR(Robinson et al., 2010) and limma(Ritchie et al., 2015) R packages to log2 transform these gene-level counts, estimate the mean-variance relationship, and calculate weights for each observation. In order to account for the correlation between technical replicates of the same clone when performing the differential analysis, we fit a mixed linear model, using the function “duplicateCorrelation” from the statmod R package(Giner and Smyth, 2016) to block on clone.
Differential analysis: limma R package, using FDR=0.05 cutoff
Principal component analysis, transcript abundances were first converted into gene-level counts using the tximport R package, with the “countsFromAbundance” parameter equal to “no”. Then, we applied a variance stabilizing transformation to these gene-level counts using the “vst” function from the DESeq2 R package(Love et al., 2014) with the parameter “blind” set to “TRUE”, and subsequently estimated the principal components using the 1000 most variable genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: expr_mat_chondrocytes (both in rda and csv format) is a gene expression matrix where the rows correspond to genes, the columns correspond to samples, and the entries correspond to the quantified expression level of a given gene in a given sample, after using tximport (see methods in the paper) and summing up the expression of a given technical replicate in the different flowcells and lanes. The column names provide information about the sample. For instance, "wt.clone1.day0.rep1" indicates the first technical replicate of wild-type clone number 1, on differentiation day 0 (ie. undifferentiated state).

source_name: mutant clone 2 (technical replicate 2)

growth_protocol: Stable ATDC5 cell lines (Kmt2d-/- with bi-allelic deletions of the catalytic SET domain and Kmt2d+/+ cells) were maintained in standard medium: DMEM/Ham’s F12 medium containing 5% fetal bovine serum (FBS), antibiotics (100 units/ml penicillin, 100 μg/ml streptomycin), and 2 mM L-glutamine in 5% CO2 in a 37 °C incubator.

extract_protocol:
Total RNA was isolated using TRIZOL reagent and RNA Clean & Concentrator-5 kit (Zymo Research). After DNAse treatment, RNA was assessed for quantity and quality using Qubit RNA BR Assay Kit (ThermoFisher Scientific) and RNA 6000 Nano Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies). mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module for Illumina (New England Biolabs).
Sequencing libraries were generated using NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs) and were validated using the Agilent High Sensitivity DNA assay on the Agilent Bioanalyzer 2100 system and quantified by NEBNext Library Quant Kit for Illumina (New England Biolabs).

treatment_protocol: ATDC5 stable cell lines (Kmt2d+/+ and Kmt2d-/-) were seeded in the above standard growth medium at 1× 10^5 cells/well in 6-well plates. The next day and every 2-3 days thereafter, medium was replaced with chondrogenic differentiation medium: DMEM/ Ham’s F12 supplemented with 5% FBS, 100 units/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 1X Insulin-Transferrin-Selenium (Gibco), 50 μg/ml L-ascorbic acid, and 10 mM β-glycerophosphate (MilliporeSigma). Cells were harvested and RNA was isolated prior to differentation (day 0; undifferentiated cells) or 7 days after induction of differentiation (chondrocytes).

value: Kmt2d mut/mut

tag: cell line

value: ATDC5 chondrogenic cell line

tag: differentiation state

value: Chondrocyte (day 7)


title: GC077041_TACGCTGC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_TACGCTGC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from recurring_nodular triple melanoma

value: GFP+ cell from recurring_nodular triple melanoma


title: Kmt2d-/- 96-9 Chondrocytes D7 rep1

source_name: mutant clone 2 (technical erplicate 1)


title: GC077041_TACGCTGC-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_nodular triple melanoma


title: GC077041_TACGCTGC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma


title: NF_WT_3

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

institute: National Institute of Immunology

data_processing:
FastQC
Mapping with HISAT2
HTseq-count
DEseq2
Genome_build: Ensembl GRCm38.97
Supplementary_files_format_and_content: tabular format, read counts per gene.

source_name: Regulatory T (Treg) cells

growth_protocol: Ex-vivo spleen cells were suspended in complete RPMI1640 medium (Biological Industries, Beit Haemek, Israel) supplemented with 10% FBS, 2 mM L-glutamine, 1.35 g/l sodium bicarbonate, 5 mM HEPES, 50 μM β-mercaptoethanol, 100 μg/ml streptomycin and 100 IU penicillin (Millipore Sigma, Merck KGaA, Germany) and stained with the relevant antibody combinations and incubated at 4 C for 20 min. The cells were then washed, re-suspended at a density of 30 million cells/ml in complete RPMI and filtered through a 40-micron size sieve. This was followed by analysis and sorting (BD FACSAria III; BD Biosciences, CA). Sorted populations showed >90% purity.

extract_protocol:
Sorted cells were rested in complete RPMI at 37°C for 2 h before being re-suspended in 1ml TRIzol reagent (Thermofisher Scientific, CA) and stored at -80°C. Three such biological repeats of WT and Nfkb2-/- Tregs were collected. RNA was isolated by treatment with chloroform, isoporopanol and ethanol according to the RNA isolation protocol using TRIzol reagent as recommended.
TruSeq RNA Sample Prep Kit v2 (Ilumina, San Diego) according to the kit protocol

value: Regulatory T (Treg) cells

tag: genotype/variation

value: wild type


title: NF_WT_2


title: NF_KO_1


title: NF_KO_2


title: Kmt2d-/- 96-9 Undiff D0 rep1

source_name: mutant clone 2 (technical replicate 1)

value: Undifferentiated (day0)


title: NF_WT_1


title: Kmt2d-/- 96-9 Undiff D0 rep2


title: NF_KO_3


title: GC077041_TACGCTGC-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_TAGGCATG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_superficial triple melanoma


title: GC077041_TACGCTGC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: Kmt2d-/- 10-7 Chondrocytes D7 rep2

source_name: mutant clone 1 (technical replicate 2)


title: GC077041_TAGCGCTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_TAAGGCGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: Kmt2d-/- 10-7 Chondrocytes D7 rep1

source_name: mutant clone 1 (technical erplicate 1)


title: GC077041_TAAGGCGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: Kmt2d-/- 10-7 Undiff D0 rep1

source_name: mutant clone 1 (technical replicate 1)


title: Kmt2d-/- 10-7 Undiff D0 rep2


title: GC077041_TAAGGCGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_TAAGGCGA-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: Kmt2d+/+ 10-8 Chondrocytes D7 rep1

source_name: wild-type clone 3 (technical erplicate 1)

value: wild-type


title: GC077042_ACTGAGCG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_TAAGGCGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077041_GTAGAGGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: GC077041_GTAGAGGA-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077041_GTAGAGGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_GTAGAGGA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_GTAGAGGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: Kmt2d+/+ 10-7 Undiff D0 rep1

source_name: wild-type clone 2 (technical replicate 1)


title: Kmt2d+/+ 10-5 Chondrocytes D7 rep1

source_name: wild-type clone 1 (technical erplicate 1)


title: Kmt2d+/+ 10-7 Chondrocytes D7 rep1

source_name: wild-type clone 2 (technical erplicate 1)


title: Kmt2d+/+ 10-7 Chondrocytes D7 rep2

source_name: wild-type clone 2 (technical replicate 2)


title: GC077041_GTAGAGGA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_GTAGAGGA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: Kmt2d+/+ 10-5 Chondrocytes D7 rep2

source_name: wild-type clone 1 (technical replicate 2)


title: Kmt2d+/+ 10-5 Undiff D0 rep2


title: Kmt2d+/+ 10-8 Undiff D0 rep1

source_name: wild-type clone 3 (technical replicate 1)


title: Kmt2d+/+ 10-7 Undiff D0 rep2


title: GC077041_GGAGCTAC-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from recurring_nodular triple melanoma


title: GC077041_GGAGCTAC-GAGCCTTA_primary_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_superficial triple melanoma


title: GC077041_GGAGCTAC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: Kmt2d+/+ 10-5 Undiff D0 rep1

source_name: wild-type clone 1 (technical replicate 1)


title: Kmt2d+/+ 10-8 Chondrocytes D7 rep2

source_name: wild-type clone 3 (technical replicate 2)


title: GC077041_GGACTCCT-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_GGACTCCT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: PFC_ParvCRE_tdTom_ATACSeq_rep2

data_processing:
Reads were aligned to the Mus musculus genome version mm10 using bowtie2 v2.2.6 (Langmead and Salzberg, 2012). Poor quality and duplicated reads were removed using respectively samtools v1.3.1(Li et al., 2009) and Picard (http://broadinstitute.github.io/picard). To measure the reproducibility between biological replicates and to avoid arbitrary thresholding biases for both Setd1a and Mef2, we perform IDR following the ENCODE framework (Landt et al., 2012) using MACS v2.1.1 as peak caller (DOI: 10.1186/gb-2008-9-9-r137) and IDR 2.0.2 (Li et al., 2011). We defined good biological replicates when the ratio N1/N2 and Np/Nt was below 2. For all subsequent analysis, biological replicates were merged into single alignment files for each antibody using samtools v1.3.1 (Li et al., 2009) and difference in sequencing depth between the libraries was corrected by normalization for library size using HOMER v4.8.2 (Heinz et al., 2010).
We mapped the reads to the reference mouse genome (UCSC/mm10) using STAR ((Dobin et al., 2013) (version 2.5.4b). Read counts and normalization of the read count data and analysis of differentially expressed genes (DE genes) were performed by using DESeq2 (Love et al., 2014) (version 1.10.2) with default parameters.
The scRNA-Seq data were aligned using the 10x Genomics package Cell Ranger 2.1.1 on the mm10 mouse genome version. In particular, UMI reads from the different genotypes and biological replicates were counted using “cellranger count” and combined together using “cellranger aggr”. From the downstream analysis, we removed cells in which we detected less then 1000 genes expressed, using “Seurat” R-package (v. 2.3.4). This package was used for all downstream analysis. In details, counts were first normalized (using the normalization method: "LogNormalize")
Genome_build: mm10

source_name: Prefrontal cortex

extract_protocol:
Whole prefrontal cortex was dissected from 6-week old wild-type (WT) mice. Dissected tissue was thoroughly minced on ice using razor blades, then fixed with EGS for 30 min and/or for 5 min at room temperature with methanol-free formaldehyde (Pierce, Thermo Fisher Scientific) diluted to 1% in PBS. Fixation was quenched by adding 1/10th volume of 1.25 M glycine. Fixed tissue was collected by centrifugation at 200 g for 5 min at 4ºC, then washed twice with cold PBS. Washed tissue was flash-frozen with liquid nitrogen then cryofractured using a Covaris CryoPrep Impactor on power setting 6. Nuclei and chromatin immunoprecipitation were performed as in Markenscoff-Papadimitriou et al.(Markenscoff-Papadimitriou et al., 2014): briefly, the cryofractured tissue was lysed in ChIP Lysis Buffer (50 mM Tris-HCl pH 7.5, 150 nM NaCl, 0.5% NP-40, 0.25% Sodium Deoxychoalate, 0.1% SDS) in rotation for 40 min at 4ºC. Nuclei were centrifuged (1700x g, 5 min, 4ºC), and the pellet was resuspended in shearing buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8, 0.25% SDS), then sheared on a Covaris S2 sonicator (12 or 16  min, 2% Duty Cycle, Intensity 3, 200 cycles per burst, frequency sweeping). Sheared chromatin was centrifuged (10,000 g for 10 min at 4ºC) to remove insoluble material. Sheared chromatin was diluted 5-fold with ChIP Dilution Buffer (CDB: 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS) and pre-cleared for two hours at 4ºC with protein G dynabeads (Thermo Fisher Scientific). Each ChIP was set up with the appropriate antibody (10 mg of anti-Setd1a, 1 mg of anti-H3K27ac, -H3K4me2 and -H3K4me3, 3 mg of anti-H3K4me1, 5 mg of Mef2) and 10-20 mg of cleared chromatin, incubating then overnight at 4ºC. Protein G dynabeads were blocked overnight with 2 mg/ml yeast tRNA (Thermo Fisher Scientific), then added to antibody bound chromatin and rotated for 3 hr at 4ºC. Bead-bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate) and once with TE (pH7.5). DNA was eluted from beads by incubating at 65ºC for 30 min with 25 mL ChIP Elution Buffer (1% SDS, 0.1 M Sodium Bicarbonate). This elution was repeated and the combined elution fractions were incubated overnight at 65ºC with proteinase K (Thermo Fisher Scientific) and RNaseA (Thermo Fisher Scientific). ChIP DNA was purified 1.8X of AMPure XP beads and eluted in 30 ml of nuclease free water. Libraries were prepared with Ovation Ultralow System V2 1-16 (NuGEN technologies) according to manufacturers’ recommendation.
Total RNA was extracted from prefrontal cortices of 6-week-old mice using RNeasy Mini Kit (Qiagen). We analyzed each four male Setd1a+/- mice and their wild-type (WT) male littermates. Quality of RNA samples was assessed by Bioanalyzer (Agilent). Mean (± SD) RNA integrity number (RIN) was 9.3 (± 0.5) in the mutant mice and 9.7 (± 0.2) in WT. An RNA-seq library was prepared from ~400 ng of total RNA by using TruSeq RNA prep kit (Illumina). Messenger RNAs were enriched by poly-A selection. Libraries were sequenced on HiSeq2500/HiSeq4000 (Illumina) with single-end 100bp reads at Columbia Genome Center.
The tissue was incubated for 1h at 37°C on a rocking platform with papain-EBSS (1 PFC/mL). The tissue was triturated 20 times and cells were pelleted (400 g, 5 min, RT). Remaining papain was inhibited by resuspending the cell pellet with Ovomucoid protease inhibitor solution diluted 1:10 in EBSS. An extra 5 ml of Ovomucoid protease inhibitor solution was slowly layered at the bottom of the cell suspension to create a discontinuous gradient and cells were pelleted (100 g, 6 min, RT). Cells were resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4 mM MgCl2, and 500 ng/mL DAPI (Invitrogen). These cells were passed through a 40 uM cell strainer, and then FAC sorted. Live cells were selected by gating out DAPI positive cells and positive cells were gated by tdTomato fluorescence. Fifty thousand cell were used to prepare ATAC-seq libraries as described in references (Buenrostro et al., 2015; Monahan et al., 2017). In brief, cells were pelleted (500 g, 5 min, 4°C) and resuspended in ice cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were pelleted (1000 g, 10 min, 4°C) and resuspended in transposition reaction mix prepared from Illumina Nextera reagents (for 50 μL: 22.5 μL water, 25 μL 2xTD buffer, 2.5 μL Tn5 Transposase). Transposed DNA was column purified using a Qiagen MinElute PCR cleanup kit (Qiagen) and amplified using barcoded primers and NEBNext High Fidelity 2x PCR Master Mix (NEB). Amplified libraries were purified using Ampure XP beads (Beckman Coulter).
Cells were dissociated using the papain dissociation kit (Worthington) following the manufacturers’ recommendation. In brief, the PFC of 2 WT and 2 Setd1a+/- mice was dissected and transferred to ice-cold PBS. The PFC was cut in small pieces using a razor blade and dissociated with a papain dissociation system (Worthington Biochemical). The tissue was incubated for 1h at 37°C on a rocking platform with papain-EBSS (1 PFC/mL). The tissue was triturated 20 times and cells were pelleted (400 g, 5 min, RT). Remaining papain was inhibited by resuspending the cell pellet with Ovomucoid protease inhibitor solution diluted 1:10 in EBSS. An extra 5 ml of Ovomucoid protease inhibitor solution was slowly layered at the bottom of the cell suspension to create a discontinuous gradient and cells were pelleted (100 g, 6 min, RT). To enrich for living cells, we removed dead cells from single cell suspension using the MACS® Dead Cell Removal Kit (Miltenyi Biotec) with the MS Columns following manufacturer’s recommendation. In brief, 200 μl per PFC of Dead Cell Removal MicroBeads were added the pelleted cells. Cell were resuspended and incubated for 15 min at RT. The MS columns were washed once with 0.5 ml of Binding buffer. After incubation is complete, the cell suspension was diluted with 500 μl 1X Binding Buffer and the suspension was applied to the MS columns. The flowthough was collected. To increase the number of live cells recovered, the column was washed twice with 1 ml of Binding buffer at RT. Flowthough were combined and live cell were pelleted (400 g, 5 min, RT). Cells were then washed twice with PBS containing 0.04% BSA and the final pellet was resuspended in 300 ml of PBS containing 0.04% BSA and passed through a 40 uM cell strainer. Cell were counted and viability was evaluated by trypan blue staining.The scRNA-Seq was performed using the 10x Genomic platform and the “Single Cell 3' v2” by the Columbia Genome Center.


title: PFC_ParvCRE_tdTom_ATACSeq_rep1


title: Kmt2d+/+ 10-8 Undiff D0 rep2


title: GC077041_GGACTCCT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma


title: GC077041_GGACTCCT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: PFC_Emx1iCRE_tdTom_ATACSeq_rep2


title: PFC_scRNA_het_rep2


title: PFC_Emx1iCRE_tdTom_ATACSeq_rep1


title: GC077041_GGACTCCT-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_nodular triple melanoma


title: GC077041_GCTCATGA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_superficial triple melanoma


title: GC077041_GGACTCCT-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_GCTCATGA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: PFC_scRNA_het_rep1


title: GC077041_GCGTAGTA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: PFC_RNASeq_het_rep1


title: PFC_RNASeq_het_rep4


title: PFC_RNASeq_het_rep3


title: PFC_scRNA_wt_rep2


title: PFC_RNASeq_wt_rep4


title: PFC_scRNA_wt_rep1


title: PFC_RNASeq_het_rep2


title: GC077041_GCGTAGTA-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: PFC_RNASeq_wt_rep2


title: PFC_RNASeq_wt_rep3


title: GC077041_GCGTAGTA-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_GCGTAGTA-CCTAGAGT_regressed_nodular_sc

description: NexteraXT library preparation


title: PFC_Input_ChIPSeq_PFA


title: PFC_Mef2_ChIPSeq_rep2

value: sc-313, Santa Cruz Biotechnology


title: GC077041_CTCTCTAC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_CTCTCTAC-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_CTCTCTAC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: PFC_Mef2_ChIPSeq_rep1


title: PFC_H3K27ac_ChIPSeq_rep2

value: 39133, Active Motif


title: GC077041_CTCTCTAC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_CTCTCTAC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: PFC_H3K4me3_ChIPSeq_rep2

value: 04-745, Millipore


title: GC077041_CTCTCTAC-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: PFC_H3K27ac_ChIPSeq_rep1

value: 6 weeks old


title: PFC_H3K4me2_ChIPSeq_rep2

value: male

value: 05-1338, Millipore


title: GC077041_CGTACTAG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: PFC_H3K4me3_ChIPSeq_rep1


title: GC077041_CGTACTAG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGTACTAG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: 25d testes RNA-seq

city: Shanghai

first: Haixin

last: Li

state: Shanghai

address: 36 Yunxin Rd

department: Shanghai Tenth People's Hospital, School of Medicine

institute: Tongji University

data_processing:
Basic quality control processing Raw sequenced fastq data were processed to remove adaptors and low quality bases, leaving high quality reads (known as clean data, mismatch ratio<6%) to perform further analysis. All processing were conducted using in-house Python and R scripts.
We aligned clean data on the refernence genome (UCSC mm10) using bowtie, allowing: (1) hits in sub-optimal strata aren't reported (--best --strata); (2) suppress all alignments if 5 exists (-m 5); (3) max 2 mismatches in seed (-n 2); (4) max sum of mismatch quals across alignment for –n is 70 (-e 70); (5) seed length is defined as 25bp (-l 25); (6) try hard to find valid alignments, at the expense of speed (-y). Total parameters in command line by bowtie are: bowtie -q -p 4 -e 70 -y -l 25 -n 2 -m 5 --best --strata –S.  Finally, bowtie alignments got sam file for each sample. Then, SortSam and MarkDuplicates were utilized to process SAM file. Bigwig format was converted from BAM file and submitted to UCSC genome browser for customer visualization.   Then, the sense, antisense and total aligned reads number were counted and plotted in pir or bar plots (See specific files). Meanwhile, using UCSC gene-model annotation, reads number and deduplicated reads aligned on exon/intron, UTR3/UTR5, downstream 1kb, and upstream 1kb regions were also counted (See tables/figures). The coverage of each region and reads covered numbers were counted using samtools and bedtools.
Homer software was used to call peaks of CLIP-Seq data, when input file (RNA-Seq data) was given as background signal to remove noises. Tag directories for samples were constructed using makeTagDirectory in Homer package and peak regions were called using findPeaks in Homer package, too. The parameters for find Peaks are: -F 2 -L 2 -poisson 0.05 –style factor (fold enrichment over input tag count is set to 2, and fold enrichment over local tag count is set to 2, Set poisson p-value cutoff is 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: bw files

source_name: testes

extract_protocol:
We used anti-Dazl Antibody to pull down DAZL immune complex from 25dpp mouse testes by HITS-CLIP method as described previously for Mili and Miwi (Vourekas et al., 2012). 3 samples were constructed with different barcode at 5'adapter.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols by Illumina Truseq RNA kit.


title: Dazl-CLIP sample 3

tag: band molecular weight

value: 40 kDa

value: ACAGTG


title: PFC_H3K4me1_ChIPSeq_rep2

value: ab8895, Abcam


title: PFC_H3K4me2_ChIPSeq_rep1


title: GC077041_CGTACTAG-GAGCCTTA_regressed_nodular_sc

description: NexteraXT library preparation


title: PFC_RNASeq_wt_rep1


title: GC077041_CGTACTAG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: GC077041_CGTACTAG-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation


title: Dazl-CLIP sample 2

value: 33 kDa

value: CAGATC


title: GC077041_CGTACTAG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: Dazl-CLIP sample 1

value: TTAGGC


title: GC077041_CGGAGCCT-TCGACTAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGGAGCCT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_CTCTCTAC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGGAGCCT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: PFC_H3K4me1_ChIPSeq_rep1


title: GC077041_CGGAGCCT-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_superficial triple melanoma


title: GC077041_CGGAGCCT-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGATCAGT-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: Liver_high-fat-diet_PFNA_biological-rep2

city: Kingston

first: Marisa

last: Pfohl

state: RI

address: Pharmacy Building, 7 Greenhouse Road

department: BPS

institute: University of Rhode Island

description: Gene Level Differential Expression Analysis

hyb_protocol: Peformed at the Genomics Core Facility at Brown University (Providence, RI)

data_processing: data was analyzed using Transcriptome Analysis Console software, default cutoff values: p-value ≤ 0.5, FC = ≤ -1.5 or ≥ 1.5

source_name: liver tissue from mouse administered a high fat diet (45%kCal from fat) containing PFNA

growth_protocol: mice were 6 weeks old at the start of the experiment and were sacrified at 18 weeks of age

extract_protocol: liver RNA was extracted using Trizol according to the manufacturer's protocol

treatment_protocol: mice were administered dietary intervention ad libitum for 12 weeks

value: liver

tag: gender


title: GC077041_CGGAGCCT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGATCAGT-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGATCAGT-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077041_CGATCAGT-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation

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


title: GC077041_CGAGGCTG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077041_CGATCAGT-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation

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


title: GC077041_CGAGGCTG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation

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


title: Liver_high-fat-diet_PFNA_biological-rep3

scan_protocol: Peformed at the Genomics Core Facility at Brown University (Providence, RI)


title: Liver_high-fat-diet_PFOS_biological-rep3

source_name: liver tissue from mouse administered a high fat diet (45%kCal from fat) containing PFOS

label_protocol: Peformed at the Genomics Core Facility at Brown University (Providence, RI)


title: Liver_high-fat-diet_PFNA_biological-rep1


title: GC077041_CGAGGCTG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGATCAGT-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: Liver_high-fat-diet_biological-rep1

source_name: liver tissue from mouse administered a high fat diet (45%kCal from fat)


title: Liver_high-fat-diet_biological-rep2


title: Liver_high-fat-diet_PFOS_biological-rep2


title: Liver_low-fat-diet_PFOS_biological-rep1

source_name: liver tissue from mouse administered a low fat diet (10%kCal from fat) containing PFOS


title: Liver_low-fat-diet_PFNA_biological-rep3

source_name: liver tissue from mouse administered a low fat diet (10%kCal from fat) containing PFNA


title: GC077041_CGAGGCTG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: Liver_high-fat-diet_PFOS_biological-rep1


title: Liver_low-fat-diet_PFOS_biological-rep3


title: Liver_low-fat-diet_PFNA_biological-rep2


title: GC077041_CGAGGCTG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: Liver_low-fat-diet_PFNA_biological-rep1


title: Liver_high-fat-diet_biological-rep3


title: GC077041_CGATCAGT-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_CGAGGCTG-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGAGGCTG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_CGAGGCTG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: HEK293T_U1WT_2

city: Toronto

first: Michael

middle: D.

last: Taylor

state: ON

address: 686 Bay Street

department: Developmental & Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description:
Alternative splicing analysis.
mRNA (poly (A) capture)

data_processing:
Sequenced by NextSeq 550.
Sequence data were mapped using STAR aligner.
Junction files were generated using LeafCutter software.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.junc: Tab-delimited text files include junction read counts.

extract_protocol:
Trizol
Poly (A) capture.

tag: vector


title: Liver_low-fat-diet_biological-rep3

source_name: liver tissue from mouse administered a low fat diet (10%kCal from fat)


title: HEK293T_U1Mut_2


title: GC077041_CCTAAGAC-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: Liver_low-fat-diet_biological-rep2


title: HEK293T_U1Mut_1


title: Liver_low-fat-diet_PFOS_biological-rep2


title: Liver_low-fat-diet_biological-rep1


title: GC077041_CCTAAGAC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_CCTAAGAC-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATGCGCAG-TCGACTAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATGCGCAG-TTCTAGCT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_CCTAAGAC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: GC077041_ATGCGCAG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATGCGCAG-CCTAGAGT_regressed_nodular_sc

description: NexteraXT library preparation


title: PFC_Input_ChIPSeq_PFA_EGS


title: GC077041_ATGCGCAG-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: HEK293T_U1WT_1


title: GC077041_ATCTCAGG-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_ATGCGCAG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_CCTAAGAC-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATCTCAGG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: PFC_LSD1_ChIPSeq_rep2

value: ab17721, Abcam


title: GC077041_ATCTCAGG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_ATCTCAGG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATCTCAGG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: 173_TAV

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

description: Gene expression data from visceral adipose tissue from a aP2-Tagln2 female mouse

hyb_protocol: Sample was hybridized to Clariom S Mouse Array (ThermoFisher) array using an Affymetrix GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 2017)  (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from visceral depots of adipose tissue (epididymal white adipose tissue)

label_protocol: Total RNA from each sample was processed and labelled according to manuals GeneChip WT PLUS Reagent kit (P/N 703174 2017)

extract_protocol: RNA purification kit (QIAGEN, Hilden, Germany) according to standard procedures

value: Visceral adipose tissue from a aP2-Tagln2 female mouse

tag: type


title: 173_TAS

description: Gene expression data from subcutaneous adipose tissue from from a aP2-Tagln2 female mouse

source_name: Total RNA from visceral depots of adipose tissue (inguinal depots)

value: Subcutaneous adipose tissue from from a aP2-Tagln2 female mouse


title: 170_TAS

description: Gene expression data from subcutaneous adipose tissue from a wild-type female mouse

value: Subcutaneous adipose tissue from a wild-type female mouse


title: 170_TAV

description: Gene expression data from visceral adipose tissue from a wild-type female mouse

value: Visceral adipose tissue from a wild-type female mouse


title: 161_TAS

description: Gene expression data from subcutaneous adipose tissue from a wild-type male mouse

value: Subcutaneous adipose tissue from a wild-type male mouse


title: PFC_LSD1_ChIPSeq_rep1

value: 6 weeks old

value: male


title: 162_TAS


title: 161_TAV

description: Gene expression data from visceral adipose tissue from a wild-type male mouse

value: Visceral adipose tissue from a wild-type male mouse


title: 169_TAV


title: GC077041_ATCTCAGG-CTATTAAG_regressed_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.

tag: genotype


title: 159_TAS

tag: tissue


title: 169_TAS


title: GC077041_ATCTCAGG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_ATCTCAGG-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from recurring_nodular triple melanoma

value: GFP+ cell from recurring_nodular triple melanoma


title: 162_TAV


title: wt ctx-1-re-run-59

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: wt ctx-1 technical Rep

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: non-manipulated adult mouse brain

growth_protocol: All mouse gliomas were generated in the CD-1 IGS mouse background as previously described (PMID: 28166219). In utero electroporation was performed on embryonic day 15. Previously generated CRISPR constructs were used to knockout NF1, PTEN, and TRP53 (each at 1.5μg per μl) (PMID: 28166219).

extract_protocol:
tissue samples were harvested with the aid of a fluorescence microscope from end stage tumors, dissecting out the GFP-positive tumor tissue, minced into ~30mg pieces, snap frozen on dry ice, and stored at -80°C. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, #74134) according to the manufacturer’s protocol. Samples were prepared in biological replicates, n ≥ 3 per genotype. RNA integrity (RIN ≥ 8.0) was confirmed using the High Sensitivity RNA Analysis Kit (AATI, DNF-472-0500) on a 12-Capillary Fragment Analyzer.
Illumina sequencing libraries with 6-bp single indices were constructed from 1 μg total RNA using the TruSeq Stranded mRNA LT kit (Illumina, RS-122-2101). The resulting library was validated using the Standard Sensitivity NGS Fragment Analysis Kit (AATI, DNF-473-0500) on a 12-Capillary Fragment Analyzer. Equal concentrations (2nM) of libraries were pooled and subjected to sequencing of approximately 20 million reads per sample using the Mid Output v2 kit (Illumina, FC-404-2001) on a Illumina NextSeq550 following the manufacturer’s instructions.

treatment_protocol: PIK3CA alleles were genomically integrated and overexpressed through the piggyBac (PB) transposase (PBase) system. The pGlast-PBase plasmid (at 2.0μg per μl) was coelectroporated with a PBCAG-PIK3CA* construct (1.0μg per μl).

tag: strain

value: ICR (CD-1) outbred

value: adult brain

value: non-manipulated


title: GC077041_AGGCAGAA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_AGGCAGAA-CTATTAAG_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077041_AGGCAGAA-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: 158_TAV

description: Gene expression data from visceral adipose tissue from a aP2-Tagln2 male mouse

value: Visceral adipose tissue from a aP2-Tagln2 male mouse


title: 2xcr + c420r-3

description: 2xcr + c420r Rep3, with over-expression of PIK3CA C430R variant

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(C420R) constructs

value: mouse GBM model

value: over-expression of PIK3CA C430R variant


title: GC077041_AGGCAGAA-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: GC077041_AGGCAGAA-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_nodular triple melanoma


title: GC077041_ACTGAGCG-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: 2xcr + c420r-2

description: 2xcr + c420r Rep2, with over-expression of PIK3CA C430R variant


title: GC077041_ACTGAGCG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from primary_nodular triple melanoma


title: GC077041_ACTGAGCG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077041_ACTGAGCG-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_superficial triple melanoma

value: GFP+ cell from primary_superficial triple melanoma


title: 159_TAV


title: GC077041_ACTGAGCG-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: 2xcr + c420r-1

description: 2xcr + c420r Rep1, with over-expression of PIK3CA C430R variant


title: wt ctx-2

description: non-manipulated adult mouse brain, rep2


title: 2xcr + c420r-4

description: 2xcr + c420r Rep4, with over-expression of PIK3CA C430R variant


title: GC077041_ACTCGCTA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: wt ctx-1

description: non-manipulated adult mouse brain, rep1


title: 140_TAV

description: Gene expression data from visceral adipose tissue from wild-type female mouse

value: Visceral adipose tissue from wild-type female mouse


title: 158_TAS

description: Gene expression data from subcutaneous adipose tissue from a aP2-Tagln2 male mouse

value: Subcutaneous adipose tissue from a aP2-Tagln2 male mouse


title: 140_TAS

description: Gene expression data from subcutaneous adipose tissue from wild-type female mouse

value: Subcutaneous adipose tissue from wild-type female mouse


title: GC077041_ACTCGCTA-GAGCCTTA_primary_superficial_sc

description: NexteraXT library preparation


title: 2xcr+h1047r-3

description: 2xcr+h1047r Rep3, with over-expression of PIK3CA H1047R variant

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(H1047R) contructs


title: GC077041_ACTCGCTA-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation


title: 135_TAS

description: Gene expression data from subcutaneous adipose tissue from a aP2-Tagln2 female mouse

value: Subcutaneous adipose tissue from a aP2-Tagln2 female mouse


title: 135_TAV

value: Visceral adipose tissue from a aP2-Tagln2 female mouse


title: 130_TAV


title: GC077041_AAGAGGCA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077041_AAGAGGCA-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from primary_nodular triple melanoma


title: 130_TAS


title: GC077040_TGCAGCTA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_TGCAGCTA-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: 2xcr+h1047r-1

description: 2xcr+h1047r Rep1, with over-expression of PIK3CA H1047R variant


title: 2xcr+m1043i-3

description: 2xcr+m1043i Rep3, with over-expression of PIK3CA M1043I variant

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(M1043I) constructs


title: 2xcr+h1047r-2

description: 2xcr+h1047r Rep2, with over-expression of PIK3CA H1047R variant


title: 106_TAV


title: 2xcr+m1043i-2

description: 2xcr+m1043i Rep2, with over-expression of PIK3CA M1043I variant


title: GC077040_TCGACGTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: ANI_6

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

country: Germany

institute: Ruhr-University Bochum

description: protoapothecia replicate 2

data_processing:
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined with DESeq (Anders S, Huber W 2010, Genome Biol 11: R106), LOX 1.8 (Zhang et al. 2010, Bioinf 26: 1918-1919), and "classical analysis" as described in Teichert et al. 2012, BMC Genomics 13:511. RNA-seq reads from a previous analysis (Traeger et al. 2013, PLoS Genet 9: e1003820, GEO accession number GSE41631) were also included in the analysis.
a consensus for differential expression was determined from the three analyses (DESeq, LOX, classical) as described in  Teichert et al. 2012, BMC Genomics 13:511. Thresholds for differential expression were 2-fold/0.5-fold and 4-fold/0.25-fold for stringent analysis.
Genome_build: The genome was sequenced as part of the 1000 Fungal Genomes Project by the JGI (Joint Genome Institute) and is available under http://genome.jgi.doe.gov/Ascni1/Ascni1.home.html. The assembly version used for these analyses is v1.0.
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts and expression ratios (from LOX, DESeq, classical) for all annotated genes.

organism: Ascodesmis nigricans

source_name: protoapothecia

growth_protocol: Samples were grown on microdissection slides with 150-200 µl RFA (rabbit food agar) medium (+0.8 % agar) for 3d at 25 °C.

extract_protocol:
Total RNA was extracted and linearly amplified as described in Teichert et al. 2012, BMC Genomics 13: 511
RNA libraries were prepared for sequencing in a HighSeq2500 using standard Illumina protocols

treatment_protocol: Samples were fixated in ethanol at 4°C, and protoapothecia were harvested by laser microdissection as described in Teichert et al. 2012, BMC Genomics 13: 511

tag: isolation

value: laser-microdissected sample

value: protoapothecia


title: GC077040_TCCTGAGC-TTATGCGA_primary_nodular_sc

city: Edinburgh

first: Jana

last: Travnickova

address: Crewe Road South

institute: MRC Human Genetics Unit & Cancer Research UK EC

description: NexteraXT library preparation


title: 2xcr+m1043i-1

description: 2xcr+m1043i Rep1, with over-expression of PIK3CA M1043I variant

value: ICR (CD-1) outbred


title: GC077040_TCCTGAGC-CCTAGAGT_regressed_superficial_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_superficial triple melanoma


title: GC077041_AAGAGGCA-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: 2xcr+e545k-3

description: 2xcr+e545k Rep3, with over-expression of PIK3CA E545K variant

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(E545K constructs

value: over-expression of PIK3CA E545K variant


title: ANI_5

description: protoapothecia replicate 1


title: 60_sucb_TAS


title: GC077040_TCCTGAGC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation

value: GFP+ cell from recurring_nodular triple melanoma


title: ANI_4

description: veg replicate 2

source_name: total vegetative mycelium

value: total vegetative mycelium


title: GC077040_TCCTGAGC-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation

source_name: mitfa:GFP cell from regressed_nodular triple melanoma


title: 106_TAS


title: GC077040_TCCTGAGC-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_TGCAGCTA-CCTAGAGT_recurring_nodular_sc

description: NexteraXT library preparation


title: 60 visc_TAV

description: Gene expression data from visceral adipose tissue from a aP2-Tagln2 female mouse


title: GC077040_TCCTGAGC-TCGACTAG_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_TAGGCATG-TTATGCGA_primary_nodular_sc

description: NexteraXT library preparation


title: GC077040_TAGGCATG-GAGCCTTA_primary_nodular_sc

description: NexteraXT library preparation


title: 2xcr+e545k-1

description: 2xcr+e545k Rep1, with over-expression of PIK3CA E545K variant

value: mouse GBM model


title: ANI_3

description: veg replicate 1


title: ANI_2

description: sex replicate 2

source_name: total sexual mycelium

value: total sexual mycelium


title: GC077040_TAGGCATG-AAGGCTAT_regressed_nodular_sc

description: NexteraXT library preparation


title: GC077040_TAGCGCTC-TCGACTAG_regressed_nodular_sc

description: NexteraXT library preparation


title: ANI_1

description: sex replicate 1


title: GC077040_TAGCGCTC-CTATTAAG_primary_superficial_sc

description: NexteraXT library preparation


title: 2xcr+r88q-3

description: 2xcr+r88q Rep3, with over-expression of PIK3CA R88Q variant

source_name: mouse GBM model relying on in utero electroporation (IUE) and CRISPR-Cas9 mediated knockout of NF1 and p53 (termed 2xCR), and coelectroporation of pGlast-PBase plasmid with a PBCAG-GFPt2aLuc and PBCAG-PIK3CA(R88Q) constructs

value: over-expression of PIK3CA R88Q variant


title: 2xcr+r88q-4

description: 2xcr+r88q Rep4, with over-expression of PIK3CA R88Q variant


title: GC077040_TACGCTGC-GCGTAAGA_recurring_nodular_sc

description: NexteraXT library preparation


title: GC077040_TAGCGCTC-AAGGCTAT_primary_superficial_sc

description: NexteraXT library preparation


title: 2xcr+r88q-2

description: 2xcr+r88q Rep2, with over-expression of PIK3CA R88Q variant


title: 2xcr+e545k-2

description: 2xcr+e545k Rep2, with over-expression of PIK3CA E545K variant


title: GC077040_TAGGCATG-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation

value: GFP+ cell from regressed_superficial triple melanoma


title: 2xcr+r88q-1

description: 2xcr+r88q Rep1, with over-expression of PIK3CA R88Q variant


title: GC077040_TAAGGCGA-TTCTAGCT_regressed_superficial_sc

description: NexteraXT library preparation


title: GC077040_TACGCTGC-CTATTAAG_recurring_nodular_sc

description: NexteraXT library preparation