title: Osdrm2 RNA-seq

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

data_processing:
For Bisulfite-Seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The clean data were mapped against genome using bismark(v0.19.0). CGmaptools(v0.1.1) was used to calculate the methylation level of the 2-kb sequences upstream and downstream of all genes and transposable elements (http://rice.plantbiology.msu.edu/). A personal Python script was  used to visualize the methylation level.
For RNA-seq data, the adaptor sequences and low-quality reads were trimmed using trim_galore(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).The clean reads were mapped against replaced genome using Tophat2 (v2.1.1)[5] with default parameters. Cufflinks (v2.0.0) was used to quantify the relative expression of the genes and calculate any differentially expressed genes (Fold change ≥ 1, adjusted p-value<0.01). To visualize the RNA-seq expression level, bedtools was used to calculate the coverage and normalize the data per million mapped reads. A Python script was used to visualize the data.
For smallRNA-seq data, The adaptor sequences and low-quality RNA-seq reads were trimmed using trim_galore, and reads shorter than 18 nt or longer than 30 nt were discarded. MicroRNA (http://www.mirbase.org/ftp.shtml), transfer RNA (http://rice.plantbiology.msu.edu/analyses_search_tRNA.shtml), ribosomal RNA (Rice Genome Annotation MSU7.0), small nucleolar RNA, and small nuclear RNA  (https://www.arb-silva.de/no_cache/download/archive/release_132/Exports/) sequences were also removed. The remaining clean reads were aligned to the  replaced MSU7.0 rice genome using Bowtie (v 1.1.1), allowing 2 mismatches and requiring mapping to a unique site. The siRNA enrichment was calculated in 10-kb windows with normalized reads, and only windows with at least three reads were further analysed. To visualize the level of siRNA expression, bedtools was used to calculate the coverage and normalize the data per million mapping reads. A  Python script was used to visualize the data.
Genome_build: About 7-kb sequence containing LOC_Os01g41370 was amplified from ZH11 and sequenced. This sequence was used to replace the LOC_Os01g41370 sequence in the MSU7.0 rice genome assembly, which was identified using BLASTn. The replaced MSU7.0 rice genome was used in our analysis.

organism: Oryza sativa Japonica Group

source_name: Osdrm2 leaf

growth_protocol: The Epi-lf mutant was identified in a screen of an anther-cultured population of Japonica rice (Oryza sativa ssp. japonica; variety ZhongHua11; ZH11) in 2005. The mutant phenotype of Epi-lf was stably inherited over more than 20 generations. The mutant and WT rice plants were planted in paddy fields under natural conditions or in glasshouses with a day temperature of 30°C and a night temperature of 24°C.

extract_protocol:
Total RNA was extracted from different tissues using TRIzol reagent (Thermo Fisher Scientific). The first-strand cDNA was synthesized using 1 μg RNA and ReverTra Ace qPCR RT Master Mix with gDNA Remover (Toyobo), according to the manufacturer’s instructions, using 29 PCR cycles to amplify the LF transcripts and 23 PCR cycles for Actin1. The RT-PCR analysis was repeated three times with similar results. Genomic DNA was isolated from the flag leaves of WT and tillers with different phenotypes of Epi-lf using the CTAB method. Briefly, 1 μg of genomic DNA was treated with sodium bisulphite using the Qiagen EpiTect Bisulfite kit, according to the manufacturer’s instructions. The treated DNA was dissolved in 15 mL distilled water, and 3 μL of this solution was used as the template in a 50-μL PCR (94°C for 4 min; followed by 40 cycles of 94°C for 30 s , 55°C for 30 s and 60°C for 30 s; with a final 60°C for 10 min).The PCR products were purified and cloned into pEASY-T5-Blunt Zero Cloning Kit vectors.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: variety

value: leaf

tag: developmental stage

value: 50 days


title: Pooled sera_51071

status: Public on Jul 01 2021

type: SRA

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

library_source: transcriptomic

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622685.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2

molecule: total RNA

organism: Escherichia coli

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: Pooled sera

tag: strain

tag: growth time

value: 2 hrs exposure to sera

tag: growth phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: RPMI_51067

value: RPMI

value: 1 hr

value: Mid log phase


title: 168B

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

country: France

institute: INRAE

data_processing:
Base calling and prefiltering (adaptor removal) was performed by BGI
STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters
Counts of reads per gene were obtained with HTSeq v0.11.2 (gtf annotation file GRCz11.97)
Use of DESeq2 v1.24.0 for differential gene expression analysis
Genome_build: DanRer11
Supplementary_files_format_and_content: csv file including raw counts obtained from htseq (unnormalized).

organism: Danio rerio

extract_protocol:
Fish were euthanized, brains were dissected and flash frozen in liquid nitrogen, and RNA was extracted using TriPrep extraction kit (Macherey-Nagel). One microg of total RNA was sent to BGI Europe A/S for pair-ended transcriptome sequencing on BGI-Seq500
according to BGI standard protocol

tag: tissue

value: whole brain

tag: age

value: adult

value: AB line

tag: generation

tag: Sex

value: F


title: Neonatal Blood Spot, 202128330060_R07C01

type: genomic

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

country: USA

institute: Emory University

description: Illumina Infinium MethylationEPIC array- standard protocol

hyb_protocol: MethylationEPIC

scan_protocol: BeadStudio

data_processing: noob, remove SNPs and cross-reactive probes, combat

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Neonatal Blood Spot

label_protocol: MethylationEPIC

extract_protocol: QIAamp DNA Mini

tag: sex (male= 1, female=2)

tag: race

value: African American

tag: gestational age


title: Mock_FLAGp3

city: Strasbourg

first: Thomas

middle: F

last: Baumert

address: 3, rue Koeberlé

department: University of Strasbourg

institute: Inserm U1110

description:
Single-cell RNA-Seq
Control

data_processing:
Reads were aligned to the human (hg19 UCSC) and HCV (Jc1) reference genomes using TopHat with default setttings.
Human gene expression levels were quantified using Cuffquant (Cufflinks 2.2.1 suite) with default settings.
Human gene expression levels were normalized across all samples using Cuffnorm (Cufflinks2.2.1 suite) with default settings.
HCV copy number was calculated as the percentage of viral read pairs mapped relative to all human and viral read pairs mapped.
Genome_build: hg19 UCSC and HCV Jc1
Supplementary_files_format_and_content: [.txt] Tab-delimited text files with human gene expression levels (FPKM) and HCV copy number for each sample.

organism:
Homo sapiens
Hepacivirus hominis

source_name: Huh7.5.1 cell_control

growth_protocol: For proliferation arrest and differentiation, Huh7.5.1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) containing 1% DMSO for 10 days, followed by additional 7 days after HCV infection.

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen) according to manufacturer 's protocol.
Refer to Trombetta et al, 2014

treatment_protocol: DMSO-differentiated Huh7.5.1 cells were infected or not using HCV cell-culture derived particles (HCVcc Jc1E2FLAG). On day 7 post-infection, single-cells were sorted into 96-well plates using a well-established limiting dilution assay. Single-cells were lysed in 5 µl TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol. Cellular mRNA was isolated using the RNeasy mini kit (Qiagen) and sequenced using the SMART-Seq 2 procedure described by Trombetta et a, 2014 on one NextSeq500. HCV RNA was co-amplified with cellular mRNA using a SMART-compatible primer (sequence: 5'-Biotin-AAGCAGTGGTATCAACGCAGAGTACTCTGCGGAACCGGTGAGTA-3')). The modulation of specific gene signatures in association with the normalized HCV copy number in single cell RNA-Seq data was determined using the pre-ranked GSEA module implemented in GenePattern with Pearson correlation as the rank metric.

tag: cell line

tag: cell type

value: DMSO-differentiated Huh7.5.1 cell

tag: treatment

value: FLAG-peptide


title: RPMI_51068

tag: growth media

tag: strain


title: WT_rep2_RNA-seq

country: China

source_name: WT leaf

tag: variety

tag: developmental stage


title: 167B


title: WT_rep3_RNA-seq


title: RPMI_51066

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature


title: RPMI_51065

tag: bpa identifier

tag: serovar


title: Neonatal Blood Spot, 202128330122_R02C01


title: Neonatal Blood Spot, 202128330122_R01C01


title: 165B

tag: tissue

tag: age

tag: generation

tag: Sex


title: WT_rep1_RNA-seq


title: Neonatal Blood Spot, 202128330060_R08C01

tag: sex (male= 1, female=2)

tag: race

tag: gestational age


title: Osdrm2_leaf_BS-seq

library_source: genomic


title: 166B


title: 163B

value: M


title: RPMI_50906

tag: growth media


title: 161B

tag: strain


title: Neonatal Blood Spot, 202128330060_R01C01


title: LF_CHD1_rep2_BS-seq

source_name: Epi-lf dwarf leaf

tag: variety


title: Neonatal Blood Spot, 202128330122_R03C01


title: Neonatal Blood Spot, 202128330122_R04C01


title: 160B


title: Pooled sera_50876

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622695.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: 159B


title: LF_CHD2_rep2_BS-seq

tag: developmental stage


title: Pooled sera_51048

tag: growth time


title: 158B


title: Pooled sera_50875

tag: growth phase


title: WT_rep3_BS-seq


title: Neonatal Blood Spot, 202128330060_R04C01


title: Neonatal Blood Spot, 202128330059_R07C01


title: Neonatal Blood Spot, 202128330060_R05C01


title: WT_rep4_BS-seq


title: 155B


title: Pooled sera_51047

tag: od600 reading


title: Pooled sera_51046

tag: temperature


title: 157B


title: LF_Normal_rep2_BS-seq

source_name: Epi-lf normal leaf


title: Pooled sera_51045

tag: bpa identifier


title: stim.wt_rep2

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0.

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and offset of 1. Spot intensities were quantile normalized between arrays.

organism: Mus musculus

source_name: Primary isolated cells, heart fibroblasts

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: Freshly isolated fibroblasts were grown in DMEM containing 10% (v/v) FBS.

extract_protocol: RNeasy from Qiagen.

treatment_protocol: Cells were left untreated or incubated for 6 hs in a hypoxia chamber (1% O2).

tag: genotype

value: Wild-type

tag: cell type

value: Heart fibroblasts

tag: condition

value: Hypoxia


title: RPMI_51044

tag: serovar


title: RPMI_50870


title: Neonatal Blood Spot, 202128330122_R05C01


title: WT_rep2_BS-seq

tag: tissue

value: leaf

value: 50 days


title: Neonatal Blood Spot, 202128330060_R03C01

tag: sex (male= 1, female=2)


title: 156B

tag: age

tag: generation

tag: Sex


title: Neonatal Blood Spot, 202128330060_R06C01

tag: race

tag: gestational age


title: RPMI_50869

tag: growth media

tag: strain


title: ctrl.ko_rep2

value: Siah knockout

value: Normoxia


title: 37B


title: 40B


title: 36B


title: RPMI_51042

value: RPMI

tag: growth time

value: 1 hr

tag: growth phase


title: Neonatal Blood Spot, 202128330059_R08C01


title: RPMI_51041

value: Mid log phase

tag: od600 reading

tag: temperature


title: 35B

value: whole brain

value: adult


title: RPMI_51043

tag: bpa identifier


title: 38B

value: AB line


title: Pooled sera_50864

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900622635.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

value: Pooled sera

value: 2 hrs exposure to sera


title: 34B

value: F


title: paht mutant phe repl 2

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts (Novogen, Hong Kong). In this step, clean data (clean reads) were obtained by removing reads containing adapters and reads in which uncertain nucleotides (N) were more than the 10% of the read length. Reads with low quality nucleotides (base quality <20) in more than 50% of the read length were also discarded.
Paired-end clean reads were mapped to the reference genome (RAST Genome ID: 6666666.92368) using HISAT2 software v.0.6.1. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
HTSeq software was used to count the read mapped to each gene, including known and novel genes.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 package v1.20.0 in R. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.
Genome_build: RAST Genome ID: 6666666.92368
Supplementary_files_format_and_content: DESeq2 normalized abundance measurements, Log2Foldchange, pvalues and functional annotation for all genes in the three experiments

organism: Novosphingobium sp. HR1a

source_name: cell culture

growth_protocol: Strains were  grown overnight in LB medium plus the corresponding antibiotic to be used as preinocula for the different growth experiments. For Bioscreen experiments, 200 l M9 minimal medium plus the corresponding carbon source (at a final concentration of 5 mM) were dispensed into wells of honeycomb microplates (OY Growth Curves AB Ltd., Raisio, Finland). Wells were inoculated with the overnight culture at an initial optical density (DO660nm) of 0.1. Cultures were incubated at 28ºC with maximal agitation in a FP-1100-C Bioscreen C MBR analyzer system (OY Growth Curves Ab Ltd., Raisio, Finland). Growth was monitored using a type at 30ºC with continuous agitation. Turbidity was measured using a sideband filter at 420-580 nm every 60 min for 42 hours.

extract_protocol:
Total RNA was extracted using the Trizol method (TRIzol RNA Isolation Reagents, Thermofisher Scientist) and further DNAse treatment and purification with RNeasy Mini Kit (Qiagen). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantification were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
One μg RNA per sample was used to prepare the sequencing libraries which were generated by Novogen (Hong Kong) using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: A 340 base pairs internal fragment of orf1998 was amplified using oligonucleotides 1998-F and 1998-R (Suppl. Table 2) using genomic DNA of Novosphingobium sp. HR1a as template. This fragment was cloned into pMBLTM-T plasmid and the resulting plasmid, pMBL1998, was digested with BamHI and ligated with the Ω-Km cassette from plasmid pHP45ΩKm that were previously digested with BamHI and ScaI and extracted from an agarose gel . The resulting plasmid pMBL1998Km was transformed into Novosphingobium sp. HR1a by electroporation. Transformants that have integrated the plasmid into the host chromosome via homologous recombination were selected on LB plus kanamycin plates and checked by Southern blot hybridization.

tag: carbon source

value: carbon source phenanthrene

tag: genotype

value: pahT mutant


title: Pooled sera_50863

tag: serovar


title: stim.wt_rep1

value: Wild-type

tag: cell type

value: Heart fibroblasts

tag: condition


title: stim.ko_rep2

value: Hypoxia


title: paht mutant phe repl 1


title: 33B

tag: tissue

tag: age


title: ctrl.wt_rep1


title: Pooled sera_51040


title: Neonatal Blood Spot, 202128330059_R06C01

tag: sex (male= 1, female=2)

value: African American


title: AAV8-UCP1 sgRNA rep4

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
DNBSEQ-G400 platform
Read files were downloaded and quality of raw read data was checked using FastQC to identify features of the data that may indicate quality problems (i.e. low-quality scores, over-represented sequences, inappropriate GC content).
Reads were aligned to the GRCm39 reference genome and quantified using STAR. FastQC was used for the second round of quality control post-alignment to ensure that only high-quality data was input to expression quantitation and differential expression analysis.
Differential expression analysis was done using DESeq2.
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table (CSV file) with raw gene counts for every gene and every sample

source_name: Brown adipose tissue (BAT) 8-10 weeks of age

extract_protocol:
Total RNA was prepared from cells by using RNA Stat60 according to the manufacturer’s protocol (Tel-Test Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice expressing Cas9 were injected with 10^12 vg/mL AAV8-UCP1 sgRNA or AAV8-Control sgRNA directly into BAT. Mice were kept at 22ºC for 14-days and were sacrificed and mRNA isolated from BAT and used for RNAseq.

value: Interscapular brown adipose tissue


title: 32B

tag: generation

tag: Sex


title: ctrl.ko_rep1

value: Siah knockout

value: Normoxia


title: stim.ko_rep1


title: ctrl.wt_rep2


title: Neonatal Blood Spot, 202128330059_R02C01

tag: race

tag: gestational age


title: Pooled sera_51039

tag: growth media

tag: growth time

tag: strain


title: AAV8-UCP1 sgRNA rep2


title: WT phe repl 2

value: wild type


title: paht mutant phe repl 3


title: AAV8-UCP1 sgRNA rep3


title: Pooled sera_51038

tag: growth phase

tag: od600 reading

tag: temperature


title: Neonatal Blood Spot, 202128330059_R03C01


title: 29B

value: M


title: 28B

value: whole brain


title: Pooled sera_51037

tag: bpa identifier


title: AAV8-Control sgRNA rep5


title: paht mutant gluc repl 2

tag: carbon source

value: carbon source glucose

tag: genotype


title: 26B

value: adult

value: AB line


title: Neonatal Blood Spot, 202128330058_R01C01


title: AAV8-UCP1 sgRNA rep1

tag: cell type


title: AAV8-Control sgRNA rep4


title: Neonatal Blood Spot, 202128330059_R04C01


title: paht mutant gluc repl 3


title: Neonatal Blood Spot, 202128330058_R08C01


title: WT phe repl 1


title: paht mutant gluc repl 1


title: Neonatal Blood Spot, 202128330059_R05C01


title: 25B

tag: tissue


title: RPMI_50858

value: RPMI

value: 1 hr

value: Mid log phase

tag: serovar


title: Neonatal Blood Spot, 202128330058_R07C01

tag: sex (male= 1, female=2)


title: AAV8-Control sgRNA rep2


title: Neonatal Blood Spot, 202128330058_R06C01


title: WT glucose repl 3


title: RPMI_50857


title: WT glucose repl 2


title: RPMI_51034


title: Neonatal Blood Spot, 202128330060_R02C01


title: AAV8-Control sgRNA rep1


title: 24B

tag: age

tag: generation

value: F


title: AAV8-Control sgRNA rep3


title: RPMI_51035


title: WT glucose repl 1


title: RPMI_51036


title: Neonatal Blood Spot, 202128330058_R04C01

tag: race


title: 21B

tag: Sex


title: P4_ChIP_H3K4me1_Ctrl_2

status: Public on Jun 30 2021

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

institute: Washington University In St. Louis

data_processing:
ChIP-seq reads were aligned to the mm10 and hg38 genome assemblies using Bowtie2
Data were filtered using a map quality score of >10
Peaks were called using MACS2 on each dataset. Bandwidth = 200; q-value 0.05
RNA-seq reads were aligned to mm10 genome assembly using RNA STAR 2.6
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Text or excel workbooks containing raw read counts or CPM, histone enrichment, or fold change

source_name: Anterior Mouse Cerebellum

growth_protocol: Brain tissue was taken from CHD7 conditional knockout and control mice maintained under standard housing conditions.

extract_protocol:
RNA was extracted from the anterior cerebella of P4 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. ChIP lysates clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: CHD7 Ctrl

tag: sample type

value: Pooled

tag: chip antibody

value: H3K4me1 (Active Motif, #39297)


title: WTM_rep1

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

description: RNA-Seq

data_processing:
A total of 42 to 57 million sequence reads were generated from each sample on the Illumina HiSeq platform.
RNA-Seq data quality control, alignment, quantification, and statistics calculations were done using the "simple" workflow of Bacpipe RNA-seq processing pipeline v0.8a (https://github.com/apredeus/multi-bacpipe).
RNA-seq samples were aligned to the genome sequence using STAR v2.6.0c using “--alignIntronMin 20 --alignIntronMax 19 --outFilterMultimapNmax 20” options.
Read counting was done by featureCounts v1.6.4, using options “-O -M --fraction -t gene -g ID -s 1”.
TPMs were calculated using raw read counts obtained in featureCounts, with effective gene length equal to gene length in annotation.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000188735.1/
Supplementary_files_format_and_content: Tab-separated matrices of raw read counts and TPM normalized extpression values

organism: Salmonella enterica

source_name: intracellular bacteria from HeLa cells

growth_protocol: HeLa human cervical adenocarcinoma epithelial cells were purchased from American Type Culture Collection (ATCC, CCL-2) and used within 15 passages of receipt. Cells were maintained at 37°C and 5% CO2 in the growth medium (GM) recommended by ATCC i.e. Eagle’s minimum essential medium (EMEM, Corning) containing sodium pyruvate, L-glutamine and 10% (v/v) heat-inactivated fetal calf serum (FCS; Gemini Bio Products). Tissue culture plasticware was purchased from Thermo Scientific Nunc.

extract_protocol:
S. Typhimurium was enriched from infected HeLa cells (12 x 15 cm dishes for EBSS treatment, 6 x 15 cm dishes for WTM treatment) as described previously by Hautefort et al. (2008) with minor modifications. Briefly, infected HeLa cells were washed once with 30 ml chilled phosphate-buffered saline (PBS), then lysed on ice for 10-20 min in 0.1% SDS, 1% acidic phenol, 19% ethanol in water (15 ml per 15 cm dish). Pooled lysates were collected into 50 ml conical tubes and centrifuged at 3,220 xg for 30 min, 4°C. After three washes in ice-cold wash buffer (0.1% phenol, 19% ethanol in water) (30 min, 3,220 xg, 4°C each wash), the remaining bacterial pellet was resuspended in <1 ml of wash buffer, transferred to an RNase-free microcentrifuge tube and centrifuged at 16,000 xg for 2 min. The supernatant was discarded, and the pellet resuspended in 1 ml TRIzol® reagent (Life Technologies) by gently pipetting up-and-down (∼60 times), then transferred to −80°C for storage. Total RNA was extracted as described [32] and the RNA concentration quantified using a Nanodrop 2000 spectrophotometer (Thermo Scientific). RNA quality was analyzed using an Agilent Bioanalyzer 2100. RNA samples isolated from two independent experiments were sent to Vertis Biotechnologie AG (https://www.vertis-biotech.com) for RNA sequencing.
The RNA samples were fragmented with ultrasound (4 pulses of 30 sec at 4°C) followed by a  treatment with antarctic phosphatase and re-phosphorylated with polynucleotide kinase (PNK).  Afterwards, the RNA fragments were poly(A)-tailed using poly(A) polymerase and a RNA adapter was  ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-  adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 20-  30 ng/μl using a high fidelity DNA polymerase (cycle numbers and barcode sequences which are part  of the 3' TruSeq sequencing adaptor are indicated in the pool descriptions below). The cDNA was  purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary  electrophoresis. The cDNA pool was size selected and sequenced on Illumina HiSeq 2000 system using 50 bp read length.

treatment_protocol: HeLa cells were seeded 24 h prior to infection at 2.6×10e6 cells/15 cm tissue culture dish. T3SS1-induced bacterial subcultures were prepared in LB-Miller broth (Difco) and cells were infected for 10 min with bacterial subcultures (MOI ∼50). To induce autophagy, HeLa cells were shifted to Earle’s Balanced Salt Solution (EBSS, Sigma) 3 h prior to infection and maintained in EBSS until 90 min post-infection. Thereafter, infected cells were switched back to regular growth medium. To inhibit autophagy, cells were incubated in growth media containing 100 nM wortmannin (WTM, Calbiochem) for 45 min prior to infection, continuing to 90 min post-infection, whereupon cells were transferred back to regular growth media.

tag: strain

value: wildtype

tag: agent

value: wortmannin


title: 22B


title: EBSS_rep2

description: RNA-Seq

value: Earle's Balanced Salt Solution


title: Neonatal Blood Spot, 202128330058_R05C01

value: African American

tag: gestational age


title: Neonatal Blood Spot, 202128330058_R03C01


title: WTM_rep2

description: RNA-Seq


title: P4_ChIP_H3K4me1_cKO_3

value: CHD7 cKO


title: RPMI_51033

tag: growth media

tag: growth time

tag: growth phase

tag: od600 reading

tag: temperature


title: Neonatal Blood Spot, 202128330059_R01C01


title: EBSS_rep1

description: RNA-Seq

tag: genotype


title: D4M3A_pOVA_2_2

city: Boston

first: Thorsten

last: Mempel

state: Massachusetts

address: Charlestown Navy Yard Building 149

department: Center for Immunology and Inflammatory Diseases

institute: Massachusetts General Hospital

data_processing:
Software call to obtain FASTQ files: bcl2fastq --use-bases-mask y*,y*,y*,y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0
Reads were processed using the inDrop v3 pipeline implemented in bcbio-nextgen version 1.2.4-76d5c4b (https://github.com/bcbio/bcbio-nextgen). Briefly, dual cell barcodes, sample barcodes and UMIs were detected using umis (Svensson et al., 2017, Nature Methods; correcting cellular and sample barcodes of edit distance 1 from expected cell barcodes). Cell barcodes with fewer than 500 total reads assigned to them were discarded. Reads were assigned to Mus Musculus transcripts (GRCm38 (mm10) release M23) using Rapmap (Srivastava et al., 2016; Bioinformatics) and counts of reads per transcript per unique UMI were generated for each cell.
Cell barcodes with more than or equal to 350 total counts, less than or equal to 6000 total counts (to filter out doublets), less than 10% of total counts derived from mitochondrial genes, and ratio of number of genes detected to total counts (i.e., the relative number of genes detected) at least higher than 0.8 were retained. Cell counts were normalized with the SCTransform function from the Seurat package (Hafemeister and Satija, 2019).
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files for each library consist of (as the bcbio-nextgen pipeline outputs the .mtx files; see data processing):  - a .mtx file that contains raw gene counts.  - a colnames.mtx file that contains the cell barcodes.  - a rownames.mtx file that contains the gene names.  In addition, the supplementary files for all libraries together consist of:   - a counts_normalized_8757x20679.mtx file that contains filtered and normalized gene counts (see data processing).    - a corresponding cell_metadata_8757x12.tsv that contains the cell barcodes and per-cell barcode meta data.  - a corresponding gene_names_20679.tsv file that contains the gene names.

molecule: polyA RNA

growth_protocol: Mice were maintained in specific pathogen-free facilities at the Massachusetts General Hospital (MGH) and all studies were approved and performed in accordance with guidelines and regulations implemented by the MGH Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
D4M.3A-pOVA injected-mice were sacrificed at day 17 after tumor implantation, tumors were minced into small fragments, which were treated with 1.5 mg/ml collagenase IV and 50 U/ml DNAse I for 30 minutes at 37 °C under agitation. Single cell suspensions were stained with fixable viability violet dye Zombie Red and a-CD45 mAbs (30-F11) (BioLegend) and live CD45+ and CD45– cells were then sorted at a 9:1 ratio (BD FACSAria Fusion Cell Sorter).
Single cell barcoding and library preparation were performed using the inDrops protocol as described in (Zilionis et 2017, Nature Protocols). inDrops Libraries were sequenced on the NextSeq Illumina platform, paired-end mode.

treatment_protocol: The BRAFV600E x PTENnull melanoma D4M.3A-H2B-SIINFEKL-Cerulean cell line (D4M.3A-pOVA; Di Pilato et al., 2019, Nature) was grown in DMEM with 10% FCS and used for experiments when in exponential growth phase. 10^6 tumor cells were s.c. injected in 100 μl PBS into the flanks of 6-8 weeks-old male mice. Tumor volumes were measured on and then every second to third day following the start of treatments and calculated as V = (length x width^2)/2.

tag: gender

value: Male

tag: tumor cell line injected

value: BRAFV600E x PTENnull D4M.3A-H2B-Cerulean-SIINFEKL

tag: age at injection of tumor cell line (weeks)

tag: age at sacrifice (weeks)

tag: purification

value: CD45+ and CD45- cells at a 9:1 ratio


title: P4_ChIP_H3K4me1_Ctrl_3


title: D4M3A_pOVA_1_1


title: D4M3A_pOVA_2_4


title: D4M3A_pOVA_2_3


title: WT phe repl 3

tag: carbon source

value: carbon source phenanthrene

value: wild type


title: D4M3A_pOVA_1_3


title: D4M3A_pOVA_1_2


title: CO2E_4

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

data_processing:
The preprocessing step was carried out with Trimmomatic v0.36 to remove adapters and filter raw reads by quality.
The filtered quality reads were aligned to the most recent version (v3) of the Sorghum bicolor genome downloaded from the Phytozome database using the Hisat2 software with its default parameter values.
The aligned read counts, the fragments per kilobase of transcript per million mapped reads (FPKM) normalization values, and the differential expression analysis were carried out using the Cuffdiff package from Cufflinks v2.2.1 and its default parameter values. Genes with FDR value < 0.05 were considered differentially expressed genes (DEGs).
Genome_build: Sorghum bicolor ver. 3 from Phytozome
Supplementary_files_format_and_content: File in xlsx format

organism: Sorghum bicolor

source_name: Sorghum bicolor plants under elevate concentration of CO2 and water deficit

growth_protocol: Sorghum bicolor BRS330 was cultivated in soil, as described by De Souza et al. (2015). Plants received 1.5 L of water per day during the vegetative stage (0 - 60 days after planting, DAP).

extract_protocol:
Total RNA extraction was performed with 100 mg of grounded GPR tissue using the ReliaPrep RNA Tissue to fibrous tissues (Promega).
Libraries were constructed according to the manufacturer’s protocol of the Truseq Stranded mRNA Sample Prep LS Kit (Illumina).

treatment_protocol: 60 DAP plants were submited to water deficit treatment based on reducing the irrigation to 0.45 L of water per day (70% of field capacity reduction). Control-plants were grown in ambient [CO2] (A[CO2], 400 µmol mol-1), and treated-plants in elevated [CO2] (E[CO2], 800 µmol mol-1), both submitted to chronic water-deficit (WD) for 30 days.

tag: cultivar

value: cv. BRS330

tag: tissue

value: prop roots tissue

tag: treatment

value: E[CO2] + water deficit


title: P4_ChIP_H3K4me1_cKO_2

tag: sample type

tag: strain

tag: chip antibody


title: D4M3A_pOVA_2_1


title: D4M3A_pOVA_1_4


title: CO2E_2


title: CO2A_4

source_name: Sorghum bicolor plants under normal concentration of CO2 and water deficit

value: A[CO2] + water deficit


title: CO2E_3


title: Neonatal Blood Spot, 202128330058_R02C01

tag: sex (male= 1, female=2)

tag: race

tag: gestational age


title: CO2A_3


title: CO2A_2


title: CA2 subfield rep4

city: Campinas

first: Andre

last: Schwambach Vieira

state: SP

address: Rua Monteiro Lobato, 255 - Bloco J - 1 piso - Sala 3

institute: State University of Campinas

data_processing:
Illumina Casava1.7 software used for basecalling.
All sequenced reads were aligned with the StarAligner 2.6 program (https://github.com/alexdobin/STAR, RRID:SCR_004463) with the Rattus norvegicus genome 3.1 (Rnor6 Ensembl release 6.0 - https://www.ensembl.org/Rattus_norvegicus/Info/Index).
Subsequently, DESeq2 package version 3.12(http://bioconductor.org/packages/release/bioc/html/DESeq2.html, RRID:SCR_015687) was used to calculate all differentially expressed genes(DEGs) between subfields and carry statistical analysis.
Genome_build: rnor6
Supplementary_files_format_and_content: comma-delimited text files include counts values for each pairwise comparison
Supplementary_files_format_and_content: countData.csv: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Hipocampal subfield

extract_protocol:
RNA from tissue was harvested using Trizol reagent. IlluminaTruSeq Stranded Total RNA LT was used with 200 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard IlluminaTruSeq Stranded Total RNA LT protocols

value: Wistar

value: brain

tag: age

value: three-month-old animals


title: CO2E_1


title: CA3 subfield rep4


title: CO2A_1


title: CA3 subfield rep3


title: CA1 subfield rep4


title: CA2 subfield rep3


title: CA1 subfield rep3


title: DG subfield rep3


title: CA3 subfield rep2


title: CA2 subfield rep2


title: CA1 subfield rep2


title: DG subfield rep2


title: CA2 subfield rep1


title: CA3 subfield rep1


title: DG subfield rep1


title: E13_5WtB12C11_R1_reads

city: Barcelona

first: Loris

last: Mularoni

address: Gran Via de l’Hospitalet, 199

department: P-CMR[C]

country: Spain

institute: IDIBELL

data_processing:
Reads were aligned to NCBI36/mm9 genome using Bowtie2 (v2.2.5) allowing for one mismatch
The bam files were filtered to retainreads with a minimum mapping quality of 10 (MAPQ>=10) using samtools.
The resulting bam files from biological replicates were pooled using samtools and peaks were called using MACS2 (v2.1.0) using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: mouse pancreas_E13.5

extract_protocol:
sonicated chromatin was IP with anti-REST antibody
Libraries were prepared according to Illumina's instructions.

tag: strain background

value: mixed strain with C57BL/6

value: embryonic pancraes E13.5

value: mouse monoclonal anti-REST 12C11 (Dr. David J. Anderson, California Institute of Technology, Pasadena)

value: untreated


title: E18_5WtA12C11_R1_reads

source_name: mouse pancreas_E18.5

value: embryonic pancraes E18.5


title: REST KO E18 sample 1 [RNA-seq]

data_processing:
Reads were aligned to the NCBI36/mm9 genome using star (v2.3.0)with default parameters, allowing only uniquely mapped reads
The resulting bam files were used to quantify gene expression using FeatureCounts (v1.5) using UCSC mm9 reference gene annotations
Differential expression analysis was performed using DESeq2 (Love, Huber and Anders, 2014)
Genome_build: mm9
Supplementary_files_format_and_content: E18KoVsE18Wt.counts.txt

source_name: REST KO E18

extract_protocol:
qiagen RNAeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Pdx1Cre RESTLoxP/LoxP

value: embryonic pancraes


title: E18_5WtB12C11_R1_reads


title: DG subfield rep4


title: WT E18 sample 2 [RNA-seq]

source_name: WT E18

value: Pdx1Cre RESTwt


title: WT E18 sample 1 [RNA-seq]


title: E18_5WtC12C11_R1_reads


title: E13_5WtA12C11_R1_reads


title: REST KO E18 sample 2 [RNA-seq]


title: TPR1-GFPeds1_aGFP_r3 (ChIP-Seq)

city: Cologne

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

institute: Max-Planck Institute for Plant Breeding Research

description:
TPR1-GFP ChIP
1673_D_run263_ACAAACAT_L006

data_processing:
Before mapping, remaining LinDA adapters and low quality sequences were removed from the sequencing data using a two-step procedure. Here, first Bpm and t7-Bpm sites were trimmed from the 5′ end using cutadapt (version 1.2.1) with options–e 0.2, -n 2 and–m 36 (otherwise default settings were used), and subsequently poly-A and poly-T tails and low quality ends were trimmed and reads with overall low quality or with less than 36 bases remaining after trimming were removed using PRINSEQ lite (version 0.20.2) (Schmieder and Edwards, 2011) with options–trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25. After the preprocessing steps, remaining high quality reads were mapped to the A. thaliana reference genome TAIR10 (http://www.arabidopsis.org) using Bowtie (version 2.0.5; default settings) (Langmead and Salzberg, 2012). For subsequent removal of non-uniquely mapping reads, the alignment output was filtered for mapping quality using samtools (version 0.1.18) (Li et al., 2009) view with option -q 10.
To identify genomic DNA regions (‘peak regions’) enriched in sequencing reads in the ChIP sample compared to the input control and TPR1-HA negative control, the peak calling algorithm of the QuEST program (version 2.4) (Valouev et al., 2008) was applied using the TF mode (option ‘2’), with permissive parameter settings for peak calling (option ‘3’). Each of three biological replicates was first analyzed separately. To obtain more exact peak locations for consistent peaks, mapped reads of the three replicates were additionally pooled and peaks called for the pooled samples. Further analyses were performed on peak regions identified from the pooled samples . To annotate peak locations with respect to annotated gene features in TAIR10 the annotatePeaks.pl function from the Homer suite (Heinz et al., 2010) was used with default settings.
Bed files for gene regions were prepared based on TAIR10 annotation (TAIR10_GFF3_genes_transposons, 11-07-2019). Raw sequence reads were trimmed with cutadapt (version 1.9.1, -e 0.2 -n 2 -m 30) to remove overrepresented sequences detected with fastqc (version 0.11.9) (Andrews et al., 2010) and then mapped to TAIR10 using bowtie2 (version 2.2.8). The resulting BAM files from individual biological replicates were deduplicated, filtered for low-quality mapping (-q 10 in view function in samtools version 1.9) and finally merged with samtools v1.9 (Li et al., 2009; Li, 2011). BAM/BAI files of the pooled samples are provided here.
The bigwig file provided for visualization in IGV (Thorvaldsdóttir et al., 2013) was prepared with bamCompare (--operation subtract --binSize 1) using merged BAM files for input and TPR1-GFP samples.
Genome_build: A. thaliana reference genome TAIR10
Supplementary_files_format_and_content: The bigwig file provided for visualization in IGV (Thorvaldsdóttir et al., 2013) was prepared with bamCompare (--operation subtract --binSize 1) using merged BAM files for input and TPR1-GFP samples.

organism: Arabidopsis thaliana

source_name: 6-week old leaves

growth_protocol: Plants were grown on soil with a daily 10 h light period (150-200 μE/m2s) at 22 °C and 60 % relative humidity. Plant leaf material was harvested after 6 weeks of growth.

extract_protocol:
ChIP was performed on 2 g leaf tissues of 6-week-old plants according to Gendrel et al. (2005) with modifications (Birkenbihl et al., 2012). Leaf samples were cross-linked twice by infiltration with 1% formaldehyde under a vacuum for 2x 7.5 minutes. Nuclei were disrupted by sonication 10 times for 30 s each and 30 s of cooling in a Bioruptor (Diagenode). IPs were performed using α-GFP (Ab6556, Abcam) antibodies and Protein A agarose beads (Sigma). After elution of immune complexes, cross-linking was reversed with an overnight incubation at 65°C in 200 mM NaCl followed by proteinase K digestion. DNA was extracted with phenol-chloroform and precipitated with ethanol in the presence of 0.3 M sodium acetate (pH=5.2) and 10 μg/mL glycogen (overnight at -20°C). After centrifugation, DNA pellets were washed with 70% ethanol, air-dried and resuspended in water before PCR.
MiniElute PCR Purification Kit (Qiagen, Germany) was used for cleaning ChIP DNA and two rounds of in vitro transcription by T7 RNA polymerase followed according to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al., 2011). Sequencing libraries were barcoded and generated using Ovation® Ultralow DR Multiplex system (NuGEN Technologies Inc.) including a 16-cycles PCR amplification. Libraries were size-selected (200-350 bp) with an agarose gel extraction using the MinElute Gel Extraction Kit (Qiagen, Germany).

treatment_protocol: untreated

value: pTPR1:TPR1-GFP eds1-2

tag: chip/antibody

value: anti-GFP

value: 6-week old leaves


title: 30B

value: whole brain

value: adult

value: AB line

tag: generation

tag: Sex

value: M


title: TPR1-GFPeds1_aGFP_r2 (ChIP-Seq)

description:
TPR1-GFP ChIP
1580_E_run242_L007


title: TPR1-GFPeds1_aGFP_r1 (ChIP-Seq)

description:
TPR1-GFP ChIP
1143_C_run160_AAGACGAT_L002


title: Chd7WT3_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx

value: CHD7 Ctrl

value: Pooled


title: CA1 subfield rep1

value: Wistar

value: brain

value: three-month-old animals


title: Chd7WT3_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx

value: CHD7 cKO


title: Chd7WT1_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT3_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT2_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7WT1_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO3_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191024_set7

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191021_set5

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO2_191022_set6

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: n2_dxbp_sz355_rs024

city: Santa Cruz

first: Alan

middle: M

last: Zahler

state: CA

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

data_processing:
The sequencing center delivered variable length reads. The maximum read length was 75bp (for both read1 and read2), with most (over 98%) reads longer than 70bp.
All reads were trimmed at the 3' end to 70bp using cutadapt. Read-pairs were discarded if either read1 or read2 was shorter than 70bp.
Trimmed reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining trimmed reads were mapped to the indicated genome assembly using a modified version of STAR.
The STAR source code was modified to replace its search for canonical intron motif ATAC (not found in C. elegans) with a search for TTAG (expected to be present in the mutant samples).
The STAR parameters were set to use equal scoring for the canonical intron motif GTAG and the mutant motif TTAG.
Potential PCR duplicates were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events of types A5,A3 were identified from the splice junctions found in all sequencing libraries.
A5 events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3 events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
Alternative splicing events of types SE, RI, MS, MX, AF, AL were extracted from the ce10 EnsemblArchive65 transcript annotation using junctionCounts:infer_pairwise_events (github ajw2329/junctionCounts)
The program junctionCounts (github ajw2329/junctionCounts) was used to determine PSI (percent spliced in) for all events in all samples.
The junctionCounts PSI estimates for a sample were merged into a gtf with the scores for the 2 alternative transcripts of an event representing (1000 times) its PSI (and 1-PSI) values. If junctionCounts reported a non-zero span of the PSI estimate, these scores were reduced by a factor of (1-spanPSI).
Genome_build: Oct. 2010 (WS220/ce10)
Supplementary_files_format_and_content: The ensArch65 gtf file for a sample contains the 2 alternative transcripts for each event of type SE, RI, MS, MX, AF, AL derived from the ce10 EnsembleArchive65 annotation. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. This score is modified by a factor of (1-spanPSI) if there is a non-zero span in the estimate of PSI.
Supplementary_files_format_and_content: The libIntrons gtf file for a sample contains the 2 alternative transcripts for each event of type A3, A5 derived from the introns found in all sample sequencing libraries. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. For these event types the span in the estimate of PSI is always zero.

organism: Caenorhabditis elegans

growth_protocol: Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli

extract_protocol:
Worms were lysed in Trizol and total RNA recovered according to manufacturers protocol.
mRNA libraries for high throughput sequencing were prepared from polyA selected mRNAs using the NuGen Universal mRNA kit. Paired directional 75nt reads, 9 libraries per lane, were obtained from an Illumina NovaSeq 6000 operated by RealSeq Biosciences of Santa Cruz, CA.

treatment_protocol: Mixed-stage worms were harvested from the plates by washing them off with M9 media

value: whole worm - mixed stage


title: Chd7KO1_191016_set2

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: n2_dxbp_sz345_rs006


title: n2_prcc_sz346_rs007


title: n2_dxbp_sz355_rs026


title: Chd7KO1_191017_set3

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: n2_prcc_sz346_rs009


title: n2_dxbp_sz345_rs005


title: Chd7KO2_191020_set4

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: Chd7KO1_191024_set8

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx


title: n2_prcc_sz356_rs027


title: n2_prcc_sz356_rs029


title: n2_dxbp_sz345_rs004


title: n2_ctrl_sz340_rs003


title: n2_prcc_sz346_rs008


title: n2_dxbp_sz355_rs025


title: n2_ctrl_sz340_rs002


title: Sham_spleen_17

city: Iowa City

first: Peter

middle: S

last: Thorne

state: IA

address: 51 Newton Rd

department: Occupational and Environmental Health

institute: University of Iowa

data_processing:
Raw sequencing reads were aligned to Ratus norvegicus genome rn6 using STAR version 2.2.1. On average, 74.2% of reads mapped uniquely, 9.0% mapped to multiple loci, and 16.2% were too short to map.
Sequenced reads were trimmed for adaptor sequence. Reads were quantified at the gene level against known transcripts from Ensembl release 89, requiring correct strand orientation.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Total RNA in brain, liver, spleen and thymus was isolated using RNeasy Mini Kit (QIAGEN, Hilden, Germany) . Illumina TruSeq stranded mRNA sample preparation kit (Illumina Inc., San Diego, CA) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: Spleen

value: 7 months

value: Sham


title: Sham_spleen_14


title: Sham_spleen_15


title: SAM_spleen_5

value: SAM-exposed


title: SAM_spleen_1


title: SAM_spleen_3


title: n2_prcc_sz356_rs028


title: n2_ctrl_sz340_rs001


title: Sham_thymus_17

source_name: Thymus

value: Thymus


title: Sham_thymus_14


title: Sham_brain_15

source_name: Brain

value: Brain


title: Sham_brain_16


title: SAM_thymus_1


title: Sham_liver_14

source_name: Liver

value: Liver


title: Sham_brain_13


title: Sham_liver_15


title: SAM_brain_3


title: SAM_brain_2


title: P21_LQ

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: 10x 3' v3 scRNA-seq

data_processing:
Read alignment and gene-expression quantification of mouse single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 3.0.2 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built mouse (mm10) reference package was used.
Genome_build: mm10
Supplementary_files_format_and_content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

source_name: LQ mutation postnatal day 21 lungs

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols

extract_protocol:
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol

treatment_protocol: Postnatal day 4 and 21 lungs were inflated with 1 ml dispase, resected and incubated in dispase for 6 minutes at 37°C. Lung lobes were separated and placed in C-tubes containing 5 ml RPMI (Gibco 11875-093) supplemented with10% FBS (Sigma F4135), 1M HEPES and 1% Penicillin/Streptomycin. Single cell suspensions were prepared using the gentleMACS dissociator with 120 U/ml DNaseI and filtered through a 40 mm strainer, washed with media and incubated in RBC lysis buffer (BioLegend 420301) for 4 minutes at 4°C. Suspensions were washed with media, cell counts were performed and cells were resuspended in RPMI at a final concentration of 100 cells/ml.

tag: developmental stage

value: postnatal day 21 lungs

value: lung

value: surfactant protein C (SP-C) mutation (L184Q)


title: SAM_liver_3


title: Sham_thymus_15


title: P21_WT

description: 10x 3' v3 scRNA-seq

source_name: Wild Type postnatal day 21 lungs

value: Wild Type


title: SAM_brain_1


title: SAM_liver_2


title: Sham_liver_13


title: P4_WT

description: 10x 3' v3 scRNA-seq

source_name: Wild Type postnatal day 4 lungs

value: postnatal day 4 lungs


title: Chd7WT1_191015_set1

description:
MyONE Streptavidin T1
Hi-C_Summary.xlsx

source_name: Anterior Mouse Cerebellum

value: CHD7 Ctrl

value: Pooled


title: P4_LQ

description: 10x 3' v2 scRNA-seq

source_name: LQ mutation postnatal day 4 lungs


title: 567_TRIM24 COE

status: Public on Jun 29 2021

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
567

data_processing:
Sequences were checked for qulaity of reads using FastQC.
Sequences were aligned to genome assembly mm10 for ucsc using tophat.
Sequences were annotated using ucsc genome annotation and cufflinks.
Annotated gtf files were processed and also converted to transcripts per million using RSEM.
Raw reads were used for post-analysis using R packages DESeq and EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with transcripts per million

source_name: mammary tumor

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from three individual tumors along with five freshly isolated, disease free mammary glands (controls) using size-selection, glass fiber filter-based mirVana RNA isolation kits (Ambion, REF#AM1560, Lot#00310947). Sequencing was performed by the M.D. Anderson Next Generation Sequencing Core Facility. The sequencing data were analyzed using DESeq and edgeR to determine differentially expressed genes (DEGs). The edgeR is also used to perform GSEA and pathway analysis upon TRIM24 over-expression
TruSeq Stranded Total RNA

value: FVB

value: TRIM24 overexpression

tag: subtype

value: Carcinosarcoma

tag: sequencing batch


title: 3956_TRIM24 COE

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
3956

value: Carcinoma


title: 897_TRIM24 COE

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
897


title: SAM_thymus_3

value: Sprague-Dawley

tag: tissue

value: 7 months


title: 517_3_Cre_control

description:
This is a control sample obtained from mammary gland of a Cre only mouse.
shah.txt
517_3

source_name: Mammary gland

value: Cre control

value: normal mammary gland


title: 417_3_Cre_control

description:
This is a control sample obtained from mammary gland of a Cre only mouse.
shah.txt
417_3


title: SAM_liver_1

tag: treatment

value: SAM-exposed


title: SAM_thymus_5

value: Thymus


title: 64_TRIM24 COE

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
64


title: 133_Cre_control

description:
This is a control sample obtained from mammary gland of a Cre only mouse.
shah.txt
133


title: FVB002_Non-TRIM24

description:
This is a tumor sample obtained from a non-TRIM24-expressing mammary gland.
shah2.txt
FVB002

value: unknown (spontaneously arising tumor)


title: control_S_W8S Normalization control - complete sagittal suture at E18.5, replicate 1

status: Public on Jun 26 2021

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and then mapped to mm10 whole genome using STAR_2.5.3a with parameters --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outSAMstrandField intronMotif --runThreadN 12 --twopassMode Basic --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverReadLmax 0.04 --outStd SAM --outSAMmode Full --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within –quantMode TranscriptomeSAM GeneCounts --outWigType bedGraph --outWigNorm RPM --outWigStrand Unstranded --outFileNamePrefix  Raw counts per gene model (GENCODE M22) were extracted with featureCounts v1.6.4
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited featurecounts output file with the following columns: GENCODE M22 gene ID, Chr, Start, End, Strand, Length, total_read_count

source_name: complete suture of the sagittal suture at E18.5

extract_protocol:
Laser-capture microdissection, followed by RNA extraction using the Arcturus Picopure RNA Isolation Kit with on-column DNase digestion as described by the manufacturer
Following RNA extraction, cDNA synthesis was performed using Ovation RNA-Seq System V2 amplification. Libraries were then prepared using the Nextera XT tagmentation protocol.

tag: suture

value: sagittal

tag: region

value: complete suture

tag: litter id


title: 219_Non-TRIM24

description:
This is a tumor sample obtained from a non-TRIM24-expressing mammary gland.
shah2.txt
219

tag: strain


title: 3956_T_TRIM24 COE

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland. This is a re-sequenced technical replicate of 3956_TRIM24 COE (GSM5404070). Because we had sequenced the samples in two batches, we repeated this sample to monitor for batch effects.
shah2.txt
3956_T


title: control_S_W8F Normalization control - complete frontal suture at E18.5, replicate 1

source_name: complete suture of the frontal suture at E18.5

value: frontal


title: 392_Cre_control

description:
This is a control sample obtained from mammary gland of a Cre only mouse.
shah.txt
392


title: FVB001_Non-TRIM24

description:
This is a tumor sample obtained from a non-TRIM24-expressing mammary gland.
shah2.txt
FVB001


title: control_L_W8C Normalization control - complete coronal suture at E18.5, replicate 1

source_name: complete suture of the coronal suture at E18.5

value: coronal


title: control_L_W8F Normalization control - complete frontal suture at E18.5, replicate 1


title: control_L_W8L Normalization control - complete lambdoid suture at E18.5, replicate 1

source_name: complete suture of the lambdoid suture at E18.5

value: lambdoid


title: control_S_W8C Normalization control - complete coronal suture at E18.5, replicate 1


title: control_IF_W8S_C Normalization control - complete sagittal suture at E18.5, replicate 1


title: control_S_W8L Normalization control - complete lambdoid suture at E18.5, replicate 1


title: cre133_MG_Cre_control

description:
This is a control sample obtained from mammary gland of a Cre only mouse.  This is a re-sequenced technical replicate of 133_Cre_control (GSM5404063). Because we had sequenced the samples in two batches, we repeated this sample to monitor for batch effects.
shah2.txt
cre133_MG


title: control_IF_W8C_C Normalization control - complete coronal suture at E18.5, replicate 1


title: control_L_W8S Normalization control - complete sagittal suture at E18.5, replicate 1


title: control_C_W8L_C Normalization control - complete lambdoid suture at E18.5, replicate 1


title: W8S5SM suture mesenchyme of the sagittal suture at E18.5, replicate 5

value: suture mesenchyme


title: control_C_W8S_C Normalization control - complete sagittal suture at E18.5, replicate 1


title: W8S4SM suture mesenchyme of the sagittal suture at E18.5, replicate 4


title: control_C_W8F_C Normalization control - complete frontal suture at E18.5, replicate 1


title: W8S5PA parietal osteogenic front of the sagittal suture at E18.5, replicate 5

value: parietal osteogenic front


title: control_C_W8C_C Normalization control - complete coronal suture at E18.5, replicate 1


title: control_IF_W8F_C Normalization control - complete frontal suture at E18.5, replicate 1


title: W8S4PA parietal osteogenic front of the sagittal suture at E18.5, replicate 4


title: 273_5_TRIM24 COE

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
273_5

value: FVB

value: TRIM24 overexpression


title: W8S3PA parietal osteogenic front of the sagittal suture at E18.5, replicate 3


title: W8S2PA parietal osteogenic front of the sagittal suture at E18.5, replicate 2


title: W8S3SM suture mesenchyme of the sagittal suture at E18.5, replicate 3


title: control_IF_W8L_C Normalization control - complete lambdoid suture at E18.5, replicate 1


title: W8S2SM suture mesenchyme of the sagittal suture at E18.5, replicate 2


title: W8S1PA parietal osteogenic front of the sagittal suture at E18.5, replicate 1


title: W6S5PA parietal osteogenic front of the sagittal suture at E16.5, replicate 5


title: W6S5SM suture mesenchyme of the sagittal suture at E16.5, replicate 5


title: W6S3SM suture mesenchyme of the sagittal suture at E16.5, replicate 3


title: W6S3PA parietal osteogenic front of the sagittal suture at E16.5, replicate 3


title: W6S4SM suture mesenchyme of the sagittal suture at E16.5, replicate 4


title: W6S2SM suture mesenchyme of the sagittal suture at E16.5, replicate 2


title: W6S1PA parietal osteogenic front of the sagittal suture at E16.5, replicate 1


title: W6S1SM suture mesenchyme of the sagittal suture at E16.5, replicate 1


title: W8L5PA parietal osteogenic front of the lambdoid suture at E18.5, replicate 5


title: W8L5SM suture mesenchyme of the lambdoid suture at E18.5, replicate 5


title: W8L4IP interparietal osteogenic front of the lambdoid suture at E18.5, replicate 4

value: interparietal osteogenic front


title: W8L4SM suture mesenchyme of the lambdoid suture at E18.5, replicate 4


title: W8L2SM suture mesenchyme of the lambdoid suture at E18.5, replicate 2


title: W8L3PA parietal osteogenic front of the lambdoid suture at E18.5, replicate 3


title: W8L3SM suture mesenchyme of the lambdoid suture at E18.5, replicate 3


title: W8L5IP interparietal osteogenic front of the lambdoid suture at E18.5, replicate 5


title: W8L3IP interparietal osteogenic front of the lambdoid suture at E18.5, replicate 3


title: W8L2IP interparietal osteogenic front of the lambdoid suture at E18.5, replicate 2


title: W8L4PA parietal osteogenic front of the lambdoid suture at E18.5, replicate 4


title: W8S1SM suture mesenchyme of the sagittal suture at E18.5, replicate 1


title: W8L1PA parietal osteogenic front of the lambdoid suture at E18.5, replicate 1


title: W8L1SM suture mesenchyme of the lambdoid suture at E18.5, replicate 1


title: W8L2PA parietal osteogenic front of the lambdoid suture at E18.5, replicate 2


title: W6L5SM suture mesenchyme of the lambdoid suture at E16.5, replicate 5


title: W6S4PA parietal osteogenic front of the sagittal suture at E16.5, replicate 4


title: W8L1IP interparietal osteogenic front of the lambdoid suture at E18.5, replicate 1


title: W6L5PA parietal osteogenic front of the lambdoid suture at E16.5, replicate 5


title: W6S2PA parietal osteogenic front of the sagittal suture at E16.5, replicate 2


title: W6L4SM suture mesenchyme of the lambdoid suture at E16.5, replicate 4


title: W6L4PA parietal osteogenic front of the lambdoid suture at E16.5, replicate 4


title: W6L5IP interparietal osteogenic front of the lambdoid suture at E16.5, replicate 5


title: W6L3SM suture mesenchyme of the lambdoid suture at E16.5, replicate 3


title: W6L4IP interparietal osteogenic front of the lambdoid suture at E16.5, replicate 4


title: W6L3PA parietal osteogenic front of the lambdoid suture at E16.5, replicate 3


title: W6L3IP interparietal osteogenic front of the lambdoid suture at E16.5, replicate 3


title: W6L2SM suture mesenchyme of the lambdoid suture at E16.5, replicate 2


title: W6L2PA parietal osteogenic front of the lambdoid suture at E16.5, replicate 2


title: W6L1PA parietal osteogenic front of the lambdoid suture at E16.5, replicate 1


title: W6L2IP interparietal osteogenic front of the lambdoid suture at E16.5, replicate 2


title: W6L1SM suture mesenchyme of the lambdoid suture at E16.5, replicate 1


title: W6L1IP interparietal osteogenic front of the lambdoid suture at E16.5, replicate 1


title: W8C5FR_C frontal osteogenic front of the coronal suture at E18.5, replicate 5

value: frontal osteogenic front


title: W8C4SM_C suture mesenchyme of the coronal suture at E18.5, replicate 4


title: W8C4PA_C parietal osteogenic front of the coronal suture at E18.5, replicate 4


title: W8C1PA_C parietal osteogenic front of the coronal suture at E18.5, replicate 1


title: W6C3SM_C suture mesenchyme of the coronal suture at E16.5, replicate 3


title: W6C3PA_C parietal osteogenic front of the coronal suture at E16.5, replicate 3


title: W8C1SM_C suture mesenchyme of the coronal suture at E18.5, replicate 1


title: W6C1SM_C suture mesenchyme of the coronal suture at E16.5, replicate 1


title: W6C2PA_C parietal osteogenic front of the coronal suture at E16.5, replicate 2


title: W6C1PA_C parietal osteogenic front of the coronal suture at E16.5, replicate 1


title: W8C3FR_C frontal osteogenic front of the coronal suture at E18.5, replicate 3


title: W8C5SM suture mesenchyme of the coronal suture at E18.5, replicate 5


title: W8C1FR_C frontal osteogenic front of the coronal suture at E18.5, replicate 1


title: W8C5FR frontal osteogenic front of the coronal suture at E18.5, replicate 5


title: W8C4PA parietal osteogenic front of the coronal suture at E18.5, replicate 4


title: W6C2SM_C suture mesenchyme of the coronal suture at E16.5, replicate 2


title: W6C3FR_C frontal osteogenic front of the coronal suture at E16.5, replicate 3


title: W8C3SM_C suture mesenchyme of the coronal suture at E18.5, replicate 3


title: W8C3SM suture mesenchyme of the coronal suture at E18.5, replicate 3


title: W6C2FR_C frontal osteogenic front of the coronal suture at E16.5, replicate 2


title: W8C5PA parietal osteogenic front of the coronal suture at E18.5, replicate 5


title: W8C2PA parietal osteogenic front of the coronal suture at E18.5, replicate 2


title: W8C3FR frontal osteogenic front of the coronal suture at E18.5, replicate 3


title: W8C1PA parietal osteogenic front of the coronal suture at E18.5, replicate 1


title: W8C2FR frontal osteogenic front of the coronal suture at E18.5, replicate 2


title: W8C3PA parietal osteogenic front of the coronal suture at E18.5, replicate 3


title: W8C4SM suture mesenchyme of the coronal suture at E18.5, replicate 4


title: W8C3PA_C parietal osteogenic front of the coronal suture at E18.5, replicate 3


title: W6C1FR_C frontal osteogenic front of the coronal suture at E16.5, replicate 1


title: W6C5PA parietal osteogenic front of the coronal suture at E16.5, replicate 5


title: W8C4FR frontal osteogenic front of the coronal suture at E18.5, replicate 4


title: W6C3PA parietal osteogenic front of the coronal suture at E16.5, replicate 3


title: W6C2SM suture mesenchyme of the coronal suture at E16.5, replicate 2


title: W6C3FR frontal osteogenic front of the coronal suture at E16.5, replicate 3


title: W8C1FR frontal osteogenic front of the coronal suture at E18.5, replicate 1


title: W6C4PA parietal osteogenic front of the coronal suture at E16.5, replicate 4


title: W8C1SM suture mesenchyme of the coronal suture at E18.5, replicate 1


title: W6C2PA parietal osteogenic front of the coronal suture at E16.5, replicate 2


title: W6C3SM suture mesenchyme of the coronal suture at E16.5, replicate 3


title: W6C4SM suture mesenchyme of the coronal suture at E16.5, replicate 4


title: W6C4FR frontal osteogenic front of the coronal suture at E16.5, replicate 4


title: W6C1SM suture mesenchyme of the coronal suture at E16.5, replicate 1


title: W6C1PA parietal osteogenic front of the coronal suture at E16.5, replicate 1


title: W8IF4SM suture mesenchyme of the frontal suture at E18.5, replicate 4


title: W8C2SM suture mesenchyme of the coronal suture at E18.5, replicate 2


title: W6C5FR frontal osteogenic front of the coronal suture at E16.5, replicate 5


title: W8IF3FR frontal osteogenic front of the frontal suture at E18.5, replicate 3


title: W6C2FR frontal osteogenic front of the coronal suture at E16.5, replicate 2


title: W6C1FR frontal osteogenic front of the coronal suture at E16.5, replicate 1


title: W8IF3SM suture mesenchyme of the frontal suture at E18.5, replicate 3


title: W8IF5FR frontal osteogenic front of the frontal suture at E18.5, replicate 5


title: W8IF1SM suture mesenchyme of the frontal suture at E18.5, replicate 1


title: W6IF5SM suture mesenchyme of the frontal suture at E16.5, replicate 5


title: W8IF5SM suture mesenchyme of the frontal suture at E18.5, replicate 5


title: W6C5SM suture mesenchyme of the coronal suture at E16.5, replicate 5


title: W8IF2FR frontal osteogenic front of the frontal suture at E18.5, replicate 2


title: W6IF3FR frontal osteogenic front of the frontal suture at E16.5, replicate 3


title: W6IF3SM suture mesenchyme of the frontal suture at E16.5, replicate 3


title: W6IF2FR frontal osteogenic front of the frontal suture at E16.5, replicate 2


title: W8IF4FR frontal osteogenic front of the frontal suture at E18.5, replicate 4


title: W8IF2SM suture mesenchyme of the frontal suture at E18.5, replicate 2


title: W6IF5FR frontal osteogenic front of the frontal suture at E16.5, replicate 5


title: W6IF4FR frontal osteogenic front of the frontal suture at E16.5, replicate 4


title: W6IF1FR frontal osteogenic front of the frontal suture at E16.5, replicate 1


title: W6IF2SM suture mesenchyme of the frontal suture at E16.5, replicate 2


title: W6IF4SM suture mesenchyme of the frontal suture at E16.5, replicate 4


title: Adult Lineage-Kit+ BM Cells mRNA

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

description:
Sample 15
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH001

data_processing:
Following Illumina sequencing, raw data was processed with CellRanger (v3.1.0, 10X Genomics) using the ‘count’ and ‘aggregate’ functions with default settings.
Aggregated count matrices were imported into R version 4.0 and all analysis was performed using the Seurat R package version 3.1.5 (Butler et al., 2018). All genes present in at least 30 cells were retained for analysis.
Each sample was filtered separately, excluding cells with >= the 98th percentile of the number of genes per cell or the number of UMIs per cell (to exclude putative doublets), and also excluding cells with >= 7.5% mitochondrial expression or less than 300 UMIs (to exclude putatively dead or dying cells).
Expression data were log-normalized using default parameters, whereas CITE-Seq data were normalized using the “CLR” method.
Genome_build: mm10 v3.0.0
Supplementary_files_format_and_content: TSV (scRNA-Seq raw count matrix) & XLSX (scRNA-Seq meta data (annotations) of the samples)

source_name: Adult Lineage-Kit+ BM Cells

extract_protocol:
Cells were isolated by flow cytometry and processed according to the Chromium single cell 3' reagent v3.1 protocol for downstream library construction.
mRNA expression libraries were constructed according to the Chromium single cell 3’ reagent v3.1 protocol, while CITE-Seq expression libraries were constructed according to the protocol described in Stoeckius et al., (Stoeckius et al., 2017)

value: Bone Marrow

tag: cell type2

value: Hematopoietic progenitors

tag: cell type

value: Lineage-Kit+ Cells

value: Adult


title: Adult CD45-Ter119- BM Cells ADT

description:
Sample 18
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH010

molecule: protein

source_name: Adult CD45-Ter119- BM Cells

value: Stromal cells

value: CD45-Ter119- Cells


title: Adult Lineage-Kit+ BM Cells ADT

description:
Sample 16
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH009


title: W6IF1SM suture mesenchyme of the frontal suture at E16.5, replicate 1


title: E18.5 Lineage-Kit+ BM Cells ADT

description:
Sample 8
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH013

source_name: E18.5 Lineage-Kit+ BM Cells

value: Embryonic day 18.5


title: E16.5 Lineage-Kit+ BM Cells ADT 2

description:
Sample 6
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH024

source_name: E16.5 Lineage-Kit+ BM Cells

value: Embryonic day 16.5


title: E18.5 Lineage-Kit+ BM Cells mRNA

description:
Sample 7
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH005


title: E18.5 CD45-Ter119- BM Cells ADT

description:
Sample 10
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH014

source_name: E18.5 CD45-Ter119- BM Cells


title: P0 Lineage-Kit+ BM Cells mRNA

description:
Sample 11
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH007

source_name: P0 Lineage-Kit+ BM Cells

value: Postnatal day 0


title: E18.5 CD45-Ter119- BM Cells mRNA

description:
Sample 9
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH006


title: P0 CD45-Ter119- BM Cells mRNA

description:
Sample 13
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH008

source_name: P0 CD45-Ter119- BM Cells


title: P0 Lineage-Kit+ BM Cells ADT

description:
Sample 12
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH015


title: P0 CD45-Ter119- BM Cells ADT

description:
Sample 14
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH016


title: E16.5 CD45-Ter119- BM Cells ADT

description:
Sample 4
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH012

source_name: E16.5 CD45-Ter119- BM Cells


title: E16.5 Lineage-Kit+ BM Cells mRNA 2

description:
Sample 5
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH020


title: E16.5 Lineage-Kit+ BM Cells ADT 1

description:
Sample 2
Antibody-derived oligos
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH011


title: E16.5 CD45-Ter119- BM Cells mRNA

description:
Sample 3
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH004


title: Adult CD45-Ter119- BM Cells mRNA

description:
Sample 17
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH002


title: W8IF1FR frontal osteogenic front of the frontal suture at E18.5, replicate 1

value: frontal


title: E16.5 Lineage-Kit+ BM Cells mRNA 1

description:
Sample 1
mRNA
scRNASeq_Raw_Count_Matrix.tsv
scRNASeq_Samples_Metadata.tsv
TDH003


title: mice ID: ER72 [apoptotic cells]

status: Public on Jun 25 2021

city: Montpellier

first: Nicole

last: Hannemann

address: 80 Avenue Augustin Fliche

department: IRMB

institute: INSERM U1183

data_processing:
Quality filtering with FASTX Toolkit 0.0.14 fastq_quality_filter (-q 30 -p 50).
Sdapter clipping with FASTX Toolkit 0.0.14 fastx_clipper (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n -C).
End trimming with FASTX Toolkit 0.0.14 fastx_trimmer (-f 7 -l 98).
Alignment to the mm10 reference with bwa mem v0.7.14.
Peak calling with macs v1.3.7.1 (--gsize 1870000000).
Determining intersect of peaks of all 3 samples for every treatment group using bedtools intersect.
Genome_build: (GRCm38) mm10
Supplementary_files_format_and_content: *.txt: Tab-separated text files containing intersected macs peaks.

source_name: peritoneal elicited macrophages

growth_protocol: The mice were bred and maintained on a 129/C57Bl6 background. All experiments were performed with male or female mice at the age of 8 weeks. Animals were housed in standardized conditions following the guidelines of the German Animal Welfare Act. Animals were kept in a standard diet and water ad libitum and kept with a 12 hour day/night cycle. All experiments with animals are authorized by the local ethics committee.

extract_protocol:
ChIP was performed as described previously: Carey MF, Peterson CL, and Smale ST. Chromatin immunoprecipitation (ChIP). Cold Spring Harbor protocols. 2009;2009(9):pdb.prot5279.
Libraries are prepared using the Illumina TruSeq ChIP Sample Preparation Kit. After quantification and profiling ChIP DNA >5 ng ChIP-enriched fragmented input DNA is used to repair the ends of fragments. After adenylation of the 3' ends indexed paired-end adapters are ligated. After purification of ligated products and PCR amplification a QC is performed in order to normalize and pool the indexed libraries. The indexed libraries are the sequenced as single read 1x100 bp fragments on the HiSeq-2500.

treatment_protocol: Thioglycollate-elicited macrophages were generated by injecting mice i.p. with 2.5 ml of 4% (w/v) Brewer’s thioglycollate medium. Peritoneal cavity cells were harvested 72 h later by lavage. Cells were washed and plated in RPMI-1640 supplemented with 10% (v/v) FCS and 1% (v/v) penicillin/streptomycin. Cells were incubated overnight, and adherent cells were stimulated with 1 μg/ml LPS (Sigma-Aldrich), or ACs (with a 1:5 ratio).

value: Peritoneal macrophages

value: apoptotic cells

tag: precipitated for

tag: mice id


title: mice ID: ER73 [apoptotic cells]


title: mice ID: ER72 [LPS]

value: LPS


title: mice ID: EP92 [LPS]


title: mice ID: EP92 [unstimulated]

value: unstimulated control


title: mice ID: ER73 [unstimulated]


title: mice ID: ER72 [unstimulated]


title: pooled samples [input 2]

value: Input


title: pooled samples [input 1]


title: POLY_FU10_S3

city: MONTPELLIER

first: Julie

last: Ripoll

state: OCCITANIE

address: 860 rue de St Priest

department: Informatics

institute: LIRMM

description: POL-seq

data_processing:
Translatome libraries read quality were assessed using FastQC v0.11.9 (Babraham Institute, Cambridge, UK). Reads were filtered according to quality threshold Q35 and were trimmed of 4 and 2 bases at their start and end, respectively, using Cutadapt v3.2. With Cutadapt we set the minimal length of trimmed reads at 50 nucleotides: all trimmed reads shorter than 50 were removed from the analysis.
High quality reads were then aligned using STAR v2.7.7, on the Homo sapiens reference genome, version GRCh38.dna.primary_assembly release v100, and annotated with GRCh38.100 gtf Ensembl annotation file. Quantification of mapped reads was performed using HTSeq-count v0.13.5, using the following parameters: strand = reverse, mode = intersection-nonempty, typesearch = exon, id_attributes = gene_id, additional attributes = gene_name, and ignoringi chimeric reads.
Statistical differential analyses were performed between the control and each 5-FU conditions (10 or 50 μM) using Wald test from DESeq2 R package. For each dataset, the read counts were filtered with a minimum of 1 count per million per biological sample after size factors estimation (method RLE for Relative Log Expression normalisation), and then dispersion was estimated (using DESeq2). P-value adjustment that corrects for multiple tests to lower the risk of false discovery was performed with the method of Benjamini and Hochberg. Genes with corrected p-values below 0.05 were kept.
Gene identifications were performed with biomaRt R package. Functional annotations were performed with gProfileR using a g:SCS threshold < at 0.80, and Ensembl release v103. Go terms were then clustered using CateGOrizer according to the Goslim2 classification in multiple mode, which is well suited for the general purpose analyses.
Gene ontology classification of mRNA of Survival genes was performed using the "functional annotation clustering" tool of the Database for Annotation, Visualization and Integrated Discovery (DAVID) version 6.8, using default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited text files include count values for each Sample.

growth_protocol: Cells were maintained in Dulbecco Minimum Essential Medium – GlutaMax (Invitrogen) supplemented with 10% foetal bovine serum (FBS) at 37°C with 5% CO2. Cells were plated 48h before 5-FU treatment. 5-FU was kindly provided by the Centre Léon Bérard (Lyon, FRANCE) and was purchased from Sanofi-Aventis. The stock solution was diluted immediately before use in DMEM.

extract_protocol:
RNAs were extracted from the fractions containing 2 to 9 ribosomes per RNA. 150 µL of each fraction was collected and pooled and RNA were extracted using TRIzolTM LS reagent (Invitrogen) following manufacturer instruction and suspended in RNAse-free water.
For sequencing, RNA samples were processed using Stranded mRNA Prep kit (Illumina) according to manufacturer’s protocol. Briefly, mRNA molecules containing polyA tails were capture by oligo(dT) magnetic beads. Then, purified mRNA was fragmented and copied into first strand complimentary DNA (cDNA) using reverse transcriptase and random primers. In a second strand cDNA synthesis step, dUTP replaced dTTP to achieve strand specificity. In the final steps adenine and thymine bases were added to fragment ends and adapters were ligated. The resulting library was purified and selectively amplified for sequencing. Next generation sequencing was performed on NextSeq 500 System (Illumina) using high output 2x75bp Flowcell (Illumina).

treatment_protocol: Cells were seeded at 106 cells/15 cm dish and treated with 5-FU 48 h later as indicated. Cells were then incubated for 5 min with 25 µg/mL Emetin (Sigma) and washed twice with cold 1X PBS before harvesting. Cytosolic lysates were prepared by incubation of cells 10 min in hypotonic buffer (10 mM Tris-HCl pH 7.4, 0.5 mM MgCl2, 10 mM KCl, 1X CompleteTM EDTA free protease inhibitor (Roche) and 10 u/mL RNAseOutTM (Invitrogen)) followed by addition of 0.5 % NP-40. Nuclei were pelleted by centrifugation 5 min at 750g and mitochondria were pelleted by centrifugation at 12,000g for 10 min. 4 mg of cytosolic proteins was loaded onto a 10-50 % sucrose gradient, sedimented by ultra-centrifugation for 2 h at 240,000 g at 4°C on a SW-41 rotor (Beckman). Fractions of 750 µL were collected and absorbance profiles were generated at 245 nm using an ISCO UA-6 detector.

tag: paired

value: Paired-end data

value: 10 µM 5-FU

value: ATCC:HCT116 (ATCC CCL-247)


title: POLY_CTL_S3

description: POL-seq

value: control


title: POLY_FU50_S3

description: POL-seq

value: 50 µM 5-FU


title: POLY_FU10_S1

description: POL-seq


title: mice ID: EP92 [apoptotic cells]


title: POLY_FU10_S2

description: POL-seq


title: POLY_CTL_S1

description: POL-seq


title: POLY_FU50_S1

description: POL-seq


title: YTHDC1 shRNA 1# CD3

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description:
YTHDC1 shRNA 1#
Cell culture
Cells were harvested and washed by PBS, following RNA extraction by TRIzol (Invitrogen) according to the manufactory's instructions.

data_processing:
Quality check of raw reads by FastQC
STAR V2.7.2b for reads alignment and counts summary
Reads count data were processed using R/Bioconductor packages "edgeR", "limma"
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files raw counts data and cpm (counts per million reads).

source_name: Cell culture

extract_protocol:
mRNA libraries were constructed by Novogene company.
TruSeq RNA Library Prep Kit v2

value: MOLM-13 AML cells

value: YTHDC1 shRNA 1#


title: POLY_FU50_S2

description: POL-seq


title: YTHDC1 shRNA 2# CD6

description:
YTHDC1 shRNA 2#
Cell culture
Cells were harvested and washed by PBS, following RNA extraction by TRIzol (Invitrogen) according to the manufactory's instructions.

value: YTHDC1 shRNA 2#


title: YTHDC1 shRNA 2# CD5


title: YTHDC1 shRNA 1# CD4


title: Scramble CD2

description:
Scramble
Cell culture
Cells were harvested and washed by PBS, following RNA extraction by TRIzol (Invitrogen) according to the manufactory's instructions.

value: Scramble


title: pooled samples [input 3]


title: dK9.2_d6_rep3

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Alignment was done using STAR, with additional options “ --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 --paired-end”
Gene expression estimates were obtained using RSEM.
Differentially expressed genes were assessed with DESEQ.
Genome_build: mm10
Supplementary_files_format_and_content: wt_dK9_EB_tpm_deseq.txt file with TPM for all considered genes across samples, with corresponding DESeq FC and FDR.

source_name: E14Tg2a ES cell derivative

growth_protocol: ES cells were cultured on 0.1% gelatine in DMEM-FCS10%-LIF.

extract_protocol:
NucleoSpin RNA Mini kit (Macherey Nagel, Cat# 740955.50) according to the manufacturer’s protocol.
Poly-A enriched strand-specific library.

treatment_protocol: Embryoid Body differentiation in DMEM-FCS10%.

tag: cell line

tag: genotype

tag: differentiation stage

value: 6 days embryoid differentiation


title: dK9.2_d8_rep2

value: 8 days embryoid differentiation


title: dK9.2_d4_rep2

value: 4 days embryoid differentiation


title: dK9.2_d0_rep3

value: Undifferentiated


title: dK9.2_d4_rep3


title: Scramble CD1


title: dK9.2_d8_rep1


title: dK9.2_d6_rep2


title: POLY_CTL_S2

description: POL-seq


title: dK9.2_d8_rep3


title: dK9.2_d4_rep1


title: dK9.1_d6_rep3


title: dK9.1_d8_rep1


title: dK9.1_d4_rep3


title: dK9.1_d0_rep3


title: dK9.1_d8_rep2


title: E14Tg2a_d8_rep3

source_name: wild-type ES cell

value: WT


title: dK9.1_d6_rep2


title: dK9.1_d0_rep1


title: E14Tg2a_d0_rep3


title: dK9.1_d4_rep1


title: dK9.1_d4_rep2


title: E14Tg2a_d4_rep3


title: dK9.1_d0_rep2


title: E14Tg2a_d8_rep2


title: E14Tg2a_d6_rep2


title: E14Tg2a_d4_rep2


title: dK9.2_d0_rep1


title: dK9.1_d8_rep3


title: E14Tg2a_d4_rep1


title: E14Tg2a_d0_rep2


title: Normal Muscle Control 2

status: Public on Jun 24 2021

city: Calgary

first: Reid

last: Mcneil

state: Alberta

address: 18 Simcrest Manor Sw

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

data_processing:
RNA samples were prepared and sequenced by Novogene Corporation Ltd 187 (Sacramento, CA) using an Illumina Hiseq4000 platform.
Quality management - Novogene has strict quality control standards; only qualified samples can be used for NGS. Before downstream bioinformatic analysis, quality testing is applied. We validate the quality of the sample, the library and the data.
Sample QC -  To ensure successful library preparation and sequencing, all samples received by Novogene first undergo quality control assessment. DNA sample quality is measured using agarose gel electrophoresis, and Qubit 2.0. RNA sample quality is assessed using NanoDrop, agarose gel electrophoresis, and the Agilent 2100 BioAnalyzer.
Library QC - During NGS library preparation, initial samples will be fragmented/sheared, tailed, ligated with modified oligos, size selected and amplified. Accurate qualification and quantification of the library is crucial to successful sequencing. Novogene library quality control process includes four steps:
Raw Data QC - QC of raw data is an important measure for determining the quality of the libraries and indicating whether the sequencing succeeded or failed. Novogene will stringently analyze the sequencing data to ensure accuracy and reliability, including quality, error rate, Q20, Q30, adapter contamination rate, etc. Raw reads with low quality, containing adapter sequences, or with >10% of “N” base calls will be removed to obtain the clean reads.
Genome_build: GRCm38 (Mus musculus)
Supplementary_files_format_and_content: raw counts and tpm normalized counts

source_name: Contralateral muscle

growth_protocol: spontaneous tumor and muscle control developed in the p53-/-/;KrasG12D/+ mouse

extract_protocol:
RNA from fresh spontaneous hindlimb sarcomas was isolated using the RNeasy MiniKit 186 (Qiagen).
RNA samples were prepared and sequenced by Novogene Corporation Ltd 187 (Sacramento, CA) using an Illumina Hiseq4000 platform.

treatment_protocol: Untreated

value: Contralateral muscle tissue

value: Untreated


title: E14Tg2a_d8_rep1


title: dK9.2_d0_rep2


title: Tumor 3

source_name: Spontaneous tumor

value: Spontaneous tumor tissue


title: Normal Muscle Control 1


title: Tumor 2


title: Tumor 1


title: E14Tg2a_d6_rep3


title: Tbx18 Stroke Infarct

status: Public on Jun 19 2021

city: Los Angeles

first: Reza

last: Ardehali

address: 675 Charles E Young Dr S

department: Internal Medicine, Division of Cardiology

institute: David Geffen School of Medicine at UCLA

data_processing:
CellRanger mkfastq was used to demultiplex the base call files
CellRanger (v3.0.2) count with mm10 genome reference was used to perform read alignment and UMI counting and generate filtered feature barcode matrices
Filtering cells (Seurat v3): minimum features >500
Filtering features (Seurat v3): minimum cells >3
Normalization (Seurat v3): logNormalization
Number of variable features: (Brain) 7500; (Heart) 2000
Scaling (Seurat v3, default): ScaleData
Batch correction (Seurat v3): FindIntegrationAnchors & IntegrateData; Heart(dim=20, anchor.features=2000); Brain(dim=75, anchor.features=7500)
Dimensional reduction (Seurat v3): RunPCA; Heart (pca, dim = 30); Brain (pca, dim = 50)
Clustering (Seurat v3): FindNeighbors (Heart: dim = 20; Brain: dim = 50); FindClusters (resolution = 0.5)
Differential expression (Seurat v3):FindMarkers (min.pct=0.25)
Genome_build: mm10
Supplementary_files_format_and_content: Data is from filtered feature-barcode matrices generated by cellranger count. mtx (matrix table of count values for genes and samples) and tsv files (features/cellular barcodes)

source_name: Infarct necrotic core of brain

growth_protocol: Intraperitoneal tamoxifen administration for 4 days followed by week washout period.

extract_protocol:
In the heart, atria were removed, and enzymatic digestion was performed using a Collagenase (Worthington) and Dispase (Sigma) mix. Cells were then sorted for tdT expression using fluorescence activated cell sorting. In the brain, cortical tissue was dissected and digested using the Miltenyi® Adult Brain Dissociation Kit. Cells were sorted for tdT expression using fluorescence activated cell sorting.
RNA libraries were prepared for sequencing using 3' 10X Genomics v.3

treatment_protocol: LAD ligation in the heart tissue. Photothrombosis in the brain tissue.

value: brain

value: PT Stroke


title: E14Tg2a_d0_rep1


title: Tbx18 MI Infarct

source_name: Left Ventricle Infarct area

value: heart

value: LAD Ligation