title: KO-P10-2

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Paired-end sequencing reads of Single nucleus RNA-seq were processed using publicly available the Drop-Seq Tools v1.12 software. Briefly, each mRNA read (read2) was tagged with the cell barcode (bases 1 to 12 of read 1) and unique molecular identifier (UMI, bases 13 to 20 of read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned using STAR v 2.5.2a to the mouse (mm10, Gencode release vM13). The intronic reads were also retained for downstream analysis. A custom Perl script was implemented in the Drop-Seq Tools pipeline to retrieve both exonic and intronic reads mapped to predicted strands of annotated genes. Uniquely mapped reads were grouped by cell barcodes. Cell barcodes were corrected for possible bead synthesis errors, using the DetectBeadSynthesisErrors program from the Drop-Seq Tools v1.12 software. To generate digital expression matrix, a list of UMIs in each gene (as rows), within each nucleus (as columns), was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given nucleus.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression matrix containing read counts for each gene (rows) in each cell/nucleus (columns)

molecule: nuclear RNA

source_name: Ventricle

extract_protocol:
Control (ERRαHet/ERRγWT) and KO (ERRαKO/ERRγKO) mouse hearts were rapidly dissected on ice 10am – 12pm of the day.  Ventricles were freshly processed or flash frozen in liquid nitrogen and subsequently kept at -80°C before nuclear isolation. Tissues were dounced 15 times with loose pestle and then 10 times with tight pestle. For nuclei purification, samples were ultracentrifuged at 25,000 rpm at 4 °C for 2 hours.
Single nucleus RNA sequencing was performed using the Drop-Seq method. Briefly, single nuclei, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (uFluidix). Nuclei in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by tagmentation of cDNA (Illumina), and amplified by PCR and purified by SPRI beads.

tag: developmental stage

value: postnatal 9-10 days

value: ERRalphaKO/ERRgammaKO

value: not determined

tag: datatype

value: sNucDrop-Seq


title: KO-P10-3

status: Public on Oct 01 2018

type: SRA

city: Philadelphia

state: PA

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: strain

tag: genotype

tag: Sex


title: KO-P10-1


title: Silc1+/+, sham, rep1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

library_source: genomic

data_processing:
Three replicates were combined for all the analysis into four groups (WT/KO, injury/sham).
Reads were mapped to the mouse genome (mm10 assembly) using Bowtie2 with the “-X 2000” parameter.
As ATAC-seq libraries typically contain multimodal fragment length distributions, and those were slightly different for different repeats, we performed the following subsampling procedure to unify the fragment length distribution. All the reads were first binned by their inferred insert length (obtained from the BAM file). We then traversed the bins, and kept in each bin an equal number of reads from each of the four groups (matching the read number in each bin to number of reads in the group which had the least reads in the bin), subsampling reads at random. This procedure resulted in 73,944,617 paired-end read mappings per group.
Peaks of accessible chromatin where then found in each group using MACS2 with the following parameters “callpeak -B -format BAMPE -g mm”.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peak coordinates and score

molecule: genomic DNA

source_name: DRG

growth_protocol: The study was conducted in accordance with the guidelines of the Weizmann Institutional Animal Care and Use Committee (IACUC). C57black6 Ola HSD male mice were purchased from Harlan Laboratories (Rehovot, Israel). All other mouse strains were bred and maintained at the Veterinary Resources Department of the Weizmann Institute.

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adjustment for application to tissue material. Six fresh L4-L6 DRGs were extracted in 100 µl ice cold cell lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630) for 5 minutes on ice, then a 21g needle on a 1 mL syringe was used to shear the tissue through the needle 5 times.
As in Buenrstro et al. 2013

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of xylazine and ketamine (10 mg/kg body weight). A 1-cm-long incision was made in the skin of the thigh perpendicular to the femur. A small incision was made between the thigh muscles and the muscles were separated by insertion and opening of the tip of the scissors between the muscles. The sciatic nerve was identified and pulled out using 45º forceps.  The tissue was crushed using fine forceps (Dumont no. 4) two times for 30 seconds at mid- thigh level. The sciatic was positioned back in its place by gently pooling the hind leg. The incision was closed using reflex wound clips.    Adult mouse DRGs were dissociated for neuron cultures with 100 U of papain followed by 1 mg/ml collagenase-II and 1.2 mg/ml dispase. The ganglia were then triturated in HBSS, 10 mM glucose, and 5 mM HEPES (pH 7.35). Neurons were recovered through percoll, plated on laminin, and grown in F12 medium for 48 hours (Hanz et al., 2003; Perlson et al., 2005; Rishal et al., 2010). Adult mouse DRG cultures were transfected with siGenome siRNAs using DharmaFect 4 (Dharmacon), replated 24 hr later

tag: tissue

value: dorsal root ganglia (DRG)

value: wildtype

tag: treatment

value: sham


title: Ctrl-P10-2

value: ERRalphaHet/ERRgammaWT


title: 515403A12_SLOT01_S01_Red_al

status: Public on Oct 02 2018

type: genomic

city: Vigo

first: Humberto

last: Quesada

address: Campus As Lagoas-Marcosende

department: Departamento de Bioquímica, Genética e Inmunología,

country: Spain

institute: Universidad de Vigo

description: DNA pool fropm British populations used in the array design

hyb_protocol: For each sample 20 μg of Cy3 (and Cy5) labeled cDNA was resuspended in 12 μL of hybridization solution, of which 6 μL was applied onto a subarray. Samples were randomly distributed in the subarrays.   Hybridization was carried out at 42°C for 72 h on a NimbleGen Hybridization System with continuous mixing. After hybridization, the arrays were washed in buffers of various stringencies using the NimbleGen Washing kit.

scan_protocol: Arrays were scanned using an Agilent G2565AA microarray scanner (Agilent Technologies) with a resolution of 2 μm.

data_processing:
For the analysis of variation in genomic sequence, each subarray hosted the DNA of one single individual and the DNA of a common reference sample. The data from scanning pictures generated by NimbleScan were parsed using ringo   (Toedling et al. 2007.BMC Bioinformatics 8, p. 221), an R/Bioconductor package.
The signal intensity data for each channel was corrected for the local background signal using the normexp + offset method (Ritchie et al. 2007. Bioinformatics 23: 2700-2707), log2-transformed, and quantile normalized using the method proposed   by Yang and Thome 2003. Notes Monogr Ser. 40: 403-418 for two channels, as implemented in the package limma for R/Bioconductor (Smyth 2005. Linear Models for Microarray Data). We performed a probe-level data analysis to test DNA sequence   differences between the distinct gene fragments included in a probe set and the hybridized DNA. To exclude probes that were not accurately detected in the array, probes with an average hybridization signal lower than the “background signal” of each   channel were disregarded. Only genes containing probes that simultaneously passed genome and expression profiling filters were used in the subsequent analyses.

organism: Littorina saxatilis

source_name: Foot muscle CGH

label_protocol: The NimbleGen/Roche Dual label kit was used to label the reference sample (Cy5 dye) and the DNA of each specimen (Cy3 dye) following manufacturer´s instructions.

extract_protocol: Genomic DNA was isolated from the foot muscle tissue of single snails using a CTAB extraction method (Wilding et al. 2001. Evol Biol. 14: 611-619) modified to include RNAse treatment. DNA samples were further cleaned with NucleoSpin columns   (Macherey- Nagel) following manufacturer´s instructions. DNA purity was assessed using a NanoDrop spectrophotometer (NanoDrop Tech. Inc., Wilmington, DE). All extractions were standardized to 100ng/μL after checking their integrity in agarose gels.

tag: sample number

tag: ecotype

value: SU

tag: locality

value: Silleiro

tag: reference

value: DNA pool of 100 snails from two British L. saxatilis populations (Dunvar and Thornwick)


title: Ctrl-P10-1


title: Silc1-/-, injury, rep3

value: injured


title: Silc1+/+, injury, rep1


title: wt_VSV

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

country: China

institute: Peking University

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

molecule: total RNA

source_name: Bone marrow

growth_protocol: Immortalized bone marrow derived macrophages were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin on 6-well for further experiments.

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by VSV for 0 or 6 hours

value: Bone marrow

tag: cell type

value: wild type

tag: infection

value: vesicular stomatitis virus


title: Silc1-/-, sham, rep2


title: Ctrl-P6-2

value: postnatal 6 days


title: Ctrl-P10-3


title: Silc1-/-, injury, rep1


title: Ctrl-P6-1


title: DRG WT sham day 7 1

data_processing:
Quantification using RSEM
Alignment to the mm10 mouse genome using STAR2
Preparation of bigWig files using wigToBigWIg
Genome_build: mm10
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from total DRGs pooled from 3 animals, using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s protocol.
TruSeq stranded mRNA kit

tag: genotype/variation

value: sham day 7


title: Silc1-/-, sham, rep1


title: DRG Silc1 KO injury day 7 2

value: Silc1 KO

value: injury day 7


title: DRG Silc1 KO sham day 4 5

value: sham day 4


title: DRG Silc1 KO sham day 4 2


title: DRG Silc1 KO sham day 4 1


title: DRG Silc1 KO injury day 4 4

value: injury day 4


title: DRG Silc1 KO injury day 4 3


title: DRG WT sham day 4 3


title: DRG WT sham day 4 5


title: DRG WT injury day 7 1


title: DRG Silc1 KO injury day 4 1


title: DRG Silc1 KO sham day 7 1


title: DRG WT sham day 7 2


title: DRG Silc1 KO sham day 4 4


title: DRG WT injury day 4 3


title: DRG WT injury day 7 2


title: DRG Silc1 KO sham day 7 2


title: DRG Silc1 KO injury day 4 5


title: Silc1 KO brain 1

source_name: Adult brain


title: DRG Silc1 KO injury day 7 1


title: DRG WT injury day 4 5


title: WT brain 1


title: DRG WT injury day 4 1


title: DRG Silc1 KO sham day 4 3


title: WT brain 5


title: Silc1 KO brain 3


title: DRG Silc1 KO injury day 4 2


title: DRG WT injury day 4 2


title: DRG WT sham day 4 2


title: Ctrl-P6-3

value: not determined

value: sNucDrop-Seq


title: WT brain 2


title: Silc1 KO brain 4


title: Silc1 siRNA, rep1

source_name: Cultured DRG neurons

value: Silc1 siRNA


title: Control siRNA, rep3

value: Control siRNA


title: Norris1 siRNA, rep3

value: Norris1 siRNA


title: Silc1 siRNA, rep2


title: WT brain 3


title: Norris1 siRNA, rep1


title: Silc1 KO brain 2


title: Atf3 siRNA, rep1

value: Atf3 siRNA


title: Sox11 siRNA, rep1

value: Sox11 siRNA


title: Control siRNA, rep2


title: Silc1 KO brain 5


title: Control siRNA, rep1


title: WT brain 4


title: DRG 7 days after sham operation, rep1

value: 7 days after sham operation


title: DRG 7 days after sham operation, rep3


title: DRG 7 days after sciatic nerve injury, rep3

value: 7 days after sciatic nerve injury


title: DRG 7 days after sciatic nerve injury, rep1


title: DRG 7 days after sciatic nerve injury, rep2


title: DRG 4 days after sciatic nerve injury, rep3

value: 4 days after sciatic nerve injury


title: DRG 1 day after sham operation, rep3

value: 1 day after sham operation


title: DRG 4 days after sciatic nerve injury, rep1


title: DRG 4 days after sham operation, rep3

value: 4 days after sham operation


title: DRG 4 days after sham operation, rep1


title: Naïve DRG, rep1

value: naïve


title: DRG 1 day after sciatic nerve injury, rep2

value: 1 day after sciatic nerve injury


title: Peak2 [Trypanosoma brucei]

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw sequence files were QC assessed using FASTQC
Paired sequences were aligned to the T. brucei genome using bowtie2 (version version 2.2.7; parameters: --very-sensitive -p 12 –no-unal –trim5 10)
BAM files were sorted and indexed using samtools (version 1.3)
Read counts were extracted from gene regions using bedtools (version v2.23.0; parameters: multicov)
All subsequent processing was undertaken in R using Bioconductor packages
Genome_build: Genome obtained from ftp.sanger.ac.uk/pub/project/pathogens/gff3/CURRENT/ Jan 2015
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts

organism: Trypanosoma brucei brucei

source_name: mouse blood

extract_protocol:
Trypanosomes were purified from whole blood by passage through a DE52 column, and RNA samples were prepared using the Qiagen RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions..
RNA-Seq was carried out by BGI Hong Kong.

tag: condition

value: peak/stumpy


title: DRG 1 day after sham operation, rep1


title: Peak1 [Trypanosoma brucei]


title: DRG 4 days after sciatic nerve injury, rep2


title: DRG 1 day after sciatic nerve injury, rep1


title: DRG 7 days after sham operation, rep2


title: Ascend3 [Trypanosoma brucei]

value: ascending/slender


title: DRG 1 day after sham operation, rep2


title: Naïve DRG, rep3


title: Peak3 [Trypanosoma brucei]


title: Ascend2 [Trypanosoma brucei]


title: Naïve DRG, rep2


title: Ascend1 [Trypanosoma brucei]


title: 47_MOLZ: mouse fed olanzapine (54mg/kg)  compacted in diet and minocycline in the drinking water (0.6mg/ml)

city: La Jolla

first: Olivia

last: Osborn

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

data_processing:
Reads were mapped to the mouse transcriptome using Bowtie2 algorithm
reads counted as reads per gene using RSEM
analyzed using the statistical algorithm limma
Genes were then sorted by their posterior error probability (local false discovery rate, FDR)
Genome_build: mm9
Supplementary_files_format_and_content: differentially expressed genes analyzed by limma:  contains normalized gene counts for each sample as well as average expression and fold change and local false discovery rate between groups

source_name: hypothalamus

extract_protocol:
mice were sacrificed and hypothalamus dissected. RNA extracted by TRIZOL according to manufacturers instructions.
TruSeq Library prep kits (Illumina)

value: female

value: hypothalamus

value: Olanzapine was compounded into high fat diet (HFD) (45 kcal% from fat) at a concentration of 54 mg/kg of diet (OLZ-HFD, Research Diets, Inc., D09092903, New Brunswick, NJ)


title: 40_MOLZ: mouse fed olanzapine (54mg/kg)  compacted in diet and minocycline in the drinking water (0.6mg/ml)


title: 37_MOLZ: mouse fed olanzapine (54mg/kg)  compacted in diet and minocycline in the drinking water (0.6mg/ml)


title: Jones-OM1

city: San Francisco

first: Pauline

middle: Anne Catherine

last: Marangoni

address: 513 Parnassus Avenue, HSE15

department: OFS

institute: UCSF

data_processing:
initial quality assessment using Cell Ranger pipeline
all additional filtering was done using SPRING tools (https://github.com/AllonKleinLab/SPRING_dev)
cells with less than 1000 total counts or more than 10% counts from mitochondrial genes were filtered out
cells characterized by distinct expression of immune genes and salivary duct markers were excluded from the analysis
Doublets were removed
Data was visualized in 2D as a force directed layout of a k nearest neighbors graph using SPRING Viewer
Genome_build: mm10
Supplementary_files_format_and_content: Jones-OM1_barcodes.tsv: table of all barcodes in sample OM1
Supplementary_files_format_and_content: Jones-OM2_barcodes.tsv: table of all barcodes in sample OM2
Supplementary_files_format_and_content: Jones-OM1_genes.tsv: table of all genes detected in sample OM1
Supplementary_files_format_and_content: Jones-OM2_genes.tsv: table of all genes detected in sample OM2
Supplementary_files_format_and_content: Jones-OM1_matrix.mtx: expression matrix for sample OM1
Supplementary_files_format_and_content: Jones-OM2_matrix.mtx: expression matrix for sample OM2

source_name: oral muccosa (buccal mucosa)

extract_protocol:
Cell Suspension from the buccal mucosa of 10 mice was submitted to the IHG 10X genomics platform (UCSF) for cell capture and barcoding using the Chromium Strategy. Single cell suspension was split into 2  technical replicates to assess batch effect.
cDNA libraries were prepared using the 10x Chromium Controller and the manufacturer's reagent kit. R2 are the biological reads, R1 are for Cell barcode / UMI and the remaining index read is for sample index.

tag: mouse strain

tag: mouse sex

value: females

tag: age

value: 12 week old


title: Jones-OM2


title: 48_MOLZ: mouse fed olanzapine (54mg/kg)  compacted in diet and minocycline in the drinking water (0.6mg/ml)


title: 31_MINO: mouse fed control diet and minocycline in the drinking water (0.6mg/ml)

value: control diet 45 kcal % from fat D09092903


title: 36_MINO: mouse fed control diet and minocycline in the drinking water (0.6mg/ml)


title: 35_MINO: mouse fed control diet and minocycline in the drinking water (0.6mg/ml)


title: 26_MINO: mouse fed control diet and minocycline in the drinking water (0.6mg/ml)


title: 14_OLZ: mouse fed olanzapine compacted in diet (54mg/kg)


title: 4_CNTL: mouse fed control diet


title: 5_CNTL: mouse fed control diet


title: 13_OLZ: mouse fed olanzapine compacted in diet (54mg/kg)


title: SGET8.2 D6 PGCLC

city: Rome

first: Jamie

last: Hackett

address: via Ramarini 32

department: Epigenetics & Neurobiology

country: Italy

institute: European Molecular Biology Laboratory (EMBL)

description: CRISPR screen; PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; replicate 1

data_processing:
Library strategy: Amplicon-seq
RNA-seq reads were quality-trimmed and aligned to mm10 with TopHat2 version: 2.0.13
Differentially expressed genes were called using DESeq2
Datastore analysis was performed with SeqMonk version: 1.36
CRISPR libraries were processed using MaGECK software version 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Fastq raw read files

molecule: other

source_name: D6 PGCLC

growth_protocol: Stella-GFP; Esg1-tdTomato (SGET) embryonic stem cells (ESC) were maintained and differentiated into epiblast-like cells (EpiLC) and primordial germ cell-like cells (PGCLC). For EpiLC, ESC were transferred to a well of a 12-well plate coated with human plasma fibronectin (Merck Millipore; 16.7 mg/ml) in N2B27 medium containing Activin A (20 ng/ml), bFGF (12 ng/ml) and knockout serum replacement (KSR; 1 %) for 42hrs. Purified EpiLC were seeded in ultra-low cell binding U-bottom 96-well plates (Nunc; 3x10e3 cells per well) in GK15 medium (GMEM, 15% KSR, NEAA, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine) supplemented with cytokines: BMP4 (500 ng/ml), LIF (1000 U/ml), SCF (100 ng/ml), BMP8a (500 ng/ml), and EGF (50 ng/ml) and collected on day2 or day6 of differentiation.

extract_protocol:
For fluorescence-activated cell sorting (FACS), cultured cells or embryoids were dissociated into single cells with TrypLE, and suspended in phosphate buffered saline (PBS) with 0.5% BSA or 3% FBS. Filtered cell suspensions were subsequently sorted using a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) or analysed with BD LSRFortessa X-20 (BD Biosciences). For exit from pluripotency analyses, cells were sorted/analysed based on absence or presence of Stella-GFP expression, whilst maintaining Esg1-tdTomato activitaion (SG+/-ET+). For PGCLC, cells were sorted/analysed based on Stella-GFP re-activation coupled with low Esg1-tdTomato. The threshold(s) levels for sorting was set and normalised based on expression levels in pre-optimised SGET ESC. A negative population of ESC without any fluorescence was used to set absolute thresholds. Forward and side scatters were used to gate for the cell population and doublets. For each sort the maximum number of cells was collected.
Sample1-36: For RNA-seq of Nr5a2-/-, Zfp296-/- and matched WT control cell lines, 100 ng of total RNA from triplicate biological independent experiments was used as inputs for the NEBNext Ultra RNA library Prep Kit for Illumina (NEB), with the library generated as per manufacturer’s instructions. During the final PCR amplification stage, 15 cycles of amplifications were performed to generate the adaptor ligated, fragmented cDNA for sequencing. Samples were assessed using the High Sensitivity D1000 ScreenTape assay (Agilent) to ensure the library did not contain primer-dimer contamination after last round of AMPure beads cleaning. The Qubit dsDNA HS assay kit (ThermoFisher Scientific) and the NEBNext Library Quant Kit for Illumina was used to accurately quantify the concentration of each library preparation. Samples were multiplexed with 12 indexes per lane and a total of 2 lanes of sequencing on Illumina HiSeq4000, single-end 50bp with an average depth of approximately 20 million reads per sample. Sample 37-42: ESC, EpiLC, or day 6 PGCLC (from the CRISPR screen) were dissociated into single cell solutions with TrypLE and sorted with a Sony SH800Z or a MoFlow high-speed cell sorter (Beckman Coulter) based on appropriate Stella-GFP and Esg1-tdTomato expression. Samples were sorted into 150ul of extraction buffer from the PicoPure RNA isolation kit (Life Technologies) and rapidly frozen on dry ice or liquid nitrogen. Total RNA was subsequently extracted using the PicoPure RNA isolation Kit, including a 15 minute on-column DNaseI digestion. RNA integrity number was assessed with RNA HS ScreenTape (Agilent), and all samples confirmed to have a RIN >8.5. For RNA-seq from CRISPR screen samples, 50 ng of total RNA was used as input for the Ovation RNA-seq System v2 (Nugen) as per manufacturer’s instructions. Amplified double-stranded (ds) cDNA was diluted into EDTA-low TE (Agilent) and sheared into ~230bp in length using S220 Focused-Ultrasonicator (Covaris) using settings: duty factor 10%, cycle burst 200, intensity 5, temp at 4°C and treatment time of 5 minutes per sample.  A high Sensitivity D1000 ScreenTape assay (Agilent) was used to assess the efficiency of library fragmentation. Fragmented ds-cDNA was concentrated with Qiagen Reaction Clean Up kit (MiniElute) and 1μg of the fragmented ds-cDNA used as input for the library preparation using Encore Rapid DR Multiplex Library System (Nugen). This kit ligated the adaptors to repaired-end ds-cDNA without amplification, which eliminated biases introduced during PCR amplification. The KAPA Library Quantification Kit (Kapa bioscience) was used to quantify the concentration of each adaptor-ligated libraries prior to multiplexing. The ESC, EpiLC and PGCLC RNA sequencing libraries were generated in parallel for each replicate, and the biological replicates were generated on independent occasions. Samples were multiplexed and sequenced with Illumina HiSeq1500, single-end 50bp read length with a minimum depth of approximately 15 million reads per sample.  Sample43-52: To quantify the relative frequencies of integrated gRNAs during the CRISPR screen in each population during cell fate transitions, genomic DNA was isolated from day 12 ESC post-lentiviral transduction, from SG–ET+ and SG+ET+ EpiLC populations at 42hr, and from SG+ETlow PGCLCs from day 6 embryoids, in biological duplicate using the DNeasy Blood & Tissue kit (Qiagen). Purified genomic DNA was used as template for custom primers that specifically amplify the gRNA region, and include overhanging Illumina adaptors and indexes to allow deep sequencing and multiplexing, respectively (synthesised as Ultramers from IDT) (see oligo tables). Prior to PCR, genomic DNA was sonicated with a Biorupter (Diagenode) for 15 seconds on ‘LOW’ power to improve efficiency of amplification. gRNA sequences were amplified in multiple PCR reactions to enable all isolated DNA to be utilised, each with NEBNext Q5 HotStart HiFi PCR Master Mix (NEB), 0.2 uM of universal forward primer (mix of staggers), 0.2 uM of indexed reverse primer and genomic DNA (~650 ng / 50 ul rxn). For amplification from the plasmid vector, 15 ng was used as template for replicate amplifications. The following cycling conditions were used: 95°C for 2 minutes, then between 21-26 cycles of (98°C for 20 seconds, 62°C for 20 seconds and 72°C for 20 seconds) followed by 72°C for 1 minute and hold at 4°C. The number of cycles was optimised for the point at which PCR products can be first visualised on an agarose gel. The PCR reaction was subsequently purified with AMPure XP beads (Beckman Coulter) using double size selection to remove primer dimers and genomic DNA. Briefly, 0.55x of AMPure beads were added to PCR reaction (1x) and incubated for 5 minutes at room temperature. The supernatant was collected; the beads contained the unwanted larger fragments and were discarded. An additional 0.3x of AMPure beads was subsequently added to the supernatant (1x) and incubated for 5 minutes at room temperature. The supernatant was removed and beads washed twice with 200 ul of 80% EtOH, air dried for 5 minutes and DNA was eluted from AMPure beads with EDTA-low TE buffer. The concentration of adaptor ligated gRNA amplicons was measured with the Qubit DNA Assay kit (ThermoFisher Scientific) and the fragment distribution determined with an Agilent D1000 ScreenTape System (Agilent Technologies). Libraries were subsequently multiplexed and sequenced with an Illumina HiSeq 1500 using single-end 50bp reads. As the sequences for all samples were identical up to the gRNA region, these types of low complexity libraries can produce low quality data. To counteract this, forward staggered primers were introduced at equal ratios during PCR amplification, generating offset reads. In addition, libraries were sequenced with 4 dark cycles and low density (70%) clustering.
Sample 1-42: RNA-seq; Sample 43-52: amplicon

value: mixed B6CBA background

tag: fluorescent reporter

value: Stella-GFP; Esg1-tdTomato

tag: facs

value: GFP+; Tomato_low


title: SGET8.5 D6 PGCLC

description: CRISPR screen; PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; replicate 2

tag: strain


title: SGET8.5 ESC

description: CRISPR screen; ESCs; replicate 2

source_name: ESC

value: GFP+; Tomato+


title: SGET8.5 EpiLC SG+ET+

description: CRISPR screen; EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; replicate 2

source_name: EpiLC SG+ET+


title: SGET8.5 EpiLC SG-ET+

source_name: EpiLC SG-ET+

value: GFP-; Tomato+


title: SGET8.2 EpiLC SG-ET+

description: CRISPR screen; EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; replicate 1


title: 17_OLZ: mouse fed olanzapine compacted in diet (54mg/kg)

tag: Sex


title: 3_CNTL: mouse fed control diet

tag: tissue


title: SGET8.2 ESC

description: CRISPR screen; ESCs; replicate 1


title: Silc1+/+, sham, rep3

value: dorsal root ganglia (DRG)

tag: genotype

value: wildtype

tag: treatment

value: sham


title: 11_CNTL: mouse fed control diet


title: SGET8.2 EpiLC SG+ET+


title: wild type parental (Zfp296) EpiLC

description: EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; wild type parental to Zfp296-/-

data_processing:
RNA-seq reads were quality-trimmed and aligned to mm10 with TopHat2 version: 2.0.13
Differentially expressed genes were called using DESeq2
Datastore analysis was performed with SeqMonk version: 1.36
CRISPR libraries were processed using MaGECK software version 1.5.2
Genome_build: mm10
Supplementary_files_format_and_content: Fastq raw read files

source_name: EpiLC


title: wild type clone #8 EpiLC

description: EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; matched wild type control clone to Zfp296-/-


title: 19_OLZ: mouse fed olanzapine compacted in diet (54mg/kg)


title: Zfp296-/- clone #42 EpiLC

description: EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF


title: wild type clone #11 EpiLC


title: Zfp296-/- clone #14 EpiLC


title: Nr5a2-/- clone #130 D6 PGCLC

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF


title: wild type clone #45 D6 PGCLC

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; matched wild type control clone to Nr5a2-/-


title: Nr5a2-/- clone #73 D6 PGCLC


title: wild type clone #72 D6 PGCLC


title: Nr5a2-/- clone #119 D6 PGCLC


title: wild type clone #72 D2 PGCLC

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; matched wild type control clone to Nr5a2-/-

source_name: D2 PGCLC


title: Nr5a2-/- clone #73 D2 PGCLC

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF


title: Nr5a2-/- clone #130 EpiLC


title: Zfp296-/- clone #18 EpiLC


title: Nr5a2-/- clone #130 D2 PGCLC


title: wild type parental D2 PGCLC 1

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; wild type parental to Nr5a2-/-


title: MPC2RAS2: CD11cLO macrophages from RAS kidneys

city: Rochester

first: Lilach

last: Lerman

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Paired-end reads were aligned to the mm10 mouse genome QIAGEN OmicSoft software’s OSA aligner and genes were annotated using Ensembl.R83
Raw counts were used to calculate differentially expressed genes using DESeq2
Transcripts per Million (TPM) scaling was performed using QIAGEN OmicSoft software
TPM values were quantile normalized using preprocessCore package in Bioconductor
Genome_build: mm10

source_name: CD11cLO macrophages from RAS kidneys

growth_protocol: Cells were flow sorted from mouse and no in vitro treatment was involved.

extract_protocol:
RNA-Seq was carried out using v4 Ultra Low-Input RT kit from Clontech (Catalogue#634889)
Nextera XT Library Preparation Kit from Illumina (FC-131-1024).

treatment_protocol: Control = Sham; Treatment = RAS; For RNA-seq, cells were prepared and stained with antibodies, washed with flow buffer, and subjected to flow sorter (BD Aria III). F4/80+CD64+macrophages from CD11chi, CD11clo and KRM and CD45+CD11b/cneg (Figure 1A-C) were sorted (n=2-5 samples/group) in RNA isolation lysis buffer (Qiagen Inc.; Flow sorting strategy, Figure 1).

value: 24 weeks

value: male

tag: flow sort time

value: 5 hours

value: Monocyte-derived macrophages from ischemic (RAS) kidneys


title: MPC3SHAM1: Kidney resident macrophages (KRM) from sham kidneys

value: Kidney-resident macrophages (KRM) from control kidneys


title: wild type clone #72 EpiLC

description: EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; matched wild type control clone to Nr5a2-/-


title: Nr5a2-/- clone #119 D2 PGCLC


title: MPC2RAS4: CD11cLO macrophages from RAS kidneys


title: MPC2RAS3: CD11cLO macrophages from RAS kidneys


title: wild type clone #45 D2 PGCLC


title: wild type parental D6 PGCLC 1

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; wild type parental to Nr5a2-/-


title: MPC3SHAM2: Kidney resident macrophages (KRM) from sham kidneys


title: Nr5a2-/- clone #73 EpiLC


title: MPC3RAS1: Kidney resident macrophages (KRM) from RAS kidneys

value: Kidney-resident macrophages (KRM) from ischemic (RAS) kidneys


title: wild type clone #45 EpiLC


title: MPC3RAS2: Kidney resident macrophages (KRM) from RAS kidneys


title: MPC2RAS1: CD11cLO macrophages from RAS kidneys


title: MPC2SHAM3: CD11cLO macrophages from sham kidneys

source_name: CD11cLO macrophages from sham kidneys

value: Monocyte-derived macrophages from control kidneys


title: Nr5a2-/- clone #119 EpiLC


title: MPC3SHAM4: Kidney resident macrophages (KRM) from sham kidneys


title: MPC2SHAM2: CD11cLO macrophages from sham kidneys


title: MPC3RAS3: Kidney resident macrophages (KRM) from RAS kidneys


title: MPC1RAS2: CD11cHI macrophages from RAS kidneys

source_name: CD11cHI macrophages from RAS kidneys


title: MPC1RAS1: CD11cHI macrophages from RAS kidneys


title: MPC1RAS3: CD11cHI macrophages from RAS kidneys


title: wild type parental EpiLC

description: EpiLC were collected at day2 of differentiation from ESC with ActA and bFGF; wild type parental to Nr5a2-/-


title: MPC1RAS4: CD11cHI macrophages from RAS kidneys


title: MPC3SHAM3: Kidney resident macrophages (KRM) from sham kidneys


title: MPC1SHAM2: CD11cHI macrophages from sham kidneys

source_name: CD11cHI macrophages from sham kidneys


title: MPC1SHAM3: CD11cHI macrophages from sham kidneys


title: MPC1SHAM1: CD11cHI macrophages from sham kidneys


title: N3

city: Guangzhou

first: Yi

last: Xiaochun

state: Guangdong

address: No. 107  West Road along the river, Yuexiu District

institute: Sun Yat-sen Memorial Hospital of the Sun Yat-sen University

description: total RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using TopHat v2.0.9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated usingusing a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: placenta

extract_protocol:
Placentas were removed, pulverized in liquid nitrogen. Total RNA was isolated using Trizol reagent (Life techologies) and puriﬁed with GeneJET RNA purification kit (Thermo) and RNase-free DNase set (QIAGEN) following manufacturer’s instructions.RNA electrophoresis was conducted to inspect RNA integration.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were killed by neck dislocation on day 13.5 of gestation

value: placenta

tag: group

value: normal


title: N2

description: total RNA


title: MPC2SHAM1: CD11cLO macrophages from sham kidneys


title: P53KO_UV_replicate1

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.35) tool: (1) removing the reads with adaptor contamination; (2) filtering the low-quality reads with ambiguous sequences ‘N’; (3) removing the low-quality bases (quality score < Q30).
All downstream analyses were based on clean, high quality data. Mapping of sequence reads were performed with STAR Aligner (v2.5.2) and differential expression analysis was performed using Cuffdiff tool of the Cufflinks suite. A Pearson’s correlation analysis was conducted to obtain the transcript-level R2 value between replicates.
We used the q-value < 0.01 (FDR) and the absolute value of |Fold change| ≥ 2 as the threshold to judge the significant differences of gene expression.
Genome_build: GRCm38.75
Supplementary_files_format_and_content: Microsoft Office Open XML Spreadsheet (RNA-seq abundance measurements in FPKM values across samples)

source_name: mouse emryonic fibroblasts

growth_protocol: Mouse embryonic fibroblast (MEF) cells from p53-/- knockout and p53-/-Cry1-/-Cry2-/- triple knockout mice in a C57BL/6J background were kindly provided from the laboratory of Aziz Sancar (University of North Carolina at Chapel Hill). Knockout MEF cells were maintained and grown in Dulbecco modified Eagle medium (DMEM) supplemented with penicillin at 50 U/ml, streptomycin at 50 μg/ ml, and 10% fetal bovine serum. The cells were maintained in an incubator at 37 °C under 5% CO2.

extract_protocol:
Total RNA was extracted from 8x10^5 UV-treated and non-treated cells using RNeasy mini kit (Qiagen, USA) according to the manufacturer’s instructions, and subjected to poly-A selection. The quality and quantity of RNA samples were assessed using Nanodrop 2000 spectrophotometer (Thermo Scientific, USA) and 2100 BioAnalyzer (Agilent, USA). Only the RNA samples with OD260/280 between 1.8 and 2.2, 28S:18S ≥ 1 and the RNA integrity number (RIN) ≥ 8 were used for library construction. After quality and quantity measurements, to remove residual genomic DNA, samples were treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg. Then, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA). Briefly, polyadenylated RNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. After that, the cleaved short RNA fragments were used as a template for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. AMPure XP beads (Beckman Coulter, USA) were used to clean up the double stranded cDNAs.
3’end adenine nucleotides were added and sequencing adaptors were ligated to the cDNA fragments followed by enrichment of libraries by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. 100X2 paired-end sequencing of four cDNA libraries with two biological replicates were performed using the Illumina HiSeq 2500 sequencing platform (Illumina, USA).

treatment_protocol: For UV-treatment assays, cells were seeded into six-well plates at 4x10^5 cells per well and incubated in growth medium for 16-20 h. Then, the cells were washed with 1x PBS (Phosphate Buffered Saline) and exposed to UV light (General electric germicidal lamp GT5, emitting mainly at 254 nm) for 40 seconds at a fluence of 40 J.m-2 with a fluence rate 1 J.m-2.s-1. UV light intensity was measured using a UVX Digital Radiometer (UVP, USA) at 264 nm. After UV-treatment, the cells were washed with 1xPBS, growth medium was added, and cells were incubated for 16 hours. After 16 hours incubation, cells were harvested for RNA extraction followed by RNA-seq library preparation. Non UV-treated cells were also used as control samples. RNA-seq was performed using two biological replicates for each of the conditions.

value: mouse embryonic fibroblasts

value: UV


title: A1

description: total RNA

value: abortion prone


title: P53KO_NT_replicate1

value: not treated


title: P53KO_NT_replicate2


title: mouse_brain_adult_male3

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

description: sample id: 1892sTS

data_processing:
RNA-seq reads were aligned to the assembled genomes of their corresponding species using STAR (version 2.2.1) using the 2-pass mapping mode and standard settings.
Aligned reads from all replicates of each organ were used to reconstruct transcripts through a genome-guided de novo transcriptome assembly using StringTie (version 1.3.4d) with the following parameters: -j 5 –g 50.
Assembled transcripts from each organ were then merged using Cuffmerge to define a unique set of transcripts. Expression levels (measured in FPKM) of the assembled transcripts were calculated with Cuffnorm (version 2.2.1) with --library-norm-method classic-fpkm.
Genome_build: human: hg38; macaque: rheMac8; marmoset: calJac3; mouse: mm10; rat: rn6; rabbit: oryCun2
Supplementary_files_format_and_content: *sample_name*.Signal.UniqueMultiple.str*N*.out.bw: STAR-generated bigWig tracks of the RPM-normalized read coverage from each sample. Files represent reads mapped on the forward (N=1) or reverse (N=2) strand.

source_name: Adult brain

extract_protocol:
QIAGEN RNeasy Kit
Single-end strand-specific RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit according to manufacturer instructions. Libraries were sequenced using the Illumina HiSeq 2500.

value: brain

tag: developmenta stage

value: adult


title: A3

description: total RNA


title: mouse_heart_adult_male3

description: sample id: 2659sTS

source_name: Adult heart

value: heart


title: N1

description: total RNA


title: mouse_liver_adult_male3

description: sample id: 1894sTS

source_name: Adult liver

value: liver


title: P53CRYKO_UV_replicate1

tag: cell type


title: mouse_heart_adult_male4

description: sample id: 2661sTS


title: mouse_liver_adult_male4

description: sample id: 1898sTSm


title: A2

description: total RNA


title: P53KO_UV_replicate2


title: P53CRYKO_UV_replicate2


title: mouse_kidney_adult_male3

description: sample id: 2660sTS

source_name: Adult kidney

value: kidney


title: P53CRYKO_NT_replicate2


title: mouse_kidney_adult_male2

description: sample id: 1957sTS

value: male


title: P53CRYKO_NT_replicate1


title: mouse_brain_adult_male4

description: sample id: 1896sTS


title: mouse_kidney_adult_male4

description: sample id: 2662sTS


title: HEK293T_560+198ZNF830_gene_rep3

type: RNA

first: Tara

last: Davis

department: Biochemistry and Molecular Biology

institute: Drexel University College of Medicine

hyb_protocol: Hybridization was conducted by the Molecular Profiling Facility at the University of Pennsylvania. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Transcriptome 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Scanning was conducted by the Molecular Profiling Facility at the University of Pennsylvania. A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Probeset and gene normalized data was calculated from cel files in Affymetrix Expression Console software using RMA with default parameters.

label: biotin

organism: Homo sapiens

label_protocol: Labeling was conducted by the Molecular Profiling Facility at the University of Pennsylvania. All protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: HeLa cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.

extract_protocol: total RNA was extracted and purified using the Bioline ISOLATE II kit according to manufacturer's instructions.

treatment_protocol: Cells were washed with 1X PBS before freezing in preparation for RNA extraction.

tag: cell line

value: ZNF830 knockdown


title: HEK293T_560+198ZNF830_gene_rep2

tag: genotype/variation


title: HEK293T_5104SCR_gene_rep1

source_name: HEK293T, SCR, rep1

growth_protocol: HEK293T cells were transduced with titered lentivirus containing either shRNA from the MISSION library or with scrambled shRNA. Puromycin was used to select for incorporation. Cells were grown to 80% confluency and harvested.

value: SCR control


title: HEK293T_560+198ZNF830_gene_rep1


title: HEK293T_5104SCR_gene_rep3

source_name: HEK293T, SCR, rep3


title: HEK293T_755+769PRPF4_gene_rep2

value: PRPF4 knockdown


title: HEK293T_470PPIL1_gene_rep1

source_name: HEK293T, 470PPIL1, rep1

value: PPIL1 knockdown


title: HEK293T_755+769PRPF4_gene_rep1


title: HEK293T_470PPIL1_gene_rep3

source_name: HEK293T, 470PPIL1, rep3


title: HEK293T_5104SCR_gene_rep2

source_name: HEK293T, SCR, rep2


title: HEK293T_470PPIL1_gene_rep2

source_name: HEK293T, 470PPIL1, rep2


title: HEK293T_165PPWD1_gene_rep1

source_name: HEK293T, 165PPWD1, rep1

value: PPWD1 knockdown


title: HEK293T 368PPIL3 gene rep1

source_name: HEK293T, 185PPIL3, rep1

value: PPIL3 knockdown


title: HEK293T 368PPIL3 gene rep2

source_name: HEK293T, 185PPIL3, rep2


title: HEK293T_165PPWD1_gene_rep3

source_name: HEK293T, 165PPWD1, rep3


title: HEK293T_5191SCR_gene_rep1


title: HEK293T 368PPIL3 gene rep3

source_name: HEK293T, 185PPIL3, rep3


title: HEK293T_5191SCR_gene_rep3


title: HEK293T_475PPIL2_gene_rep2

source_name: HEK293T, 475PPIL2, rep2

value: PPIL2 knockdown


title: HEK293T_165PPWD1_gene_rep2

source_name: HEK293T, 165PPWD1, rep2


title: HEK293T_5191SCR_gene_rep2


title: HEK293T_475PPIL2_gene_rep3

source_name: HEK293T, 475PPIL2, rep3


title: HEK293T_368PPIE_gene_rep2

source_name: HEK293T, 368PPIE, rep2


title: HEK293T_368PPIG_gene_rep2

source_name: HEK293T, 368PPIG, rep2


title: HEK293T_368PPIG_gene_rep3

source_name: HEK293T, 368PPIG, rep3


title: HEK293T_755+769PRPF4_gene_rep3


title: HEK293T_368PPIE_gene_rep1

source_name: HEK293T, 368PPIE, rep1


title: HEK293T_368PPIE_gene_rep3

source_name: HEK293T, 368PPIE, rep3


title: HEK293T_475PPIL2_gene_rep1

source_name: HEK293T, 475PPIL2, rep1


title: HEK293T_368PPIG_gene_rep1

source_name: HEK293T, 368PPIG, rep1


title: HEK293T_SCR_gene_rep1

source_name: HEK293T, SCR, rep1


title: HEK293T_SCR_gene_rep2

source_name: HEK293T, SCR, rep2


title: HEK293T_139CWC27_gene_rep2


title: HEK293T_139CWC27_gene_rep1


title: HEK293T_139CWC27_gene_rep3


title: NHDF_t=23 (set3)

first: Tom

middle: C

last: Freeman

address: Easter Bush Campus, Midlothian

department: Genetics and Genomics

institute: Roslin Institute

description:
NHDF, 23 h
Gene expression data of NHDF in synchronous late proliferation

hyb_protocol: Samples were hybridized to GeneChip Human Transcriptome Arrays 2.0. Hybridization, wash and staining was done using a GeneChip Instrument System including Fluidics Station 450, Hybdrization Oven 640 and GeneChip Scanner with the GeneChip Hybridization, Wash and Stain Kit (Thermo Fisher).

scan_protocol: Arrays were scanned using the GeneChip scanner (Affymetrix)

data_processing: Data were pre-processed with Bioconductor package oligo. After QC data was RMA normalised.

source_name: NHDF late proliferation

label_protocol: fragmented cDNA was labeled  by TdT DNA labelling reagent using GeneChip® WT Terminal Labelling Kit (Affymetrix, Buckinghamshire, UK) according to manufacturer’s instructions

growth_protocol: Primary human dermal fibroblasts (NHDF) isolated from neonate foreskins were plated on 175 cm2 tissue culture flasks (Thermo Fisher, Perth, UK) at density of 6x103 cells/cm2. Cells were cultured in DMEM (Sigma-Aldrich, Missouri, US) with 10% (v/v) foetal calf serum (FCS) (GE Healthcare, Little Chalfont, UK) and antibiotics (25 U/ml penicillin and 25 µg/ml streptomycin (Life technologies, Paisley, UK).

extract_protocol: total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Manchester, UK) according to manufacturer’s instructions

treatment_protocol: Starvation-induced synchronisation was achieved by replacing full medium with DMEM containing 0.5% FCS for 48 h. After this time, medium was replaced with DMEM containing 10% FCS promoting the synchronised entry of the NHDF back into the cell cycle.

value: Primary human fibroblasts (NHDF)

value: early passage NHDF


title: NHDF_t=22 (set3)

description:
NHDF, 22 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=28 (set3)

description:
NHDF, 28 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=24 (set3)

description:
NHDF, 24 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=19 (set3)

description:
NHDF, 19 h
Gene expression data of NHDF in synchronous late proliferation


title: HEK293T_SCR_gene_rep3

source_name: HEK293T, SCR, rep3


title: NHDF_t=21 (set3)

description:
NHDF, 21 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=20 (set3)

description:
NHDF, 20 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=26 (set3)

description:
NHDF, 26 h
Gene expression data of NHDF in synchronous late proliferation


title: SH_TS_BC99

city: Chapel Hill

first: Zhiyuan

last: Hu

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC99

data_processing:
Illumina Casava1.7 software used for basecalling and sequencing data were demultiplexed based on dual indexes.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, demultiplexed and then only read 1 in each sample were mapped to known Targeted regions of human genomes for counts using R package "ShortRead".
Raw counts of all samples were imported to edgeR for normalization by the size of the transcripts and by the size of the library and then calculation of CPM per sample as a gene expression matrix
Gene expression CPM dataset were median-centered and column-standardized using DWD
DWD dataset were used for iRDM data analysis including subtype classification, iRDM risks,  immunity scores, and proliferation scores.
Genome_build: hg19
Supplementary_files_format_and_content: csv files were generated including raw counts and normalized gene expression data

source_name: Breast cancer

extract_protocol:
FFPE tissues total RNA extraction was routinely performed using Roche FFPE RNA extraction kit according to the manufacturer’s protocol.
The Illumina TruSeq Targeted RNA expression kit was used to build libraries of the targeted 72-genes. To synthesize cDNA, 200 to 800 nanograms of purified FFPE RNA in a total volume of 3 µl was mixed with 4.0 µl RCS1, 2.0 µl ProtoScrip II Reverse Transcriptase, 1.0 µl 10mM DTT at 42OC for 30 min and 94OC for 10 min. The cDNA was hybridized with custom oligo pools in a thermal cycler programed to gradually decrease temperature from 70 OC to 30 OC in 30 minutes. The RNA/Oligo hybrid products were washed, extended and ligated. The ligated DNA was amplified by DNA polymerase on the thermal cycler with 35 PCR cycles of 98 OC for 30 seconds, 62 OC for 30 seconds and 72 OC for 60 seconds. The PCR products were purified with AMPure XP beads and eluted in 15 µl of buffer, measured using Agilent Bioanalyzer2100 and DNA1000 chips, pooled with equal amounts of DNA from each sample’s library, and finally diluted to 4 nM, denatured, and loaded to Nextseq500 according to the manufacturer’s protocol.
Libraries were multiplexed and sequenced on Illumina Nextseq500  to generate 75bp single read R1.

tag: gender

value: female

tag: dmfs time

tag: dmfs event

tag: sample type

value: Solid tumor

tag: irdm subtype

value: LumA

tag: pam50 subtype

tag: immunity group

value: iweak

tag: proliferation group

value: low

tag: er status rna

value: ER+

tag: pr status rna

value: PR+


title: NHDF_t=15 (set3)

description:
NHDF, 15 h
Gene expression data of NHDF in synchronous late proliferation

tag: tissue

tag: age


title: NHDF_t=18 (set3)

description:
NHDF, 18 h
Gene expression data of NHDF in synchronous late proliferation


title: NHDF_t=17 (set3)

description:
NHDF, 17 h
Gene expression data of NHDF in synchronous late proliferation


title: SH_TS_BC94

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC94

value: istrong


title: SH_TS_BC95

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC95


title: NHDF_t=10 (set3)

description:
NHDF, 10 h
Gene expression data of NHDF in synchronous mid proliferation

source_name: NHDF mid proliferation


title: SH_TS_BC88

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC88


title: SH_TS_BC93

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC93


title: SH_TS_BC92_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC92_2

value: Immuno

value: LumB

value: high


title: NHDF_t=4 (set3)

description:
NHDF, 4 h
Gene expression data of NHDF in synchronous early proliferation

source_name: NHDF early proliferation


title: NHDF_t=16 (set3)

description:
NHDF, 16 h
Gene expression data of NHDF in synchronous late proliferation


title: SH_TS_BC81

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC81

value: Basal


title: NHDF_t=6 (set3)

description:
NHDF, 6 h
Gene expression data of NHDF in synchronous mid proliferation


title: NHDF_t=2 (set3)

description:
NHDF, 2 h
Gene expression data of NHDF in synchronous early proliferation


title: NHDF_t=0 (set3)

description:
NHDF, 0 h
Gene expression data of NHDF in a quiescent state

source_name: NHDF quiescent


title: NHDF_t=14 (set3)

description:
NHDF, 14 h
Gene expression data of NHDF in synchronous late proliferation


title: SH_TS_BC86

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC86


title: SH_TS_BC74

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC74

value: Mixed


title: NHDF_t=12 (set3)

description:
NHDF, 12 h
Gene expression data of NHDF in synchronous mid proliferation


title: SH_TS_BC97

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC97


title: SH_TS_BC71

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC71

value: ER-


title: SH_TS_BC68

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC68


title: NHDF_t=1 (set3)

description:
NHDF, 1 h
Gene expression data of NHDF in synchronous early proliferation


title: SH_TS_BC96

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC96


title: SH_TS_BC76

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC76


title: SH_TS_BC98

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC98


title: SH_TS_BC67

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC67


title: NHDF_t=8 (set3)

description:
NHDF, 8 h
Gene expression data of NHDF in synchronous mid proliferation


title: NHDF_t=13 (set3)

description:
NHDF, 13 h
Gene expression data of NHDF in synchronous mid proliferation


title: SH_TS_BC92

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC92


title: SH_TS_BC75

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC75


title: SH_TS_BC87

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC87

value: Normal


title: SH_TS_BC61

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC61


title: SH_TS_BC82

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC82


title: SH_TS_BC57

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC57

value: PR-


title: SH_TS_BC56

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC56


title: SH_TS_BC73

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC73


title: SH_TS_BC53

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC53


title: SH_TS_BC62

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC62


title: NHDF_control (set3)

description:
NHDF, unsynchronised
Gene expression data of NHDF unsynchronised

source_name: NHDF unsynchronised

value: Primary human fibroblasts (NHDF)

value: early passage NHDF


title: SH_TS_BC72

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC72

value: female

value: Solid tumor


title: SH_TS_BC66

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC66

value: iweak


title: SH_TS_BC49

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC49


title: SH_TS_BC47

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC47


title: SH_TS_BC48

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC48

value: LumA

value: low


title: SH_TS_BC44

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC44

value: ER+

value: PR+


title: SH_TS_BC45

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC45

value: istrong


title: SH_TS_BC42

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC42


title: SH_TS_BC43

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC43


title: SH_TS_BC64

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC64


title: SH_TS_BC41

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC41


title: SH_TS_BC58

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC58

value: Immuno

value: LumB


title: SH_TS_BC65

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC65


title: SH_TS_BC46

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC46


title: SH_TS_BC51

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC51

value: high


title: SH_TS_BC59

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC59


title: SH_TS_BC63

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC63


title: SH_TS_BC37

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC37


title: SH_TS_BC50

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC50


title: SH_TS_BC52

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC52


title: SH_TS_BC70

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC70


title: SH_TS_BC36

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC36


title: SH_TS_BC343

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC343


title: SH_TS_BC38

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC38


title: SH_TS_BC39

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC39


title: SH_TS_BC60

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC60


title: SH_TS_BC341

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC341

value: Basal


title: SH_TS_BC336

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC336


title: SH_TS_BC340

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC340


title: SH_TS_BC335

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC335

value: ER-


title: SH_TS_BC319

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC319


title: SH_TS_BC33

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC33


title: SH_TS_BC40

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC40


title: SH_TS_BC337

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC337


title: SH_TS_BC318

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC318


title: SH_TS_BC315

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC315


title: SH_TS_BC333

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC333


title: SH_TS_BC321

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC321


title: SH_TS_BC313

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC313


title: SH_TS_BC338

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC338


title: SH_TS_BC344

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC344

value: Normal


title: SH_TS_BC339

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC339

value: Mixed


title: SH_TS_BC305

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC305

value: PR-


title: SH_TS_BC310

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC310


title: SH_TS_BC311

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC311


title: SH_TS_BC308

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC308


title: SH_TS_BC306

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC306


title: SH_TS_BC314

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC314


title: SH_TS_BC303

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC303


title: SH_TS_BC304

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC304


title: SH_TS_BC302_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC302_2


title: SH_TS_BC312

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC312


title: SH_TS_BC299

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC299


title: SH_TS_BC30

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC30


title: SH_TS_BC307

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC307


title: SH_TS_BC297

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC297


title: SH_TS_BC309

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC309


title: SH_TS_BC300

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC300


title: SH_TS_BC301

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC301


title: SH_TS_BC281

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC281


title: SH_TS_BC296

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC296


title: SH_TS_BC291

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC291


title: SH_TS_BC27

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC27


title: SH_TS_BC298

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC298


title: SH_TS_BC287

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC287


title: SH_TS_BC29

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC29


title: SH_TS_BC265

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC265


title: SH_TS_BC284

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC284


title: SH_TS_BC289

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC289


title: SH_TS_BC273

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC273


title: SH_TS_BC272

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC272


title: SH_TS_BC271

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC271


title: SH_TS_BC28_1

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC28_1


title: SH_TS_BC262

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC262


title: SH_TS_BC258

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC258


title: SH_TS_BC257

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC257


title: SH_TS_BC255

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC255


title: SH_TS_BC283

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC283


title: SH_TS_BC266

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC266


title: SH_TS_BC286

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC286


title: SH_TS_BC285

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC285


title: SH_TS_BC253

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC253


title: SH_TS_BC252

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC252


title: SH_TS_BC290

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC290


title: SH_TS_BC237

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC237


title: SH_TS_BC247

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC247


title: SH_TS_BC264

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC264


title: SH_TS_BC235

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC235


title: SH_TS_BC233

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC233


title: SH_TS_BC249

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC249


title: SH_TS_BC24

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC24


title: SH_TS_BC236

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC236


title: SH_TS_BC226

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC226


title: SH_TS_BC213

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC213


title: SH_TS_BC212

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC212


title: SH_TS_BC239

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC239


title: SH_TS_BC251

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC251


title: SH_TS_BC246

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC246


title: SH_TS_BC210

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC210


title: SH_TS_BC222

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC222


title: SH_TS_BC243

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC243


title: SH_TS_BC240

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC240


title: SH_TS_BC211

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC211


title: SH_TS_BC232

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC232


title: SH_TS_BC219

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC219


title: SH_TS_BC260

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC260


title: SH_TS_BC214

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC214


title: SH_TS_BC209

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC209


title: SH_TS_BC21

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC21


title: SH_TS_BC204

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC204


title: SH_TS_BC203

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC203


title: SH_TS_BC207

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC207


title: SH_TS_BC202

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC202


title: SH_TS_BC200

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC200


title: SH_TS_BC20_1

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC20_1


title: SH_TS_BC220

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC220


title: InputR4

city: Missoula

first: Ekaterina

last: Voronina

state: MT

address: 32 Campus Drive

department: Division of Biological Sciences

institute: University of Montana

data_processing:
Sequenced reads were trimmed and filtered with Trim Galore! to remove Illumina adapter sequences (v 0.4.2).
Trimmed reads were filtered for rRNA sequences in both the Total and IP RNA libraries using Bowtie2 (2.3.0) with a reference file containing only C. elegans rRNA sequences.
Unaligned reads that did not map to the rRNA sequences were then mapped to WBcel235/ce11 genome using RNA Star (v 2.5.2b-0)
Normalization and enrichment calculations for the RIP experiments were performed using DESeq2 (version 1.12.3). Genes were considered enriched when they had a log2foldchange > 1 and Padj < 0.01. Genes that did not correspond to the annotated features of the current reference genome were removed from the list of enriched genes. The final list of genes are reported in File S2
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: Excel spreadsheet reporting Wbgene ID, gene name, baseMean,log2FoldChange, lfcSE, stat, pvalue, padj

organism: Caenorhabditis elegans

source_name: Whole worm extract

growth_protocol: synchronized 3xFLAG::DLC-1 C. elegans were grown to high density on NA22 plates to young adult stage.

extract_protocol:
Extracts were prepared and cleared of debris and used for RNA immunoprecipitation. DLC-1-RNP complexes were isolated by FLAG tag immunosprecipitations. Eluents and Input samples were stored in Trizol Reagent and extracted using ZymoResearch Directzol RNA extraction kit
Total RNA was oligo-dT primed to generate the input libraries while immunoprecipitated RNA was processed without enrichment.

tag: genotype

tag: replicate experiment

value: Replicate 4

value: Whole Worm tissue

tag: Stage

value: Young adult

tag: rip antibody


title: InputR5

value: Replicate 5


title: SH_TS_BC199

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC199

value: female

value: Solid tumor


title: InputR2

value: Replicate 2


title: FLAGr5

value: FLAG (Sigma, Cat#:F1804, Lot # SLBJ4607V)


title: FLAGr4


title: InputR3

value: Replicate 3


title: SH_TS_BC198

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC198

value: iweak

value: ER+

value: PR+


title: SH_TS_BC19_1

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC19_1

value: LumA

value: low


title: SH_TS_BC196

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC196

value: Basal

value: high


title: InputR1

value: Replicate 1


title: SH_TS_BC193

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC193

value: Immuno

value: istrong

value: ER-


title: FLAGr3

value: Whole Worm tissue

value: Young adult


title: SH_TS_BC206

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC206

value: female

value: Solid tumor


title: SH_TS_BC188

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC188


title: SH_TS_BC182

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC182

value: Mixed


title: SH_TS_BC177

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC177

value: PR-


title: FLAGr2

value: Replicate 2

value: FLAG (Sigma, Cat#:F1804, Lot # SLBJ4607V)


title: SH_TS_BC180

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC180

value: ER+

value: PR+


title: SH_TS_BC178

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC178

value: LumA

value: low


title: SH_TS_BC184

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC184

value: Basal

value: iweak

value: high


title: macaque_liver_adult_male2

description: sample id: 5425sTS

organism: Macaca mulatta

source_name: Adult liver

value: liver

tag: Sex

value: male

tag: developmenta stage

value: adult


title: SH_TS_BC175

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC175

tag: gender

tag: dmfs time

value: Immuno

value: istrong

value: ER-


title: SH_TS_BC181

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC181

value: female

tag: dmfs event

tag: sample type

value: Solid tumor


title: SH_TS_BC1700216

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC1700216

tag: irdm subtype

tag: pam50 subtype


title: FLAGr1

value: Replicate 1

value: Whole Worm tissue

value: Young adult


title: SH_TS_BC183

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC183

tag: immunity group

tag: proliferation group

value: PR-


title: macaque_kidney_adult_male3

description: sample id: 5445sTS

source_name: Adult kidney

value: kidney


title: 254706910113_b4 - OXPMT7-7.4_rep3 vs WT4_rep3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What biochemical function? What consequence on lignification when overexpressed in Arabidopsis thaliana?

hyb_protocol: WT4_rep3 Cy5 / OXPMT7-7.4_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green). For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias. Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA.

growth_protocol: stem - Media: soil Hygrometry: relative humidity (60%) Temperature: 22℃ day and 16℃ night, 150 μmol/m2 × s

extract_protocol: WT4_rep3:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

value: WT

tag: developmental stage

value: (boyes et al. plant cell 2001):boyes:6.30

value: stem

value: mutant (mutant_oxpmt980)


title: 254706910114_b1 - WT1_rep1 vs OXPMT7-7.1_rep1

hyb_protocol: OXPMT7-7.1_rep1 Cy5 / WT1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue

extract_protocol: WT1_rep1:100mg. (Qiagen_RNeasy.pdf)


title: macaque_liver_adult_male3

description: sample id: 5395sTS

value: liver

value: male


title: SH_TS_BC185

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC185

value: Basal

value: iweak

value: high

tag: er status rna

tag: pr status rna

value: PR+


title: macaque_kidney_adult_male1

description: sample id: 5476sTS

value: adult


title: SH_TS_BC1700115

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC1700115

value: female

value: Solid tumor

value: LumA

value: low

value: ER+


title: SH_TS_BC176

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC176

value: PR-


title: macaque_kidney_adult_male2

description: sample id: 5391sTS

value: kidney


title: SH_TS_BC171

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC171

value: Immuno

value: Normal

value: istrong


title: 254706910114_b3 - WT3_rep2 vs OXPMT7-7.3_rep2

hyb_protocol: OXPMT7-7.3_rep2 Cy5 / WT3_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

tag: genotype

value: mutant (mutant_oxpmt980)

value: (boyes et al. plant cell 2001):boyes:6.30

value: stem

extract_protocol: WT3_rep2:100mg. (Qiagen_RNeasy.pdf)

value: WT


title: 254706910114_b4 - OXPMT7-7.3_rep2 vs WT3_rep2

hyb_protocol: WT3_rep2 Cy5 / OXPMT7-7.3_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SH_TS_BC1700217

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC1700217

value: PR+


title: SH_TS_BC166

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC166

value: Basal

value: high

value: ER-


title: macaque_liver_adult_male4

description: sample id: 5416sTS

value: liver

value: male

value: adult


title: SH_TS_BC173

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC173

value: female

value: Solid tumor

value: iweak

value: PR-


title: macaque_heart_adult_male2

description: sample id: 5450sTS

source_name: Adult heart

value: heart


title: SH_TS_BC170

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC170

value: Immuno

value: istrong

value: low

value: ER+


title: SH_TS_BC172

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC172


title: macaque_heart_adult_male1

description: sample id: 5441sTS


title: macaque_heart_adult_male3

description: sample id: 5401sTS


title: SH_TS_BC160

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC160


title: 254706910113_b3 - WT4_rep3 vs OXPMT7-7.4_rep3

hyb_protocol: OXPMT7-7.4_rep3 Cy5 / WT4_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: mutant (mutant_oxpmt980)

value: (boyes et al. plant cell 2001):boyes:6.30

value: stem

value: WT


title: CEBPβ-A, rep3

city: Beijing

first: shanshan

last: liu

address: No.1 Xian Nong Tan St. Xi Cheng District

institute: Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
Transcription abundance was estimated using String Tie software.
Fragments Per Kilobase of gene/transcript model per Million mapped fragments (FPKM) were calculated using Ballgown.
rMATs used for alternative splicing
Coding potential of the novel transcript was predicted using CPAT
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: CEBPβ-overexpressed alveolar macrophages after A20-Ad treatment

extract_protocol:
Alveolar macrophages were isolated, treated with indicated Ad virus, and flash frozen on dry ice, and RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lung

tag: cell type

value: alveolar macrophage


title: 254706910114_b2 - OXPMT7-7.1_rep1 vs WT1_rep1

hyb_protocol: WT1_rep1 Cy5 / OXPMT7-7.1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Sorted library (160718Kea)

first: Amy

middle: E

last: Keating

address: 77 Massachusetts Ave

department: Biology and Biological Engineering

institute: Massachusetts Institute of Technology

description:
DNA encoding BH3 peptide
Sorted library for Bfl-1 at 100 nM

data_processing:
The SORTCERY pipeline was applied as described at https://github.com/KeatingLab/sortcery_design
Supplementary_files_format_and_content: .csv files that describe the distribution of the reads across SORTCERY gates. The columns describe the raw counts and normalized distribution of reads across gates. The .csv column headers are indexed from 0-11 which refer to gates 1-12.  Each sequence is summarized by a mean affinity coordinate.

organism: Saccharomyces cerevisiae

source_name: Sorted library for Bfl-1 at 100 nM

growth_protocol: The libraries were grown from glycerol stocks in selective media containing glucose (SD+CAA) at 30 °C to passage. To induce expression, cultured were diluted (40 mL inoculate/L) into selective media containing galactose (SG+CAA) for 16-24h at 30 °C.

extract_protocol:
The plasmid DNA from yeast was extracted using the Zymoprep Yeast Plasmid Miniprep II (Zymo Research) reagents and Qiagen miniprep columns.
The BH3 library was amplified with PCR using primers that encoded an MmeI restriction enzyme binding site at 5′ end and a universal Illumina sequencing region on the 3′ end. After purification with the Qiagen PCR purification kit, the PCR products were digested with MmeI for 1 h at 37 °C before being heat inactivated. Each digestion product was then ligated to double-stranded DNA fragments containing Illumina adapters, with the adapter containing a unique barcode.

tag: yeast display vector

value: pCT

tag: protein

tag: concentration of protein used during sortcery assay


title: SH_TS_BC169

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC169

tag: gender

value: female

tag: dmfs time

tag: dmfs event

value: Mixed

value: high


title: SH_TS_BC17

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC17

tag: sample type

value: Solid tumor

tag: irdm subtype

tag: pam50 subtype

value: ER-

value: PR+


title: CEBPβ-A, rep2


title: CEBPβ-A, rep1


title: CEBPβ, rep3


title: Sorted library (161011Kea)

description:
DNA encoding BH3 peptide
Sorted library for Bcl-xL at 1 nM
Sorted library for Mcl-1 at 1 nM
Sorted library for Mcl-1 at 1 nM
Sorted library for Bcl-xL at 100 nM

source_name: Sorted libraries

value: mixed sample (non-demultiplexed)


title: CEBPβ, rep2


title: SH_TS_BC161

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC161

tag: immunity group

value: iweak

tag: proliferation group

value: PR-


title: macaque_brain_adult_male2

description: sample id: 5382sTS

source_name: Adult brain

tag: tissue

value: brain

tag: Sex

value: male

tag: developmenta stage

value: adult


title: Sorted library (140828Kea)

description:
DNA encoding BH3 peptide
Sorted library for Bcl-xL at 1 nM
Sorted library for Bfl-1 at 100 nM
Sorted library for Bcl-xL at 100 nM


title: macaque_brain_adult_male3

description: sample id: 5461sTS


title: SH_TS_BC15

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC15

value: LumB

value: istrong

tag: er status rna

value: ER+

tag: pr status rna


title: SH_TS_BC146

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC146

value: Basal


title: SH_TS_BC163

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC163


title: wild type mice, rep3

source_name: alveolar macrophage

extract_protocol:
Alveolar macrophages were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lung

tag: genetype

value: wild type


title: SH_TS_BC165

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC165

value: female

value: Immuno

value: low


title: SH_TS_BC154

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC154

value: Solid tumor

value: high

value: ER-


title: SH_TS_BC155

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC155

value: iweak


title: SH_TS_BC153

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC153

value: PR-


title: SH_TS_BC151

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC151


title: SH_TS_BC152

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC152


title: A20 conditional knockout mice, rep3

value: A20 conditional knockout


title: 090717 MLN 48h WT Sham 2

first: Mukund

last: Varma

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Alignment with Tophat+Bowtie
Counting of transcripts with htseq-count
QC with RSeqC
Differential expression with EdgeR
Scripts to tie these together available at bitbucket.org/mukundvarma/dge-pipeline
Genome_build: mm10
Supplementary_files_format_and_content: counts matrix - Samples for columns, genes for rows, tab-delimited text file, includes log2cpm

source_name: Mesenteric lymph nodes cell suspension

extract_protocol:
RNA was extracted using the Qiagen Rneasy plus mini kit
RNA-seq libraries were prepared using the Illumina TruSeq protocol and sequenced with single-end 50bp reads on an Illumina HiSeq4000

treatment_protocol: C57BL/6 mice were inoculated with medium (n = 5 mice), CW3 5e7 (n = 5 mice), CW3-VP1CR6 5e7 (n = 5 mice), CR6 5e7 (n = 5 mice) or T1L 10e8 pfu (n = 5 mice) and mLN were harvested 48 hpi. Transcriptional responses to each of the viruses indicated were analyzed by RNAseq

value: Mesenteric lymph nodes cell suspension

tag: age

value: 8 weeks old

tag: virus

value: Sham infected


title: CEBPβ, rep1

tag: cell type

value: alveolar macrophage


title: SH_TS_BC16

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC16

tag: gender

tag: dmfs time

value: Mixed

value: istrong

value: ER+


title: SH_TS_BC150

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC150

tag: dmfs event

tag: sample type

value: LumA

value: PR+


title: macaque_brain_adult_male1

description: sample id: 5413sTS

value: brain

value: male

value: adult


title: A20 conditional knockout mice, rep2

value: lung


title: SH_TS_BC147

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC147

value: female

value: Solid tumor

tag: irdm subtype

value: LumB

tag: pam50 subtype

value: high


title: 090717 MLN 48h WT CR6 5e7 3

value: Mesenteric lymph nodes cell suspension

value: MNV CR6 5e7


title: SH_TS_BC133

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC133

value: Basal

tag: immunity group

value: iweak

tag: proliferation group

value: PR-


title: A20 conditional knockout mice, rep1

tag: tissue

value: A20 conditional knockout


title: 090717 MLN 48h WT CW3 5e7 3

value: 8 weeks old

value: MNV CW3 5e7


title: SH_TS_BC141

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC141

value: low

value: ER+

value: PR+


title: SH_TS_BC116_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC116_2

value: Immuno

value: istrong


title: 122017 MLN 48h WT CW3CR6VP1 5e7 1

value: MNV CW3CR6VP1 5e7


title: 090717 MLN 48h WT T1L 1e8 2

value: Reovirus T1L 1e8


title: wild type mice, rep2

value: lung

value: wild type


title: SH_TS_BC139

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC139

value: female

value: Solid tumor

value: high


title: SH_TS_BC134

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC134

value: LumA

value: Mixed

value: iweak


title: 122017 MLN 48h WT Sham 1

value: Mesenteric lymph nodes cell suspension

value: 8 weeks old

value: Sham infected


title: 090717 MLN 48h WT CR6 5e7 1

value: MNV CR6 5e7


title: SH_TS_BC12

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC12

value: ER-

value: PR-


title: wild type mice, rep1


title: 121217 MLN 48h WT CW3CR6VP1 5e7 3


title: SH_TS_BC13

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC13

value: LumB

value: ER+

value: PR+


title: 090717 MLN 48h WT T1L 1e8 1

value: Reovirus T1L 1e8


title: 090717 MLN 48h WT CW3 5e7 1

value: MNV CW3 5e7


title: SH_TS_BC14

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC14

value: female

value: Immuno

value: Basal

value: istrong


title: SH_TS_BC117

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC117

value: Solid tumor

value: LumA

value: low


title: 122017 MLN 48h WT CW3CR6VP1 5e7 3

value: Mesenteric lymph nodes cell suspension

value: 8 weeks old

value: MNV CW3CR6VP1 5e7


title: SH_TS_BC11

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC11

value: iweak


title: SH_TS_BC118

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC118

value: high


title: 121217 MLN 48h WT Sham 1

value: Sham infected


title: 101317 MLN 48h WT T1L 1e8 2


title: 090717 MLN 48h WT Sham 1


title: SH_TS_BC105

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC105

value: ER+


title: SH_TS_BC115_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC115_2

value: PR+


title: SH_TS_BC119

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC119

value: ER-


title: SH_TS_BC104

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC104


title: SH_TS_BC112

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC112

value: Normal


title: SH_TS_BC113

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC113

value: female


title: SH_TS_BC114

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC114


title: SH_TS_BC1700116

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC1700116

value: Mixed


title: SH_TS_BC107

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC107

value: LumB


title: 121217 MLN 48h WT CW3CR6VP1 5e7 1


title: 122017 MLN 48h WT CW3CR6VP1 5e7 2


title: 121217 MLN 48h WT CW3 5e7 2

value: MNV CW3 5e7


title: 122017 MLN 48h WT CW3 5e7 2


title: SH_TS_BC108

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC108

value: Solid tumor

value: Immuno

value: istrong


title: 101317 MLN 48h WT T1L 1e8 1

value: Mesenteric lymph nodes cell suspension

value: Reovirus T1L 1e8


title: SH_TS_BC102

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC102

value: LumA

value: low


title: SH_TS_BC101

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC101

value: iweak


title: 090717 MLN 48h WT CR6 5e7 2

value: 8 weeks old

value: MNV CR6 5e7


title: SH_TS_BC111

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC111

value: high

value: ER+

value: PR+


title: 101317 MLN 48h WT CW3 5e7 1


title: SH_TS_BC106

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC106

value: female

value: ER-

value: PR-


title: 101317 MLN 48h WT CR6 5e7 2


title: 101317 MLN 48h WT Sham 1

value: Sham infected


title: SH_TS_BC07

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC07

value: Solid tumor


title: SH_TS_BC09

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC09


title: SH_TS_BC10

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC10

value: Immuno


title: SH_TS_BC06

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC06

value: LumB


title: Zfp296-/- clone #14 D6 PGCLC

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF

source_name: D6 PGCLC

value: mixed B6CBA background

tag: fluorescent reporter

value: Stella-GFP; Esg1-tdTomato

tag: facs

value: GFP+; Tomato_low


title: Zfp296-/- clone #18 D6 PGCLC


title: Zfp296-/- clone #42 D6 PGCLC


title: SH_TS_BC05

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC05

value: LumA

value: low

tag: er status rna

tag: pr status rna


title: SH_TS_BC100

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC100

value: iweak


title: wild type clone #8 D6 PGCLC

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; matched wild type control clone to Zfp296-/-

tag: strain


title: wild type parental D6 PGCLC 2

description: PGCLC were collected at day6 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; wild type parental to Zfp296-/-


title: Zfp296-/- clone #18 D2 PGCLC

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF

source_name: D2 PGCLC


title: SH_TS_BC02

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC02

source_name: Breast cancer


title: macaque_liver_adult_male1

description: sample id: 5404sTS

value: liver

tag: Sex

value: male

tag: developmenta stage

value: adult


title: SH_TS_BC010_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC010_2

value: istrong

value: ER+

value: PR+


title: wild type clone #11 D6 PGCLC


title: 090717 MLN 48h WT T1L 1e8 3

value: Mesenteric lymph nodes cell suspension

tag: age

value: 8 weeks old

tag: virus

value: Reovirus T1L 1e8


title: Zfp296-/- clone #14 D2 PGCLC


title: SH_TS_BC07_2

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC07_2

tag: gender

value: female

tag: dmfs time

value: Solid tumor

value: high


title: 101317 MLN 48h WT CR6 5e7 1

value: MNV CR6 5e7


title: Zfp296-/- clone #42 D2 PGCLC

value: mixed B6CBA background

value: Stella-GFP; Esg1-tdTomato

value: GFP+; Tomato_low


title: wild type clone #8 D2 PGCLC

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; matched wild type control clone to Zfp296-/-


title: wild type parental D2 PGCLC 2

description: PGCLC were collected at day2 of differentiation from EpiLC with BMP4, BMP8b, SCF, EGF, LIF; wild type parental to Zfp296-/-


title: SH_TS_BC04

description:
FFPE RNA
Targeted RNA-seq
SH_TS_BC04

tag: dmfs event

tag: sample type

value: LumB

value: LumA

value: iweak

value: low


title: wild type clone #11 D2 PGCLC