title: cDNA Dilution

description:
custom fa file:
Barcodes_Dilution.fa
Amplicons_Pluripotency.fa

source_name: HMGU1 iPSC bulk RNA

value: H9 hESCs

tag: range of template concentration


title: Dysplastic-Pt12

status: Public on Jul 05 2019

type: genomic

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

description:
Sample name: NY822
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Genotype, Log R ratio (LRR, reflecting total copy number) and B-allele frequency (BAF) obtained from GenomeStudio were used for CNV detection.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Pre-malignant dysplastic nodule from cirrotic liver

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from seven to ten macrodissected FFPE sections (5 μm) using the automated procedure QIAcube and QIAGEN spin columns (Qiagen, Hilden, Germany). For fresh-frozen samples, tissues were processed for gDNA extraction using the Invitrogen ChargeSwitch genomic DNA Mini Tissue.

treatment_protocol: Previous treatment with the Infinium FFPE restoration kit (Illumina) was performed for FFPE samples.

tag: tissue

tag: pathologic classification

value: DN

tag: pathologic subclassification

value: HGDN

tag: tissue preparation

value: FFPE


title: Hela cells transfected with siTHOC1 for 72 h, biological rep3

type: RNA

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

description: Gene expression from HeLa cells after 72 h of siTHOC1 transfection

hyb_protocol: Following fragmentation, 5.2 µg of ss-cDNA were hybridized for 16 h at 45 ºC on GeneChipTM Human Transcriptome (HTA) Array 2.0 . GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix GeneChip Comand Console®  (AGCC) Software.

data_processing:
The .CEL files generated with AGCC software were processed and normalized  into expression values using the SST (Signal Space transformation)-RMA (Robust Microarray Average) method by Expression Console (Affymetrix). The following gene level and alternative splicing analysis (ANOVA unpaired one-way) were performed using the Transcriptome Analysis Console (TAC) Software developed by Affymetrix.
affymetrix-algorithm-name = 'sst-rma-gene-full' -or- 'sst-rma-alt-splice: sst-dabg'
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

molecule: total RNA

source_name: THOC1-depleted HeLa cells

label_protocol: Total RNA from each sample (100 ng) was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix)

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO, Thermo Scientific, Waltham, MA) supplemented with 10% heat-inactivated fetal bovine serum at 37°C (5% CO2). ON-TARGETplus Non-targeting Pool (control siRNA) and ON-TARGETplus SMARTpool human MFAP1 and human THOC1 from Dharmacon were used for depletions. Transient transfection of siRNA was performed using DharmaFECT 1 (Dharmacon) according to the manufacturer’s instructions. Assays were performed 72 h after siRNA transfection.

extract_protocol: Total RNA was isolated from HeLa cells transfected with siRNA for 72 h using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: cell line

value: HeLa

tag: sirna transfection

value: siTHOC1 for 72 h


title: Hela cells transfected with siTHOC1 for 72 h, biological rep2


title: Differentiation, replicate 3

type: SRA

city: Neuherberg

first: Fatma

last: Uzbas

address: Ingolstaedter Landstr. 1

department: Institute of Stem Cell Research

country: Germany

institute: Helmholtz Center Munich

description:
Amplicons_Differentiation.fa
Barcodes_Differentiation_Lib1_3.fa

library_source: transcriptomic

data_processing:
FASTQ files from sequencing run were processed  to assign the reads to barcode combinations and amplicons, using the demultiplexing pipeline provided with the BART-Seq method.
Genome_build: Custom reference consisting of target amplicon sequences
Supplementary_files_format_and_content: Count matrices (*.csv) contain the processed read counts assigned to each forward × reverse barcode combination per amplicon. Fasta files (*.fa) contain the Barcode and Amplicon sequences used for demultiplexing.

source_name: Single cells and bulk RNA derived from differentiating H9 hESCs

extract_protocol:
Bulk RNA was extracted using Qiagen RNeasy Mini Kit. Single cells were sorted using FACS directly into the reverse transcription reaction mixture and lyzed by a freeze-thaw cycle (RNA was not purified).
Adapted protocol from NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (provided with the BART-Seq method)

tag: inducer

value: rWnt3a protein, CHIR99021, Dox induced bCat<delta>N90

tag: cell lines

value: H9 hESCs, H9-bCat<delta>N90 hESCs


title: Hela cells transfected with siMFAP1 for 72 h, biological rep3

description: Gene expression from HeLa cells after 72 h of siMFAP1 transfection

source_name: MFAP1-depleted HeLa cells

value: siMFAP1 for 72 h


title: Dplus [miRNA-seq]

city: Dublin

first: Thomas

last: Hall

state: Select One

address: 2, Taney Grove

department: Vet sciences

country: Ireland

institute: UCD

data_processing:
At each step of data processing, read quality was assessed via fastqc version 0.11.5
Any samples that indicated adapter contamination were trimmed via Cutadapt (version 1.15)
Raw reads were mapped to the bovine reference genome via Bowtie (version 1.2.2).
miRNA detection, identification and quantification was carried out via mirdeep2 (version 0.0.91).
Supplementary_files_format_and_content: Alignment output via mirdeep2 Is in .arf.txt format

organism: Bos taurus

source_name: Dplus_Bovine alveolar macrophages

growth_protocol: Centrifuged cell pellet was resuspended in 15 ml of R10+ media and placed in a 75 cm [2] vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed together with non-adherent cells and adherent cells were washed with 15 ml HBSS pre-warmed to 37 °C (Note: all pre-warmed media and solutions were heated to 37 °C prior to use). Adherent cells were dissociated by adding 10 ml pre-warmed 1× non-enzymatic cell dissociation solution (Sigma–Aldrich Ltd.) to each culture flask and incubating at room temperature for 10 min. Cells were then pelleted (200× g for 5 min at room temperature), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., High Wycombe, UK).

extract_protocol: RNA was extracted from infected (n = 4) and control (n = 4) bAM samples using the RNeasy Plus Mini Kit (Qiagen) as previously outlined (10.1095/biolreprod.111.094946). All RNA samples were of excellent quality (RIN >9).

treatment_protocol: 2 x 10^6 macrophages were seeded in 60 mm tissue culture plates and challenged with M. bovis at an MOI of 10:1 (2 X 107 bacteria per plate) for 24 hours, parallel non-infected controls were prepared simultaneously.

tag: animal

value: Animal 4

tag: condition

value: Infected

tag: timpoint

value: 24 HPI

tag: cell type

value: Bovine alveolar macrophages


title: Differentiation, replicate 2

source_name: Single cells derived from differentiating H9 hESCs


title: HeLa cells transfected with control siC for 72 h, biological rep2

description: Gene expression from HeLa cells after 72 h of siC transfection

source_name: Control HeLa cells

value: control siC for 72 h


title: Dysplastic-Pt10

description:
Sample name: NY818
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Pre-malignant dysplastic nodule from cirrotic liver


title: Hela cells transfected with siMFAP1 for 72 h, biological rep2


title: HeLa cells transfected with control siC for 72 h, biological rep3


title: Genotyping [barcodes with 5'CCA]

description: custom FASTA file: Amplicons_Genotyping.fa

library_source: genomic

source_name: breast cancer patient samples

extract_protocol:
Patient gDNAs were received from the Hadassah Medical Center.
Adapted protocol from NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (provided with the BART-Seq method)

value: patient samples

tag: target genes

value: BRCA1, BRCA2

tag: sample size


title: Differentiation, replicate 1


title: Dminus [miRNA-seq]

source_name: Dminus_Bovine alveolar macrophages

value: Control


title: Hela cells transfected with siMFAP1 for 72 h, biological rep1


title: HeLa cells transfected with control siC for 72 h, biological rep1


title: Genotyping [barcodes with 5'NNN]

source_name: cell line


title: Dysplastic-Pt9

description:
Sample name: NY816
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: DN


title: RNA Dilution

extract_protocol:
Bulk RNA was extracted from HMGU1/H9 cells using Qiagen RNeasy Mini Kit. Single/multiple cells are FACS-sorted directly into the reverse transcription reaction mixture and lyzed by a freeze-thaw cycle (RNA was not purified).
Adapted protocol from NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (provided with the BART-Seq method)

value: H9 hESCs

tag: growth media

tag: primer concentration

value: 0.75 uM in PCR


title: LMD_niche_p4

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

description: HPCs and their surrounding niche

data_processing:
Each fastq file was trimmed and filtered to remove adaptors, polyN nucleotides and low quality sequences and subsequently confirmed by performing a second quality control.
All reads were mapped by Tophat2 on the homo sapiens genome h19.
Transcript compilation was performed using Cufflinks with homo sapiens hg19 UCSC transcript annotation.
Differential expression was calculated by Cuffdiff and subsequently we converted FPKM to TPM (median gene expression) using RStudio.
The data were further analysed with IPA (Inguinity Pathway Analysis) and Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: commapoint-delimited csv file include TPM values for each gene and each sample

source_name: HPC niche

extract_protocol:
Qiagen RNeasy Plus Micro Kit
TruSeq LT Library Prep Kit

treatment_protocol: Liver tissue samples were dissociated, after which the single cell suspension was incubated with Hoechst, Hoechst+verapamil or TROP-2 or EpCAM fluorophore-coupled antibody. SP, EpCAM+ and TROP-2+ populations were extracted with FACS. Frozen, chresyl violet stained sections  were used for LMD isolation of HPCs and niche.

tag: sample type

value: Tissue

tag: subject

value: Patient 4


title: Dysplastic-Pt8

description:
Sample name: NY814
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

tag: tissue

tag: pathologic classification

value: HGDN

value: FFPE


title: LMD_niche_p1

description: HPCs and their surrounding niche

value: Patient 1


title: Cplus [miRNA-seq]

source_name: Cplus_Bovine alveolar macrophages

value: Animal 3


title: LMD_niche_p2

description: HPCs and their surrounding niche

value: Patient 2


title: Dysplastic-Pt4

description:
Sample name: NY806
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

tag: pathologic subclassification

tag: tissue preparation


title: Dysplastic-Pt2

description:
Sample name: NY802
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: RNA-Seq A549 p-Babe LKB1

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

country: USA

institute: Salk Institute For Biological Studies

data_processing:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff alignment
Genome_build: hg19
Supplementary_files_format_and_content: .diff file from cuffdiff comparing the two samples

source_name: A549 cells

growth_protocol: DMEM 10% FBS

extract_protocol:
total RNA extracted with Qiagen Rneasy kit
polyA RNA isolated and library prepared with NEBnext Ultra kit

treatment_protocol: stable expression of pBabe vector or pBabe-LKB1 selected with puromycin

value: NSCLC cells

tag: transduction

value: retrovirus mediated transduction of pBabe-LKB1 (WT)

tag: expression

value: stable expression of pBabe-LKB1(WT) vector selected with puromycin


title: Bplus [miRNA-seq]

source_name: Bplus_Bovine alveolar macrophages

value: Animal 2

value: Infected

value: 24 HPI

value: Bovine alveolar macrophages


title: SP_p4

description: SP

source_name: HPC

value: Cells


title: Cminus [miRNA-seq]

source_name: Cminus_Bovine alveolar macrophages

value: Control


title: RNA-Seq A549 p-Babe

value: retrovirus mediated trasduction of pBabe vector

value: stable expression of pBabe vector selected with puromycin


title: Dysplastic-Pt1

description:
Sample name: NY800
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Pre-malignant dysplastic nodule from cirrotic liver

value: DN


title: SP_p3

description: SP

value: Patient 3


title: Aplus [miRNA-seq]

source_name: Aplus_Bovine alveolar macrophages

value: Animal 1


title: Dysplastic-Pt23

description:
Sample name: NY844
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

source_name: Pre-malignant dysplastic nodule from cirrotic liver

value: LGDN

value: FFPE


title: Genotyping [barcodes without a protection group]

value: patient samples

value: BRCA1, BRCA2


title: SP_p2

description: SP

value: Patient 2


title: SP_p1

description: SP

value: Patient 1


title: Aminus [miRNA-seq]

source_name: Aminus_Bovine alveolar macrophages


title: Dysplastic-Pt20

description:
Sample name: NY838
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Dysplastic-Pt21

description:
Sample name: NY840
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Trop2_p3

description: TROP-2+ population


title: Dysplastic-Pt14

description:
Sample name: NY826
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Dysplastic-Pt11

description:
Sample name: NY820
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Trop2_p2

description: TROP-2+ population


title: Dysplastic-Pt82

description:
Sample name: NY89
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: FFz


title: Bminus [miRNA-seq]

source_name: Bminus_Bovine alveolar macrophages

value: Animal 2

value: 24 HPI


title: Dysplastic-Pt80

description:
Sample name: NY69
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Trop2_p1

description: TROP-2+ population

value: Cells


title: Dysplastic4-Pt79

description:
Sample name: NY63
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Trop2_p4

description: TROP-2+ population

value: Patient 4


title: Dysplastic3-Pt79

description:
Sample name: NY60
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Epcam_p2

description: EpCAM+ population


title: WT_37_rep3

data_processing:
Raw reads were filtered and trimmed with FASTQ toolkit 1.0.0 by BaseSpace Sequence Hub Illumina website
Mapped to sacCer3 with the HISAT2 aligner and filtered for MapQuality ≥ 30 using BAM tools
Counts were generated using Feature Counts v1.6.2  and Differential expression analysis was performed using limma pipeline.
Data was further annotated for functional classification using DAVID bioinformatics resources 6.8
Genome_build: sacCer3
Supplementary_files_format_and_content: Coverage bigWig file provided for each sample were generated by deeptools

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in rich media YPAD.

extract_protocol:
RNA was extracted with the RNeasyMini Kit (Qiagen, Hilden, Germany)  and treated with the RNase-Free DNase Set (Qiagen) to remove any contaminating genomic DNA
RNA libraries for sequencing were performed from 150 ng RNA samples using the TruSeq® Stranded mRNA Library preparation kit (20020594, Illumina )

treatment_protocol: 1h heat-shock at 37ºC to induce the spp381-ts mutation.

tag: strain

value: YDR007W (BY4741 background)

tag: genotype

value: BY4741 trp1{delta}::KanMX4


title: WT_37_rep2


title: WT_37_rep1


title: Dysplastic2-Pt79

description:
Sample name: NY59
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Pre-malignant dysplastic nodule from cirrotic liver


title: Epcam_p1

description: EpCAM+ population


title: Epcam_p4

description: EpCAM+ population


title: liver_p4

description: whole liver sample containing all types of liver cells

source_name: Total liver

value: Tissue


title: p65_ID206_S4

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

data_processing:
Reads were aligned using bowtie2 version 2.2.9
Following removal of chrM reads we filtered with samtools version 1.4 and-f 2 and -F 1804 and MAPQ > 30, and removed duplicate reads with picard version 1.134
Used get_count function from nucleoATAC
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including read count for each sample in each peak

source_name: primary blood

growth_protocol: Isolated CD4+ T cells were stimulated for 24 hours with anti-human CD3/CD28 dynabeads (Thermo Fisher Scientific, MA, USA) at a 1:1 cell to bead ratio and 50 unit/ml of human IL-2 (UCSF Pharmacy).

extract_protocol:
The cells were harvested, fixed with 1% formaldehyde (Thermo Fisher Scientific, MA, USA) for 10 min, washed twice with cold PBS and frozen at -80C. The chromatin was sonicated to generate fragments of 200-500bp in length, followed by incubation with rabbit polyclonal p50 (#3035, Cell Signaling, Danvers, MA, USA) and p65 (ab16502, Abcam, Cambridge, UK) antibodies overnight. Precipitated chromatin was washed, de-crosslinked and DNA extraction was carried out using phenol-chloroform (Sigma).
ChIP DNA was prepared for high throughput sequencing using Accel-NGS 2S Plus DNA library kit (Swift Biosciences) as per manufacturer’s protocol. DNA libraries were sequenced on an Illumina Hiseq4000 with a paired-end 75bp run (CAT, UCSF).

tag: individual

value: donor 206

tag: lineage

tag: chip antibody

value: p65 (ab16502, Abcam, Cambridge, UK)


title: Root Ribo-seq sample 1

city: East Lansing

first: Polly

last: Hsu

state: MI

address: 603 Wilson Road

department: Biochemistry and Molecular Biology

institute: Michigan State University

description:
ribosome-protected mRNA fragment
P_sites_sort_count and translated_ORFs_filtered_sorted.bed

data_processing:
RNA-seq: step A: remove contamination sequences with bowtie2 v2.3.4. with the following steps: 1. remove contamination sequences. Used bowtie2 -L 20 -p 24 parameters. Contamination sequences are from SL3.0 repeat aggressive sequences and SL2.5 snRNA, snoRNA, rRNA and tRNA sequences) 2. samtools v1.8: convert sam to bam with samtools view. 3. Extract unmapped reads: Used samtools view -b -f 12 -F 256 parameters. 4. Sort bam file by read names with samtools 5. Split paired-end reads into separated fastq files with bamToFastq. 6. gzip the fastq files.
Ribo-seq: step A: remove adapter and contamination sequences: remove adaptors with fastx_clipper (FASTX_Toolkit v0.0.14) with the following parameters -a AGATCGGAAGAGCACACGTCT -l 20 -c -n -v -Q33 2. remove contamination sequences with bowtie2 using the following parameters -L 20 -p 16
RNA-seq: step B: mapping of the RNA-seq reads: STAR v2.6.0c 1. Create STAR index for RNA-seq reads: STAR --runThreadN 24 --runMode genomeGenerate --genomeDir $newINDEX --genomeFastaFiles $FASTA --sjdbGTFfile $GTF --sjdbOverhang 99 (here the $newINDEX is the directory for the STAR index file, $GTF is the standard ITAG3.2 annotation, and $FASTA is the SL3.0 fasta). 2. mapping: STAR --runThreadN 24 --genomeDir $newINDEX --readFilesCommand zcat --readFilesIn R1_r1.fastq.gz R1_r2.fastq.gz --alignIntronMax 15000 --alignIntronMin 15 --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --outSAMmultNmax 1 --outMultimapperOrder Random --outFileNamePrefix "star_R1” 3. index the bam file: samtools index star_R1_Aligned.sortedByCoord.out.bam
RNA-seq: step C: de novo assembly with for each stringtie v1.3.5 and compare with ITAG3.2b with gffcompare v.o.10.1: 1. assemble for each replicate (here show R1 example): stringtie --rf -p 16 -G ITAG3.2.gtf -o R1.gtf -l star_R1_Aligned.sortedByCoord.out.bam 2. combine the 3 root gtfs: stringtie --merge -p 12 -T 0.05 -G ITAG3.2.gtf -o Tomato_Root_merged.gtf mergeList.txt (here mergeList.txt is a list of gtf file names in rows). 3. compare with ITAG3.2: gffcompare -V -r $GTF -o Tomato_Root_ITAG_vs_de_novo Tomato_Root_merged.gtf
RNA-seq and Ribo-seq: step D: The i, x, y, o, u, s classes of the novel transcripts from Tomato_Root_ITAG_vs_de_novo.annotated.gtf (in the gffcompare output folder) were extracted and combined with ITAG3.2 in R (v3.4.3) to generate Tomato_Root_ixyous+IATG3.2.gtf file. Both RNA-seq and Ribo-seq reads are mapped to the new gtf and SL3.0 genome assembly using STAR with the same parameter listed above. Next, resulting bam files for three RNA-seq and three Ribo-seq data were merged with samtools merge, sorted by genome coordinates with samtools sort and indexed with samtools index.
Preparing ribotaper annotation file: use the SL3.0 genome sequence fasta and Tomato_Root_ixyous+IATG3.2.gtf files to generate the annotation files for RiboTaper (v1.3.0). Load bedtools v2.17.0 and run create_annotations_files.bash Tomato_Root_ixyous+IATG3.2.gtf SL3.0.fa false false $path_to_OUTPUT $path_to_BEDTOOL $path_to_riboTaper_scripts/
Run riboTaper (v1.3.0) parameter: 24,25,26,27,28 8,9,10,11,12
Genome_build: ITAG3.2

organism: Solanum lycopersicum

source_name: 4-day old roots

growth_protocol: For each replicate, ~300 tomato seeds (Heinz HG1706) were surface-sterilized by 70% ethanol 5 minutes followed by bleach solution (~2.4% NaHClO, 0.3% Tween20) for 30 minutes with shaking. The seeds were then washed with sterile water for 5 times. Next, the seeds were stratified on 1x MS media (4.3 g/L MS salt, 1% sucrose, 0.5 g/L MES, pH 5.7, 1% agar), kept at 22 °C in the dark for 3 days before grown under 16-hour light/8-hour dark at 22°C for 4 days.

extract_protocol:
The frozen tissues were pulverized with liquid nitrogen using a pestle and a mortar. About 0.4 g tissue powder was resuspended in 1.2 ml lysis buffer described in Hsu et al. 2016 (100 mM Tris·HCl (pH 8), 40 mM KCl, 20 mM MgCl2, 2% (vol/vol) polyoxyethylene (10) tridecyl ether (Sigma P2393), 1% sodium deoxycholate (Sigma D6750), 1 mM DTT, 100 μg/mL cycloheximide, and 10 unit/mL DNase I (Epicenter D9905K)). After incubation on ice with gentle shaking for 10 minutes, the lysate was spun at 4°C at 20,000 g for 10 minutes. The supernatant was transferred to new tube, and 100 µL and 200 µL aliquots were created. The aliquoted lysates were flash frozen with liquid nitrogen and stored at -80°C until ready to be processed.
For RNA-seq samples, 10 µL 10% SDS was added to the above 100 µL lysate. RNA greater than 200 nt was extracted using Zymo RNA clean and concentrator kit (Zymo Research R1017). The obtained RNA was checked by a Bioanalyzer (Agilent) RNA pico chip to access the RNA integrity, and a RIN value ranging from 9.2 to 9.4 was obtained for each replicate. Ribosomal RNAs (rRNAs) were depleted using RiboZero Plant Leaf kit (Epicenter/illumina MRZPL1224). Next, 100 ng of the rRNA-depleted RNA was used as the starting materials and fragmented to ~200 nt size based on the RIN reported by Bioanalyer following the NEBNext Ultra Directional RNA Library Prep Kit (NEB E7420S) to create strand-specific libraries. The libraries were barcoded and enriched using 11 cycles of PCR amplification. Equal molarity of the libraries was pooled and sequenced using Hi-Seq 4000 PE-100. The Ribo-seq samples were prepared according to Hsu et al. 2016 with minor modifications. Briefly, the RNA concentration of each lysate was first determined by Qubit RNA HS assay using a 10-fold dilution. Next, the 200 µL lysate above was treated with 100 units of Nuclease (provided by the TruSeq Mammalian Ribo Profile Kit, illumina RPHMR12126) per 40 µg of RNA with gently shaking at room temperature for one hour. The nuclease reaction was stopped by immediately transferred to ice and adding 15 µL of SUPERase-IN (Invitrogen AM2696). The ribosomes were isolated using illustra MicroSpin S-400 HR Columns (GE Healthcare 27514001). The RNA greater than 17 nt was purified first, and then RNA smaller than 200 nt was enriched using the RNA Clean & Concentrator Kit (Zymo Research R1017). Next, the rRNAs were depleted using the RiboZero Plant Leaf kit (Epicenter/illumina MRZPL1224). The rRNA-depleted RNA was then separated by 15% (wt/vol) TBE-urea PAGE (Invitrogen EC68852BOX), and gel slices ranging from 28 to 30 nt were excised. Ribosome footprints were recovered from the excised gel slices following the overnight elution method and the sequencing libraries were constructed according to the TruSeq Mammalian Ribo Profile Kit manual. The final libraries were amplified by 9 cycles of PCR. Equal molarity of the libraries was pooled and sequenced using Hi-Seq 4000 SE-50.

treatment_protocol: Seedlings that germinated around the same time and of similar size were selected for the experiments. Root (2.5-3 cm from the tip) from ~180 plants were harvested at ZT 3 (3 hours after light on) in batches and immediately frozen in liquid nitrogen.

tag: organ

value: roots

tag: cultivar

value: Heinz 1706-BG


title: Root Ribo-seq sample 3


title: Root Ribo-seq sample 2


title: p50_ID171_S1

value: donor 171

tag: cell type

value: p50 (#3035, Cell Signaling, Danvers, MA, USA)


title: Dysplastic1-Pt79

description:
Sample name: NY54
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: DN

value: LGDN


title: Epcam_p3

description: EpCAM+ population

value: Patient 3


title: Root RNA-seq sample 3

description: rRNA depleted RNA


title: liver_p3


title: Dysplastic2-Pt77

description:
Sample name: NY49
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: FFz


title: p65_ID171_S2


title: Input_ID206_S6


title: Root RNA-seq sample 2

description: rRNA depleted RNA


title: Dysplastic1-Pt77

description:
Sample name: NY48
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: p50_ID206_S3


title: Input_ID171_S5


title: Dysplastic1-Pt75

description:
Sample name: NY14
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: liver_p1

value: Patient 1


title: Root RNA-seq sample 1

description: rRNA depleted RNA


title: liver_p2

value: Patient 2


title: Ad5LO_rep_3

status: Public on Jul 04 2019

city: Stanford

first: Mark

last: Nicolls

state: California

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

institute: Stanford University School of Medicine

data_processing:
RNA-seq sample processing was performed according to Bulk RNA-seq pipeline as part of the ENCODE Uniform Processing Pipeline.
Paired end reads were mapped to human genome hg38 using STAR program.
The quantification of genes and transcripts is done with the RSEM program
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files generated by RSEM detailing quantification of genes in expected count, TPM, FPKM.

source_name: Human pulmonary artery endothelial cells  (hPAECs)

growth_protocol: PAECs, at passage number 3–5 from control subjects, infected by lentivirus expressing control shGFP or shBmpr2 to silent BMPR2 signaling were treated with control AdGfp vector or AdAlox5.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and subjected to sequencing on 1–2 Illumina HiSeq 2000 lanes to obtain an average of approximately 100-150 million uniquely mapped reads for each sample (Stanford Personalized Medicine Sequencing Core).

tag: passages

tag: condition


title: shBMPR2+Ad5LO_rep_3

value: Human pulmonary artery endothelial cells  (hPAECs)


title: shBMPR2_rep_1


title: Ad5LO_rep_2


title: shBMPR2_rep_2


title: Ad5LO_rep_1


title: shGFP_rep_3

value: shGFP


title: shBMPR2+Ad5LO_rep_1


title: shBMPR2+Ad5LO_rep_2


title: shBMPR2_rep_3


title: shGFP_rep_1


title: shGFP_rep_2


title: AdGFP_rep_3

value: AdGFP


title: AdGFP_rep_2


title: AdGFP_rep_1


title: RPE_24W_emb1_rep1

city: Beijing

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

country: China

institute: Peking university

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
A custom script was used to trim the primer, TSO and polyA sequences for the raw input read. At the same time, the cell barcode was also extracted and put into the read.id information of the fastq file.
Then the extracted reads were mapped to hg38 genome using Hisat2 v2.0.5. The unique mapped reads were than counted by FeatureCounts v1.5.2 using the Ensembl release 84 GTF transcriptome annotation.
In order to get the sample-gene count matrix, Spark v1.6.2 were used to identify cells with at least 500 genes and then cast the table into a sample (2553)-gene (58830) count matrix.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files which include theTPM values of RefSeq genes.

source_name: Human Embryonic Retinal Cells

extract_protocol:
The modified Smart-seq2 protocol for multiplexed single-cell RNA-seq was described previously. Briefly, after digestion, a single retinal cells was randomly picked into 2μL cell lysis buffer using a mouth pipette. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 19 cycles. Then the amplified cDNA were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads. RNA-seq library was constructed using Kapa Hyper Prep Kit and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform.

value: retinal pigment epithelium

tag: developmental stage

value: 24 week gestation

tag: gender

value: female


title: Ctrl_rep_2

value: Ctrl


title: RPE_23W_emb1_rep1_r1

description: polyA RNA

tag: tissue

value: 23 week gestation


title: RPE_11W_emb1_rep1_r2

description: polyA RNA

value: 11 week gestation

value: male


title: Ctrl_rep_1


title: RPE_9W_emb1_rep1

description: polyA RNA

value: 9 week gestation


title: RPE_9W_emb2_rep1_r1

description: polyA RNA


title: RPE_7W_emb2_rep1

description: polyA RNA

value: 7 week gestation


title: RPE_8W_emb3_rep1

description: polyA RNA

value: 8 week gestation


title: Ctrl_rep_3


title: RPE_6W_emb1_rep1

description: polyA RNA

value: 6 week gestation


title: RPE_5W_6W_emb1_rep1_r1

description: polyA RNA

value: 5 and 6 week gestation


title: RET_24W_emb1_rep2

description: polyA RNA

value: neural retina


title: RET_24W_emb1_rep1

description: polyA RNA


title: RET_23W_emb2_rep2_r2

description: polyA RNA


title: RPE_7W_emb1_rep1

description: polyA RNA


title: RPE_13W_emb1_rep1

description: polyA RNA

value: 13 week gestation


title: RET_23W_emb2_rep2_r1

description: polyA RNA


title: RET_23W_emb2_rep1_r2

description: polyA RNA


title: RET_23W_emb2_rep1_r1

description: polyA RNA


title: RPE_9W_emb2_rep1_r2

description: polyA RNA


title: RPE_5W_6W_emb1_rep1_r2

description: polyA RNA


title: RPE_23W_emb2_rep1_r2

description: polyA RNA


title: RPE_23W_emb2_rep1_r1

description: polyA RNA


title: RPE_8W_emb1_rep1

description: polyA RNA


title: RET_23W_emb1_rep1_r2

description: polyA RNA


title: RPE_13W_emb2_rep1

description: polyA RNA


title: RET_23W_emb1_rep1_r1

description: polyA RNA


title: RPE_17W_emb2_rep1

description: polyA RNA

value: 17 week gestation


title: RPE_17W_emb1_rep1

description: polyA RNA


title: RET_17W_emb2_rep2

description: polyA RNA


title: RPE_11W_emb1_rep1_r1

description: polyA RNA


title: RPE_23W_emb1_rep1_r2

description: polyA RNA


title: RET_23W_emb1_rep2_r1

description: polyA RNA


title: RET_17W_emb2_rep1

description: polyA RNA


title: RET_17W_emb1_rep1

description: polyA RNA


title: RET_23W_emb1_rep2_r2

description: polyA RNA


title: RET_11W_emb1_rep2_r2

description: polyA RNA


title: RET_13W_emb1_rep1

description: polyA RNA


title: RET_11W_emb1_rep2_r1

description: polyA RNA


title: RET_13W_emb1_rep2

description: polyA RNA


title: RET_9W_emb2_rep2_r2

description: polyA RNA


title: RET_11W_emb1_rep1_r1

description: polyA RNA


title: RET_11W_emb1_rep1_r2

description: polyA RNA


title: RET_13W_emb2_rep1

description: polyA RNA


title: RET_9W_emb2_rep1_r2

description: polyA RNA


title: RET_9W_emb1_rep2

description: polyA RNA


title: RET_17W_emb1_rep2

description: polyA RNA


title: RET_9W_emb1_rep1

description: polyA RNA


title: RET_8W_emb2_rep2_r2

description: polyA RNA


title: RET_9W_emb2_rep1_r1

description: polyA RNA


title: Hela cells transfected with siTHOC1 for 72 h, biological rep2 [alternative splicing]

description: alternative splicing data from HeLa cells after 72 h of siTHOC1 transfection

source_name: THOC1-depleted HeLa cells

tag: cell line

value: HeLa

tag: sirna transfection

value: siTHOC1 for 72 h


title: RET_8W_emb2_rep2_r1

description: polyA RNA


title: RET_8W_emb1_rep2_r1

description: polyA RNA


title: RET_8W_emb1_rep2_r2

description: polyA RNA


title: RET_8W_emb1_rep1_r2

description: polyA RNA


title: Hela cells transfected with siTHOC1 for 72 h, biological rep3 [alternative splicing]


title: RET_7W_emb3_rep1

description: polyA RNA


title: RET_8W_emb1_rep1_r1

description: polyA RNA


title: RET_7W_emb2_rep2

description: polyA RNA


title: RET_8W_emb3_rep1

description: polyA RNA


title: RET_9W_emb2_rep2_r1

description: polyA RNA


title: Hela cells transfected with siMFAP1 for 72 h, biological rep2 [alternative splicing]

description: alternative splicing data from HeLa cells after 72 h of siMFAP1 transfection

source_name: MFAP1-depleted HeLa cells

value: siMFAP1 for 72 h


title: RET_7W_emb2_rep1

description: polyA RNA


title: RET_5W_6W_emb1_rep1_r2

description: polyA RNA


title: RET_7W_emb1_rep2

description: polyA RNA


title: RET_6W_emb1_rep1

description: polyA RNA


title: RET_5W_6W_emb1_rep1_r1

description: polyA RNA


title: HeLa cells transfected with control siC for 72 h, biological rep1 [alternative splicing]

description: alternative splicing data from HeLa cells after 72 h of siC transfection

source_name: Control HeLa cells

value: control siC for 72 h


title: Hela cells transfected with siMFAP1 for 72 h, biological rep3 [alternative splicing]


title: Hela cells transfected with siMFAP1 for 72 h, biological rep1 [alternative splicing]


title: HeLa cells transfected with control siC for 72 h, biological rep3 [alternative splicing]


title: RET_7W_emb1_rep1

description: polyA RNA


title: Hela cells transfected with siTHOC1 for 72 h, biological rep1 [alternative splicing]


title: HeLa cells transfected with control siC for 72 h, biological rep2 [alternative splicing]


title: JFC_Hep-i(-) Experiment2

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

description: SAMPLE 17

hyb_protocol: For each hybridization, 0.60 μg of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID: 72363).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software, which performs background subtractions.

source_name: Lot JFC hCLiPs cultured for 8 days without hepatic inducing factors

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA)

growth_protocol: hCLiPs were generated from 3 donor-derived PHHs by culture under SHM+10%FBS + AC for 2 week culture, and then passaged to collagen coated plates. Until reaching 50-80% confluency, the cells were grown in SHM+10%FBS+AC.

extract_protocol: RNA was extracted using the miRNAeasy mini kit (QIAGEN).

treatment_protocol: hCLiPs at 50-80% confluency were treated with SHM+2%FBS+AC with a high dose of dexamethasone (10^-6 M) and human oncostatin M (10 ng/ml) for another 8 days (termed Hep-i(+) cells). Control cells (Hep-i(-) cells) were cultured in SHM with 2%FBS+AC with a normal dose of dexamethasone (10^-7 M) without human oncostatin M for the same period (8 days). PHHs were thawed and seeded in William's E medium with 10%FBS and insulin (10^-7 M). 4-7 hours after plating, the culture medium was replaced with SHM+2%FBS and cultured for one day.

tag: Sex

value: Male

tag: donor age

value: 1 year

value: human chemically induced liver progenitors (hCLiPs)

tag: treatment/timepoint


title: HC5-25 PHH

description: SAMPLE 20

source_name: Primary culture of lot HC5-25 human hepatocytes

growth_protocol: Magnetically purified human hepatocytes were seeded to collagen coated plates and cultured in SHM containing 2% FBS for one day, and RNA was prepared for microarray analysis. PHHs were thawed and seeded in William's E medium with 10%FBS and insulin (10^-7 M). 4-7 hours after plating, the culture medium was replaced with SHM + 2%FBS and cultured for one day.

value: 56 year


title: FCL P7

description: SAMPLE 7

source_name: Lot FCL PHH-derived CLiPs at P7

growth_protocol: Cells were cultured in SHM supplemented with 10%FBS and 0.5 microM A83-01 and 3 microM CHIR99021.

treatment_protocol: Long term culture was performed until passage 10.

tag: donor gender

value: Female

value: 12 months

value: PHH-derived CLiPs

tag: passage


title: JFC_D0 Experiment1

description: SAMPLE 13

source_name: Lot JFC hCLiPs before hepatic induction

value: before hepatic induction


title: DUX P10

description: SAMPLE 10

source_name: Lot DUX PHH-derived CLiPs at P10

value: 10 months


title: Chimera-JFC

description: SAMPLE 6

source_name: PHHs isolated from chimeric liver generated by transplantation of hCLiPs (lot JFC)


title: JFC_Hep-i(-) Experiment1

description: SAMPLE 14

value: cultured for 8 days without hepatic inducing factors


title: PXB cells-JFC

description: SAMPLE 7

source_name: PHHs isolated from chimeric liver generated by transplantation of PHHs (lot JFC)


title: JFC PHH

description: SAMPLE 19

source_name: Primary culture of lot JFC human hepatocytes


title: JFC_D0 Experiment2

description: SAMPLE 16


title: DUX P3

description: SAMPLE 4

source_name: Lot DUX PHH-derived CLiPs at P3


title: FCL P5

description: SAMPLE 5

source_name: Lot FCL PHH-derived CLiPs at P5


title: JFC_Hep-i(+) Experiment2

description: SAMPLE 18

source_name: Lot JFC hCLiPs cultured for 8 days with hepatic inducing factors


title: DUX_Hep-i(+) Experiment2

description: SAMPLE 12

source_name: Lot DUX hCLiPs cultured for 8 days with hepatic inducing factors


title: FCL P3

description: SAMPLE 3

source_name: Lot FCL PHH-derived CLiPs at P3


title: RET_8W_emb3_rep2

description: polyA RNA

source_name: Human Embryonic Retinal Cells

value: neural retina

value: 8 week gestation


title: DUX P7

description: SAMPLE 8

source_name: Lot DUX PHH-derived CLiPs at P7


title: DUX P0

description: SAMPLE 1

source_name: Lot FCL PHH-derived CLiPs at P0


title: FCL P10

description: SAMPLE 9

source_name: Lot FCL PHH-derived CLiPs at P10


title: Chimera-DUX

description: SAMPLE 5

source_name: PHHs isolated from chimeric liver generated by transplantation of hCLiPs (lot DUX


title: DUX P5

description: SAMPLE 6

source_name: Lot DUX PHH-derived CLiPs at P5


title: Chimera-FCL

description: SAMPLE 4

source_name: PHHs isolated from chimeric liver generated by transplantation of hCLiPs (lot FCL)


title: HC7-4 PHH

description: SAMPLE 21

source_name: Primary culture of lot HC7-4 human hepatocytes

value: 7 year


title: DUX_Hep-i(-) Experiment2

description: SAMPLE 11

source_name: Lot DUX hCLiPs cultured for 8 days without hepatic inducing factors


title: DUX_D0 Experiment2

description: SAMPLE 10

source_name: Lot DUX hCLiPs before hepatic induction


title: JFC_Hep-i(+) Experiment1

description: SAMPLE 15

value: cultured for 8 days with hepatic inducing factors


title: FCL P0

description: SAMPLE 2

source_name: Lot DUX PHH-derived CLiPs at P0


title: DUX_Hep-i(-) Experiment1

description: SAMPLE 8


title: DUX_Hep-i(+) Experiment1

description: SAMPLE 9


title: ΔLD Sample 6

city: Evanston

last: Bozza

state: IL

address: 2205 Tech Drive, Hoga 2-160

department: Neurobiology

institute: Northwestern University

data_processing:
Reads were aligned to the GRCm38.p6 genome using STAR v2.6.0 with default parameters with the exception of --outFilterMultimapNmax 1
Reads were normalized using DESeq2 with default paramaters after filtering for nonexpressed genes
Differential expression was performed with DESeq2 using contrast argument
Genome_build: Mus musculus Gencode build M21: GRCm38.p6
Supplementary_files_format_and_content: Excel file of DESeq2 output including normalized counts, p-value, error and significance

organism: Mus musculus

source_name: olfactory mucosa

extract_protocol:
Olfactory mucosae were dissected and total RNA was isolated using Qiagen RNeasy Kit according to manufacturer's protocol.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit (ribodepleted) and 1 ug of total RNA according to standard Illumina protocols.

value: olfactory mucosa

tag: genotype

value: delta large deletion

tag: strain

tag: age


title: FCL_Hep-i(+) Experiment2

description: SAMPLE 3

source_name: Lot FCL hCLiPs cultured for 8 days with hepatic inducing factors


title: ΔLD Sample 3


title: ΔLD Sample 4


title: FCL_D0 Experiment2

description: SAMPLE 1

source_name: Lot FCL hCLiPs before hepatic induction


title: DUX_D0 Experiment1

description: SAMPLE 7


title: JFC-F_D7

description: SAMPLE 15

source_name: Lot JFC PHHs cultured for 7 days without AC

treatment_protocol: Primary human hepatocytes were cultured for 2 weeks in SHM supplemented with 10%FBS in the presence or absence of 0.5 microM A83-01 and 3 microM CHIR99021.

value: Primary human hepatocytes (PHHs)

tag: treatment

value: cultured for 7 days without AC


title: JFC-FAC_D7

description: SAMPLE 16

source_name: Lot JFC PHHs cultured for 7 days with AC

value: Male

value: 1 year

tag: cell type

value: cultured for 7 days with AC


title: JFC-F_D1

description: SAMPLE 13

source_name: Lot JFC PHHs cultured for 1 day without AC

value: cultured for 1 day without AC


title: DUX-F_D14

description: SAMPLE 11

source_name: Lot DUX PHHs cultured for 14 days without AC

value: cultured for 14 days without AC


title: FCL_Hep-i(+) Experiment1

description: SAMPLE 6

value: Female

value: 12 months

value: human chemically induced liver progenitors (hCLiPs)


title: ΔLD Sample 5


title: JFC-FAC_D14

description: SAMPLE 18

source_name: Lot JFC PHHs cultured for 14 days with AC

value: cultured for 14 days with AC


title: JFC-FAC_D1

description: SAMPLE 14

source_name: Lot JFC PHHs cultured for 1 day with AC

value: cultured for 1 day with AC


title: FCL_Hep-i(-) Experiment1

description: SAMPLE 5

source_name: Lot FCL hCLiPs cultured for 8 days without hepatic inducing factors


title: ΔLD Sample 2


title: FCL-F_D14

description: SAMPLE 5

source_name: Lot FCL PHHs cultured for 14 days without AC


title: FCL_D0 Experiment1

description: SAMPLE 4

value: before hepatic induction


title: FCL-F_D7

description: SAMPLE 3

source_name: Lot FCL PHHs cultured for 7 days without AC


title: FCL-F_D1

description: SAMPLE 1

source_name: Lot FCL PHHs cultured for 1 day without AC


title: DUX-F_D1

description: SAMPLE 7

source_name: Lot DUX PHHs cultured for 1 day without AC

value: 10 months


title: DUX-FAC_D14

description: SAMPLE 12

source_name: Lot DUX PHHs cultured for 14 days with AC


title: ΔLD Sample 1


title: FCL-FAC_D1

description: SAMPLE 2

source_name: Lot FCL PHHs cultured for 1 day with AC


title: DUX-F_D7

description: SAMPLE 9

source_name: Lot DUX PHHs cultured for 7 days without AC


title: LD wt Sample 5

source_name: olfactory mucosa

value: wildtype


title: DUX-FAC_D7

description: SAMPLE 10

source_name: Lot DUX PHHs cultured for 7 days with AC


title: FCL-FAC_D7

description: SAMPLE 4

source_name: Lot FCL PHHs cultured for 7 days with AC


title: FCL_Hep-i(-) Experiment2

description: SAMPLE 2

value: cultured for 8 days without hepatic inducing factors


title: JFC-F_D14

description: SAMPLE 17

source_name: Lot JFC PHHs cultured for 14 days without AC


title: DUX-FAC_D1

description: SAMPLE 8

source_name: Lot DUX PHHs cultured for 1 day with AC


title: LD wt Sample 4

value: olfactory mucosa


title: LD wt Sample 3


title: LD wt Sample 2


title: LD wt Sample 1


title: ΔeC Sample 3

data_processing:
Reads were aligned to the GRCm38.p6 genome using STAR v2.6.0 with default parameters with the exception of --outFilterMultimapNmax 1
Reads were normalized using DESeq2 with default paramaters after filtering for nonexpressed genes
Differential expression was performed with DESeq2
Genome_build: Mus musculus Gencode build M21: GRCm38.p6
Supplementary_files_format_and_content: Excel file of DESeq2 output including normalized counts, p-value, error and significance

value: delta eC


title: ΔeC Sample 1


title: LD wt Sample 6


title: eC wt Sample 3


title: eC wt Sample 2


title: eC wt Sample 1


title: ΔeB Sample 3

value: delta eB


title: ΔeB Sample 4

value: Male


title: ΔeB Sample 5


title: ΔeB Sample 2


title: ΔeB Sample 1


title: eB wt Sample 5


title: FCL-FAC_D14

description: SAMPLE 6

source_name: Lot FCL PHHs cultured for 14 days with AC

value: Primary human hepatocytes (PHHs)


title: eB wt Sample 2


title: ΔeA Sample 5

value: enhancer A deletion


title: eB wt Sample 1


title: ΔeC Sample 2


title: ΔeA Sample 6


title: ΔeA Sample 2


title: ΔeA Sample 1


title: eB wt Sample 3


title: ΔeA Sample 4


title: eB wt Sample 4


title: eA wt Sample 5

value: wt


title: eA wt Sample 6


title: eA wt Sample 4


title: ΔeA Sample 3


title: eA wt Sample 3


title: eA wt Sample 1


title: ΔeB Sample 6


title: eA wt Sample 2


title: WD.CD45lo.2

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
bcl2fastq/2.18.0.12 software was used for basecalling
NGSQCToolkit v2.3 for the removal of adapters and trimming low quality bases (Phred < 30)
RSEM v1.2.12 to quantify gene expression as counts per million (cpm), TPM or FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM, TPM and FPKM values for each sample, but only CPM values were used for downstream analysis

source_name: Brain myeloid cells

extract_protocol:
Brain myeloid cells were isolate into CD11b+CD45lo and CD11b+CD45hi cells using FACS, snapfozen on dry ice. Samples were processed in TRIzol (Invitrogen, cat #: 15596026) solution for total RNA extraction using QIAGEN miRNeasy mini extraction kit.
Poly(A) selected RNA-seq libraries were generated using the TruSeq RNA Sample preparation kit v2 (Illumina)

value: brain myeloid cells

tag: mouse strain

tag: diet

value: WD

value: wild type


title: eB wt Sample 6


title: colon spf 3

city: Los Angeles

middle: C

last: Fung

address: 610 Charles E Young Dr. East

institute: University of California, Los Angeles

description:
colon SPF 3
colon_read_counts.xlsm
colon.ANOVA_GFvSPF.csv
colon.WALD_GFvSPF.csv

data_processing:
BlueBee data analysis platform was used for read trimming, read alignment and gene read counting
DESeq2 was used to determine differential gene expression between groups. Wald test and 2-way ANOVA were used as statistical tests.
Genome_build: mm10
Supplementary_files_format_and_content: Gene read counts were generated using BlueBee; ANOVA and Wald test p- and q-values were generated using DESeq2

source_name: specific pathogen free

growth_protocol: Germ-free (GF) and Turicibacter-monocolonized mice were maintained in a sterile environment to maintain GF and monocolonization status

extract_protocol:
Total RNA from tissue was extracted using Trizol and with the RNAeasy Mini Kit with on-column DNAse digestion
Library construction was performed using the QuantSeq FWD Kit (Lexogen)

treatment_protocol: To generate Turicibacter-monocolonized mice, germ-free (GF) mice were orally gavaged with overnight cultures of Turicibacter sanguinis MOL361 and  the terminal ileum and distal colon were harvested

value: colon

value: male


title: WD.CD45lo.4

value: 12 months


title: WD.CD45lo.1


title: colon spf 5

description:
colon SPF 5
colon_read_counts.xlsm
colon.ANOVA_GFvSPF.csv
colon.WALD_GFvSPF.csv

value: female


title: colon spf 1

description:
colon SPF 1
colon_read_counts.xlsm
colon.ANOVA_GFvSPF.csv
colon.WALD_GFvSPF.csv


title: WD.CD45hi.3


title: colon turi 3

description:
colon Turi 3
colon_read_counts.xlsm
colon.ANOVA_GFvTURI.csv
colon.WALD_GFvTURI.csv

source_name: Turicibacter-monocolonized


title: colon turi 1

description:
colon Turi 1
colon_read_counts.xlsm
colon.ANOVA_GFvTURI.csv
colon.WALD_GFvTURI.csv


title: Chow.CD45lo.3

value: Chow


title: Chow.CD45lo.4


title: colon turi 4

description:
colon Turi 4
colon_read_counts.xlsm
colon.ANOVA_GFvTURI.csv
colon.WALD_GFvTURI.csv


title: colon gf 5

description:
colon GF 5
colon_read_counts.xlsm

source_name: germ-free


title: colon turi 2

description:
colon Turi 2
colon_read_counts.xlsm
colon.ANOVA_GFvTURI.csv
colon.WALD_GFvTURI.csv


title: WD.CD45hi.1


title: Chow.CD45lo.1


title: colon gf 4

description:
colon GF 4
colon_read_counts.xlsm


title: colon gf 3

description:
colon GF 3
colon_read_counts.xlsm


title: colon spf 4

description:
colon SPF 4
colon_read_counts.xlsm
colon.ANOVA_GFvSPF.csv
colon.WALD_GFvSPF.csv


title: Chow.CD45hi.3


title: WD.CD45hi.2


title: Chow.CD45lo.2


title: Chow.CD45hi.4


title: colon gf 2

description:
colon GF 2
colon_read_counts.xlsm


title: colon gf 1

description:
colon GF 1
colon_read_counts.xlsm


title: WD.CD45lo.3


title: Chow.CD45hi.2


title: 3496-SP-16

city: Nashville

first: Matthew

middle: Tyler

last: Stier

state: TN

address: 1161 21st Avenue South

department: Internal Medicine

institute: Vanderbilt University Medical Center

description: poly-A enriched RNA

data_processing:
RTA (version 2.7.6; Illumina) was used for base calling
Analysis was completed using MultiQC v1.2
On paired fastq files, transcript abundance was estimated, and these read counts were imported into edgeR for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains read counts for each sample

source_name: Bone marrow

extract_protocol:
Bone marrow was isolated, CD19+ cells were enriched by MACS (Miltenyi), and pro-B and large pre-B cells were FACS-purified into PBS and processed for RNA using the QIAGEN Rneasy Mini Kit (Cat. #74104); 20-50 ng of total RNA was prepared for sequencing
Prepared using Illumina's TruSeq Stranded mRNA kit (Cat. #20020595) per manufacturer instructions with mRNA enriched via poly-A selection using oligoDT beads

value: BALB/c

value: FACS-purified large pre-B


title: colon spf 2

description:
colon SPF 2
colon_read_counts.xlsm
colon.ANOVA_GFvSPF.csv
colon.WALD_GFvSPF.csv


title: 3496-SP-15

description: poly-A enriched RNA


title: 3496-SP-14

description: poly-A enriched RNA


title: small intestine spf 5

description:
SI SPF 5
SI_read_counts.xlsm
SI.ANOVA_GFvSPF.csv
SI.WALD_GFvSPF.csv

value: small intestine


title: Chow.CD45hi.1


title: 3496-SP-13

description: poly-A enriched RNA


title: small intestine spf 4

description:
SI SPF 4
SI_read_counts.xlsm
SI.ANOVA_GFvSPF.csv
SI.WALD_GFvSPF.csv


title: 3496-SP-11

description: poly-A enriched RNA


title: 3496-SP-12

description: poly-A enriched RNA


title: R2b

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

institute: University of Oklahoma Health Sciences Center

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw fastq reads were aligned with STAR version 2.5.3 with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Following alignment, htseq-count version 0.9.1 with parameters -r pos -m union -t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used to normalize and identify differentially expressed genes
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab delimited Excel file containing raw count values for each gene in each sample

source_name: CD11c- Kidney resident macrophages

extract_protocol:
After perfusion of the mouse with PBS, kidneys were minced and digested in 1 ml of RPMI 1640 containing 1 mg/ml collagenase type I (Sigma-Aldrich) and 100 U/ml DNase I (Sigma-Aldrich) for 30 min at 37ºC with agitation. Kidney fragments were passed through a 70-µm mesh (Falcon; BD Biosciences) yielding single-cell suspensions. Red blood cells were lysed and cells were resuspended in 1 ml PBS containing 1% BSA with Fc blocking solution for 30 minutes on ice. 2 X 106 cells were stained for 30 minutes at room temperature with primary antibody. Following staining, R2a and R2b resident macrophages were sorted and collected using a BD FACS AriaII. RNA was isolated from FACS sorted cells using the RNeasy Plus Mini Kit (Qiagen cat. 74134) according to standard procedures.
For RNA sequencing, the NEBNext mRNA library prep kit for Illumina with ribosome reduction was used to generate the library, which was subsequently sequenced using Illumina NextSeq500 with paired end 75bp sequencing and aligned to the University of California, Santa Cruz (UCSC) GRCm38/mm10 reference genome using the STAR software package. For each sample, at least 25 million reads were obtained.  Following alignment, HTSeq-count (version 0.9.1) was used to count the number of reads mapping to each gene.  Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using the Cufflinks suite (https://github.com/cole-trapnell-lab/cufflinks) and differential expression was then applied to the count files using DESeq2.

value: Kidney

value: 8 weeks old


title: R2a

source_name: CD11c+ Kidney resident macrophages


title: small intestine spf 2

description:
SI SPF 2
SI_read_counts.xlsm
SI.ANOVA_GFvSPF.csv
SI.WALD_GFvSPF.csv


title: 3496-SP-7

description: poly-A enriched RNA

value: FACS-purified pro-B


title: BCELL_PRDM15KO_3

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
Sequenced reads were mapped to mm9 genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the htseq package and edgeR
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Primary mouse lymphoma

growth_protocol: Lymphoma cells were maintained in 500ml DMEM (Hyclone #30022.01, DMEM with high glucose, with 4.0mM L-glutamine, without Sodium Pyruvate) +500ml IMDM (Lonza #12-722F) +10% FBS +Penicillin/streptomycin +0.1mM Asparagine +2mM L-glutamine +11ug IL7 +2.2ul B-mercaptoethanol +Non-essential amino acids (100uM each of Glycine, L-alanine, L-asparagine, L-aspartic acid, L-glutamic acid, L-proline, L-serine)

extract_protocol:
RNA was isolated from lymphoma cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.

treatment_protocol: Lymphoma cells were treated with OHT (50nM) to induce PRDM15 deletion or EtOH (control) for 24 hours and reseeded for collection 3 days post EtOH/OHT treatment.

value: Primary mouse lymphoma

value: B-cells

value: E mu-Myc transgenic

value: PRDM15 KO


title: BCELL_PRDM15KO_2


title: 3496-SP-9

description: poly-A enriched RNA


title: 3496-SP-10

description: poly-A enriched RNA


title: small intestine spf 1

description:
SI SPF 1
SI_read_counts.xlsm
SI.ANOVA_GFvSPF.csv
SI.WALD_GFvSPF.csv


title: small intestine spf 3

description:
SI SPF 3
SI_read_counts.xlsm
SI.ANOVA_GFvSPF.csv
SI.WALD_GFvSPF.csv


title: 3496-SP-5

description: poly-A enriched RNA


title: 3496-SP-6

description: poly-A enriched RNA


title: BCELL_PRDM15KO_1


title: 3496-SP-3

description: poly-A enriched RNA


title: small intestine turi 3

description:
SI Turi 3
SI_read_counts.xlsm
SI.ANOVA_GFvTURI.csv
SI.WALD_GFvTURI.csv


title: 3496-SP-2

description: poly-A enriched RNA


title: 3496-SP-1

description: poly-A enriched RNA


title: BCELL_WT_2


title: small intestine turi 2

description:
SI Turi 2
SI_read_counts.xlsm
SI.ANOVA_GFvTURI.csv
SI.WALD_GFvTURI.csv


title: BCELL_WT_1


title: 3496-SP-4

description: poly-A enriched RNA


title: small intestine turi 1

description:
SI Turi 1
SI_read_counts.xlsm
SI.ANOVA_GFvTURI.csv
SI.WALD_GFvTURI.csv


title: U937 infected or not with Y. pestis WT, targeting infected, rep2

city: Chicago

first: Yan

last: Li

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

description: Sample 6

data_processing:
Sequencing reads were first de-multiplexed by using the barcode in the reverse primer, and processed by Cutadapt to remove sequences from beginning to sgRNA priming site primers.
Trimmed reads were used to map sgRNA sequences to pooled GeCKO v2 libraries A. Read counts of sgRNA for each sample were quantified by MAGeCK v5.6.0.
Count data were filtered and normalized, and essential sgRNA and genes were ranked by MAGeCK v5.6.0.
Enriched genes were identified via MAGeCK v5.6.0.
Genome_build: GeCKO v2 libraries A
Supplementary_files_format_and_content: excel files include the occurrence of each sgRNA indexes in LibraryA for all samples

growth_protocol: U937 cells were transduced with the pooled human GeCKO v2.0 lentiviral library via spinfection. Briefly, 3x10^6 cells per well were plated into a 12-well plate in RPMI 1640 containing 10% FCS (RPMI-FCS), and polybrene (8 µg/ml). Wells received between 0 to 50 µl of the viral preparation. Next, the 12-well plate was centrifuged at 1,500 x g for 2 hours at 37°C. Cell pellets were suspended in fresh RPMI-FCS and incubated for 48 hours at 37°C under 5% CO2. Cells were centrifuged, counted, and samples split into two wells with one well containing 2.5 µg/ml puromycin (Gibco). After 3 days, cells were counted, and the transduction efficiency was calculated as cell count from wells containing puromycin divided by cell count from wells without puromycin, and multiplied by 100.

extract_protocol:
Genomic DNA was extracted with a Blood & Cell Culture Midi kit (Qiagen) and used to prepare a sgRNA library with a two-step PCR protocol. The first PCR was used to amplify the sgRNA containing cassette. Amplified products were subjected to a second PCR with a primer pair encoding a unique 8-bp barcode required for multiplexing along with a stagger sequence to increase library complexity. The resulting amplicons from the second PCR were gel extracted, quantified, mixed and sequenced using a HiSeq 2500 (Illumina).
The pooled human GeCKO v2.0 lentiviral library was obtained from Addgene (Feng Zhang, Massachusetts Institute of Technology, Cambridge, MA).
The GeCKO v2.0 lentiviral library expresses RNA guided endonuclease Cas9 and short guide RNAs (sgRNA) targeting 19,052 genes (three sgRNAs per gene).

treatment_protocol: U937 cells transduced with the GeCKO lentiviral library were infected with Y. pestis or mock for 12 hours at MOI of 100. Following infection, resistant cells were cultured in the presence of 2.5 μg/ml puromycin until reaching approximately 70% confluence and then reseeded and re-infected. Following incubation for 12 hours, the resistant cells were cultured in the presence of 2.5 µg/ml puromycin.

value: macrophage


title: BCELL_WT_3

value: wild type


title: U937 infected or not with Y. pestis WT, targeting un-infected, rep2

description: Sample 5


title: 3496-SP-8

description: poly-A enriched RNA


title: small intestine gf 4

description:
SI GF 4
SI_read_counts.xlsm


title: U937 infected with Y. pestis WT and lcrV mutant, targeting WT

description: Sample 3


title: small intestine gf 3

description:
SI GF 3
SI_read_counts.xlsm


title: U937 infected or not with Y. pestis WT, targeting un-infected, rep1

description: Sample 1


title: small intestine gf 1

description:
SI GF 1
SI_read_counts.xlsm


title: small intestine gf 5

description:
SI GF 5
SI_read_counts.xlsm


title: SI2

city: Guangzhou

first: Xiang

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

description: SI.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean  reads were than mapped to mm10 genome with HISAT2 compares software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Heart

extract_protocol:
Total RNAs from C57BL/6J and Slit2-Tg hearts after IR or non-IR were isolated using TRIzol® Reagent(Thermo Fisher Scientific, USA). Each group contains three independent samples. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart


title: Testis, 1/6738 E2F3 lox/lox  Rb lox/lox

city: Turku

first: Emmi

last: Rotgers

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA44

data_processing:
The 44 libraries were pooled into a single pool
The samples were sequenced in a single run with Illumina MiSeq instrument using v2 sequencing chemistry.
Single-read sequencing with 1 x 50 bp read length was used, followed by 6 bp + 8 bp dual index run.
Technical quality of the MiSeq run was good and the cluster amount was as expected. Greater than 90% of all bases above Q30 was requested.
The results were submitted to the Illumina BaseSpace data-management and analysis interphase.
The TruSeq Targeted RNA sequencing application v1.0 was used to analyze differential expression of the transcripts in the experimental groups. Briefly, the depth of sequencing between samples was estimated and the expression level for each replicate were normalized based on the total number of aligned reads. The normalized transcript abundance was modeled by a negative binomial distribution model and this model was used to derive a p-value for the differential expression of each transcript. Finally, the application corrected for multiple hypothesis testing by adjusting the p-value for false discovery rate (FDR) by using the Benjamini-Hochberg method.
Genome_build: Hprt, Rpl19 and Ppia were used as reference genes for normalization during the analysis.
Supplementary_files_format_and_content: The TruSeq Targeted RNA sequencing application v1.0 was used to analyze differential expression of the transcripts in the experimental groups.

source_name: testis

extract_protocol:
Testes were removed, flash frozen on dry ice and total RNA was isolated from P10 (control only) and adult mouse testis (n=4-5/group) using the RNeasy Mini kit (cat. # 74104, Qiagen). Subsequently, the obtained total RNA was treated with RNase-free DNase (cat. # 79254, Qiagen) and purified using the RNeasy MinElute Clean-up kit (cat. # 74204, Qiagen). RNA quality and concentration were determined using Nanodrop.
The library preparation and sequencing were performed at the FFGC (Finnish Functional Genomics Centre, Turku, Finland). Prior to the library preparation the quality of the total RNA samples was ensured using Agilent Bioanalyzer 2100 and Advanced Analytical Fragment Analyzer. Total RNA samples were pure, intact and all samples had similar quality. Bioanalyzer RIN values were > 9.0. Fifty ng of RNA was taken for the library preparation. Library preparation was done according to Illumina TruSeq® Targeted RNA Expression Guide (part # 15034665).

value: mix:B6, C57BL/6, FVB

value: WT

value: testis


title: SI3

description: SI.txt


title: SI1

description: SI.txt


title: Testis, 10/6731  cre-  E2F3 lox/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA42


title: small intestine gf 2

description:
SI GF 2
SI_read_counts.xlsm

value: male


title: small intestine turi 4

description:
SI Turi 4
SI_read_counts.xlsm
SI.ANOVA_GFvTURI.csv
SI.WALD_GFvTURI.csv

value: female


title: U937 infected with Y. pestis WT and lcrV mutant, targeting mutant

description: Sample 4


title: Testis, 30/6678   cre-  E2F3 wt/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA41


title: SC2

description: SC.txt


title: U937 infected or not with Y. pestis WT, targeting infected, rep1

description: Sample 2


title: SC1

description: SC.txt


title: Testis, 10/7037 cre+   E2F3 lox/lox  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA39

value: SCdKO


title: keratinocyte pLXSN-HPV8-E7 #3

city: Cologne

first: Matthias

last: Kirschberg

state: NRW

address: Fürst-Pückler-Str. 56

department: Institute of Virology

institute: University of Cologne

description: gene expression data from primary human adult skin keratinocytes expressing the pLXSN-HPV8-E7

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data processing was carried using the Transcriptome Analysis Console v.4.0.1.36 and Excel
RMA

label: not applicable

source_name: primary human adult skin keratinocytes

label_protocol: standard Affymetrix protocol

growth_protocol: keratinocytes were cultured on 3T3 feeder cells (passage 0). For retroviral transduction, cells were cultivated in Defined Keratinocyte-SFM (Thermo Fisher Scientific)

extract_protocol: Total cellular RNA was extracted using the QIAGEN RNeasy Mini Kit

value: keratinocytes isolated from adult skin, retrovirally transduced in passage 1, selected in passage 2, total RNA extracted in passage 3 for analysis


title: CI3

description: CI.txt


title: CI2

description: CI.txt


title: keratinocyte pLXSN-HPV8-CE #2

description: gene expression data from primary human adult skin keratinocytes expressing the pLXSN-HPV8-CE


title: Blastocysts, W-XY-8

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

hyb_protocol: The fragmented and labeled sample was hybridized for 17 (+/- 1) hours on an Mouse Gene 1.0 ST Affymetrix GeneChip™ (Thermo Fisher Scientific) using the respective Hybridization, Wash and Stain Kit  (Thermo Fisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Affymetrix microarrays were scanned using a GeneChip® Scanner 3000.

data_processing: The data was normalized using the Robust Multi-Array (RMA) in the BioConductor package affy.

source_name: Blastocyst

label_protocol: Purified target cDNA was fragmented and Biotin-labeled using the FL-modul (NuGEN) according to the manufacturer’s instructions.

growth_protocol: For a period of nine weeks a three-week-old cohort of seven male and female NMRI mice were fed a modified D12492 high-fat, high-calorie diet (HFD, E15741-34; ssniff, Soest, Germany), and another cohort of 14 male and female animals received a control diet to D12492 (CD, ssniff).

extract_protocol: Single blastocysts were lysed in 10 µl buffer using Direct Lysis Kit (NuGEN, Leek, Netherlands) according to the manufacturer’s instructions. For whole-transcriptome gene expression analysis the lysate of three sex-matched blastocysts from one mother were pooled. Targets for the microarray analysis were generated using the Ovation One-Direct System (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: At the age of 12 weeks, HFD mice were mated with CD mice and as control group, CD fed animals were mated with each other. During mating all animals were fed the CD and screened for vaginal plugs every morning and evening. At day 3.5 post coitum (dpc), female mice were sacrificed by cervical dislocation and blastocysts were isolated in M2 medium. Blastocysts were washed three times in PBS, separately snap frozen in PBS, and stored at -80 °C until used for further analysis. For whole-transcriptome gene expression analysis the lysate of three sex-matched blastocysts from one mother were pooled (n=4) and analyzed on an Affymetrix GeneChip™ (Thermo Fisher Scientific) according to the manufacturer’s instructions.

tag: diet of parents

value: High fat diet (HFD) (obese mother)

tag: sex of blastocyst

value: blastocyst


title: keratinocyte pLXSN-HPV8-E7 #2


title: Blastocysts, W-XY-6

tag: tissue


title: Testis, 3/6613 cre- E2F3 lox/wt  Rb lox/wt

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA40


title: CI1

description: CI.txt


title: keratinocyte control #1

description: gene expression data from primary human adult skin keratinocytes harboring the pLXSN vector


title: keratinocyte pLXSN-HPV8-CE #1


title: Testis, 3/6969 cre+  E2F3 lox/lox  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA37


title: keratinocyte control #3


title: keratinocyte pLXSN-HPV8-E7 #1


title: Testis, 10/6977 cre+  E2F3 lox/lox  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA38


title: Blastocysts, W-XY-5


title: Blastocysts, W-XY-7


title: CC3

description: CC.txt


title: Blastocysts, W-XX-20


title: keratinocyte pLXSN-HPV8-CE #3


title: CC1

description: CC.txt


title: p53activation rep5

first: Margot

middle: Elizabeth

last: Bowen

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Reads were aligned to the genome using HISAT2 version 2.0.4
Sorted BAM files were generated using SAMtools version 1.3.1
The number of reads mapping to each gene in the Ensembl database (version GRCm38.87) was counted using HTSeq-count version 0.6.1
Differential gene expression analysis was performed using DESeq2 version 1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Bowen_Counts.txt: file containing the number of reads in each library that mapped to each gene in the Ensembl database
Supplementary_files_format_and_content: Bowen_Deseq2.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing embryos with activated p53 (n=5)  to embryos with basal p53 (n=5).

molecule: polyA RNA

source_name: FACS-isolated neural crest cells

extract_protocol:
E10.5 mouse embryos were harvested in cold PBS and were digested in 0.1% Trypsin for 15 min at 37 °C with intermittent agitation. Cells were resuspended in sorting buffer (PBS, 1% fetal calf serum, 1 mM EDTA), filtered through a 35 μm nylon mesh (Corning), and stained with the viability dye 7AAD (Biolegend). FACS-based isolation of GFP-positive cells was performed on instruments at the Stanford Shared FACS Facility. After sorting, cells were pelleted and lysed in TRIzol (ThermoFisher) and RNA was extracted using the RNeasy mini kit (Qiagen).  RNA quality was assessed using a Bioanalyzer, and only samples with an RNA integrity number (RIN) greater than 8.0 were used for library preparation.
RNA-Seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina). Each library was prepared from 300ng to 1ug of RNA that had been obtained from FACS-isolated cells from a single E10.5 embryo.

value: mixed 129/Sv-C57BL/6

value: embryonic day 10.5


title: Testis, 1/6729  cre+  E2F3 lox/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA32


title: keratinocyte control #2


title: Testis, 30/6931 cre+ E2F3 lox/lox   Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA36


title: Testis, 3/6730   cre+  E2F3 lox/wt Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA33


title: Blastocysts, W-XX-18


title: Blastocysts, M-XY-9

value: High fat diet (HFD) (obese father)


title: Testis, 10/6930 cre+ E2F3 lox/lox   Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA35


title: Blastocysts, W-XX-17


title: Blastocysts, M-XY-11


title: Blastocysts, M-XY-12


title: Blastocysts, M-XX-23


title: Blastocysts, M-XX-22


title: Blastocysts, M-XY-10


title: CC2

description: CC.txt


title: Blastocysts, W-XX-19


title: Blastocysts, K-XY-4

value: Control Diet (CD) (lean parents)


title: Blastocysts, M-XX-24


title: Blastocysts, K-XY-2


title: Blastocysts, K-XY-1


title: Blastocysts, K-XX-16


title: Testis, 4/6679  cre+    E2F3 lox/wt Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA31


title: p53activation rep3


title: Blastocysts, M-XX-21


title: Blastocysts, K-XY-3


title: Blastocysts, K-XX-15


title: Testis, 1/6797 cre+  E2F3 lox/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA34


title: p53activation rep4


title: Blastocysts, K-XX-14


title: p53activation rep2


title: p53activation rep1


title: DCMA4

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw FASTQ files were generated using Illumina NextSeq Control software (version 2.02). For RNA-Seq analysis, initial sequencing quality was inspected using FASTQC. Next,transcript counts were estimated using kallisto with human reference transcriptome built from refseq database using linux command ;wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.*.rna.fna.gz;
Quantification of raw transcript counts for each dataset by using following command:    kallisto --single -l 180 -s 20 ; pachterlab.github.io/kallisto/
Expression testing:  Differential gene expression from the kallisto counts data was performed using the Bioconductor package DESeq2. Read counts for control and patient fibroblasts were compared to determine the log2-fold change in abundance for each transcript. Raw p-values were adjusted for multiple comparisons with the Benjamini-Hochberg method
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: DCMA_dermal fibroblasts

extract_protocol:
Total RNA was extracted from DCMA fibroblasts (n=4) and control fibroblasts (n=4) using the RNA extraction Mini kit (Invitrogen) according to the manufacturer’s protocol. RNA purity was assessed and quantified using Nanodrop and a Qubit 2.0 fluorometer (ThermoFisher Scientific). The sequencing library was prepared using 2 μg of RNA and the TruSeq Stranded mRNA library preparation kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: pediatric patient with dilated cardiomyopathy with ataxia syndrome (DCMA)

value: dermal fibroblasts

tag: passages


title: Testis, 30/6849 cre+    E2F3 wt/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA28

value: SCRbKO


title: Blastocysts, K-XX-13


title: spp1 knockout galactose 15 mins

city: Oxford

first: Jane

last: Mellor

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: NET-Seq
FASTQ files with sanger (+33) encoded quality scores were uploaded to Galaxy (Blankenberg et al., 2010). Adaptor sequences were clipped and reads shorter than 15nt after clipping were discarded. Reads were aligned to the S. cerevisiae genome (2011 assembly) using Bowtie for Illumina (Langmead, 2010). Parameters were chosen so non-uniquely aligned reads were discarded (-n 1, -e 70, -l 28, -k 1, -m 1). The SAM file output was converted to a BAM file and downloaded
Read counts were determined at individual S cerevisiae genes using codes written in MATLAB.
Genome_build: sacCer3
Supplementary_files_format_and_content: Excel file contains nascent transcription levels at 5,222 S cerevisiare genes in a window between the TSS and a point 300bp downstream.

organism: Saccharomyces cerevisiae BY4741

source_name: Log-phase budding yeast

growth_protocol: Cells were grown in 25 mL YPD (1% yeast extract (Difco), 1% bactopeptone, 2% glucose) overnight. This was used to inoculate 1 L of YPD in a 2 L flask to give a starting OD600 of 0.2. 2 L of cells were grown (30°C, 170 rpm) to OD600 of 0.65 (mid-log) and harvested by filtration onto a 0.45 μm pore size, 90 mm diameter nitrocellulose filter paper (Whatman). Cells were scraped off the filter paper with a spatula pre-cooled in liquid nitrogen and flash frozen in liquid nitrogen. Cells were ground in 6 cycles of 3 min at a 15 Hz shaking frequency in a 50 mL grinding jar (Retch) with a 25 mm stainless steel ball using a Retsch MM400 mixer mill. The grinding chamber was cooled in liquid nitrogen in between cycles. 1 g of yeast grindate was stored at −80°C.

extract_protocol:
1 g of yeast grindate was resuspended in Lysis buffer A (20 mM HEPES (pH 7.4), 110 mM KOAc, 0.5% Triton X-100, 0.1% Tween 20, 10 mM MnCl2, 1x proteinaseinhibitors (complete, EDTA-free (Roche)), 50 U/ml SUPERase.In (Invitrogen)). Resuspended grindate was incubated (4°C, 20 min) with 660 U of DNase I (Promega). Insoluble cell debris was pelleted by spinning (16,000 g, 4°C, 10 min). Supernatantswere combined (a 20 μL input sample was taken and combined with 20 μL 2 × SDS loading buffer (80 mM Tris-HCl (pH 6.8), 200 mM DTT, 3.2% SDS, 0.1% Bromophenol Blue, 1.6% glycerol)) and added to 0.5 mL of anti-FLAG M2 affinity agarose beads (Sigma) pre-washed with 2 × 10 mL Lysis buffer A (without SUPERase.In). Beads and supernatant were incubated (4°C, 2.5 h) on a nutator, before spinning (1,000 g, 4°C, 2 min). A 20 μL unbound sample was taken and combined with 20 μL 2 × SDS loading buffer. Beads were washed four times with 10 mL Wash buffer A (20 mM HEPES (pH 7.4), 110 mM KOAc, 0.5% Triton X-100, 0.1% Tween 20, 1 mM EDTA). Beads were incubated (30 min, 4°C) twice with 300 μL of Elution buffer (Lysis buffer A with 1 mg/mL 3 × FLAG peptide (Sigma)). The elution supernatants were combined (a 20 μL elute sample was taken and combined with 20 μL 2 × SDS loading buffer) and RNAs were extracted using a miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. For the sequential IP procedure, the elution supernatants from two IPs were combined giving a total of 1200 ul and added to 15 ul anti-HA dynabeads (Pierce) pre-washed with 2 × 1 mL Lysis buffer A. Beads and supernatant were incubated (4°C, 2.5 h) on a nutator. A 20 μL secondary unbound sample was taken and combined with 20 μL 2 × SDS loading buffer. Beads were washed five times with 1 mL Wash buffer A. Beads were resuspended in 100 uL Lysis buffer A (a 5 uL secondary elute sample was taken and combined with 15 uL Lysis buffer A and 20 uL 2 × SDS loading buffer) and RNAs were extracted using a miRNeasy kit (QIAGEN) according to the manufacturer’s instructions.
Samples were submitted to Harvard Biopolymers facility. They determined DNA quality and quantity using the TapeStation (Agilent) and qPCR and then sequenced samples on an Illumina HiSeq 2000 machine. 50nt were sequenced from one end using the sequencing primer.

treatment_protocol: For galactose induction experiments 2 L of cells were grown to mid-log in 2 × 2 L flasks, then centrifuged (3000 rpm, 3 min) and then resuspended in 2 L YPG (1% yeast extract (Difco), 1% bactopeptone, 2% galactose) prewarmed to 30°C. Resuspended cells were returned to 2 L flasks, incubated (30°C, 170 rpm) and harvested by filtration as above after the requisite incubation time.

value: BY4741 RPB3-3xFLAG spp1{delta}

value: RPB3-3xFLAG-HisMX6, spp1::KanMX6

value: Log-phase budding yeast


title: Testis, 30/6780 cre+   E2F3 wt/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA27

value: mix:B6, C57BL/6, FVB

value: testis


title: DCMA2


title: spp1 knockout glucose


title: WT rep5


title: DCMA1


title: Testis, 1/6777 cre+   E2F3 wt/wt  Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA26


title: WT rep4


title: wild-type galactose 60 mins

value: BY4741 RPB3-3xFLAG


title: Testis, 30/6335  cre-   lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA25

value: WT


title: wild-type galactose 15 mins


title: WT rep3


title: control3

source_name: control_dermal fibroblasts

value: healthy control


title: WT rep2


title: H3K4me3 60mins after rapamycin Input

data_processing:
Reads were aligned to the S cerevisiae genome (build sacCer3) using bowtie2 with standard parameters. Prior to this, reads were first aligned to S. Pombe 2007 build (ASM294v2) to determine normalisation factors, and these aligned reads removed from subsequent analysis.
File type conversion from .sam to .bam, filtering of low quality reads, sorting, and other formattting were performed with Samtools. Genome wide coverage files were generatived with bedtools.
Data-sets were normalised according to total S pombe read counts, and read counts determined at individual S cerevisiae genes using codes written in MATLAB.
Genome_build: sacCer3
Supplementary_files_format_and_content: Excel file contains spike-in normalised H3K4me3 and H3K36me3 levels at 5,222 S cerevisiare genes in a window between the TSS and a point 300bp downstream, approximately corresponding to positions of +1 and +2 nucleosomes.

growth_protocol: Cells were grown in 25 mL YPD (1% yeast extract (Difco), 1% bactopeptone, 2% glucose) overnight. This was used to inoculate 1 L of YPD in a 2 L flask to give a starting OD600 of 0.2. 2 L of cells were grown (30°C, 170 rpm) to OD600 of 0.65 (mid-log) .

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 10 uL of anti-H3K4me3 (Millipore, 05-745R) or anti-H3K36me3 (abcam, ab9050) were used for precipitation
500 ng of RNA was used for library preparation with the Lexogen 3’ end RNA-seq library prep kit.

treatment_protocol: Before DNA purification, 25 % S. pombe cells were added (vol. at OD 0.6) as a spike-in control. . Rapamycin was added to a final concentration of 1 ug/mL and samples for RNA-seq were taken at indicated timepoints.

value: BY4741 Anchor-Away

value: MATa; his3D1; leu2D0; ura3D0; tor1D1; fpr1D; RPL13-2xFKBP12-NATMX6.


title: Testis, 1/6350 cre-   lox/wt

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA24


title: WT rep1

value: mixed 129/Sv-C57BL/6


title: wild-type glucose


title: Testis, 3/6343  cre-  lox/wt

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA23


title: control2


title: control1


title: H3K4me3 60mins after rapamycin IP


title: H3K4me3 40mins after rapamycin Input


title: control4


title: Testis, 10/6420 cre-     lox/wt

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA20


title: H3K4me3 40mins after rapamycin IP


title: Testis, 1/6155 cre- lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA21


title: H3K4me3 20mins after rapamycin Input


title: Irf5-/- BMDMs, infected with Rickettsia parkeri, with IFN-I

city: Berkeley

first: Thomas

middle: Patrick

last: Burke

address: 301 LSA

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Infections were performed with Rickettsia parkeri strain Portsmouth (30% prepared purity) at an MOI of 2.3 and RNA was harvested at 12 hpi. At this time, 71% of cells contained at least 1 bacterium (as determined by immunofluorescence microscopy).

data_processing:
Data was demultiplexed using CASAVA
Sequence data were aligned to the Mus musculus C57BL/6 reference genome (reference assembly GCA_000001635.8) using CLC Genomics Workbench (Qiagen).
Transcripts with Reads Per Kilobase of exon per Megabase of library size (RPKM) below 10.0 were excluded from the analysis.
Fold regulation of genes for each genotype was determined by referencing the sample to WT BMDMs that were infected with R. parkeri but not treated with IFN-I. Each data set was composed of at least 55 million reads and 98.3% of the reads aligned with the reference.
Genome_build: reference assembly GCA_000001635.8
Supplementary_files_format_and_content: Excel file containing fold change data

source_name: Bone marrow derived macrophages

growth_protocol: To obtain bone marrow: male or female mice were euthanized and femurs, tibias, and fibulas were excised. Visible muscle and connective tissue was removed from the bones and the bones were sterilized with 70% ethanol. Bones were washed with BMDM media (20% HyClone FBS, 1% sodium pyruvate, 0.1% β-mercaptoethanol, 10% conditioned supernatant from 3T3 fibroblasts, in Gibco DMEM containing glucose and 100 U/ml penicillin and 100 ug/ml streptomycin) and ground using a mortar and pestle. Bone homogenate was passed through a 70 μm nylon Corning Falcon cell strainer (Thermo Fisher Scientific, 08-771-2) to remove particulates. Filtrates were centrifuged in an Eppendorf 5810R at 1,200 RPM for 8 min, supernatant was aspirated, and the remaining pellet was resuspended in 30 ml BMDM media. Cells were then plated in 15 cm (non-TC treated) petri dishes and incubated at 37˚C. An additional 30 ml BMDM media was added 3 d later. At 7 d the media was aspirated and cells were incubated at 4˚C with 15 ml cold PBS (Gibco, 1x pH 7.4, no ions) for 10 min. BMDMs were then scraped from the plate, collected in a 50 ml conical tube, and centrifuged at 1,200 RPM for 5 min. The PBS was then aspirated, cells were resuspended in BMDM media and cell numbers were counted using trypan blue and a hemocytometer. For freezing, the pellet was resuspended in BMDM media with 30% FBS and 10% DMSO at 107 cells/ml. 1 ml aliquots were frozen in a styrofoam box at -80˚C for one day and then moved to liquid nitrogen.

extract_protocol:
At 12 hpi, cells were lysed and RNA was purified using an RNeasy purification kit (Qiagen). Dnase-treatment was performed on column according to the manufacturer's protocol.
RNA quality was assessed using an Agilent 2100 Bioanalyzer, and all samples had RIN values above 8.0. Transcripts were selected using polyA selection (using Dynabeads mRNA Purification Kit, Invitrogen) and enzymatically fragmented as part of the Apollo library prep kits (Wafergen PrepX RNA library prep for Illumina). Libraries were constructed by using Apollo 324 (IntegenX Inc.), PCR amplified, and multiplexed at the Functional Genomics Lab at the University of California, Berkeley (http://qb3.berkeley.edu/qb3/fgl/). The resulting libraries were sequenced at the Vincent J. Coates Genomics Sequencing Facility at the University of California, Berkeley using single-end reads, 50 base length, with a Hiseq 2000 Illumina platform.

treatment_protocol: For plating macrophages and infections: aliquots of BMDMs were thawed on ice, diluted into 9 ml of DMEM, centrifuged in an Eppendorf 5810R at 1,200 RPM for 5 minutes, and the pellet was resuspended in 10 ml BMDM media. The number of cells was counted and 5 x 10^5 cells were plated into 24 well plates. For infected cells, approximately 16 h later, 30% prep R. parkeri were thawed on ice and diluted into fresh BMDM media and added to the BMDMs to a multiplicity of infection (MOI) of 2.3. Media was then aspirated from the BMDMs, replaced with the media containing R. parkeri, and plates were spun at 300 G for 5 mins in an Eppendorf 5810R. For cells treated with recombinant type I interferon (IFN-I), approximately 4 ul of IFN-I (10,000 activity units, PBL, Cat # 12405-1) was added to each well at time=0. All cells were then incubated in a humidified CEDCO 1600 incubator set to 33˚C and 5% CO2 for the duration of the experiment. At 12 hpi, BMDMs were lysed according to the Qiagen RNeasy manufacturer's protocol.

value: Bone marrow derived macrophages

tag: genotype/variation

value: Irf5-/- BMDMs

tag: agent

tag: confluency

value: 5x10^5 in a 24 well plate


title: Testis, 3/6147 cre-lox/wt

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA19


title: Irf1-/- BMDMs, infected with Rickettsia parkeri, with IFN-I

description: Infections were performed with Rickettsia parkeri strain Portsmouth (30% prepared purity) at an MOI of 2.3 and RNA was harvested at 12 hpi. At this time, 71% of cells contained at least 1 bacterium (as determined by immunofluorescence microscopy). This sample was treated at the time of infection with 10,000 activity units of recombinant murine IFN-beta (PBL, Catalog number 12405-1).

value: Irf1-/- BMDMs


title: WT BMDMs, infected with Rickettsia parkeri, with IFN-I

description: Infections were performed with Rickettsia parkeri strain Portsmouth (30% prepared purity) at an MOI of 2.3 and RNA was harvested at 12 hpi. At this time, 71% of cells contained at least 1 bacterium (as determined by immunofluorescence microscopy). This sample was not treated with IFN-I.

value: WT BMDMs


title: H3K4me3 20mins after rapamycin IP


title: Testis, 31/6093 cre- lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA18


title: H3K4me3 0mins after rapamycin Input


title: Testis, 10/6256  cre-  lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA22


title: WT BMDMs, infected with Rickettsia parkeri, no IFN-I


title: H3K4me3 0mins after rapamycin IP


title: Testis, 1/6612 cre+ E2F3 lox/wt Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA30


title: Testis, 11/6091 cre- lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA17


title: WT BMDMs, uninfected, no IFN-I

description: Uninfected, untreated with IFN-I

value: uninfected, no IFN-I


title: Testis, 10/6088 cre- lox/lox

description:
2 months SC_E2F3_NormalizedHitsPerSample_M1
RNA16


title: Irf3/7-/- BMDMs, infected with Rickettsia parkeri, with IFN-I

value: Irf3/7-/- BMDMs


title: Liver_Male_Age_24

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

description: Gene expression data

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven

scan_protocol: Arrays were scanned on an Affymetrix GeneChip® scanner.

data_processing: Microarray data analysis was performed using Rosetta Resolver®

label_protocol: Affymetrix recommended protocol using Affymetrix Human Genome U133 Plus 2.0 GeneChips®

extract_protocol: Total RNA was isolated from human livers according to the TriReagent procedure

treatment_protocol: Human livers, male and female, approximately 21-45 years old and 69+ years old, were obtained frozen from CellzDirect (Durham, NC).

tag: gender

value: Male

value: young


title: Liver_Male_Age_44

description: Gene expression data

growth_protocol: Human livers, male and female, approximately 21-45 years old and 69+ years old


title: Liver_Male_Age_39

description: Gene expression data


title: Liver_Male_Age_43

description: Gene expression data


title: H3K36me3 60mins after rapamycin Input

value: Log-phase budding yeast


title: Liver_Male_Age_42

description: Gene expression data


title: Liver_Male_Age_21

description: Gene expression data


title: Testis, 11/6458 cre + lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA15

value: testis


title: hSMCs-Nutlin3a-rep3

city: Stanford

data_processing:
Reads were aligned to the genome using HISAT2 version 2.0.4
The number of reads mapping to each gene in the Ensembl database was counted using HTSeq-count version 0.6.1
Differential gene expression analysis was performed using DESeq2 version 1.14.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Bowen_hNCCs_hSMCs_counts.txt: file containing the number of reads in each library that mapped to each gene in the Ensembl database
Supplementary_files_format_and_content: Bowen_Deseq2_NCCNutlin_NCCDMSO.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing Nutlin3a-treated hNCCs (n=3) to DMSO-treated hNCCs (n=3)
Supplementary_files_format_and_content: Bowen_Deseq2_SMCNutlin_SMCDMSO.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing Nutlin3a-treated hSMCs (n=3) to DMSO-treated hSMCs (n=3)
Supplementary_files_format_and_content: Bowen_Deseq2_SMC_NCC.txt: output from DESeq2. Contains the mean expression values, fold changes and p values for each gene. Fold change was calculated by comparing DMSO-treated hSMCs (n=3) to DMSO-treated hNCCs (n=3)

source_name: early-stage smooth muscle cells, generated from H9 human embryonic stem cells

growth_protocol: H9 human embryonic stem cell colonies were detached using collagenase (2mg/ml, diluted in KnockOut DMEM) and clusters of 100-200 cells were plated in cranial neural crest cell (CNCC) differentiation medium (1:1 Neurobasal medium and D-MEM F-12 medium [Invitrogen]) supplemented with 0.5x B-27 supplement with Vitamin A (50x stock, Gemini Bio-Products), 0.5x N-2 supplement (100x stock, Gemini Bio-Products), 0.5x Glutamax-I supplement (100x stock, ThermoFisher), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich) and 5 μg/ml bovine insulin (Sigma-Aldrich)) to form neuroepithelial spheres. After seven days of differentiation, neuroepithelial spheres attached to the dish and migratory CNCCs began to form at the periphery of the spheres. After a further 3-4 days of differentiation, cells were passaged using Accutase onto fibronectin-coated plates in CNCC early maintenance media (1:1 Neurobasal medium and D-MEM F-12 medium (Invitrogen) supplemented with 0.5x B-27 supplement with Vitamin A (50x stock, Gemini Bio-Products ##400-160), 0.5x N-2 supplement (100x stock, Gemini Bio-Products #400-163), 0.5x Glutamax-I supplement (100x stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich) and 1 mg/ml bovine serum albumin (serum replacement grade, Gemini Bio-Products #700-104P)). After 1-2 passages, CNCCs were transitioned into long term maintenance media (CNCC early maintenance media supplemented with 3µM ChIRON 99021 (Selleck, CHIR-99021) and 50pg/ml BMP2 (Peprotech)). After 4 passages, CNCCs were either maintained in long term maintenance media for an additional 2 days, or were differentiated towards the smooth muscle cell lineage for 2 days in DMEM (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Omega).

extract_protocol:
RNA was extracted using Trizol
RNA-seq libraries were prepared for Illumina sequencing by Novogene Corporation

treatment_protocol: Cells were treated with 10 µM Nutlin-3a (Millipore Sigma) or 0.001% DMSO (vehicle control) and harvested after 8 hours for RNA-seq


title: H3K36me3 60mins after rapamycin IP


title: Testis, 10/6334  cre+    lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA14


title: H3K36me3 40mins after rapamycin Input


title: Testis, 10/6329  cre+    lox/lox

description:
5 months SC_E2F3_NormalizedHitsPerSample_M1
RNA13


title: Testis, 30/6732   cre-  E2F3 lox/wt Rb lox/lox

description:
2.5 months SC_RB_E2F3_NormalizedHitsPerSample_M1
RNA43

value: mix:B6, C57BL/6, FVB


title: hNCCs-Nutlin3a-rep3

source_name: neural crest cells, generated from H9 human embryonic stem cells


title: H3K36me3 40mins after rapamycin IP


title: Liver_Male_Age_79

description: Gene expression data

value: old


title: hSMCs-DMSO-rep3

value: DMSO