title: Gfi1b Wild-Type ROSA-Cre

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 v77 Ensembl genes

source_name: Megakaryocytes

extract_protocol:
Lin- cKit+ CD41+ CD61+ Megakaryocytes were sorted from mice tibiae, femora and humeri using a MoFlo cell sorter and RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion).
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

value: 8 weeks

value: Gfi1b WT

tag: cre status

value: ROSA-Cre

tag: cell type

value: megakaryocyte


title: Gfi1b KO ROSA-Cre

status: Public on Jan 21 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: genotype

value: Gfi1b KO


title: 10F: ski2KO long footprints previous replicate

status: Public on Jan 22 2017

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

country: USA

institute: National Institutes of Health

description: Serves as biological replicate to long reads in 33F2

data_processing:
Library strategy: ribosome profiling
Base calling was performed at UC Riverside or Johns Hopkins sequencing facilities with CASAVA 1.8
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009) and the parameters: -y -a -m 1 --best --strata. Reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files. Wig files beginning with "end3" are aligned by 3' ends, all others by 5' ends.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

tag: target molecule

value: Ribosome-protected RNA 25-34 nt


title: Gfi1b KO PF4-Cre


title: Dist 3

city: Seattle

first: Jeremy

last: Rabinowitz

state: WA

address: 850 Republican St

institute: University of Washington

description:
DESeq_distal_vs_proximal
DESeq_distal_vs_middle
monotonic_genes_v2

data_processing:
FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings.
HTSeq-count was used to get read counts for each sample.
Ensembl GRCz10 gene annotation file was used for gene expression quantification
Differential analysis was performed with DESeq.
Genome_build: Zebrafish GRCz10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Danio rerio

source_name: Distal region of caudal fin

extract_protocol:
Collected fin regions were flash frozen in liquid nitrogen and stored at -80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA-depleted using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA).
Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform (Illumina, San Diego, CA) with 20-30 million 50 base pair, paired-end sequences per sample. RNA extraction, rRNA depletion, library construction and sequencing were done by Covance Genomics Laboratory (Seattle, WA).

value: AB WT

tag: position

value: distal

tag: barcode sample name for sequencing


title: Dist 2


title: Gfi1b Wild-Type PF4-Cre


title: Dist 5


title: Dist 1


title: yes_kcl5_CACAGAAGG_RF

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Library strategy: Ribosomal footprinting
Excluded one KCl replicate due to low library size
Using Trimmomatic v. 0.32, trimmed adapters and set min. read length to 25 (RF) or 20 (RNA-seq) and set max length to 35 (RF)
Removed rRNA reads using STAR v. 2.3.1z8
Aligned RF and RNA-seq reads to non-degenerate mouse transcriptome using Bowtie2 v. 2.2.2
Counted reads using BEDTools v. 2.20.1
Differentially transcribed or translated genes were identified using a permuted t-test with replacement after integration into a digital gene expression (DGE) object using the edgeR package
Genome_build: Ensembl 75 (mouse) transcriptome with degenerate sequences removed. We also removed several positions in the transcriptome for translation efficiency calculations: 9 nt before the first nt of each start codon, 15 nt after the last nt of each start codon, 15 nt before the first nt of each stop codon, and 15nt after the last nt of each stop codon
Supplementary_files_format_and_content: ASCII files with counts for each sample

source_name: Mouse neurons_yes_kcl

extract_protocol:
Cell lysate was treated with DNase and clarified, and a portion was taken for RNAseq analysis. Remainder was treated with RNaseI(100U/ul; Invitrogen)for 45 min at room temperature and gentle mixing on a Nutator followed by inactivation of RNase by treatment with SUPERase-In(Thermo Fisher). Ribosomes and protected mRNA fragments were separated from free RNA by pelleting with ultracentrifugation on 1M Sucrose cushion at 200,000g for 4 h at 40C. RNA was isolated from the pellet using miRNeasy kit from Qiagen. Ribosome protected fragments (26-nt to 34-nt size)were purified on a 15% polyacrylamide TBE-urea gel and after dephosphorylation linker ligation was performed at room temperature for 2.5h using miRNA cloning linker from NEB. Linker ligated product was separated from unligated product on a 15% polyacrylamide gel.
Reverse transcription was performed using SuperScript III(Invitrogen)per the manufacturer’s protocol. Left over RNA was hydrolysed by treatment with 1N NaOH and precipitated cDNA was circularized using CircLigase(NEB). Circularized cDNA was subjected to rRNA depletion using biotinylated subtraction oligo pool directed against rRNA. Ribosome depleted product was PCR amplified using Phusion polymerase(NEB)and different indexing primers and the final product was purified on 8% polyacrylamide non-denaturing gels. Resuspended library was quantified and fragment size measured on high-sensitivity DNA chip on the Agilent BioAnalyzer.

value: FVB

tag: tissue

value: brain cortex


title: Mid 4

description:
DESeq_distal_vs_middle
DESeq_middle_vs_proximal
monotonic_genes_v2

source_name: Middle region of caudal fin

value: middle


title: Mid 5


title: Dist 4


title: lincRNA11195 mutant Arabidopsis under ABA treatment

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

country: China

institute: Nanchang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.3.3, --stringency 6); Clean reads were aligned to reference genomes (TAIR10) using STARv2.5.2a  with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 30.
Raw counts of refrence genes were calculated with function "summarizeOverlaps" in R package "GenomicAlignments"; "edgeR" was used to do differential expression (DE) analysis.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Text file including raw count table for reference genes

organism: Arabidopsis thaliana

source_name: total RNAs, seedling

growth_protocol: For growing Arabidopsis thaliana, seeds were grown on the half MS media.

extract_protocol:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.

treatment_protocol: Under ABA treatment for 12 hours.

tag: strain/ecotype

tag: genotype/variation

value: lincRNA11195 mutant

value: seedlings

tag: developmental stage

value: two weeks old

tag: treatment

value: ABA


title: yes_kcl4_TTAGGGACC_RF


title: Mid 3


title: lincRNA11195 mutant Arabidopsis


title: no_kcl3_TGTGTGAAG_RF

source_name: Mouse neurons_no_kcl


title: Mid 2


title: Mid 1


title: ddm1 Mutant Arabidopsis

description: Paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.3.3, --stringency 6); Clean reads were aligned to reference genomes (TAIR10 for Arabidopsis, TIGR release 7 for rice and AGPv2 for maize) using Tophat2 with following parameters: -N 5 --read-edit-dist 5 (v2.0.14).
Mapped reads from three biological replicates for Arabidopsis and rice were merged and then assembled with Cufflinks respectively (v2.2.1) (15).  For maize, mapped reads were assembled with Cufflinks firstly and then merged with Cuffmerge.
Genome_build: Arabidopsis TAIR10; Rice TIGR release 7; Maize AGPv2
Supplementary_files_format_and_content: GTF files including assembled transcripts, FPKM

growth_protocol: For growing Arabidopsis thaliana and rice, seeds were grown on the half MS media. And maize seeds were planted on soil in the growth room.

value: two-weeks-old


title: Prox 4

description:
DESeq_distal_vs_proximal
DESeq_middle_vs_proximal
monotonic_genes_v2

source_name: Proximal region of caudal fin

value: proximal


title: Wild type Arabidopsis

description: strand-specific RNA-seq


title: Prox 2


title: Prox 3


title: Prox 1


title: Wild type Maize

description: strand-specific RNA-seq

organism: Zea mays subsp. mays


title: Wild type Rice

description: strand-specific RNA-seq

organism: Oryza sativa Japonica Group

value: Nipponbare


title: DDX5+/+ mESCs Rep #2

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: Ddx5 wild-type MPI-II embryonic stem cells

data_processing:
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file containing ensembl transcript accession, gene name and normalised abundance estimates for each transcript

source_name: embryonic stem cells_wildtype

growth_protocol: Wild-type (MPI-II) and DDX5 knockout mESCs were cultured in plates coated with feeder cells in DMEM/High Glucose medium (Hyclone) supplemented with b-mercaptoethanol(10mM), sodium pyruvate(10mM), non-essential amino acids(10mM), GlutaMAX(10mM), 15% fetal bovine serum (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and 1 μM MEK inhibitor PD0325901 and 3μM GSK3 inhibitor CH99021.

extract_protocol:
Extracted using TRIzol using the manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Generation of DDX5 Knockout mESCs: Two sets of oligonucleotides were separately cloned into a U6-gRNA vector to create paired sgRNA target sites for SpCas9-nickase in the second exon of Ddx5, encoding the DDX5 protein. CRISPR/Cas9 target sites in Ddx5 (NM_007840.3) were designed by http://zifit.partners.org/ZiFiT/CSquare9Nuclease.aspx. Then these two sets of oligonucleotides were synthesized and inserted into the Bbs I site of the U6-gRNA vector. The sequences of two sets of oligonucleotides were as follow: Ddx5-Target1-F: 5’-CACCGAGACCGCGGCCGGGATCGA-3’, Ddx5-Target1-R: 5’-AAACTCGATCCCGGCCGCGGTCTC-3’, Ddx5-Target2-F: 5’-CACCGGAAAGAAGTTTGGAAATCC-3’, Ddx5-Target2-R: 5’-AAACGGATTTCCAAACTTCTTTCC-3’.  To generate a stable DDX5-/- mESC line, 2 × 106 mESCs were transfected with 20 μg U6-gRNA vector and 50 μg U6-cas9 plasmids. Cells were selected with 500 μg/ml of G418 (Sigma) after 24 hr of infection and were maintained in selection for 72 hr. Single clones were separated and were seeded in each well of a 48-well plate. Individual wells were inspected by microscopy to exclude polyclonal cell lines. Monoclonal cell lines were expanded. Then, DNA and protein of monoclonal cell lines were extracted to detect the genotype through DNA sequencing after PCR and Western blot.

value: embryonic stem cells

value: MPI-II

tag: passages

value: wild type


title: Wild type Arabidopsis under ABA treatment


title: SUM229pos_30nMtrametinib_24h

status: Public on Jan 20 2017

city: Chapel Hill

first: Gary

middle: L

last: Johnson

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina School of Medicine

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
Differential expression analysis was performed as follows:  RSEM gene-level expected read counts were imported into R version 3.2.2 and were analyzed using DESeq2 v1.12.3  to detect genes that were differentially expressed between pre-treatment and trametinib-treated conditions for claudin-low cell lines (DESeq2_Figure2_claudin.xlsx) or basal-like cell lines (DESeq2_Figure2_basal.xlsx), or to detect genes that were differentially expressed between claudin-low and basal-like cell line groups (DESeq2_Figure2_subtype_group_comparison.xlsx).  DESeq2 v1.12.3 was also used to detect differentially expressed transcripts in response to trametinib among biological replicates of an individual cell line (DESeq2_SUM159replicates.xlsx).  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.  Significantly differentially expressed genes were selected based on adjusted p-values, utilizing a threshold of 0.05 for significance.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: Processed files (.xlsx and .normalized_results) contain upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.

molecule: polyA RNA

organism: Homo sapiens

source_name: EpCAM/CD49f positive SUM229 breast carcinoma subpopulation

growth_protocol: culture media: F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libraries constructed with Illumina TruSeq RNA Library Prep Kit v2. 4 µg total RNA and 10 cycles of amplification (using 0.5X recommended DNA template) were used for libraries constructed with KAPA Stranded mRNAseq kit or Illumina TruSeq RNA library kit v2.
library preparation kit: Illumina TruSeq RNA library kit v2

tag: cell line

value: SUM229 breast carcinoma cell line, EpCAM/CD49f positive subpopulation

value: 30nM trametinib

tag: time


title: Figure3_HCC1806_10nMtrametinib_48h

source_name: HCC1806 breast carcinoma cell line

growth_protocol: culture media: RPMI 1640 supplemented with 10% FBS

value: HCC1806 breast carcinoma cell line

value: 10nM trametinib


title: Figure3_HCC1806_DMSO_48h

value: DMSO


title: Figure3_HCC1806_300nMJQ1_48h

value: 300nM JQ1


title: Prox 5

value: AB WT


title: SUM159_H3K4me3_500nMtrametinib_24h

description: SupplementaryTableS4_peakclassification.xlsx

library_source: genomic

data_processing:
Reads were aligned to hg19_M_rCRS using Bowtie v1.1.2 with parameters -v 2 -m 1.
For libraries constructed with Clontech DNA SMART ChIP Seq kit, the first three bases of the sequencing read, corresponding to the template switching oligo, were trimmed prior to mapping.
The following processing steps were performed to generate peakclassification files:  Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm).  The read density of the input chromatin was subtracted from the ChIP read density for normalization.  Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions.  We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage.   Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153.  We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions.  Peak genic classification:  A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations.  If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak.   If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak.  If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak.  If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer.   All remaining peaks were designated as "other".
Genome_build: hg19
Supplementary_files_format_and_content: .bed and .xls

molecule: genomic DNA

source_name: SUM159 breast carcinoma cell line

growth_protocol: culture media: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification, except where indicated, whereby the libraries were constructed using DNA SMART ChIP Seq kit (Clontech) with dual SPRI size selection following 18 cycles of amplification.
library preparation kit: Illumina TruSeq ChIP Library Prep kit

value: SUM159 breast carcinoma cell line

value: 500nM trametinib

tag: chip antibody

value: histone H3K4me3 EMD Millipore 07-473


title: SUM229neg_30nMtrametinib_24h

source_name: EpCAM/CD49f negative SUM229 breast carcinoma subpopulation

value: SUM229 breast carcinoma cell line, EpCAM/CD49f negative subpopulation


title: SUM159_H3K4me3_DMSO_24h


title: SUM229pos_DMSO_24h


title: Figure3_HCC1806_10nMtrametinib300nMJQ1_48h

value: 10nM trametinib 300nM JQ1


title: mmHeartMiseqPre

city: Barcelona

first: Julien

last: Lagarde

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: “*Post*” and “*Pre*” contain post- and pre-capture data, respectively

data_processing:
Read mapping software: STAR v.2.4.0.1
Read merging: compmerge v.1.3
Genome_build: hg38, mm10
Supplementary_files_format_and_content: “Compmerge” BED files contain merged transcript models generated using compmerge on the BAM files produced by STAR, with PacBio reads as input. Four flavors are provided per sample: “*.all.bed”: all merged transcript models from confidently mapped reads, “*.cage+polyASupported.bed”: subset of “*all.bed” containing full-length (i.e., with CAGE support at their 5’ end and polyA support at their 3’ end) merged transcript models, “*.cageSupported.bed”: subset of “*all.bed” containing merged transcript models with 5’ end CAGE support, “*.polyASupported.bed”: subset of “*all.bed” containing merged transcript models with 3’ end polyA support

source_name: Heart

extract_protocol:
See Samples – RNA source
Ribo-depleted, oligodT-primed cDNA, barcoded, captured separately in human and mouse

value: Heart

value: adult

tag: rna source

value: Clontech 636644


title: mmLiverMiseqPre

source_name: Liver

value: Liver


title: mmBrainMiseqPre

source_name: Brain

value: Brain


title: mmE7MiseqPre

source_name: Whole embryo day 7

value: Whole embryo day 7

value: embryo day 7


title: mmTestesMiseqPre

source_name: Testes

value: Testes


title: mmE15MiseqPre

source_name: Whole embryo day 15

value: Whole embryo day 15

value: embryo day 15


title: FL_RNA 1

city: Stanford

first: Zhen

last: Shi

state: California

address: 279 Campus Drive

institute: Stanford

description:
mRNA
E11.5_NT_FL_normalizedReads.txt

data_processing:
Sequencing reads were parsed by cutadapt to remove the 3’ adapter sequence and reads with good sequencing qualities (phred quality score>33) were kept.
A layered alignment employing Bowtie 2 was performed to first discard reads mapping to rRNA, tRNA or snRNA sequences. Non-rRNA/tRNA/snRNA reads were then aligned against the canonical isoform of UCSC known gene transcripts (mm10).
Mapped footprints were assigned to a specific position based on the A sites. The position of A site in relative to the 5’ end of each read is calculated as follows: 29-30 nt: +15; 31-33 nt: +16 and 34-35 nt: +17.
For each gene, the total number of ribosome footprints mapping to the CDS excluding the first 15 or last 5 codons were counted. The density of ribosome footprints was calculated as Reads Per Kilobase per Million mapped reads (RPKM). Genes having ≥5 RPKM were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized read counts (DESeq) for each analyzed protein-coding genes

source_name: Mouse

growth_protocol: Mice were housed under a 12 hr light/dark cycle with free access to food and water. All animal work was performed in accordance with protocols approved by Stanford University’s Administrative Panel on Laboratory Animal Care.

extract_protocol:
For Ribo-Seq, the cell pellet was re-suspended in 200 μl of cold lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 100 μg/ml cycloheximide, 1 mM DTT, 1% Triton X-100, 8% glycerol, 20 U/ml TURBO™ DNase (Ambion, AM1907)) and incubated for 30 min at 4°C with occasional vortexing. The lysate was clarified by sequential centrifugation for 5 min at 1800 x g and 10000 x g at 4°C to remove nuclei and mitochondria. The lysate was then treated with RNase I (Ambion, AM2294) for 30 min at RT to digest mRNAs not protected by the ribosome. The digestion was stopped by adding 4.5 μl of SUPERaseIn™ RNase Inhibitor (20 U/μl, Ambion AM2696). Lysate was then loaded onto a 1 M sucrose cushion. Ribosomes were pelleted by ultracentrifugation at 70000 rpm for 4 hr at 4°C by TLA120.2 rotor. The pellet was re-suspended in Trizol (Invitrogen, 15596) and RNAs were extracted by following manufacturer’s protocol. For RNA-Seq, after centrifugation, the cell pellet was re-suspended in Trizol (Invitrogen, 15596) for RNA extraction. RNA was extracted and polyA mRNA was isolated using Oligotex mRNA Mini Kit (Qiagen, 70022) following manufacturer’s protocol. Purified mRNAs were fragmented in alkaline fragmentation buffer (100 mM NaCO3 pH9.2, 2 mM EDTA).
Briefly, ribosome protected fragments (RPFs) and fragmented RNAs were loaded onto a 15% urea gel. 28-31 nt RPFs and 30-50 nt fragmented RNAs were excised from the gel for Ribo-Seq and RNA-Seq respectively. RNAs were eluted, dephosphorylated by PNK (NEB, M0201S), and ligated to the miRNA Cloning linker (NEB, S1315S) by T4 RNA Ligase2 truncated K227Q (NEB, M0242S). Ligated RNA was gel purified and reverse transcribed by Superscript III (Invitrogen, 18080). Gel purified cDNAs were circularized by Circligase (Epicentra, CL4111K) and rRNA sequence were subtracted using biotinylated oligos. Amplification was done using Phusion High Fidelity DNA Polymerase (NEB, M0530S). PCR amplification was performed for 10-15 cycles and products were loaded onto non-denaturing 8% PAGE gel. DNA fragment were purified for Illumina sequencing.

treatment_protocol: Cells of mesodermal lineage derived from the primitive streak were isolated by Fluorescence Activated Cell Sorting (FACS) at E11.5 embryos. Neural tubes (NT) and forelimb buds (FL) were microdissected from E11.5 embryos.

tag: cell type

value: microdissected forelimb buds (FL) at E11.5 embryos

value: FVB


title: FL_RNA 2

description:
mRNA
E11.5_NT_FL_normalizedReads.txt


title: FL_RPF 2

description:
Ribosome-Protected Fragments (RPFs)
E11.5_NT_FL_normalizedReads.txt


title: FL_RPF 3


title: FL_RPF 1


title: NT_RNA 2

description:
mRNA
E11.5_NT_FL_normalizedReads.txt

value: microdissected neural tubes (NT) at E11.5 embryos


title: NT_RNA 3

description:
mRNA
E11.5_NT_FL_normalizedReads.txt


title: SUM229neg_DMSO_24h

value: DMSO


title: NT_RPF 2


title: NT_RPF 3


title: NT_RPF 1


title: Mesoderm_RNA 3

description:
mRNA
We used the double fluorescent T-Cre (T-Cre; mT/mG) reporter system in which membrane-bound Tomato (mT) is expressed in all cells of the mouse embryo prior to Cre-activation and membrane-targeted enhanced Green Fluorescent Protein (mG) is expressed after activation of T-Cre which labels the mesodermal lineage derived from the primitive streak. This enabled us to mark all of the lineages derived from the paraxial mesoderm (PM) (somites), lateral plate mesoderm (LPM) (limbs) and intermediate mesoderm, and to isolate the GFP+ cells by Fluorescence Activated Cell Sorting (FACS)
E11.5_mesoderm_normalizedReads.txt

value: Cells of mesodermal lineage derived from the primitive streak, isolated by Fluorescence Activated Cell Sorting (FACS) at E11.5 embryos

value: R26-mTmGflox/+; Tg(T-cre)1LWD/J/+

tag: tag

value: GFP+


title: Mesoderm_RNA 2


title: FL_RNA 3

description:
mRNA
E11.5_NT_FL_normalizedReads.txt


title: Mesoderm_RNA 1


title: Mesoderm_RPF 1

description:
Ribosome-Protected Fragments (RPFs)
We used the double fluorescent T-Cre (T-Cre; mT/mG) reporter system in which membrane-bound Tomato (mT) is expressed in all cells of the mouse embryo prior to Cre-activation and membrane-targeted enhanced Green Fluorescent Protein (mG) is expressed after activation of T-Cre which labels the mesodermal lineage derived from the primitive streak. This enabled us to mark all of the lineages derived from the paraxial mesoderm (PM) (somites), lateral plate mesoderm (LPM) (limbs) and intermediate mesoderm, and to isolate the GFP+ cells by Fluorescence Activated Cell Sorting (FACS)
E11.5_mesoderm_normalizedReads.txt


title: Mesoderm_RPF 2


title: shRNA2_ATRA [RNA-Seq]

city: Garching

first: Christian

last: Mertes

state: BY

address: Boltzmannstraße 3

department: Informatics

country: Germany

institute: Technical University Munich

data_processing:
Illumina bcl2fastq version v2.17.1.14 to extract fastq files from raw intensities.
STAR version v2.5.0a to align the reads against the reference
PICARD tools 2.5.0 to remove PCR duplicates
R/Bioconductor package GenomicAlignments to count raw reads per gene
R/Bioconductor package DESeq2 to call differentiall gene expression between CTRL and shRNA treatment
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text file containing the raw and normalized read counts and DESeq2 statistics per gene

source_name: acute promyelocytic leukemia cell line (NB4)

growth_protocol: log growth about 0.5-1 cells x10^6/ml in FCS, L-Glu, PenStrep, HEPES supplemented RPMI

extract_protocol:
GeneJET RNA Purification Kit
NEBNext Ultra RNA Library Prep kit for Illumina
Mid output cartridge, reaching approx 2x5 GB per sample
total cell number: 1 million cells per condition

treatment_protocol: 1µM ATRA in RPMI medium or DMSO 1:10.000

tag: Stage

value: differentiated

tag: smarcd2 expression

value: SMARCD2 k/d


title: CTRL_ATRA [RNA-Seq]

value: Control


title: shRNA2_DMSO [RNA-Seq]

value: undifferentiated


title: Wild type Arabidopsis NT

value: wild type

value: seedlings

value: two weeks old


title: shRNA1_ATRA [ATAC-Seq]

description:
Tn5 treated DNA
atac_463_atra

data_processing:
Library strategy: ATAC-Seq
Illumina bcl2fastq version v2.17.1.14 to extract fastq files from raw intensities.
STAR version v2.5.0a to align the reads against the reference
PICARD tools 2.5.0 to remove PCR duplicates
MACS2 to do a joined peak calling on all files
EdgeR to call differentiall binding between CTRL and shRNA treatment
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text file containing the raw and normalized read counts and EdgeR statistics for the joined called peaks by MACS2

extract_protocol:
Buenrostro et al. Curr. Protoc. Mol. Biol. 2015
NEBNext Multiplex Oligos for Illumina
Illumina NextSeq 500, reaching approx 2x1.8GB per sample
total cell number: 50000 cells per condition

treatment_protocol: 1µM ATRA in supplemented RPMI medium or DMSO 1:10.000


title: shRNA1_DMSO [RNA-Seq]


title: shRNA2_DMSO [ATAC-Seq]

description:
Tn5 treated DNA
atac_374_dmso


title: shRNA1_ATRA [RNA-Seq]


title: CTRL_DMSO [ATAC-Seq]

description:
Tn5 treated DNA
atac_scr_atra


title: shRNA2_ATRA [ATAC-Seq]

description:
Tn5 treated DNA
atac_374_atra


title: shRNA1_DMSO [ATAC-Seq]

description:
Tn5 treated DNA
atac_463_dmso


title: NT_RNA 1

description:
mRNA
E11.5_NT_FL_normalizedReads.txt

tag: genotype


title: SUM159_DMSO_24h_500nMtrametinib_replicate1

description:
processed data file:
DESeq2_Figure2_claudin.xlsx
DESeq2_Figure2_subtype_group_comparison.xlsx

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files (.xlsx and .normalized_results) contain upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libaries constructed with Illumina TruSeq RNA Library Prep Kit v2.   4 µg total RNA and 10 cycles of amplification (using 0.5X recommended DNA template) were used for libraries constructed with KAPA Stranded mRNAseq kit.

value: SUM159 breast carcinoma cell line

tag: culture media

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone

tag: library preparation kit

value: KAPA Stranded mRNAseq kit


title: SUM159_DMSO_24h_500nMtrametinib_replicate2


title: WHIM12_500nMtrametinib_24h_replicate2

value: PDX breast carcinoma cell line

value: RPMI 1640 supplemented with 10% FBS


title: WHIM12_DMSO_24h_replicate1


title: HS578T_500nMtrametinib_24h_replicate1

value: HS578T breast carcinoma cell line


title: HS578T_500nMtrametinib_24h_replicate2


title: Mesoderm_RPF 3


title: HS578T_DMSO_24h_replicate2


title: SUM159_500nMtrametinib_24h_replicate1


title: HS578T_DMSO_24h_replicate1


title: SUM159_500nMtrametinib_24h_replicate2


title: CTRL_DMSO [RNA-Seq]


title: MDAMB468_500nMtrametinib_24h_replicate1

description:
processed data file:
DESeq2_Figure2_basal.xlsx
DESeq2_Figure2_subtype_group_comparison.xlsx

value: MDAMB468 breast carcinoma cell line


title: CTRL_ATRA [ATAC-Seq]

description:
Tn5 treated DNA
atac_scr_atra


title: SUM149pos_DMSO_24h_replicate2

value: EpCAM/CD49f positive SUM149 breast carcinoma subpopulation

value: HuMEC supplemented with 5% FBS and Gibco defined HuMEC supplements


title: SUM149pos_500nMtrametinib_24h_replicate1


title: MDAMB468_500nMtrametinib_24h_replicate2


title: MDAMB468_DMSO_24h_replicate1


title: MDAMB468_DMSO_24h_replicate2


title: SUM149pos_500nMtrametinib_24h_replicate2


title: SUM149pos_DMSO_24h_replicate1


title: HCC1806_DMSO_24h_replicate1

value: HCC1806 breast carcinoma cell line


title: HCC1806_500nMtrametinib_24h_replicate2


title: SUM159xenograft_mouse2_control_48h

source_name: SUM159 breast carcinoma cell line: xenograft

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libraries constructed with Illumina TruSeq RNA Library Prep Kit v2. 4 µg total RNA and 10 cycles of amplification (using 0.5X recommended DNA template) were used for libraries constructed with KAPA Stranded mRNAseq kit or Illumina TruSeq RNA library kit v2.
library preparation kit: KAPA Stranded mRNAseq kit

tag: xenograft

value: SUM159 breast carcinoma cell line xenograft

value: control


title: SUM159xenograft_mouse3_control_48h


title: WHIM12_500nMtrametinib_24h_replicate1


title: HCC1806_DMSO_24h_replicate2


title: SUM159xenograft_mouse3_30mpkIBET151_48h


title: SUM159xenograft_mouse1_control_48h


title: SUM159xenograft_mouse2_30mpkIBET151_48h


title: WHIM12_DMSO_24h_replicate2


title: SUM159xenograft_mouse1_30mpkIBET151_48h


title: SUM159xenograft_mouse3_2mpktrametinib30mpkIBET151_48h

value: 2mpk trametinib 30mpkIBET151


title: hsTestesPacbioPost

tag: tissue

value: Testes

value: adult

value: Ambion AM6000


title: SUM159xenograft_mouse1_2mpktrametinib30mpkIBET151_48h


title: hsLiverPacbioPost

value: Liver


title: hsK562PacbioPost

value: Gingeras lab, CSHL (ENCODE cell cultures)


title: SUM159xenograft_mouse3_2mpktrametinib_48h

value: 2mpk trametinib


title: hsHelaPacbioPost

source_name: Hela

value: Hela


title: HCC1806_500nMtrametinib_24h_replicate1

value: KAPA Stranded mRNAseq kit


title: SUM159xenograft_mouse2_2mpktrametinib_48h


title: SUM159xenograft_mouse1_2mpktrametinib_48h


title: hsBrainPacbioPost

value: Brain


title: Figure7_SUM159_100nMtrametinib500nMIBET151_24h

value: SUM159 breast carcinoma cell line

value: 100nM trametinib 500nM IBET151


title: Figure7_SUM159_100nMtrametinib3uMSGCCBP30_24h

value: 100nM trametinib 3uMSGCCBP30


title: hsHeartPacbioPost

value: Heart


title: SUM159_100nM_trametinib_24h_replicate3

description:
DESeq2_SUM159replicates.xlsx
SUM159_replicate3_normalizedRSEM.xlsx

value: 100nM trametinib


title: SUM159_300nMJQ1_24h_replicate3

value: 300nM JQ1


title: Figure7_SUM159_3uMSGCCBP30_24h


title: hsTestesMiseqPre


title: hsLiverMiseqPre


title: SUM159_DMSO_24h_replicate3

value: DMSO


title: Figure7_SUM159_500nMIBET151_24h

value: 500nM IBET151


title: hsK562MiseqPre


title: SUM159_100nM_trametinib_24h_replicate2

description:
DESeq2_SUM159replicates.xlsx
SUM159_replicate2_normalizedRSEM.xlsx


title: SUM159_100nMtrametinib300nMJQ1_24h_replicate2

value: 100nM trametinib 300nM JQ1


title: hsHelaMiseqPre

value: adult


title: SUM159xenograft_mouse2_2mpktrametinib30mpkIBET151_48h

value: SUM159 breast carcinoma cell line xenograft

value: 2mpk trametinib 30mpkIBET151


title: SUM159_100nMtrametinib300nMJQ1_24h_replicate3


title: SUM159_300nMJQ1_24h_replicate2


title: hsHeartMiseqPre

value: Ambion AM6000


title: SUM159_DMSO_24h_replicate2


title: SUM159_300nMJQ1_24h_replicate1


title: SUM159_100nMtrametinib300nMJQ1_24h_replicate1


title: Apis mellifera larvae in diet with 0.25mM quercetin replication 3

city: Urbana

first: May

last: Berenbaum

state: Illinois

address: 505 S. Goodwin Avenue

department: Entomology

institute: University of Illinois at Urbana-Champaign

data_processing:
Basecalls performed using CASAVA version 1.8 (pipeline 1.9)
Reads were mapped to the Bee reference genome (version 3.2)
Read count was performed using HTSeq-count(www-huber.embl.de/users/anders/HTSeq/doc/overview.html) using the genome annotation version amel_OGSv3.2.gff3.
EdgeR was used to calculate normalized expression counts, differential expression, and statistics on pairwise comparissons
Genome_build: OGSv3.2
Supplementary_files_format_and_content: A tab delimited matrix containing the raw read counts per sample for each transcript feature of the Apis mellifera genome

organism: Apis mellifera

source_name: whole larvae

growth_protocol: All honeybees in these experiments were obtained from the University of Illinois Bee Research Facility in Urbana, IL.  To collect eggs, a previously occupied empty frame with an excluder cage was placed into a hive with a healthy colony in the afternoon for cleaning by workers. A queen was transferred into the excluder cage in the evening of the next day, confined overnight, and released. In the morning of the fourth day after egg collection, the frame with newly hatched larvae was removed from the hive and brought to the laboratory for larval grafting.

extract_protocol:
RNA was extracted from the frozen midguts using TRIzol reagent (Thermo Fisher) following manufacturer protocol. RNA was cleaned up with an RNeasy Mini Kit, and the RNase-free DNase set for on-column DNase digestion (Qiagen).
The RNA-seq libraries were prepared using the TruSeq RNA-seq Sample Prep kit according to the manufacturer’s instructions (Illumina)

treatment_protocol: 10 -12 newly emerged larvae per treatment per replication were grafted into the wells of a 24-well cell culture plate with 30 μl of the corresponding semi-aritificial diet in each well. The semi-artificial diet was prepared with 50% royal jelly and 50% aqueous solution containing 12% d-glucose, 12% fructose, and 2% yeast extract. Diet treatments consisted of the semi-artificial diets with either none, 0.1mM quercetin, or  0.25 mM quercetin for three days. Each of the three treatments were independently replicated three times. On the third day, the larvae were collected and flash-forzen in liquid nitrogen for further RNA extraction

value: diet with 0.25mM quercetin

value: larva


title: Apis mellifera larvae in diet with 0.25mM quercetin replication 2


title: SUM159_DMSO_24h_replicate1


title: Apis mellifera larvae in diet with 0.1mM quercetin replication 3

value: diet with 0.1mM quercetin


title: SUM229neg_input_DMSO_24h

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification, except where indicated, whereby the libraries were constructed using DNA SMART ChIP Seq kit (Clontech) with dual SPRI size selection following 18 cycles of amplification.
library preparation kit: KAPA Hyper Prep

value: SUM229 breast carcinoma cell line, EpCAM/CD49f negative subpopulation


title: Apis mellifera larvae in diet with 0.25mM quercetin replication 1


title: SUM229neg_BRD4_30nMtrametinib_24h

value: 30nM trametinib

value: BRD4 Bethyl Laboratories A301-985A


title: Apis mellifera larvae in diet with 0.1mM quercetin replication 2


title: Apis mellifera larvae in control diet replication 2

value: control diet


title: SUM229pos_input_DMSO_24h

value: SUM229 breast carcinoma cell line, EpCAM/CD49f positive subpopulation


title: SUM229pos_BRD4_30nMtrametinib_24h


title: Apis mellifera larvae in diet with 0.1mM quercetin replication 1


title: SUM229pos_BRD4_DMSO_24h


title: Apis mellifera larvae in control diet replication 3


title: Apis mellifera larvae in control diet replication 1


title: hsBrainMiseqPre

value: Brain


title: Epc_soma_input1

city: baltimore

first: Xin

last: Chen

address: 3400 N Charles St

department: Biology

institute: The Joihns Hopkins University

data_processing:
Basecalls performed using CASAVA version 1.7 default
Bowtie aligner (version 0.12.7) following configuration (-a --phred33-quals -n 2 -e 70 -l 28 -m 1 --best –strata)
non-redundant reads are filtered through;SAMtools software suite was utilized to convert between related read formats to BAM
edgeR R package TMM normalization
MACS2.0 peakcall default settings
Genome_build: flybase d_melanogaster r5.43
Supplementary_files_format_and_content: bedgraph generated by 500bp interval inhouse software; raw_count_per_gene_RNAseq.txt is summarized by inhouse software; RPKM is calculated by edgeR

organism: Drosophila melanogaster

source_name: somatic gonadal cells in fly testis

extract_protocol:
[ChIP-seq] Sonication of fly testes was performed. Then sonicated chromatin was incubated with GFP antibody.
[ChIP-seq] Libraries were generated using reagents provided in the Illumina TruSeq ChIP Sample Preparation Kit (IP-202-1012).
[RNA-seq] Total RNA was purified following the manufacturer’s instruction of PicoPure RNA isolation kit (KIT0204, Life technologies)
[RNA-seq] libraries were generated using reagents provided in Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001).

tag: strain

value: Tj-Gal4/ UAS-E(Pc) cDNA-GFP; UAS-E(Pc)shRNA/+

tag: age

value: 5 days old


title: Epc_soma_input2

tag: developmental stage


title: Epc_soma_GFPChIP1

value: GFP (Abcam, ab290)


title: SUM229neg_BRD4_DMSO_24h

tag: treatment

value: DMSO


title: timecourse_SUM159_BRD4_100nMtrametinib_72h

description: peakclassification_trametinib_timecourse.xlsx

tag: cell line

value: SUM159 breast carcinoma cell line

value: 100nM trametinib


title: timecourse_SUM159_BRD4_100nMtrametinib_1h

tag: time


title: timecourse_SUM159_BRD4_100nMtrametinib_4h

tag: chip antibody


title: timecourse_SUM159_BRD4_100nMtrametinib_24h


title: SUM159shMYC_BRD4_dox_48h

value: shMYC, dox


title: SUM159shMYC_input_DMSO_48h

value: shMYC, DMSO


title: SUM159_100nM_trametinib_24h_replicate1


title: timecourse_SUM159_BRD4_DMSO_72h


title: SUM159shMYC_BRD4_100nMtrametinib_48h

value: shMYC, 100nM trametinib


title: SUM159shMYC_BRD4_DMSO_48h


title: SUM159_input_DMSO_48h


title: SUM159_BRD4_100nMtrametinib_48h


title: SUM159_BRD4_dox_48h

value: dox


title: SUM159_BRD4_30nMbortezomib_8h

value: 30nM bortezomib


title: SUM159_BRD4_100nMtrametinib30nMbortezomib_8h

value: 100nM trametinib 30nM bortezomib


title: Epc_soma_GFPChIP2

value: adult


title: SUM159_BRD4_100nMtrametinib_8h

value: BRD4 Bethyl Laboratories A301-985A


title: SUM159_BRD4_DMSO_8h


title: Figure7_SUM159_p300_100nMtrametinib1uMSGCCBP30_24h

value: 100nM trametinib 1uM SGCCBP30

value: p300 Santa Cruz Biotechnology sc-585X


title: Figure7_SUM159_p300_DMSO_24h


title: Figure7_SUM159_p300_100nMtrametinib_24h


title: Figure7_SUM159_BRD4_100nMtrametinib1uMSGCCBP30_24h


title: HCC1806_input_DMSO_24h

value: HCC1806 breast carcinoma cell line


title: HCC1806_BRD4_100nMtrametinib300nMJQ1_24h

description: SupplementaryTableS5_peakclassification.xlsx

value: 100nM trametinib 300nM JQ1


title: Figure7_SUM159_BRD4_100nMtrametinib_24h


title: ID4-GFP Bright 3

city: Pullman

first: Jon

last: Oatley

address: 1770 NE Stadium Way

institute: Washington State University

description: Helsel 05

data_processing:
TopHat 2.1.1
Cufflinks 2.2.1
Genome_build: mm9

source_name: Postnatal Day 8 pup testis

extract_protocol:
Trizol
cDNA libraries were generated using oligo d(T) priming

value: Testis

value: Id4-eGfp (LT11)

value: Postnatal Day 8

tag: level of id4 expression

value: High


title: HCC1806_BRD4_300nMJQ1_24h

value: 300nM JQ1


title: ID4-GFP Dim 2

description: Helsel 04

value: Low


title: HCC1806_BRD4_DMSO_24h

value: DMSO


title: ID4-GFP Dim 3

description: Helsel 06


title: SUM159_input_DMSO_24h

value: SUM159 breast carcinoma cell line


title: ID4-GFP Bright 2

description: Helsel 03


title: ID4-GFP Dim 1

description: Helsel 02


title: Figure7_SUM159_BRD4_DMSO_24h


title: SUM159_H3K4me1_100nMtrametinib_24h

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification, except where indicated, whereby the libraries were constructed using DNA SMART ChIP Seq kit (Clontech) with dual SPRI size selection following 18 cycles of amplification.
library preparation kit: Clontech DNA SMART ChIP Seq kit

value: 100nM trametinib

value: histone H3K4me1 Active Motif 39297


title: SUM159_BRD4_DMSO_48h


title: HCC1806_BRD4_100nMtrametinib_24h


title: ID4-GFP Bright 1

description: Helsel 01


title: 7802: ID4 Germ Cell Overexpression

data_processing:
TopHat
Cufflinks
Genome_build: mm9

source_name: Testis


title: SUM159_H3K4me1_DMSO_24h


title: SUM159_CEBPB_100nMtrametinib300nMJQ1_24h

value: CEBPβ Santa Cruz Biotechnology sc-150X


title: 6125: ID4 Germ Cell Overexpression


title: Figure7_SUM159_p300_100nMtrametinib300nMJIB04_24h

value: 100nM trametinib 300nM JIB04


title: 6124: Control


title: SUM159_CEBPB_300nMJQ1_24h


title: Figure7_SUM159_BRD4_100nMtrametinib300nMJIB04_24h

value: BRD4 Bethyl Laboratories A301-985A


title: SUM159_CEBPB_100nMtrametinib_24h


title: 6122: Control


title: SUM159_CEBPB_DMSO_24h


title: SUM159_H3K27ac_100nMtrametinib300nMJQ1_24h

value: histone H3K27ac Active Motif 39133


title: 6120: Control


title: SUM159_H3K27ac_300nMJQ1_24h


title: 6121: ID4 Germ Cell Overexpression


title: Chd7-Het-Atac-Seq2

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

description: Chd7 Heterzygous

data_processing:
The reads were first trimmed with trim-galore_0.4.1 to remove the adapters.
The trimmed reads are mapped with bowtie 1.0.0  to mm10 with parameters -X 2000 -m 1
Duplicated reads were removed with picard_1.139. Reads mapped to chrM were also removed
To get the peaks macs2 2.1.0.20150731 were applied for Chd7 wild type, het  and Chd7 het mutant and Chd7 hom mutant  respectively with parameters   –nomodel --shift -100 --extsize 200.
Genome_build: mm10
Supplementary_files_format_and_content: macs2 peak calling, xls file

source_name: Granule NeuronProgenitors

growth_protocol: P7 GNPs were freshly isolated from mice

extract_protocol:
nuclei was extracted with hypotonic buffer
Tn5 mediated tagging

treatment_protocol: no treatment

value: cerebellum

tag: cell type

value: Granule Neuron Progenitors

value: Chd7 het


title: Chd7-Het-Atac-Seq1

description: Chd7 Heterzygous


title: Hom-4

data_processing:
RSEM-1.2.15 with Bowtie-1.0.0 is used for mapping, default setting is used.
ComBat with default setting was used to remove batch effect
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Cerebellar granule neuron progenitors

growth_protocol: Primary cells without culture

extract_protocol:
Tri-Reagent combined with QIAGEN RNAeasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were freshly isolated from P7 pups

value: Atoh1-Cre::Chd7 f/f


title: SUM159_H3K27ac_100nMtrametinib_24h

source_name: SUM159 breast carcinoma cell line


title: Hom-3


title: SUM159_H3K27ac_DMSO_24h


title: SUM159_p300_100nMtrametinib300nMJQ1_24h

value: 100nM trametinib 300nM JQ1

value: p300 Santa Cruz Biotechnology sc-585X


title: IVBL, rep2

city: Buffalo

first: Hai

state: NY

address: Elm and Carlton Streets, MRC 328

department: Molecular and Cellular Biology

institute: Roswell Park Cancer Institute

description:
Sample 15
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData

data_processing:
Illumina NextSeq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from xenograft materials contain a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DESeq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: Human: GRCh38.83
Genome_build: Mouse: GRCm38.83
Supplementary_files_format_and_content: BICA_RNAseq.RData: Rdata object; RSEM read counts.
Supplementary_files_format_and_content: BICA_RNAseq.Normalized.RData: Rdata object; DESeq2 normalized gene/isoform expression matrix.

organism:
Homo sapiens
Mus musculus

source_name: xenograft bone lesion

growth_protocol: For MCF-7, cells are cultured in DMEM with 2% FBS. For BICA, bone pieces were prepared from metaphysis of femurs and tibias harvested from mice receiving intra-iliac injection. The bones were crushed with a bone plier (F.S.T. 16025-14) and transferred to low attachment 96-well plate. Bone pieces bearing tumor cells were cultured in media comprised of DMEM/F12.

extract_protocol:
After homogenization, total RNA were extracted by Direct-zol RNA miniprep kit. The first and second strand cDNA were prepared by SuperScript III First-Strand Synthesis System and NEBNext mRNA Second Strand Synthesis Module from at least 200ng total RNA for each sample.
Illumina Nextera XT DNA Sample Prep Kit was used with 1 ng of dsDNA for the construction of sequencing libraries.

value: MCF-7 and local mouse cells

tag: passage

tag: reporter gene

value: Firefly Luciferase (MCF-7)


title: IVBL, rep4

description:
Sample 17
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: IVBL, rep1

description:
Sample 14
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: IVBL, rep3

description:
Sample 16
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: SUM159_p300_100nMtrametinib_24h


title: WT-5

value: Atoh1-Cre negative


title: SUM159_MED1_100nMtrametinib300nMJQ1_24h

value: MED1/CRSP1/TRAP220 Bethyl Laboratories A300-793A


title: Het-3

value: Atoh1-Cre::Chd7 f/+


title: SUM159_MED1_300nMJQ1_24h

value: SUM159 breast carcinoma cell line

value: 300nM JQ1


title: BICA, rep5

description:
Sample 12
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData

source_name: cancer-containing bone-in-culture array


title: BICA, rep6

description:
Sample 13
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: WT-4


title: BICA, rep4

description:
Sample 11
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: SUM159_MED1_100nMtrametinib_24h

description: SupplementaryTableS4_peakclassification.xlsx

value: 100nM trametinib


title: BICA, rep3

description:
Sample 10
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: BICA, rep2

description:
Sample 9
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: CGN Top2b

data_processing:
Trim with trim_galore
Map with bowtie 1.0.0 with parameter -X 1000 -m 1.
Peaks were called with macs2 with default parameters. For Top2b, peaks were called with homer findPeaks with parameter -F 2.0 -P 0.001 -L 2.0 -LP 0.001 -fdr 0.01 - style factor
Super-enhancer was called using homer findPeaks with parameter -style super
Genome_build: mm10

source_name: Cerebellar granule neuron

growth_protocol: GNPs were freshly isolated from P7 pups. CGNs were cultured from GNPs without SHH for 48 hours.

extract_protocol:
Cells were fixed with formadehyde.
Lysates were sonicated and precipitated with antibody.

treatment_protocol: No treatment

value: granule neuron

tag: antibody

value: Top2b (Santa Cruz)


title: CGN Chd7 KO Top2b


title: SUM159_BRD4_100nMtrametinib300nMJQ1_24h

value: BRD4 Bethyl Laboratories A301-985A


title: SUM159_p300_300nMJQ1_24h


title: SUM159_MED1_DMSO_24h

value: DMSO


title: CGN input


title: Het-5

value: cerebellum

value: Granule Neuron Progenitors

tag: genotype


title: BICA, rep1

description:
Sample 8
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: SUM159_BRD4_300nMJQ1_24h


title: Het-4


title: Orth, rep3

description:
Sample 7
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData

source_name: xenograft breast tumor


title: SUM159_p300_DMSO_24h


title: Orth, rep2

description:
Sample 6
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: GNP Chd7

source_name: Cerebellar granule neuron progenitor

value: granule neuron progenitor

value: Chd7 (Cell Siganling)


title: GNP Chd7 KO Chd7


title: SUM159_BRD4_DMSO_24h


title: Orth, rep1

description:
Sample 5
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: MCF-7, rep4

description:
Sample 4
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData

source_name: MCF-7 breast cancer cells

value: breast cancer cell line


title: Mll2 4-OHT rep2

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
Sample name: YC47
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

data_processing:
Quality trim to a minimum of Q15.
Map to the mm10 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20141217_250/gsnap -d mm10_total -v mm10_total.snp138 --use-splicing=mm10_total.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $file > ./${j}.sam
Sort and index using SAMTOOLS.
Split forward and reverse reads using SAMTOOLS.
Call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_expression_matrix.xlsx: Tab-delimited text file containing FPKM values.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll2 deletion

growth_protocol: Bone marrow cells were transformed by MLL-AF9 in M3434 methylcellulose, then liquid culture in IMDM-based medium supplemented with 50ng/mL SCF, 10ng/mL IL-3 and 10ng/mL IL6.

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Mini Kit.
Illumina directional mRNA prep.
HiSeq4000 using 1x152bp format.

treatment_protocol: Cells were treated with ethanol or 100nM 4-OHT for 24 hours. Then remove the drug and continue to culture for 2 days.

value: MLL-AF9-transformed cells

tag: genotype/variation

tag: treatment time

value: 72 hours since initiating the treatment


title: screen4_postHYG

first: Eric

middle: Jan

last: Foss

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: shRNA

data_processing:
shRNAs present in the library were enumerated using a perl script that accepted sequences with 0 or 1 mismatches.
Genome_build: MM10
Supplementary_files_format_and_content: count shRNA library inserts

source_name: Open Biosystems library

growth_protocol: pre- and post-hygromycin treatment

extract_protocol:
DNA extraction
Illumina TruSeq DNA LT Sample Prep Kit

treatment_protocol: hygromycin B

tag: group

value: after selection for hygromycin resistance


title: MCF-7, rep3

description:
Sample 3
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData

value: Firefly Luciferase (MCF-7)


title: MCF-7, rep2

description:
Sample 2
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: Mll2 4-OHT rep1

description:
Sample name: YC46
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: screen4_preHYG

description: shRNA

value: before selection for hygromycin-resistance


title: MCF-7, rep1

description:
Sample 1
Processed data file: BICA_RNAseq.RData
Processed data file: BICA_RNAseq.Normalized.RData


title: GNP H3K27ac

tag: tissue

value: H3K27ac (Diagenode)


title: Mll2 EtOH rep1

description:
Sample name: YC43
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll2 control

value: EtOH


title: screen3_postHYG

description: shRNA


title: screen2_postHYG

description: shRNA


title: screen3_preHYG

description: shRNA


title: SUM159_BRD4_100nMtrametinib_24h

value: SUM159 breast carcinoma cell line

value: 100nM trametinib


title: RODI-3

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

data_processing:
Quality of the sequences was verified with FastQC 0.11.2
EDGE-pro 1.3.1 workflow was employed for read processing. The pipeline as described by T.Magoc, et al., Evolutionary Bioinformatics, 2013, employs Bowtie2 (v2.2.3) to map reads to the reference genome (NCTC 8325), filters multimapped reads based on scoring alignments and determines read coverage for each genomic position and gene.
EDGE-pro output files were formated using the edgeToDeseq script provided in the EDGE-pro package and used as input for DESeq2 (v1.12.4) to calculate RPKMs per gene and quantify differential expression between conditions.
Unaligned reads for RODI replicates to the NCTC 8325 reference genome were collected and reprocessed using the EDGE-pro 1.3.1 and DESeq2, using phiIPLA-RODI's reference genome.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly GCA_000013425.1, Mar 2010) and phage phiIPLA-RODI (Assembly GCF_001504675.1, May 2015)
Supplementary_files_format_and_content: SM_vs_RODI.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in SM and RODI replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
Supplementary_files_format_and_content: phiIPLA-RODI_RPKMs.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phiIPLA-RODI genes in each RODI replicate.

organism: Staphylococcus aureus

source_name: Biofilm cells

growth_protocol: Biofilms were formed for 24 hours at 37ºC, then adhered cells were harvested

extract_protocol:
Bacterial cells were harvested, treated with RNA protect (Qiagen) and kept at -80ºC until RNA purification. RNA was obtained by mechanical disruption in the presence of acid phenol and subsequent purification was carried out with illustra RNA spin minikit (GE Healthcare)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: IPLA 1

value: Biofilm cells

value: phage phiIPLA-RODI


title: screen1_preHYG

description: shRNA


title: Mll1;Mll2 EtOH rep2

description:
Sample name: YC38
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll1;Mll2 control


title: Mll1;Mll2 4-OHT rep2

description:
Sample name: YC41
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll1;Mll2 deletion


title: GNP input


title: RODI-2


title: SM-3

value: untreated control


title: SM-2


title: Mll1;Mll2 4-OHT rep1

description:
Sample name: YC40
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: RODI-1


title: SM-1


title: screen2_preHYG

description: shRNA


title: Mll1 4-OHT rep2

description:
Sample name: YC35
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll1 deletion


title: screen1_postHYG

description: shRNA


title: Mll1;Mll2 EtOH rep1

description:
Sample name: YC37
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: C3TAgT2_500nMtrametinib_24h

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
Differential expression analysis was performed as follows:  RSEM gene-level expected read counts were imported into R version 3.2.2 and were analyzed using DESeq2 v1.12.3  to detect genes that were differentially expressed between pre-treatment and trametinib-treated conditions for claudin-low cell lines (DESeq2_Figure2_claudin.xlsx) or basal-like cell lines (DESeq2_Figure2_basal.xlsx), or to detect genes that were differentially expressed between claudin-low and basal-like cell line groups (DESeq2_Figure2_subtype_group_comparison.xlsx).  DESeq2 v1.12.3 was also used to detect differentially expressed transcripts in response to trametinib among biological replicates of an individual cell line (DESeq2_SUM159replicates.xlsx).  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.  Significantly differentially expressed genes were selected based on adjusted p-values, utilizing a threshold of 0.05 for significance.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: Processed files (.xlsx and .normalized_results) contain upper-quartile normalized RSEM transcript abundance estimates, organized by official gene symbol and Entrez Gene ID.

source_name: C3TAg GEMM cell line

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
2 µg total RNA and 15 cycles of amplification were used for libraries constructed with Illumina TruSeq RNA Library Prep Kit v2. 4 µg total RNA and 10 cycles of amplification (using 0.5X recommended DNA template) were used for libraries constructed with KAPA Stranded mRNAseq kit or Illumina TruSeq RNA library kit v2.
library preparation kit: Illumina TruSeq RNA library kit v2

value: C3TAg GEMM cell line

value: 500nM trametinib


title: Mll2 EtOH rep2

description:
Sample name: YC44
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: mmTestesHiseqPost

description: “*Post*” and “*Pre*” contain post- and pre-capture data, respectively

data_processing:
Read mapping software: STAR v.2.4.0.1
Read merging: compmerge v.1.3
Genome_build: hg38, mm10
Supplementary_files_format_and_content: “Compmerge” BED files contain merged transcript models generated using compmerge on the BAM files produced by STAR, with PacBio reads as input. Four flavors are provided per sample: “*.all.bed”: all merged transcript models from confidently mapped reads, “*.cage+polyASupported.bed”: subset of “*all.bed” containing full-length (i.e., with CAGE support at their 5’ end and polyA support at their 3’ end) merged transcript models, “*.cageSupported.bed”: subset of “*all.bed” containing merged transcript models with 5’ end CAGE support, “*.polyASupported.bed”: subset of “*all.bed” containing merged transcript models with 3’ end polyA support

source_name: Testes

extract_protocol:
See Samples – RNA source
Ribo-depleted, oligodT-primed cDNA, barcoded, captured separately in human and mouse

value: Testes

value: adult

tag: rna source

value: Clontech 636644


title: Mll1 4-OHT rep1

description:
Sample name: YC34
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

value: MLL-AF9-transformed cells

value: 72 hours since initiating the treatment


title: mmLiverHiseqPost

source_name: Liver

value: Liver

tag: developmental stage


title: Mll1 EtOH rep2

description:
Sample name: YC32
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: MLL-AF9-transformed cells from c-Kit+ bone marrow cells, Mll1 control

tag: treatment


title: C3TAgT2_DMSO_24h

tag: cell line

value: DMSO


title: Mll1 EtOH rep1

description:
Sample name: YC31
Processed data file: gene_expression_matrix.txt
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: mmTestesPacbioPost


title: T11_DMSO_24h

source_name: T11 orthotopic serial transplant cell line

tag: time


title: mmHeartHiseqPost

source_name: Heart

value: Heart


title: mmE7HiseqPost

source_name: Whole embryo day 7

value: Whole embryo day 7

value: embryo day 7


title: mmBrainHiseqPost

source_name: Brain

value: Brain


title: mmE7PacbioPost


title: mmE15HiseqPost

source_name: Whole embryo day 15

value: Whole embryo day 15

value: embryo day 15


title: Chd7-mutant-Atac-Seq1

data_processing:
Library strategy: ATAC-seq
The reads were first trimmed with trim-galore_0.4.1 to remove the adapters.
The trimmed reads are mapped with STAR_2.5.0b to mm10 with parameters -alignMatesGapMax 10000   --outFilterMultimapNmax 1  --outFilterMismatchNmax 4  to get uniq mapping with few mismatches.
Duplicated reads were removed with picard_1.139. Reads mapped to chrM were also removed
To get the peaks macs2 2.1.0.20150731 were applied for Chd7 wild type  and Chd7 mutant respectively with parameters   –nomodel --shift -100 --extsize 200.
Genome_build: mm10
Supplementary_files_format_and_content: macs2 peak calling, plain text file

source_name: Granule Neuron Progenitors

value: cerebellum

value: Granule Neuron Progenitors

value: Chd7 mutant


title: Chd7-wt-Atac-Seq3

value: Chd7 wild type


title: mmHeartPacbioPost


title: Chd7-mutant-Atac-Seq2


title: Chd7-wt-Atac-Seq2


title: mmBrainPacbioPost


title: mmE15PacbioPost


title: Chd7-wt-Atac-Seq1


title: 2776-TL-0034 miRNA

city: Gainesville

first: Tanmay

last: Lele

state: FL

address: Bldg 723, Room 329

department: Chemical Engineering

institute: University of Florida

data_processing:
Post processing of the sequencing reads from miRNA-seq experiments from each sample was performed as per the Genomic Services Laboratory unique in-house pipeline. Briefly, quality control checks on raw sequence data from each sample was performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were imported on a commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). Adapter trimming was done to remove ligated adapter from 3' end of the sequenced reads with only one mismatch allowed, poorly aligned 3' ends were also trimmed. Sequences shorter than 15 nucleotides length were excluded from further analysis. Trimmed Reads with low qualities (base quality score less than 30, alignment score less than 95, mapping quality less than 40) were removed. Filtered reads were then used to extract and count the small RNA which was annotated with micro RNAs from the miRBase release 20 database. The quantification operation carries out measurement at both the gene level and at the active region level. Active region quantification considers only reads whose 5' end matches the 5' end of the mature miRNA annotation. The expression values obtained thus are called `raw counts', candidate miRNAs having less than 10 counts were filtered. Samples were then grouped as identifiers and the differential expression of miRNA was calculated on the basis of their fold change (default cut-off ≥ ±2.0) observed between different groups, p-value of differentially expressed miRNA's was estimated by implementing z-score calculations using Benjamini Hochberg FDR corrections of 0.05 (Benjamini and Hochberg 1995).
Genome_build: mm9
Supplementary_files_format_and_content: excel file contains normalized expressions for each sample

source_name: Fibroblast

growth_protocol: The SS-GFP-KDEL (control) and SS-HA-SUN1L-KDEL (LINC complex disrupted) cells were cultured in Dulbecco’s modified Eagle’s medium with 4.5 g/l glucose (Mediatech, Manassas, VA, USA) supplemented with 10% Donor Bovine Serum (DBS) (Gibco, Grand Island, NY, USA) and 1% penicillin-streptomycin (Mediatech), and were maintained at 37°C in a humidified environment with 5% CO2. Cells were trypsinized, seeded on hydrogel, and induced by adding 1 µg/ml doxycycline hyclate (Sigma, St. Louis, MO, USA) for 48 hr prior to lysis or fixation. For myosin inhibition, Y27 (EMD Millipore, Billerica, MA, USA) and blebbistatin (EMD Millipore) were added to the cell medium at final concentrations of 25 μM and 10 μM, respectively, for 48 hr prior to lysing or fixing.

extract_protocol:
After 48 hr of seeding on substrates, cells were lysed using QIAzol Lysis Reagent (Qiagen Sciences, Germantown, MD USA) following the manufacturer’s protocol. The cell lysate was immediately stored at -80°C and transported on dry ice to the Genomic Services Laboratory (HudsonAlpha, Huntsville, AL, USA) for RNA isolation and sequencing. Total RNA containing both mRNA as well as microRNA fractions was extracted from the cell lysate using the miRNeasy Kit with on-column DNase treatment (Qiagen Inc., Valencia, CA, USA) according to the manufacturer's protocol. The final elution was performed in 30 µl of RNase-free sterile distilled water. The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen)and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. RNA samples with RNA integrity numbers (RIN) of at least 7.0 were used for further processing.
Total RNA from each sample was taken into small RNA library preparation protocol using NEBNext Small RNA Library Prep Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer’s protocol. Briefly, 3` adapters were ligated to total input RNA followed by hybridization of multiplex SR RT primers and ligation of multiplex 5` SR adapters. Reverse transcription (RT) was done using ProtoScript II RT for 1 hour at 50°C. Immediately after RT reaction, PCR amplification was performed for 15 cycles using LongAmp Taq 2X master mix. Illumina indexed primers were added to uniquely barcode each sample. Post- PCR material was purified using QIAquick PCR purification kit (Qiagen Inc., Valencia, CA, USA). Post-PCR yield and concentration of the prepared libraries were assessed using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, California, USA) and DNA 1000 chip on Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. Size selection of small RNA was done using a 3% dye free agarose gel cassettes on Pippin prep instrument (Sage Science Inc., Beverly, MA, USA). Post-size selection yield and concentration of the libraries were assessed using Qubit 2.0 Fluorometer and DNA High sensitivity chip on Agilent 2100 Bioanalyzer, respectively. Accurate quantification for sequencing applications was performed using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was diluted to a final concentration of 1.25nM and pooled in equimolar ratios prior to clustering. Single End (SE) sequencing (50bp) was performed to generate approximately 15 million reads per sample on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA).

value: NIH 3T3 TetON

tag: substrate stiffness (kpa)

tag: linc complex

value: Control

tag: myosin inhibition

value: Yes, with blebbistatin


title: Tj-Epc_shRNA_RNAseq2

source_name: fly testis

value: Tj-Gal4/+; UAS-E(Pc) shRNA/+

value: adult

tag: age

value: 5 days old


title: 2776-TL-0052 miRNA

value: No


title: Chd7-mutant-Atac-Seq3

tag: cell type


title: 2776-TL-0051 miRNA

value: LINC disrupted


title: 2776-TL-0050 miRNA


title: Tj-Epc_shRNA_RNAseq1


title: T11_500nMtrametinib_24h

value: T11 orthotopic serial transplant cell line

value: 500nM trametinib


title: Tj-Gal4_RNAseq2


title: 2776-TL-0049 miRNA


title: Tj-Gal4_RNAseq1


title: Chd7-hom-RNA-Seq2

extract_protocol:
RNA was extracted from freshly isolated GNPs with Tri-Reagent and purified with RNeasy Minin Kit
Library were preparied according to Illumina's instruction

value: Chd7 hom mutant


title: Chd7-het-RNA-Seq1

value: Chd7 het mutant


title: Chd7-het-RNA-Seq2


title: 2776-TL-0053 miRNA

value: Yes, with Y27632


title: Chd7-hom-RNA-Seq1

value: cerebellum


title: 2776-TL-0044 miRNA


title: 2776-TL-0043 miRNA


title: Chd7-wt-RNA-Seq1

value: Granule Neuron Progenitors


title: Chd7-wt-RNA-Seq3


title: 2776-TL-0042 miRNA


title: Chd7-wt-RNA-Seq2


title: 2776-TL-0054 miRNA


title: 2776-TL-0040 miRNA


title: hsTestesHiseqPost

value: Testes

value: Ambion AM6000


title: hsLiverHiseqPost

value: Liver


title: 2776-TL-0038 miRNA

value: NIH 3T3 TetON

value: Control


title: 2776-TL-0037 miRNA


title: 2776-TL-0039 miRNA


title: hsK562HiseqPost

value: Gingeras lab, CSHL (ENCODE cell cultures)


title: 2776-TL-0034

data_processing: Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using the Genomic Services Laboratory unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference mouse genome mm9 using TopHat v2.0 (Langmead et al. 2009). The alignment metrics of the mapped reads were estimated using SAMtools (Li et al. 2009). Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics; reads with a base quality score of less than 30, alignment score of less than 95, and mapping quality of less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics; missing mates, translocated, unaligned, and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and transcript abundance was quantified for this final read list using Trimmed Means of M-values as the normalization method (Robinson and Oshlack 2010). Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-score calculations using Benjamini Hochberg corrections of 0.05 for false-discovery rate (Benjamini and Hochberg 1995). A   gene   ontology (GO)  analysis  was  performed  on  the  list  of  differentially expressed  mRNAs  between  samples.  Database for Annotation, Visualization   and Integrated Discovery (DAVID) v6.7 (Huang et al., 2009a; Huang et al., 2009b) was used for this analysis.   A functional annotation enrichment analysis was performed; functional annotation clustering based on biological processes, cellular components, and molecular functions demonstrating enrichment in the dataset was examined. Ingenuity Pathway Analysis (IPA,  Ingenuity® Systems, Redwood City, CA, USA) software was used to analyze the unique canonical pathways, biological functions, and networks  affected by LINC complex disruption on each substrate.  Additionally, a two-way analysis of variance was applied to significant substrate rigidity and LINC complex disruption main effects as well as their interaction. Additional GO-based analyses were performed using DAVID for genes that were significantly affected in the interaction analysis.

source_name: Empty Vector-308 kPa-Y27

extract_protocol:
After 48 hr of seeding on substrates, cells were lysed using QIAzol Lysis Reagent (Qiagen Sciences, Germantown, MD USA) following the manufacturer’s protocol. The cell lysate was immediately stored at -80°C and transported on dry ice to the Genomic Services Laboratory (HudsonAlpha, Huntsville, AL, USA) for RNA isolation and sequencing. Total RNA containing both mRNA as well as microRNA fractions was extracted from the cell lysate using the miRNeasy Kit with on-column DNase treatment (Qiagen Inc., Valencia, CA, USA) according to the manufacturer's protocol. The final elution was performed in 30 µl of RNase-free sterile distilled water. The concentration and integrity of the extracted total RNA were estimated using the Qubit® 2.0 Fluorometer (Invitrogen)and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA), respectively. RNA samples with RNA integrity numbers (RIN) of at least 7.0 were used for further processing.
Five hundred nanograms of total RNA for samples with RIN values of greater than 7.0 was required for downstream RNA-seq applications. One microliter of a 1:100 dilution of ERCC spike-in consisting of either Mix 1 or Mix 2 (Invitrogen) was added to each sample. Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads. The NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was used to prepare individually bar-coded next-generation sequencing expression libraries. Library quality was assessed using the Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was diluted to a final concentration of 12.5 nM and pooled in an equimolar ratio prior to clustering. Paired-end sequencing (25 million reads per sample, 50-bp) was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA)

value: NIH 3T3

value: Control (empty vector)

value: Yes, with blebbistatin


title: 2776-TL-0048 miRNA


title: hsHelaHiseqPost

source_name: Hela

value: Hela

value: adult


title: 2776-TL-0047 miRNA


title: 2776-TL-0032

source_name: SS-GFP-KDEL-308 kPa

value: Control (SS-GFP-KDEL)

value: No


title: 2776-TL-0031

source_name: SS-HA-Sun1L-KDEL-308 kPa

value: LINC disrupted (SS-HA-Sun1L-KDEL)


title: mmLiverPacbioPost

value: Clontech 636644


title: 2776-TL-0046 miRNA


title: 2776-TL-0027

source_name: SS-HA-Sun1L-KDEL-1 kPa


title: 2776-TL-0028

source_name: SS-GFP-KDEL-1 kPa


title: 2776-TL-0045 miRNA

value: LINC disrupted


title: 2776-TL-0024

source_name: SS-GFP-KDEL-308 kPa-Y27

value: Yes, with Y27632


title: SUM229pos

description:
SUM229variantcalling.xlsx
whole exome sequencing

data_processing:
Alignment to hg19 was performed using BWA-mem.
Variants from the reference were identified using FreeBayes and Strelka was used to call cell line specific mutations in a paired fashion by tretating each cell line individually as the somatic sample.
Variants of high quality (Q>=50) were annotated with SNPeff.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet containing variant coordinate, gene name, dbSNP ID, minor allele frequency, Q score, and COSMIC overlaps.

source_name: EpCAM/CD49f positive SUM229 breast carcinoma subpopulation

growth_protocol: F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES

extract_protocol:
Genomic DNA was isolated from EpCAM+/CD49f+ and EpCAM-/CD49f- FACS populations using Qiagen DNeasy Blood and Tissue Kit and subquently treated with Rnase A.
300 ng genomic DNA was submitted to the UNC High Throughput Sequencing Facility for Illumina Nextera Rapid Capture exome enrichment.

value: triple negative breast cancer cell line SUM-229PE

tag: cell subpopulation


title: hsHeartHiseqPost

value: Heart

value: Ambion AM6000


title: hsBrainHiseqPost

value: Brain


title: 2776-TL-0022

source_name: SS-GFP-KDEL-308 kPa-Blebb


title: SUM229neg

source_name: EpCAM/CD49f negative SUM229 breast carcinoma subpopulation


title: 2776-TL-0019


title: 2776-TL-0015


title: 2776-TL-0016


title: 2776-TL-0012


title: Wild-type2_1

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Fastq files were quality controlled using FastQC (Babraham Bioinformatics) and any adapter sequences, as well as twelve bases from the five prime end, were removed and mapped to hg19 using STAR (v. 2.4.0a
Samtools (version 0.1.19) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes and annotated using RefSeq (archive-2012-03-09-03-24-410). Genes that did not have at least one sample with at least ten reads were removed from the analysis.
The gene count file was then normalized and differential expression was performed by the R (v.3.0.1) package DESeq (v.1.16.0)
Transcripts with an adjusted P-Value less than 0.05 and an absolute log fold change of more than 1.2 were considered differentially expressed.
All KEGG pathway enrichment analysis was performed using DAVID Bioinformatics Resource 6.7 (http://david.abcc.ncifcrf.gov/home.jsp)
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx including DESeq normalized counts filtered for genes with at least 10 reads in at least one sample

growth_protocol: The four WA09 clones (2 wild-type and 2 mutant) were initially grown on MEF feeder layers in standard hPSC medium. These initial cultures were transitioned to feeder-free conditions in a stepwise fashion by passaging them with Accutase onto Geltrex (Gibco) with MEF-conditioned medium (MEF-CM) supplemented with 12 ng/ml basic FGF. After one passage in MEF-CM, the cultures were either continued in MEF-CM or passaged into E8 medium (Life Technologies). For all cultures, cells were grown at 37°C and 5% CO2 and passaged every three to four days, when they were ~80% confluent. At each passage, 150,000 cells were seeded per well of a 6-well plate (equivalent to a cell plating density of ~15,600 cells/ cm2). The medium was changed daily.

extract_protocol:
RNA was isolated using the mirVana miRNA Isolation Kit (Life Technologies, Inc.). The RNA was then quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 500 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Second strand cDNA synthesis was then done using DNA Polymerase I and RNase H. The cDNA was then ligated to adapters and enriched with PCR to create the final cDNA library. The library was then pooled and sequenced on a HiSeq 2500 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

treatment_protocol: Single-cell cloning was used to derive pure subpopulations of mutant and wild-type cells from the original mosaic MefEnz culture. MefEnz cells cultured on irradiated mouse embryonic fibroblasts (MEFs) in standard hPSC medium, consisting of Dulbecco’s modified eagle medium DMEM/F12 (Life Technologies) with 20% Knockout Serum Replacement (Life Technologies), 1 mM GlutaMAX (Life Technologies), 0.1 mM nonessential amino acids (NEAA, Life Technologies), 0.1 mM -mercaptoethanol, and 12 ng/ml basic FGF (Life Technologies), were treated for 1 hour with 10 M ROCK inhibitor Y-27632 (Calbiochem) before dissociation. The medium was supplemented with SMC4 (0.58 l SMC4/ 1 ml medium) (BD Biosciences) for one day.

value: WA09 Human Embryonic Stem Cell

value: wild-type


title: 2776-TL-0010

value: NIH 3T3


title: Wild-type1_1


title: Mutant1_3

value: a single-copy deletion of chr17p13.1


title: Wild-type1_2


title: 2776-TL-0007


title: 2776-TL-0008


title: Wild-type2_3


title: 2776-TL-0003


title: Mutant2_3


title: Mutant1_1


title: Mutant2_2


title: Mutant1_2


title: 2776-TL-0020


title: Wild-type2_2


title: 2818-CPP-0019 L635

city: Huntsville

first: Nripesh

last: Prasad

state: Alabama

address: 601 Genome way

institute: Hudson Alpha Institute for Biotechnology

description: intestinalized SPEM-associated macrophages

data_processing:
Post processing of the sequencing reads from RNA-seq experiments from each sample was performed as per our unique in-house pipeline. Briefly, quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were mapped to the reference mouse genome mm9 using TopHat v1.4 with two mismatches allowed and other default parameters. The alignment metrics of the mapped reads was estimated using SAMtools. Aligned reads were then imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were then grouped as treatment and control identifiers and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) as the normalization method. Differential expression of genes was calculated on the basis of fold change (using default cut-off ≥ ±2.0) observed between defined conditions, and the p-value of the differentially expressed gene list was estimated by z-score calculations with Benjamini Hochberg False discovery rate (FDR) correction of 0.05 (Supplemental Table 1).  Differentially expressed genes underwent gene ontology (GO) analysis and pathway analysis using DAVID and Ingenuity Pathway Analysis tool.
Genome_build: mm9
Supplementary_files_format_and_content: excel file contains normalized expressions for each sample

source_name: Corpus macrophage

extract_protocol:
Stomach corpus was isolated and diced into 1mm cubed pieces, ezymatically digested for 7 minutes in DMEM/Dispase.  Stomach then put over a 70micron filter and pushed through filter using rubber syringe.  Cells then spun down, washed, antibody labeled and FAC sorted.
RNA samples that had RNA integrity numbers (RIN) ≥7.0 were used. RNA was amplified using the NuGEN Technologies Ovation RNA-Seq System V2 kit (Part # 7102-08) using manufacturer's instructions.  Approximately, 2.5 µg amplified DNA from each sample was sheared on a Covaris S200 focused-ultrasonicator (Woburn, MA, USA) with a target yield of an average 200bp fragment size. The fragmented DNA was taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house genomics service lab (GSL) primers and amplified through 8 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa  Biosystems,  Inc.,  Woburn,  MA,  USA).  The quantity of the libraries were assessed by Qubit® 2.0 Fluorometer, and the quality of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA, USA). Each library was then diluted to a final concentration of 12.5nM and pooled equimolar prior to clustering. Single End (SE) sequencing was performed on an Illumina HiSeq2500 following the manufacturer's protocols.

value: macrophage

tag: passages

value: isolated from stomach corpus


title: 2818-CPP-0015 L635


title: 2818-CPP-0009 L635


title: 2818-CPP-0010 DMP

description: SPEM-associated macrophages


title: Total 0-180 MAF Slbp10/15 Drosophila embryo (replicate 2)

city: Montreal

first: Fabio

middle: Alexis

last: Lefebvre

address: 110 Ave des Pins

department: RNA biolog

institute: IRCM

description:
Slbp10_15_0_3h_2
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx

data_processing:
Read quality was assessed with FastQC v0.10.1.
No trimming was deemed necessary
Read alignment was performed with TopHat on dm3
Featurecount was used to extract read counts
The count files were used with DESeq for differential expression
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited files include normalized read counts for each sample

growth_protocol: Oregon R was used as wt. The grpfs1 stock was kindly provided by the Theurkauf lab, and the Slbp10, Slbp12 and Slbp15 stock were obtained from the Duronio lab. Embryos were collected and dechorionated as previously described. 90-180 minutes AEL samples were collected over 90 minutes and kept at 25 C for 90 additional minutes, while 0-45 minutes AEL embryos.

extract_protocol:
For DAPI staining, embryos were fixed with formaldehyde as previously described and imaged by epifluorescence on a Leica DM5500B microscope equipped with a QImaging ExiAqua camera (QImaging). Cytoplasmic and nuclear extracts were derived from 90-180 minutes AEF wt embryos as previously described.
RNA-seq libraries were prepared for deep-sequencing using standard Illumina sequencing protocol with ribosomal depletion

tag: strain background

value: Oregon R

tag: embryonic stage

tag: genotype/variation

value: from transheterozygous mothers bearing the Slbp10/15 mutation

tag: sample type

value: Total mutant embryo extract


title: Total 0-180 MAF Slbp10/15 Drosophila embryo (replicate 1)

description:
Slbp10_15_0_3h_1
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx


title: Wild-type1_3


title: Mutant2_1


title: 2818-CPP-0004 DMP

description: SPEM-associated macrophages


title: 2818-CPP-0006 DMP

description: SPEM-associated macrophages


title: Total 0-180 MAF Slbp10/12 Drosophila embryo (replicate 2)

description:
Slbp10_12_0_3h_2
processed data file: SLBP_Grp_mutants_normalized_counts.xlsx

value: from transheterozygous mothers bearing the Slbp10/12 mutation