title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 P95H/+_2

status: Public on Jun 18 2018

description:
Srsf2 P95H KI/+
S233_KI.cpm

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
Sequences aligning to rRNA (NR_003278.3, NR003279.1,  NR_003280.2, NR_046144.1) were removed using BBMap (bbsplit.sh).
Sequenced reads were trimmed for adaptor sequence using Trim_galore (a wrapper to cutAdapt).
Reads were aligned using STAR (version STAR_2.5.3a) against mm10 (Annotation: gencode.mm10.vM14.annotation.gtf).
Duplicate reads were marked using Picard (v 1.96).
Read counting was performed using the featureCounts (subread-1.5.1).  "-T 16 --ignoreDup -p -t exon -g gene_id"
Data was normalised to cpm using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.).
Filtering and differential expression was performed using degust (http://degust.erc.monash.edu/). Data was filtered to keep only genes with: a) Min gene read count: 5, and b) min gene CPM: 1 (in at least 2 samples) resulting in 15,466 expressed genes. Differential expression was performed using voom with sample weighting.
Genome_build: mm10
Supplementary_files_format_and_content:
RAW_counts_unfiltered_n26027.gct (GCT): Raw counts from featureCounts. ENSEMBL gene level annotation.
Normalised_counts_unfiltered_cpm_n26027.gct (GCT): CPM normalised counts from featureCounts processed with Degust. ENSEMBL gene level annotation.
Normalised_counts_filtered_cpm_n15666.gct (GCT): Filtered CPM normalised counts from featureCounts processed with Degust, with filtering to remove lowly expressed genes. ENSEMBL gene level annotation.
Differential_expression_voom_weighted_n15466.odf (ODF): Differential expression results.
SVI_SRSF2_RNAseq_LinNeg_cKitPos_eYFPPos_differential_expression_supplementary.xlsx: Raw counts, CPM, annotation and differential expression in excel format.

source_name: Lin-/cKit+/eYFP+ Srsf2 P95H KI/+

extract_protocol:
Total RNA was isolated from Lin-/cKit+/eYFP+ (Immature haematopoietic multipotent progenitors) cells from whole bone marrow of 3 replicates from Srsf2+/+ and Srsf2 P95H/+ mice post tamixofen using the Direct-zol RNA MicroPrep kit from Zymo Research. RNA was checked for quality using the LabChip GX Touch 24.
150ng total RNA was used as starting material. Post ribosome depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit for Illumina Platforms (Kapa Biosystems). Library amplification was performed for 13 cycles of PCR. The resultant libraries were pooled and sequenced on two lanes using the Illumina X-ten with 150bp paired end reads at  Novogene Bioinformatics Technology Co., Ltd, Hong Kong.

value: female

tag: genotype/variation

value: hScl-CreERT R26eYFP Srsf2 P95H/+

tag: srsf2 genotype

value: 32 week old

tag: tissue

value: whole Bone Marrow

tag: cell type


title: CC1

status: Public on Oct 03 2018

type: SRA

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

library_source: transcriptomic

data_processing:
Nine nucleotides were removed from read 1 fastq files, and six were removed from read 2, as suggested by the Lexogen SENSE library preparation manual using the cutadapt tool. Samples split across two lanes were merged into a single fastq file.
Transcript abundances were estimated using salmon with Ensembl v75 annotation. Abundances were then aggregated to gene level using tximport.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; salmon quantifications

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The RNA content from each fraction was extracted using TRIzol, following the manufacturer’s guidelines. All RNA samples were DNase-treated (TurboDNase, Ambion), phenol/chlorophorm extracted, ethanol precipitated, and resuspended in RNases-free water (Sigma). Fractionations were assessed by western blot analysis, using histone H3, as a chromatin marker, Alyref or Ssrp1 as nuclear markers, and Tubulin as a cytoplasmic marker.
Libraries for sequencing were prepared using the Lexogen SENSE mRNA-Seq Library Prep according to the manufacturer’s instructions and sequenced using a Hiseq 2500.

tag: cell line

tag: condition

value: Control

tag: cellular fraction

value: Cytoplasms

tag: replicate

value: Replicate 1


title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 P95H/+_3

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description:
Srsf2 P95H KI/+
S242_KI.cpm

organism: Mus musculus

tag: strain background

tag: Sex

value: male

tag: age

value: Lin-/cKit+/eYFP+ (Immature haematopoietic multipotent progenitors) cells


title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 P95H/+_1

description:
Srsf2 P95H KI/+
S232_KI.cpm


title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 +/+_3

description:
Srsf2 P95 WT
S228_WT.cpm

source_name: Lin-/cKit+/eYFP+_Srsf2 P95 WT

value: hScl-CreERT R26eYFP Srsf2 +/+

value: WT


title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 +/+_1

description:
Srsf2 P95 WT
S176_WT.cpm

value: 54 week old


title: Whole bone marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H

description:
Srsf2 P95H KI/+
58-KI-TAM

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
Sequenced reads were trimmed for adaptor sequence using Trim_galore which is a wrapper to cutAdapt.
Reads were aligned using STAR (version STAR_2.5.3a) against mm9 (Annotation: gencode.mm9.vM1.annotation.gtf), using the following parameters  XXXX
Duplicate reads were marked using Picard (v 1.96).
Read counting was performed using the featureCounts function in Rsubread (v1.26.0).
Data was normalised to cpm using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.).
Genome_build: mm9
Supplementary_files_format_and_content: SVI_SRSF2_RNAseq_CPM_gr1_supplementary.xlsx : CPM, annotation and logFC information for genes detected above 1 cpm in WT or KI in excel format.

source_name: Whole Bone Marrow

extract_protocol:
Total RNA was isolated from the whole bone marrow from a single replicate from a 12 week old male Srsf2+/+ and a 14 week old female Srsf2 P95H/+ mouse.
Post ribosome depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit for Illumina Platforms (Kapa Biosystems). Library amplification was performed for 9 cycles of PCR. The resultant libraries were pooled and sequenced on a single run using the Illumina NextSeq500 with 75bp paired end reads at the Ramaciotti Centre for Genomics (UNSW, Australia).

value: 14 week old

value: Whole bone marrow


title: Whole bone marrow in vivo tamoxifen treated R26CreERT2 Srsf2 WT

description:
Srsf2 P95 WT
60-WT-TAM

value: 12 week old


title: Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 54

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
The datasets were assessed using FastQC and all reads having quality greater than 30 (Phred score) were kept for further analysis.
Raw data was aligned to Mus musculus genome (Ensembl GRCm38.72) using the Bowtie2 aligner with allowance for one mismatch. More than 98% of reads aligned to reference genome in all samples.
Variants (SNP and Indels) were detected using samtools mpileup from each sample. Identified variants were filtered for ≥ 10 reads supporting allele (Sum of reads supporting (DP4): reference forward, reference reverse, alternate forward and alternate reverse bases).
Somatic mutations were identified using two algorithms (Strelka & VarScan2) by considering ear sample as germline control and bone marrow as tumour. Strelka detects somatic SNVs and small Indels from the aligned sequencing reads of matched tumour (BM) – normal (Ear) samples. Passed somatic variants (SNPs and Indels) are the somatic variants which have passed all filters and have a quality score of at least 15 (SNPs) or 30 (Indels) assuming a homozygous reference genotype in the normal.
Genome_build: mm9
Supplementary_files_format_and_content: *BM_All_variant_calling_samtools_RD10.vcf. VCF format. All variants called using samtools.
Supplementary_files_format_and_content: *BM_All_variants_samtools_RD10_SnpEff_Annotated.txt TXT format. All variants called using samtools, with SnpEff annotations.
Supplementary_files_format_and_content: *Somatic_mutation_detection_Stelka_Passed_Somatic_Indels.vcf. VCF format. Stelka somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_Stelka_Passed_Somatic_SNPs.vcf. VCF format. Stelka somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_VarScan2_Filtered_Somatic_Indels.txt. TXT format. VarScan2 called somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_VarScan2_Filtered_Somatic_SNPs.txt TXT format. VarScan2 called somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_variants_strelka_Passed_Somatic_Indels_SnpEff_Annotated.txt TXT format. Stelka somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal)). Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_strelka_Passed_Somatic_SNPs_SnpEff_Annotated.txt TXT format. Stelka somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal)). Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_VarScan2_Filtered_Somatic_Indels_SnpEff_Annotated.txt TXT format. VarScan2 called somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal)) Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_VarScan2_Filtered_Somatic_SNPs_SnpEff_Annotated.txt TXT format. VarScan2 called somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal)) Annotated by SnpEff.

molecule: genomic DNA

extract_protocol:
Exome sequencing data was acquired for 6 samples from 50-60 weeks post tamoxifen treatment (time of euthanasia due to animals becoming moribund). Genomic DNA was isolated from both whole BM and matched ear tissue from three independent animals (two R26-CreERT2 Srsf2P95H/+ and one hScl-CreERT R26eYFP Srsf2P95H/+ ). The genomic DNA was isolated using the PureGene DNA isolation kit (Qiagen) as directed by the manufacturer.
The gDNA was subjected to exome capture using the Agilent SureSelect Mouse Exon (50Mb; performed by BGI) system and sequenced using the Illumina X10 platform at a mean depth of 100x coverage by BGI Ltd (Hong Kong).

tag: strain

tag: animal id

value: animal 54

value: 50-60 weeks

value: R26CreERT2 Srsf2 P95H

value: Bone Marrow


title: Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 136

value: animal 136

value: female


title: Ear in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 136

value: Ear


title: Ear in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 108

value: animal 108


title: CC3

value: Control

value: Cytoplasms

value: Replicate 3


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 1 (75B)

status: Public on Aug 14 2017

description:
MDA5 knockout mouse
Adar75B_MDA5_KO

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (v 0.36, Bolger AM, Lohse M and Usadel B: "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics. 2014 Apr 28. ). Command line used: java -jar trimmomatic-0.36.jar PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned using STAR (version STAR_2.5.2a_modified) against mm9 (Annotation: gencode.mm9.vM1.annotation.gtf), using the following parameters  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMismatchNmax 30 --outFilterMultimapNmax 20 --outSAMattributes All
Gene count files were combined using a custom script. File: rawCountData.gct.
Data was normalised in Degust (http://victorian-bioinformatics-consortium.github.io/degust/) using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.). Genes with CPM > 2 in at least 3/3 samples of a given genotype were considered for further analysis (E861A_MDA5_DKO_AB_STAR_mm9_Normalised_degust_edgeR_cpm2_3reps.CPM.EdgeR_n13891.gct). Differential expression was performed in Degust using EdgeR (E861A_MDA5_DKO_AB_STAR_mm9_Normalised_degust_edgeR_cpm2_3reps.CPM.EdgeR.DifferentialExpression_n13891.tsv)
Genome_build: mm9

source_name: Adult Brain

extract_protocol:
Total RNA was isolated from the whole brain from 3 independent biological replicates from 12 week old male Adar1+/+Ifih1-/- and Adar1E861A/E861AIfih1-/- mice.
Post ribosome depleted RNA was purified and subjected to indexing and library preparation using the Kapa Stranded RNA-seq Library Preparation Kit for Illumina Platforms (Kapa Biosystems). Library amplification was performed for 9 cycles of PCR. The resultant libraries were pooled and sequenced on a single run using the Illumina NextSeq500 with 75bp paired end reads at the Ramaciotti Centre for Genomics (UNSW, Australia).

value: Brain

tag: adar genotype

tag: mda5 genotype

value: Knockout

value: Adult Brain

value: male


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 3 (413B)

description:
ADAR1 editing deficient and MDA5 knockout mouse
Adar413B_E861A_MDA5_DKO


title: Lin-/cKit+/eYFP+ cells from whole bone marrow in vivo tamoxifen treated hScl-CreERT R26eYFP Srsf2 +/+_2

description:
Srsf2 P95 WT
S225_WT.cpm

value: hScl-CreERT R26eYFP Srsf2 +/+

value: WT

value: 32 week old

value: whole Bone Marrow

value: Lin-/cKit+/eYFP+ (Immature haematopoietic multipotent progenitors) cells


title: GIST48_Day3_siSCR_1

status: Public on Feb 01 2018

city: New York

first: Yuedan

last: Chen

state: NY

department: HOPP

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The sequenced reads from fastq files were mapped to hg19 using STAR and and downstream processing was done usig cuffquant
Genome_build: hg19
Supplementary_files_format_and_content: xls file including FPKM values for each Sample ...

source_name: GIST48 cells with siSCR

growth_protocol: Cells were grown in F-12 media containing 15% FBS

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

treatment_protocol: Cells were transfected with siRNA and harvested 3 days after transfection

value: GIST48 cells


title: GIST48_Day3_siFOXF1_1

source_name: GIST48 cells with siFOXF1 knockdown


title: GIST48_Day3_siSCR_2


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 2 (82B)

description:
MDA5 knockout mouse
Adar82B_MDA5_KO

value: 12 week old


title: GIST48_Day3_siFOXF1_2


title: ADAR1 WT MDA5 knockout Adult Brain - Whole. Replicate 3 (84B)

description:
MDA5 knockout mouse
Adar84B_MDA5_KO


title: GIST48_Day3_siETV1_2

source_name: GIST48 cells with siETV1 knockdown


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 2 (411B)

description:
ADAR1 editing deficient and MDA5 knockout mouse
Adar411B_E861A_MDA5_DKO


title: GIST48_Day3_siETV1_1


title: ADAR1 E861A E12.5 FB - Whole. Replicate 1

description: ADAR1 editing deficient mouse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (v 0.36, Bolger AM, Lohse M and Usadel B: "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics. 2014 Apr 28. ). Command line used: java -jar trimmomatic-0.36.jar PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned using STAR (version STAR_2.5.2a_modified) against mm9 (Annotation: gencode.mm9.vM1.annotation.gtf), using the following parameters  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMismatchNmax 30 --outFilterMultimapNmax 20 --outSAMattributes All
Gene count files were combined using a custom script into rawCountData.gct
Data was normalised in Degust (http://victorian-bioinformatics-consortium.github.io/degust/) using EdgeR (McCarthy, J. D, Chen, Yunshun, Smyth and K. G (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), pp. -9.). Genes with CPM > 2 in at least 3/3 samples of a given genotype were considered for further analysis (E861A_FB_STAR_mm9_degust_edgeR_cpm2_3reps.CPM.EdgeR.gct). Differential expression was performed in Degust using EdgeR (E861A_FB_STAR_mm9_degust_edgeR_cpm2_3reps.tsv)
Genome_build: mm9

source_name: Feotal Brain

growth_protocol: RNA was harvested from Single cell suspensions of whole feotal brain using Trizol reagent . >2.5 ug of total RNA was used for the construction of sequencing libraries.

extract_protocol:
RNA-Seq
For mRNA-Seq sample preparation, the Illumina TruSeq RNA Sample Prep Kit v2 was used according to the manufacturer’s instructions, using 1 ug of total RNA as input. The libraries were enriched using 12 cycles of PCR and the insert size ranged from 90bp to 330 bp.

treatment_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols at The Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia)

value: Embryonic day 12.5

value: Feotal Brain


title: ADAR1 E861A E12.5 FB - Whole. Replicate 2

description: ADAR1 editing deficient mouse


title: ADAR1 WT E12.5 FB - Whole. Replicate 3

description: Control


title: ADAR1 WT E12.5 FB - Whole. Replicate 2

description: Control


title: ADAR1 WT E12.5 FB - Whole. Replicate 1

description: Control


title: ADAR1 E861A E12.5 FB - Whole. Replicate 3

description: ADAR1 editing deficient mouse


title: Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 108

value: animal 108

value: 50-60 weeks

value: R26CreERT2 Srsf2 P95H

value: Bone Marrow


title: E861A Ifih1 knockout Brain replicate 3

description:
original sample name: 48_Adar1 E861A/E861A Ifih1-/-
barcode: 96
96-48-Adar1_S190

data_processing:
Illumina Casava1.7 software used for basecalling.
STAR mapping to mm9 with the following parameters: --outSAMunmapped Within --outFilterType BySJout  --outSAMattributes NH HI AS NM MD    --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverReadLmax 0.1   --alignIntronMin 20 --limitBAMsortRAM 10000000000  --alignIntronMax 1000000   --alignMatesGapMax 1000000    --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1
A custom script used samtools mpileup to query the edit level of BAM files to generate the raw editing levels and coverage information for editing sites (*.EditLvl.txt files).
Raw editing level and coverage files were then combined to create: rawEditData.noFilter.coverage.gct, rawEditData.noFilter.editLevels.gct
Genome_build: mm9

source_name: Brain

growth_protocol: Whole brain, kidney, spleen, thymus, bone marrow (haematopoietic cells), heart and small intestines from 3 independent biological replicates from Adar1+/+Ifih1-/- and Adar1E861A/E861AIfih1-/- were used for mmPCR-seq.

extract_protocol:
Following tissue homogenization with a mechanical blender, RNA was isolated from TRIsure reagent (Bioline) using Direct-Zol columns (Zymo Research) as described by the manufacturer.
cDNA was synthesized using iScript Advanced Kit (BioRad) using 1.2-7.5μg RNA per tissue. 200ng of cDNA was used for mmPCR-seq (www.ncbi.nlm.nih.gov/pubmed/24270603). Loci containing known A-to-I editing sites were PCR amplified using multiplexed primer pools. PCR amplicons were used for high throughput sequencing and A-to-I editing frequencies were determined as described by Zhang and colleagues (www.ncbi.nlm.nih.gov/pubmed/24270603).

value: Brain


title: Ear in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 54

value: animal 54

value: Ear


title: E861A Ifih1 knockout Brain replicate 1

description:
original sample name: 46_Adar1 E861A/E861A Ifih1-/-
barcode: 94
94-46-Adar1_S188

value: male


title: E861A Ifih1 knockout Brain replicate 2

description:
original sample name: 47_Adar1 E861A/E861A Ifih1-/-
barcode: 95
95-47-Adar1_S189


title: Adar1wt Ifih1 knockout Brain replicate 3

description:
original sample name: 45_Adar1+/+Ifih1-/-
barcode: 93
93-45-Adar1_S187


title: E861A Ifih1 knockout Thymus replicate 2

description:
original sample name: 41_Adar1 E861A/E861A Ifih1-/-
barcode: 89
89-41-Adar1_S183

source_name: Thymus

value: Thymus


title: E861A Ifih1 knockout Thymus replicate 3

description:
original sample name: 42_Adar1 E861A/E861A Ifih1-/-
barcode: 90
90-42-Adar1_S184


title: Adar1wt Ifih1 knockout Brain replicate 1

description:
original sample name: 43_Adar1+/+Ifih1-/-
barcode: 91
91-43-Adar1_S185

value: WT


title: Adar1wt Ifih1 knockout Brain replicate 2

description:
original sample name: 44_Adar1+/+Ifih1-/-
barcode: 92
92-44-Adar1_S186


title: ADAR1 E861A MDA5 knockout Adult Brain - Whole. Replicate 1 (401B)

description:
ADAR1 editing deficient and MDA5 knockout mouse
Adar401B_E861A_MDA5_DKO

value: Knockout

value: Adult Brain


title: Adar1wt Ifih1 knockout Thymus replicate 2

description:
original sample name: 38_Adar1+/+Ifih1-/-
barcode: 86
86-38-Adar1_S180


title: Adar1wt Ifih1 knockout Thymus replicate 3

description:
original sample name: 39_Adar1+/+Ifih1-/-
barcode: 87
87-39-Adar1_S181


title: E861A Ifih1 knockout Thymus replicate 1

description:
original sample name: 40_Adar1 E861A/E861A Ifih1-/-
barcode: 88
88-40-Adar1_S182


title: E861A Ifih1 knockout Heart replicate 1

description:
original sample name: 34_Adar1 E861A/E861A Ifih1-/-
barcode: 82
82-34-Adar1_S176

source_name: Heart

value: Heart


title: Adar1wt Ifih1 knockout Thymus replicate 1

description:
original sample name: 37_Adar1+/+Ifih1-/-
barcode: 85
85-37-Adar1_S179


title: Adar1wt Ifih1 knockout Heart replicate 2

description:
original sample name: 32_Adar1+/+Ifih1-/-
barcode: 80
80-32-Adar1_S174


title: Adar1wt Ifih1 knockout Heart replicate 1

description:
original sample name: 31_Adar1+/+Ifih1-/-
barcode: 79
79-31-Adar1_S173


title: Adar1wt Ifih1 knockout Heart replicate 3

description:
original sample name: 33_Adar1+/+Ifih1-/-
barcode: 81
81-33-Adar1_S175


title: E861A Ifih1 knockout Heart replicate 3

description:
original sample name: 36_Adar1 E861A/E861A Ifih1-/-
barcode: 84
84-36-Adar1_S178


title: E861A Ifih1 knockout Heart replicate 2

description:
original sample name: 35_Adar1 E861A/E861A Ifih1-/-
barcode: 83
83-35-Adar1_S177


title: E861A Ifih1 knockout Small Intestine replicate 3

description:
original sample name: 30_Adar1 E861A/E861A Ifih1-/-
barcode: 78
78-30-Adar1_S172

source_name: Small intestine

value: Small intestine


title: Adar1wt Ifih1 knockout Small Intestine replicate 1

description:
original sample name: 25_Adar1+/+Ifih1-/-
barcode: 73
73-25-Adar1_S167

source_name: Small Intestine

value: Small Intestine

value: 12 week old


title: E861A Ifih1 knockout Spleen replicate 3

description:
original sample name: 24_Adar1 E861A/E861A Ifih1-/-
barcode: 72
72-24-Adar1_S166

source_name: Spleen

value: Spleen


title: E861A Ifih1 knockout Small Intestine replicate 2

description:
original sample name: 29_Adar1 E861A/E861A Ifih1-/-
barcode: 77
77-29-Adar1_S171


title: Adar1wt Ifih1 knockout Small Intestine replicate 2

description:
original sample name: 26_Adar1+/+Ifih1-/-
barcode: 74
74-26-Adar1_S168


title: E861A Ifih1 knockout Small Intestine replicate 1

description:
original sample name: 28_Adar1 E861A/E861A Ifih1-/-
barcode: 76
76-28-Adar1_S170


title: E861A Ifih1 knockout Spleen replicate 2

description:
original sample name: 23_Adar1 E861A/E861A Ifih1-/-
barcode: 71
71-23-Adar1_S165


title: Adar1wt Ifih1 knockout Small Intestine replicate 3

description:
original sample name: 27_Adar1+/+Ifih1-/-
barcode: 75
75-27-Adar1_S169


title: E861A Ifih1 knockout Spleen replicate 1

description:
original sample name: 22_Adar1 E861A/E861A Ifih1-/-
barcode: 70
70-22-Adar1_S164


title: Adar1wt Ifih1 knockout Spleen replicate 3

description:
original sample name: 21_Adar1+/+Ifih1-/-
barcode: 69
69-21-Adar1_S163


title: Adar1wt Ifih1 knockout Spleen replicate 2

description:
original sample name: 20_Adar1+/+Ifih1-/-
barcode: 68
68-20-Adar1_S162


title: E861A Ifih1 knockout Liver replicate 1

description:
original sample name: 16_Adar1 E861A/E861A Ifih1-/-
barcode: 64
64-16-Adar1_S158

source_name: Liver

value: Liver


title: Adar1wt Ifih1 knockout Liver replicate 1

description:
original sample name: 13_Adar1+/+Ifih1-/-
barcode: 61
61-13-Adar1_S155


title: Adar1wt Ifih1 knockout Liver replicate 2

description:
original sample name: 14_Adar1+/+Ifih1-/-
barcode: 62
62-14-Adar1_S156


title: E861A Ifih1 knockout Bone Marrow replicate 3

description:
original sample name: 12_Adar1 E861A/E861A Ifih1-/-
barcode: 60
60-12-Adar1_S154

source_name: Bone Marrow


title: MOLM13-Cas9_RNA_sgMEN1-3_d6i_d4s_CGCGGA_S12_R1_merged.fastq.gz

status: Public on Nov 06 2019

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads aligned using STAR (v2.6.1b) and UCSC hg19 genome, gene and transcriptome references from Illumina iGenomes resource.
Aligned BAM files indexed with samtools v1.2; sorted, duplicate reads marked and removed (in cell line samples) using Broad picard tools v.2.9.4; and deduplicated BAMs indexed using samtools.
Read counts per gene calculated using HTSeq v0.11 htseq-count with hg19 gene reference from Illumina iGenomes and differential expression calculated using Bioconductor DESeq2 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Summary of raw counts per gene per sample (.txt)

source_name: MOLM13-Cas9 cultured cells

growth_protocol: MOLM13 cells expressing Cas9 were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). The cells were spinfected with lentiviruses carrying sgRNA for MEN1

extract_protocol:
Cell Lines: The cells were collected and washed twice in ice-cold PBS followed by lysis and RNA extraction using RNEasy (Qiagen) kit.  Quality of RNA was tested using RNA TAPE and samples qith RIN >7 were used for library preparation.
10-100 ng of total RNA converted to illumina compatible sequencing libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: CRISPR based knock out of MEN1 using 3 independent sgRNA for 6 days post infection

tag: timepoint

value: 6 days post infection

tag: treatment

value: CRISPR based knock out of MEN1


title: E861A Ifih1 knockout Bone Marrow replicate 2

description:
original sample name: 11_Adar1 E861A/E861A Ifih1-/-
barcode: 59
59-11-Adar1_S153

value: Bone Marrow


title: E861A Ifih1 knockout Bone Marrow replicate 1

description:
original sample name: 10_Adar1 E861A/E861A Ifih1-/-
barcode: 58
58-10-Adar1_S152


title: Adar1wt Ifih1 knockout Bone Marrow replicate 1

description:
original sample name: 7_Adar1+/+Ifih1-/-
barcode: 55
55-7-Adar1_S149


title: Adar1wt Ifih1 knockout Bone Marrow replicate 3

description:
original sample name: 9_Adar1+/+Ifih1-/-
barcode: 57
57-9-Adar1_S151


title: Adar1wt Ifih1 knockout Bone Marrow replicate 2

description:
original sample name: 8_Adar1+/+Ifih1-/-
barcode: 56
56-8-Adar1_S150


title: E861A Ifih1 knockout Kidney replicate 2

description:
original sample name: 5_Adar1 E861A/E861A Ifih1-/-
barcode: 53
53-5-Adar1_S147

source_name: Kidney

value: Kidney


title: Adar1wt Ifih1 knockout Kidney replicate 2

description:
original sample name: 2_Adar1+/+Ifih1-/-
barcode: 50
50-2-Adar1_S144


title: Adar1wt Ifih1 knockout Kidney replicate 3

description:
original sample name: 3_Adar1+/+Ifih1-/-
barcode: 51
51-3-Adar1_S145


title: Adar1wt Ifih1 knockout Spleen replicate 1

description:
original sample name: 19_Adar1+/+Ifih1-/-
barcode: 67
67-19-Adar1_S161


title: Adar1wt Ifih1 knockout Kidney replicate 1

description:
original sample name: 1_Adar1+/+Ifih1-/-
barcode: 49
49-1-Adar1_S143


title: E861A Ifih1 knockout Liver replicate 2

description:
original sample name: 17_Adar1 E861A/E861A Ifih1-/-
barcode: 65
65-17-Adar1_S159


title: E861A Ifih1 knockout Liver replicate 3

description:
original sample name: 18_Adar1 E861A/E861A Ifih1-/-
barcode: 66
66-18-Adar1_S160


title: Adar1wt Ifih1 knockout Liver replicate 3

description:
original sample name: 15_Adar1+/+Ifih1-/-
barcode: 63
63-15-Adar1_S157


title: E861A Ifih1 knockout Kidney replicate 3

description:
original sample name: 6_Adar1 E861A/E861A Ifih1-/-
barcode: 54
54-6-Adar1_S148


title: FL3_ADAR_WT

status: Public on Jul 24 2016

description: Control

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression) the following protocol was used
We used a basic differential expression analysis pipeline based developed at the Life Sciences Computation Centre, University of Melbourne. It is based around the Tuxedo protocol (Tophat, Cufflinks) and EdgeR/Voom with HTSeq-count. (Source code available at: https://bitbucket.org/jessicachung/rna_seq_pipeline)
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (v 0.3, Bolger AM, Lohse M and Usadel B: "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics. 2014 Apr 28.  ). Command line used: java -jar /usr/local/trimmomatic/0.30/trimmomatic-0.30.jar PE -phred33 ILLUMINACLIP:TruSeqAdapters.fa:4:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to the mus musculus genome build mm9 using tophat (v2.0.8), which uses Bowtie (2.1.0.0) and Samtools (v0.1.19) using default parameters and --transcriptome-index NCBI build 37.2 gtf.
Raw read counts were summarised using HTSeq from Simon Anders, Paul Theodor Pyl, Wolfgang Huber. "HTSeq — A Python framework to work with high-throughput sequencing data". bioRxiv preprint (2014), doi: 10.1101/002824
Normalisation factors were calculated using the edgeR method="TMM" is the weighted trimmed mean of M-values (to the reference) proposed by Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data.
Normalised read counts (moderated log counts per million) and differential expression were generated using a protocol from Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Law CW, Chen Y, Shi W, Smyth GK. Genome Biol. 2014 Feb 3;15(2):R29.
For RNA editing the following protocol was used:
RNA-seq reads were aligned to the MM9/NCBIM37 reference genome with BWA (Li and Durbin 2009). A-to-I(G) editing sites were determined as previously described . Briefly, paired-end reads were mapped separately to mm9 reference genome and exonic sequences encompassing known splicing junctions. Samtools rmdup (Li et al. 2009) was used to remove identical reads (PCR duplicates). Unique reads were subjected to local realignment and base score recalibration using the Genome Analysis ToolKit (GATK) (McKenna et al. 2010). Subsequently, variants were called with the UnifiedGenotyper in GATK and reported at lenient call criteria (stand_call_conf 0, stand_emit_conf 0). Variants were removed from the resulting candidate list if (1) they overlapped with known genomic variation (Keane et al. 2011), (2) had a variant call quality <20 or (3) were located in the first six bases of a read, within 4bp of a splice junction, in homopolymer runs or in simple repeats. The resulting list of variants was combined with editing sites discovered in previous studies and annotated using ANNOVAR (Wang et al. 2010) based on Gencode, RefSeq and UCSC gene models. Editing level at each of these sites was quantified using samtools mpileup. Sites that were covered by >20 reads in the RNA-seq data of all Adar1+/+ and Adar1-/- duplicates were tested for differential editing using ANOVA and reported as significant for p-value<0.1.
To find hyper-edited A-to-I (G) sites, all reads were to the MM9/NCBIM37 reference genome using BWA aln 0.6.2 (default parameters) and mem 0.7.4 (minimum seed length 50) (Porath et al. 2014). Reads with potential sequencing errors, long stretches of simple repeats or an average Phred quality <25 were removed. In order to be able to realign reads with a large number of mismatches caused by A-to-G editing sites, all ‘As’ were transformed to ‘Gs’ in both the remaining RNA reads and in the genome. Transformed reads were aligned to the transformed genome, again using BWA aln 0.6.2. The original read sequences that aligned (after the transformation) to multiple locations were separately treated by selecting the location with the largest fraction of A-to-G to all mismatches. Low-quality/mismapped reads having (i) a too dense A-to-G mismatch cluster (length <10% of the read length); (ii) a cluster too close to the ends of the read (completely contained within either the first or last 20% of the read; or (iii) a cluster with a particularly large percentage (>60%) of a single nucleotide were discarded. For edited PE reads (which were treated throughout the pipeline as two separate single-end reads), also required that the mate read was mapped to a nearby region (within 500 kbp) and in an opposite orientation. Reads that passed all filters were finally designated as hyper-edited.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag counts (raw_tagcounts.gct). Normalised tag counts (normalised_tag_counts.gct) in gct format. Differential expression in txt format (all_genes_annotated_ko_vs_wt.txt).  Editing analysis in xls format (Supplemental TableS6 Identification of novel A-to-I editing sites.xls)

source_name: Fetal liver day E14.5

extract_protocol:
RNA was harvested from Single cell suspensions of FACS isolated erythroid cells (YFP+, using R26eYFP reporter) from E14.5 fetal liver using TriSure reagent (Bioline). >2.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols at The Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia)

value: liver

value: Embryonic day 14.5

tag: genotype

value: wild type

value: Female


title: FL2_ADAR_KO

description: ADAR1 Epor-ADAR knock out mouse

value: Epor-Adar / +

value: Male


title: FL8_ADAR_WT

description: Control


title: E861A Ifih1 knockout Kidney replicate 1

description:
original sample name: 4_Adar1 E861A/E861A Ifih1-/-
barcode: 52
52-4-Adar1_S146

value: male


title: FL1_ADAR_KO

description: ADAR1 Epor-ADAR knock out mouse


title: E861A-FL17wt

status: Public on Jul 23 2015

description: Control

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
We used a basic differential expression analysis pipeline based developed at the Life Sciences Computation Centre, University of Melbourne. It is based around the Tuxedo protocol (Tophat, Cufflinks) and EdgeR/Voom with HTSeq-count. (Source code available at: https://bitbucket.org/jessicachung/rna_seq_pipeline)
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (v 0.3, Bolger AM, Lohse M and Usadel B: "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics. 2014 Apr 28.  ). Command line used: java -jar /usr/local/trimmomatic/0.30/trimmomatic-0.30.jar PE -phred33 ILLUMINACLIP:TruSeqAdapters.fa:4:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to the mus musculus genome build mm9 using tophat (v2.0.8), which uses Bowtie (2.1.0.0) and Samtools (v0.1.19) using default parameters and --transcriptome-index NCBI build 37.2 gtf.
Raw read counts were summarised using HTSeq from Simon Anders, Paul Theodor Pyl, Wolfgang Huber. "HTSeq — A Python framework to work with high-throughput sequencing data". bioRxiv preprint (2014), doi: 10.1101/002824
Normalisation factors were calculated using the edgeR method="TMM" is the weighted trimmed mean of M-values (to the reference) proposed by Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data.
Normalised read counts (moderated log counts per million) and differential expression were generated using a protocol from Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Law CW, Chen Y, Shi W, Smyth GK. Genome Biol. 2014 Feb 3;15(2):R29.
For RNA editing the following protocol was used
RNA-seq reads were aligned to the MM9/NCBIM37 reference genome with BWA from Li, H. and R. Durbin, Bioinformatics, 2009.
Paired-end reads were mapped separately to mm9 reference genome and exonic sequences encompassing known splicing junctions
PCR duplicates were removed using Samtools rmdup from Li H. et al., Bioinformatics, 2009.
Identification of mismatches between RNA and DNA (putative RNA editing sites) required homozogousity in the genomic DNA and all known SNPs present in dbSNP were excluded from the analysis
The first 6bp of each read were truncated and DNA-RNA mismatches were determined according to strandedness of RNA-seq reads
Genome_build: mm9
Supplementary_files_format_and_content: raw tag counts (E861A_FL_raw_counts.txt). Normalised tag counts (normalised_tag_counts.gct) in gct format. Differential expression in txt format (all_genes_annotated_wt_vs_mu.txt). Identified A-to-I RNA editing sites (WT_E861A_comparison_editlevels_and_cover.xlsx) in xlsx format.

source_name: Fetal liver day E12.5

extract_protocol:
RNA was harvested from Single cell suspensions of whole fetal liver using Trizol reagent . >2.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols at The Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia)

value: Embryonic day 12.5


title: E861A-FL19mu

description: ADAR1 editing deficient mouse


title: E861A-FL2wt

description: Control


title: E861A-FL6mu

description: ADAR1 editing deficient mouse


title: E861A-FL16mu

description: ADAR1 editing deficient mouse


title: 54R

status: Public on Jul 06 2015

description: Osteosarcoma cell line (54R) derived from Osx-Cre shRNA p53-/- (osteoblastic)

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
We used a basic differential expression analysis pipeline based developed at the Life Sciences Computation Centre, University of Melbourne. It is based around the Tuxedo protocol (Tophat, Cufflinks) and EdgeR/Voom with HTSeq-count. (Source code available at: https://bitbucket.org/jessicachung/rna_seq_pipeline)
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (v 0.3, Bolger AM, Lohse M and Usadel B: "Trimmomatic: a flexible trimmer for Illumina sequence data." Bioinformatics. 2014 Apr 28.  ). Command line used: java -jar /usr/local/trimmomatic/0.30/trimmomatic-0.30.jar PE -phred33 ILLUMINACLIP:TruSeqAdapters.fa:4:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to the mus musculus genome build mm9 using tophat (v2.0.8), which uses Bowtie (2.1.0.0) and Samtools (v0.1.19) using default parameters and --transcriptome-index NCBI build 37.2 gtf.
Raw read counts were summarised using HTSeq from Simon Anders, Paul Theodor Pyl, Wolfgang Huber. "HTSeq — A Python framework to work with high-throughput sequencing data". bioRxiv preprint (2014), doi: 10.1101/002824
Normalisation factors were calculated using the edgeR method="TMM" is the weighted trimmed mean of M-values (to the reference) proposed by Robinson and Oshlack (2010), where the weights are from the delta method on Binomial data.
Normalised read counts ( moderated log counts per million) and differential expression were generated using a protocol from Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Law CW, Chen Y, Shi W, Smyth GK. Genome Biol. 2014 Feb 3;15(2):R29.
Genome_build: mm9
Supplementary_files_format_and_content: raw and normalised tag counts in txt format

source_name: Osteosarcoma cell line

growth_protocol: subconfluent early passage (less than passage 8) proliferative cultures were used for RNA extraction

extract_protocol:
RNA was harvested from osteosarcoma cell lines derived from tumours using Trizol reagent . >2.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols at The Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia)

value: Osteosarcoma cell line

tag: developmental stage

value: Adult

value: Osx-Cre shRNA TRE-p53.1224 pRbfl/fl

tag: primary tumor site

value: Rib

value: female


title: E861A-FL15wt

description: Control

tag: tissue


title: 148I

description: Osteosarcoma cell line (148I) derived from Osx-Cre shRNA p53-/- (osteoblastic)

tag: cell line

tag: cell type

value: Iliac Crest


title: 98S

description: Osteosarcoma cell line (98S) derived from Osx-Cre shRNA p53-/- (osteoblastic)

value: Scapula


title: 716L

description: Osteosarcoma cell line (716L) derived from Osx-CreLox p53-/- Rb-/- (fibroblastic)

value: Osx-Cre p53fl/fl Rbfl/fl

value: Tibia


title: FL11R2

type: RNA

description: Ter119-CD71+ sorted erythrocyte progenitors from mice with an erythroid restricted deletion of ADAR1

hyb_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

data_processing: samples were RMA normalised in GenePattern using NormalizeAffymetrixST (RMA, core probesets, controls included, MoGene_1_0_ST_v1.na32.mm9.transcript.chip).

label: biotin

source_name: Erythrocyte progenitors from mice with an erythroid restricted deletion of ADAR1

growth_protocol: Mouse model

extract_protocol: Qiagen RNA kit

treatment_protocol: Embryos were havested at E14.5 and erythroid progenitors were FACs sorted from fetal liver

value: Fetal Liver

tag: eporcre genotype

value: ki/+

tag: r26eyfp genotype

tag: adar1 genotype

value: fl/-

tag: genetic background


title: FL15R4

description: Ter119+CD71med sorted erythrocyte progenitors from control mice

scan_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

source_name: Erythrocyte progenitors from control mice

value: fl/+


title: FL1R2

label_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.


title: FL13R3

description: Ter119+CD71+ sorted erythrocyte progenitors from control mice


title: FL10R2


title: FL13R4


title: FL11R3

description: Ter119+CD71+ sorted erythrocyte progenitors from mice with an erythroid restricted deletion of ADAR1


title: FL2R3


title: FL13R2

description: Ter119-CD71+ sorted erythrocyte progenitors from control mice


title: FL15R3


title: FL15R2


title: FL10R3


title: 494H

description: Osteosarcoma cell line (494H) derived from Osx-CreLox p53-/- Rb-/- (fibroblastic)

value: Hip

tag: Sex


title: 493H

description: Osteosarcoma cell line (493H) derived from Osx-CreLox p53-/- Rb-/- (fibroblastic)

tag: strain


title: FL2R2


title: Osterix-Cre p53 Rb mouse model of osteosarcoma 494H

status: Public on Jul 01 2015

growth_protocol: Grown in RPMI media supplemented with 10% FCS, glutamax, penicillin/streptomycin in a humidified, 5% CO2, 37degrees incubator.

extract_protocol: Tissue homogenised in trizol, trizol extraction followed by Qiagen colum cleanup of total RNA.

treatment_protocol: Kusa4b10 cells were in vitro differentiated by exposure to growth media containing 50ug/ml ascorbate for 21 days, commencing when cells had reached 100% confluency. Growth media supplemented with ascorbate was changed three times a week, for 21 days.

tag: genotype rb

value: fl/fl

tag: genotype p53

tag: model

value: Osx-Cre+

tag: age

value: hip

value: M


title: Ren3

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 3

data_processing: samples were RMA normalised in GenePattern using NormalizeAffymetrixST (v.2.0, RMA, core probesets, controls included, MoGene_1_0_ST_v1.na32.mm9.transcript.chip).

source_name: Renilla.1309 OS80 tumour

treatment_protocol: Tumours grown on back flank in pairs (PTHR1 and Renilla shRNA on alternate flanks). Tumour grown for 4 weeks in vivo. Weekly bioimaging for luciferase measurement. Endpoint microCT analysis. Tumour weiged, dissected and stored in Trizol.

tag: host strain background

value: Balb/c nu/nu

tag: parental mouse strain background for cell line

value: mixed (C57, 129, FvBN)

tag: parental mouse strain for cell line

tag: parental mouse gender for cell line

tag: parental mouse age for cell line

value: 224 days

tag: source tissue for cell line

value: tumour on right front leg/shoulder

value: OS 80

value: Cre:lox osteosarcoma cells

tag: cell line genotype/variation

value: control renilla luciferase shRNA

tag: tumour location

value: back flank (opposite side had PTHR1.358 OS80 tumour 3)


title: Ren5

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 5

value: female

tag: cell line

tag: cell type

value: back flank (opposite side had PTHR1.358 OS80 tumour 5)


title: Differentiated KUSA4b10 rep 1 T=21 Ex1

tag: replicate


title: Ren6

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 6

value: back flank (opposite side had PTHR1.358 OS80 tumour 6)


title: Differentiated KUSA4b10 rep 3 T=21 Ex3


title: Osterix-Cre p53 Rb mouse model of osteosarcoma 716H

tag: primary tumor site

value: Tibia

tag: Sex

value: F


title: Osterix-Cre p53 Rb mouse model of osteosarcoma 493H

tag: genotype rb

value: fl/fl

tag: strain


title: Ren4

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 4

value: back flank (opposite side had PTHR1.358 OS80 tumour 4)


title: Differentiated KUSA4b10 rep 2 T=21 Ex2


title: PTHR1_5

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 5

source_name: PTHR1.358 OS80 tumour

value: PTHR1 shRNA knockdown

value: back flank (opposite side had Renilla.1309 OS80 tumour 5)


title: PTHR1_6

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 6

value: Balb/c nu/nu

value: back flank (opposite side had Renilla.1309 OS80 tumour 6)


title: PTHR1_4

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 4

value: mixed (C57, 129, FvBN)

value: 224 days

value: back flank (opposite side had Renilla.1309 OS80 tumour 4)


title: Ren2

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 2

value: tumour on right front leg/shoulder

value: OS 80

value: Cre:lox osteosarcoma cells

value: back flank (opposite side had PTHR1.358 OS80 tumour 2)


title: Ren1

description:
mouse OS xenograft, luciferase tagged
Renilla.1309 OS80 tumour 1

value: female

value: control renilla luciferase shRNA

value: back flank (opposite side had PTHR1.358 OS80 tumour 1)


title: PTHR1_3

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 3

value: back flank (opposite side had Renilla.1309 OS80 tumour 3)


title: Osteoblast (independent sample2)

status: Public on Jan 29 2015

source_name: Osteoblastic in vitro differentiation of Kusa4b10 mouse cell line.

growth_protocol: Subconfluent early passage (less than passage 8) proliferative OS cultures, undifferentiated Kusa4b10 cultures representing pre-osteoblast cells, and in vitro osteoblastic differentiated (21 days) Kusa4b10 cells representing osteoblast samples were used for RNA extraction

extract_protocol: RNA was harvested from cell samples using Trizol reagent combined with Qiagen Rneasy mini columns.

treatment_protocol: Cells representing osteoblast cultures, were cultured under osteoblastic conditions (ascorabate suppplemented medium) for 21 days.


title: Pre-osteoblast (independent sample 3)

source_name: Kusa4b10 mouse cell line

value: Kusa4b10 mouse cell line


title: PTHR1_2

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 2

value: back flank (opposite side had Renilla.1309 OS80 tumour 2)


title: Osteoblast (independent sample3)

value: Osteoblastic in vitro differentiation of Kusa4b10 mouse cell line.


title: 716H

description: Osx-CreLox p53-/- Rb-/- (fibroblastic)

value: Osteosarcoma cell line

value: Adult

tag: genotype

value: Osx-Cre p53fl/fl Rbfl/fl


title: PTHR1_1

description:
mouse OS xenograft, luciferase tagged
PTHR1.358 OS80 tumour 1

value: Balb/c nu/nu

value: mixed (C57, 129, FvBN)

value: PTHR1 shRNA knockdown

value: back flank (opposite side had Renilla.1309 OS80 tumour 1)


title: Pre-osteoblast (independent sample 2)


title: Osteoblast (independent sample1)


title: Pre-osteoblast (independent sample 1)


title: 494H

description: Osx-CreLox p53-/- Rb-/- (fibroblastic)

tag: age

value: male


title: 493H

description: Osx-CreLox p53-/- Rb-/- (fibroblastic)


title: PTHrP_6hour_rep3

status: Public on Apr 10 2013

hyb_protocol: Twenty micrograms of labeled cRNA was fragmented (50-200 bp) and quality control checked using the Agilent Bioanalyser 2100 NanoChip protocol before preparing the probe cocktail containing 0.05  g/ml cRNA in hybridization buffer. Two hundred microliters of each sample were loaded onto Affymetrix Murine 430 version 2.0 GeneChips and hybridized at 45°C for 16 h in an oven with a rotating wheel at 60 rpm.

scan_protocol: After hybridization, the chip was washed and scanned using the Affymetric GeneChip Scanner 3000 and the chip signal converted into a DAT file by the scanner operating software GCOS.

data_processing:
Normalised data were generated with GenePattern module NormalizeAffymetrix3prime (v.2.1) at
http://pwbc.garvan.unsw.edu.au/gp
RMA normalised, using quantile normalisation with background correction

label_protocol: Five micrograms of total RNA was labeled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences), and subsequent cDNA was purified using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences). In vitro transcription of cDNA to cRNA was performed using the Affymetrix IVT labeling kit (Millenium Sciences) with biotin-labeled ribonucleotides to incorporate biotin into the cRNA. cRNA was purified using the GeneChip Sample Cleanup kit and quality tested using the Agilent Bioanalyser 2100 NanoChip protocol.

extract_protocol: RNA was prepared from Kusa 4b10 cells lysed in Trizol (Invitrogen) according to the manufacturer's instructions. RNA was treated with DNase (Promega) for 30 min at 37°C and purified according to the Qiagen protocol for the RNeasy MiniElute kit (Qiagen). Total RNA was quality tested using the Agilent Bioanalyser 2100 NanoChip protocol.

value: mouse marrow stromal cells

tag: treated with

value: PTHrP(1–141) (20 nM) for 6hr


title: PTHrP_24hour_rep1

value: PTHrP(1–141) (20 nM) for 24hr


title: PTHrP_1hour_rep3

value: PTHrP(1–141) (20 nM) for 1hr


title: PTHrP_1hour_rep2


title: PTHrP_6hour_rep1


title: PTH_6hour_rep3

value: PTH(1–34) (10 nM) for 6h


title: PTHrP_1hour_rep1


title: PTH_6hour_rep2


title: PTHrP_24hour_rep2


title: PTH_24hour_rep2


title: PTHrP_24hour_rep3


title: PTH_1hour_rep3

value: PTH(1–34) (10 nM) for 1h


title: PTH_24hour_rep3


title: PTH_6hour_rep1


title: PTH_24hour_rep1


title: PTHrP_6hour_rep2


title: control_6hour_rep3

value: None (control) for 6h


title: PTH_1hour_rep2


title: control_6hour_rep1


title: control_6hour_rep2


title: control_1hour_rep3

value: None (control) for 1h


title: control_24hour_rep2

value: None (control) for 24h


title: control_24hour_rep3


title: control_24hour_rep1


title: control_1hour_rep2


title: control_1hour_rep1


title: PTH_1hour_rep1


title: Differentiated KUSA4b10 rep 3 T=21

type: genomic

hyb_protocol: standard procedures by Roche Nimblegen

scan_protocol: standard procedures by Roche Nimblegen

data_processing: Pair files were analysed using Repitools (v1.7.6) and Limma (v3.14.4).

source_name: DNAme ChIP DNA from KUSA cells

label_protocol: standard procedures by Roche Nimblegen

growth_protocol: Grown in RPMI media supplemented with 10% FCS, glutamax, penicillin/streptomycin in a humidified, 5% CO2, 37degrees incubator. Kusa4b10 cells were in vitro differentiated by exposure to growth media containing 50ug/ml ascorbate for 21 days, commencing when cells had reached 100% confluency. Growth media supplemented with ascorbate was changed three times a week,

extract_protocol: standard procedures by Roche Nimblegen

tag: antibody

value: MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen)

tag: genetic background

source_name: Input DNA from KUSA cells

value: none, input DNA


title: OS cell line derived from Osterix-Cre p53 Rb mouse model of osteosarcoma rep1

source_name: DNAme ChIP DNA from primary OS cells

tag: genotype p53

tag: model

value: Osx-Cre+

value: hip

value: F

source_name: Input DNA from primary OS cells

value: primary OS cells


title: Differentiated KUSA4b10 rep 2 T=21


title: Differentiated KUSA4b10 rep 1 T=21


title: OS cell line derived from Osterix-Cre p53 Rb mouse model of osteosarcoma rep3

value: Tibia


title: OS cell line derived from Osterix-Cre p53 Rb mouse model of osteosarcoma rep2

value: M