title: 1.5 µM PF-067446846, 60 min, rep 5 -riboseq

data_processing:
library strategy: Ribo-seq
Adapter sequences (CTGTAGGCACCATCAAT) were trimmed and reads were filtered for minimum length using FASTX-clipper version 0.0.13
Ribosomal RNA sequences were computationally removed by aligning the reads to a set of human rRNA sequences with Bowtie version 1.1.2
Nonribosomal sequences from samples 24 and 26 were pooled were pseudoaligned to a reference consiting of all transcripts annotated as "Known" and "Protien coding" in the ENSEMBL GRCh38 annotation using Kallisto version 0.42.5 to determine the relative abundance of the transcript isoforms. This was done with python version 3.5.1 . Python code used is Additional_file_S2.py
A custom reference transcriptome consisting of the most abundant transcript isoform from each gene was generated using python version 3.5.1. Python code used is "Additional_file_S4.py" and "Additional_file_S5.py"
Nonribosomal sequences were aligned with the custom transcriptome using Bowtie version 1.1.2
Reads mapping to more then five locations in the custom transcriptome were filtered out using python version 2.6.6. Python code used is "Additional_file_S6.py"
Readmaps indicating the number of reads alining to each position of the custom transcriptome were genenerated using python 2.6.6. The python code used is "Additional_file_S7.py"
Metareadmaps" showing the average distribution of reads relative to the start and stop codons for all genes were generated using python version 2.6.6 These maps were used to determine the distance between the 5' end of read alingments and the ribosomal P-site. The python code used for this step is "Additional_file_S8.py
The readmaps were converted from nucleotide-based to codon-based using python 2.6.6. The python code used is "Additional_file_S9.py"
The readmaps were normalized from raw reads to reads per million using python 2.6.6. The python code used is "Additional_file_S10.py"
Cumulative fractional readplots, Dmax values and Dmax positions were calculated using python 2.6.6. The output of "Additional_file_S9.py" is used for this step. The python code for this step is "Additional_file_S11.py"
Dmax values were Z-score transformed as described in Andreev et al. (2015) Genome Biology 16:90 using python verson 2.6.6 The python code used for this step is "Additional_file_S17.py"
For genes with a Dmax Zscore > 2 reads mapping to the CDS 3' to the position of Dmax were extracted for DeSeq analysis. For Dmax Z-score ≤ 2, reads mapping 3' to codon 50 were extracted. In all cases, the 10 3'-most codons were omitted. The python code used for this step is "Additional_file_S12.py"
The extracted reads were used for differential expression analysis with DeSeq1. Changes in the number of reads extracted in the previous step were used as a basis for determining compound-induced changes in expression levels.

ADDITIONAL ANALYSIS:
For standard differential expression analysis, raw read counts were extracted from the output of "Additional_file_S7.py" python code "Additional_file_S13.py" for mRNA-seq datasets or "Additional_file_S14.py" for riboseq datasets. The output was used as input for DeSeq for standard differential expression analysis.
Z-score transformations analysis (Andreev et al. (2015) Genome Biology 16:90) was done on raw alignment counts and tranlational efficiency values using python version 2.6.6, "Additional_file_S15.py", "Additional_file_S16.py" and "Additional_file_S18.py"
Centers of density or the mean positions of reads along each CDS, changes in the centers of density and Z-score transformations of those changes were calculated using python version 2.6.6. The code is "Additional_file_S19.py"
Potential AUG-initiating uORFs were identified and the number of reads aligning to those uORFs were extracted using python version 2.6.6 The code is "Additional_file_S20.py" and "Additional_file_S21.py"
Genome_build: GRCh38

Supplementary_files_format_and_content:
*codonmap.txt files are plain text files with three columns, the first is the transcript accession number, the second is the codon, relative to start, the third is the number of reads that align to that position based on the infered location of the ribosome P-site.
Deseq_poststall_analysis.xlsx is an Excel spreadsheet with Differential expression analysis that uses the Dmax approach to predict potential stall sites and use only alignments mapping 3' to thos sites.
Deseq_basic_analysis.xlsx is an Excel spreadsheet with basic differential expression analyses done with DeSeq
Z-score_analyses.xlsx is an Excel spreadsheet with Z-score analyses of raw readcounts as described in Andreev et al. (2015) Genome Biology 16:90
Center_of_densities.xlsx is an Excel spreadsheet with Center of density analysis as described in Andreev et al. (2015) Genome Biology 16:90
Raw_read_counts.xlsx is an Excel speadsheet summarizing raw alignment counts.
Additional_files_S1-S21.txt is an Text file containing the custom python code used to process the data.
GRCh38_known_protein_coding_cDNAs.fa is the Multifasta file with reference transcriptome used for the initial Kallisto psudoaligments.
GRCh38_Huh7_most_abundant_isoforms.fa is the Multifasta file with reference transcriptome of only the most abundant splice isoform from each locus, used in the bowtie alignments.

value: ribo-seq


title: PF-06446846, 60 min, rep 4 -mRNA-seq

status: Public on Jun 05 2017

type: SRA

city: Berkeley

first: Jamie

last: Cate

state: CA

address: 748 Stanley Hall

country: USA

institute: University of California

library_source: transcriptomic

data_processing:
library strategy: Ribo-seq
Adapter sequences (CTGTAGGCACCATCAAT) were trimmed and reads were filtered for minimum length using FASTX-clipper version 0.0.13
Ribosomal RNA sequences were computationally removed by aligning the reads to a set of human rRNA sequences with Bowtie version 1.1.2
Nonribosomal sequences from samples 24 and 26 were pooled were pseudoaligned to a reference consiting of all transcripts annotated as "Known" and "Protien coding" in the ENSEMBL GRCh38 annotation using Kallisto version 0.42.5 to determine the relative abundance of the transcript isoforms. This was done with python version 3.5.1 . Python code used is Additional_file_S2.py
A custom reference transcriptome consisting of the most abundant transcript isoform from each gene was generated using python version 3.5.1. Python code used is "Additional_file_S4.py" and "Additional_file_S5.py"
Nonribosomal sequences were aligned with the custom transcriptome using Bowtie version 1.1.2
Reads mapping to more then five locations in the custom transcriptome were filtered out using python version 2.6.6. Python code used is "Additional_file_S6.py"
Readmaps indicating the number of reads alining to each position of the custom transcriptome were genenerated using python 2.6.6. The python code used is "Additional_file_S7.py"
Metareadmaps" showing the average distribution of reads relative to the start and stop codons for all genes were generated using python version 2.6.6 These maps were used to determine the distance between the 5' end of read alingments and the ribosomal P-site. The python code used for this step is "Additional_file_S8.py
The readmaps were converted from nucleotide-based to codon-based using python 2.6.6. The python code used is "Additional_file_S9.py"
The readmaps were normalized from raw reads to reads per million using python 2.6.6. The python code used is "Additional_file_S10.py"
Cumulative fractional readplots, Dmax values and Dmax positions were calculated using python 2.6.6. The output of "Additional_file_S9.py" is used for this step. The python code for this step is "Additional_file_S11.py"
Dmax values were Z-score transformed as described in Andreev et al. (2015) Genome Biology 16:90 using python verson 2.6.6 The python code used for this step is "Additional_file_S17.py"
For genes with a Dmax Zscore > 2 reads mapping to the CDS 3' to the position of Dmax were extracted for DeSeq analysis. For Dmax Z-score ≤ 2, reads mapping 3' to codon 50 were extracted. In all cases, the 10 3'-most codons were omitted. The python code used for this step is "Additional_file_S12.py"
The extracted reads were used for differential expression analysis with DeSeq1. Changes in the number of reads extracted in the previous step were used as a basis for determining compound-induced changes in expression levels.
ADDITIONAL ANALYSIS:
For standard differential expression analysis, raw read counts were extracted from the output of "Additional_file_S7.py" python code "Additional_file_S13.py" for mRNA-seq datasets or "Additional_file_S14.py" for riboseq datasets. The output was used as input for DeSeq for standard differential expression analysis.
Z-score transformations analysis (Andreev et al. (2015) Genome Biology 16:90) was done on raw alignment counts and tranlational efficiency values using python version 2.6.6, "Additional_file_S15.py", "Additional_file_S16.py" and "Additional_file_S18.py"
Centers of density or the mean positions of reads along each CDS, changes in the centers of density and Z-score transformations of those changes were calculated using python version 2.6.6. The code is "Additional_file_S19.py"
Potential AUG-initiating uORFs were identified and the number of reads aligning to those uORFs were extracted using python version 2.6.6 The code is "Additional_file_S20.py" and "Additional_file_S21.py"
Genome_build: GRCh38
Supplementary_files_format_and_content:
*codonmap.txt files are plain text files with three columns, the first is the transcript accession number, the second is the codon, relative to start, the third is the number of reads that align to that position based on the infered location of the ribosome P-site.
Deseq_poststall_analysis.xlsx is an Excel spreadsheet with Differential expression analysis that uses the Dmax approach to predict potential stall sites and use only alignments mapping 3' to thos sites.
Deseq_basic_analysis.xlsx is an Excel spreadsheet with basic differential expression analyses done with DeSeq
Z-score_analyses.xlsx is an Excel spreadsheet with Z-score analyses of raw readcounts as described in Andreev et al. (2015) Genome Biology 16:90
Center_of_densities.xlsx is an Excel spreadsheet with Center of density analysis as described in Andreev et al. (2015) Genome Biology 16:90
Raw_read_counts.xlsx is an Excel speadsheet summarizing raw alignment counts.
Additional_files_S1-S21.txt is an Text file containing the custom python code used to process the data.
GRCh38_known_protein_coding_cDNAs.fa is the Multifasta file with reference transcriptome used for the initial Kallisto psudoaligments.
GRCh38_Huh7_most_abundant_isoforms.fa is the Multifasta file with reference transcriptome of only the most abundant splice isoform from each locus, used in the bowtie alignments.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Huh7 cells were maintained in RPMI ((Life Technologies 11875-093) supplemented with 10% FBS (Sigma F4135) 1% Penicillin/Streptomycin (Life Technologies 15410-112) and 4 mM Glutamax (Life Technologies 35050-061) at 37 ˚C under a 5% CO2 atmosphere.   The cells were tested for mycoplasma and using the Gen-Probe Mycoplasma Tissue Culture NI (MTC-IN) Rapid Detection method.

extract_protocol:
The cells were harvested by aspiration of media and immediate addition of ice-cold PBS containing 100 µg/mL cycloheximide.  The PBS plus cycloheximide was aspirated with a vacuum aspirator and 400 µL lysis buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 µg/mL cycloheximide, 1% Triton X-100 and 25 U/mL DNase I (Promega)) was added.
Cells were lysed and ribosome footprint or fragmented RNA libraries were generated as described in Ingolia et al. Curr Protoc Mol Biol Chapter 4, Unit 4 18 (2013).

treatment_protocol: Huh7 cells were grown in 10 cm plates to a confluence of 50-80%.  The cells were always passaged into fresh media within 24 hours of the experiment. The media was replaced with fresh prewarmed media containing 1.5 µM or 0.3 µM PF-06446846 or vehicle (0.5% DMSO) and the plates were immediately returned to the incubator for 10 or 60 minutes as indicated.

tag: cell line

tag: treatment time

value: 60 min

tag: library type

value: mRNA-seq


title: vehicle, 60 min, rep 5-Ribo-seq

data_processing:
Adapter sequences (CTGTAGGCACCATCAAT) were trimmed and reads were filtered for minimum length using FASTX-clipper version 0.0.13
Ribosomal RNA sequences were computationally removed by aligning the reads to a set of human rRNA sequences with Bowtie version 1.1.2
Nonribosomal sequences from samples 24 and 26 were pooled were pseudoaligned to a reference consiting of all transcripts annotated as "Known" and "Protien coding" in the ENSEMBL GRCh38 annotation using Kallisto version 0.42.5 to determine the relative abundance of the transcript isoforms. This was done with python version 3.5.1 . Python code used is Additional_file_S2.py
A custom reference transcriptome consisting of the most abundant transcript isoform from each gene was generated using python version 3.5.1. Python code used is "Additional_file_S4.py" and "Additional_file_S5.py"
Nonribosomal sequences were aligned with the custom transcriptome using Bowtie version 1.1.2
Reads mapping to more then five locations in the custom transcriptome were filtered out using python version 2.6.6. Python code used is "Additional_file_S6.py"
Readmaps indicating the number of reads alining to each position of the custom transcriptome were genenerated using python 2.6.6. The python code used is "Additional_file_S7.py"
Metareadmaps" showing the average distribution of reads relative to the start and stop codons for all genes were generated using python version 2.6.6 These maps were used to determine the distance between the 5' end of read alingments and the ribosomal P-site. The python code used for this step is "Additional_file_S8.py
The readmaps were converted from nucleotide-based to codon-based using python 2.6.6. The python code used is "Additional_file_S9.py"
The readmaps were normalized from raw reads to reads per million using python 2.6.6. The python code used is "Additional_file_S10.py"
Cumulative fractional readplots, Dmax values and Dmax positions were calculated using python 2.6.6. The output of "Additional_file_S9.py" is used for this step. The python code for this step is "Additional_file_S11.py"
Dmax values were Z-score transformed as described in Andreev et al. (2015) Genome Biology 16:90 using python verson 2.6.6 The python code used for this step is "Additional_file_S17.py"
For genes with a Dmax Zscore > 2 reads mapping to the CDS 3' to the position of Dmax were extracted for DeSeq analysis. For Dmax Z-score ≤ 2, reads mapping 3' to codon 50 were extracted. In all cases, the 10 3'-most codons were omitted. The python code used for this step is "Additional_file_S12.py"
The extracted reads were used for differential expression analysis with DeSeq1. Changes in the number of reads extracted in the previous step were used as a basis for determining compound-induced changes in expression levels.
ADDITIONAL ANALYSIS:
For standard differential expression analysis, raw read counts were extracted from the output of "Additional_file_S7.py" python code "Additional_file_S13.py" for mRNA-seq datasets or "Additional_file_S14.py" for riboseq datasets. The output was used as input for DeSeq for standard differential expression analysis.
Z-score transformations analysis (Andreev et al. (2015) Genome Biology 16:90) was done on raw alignment counts and tranlational efficiency values using python version 2.6.6, "Additional_file_S15.py", "Additional_file_S16.py" and "Additional_file_S18.py"
Centers of density or the mean positions of reads along each CDS, changes in the centers of density and Z-score transformations of those changes were calculated using python version 2.6.6. The code is "Additional_file_S19.py"
Potential AUG-initiating uORFs were identified and the number of reads aligning to those uORFs were extracted using python version 2.6.6 The code is "Additional_file_S20.py" and "Additional_file_S21.py"
Genome_build: GRCh38
Supplementary_files_format_and_content:
*codonmap.txt files are plain text files with three columns, the first is the transcript accession number, the second is the codon, relative to start, the third is the number of reads that align to that position based on the infered location of the ribosome P-site.
Deseq_poststall_analysis.xlsx is an Excel spreadsheet with Differential expression analysis that uses the Dmax approach to predict potential stall sites and use only alignments mapping 3' to thos sites.
Deseq_basic_analysis.xlsx is an Excel spreadsheet with basic differential expression analyses done with DeSeq
Z-score_analyses.xlsx is an Excel spreadsheet with Z-score analyses of raw readcounts as described in Andreev et al. (2015) Genome Biology 16:90
Center_of_densities.xlsx is an Excel spreadsheet with Center of density analysis as described in Andreev et al. (2015) Genome Biology 16:90
Raw_read_counts.xlsx is an Excel speadsheet summarizing raw alignment counts.
Additional_files_S1-S21.txt is an Text file containing the custom python code used to process the data.
GRCh38_known_protein_coding_cDNAs.fa is the Multifasta file with reference transcriptome used for the initial Kallisto psudoaligments.
GRCh38_Huh7_most_abundant_isoforms.fa is the Multifasta file with reference transcriptome of only the most abundant splice isoform from each locus, used in the bowtie alignments.

molecule: total RNA

source_name: Huh7_vehcile_60 min_Ribo-seq

value: 0 µM

value: Ribo-seq


title: Vehicle, 60 min, rep 4-ribo-seq

source_name: Huh7_Veh_60 min_Ribo-seq


title: MPP_ATAC-seq_rep2

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

country: China

institute: Shanghai Jiao Tong University

description:
Illumina Hi-Seq2000 50 nt strand-specific
MPP_ATAC-seq_peaks.bed

library_source: genomic

data_processing:
Library strategy: ATAC-seq
The pairedend reads were aligned to the mouse genome version mm10 using bowtie2 with default parameter.
Peak calling were performed using findPeaks script in HOMER software  with dnase style (Heinz et al., 2010).
The DNA sequence motif enrichment in promoter regions and enhancers were detected by Homer script findMotifsGenome with length 6 nt, 8 nt and 10 nt.
Genome_build: mm10
Supplementary_files_format_and_content: bed files, peaks

molecule: genomic DNA

organism: Mus musculus

source_name: hematopoietic stem cells

extract_protocol:
Bone marrow cells were flushed from the long bones (tibias and femurs) of mice with phosphate buffered solution (PBS) without calcium or magnesium. For detection of LSK cells, whole bone marrow cells were incubated with PE anti-mouse Lineage Cocktail antibody,  FITC-conjugated antibody to Sca1 (Ly6A/E; D7) and allophycocyanin (APC)-conjugated antibody to c-Kit (ACK2). CD150 and CD48 were measured with the following antibodies: phycoerythrin (PE)-Cy7 conjugated antibody to CD48 (HM48-1), BV421-conjugated antibody to CD150 (TC15-12F12.2), All antibodies were purchased from Biolegend except for antibodies to Sca1 and c-Kit, which were purchased from eBioscience. Antibodies to lineage, Sca1, c-Kit, CD150, CD48 were diluted 1:100. Nonviable cells were excluded using the viability dye 7-AAD (50 ug ml−1). Cells were sorted with a FACSAria (Becton Dickinson) automated cell sorter.
ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688

tag: strain

tag: chromatin state

value: multipotent progenitor

tag: genotype

value: wild-type

tag: replicate


title: LT-HSC_ATAC-seq_rep2

description:
Illumina Hi-Seq2000 50 nt strand-specific
LT-HSC_ATAC-seq_peaks.bed

value: long term


title: LT-HSC_ATAC-seq_rep1


title: ST-HSC_ATAC-seq_rep2

description:
Illumina Hi-Seq2000 50 nt strand-specific
ST-HSC_ATAC-seq_peaks.bed

value: short term


title: MPP_ATAC-seq_rep1


title: ST-HSC_ATAC-seq_rep1


title: 1.5 µM PF-067446846, 60 min, rep 4 -riboseq


title: WT1

city: New York

first: Hyung Don

last: Ryoo

state: NY

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

description: Barcode: CGATGT

data_processing:
Alignment against dm6 using Tophat/2.1.1
Gene counting against dm6 reference gtf using HTSeq-count 0.6.1
Normalization of raw counts using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: Normalized_counts.csv

organism: Drosophila melanogaster

source_name: WT, Whole Larvae (2nd instar stage)

extract_protocol:
Qiagen RNA prepkit - RNEASY
RNASeq libraries were prepared using the Illumina TruSeq Stranded Total RNA library prep, with Ribozero Gold

tag: genotype/variation

value: WT

tag: developmental stage

value: 2nd instar stage

tag: tissue

value: Whole Larvae


title: RNAseq_WT_rep1

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

data_processing:
residual adapter trimming was performed with Trimmomatic-0.32(usadellab.org)
Trimmed reads were aligned to the mm10 genome with Tophat (v.2.0.11)
Differential gene expression was determined by Cuffdiff (v.2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output gene_exp.diff; tab delimited file with fpkm, log2 fold change and p/q-value

source_name: B220+CD43+ B cells

extract_protocol:
total RNA was isolated by Trizol extraction
libraries were constructed from polyA-enriched RNA using the Illumina TrueSeq RNA library preparation kit.

treatment_protocol: B220+CD43+ B cell populations were sorted from mouse bone marrow

value: bone marrow

tag: cell type

value: B220+CD43+ B cells

value: wildtype


title: RNAseq_Hdac3KO_rep2

value: HDAC3 KO


title: vehicle, 60 min rep 3

source_name: Huh7_vehicle_60 min_ribo-seq


title: WT2

description: Barcode: TGACCA


title: RNAseq_Hdac3KO_rep1


title: Mutant1

description: Barcode: CAGATC

source_name: Mutant, Whole Larvae (2nd instar stage)

value: XBP1 Mutant


title: vehicle, 60 min rep 1

value: ribo-seq


title: RNAseq_WT_rep2


title: Mutant2

description: Barcode: CCGTCC


title: set2d_120min_Rep3

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Ribo-depleted/Stranded

data_processing:
Reads were first filtered for any adapter sequences using TagDust (v1.12) and an FDR of 0.001. For samples that had over 50 basepair reads, TagDust was used to trim 3' basepairs so all the reads were 50 bp
Bowtie (v1.1.2) was used to align reads to the sacCer3 genome. Alignment options included: -m 1, --seed=123.456, --nomaqround, and --best.
Alignments were filtered for properly mapped reads using samtools (v1.3.1).
Reads came off the sequencer with strand information reversed, and were corrected using the bedtools suite (v2.25.0).
To correct any PCR amplification artifacts, two identical reads were permitted per specific strand and alignment location, with all others being filtered.
Single base pair wiggle files were generated using the bedtools suite (v2.25.0).
Differentially expressed genes were identified using DESeq2 (v1.6.3) with default parameters. Genes with a p-value < 0.05, a minimum of log2(Fold Change) > 1 as identified by DESeq2, and an average RPKM > 1 across all replicates with a time point were considered differentially expressed.
Genome_build: sacCer3
Wig files are fixed step, with a step size of 1, wiggles containing the normalized read depth/signal at each base pair in the genome. The wigs contain either sense or antisense signal only, where sense or antisense is defined by annotated ORFs in sacCer3.

organism: Saccharomyces cerevisiae

source_name: Log Phase Yeast Cultures

growth_protocol: Yeast cells were grown in YPD overnight to saturation. New YPD cultures were then innoculated to a final concentration of 2*10^6 cells and grown until the cultures reached a concentration of 1*10^7 cells.

extract_protocol:
RNA was extracted using acid phenol, DNase treated, and cleaned up on Qiagen RNeasy columns.
Libraries were constructed using Illumina's TruSeq Stranded Total RNA Sample Preparation Kit with the yeast specific Ribo-Zero kit.

treatment_protocol: Cultures were collected and pelleted.  Pellets were washed twice with ddH20 followed by resuspension in SD media and incubated at 30C.  At 0, 30, 60, and120 minutes after the media shift, 1*10^8 cells were isolated, pelleted, and snap frozen for processing.

value: SET2 deletion


title: vehicle, 60 min rep 2

value: 60 min


title: set2d_120min_Rep2

description: Ribo-depleted/Stranded


title: set2d_120min_Rep1

description: Ribo-depleted/Stranded


title: 0.3 µM PF-067446846, 60 min, rep 3


title: set2d_60min_Rep3

description: Ribo-depleted/Stranded


title: 0.3 µM PF-067446846, 60 min, rep 2


title: 0.3 µM PF-067446846, 60 min, rep 1


title: set2d_60min_Rep1

description: Ribo-depleted/Stranded


title: set2d_60min_Rep2

description: Ribo-depleted/Stranded


title: set2d_30min_Rep2

description: Ribo-depleted/Stranded


title: 1.5 µM PF-067446846, 60 min, rep 3


title: ATACseq_Hdac3KO_rep2

data_processing:
adapter trimmed reads were aligned to the mm10 + dm3 genome using   Bowtie2 v2.2.4(bowtie2 -p 8 -X 2000 -q --no-mixed --no-discordant).
Drosophila and mitochondrial reads were removed using samtools
ATAC peaks were shifted using in house perl script
peaks were called using Macs2 (v. 2.0.10) (-q 0.001, --nomodel, --extsize 140)
differential peak quantification was determined by DiffBind (v 1.10.2) (final normalization using DiffBind w/EdgeR rather than S2 spikein)
Genome_build: mm10 + dm3
Supplementary_files_format_and_content: peak files (.txt) contain called peaks for each sample, MB1_ATAC_DiffBind_out.txt reports significantly changed peaks between wild-type and knockout samples

organism:
Drosophila melanogaster
Mus musculus

extract_protocol:
purification of transposase-treated DNA by Zymo Research DNA clean and concentrator
Tn5-mediated fragmentation and adapter insertion


title: set2d_0min_Rep2

description: Ribo-depleted/Stranded


title: 1.5 µM PF-067446846, 60 min, rep 2


title: set2d_0min_Rep1

description: Ribo-depleted/Stranded


title: set2d_30min_Rep3

description: Ribo-depleted/Stranded


title: 1.5 µM PF-067446846, 60 min, rep 1


title: WF-rep1

status: Public on Jun 06 2017

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: inducible wild type

data_processing:
Sequenced reads were mapped using rnaSTAR to the mouse reference genome
Differentially expressed genes were identified using cufflinks with default parameters
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited cufflinks transcript abundance files including FPKM values for each sample

source_name: WF

growth_protocol: Mouse hepatocytes were obtained by liver perfusion in Hank's Balanced Salt Solution followed by collagenase

extract_protocol:
Total RNA was isolated from hepatocytes using miRNease mini kit (Qiagen)
RNAseq libraries were constructed using illumina Stranded total RNA library kit

value: RNASEH1 WT

value: liver

value: hepatocyte


title: WT_120min_Rep3

description: Ribo-depleted/Stranded

value: wild type


title: ATACseq_WT_rep2


title: vehicle, 10 min rep 3

source_name: Huh7_vehicle_10 min_ribo-seq

value: 10 min


title: WT_120min_Rep2

description: Ribo-depleted/Stranded


title: WT_120min_Rep1

description: Ribo-depleted/Stranded


title: ATACseq_WT_rep1


title: ATACseq_Hdac3KO_rep1


title: Hibernating rep6

city: Guangzhou

first: Yizhao

last: Luan

state: Guangdong

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

description: Hibernating rep6

data_processing:
bcl2fastq was used for base calling.
All the reads were trimmed to be 50nt of length. Trimmed reads were aligned to Ictidomys tridecemlineatus genome reference (Ensembl spetri2)  with Tophat v2.0.11. The parameter options applied in alignment were -r 200, -g 20, -p 8, --no-coverage-search, --library-type fr-firststrand and -G corresponding GTF file.
Rsubread was used for gene feature count
Genome_build: spetri2
Supplementary_files_format_and_content: tab-delimited text files include raw count values of genes for each Sample

organism: Ictidomys tridecemlineatus

source_name: Retina

extract_protocol:
Retinas of active and hibernating ground squirrels were collected in July and August, and January and February, respectively. Total RNAs were extracted by TRIzol (Thermo Fisher Scientific)
the TruSeq stranded total RNA sample preparation kit (Illumina) were used for RNA-seq

value: retina

tag: condition

value: hibernation in winter


title: vehicle, 10 min rep 2


title: Awake rep4

description: Awake rep4

value: awake in summer


title: WT_60min_Rep3

description: Ribo-depleted/Stranded


title: vehicle, 10 min rep 1


title: 0.3 µM PF-067446846, 10 min, rep 3


title: WT_60min_Rep2

description: Ribo-depleted/Stranded


title: WT_60min_Rep1

description: Ribo-depleted/Stranded


title: 0.3 µM PF-067446846, 10 min, rep 2


title: Awake rep3

description: Awake rep3


title: 0.3 µM PF-067446846, 10 min, rep 1


title: 1.5 µM PF-067446846, 10 min, rep 3


title: set2d_30min_Rep1

description: Ribo-depleted/Stranded


title: WT_30min_Rep3

description: Ribo-depleted/Stranded


title: Awake rep1

description: Awake rep1


title: WT_30min_Rep2

description: Ribo-depleted/Stranded


title: 1.5 µM PF-067446846, 10 min, rep 2


title: Hibernating rep5

description: Hibernating rep5


title: WT_30min_Rep1

description: Ribo-depleted/Stranded


title: 1.5 µM PF-067446846, 10 min, rep 1


title: Hibernating rep4

description: Hibernating rep4


title: WT_0min_Rep4

description: Ribo-depleted/Stranded


title: Hibernating rep3

description: Hibernating rep3


title: WT_0min_Rep3

description: Ribo-depleted/Stranded


title: Hibernating rep2

description: Hibernating rep2


title: Hibernating rep1

description: Hibernating rep1


title: WT_0min_Rep1

description: Ribo-depleted/Stranded


title: WT_0min_Rep2

description: Ribo-depleted/Stranded


title: DGB129 Resting

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
Paired end RNA-seq reads in fastq format were aligned to the hg19 genome assembly using STAR aligner [Dobin et al. 2013] version 2.3.
Gene annotations were derived from GENCODE version 19.
Counts of reads mapping over gene features were obtained using the featureCounts method of the R/bioconductor subread packages [Liao et al. 2014] version 1.5.0-p1.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing counts of reads over Gencode version 19 gene features

source_name: MR1T cells

growth_protocol: T cell clones were generated from healthy donor PBMC as previously reported in De Libero et al., J. Exp. Med., 1989 Jul 1;170(1):303-8; PMID: 2501447.

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kits according to manufacturer's protocol. RNA quality was assessed using the Agilent Bioanalyzer (exhibited RIN ≥6.9).
cDNA libraries were prepared using 200ng total RNA and a 2µl volume of a 1:500 dilution of ERCC RNA Spike in Controls (Ambion). Samples were subjected to cDNA library synthesis using the TruSeq Stranded mRNA Library Preparation Kit according to manufacturer's protocol with minor modifications; 13 PCR cycles used, and 2 additional rounds of incubation with Agencourt Ampure XP SPRI beads (Beckman Courter) to remove double-stranded cDNA >600bp in size. The length distribution of the cDNA libraries was monitored using DNA 1,000 kits with the Agilent Bioanalyzer. The samples were then subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000.

treatment_protocol: T cell clones were stimulated with A375-MR1 cells (A375 melanoma cells transfected with the MR1 gene) for 20 hrs.  The CD3+ CD137+ cells were sorted, counted and immediately frozen.

tag: clone id

value: T cell clone from healthy donor PBMC

tag: stimulated with

tag: sorting


title: T1E_tol2

status: Public on Jun 04 2017

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to KT2440 or DOT-T1E whole genomes using Rockhopper
Expressions were calculated using Rockhopper
The wig file was obtained using Rockhopper software and contains the position of the differential expressed genes in all the conditions tested.
Genome_build: DOT-T1E (GCA_000281215.1); KT2440 (GCF_000007565.1)
Supplementary_files_format_and_content:.txt files include expression values (normalized abundance measurements) for each Sample

organism: Pseudomonas putida DOT-T1E

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sensitivity

value: Toluene-tolerant

tag: treatment

value: toluene vapor phase


title: T1E_gluc2

value: glucose


title: T1E_tol1


title: Awake rep2

description: Awake rep2


title: T1E_gluc1


title: T1E_shock1

value: toluene shock


title: DGB70 Activated

value: A375-MR1 cells for 20 hrs (T cells:APC ::2:1)


title: KT2440_shock2

organism: Pseudomonas putida KT2440

value: Toluene-sensitive


title: Williams_mock 3

city: West Lafayette

first: Meixia

last: Zhao

state: IN

address: 915 W State Steet

department: Agronomy

institute: Purdue University

data_processing:
base-calling
Sequenced reads were trimmed for adaptor sequences, and masked for low-quality and < 101 bp sequences, then mapped to Glycine max reference genome (v2.0) using Tophat 2.1.0, with the parameters -r 0 -g 1 -i 30 -I 100000 -p 8 --read-mismatches 2.
The raw count of each gene was calculated by HTSeq (http://www-huber.embl.de/users/anders/HTSeq) with the “intersection_nonempty” mode, and preceded to edgeR package (Robinson et al. 2009) in the R-Bioconductor tools.
Fragments per kilobase of exon per million fragments mapped (FPKM)  were caculated using cuffdiff function in cufflinks.
Genome_build: Gmax_275_v2.0.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene of each sample

organism: Glycine max

source_name: Soybean hypocotyl

growth_protocol: greenhouse

extract_protocol:
Qiagen RNeasy Plant Mini Kit, Cat. No. 74904
RNA libraries were prepared for sequencing using TrueSeq RNA Sample Preparation Kit, Cat. No. FC-122-1002 with standard Illumina protocols

treatment_protocol: Standard hypototyl inoculation

value: stem

tag: infection

value: mock-inoculated


title: Williams_Inoc 3

value: P. sojae inoculated


title: dwetA_RNA-seq-2

city: Madison

first: Ming-Yueh

last: Wu

state: WI

address: 1550 Linden Dr

department: Bacteriology

institute: University of Wisconsin-Madison

data_processing:
Reads were mapped to the A. flavus genome using Tophat version 2.1.1 with the default parameters except for --max-intron-length 4000
The number of reads that mapped to each gene were counted with HTSeq-count version 0.6.1p1 with the parameters -f bam -r pos -s no -i Note
Differential gene expression analysis was carried out with version 1.14.1 of DeSeq2 using the DESeqDataSetFromHTSeqCount function and an adjusted p-value cutoff of 0.05
After carrying out multiple quality control analyses, sample dwetA_1 was excluded from further study
Genome_build: GCF_000006275.2_JCVI-afl1-v2.0_genomic
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each gene in each sample

organism: Aspergillus flavus

growth_protocol: The fungal strains were grown on minimal medium with appropriate supplements and incubated at 30C for 2 days.The conidia were collected in ddH2O from the entire colony.

extract_protocol:
Total RNA was isolated by adding silica/zirconium beads (Biospec, Bartlesville, OK) and Trizol (Invitriogen, San Diego) and homogenizing in a Mini Bead Beater (Biospec), and then subsequently following manufacturere's instructions (Invitrogen)
Strand-specific library was prepared from total RNA using Illumina TruSeq Strand specific RNA sample preparation system.

value: {delta}wetA::AfupyrG+; pyrG-

value: conidia


title: dwetA_RNA-seq-3


title: KT2440_tol2


title: dwetA_RNA-seq-1


title: WT_RNA-seq-3

value: WT


title: WT_RNA-seq-2


title: KT2440_gluc2


title: KT2440_tol1


title: DGB129 Activated


title: T1E_shock2


title: DGB70 Resting


title: BT549_si7_rep3

status: Public on Jun 03 2017

city: shenzhen

first: Xiaolong

last: Tang

address: 3688 Nanhai Ave, Nanshan District

institute: shenzhen university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.77 whole genome using FANSe 2 with parameters -L55 -E4 -I0 -S10 -M0 -U0 -B1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: text files include RPKM values for each Sample

growth_protocol: BT549 cells were cultured in RPMI-1640 (Gibco®) with 10% FBS.

extract_protocol:
Total RNA extracts are first treated with DNase I to degrade DNA contamination. Next, by using the oligo (dT) magnetic beads the mRNA is enriched . Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. The first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with AMPure XP beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BT549 cells were transfected with control siRNAs or SIRT7-targeted siRNAs by using Lipofectamine®3000 (Thermo).

tag: cell line

value: breast cancer cells

tag: transfected with

value: SIRT7-targeted siRNAs


title: BT549_si7_rep1


title: BT549_si7_rep2


title: BT549_scramble_rep3

value: control siRNAs


title: BT549_scramble_rep1


title: HFL1-PBPA-Day5_3

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: RNA-seq

data_processing:
RNA-seq reads were trimmed for poly-A tails using fqtrim with minimum poly-A/T run of 10
The trimmed reads were mapped to the human reference genome (hg38) using STAR_2.4.0j with default parameters
Genes were quantified to iGenomes NCBI (GRCh38) annotations (BestRefSeq), using featureCounts from the Subread package
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts for each of the NCBI genes in each sample are listed the tab-delimited matrix file hg38.mRNA.NCBI.fCounts.primary.tab.txt

growth_protocol: HFL1 (ATCC-CCL-153) cells were obtained from the American Type Culture Collection (ATCC), and expanded in standard fibroblast medium. All the fibroblasts used in this study were expanded at 37 °C in 5% CO2 in fibroblast medium. The cells were then dissociated with 0.05% trypsin, spun, and frozen in 50/50 DMEM/FBS with 10% DMSO (Sigma).

extract_protocol:
miRNeasy mini kit (Qiagen) + DNase treatment
KAPA Stranded RNA-Seq Kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina HiSeq2000 for a single read 50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

treatment_protocol: DNA plasmids expressing mouse open reading frames (ORFs) for Ascl1, Brn2 or Myt1L or a combination of Ascl1 and Brn2 with or without short hairpin RNA (shRNA) targeting REST or miRNA loops for miR-9/9* and miR-124 in a third-generation lentiviral vector containing a non-regulated ubiquitous phosphoglycerate kinase (PGK) promoter were generated (Fig. 1a, 3b, 5a). All the constructs have been verified by sequencing. Lentiviral vectors were produced as previously described 30 and titrated by quantitative PCR (qPCR) analysis 31. Unless otherwise stated, transduction was performed at a multiplicity of infection (MOI) of 10 for separate vectors and MOI 20 for the single vector (all viruses used in this study tittered between 3 x108 and 6 x109). For direct neural reprogramming, fibroblasts were plated at a density of 27 800 cells per cm2 in 24-well plates (Nunc) coated with 0.1% gelatin (Sigma). Three days after viral transduction, fibroblast medium was replaced by neural differentiation medium (NDiff227; Takara-Clontech) supplemented with growth factors at the following concentrations: 2 µM LM-22A4 (R&D Systems), 2 ng/mL GDNF (R&D Systems), 10 ng/µL NT3 (R&D Systems) and 0.5 mM db-cAMP (Sigma) and the small molecules CHIR99021 (2 µM, Axon), SB-431542 (10 µM, R&D Systems), noggin (100.5 µg/ml, R&D Systems), LDN-193189 (0.5 µM, Axon), as well as valproic acid sodium salt (VPA; 1mM, Merck Millipore). Half of the neuronal conversion medium was replaced every 2-3 days. Cells were replated onto a combination of polyornithine (15 µg/mL), fibronectin (0.5 ng/µL) and laminin (5 µg/mL) coated 24-well plates at day 12 post-transduction. 18 days post-transduction, the small molecules were stopped and the neuronal medium was supplemented with only the growth factors (LM-22A4, GDNF, NT3 and db-cAMP) until the end of the experiment.

tag: vector

tag: starting cell

value: Fetal fibroblast

tag: cell source

value: HFL1 (ATCC-CCL-153), obtained from the American Type Culture Collection (ATCC)


title: HFL1-PBPA-Day5_1

description: RNA-seq


title: HFL1-PBPA-Day5_2

description: RNA-seq


title: HFL1-NEG-CTL-Day5_2

description: RNA-seq


title: KT2440_shock1

tag: strain


title: C2-REST_sh-PBPA-Day5_2

description: RNA-seq

value: Adult fibroblast

value: Adult dermal fibroblasts, obtained from the Parkinson’s Disease Research and Huntington’s disease clinics at the John van Geest Centre for Brain Repair (Cambridge, UK)


title: HFL1-NEG-CTL-Day5_1

description: RNA-seq


title: C2-REST_sh-PBmPA-Day5_3

description: RNA-seq


title: C2-REST_sh-PBPA-Day5_1

description: RNA-seq


title: C2-REST_sh-PBPA-Day5_3

description: RNA-seq


title: HFL1-NEG-CTL-Day5_3

description: RNA-seq


title: C2-REST_sh-PBmPA-Day5_1

description: RNA-seq


title: C2-REST_sh-NEG-CTL-Day5_2

description: RNA-seq


title: C2-REST_sh-NEG-CTL-Day5_3

description: RNA-seq


title: WT_RNA-seq-1

tag: genotype/variation


title: C2-PBPA-Day5_3

description: RNA-seq


title: C2-PBPA-Day5_1

description: RNA-seq


title: C2-PBPA-Day5_2

description: RNA-seq


title: C2-REST_sh-PBmPA-Day5_2

description: RNA-seq


title: C2-PBmPA-Day5_1

description: RNA-seq


title: C2-PBmPA-Day5_2

description: RNA-seq


title: C2-PBmPA-Day5_3

description: RNA-seq


title: C2-NEG-CTL-Day5_2

description: RNA-seq


title: MCF7-E2-D538G-rep4

city: Pittsburgh

first: Amir

last: Bahreini

state: PA

address: 204 Craft Ave A430

department: Human Genetics

institute: University of Pittsburgh

data_processing:
Salmon was used for quantification of the transcripts using default options and hg38 genome build as the reference
The differentially expressed (DE) genes between WT and mutants were identified by DEseq2 package using the contrast option to compare mutants vs WT and calculate adjusted p-value and fold change (FC)
Genes with a maximum transcripts per million (TPM) <1 across all samples were excluded from further analysis due to low gene expression

source_name: MCF7 cell line

growth_protocol: T47D and MCF7 cells were maintained in RPMI 1640+10% FBS and DMEM+5% FBS, respectively

extract_protocol:
RNA was isolated via Qiagen RNeasy kit
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation according to Illumina standar protocols

treatment_protocol: Individual ESR1 WT and mutant T47D and MCF7 clones were hormone deprived in CSS for three days, pooled, and plated in quadruplicates in 6-well plates. The cells were treated with veh or 1nM E2 for 24 hrs, RNA was isolated via Qiagen RNeasy kit, and RNA seq was performed obtaining >15M reads per sample

value: Estrogen

tag: genotype


title: C2-NEG-CTL-Day5_1

description: RNA-seq


title: MCF7-E2-D538G-rep3


title: BT549_scramble_rep2


title: MCF7-E2-D538G-rep1


title: MCF7-E2-Y537S-rep4


title: MCF7-E2-Y537S-rep3


title: C2-REST_sh-NEG-CTL-Day5_1

description: RNA-seq


title: MCF7-E2-Y537S-rep2


title: MCF7-E2-Y537S-rep1


title: MCF7-E2-WT-rep3

value: Wild type


title: MCF7-E2-D538G-rep2


title: MCF7-E2-WT-rep4


title: MCF7-veh-D538G-rep3

value: Vehicle


title: MCF7-veh-D538G-rep1


title: MCF7-veh-D538G-rep2


title: MCF7-E2-WT-rep2


title: MCF7-E2-WT-rep1


title: MCF7-veh-D538G-rep4


title: KT2440_gluc1

value: Toluene-sensitive

value: glucose


title: C2-NEG-CTL-Day5_3

description: RNA-seq


title: MCF7-veh-WT-rep4


title: MCF7-veh-Y537S-rep3


title: MCF7-veh-Y537S-rep4


title: MCF7-veh-Y537S-rep2


title: MCF7-veh-Y537S-rep1


title: MCF7-veh-WT-rep3


title: MCF7-veh-WT-rep1


title: T47D-E2-Y537S-rep4

source_name: T47D cell line


title: MCF7-veh-WT-rep2


title: T47D-E2-D538G-rep2


title: T47D-E2-D538G-rep4


title: T47D-E2-Y537S-rep1


title: T47D-E2-WT-rep3


title: T47D-E2-D538G-rep1


title: T47D-E2-WT-rep4


title: T47D-veh-D538G-rep3


title: T47D-veh-D538G-rep2


title: T47D-E2-WT-rep1


title: T47D-veh-D538G-rep1


title: T47D-veh-D538G-rep4


title: T47D-veh-Y537S-rep3


title: T47D-veh-Y537S-rep1


title: T47D-veh-WT-rep3


title: T47D-E2-WT-rep2


title: T47D-veh-WT-rep2


title: T47D-veh-WT-rep4


title: T47D-E2-D538G-rep3


title: T47D-E2-Y537S-rep3


title: C11_151020_run0437_female_LPS_3

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Basecalling was performed using CASAVA v1.8.2 (Illumina, San Diego, CA). BCL files were converted to FASTQ and demultiplexed using bcl2fastq v1.8 (Illumina, San Diego, CA).
D. melanogaster reads were mapped to the major chromosome arms (chr2L, chr2R, chr3L, chr3R, chr4, chrX, chrY, and chrM) of Drosophila genome assembly release 6 plus ISO1 MT and ERCC sequences using TopHat v2.1.0 (Trapnell et al., 2009. PMID: 19289445) with default options except for the following: Libraries were stranded so mapping was done with --library-type fr-firststrand, and we provided a GTF with known set of gene models (FlyBase r6.09 and ERCC) using -G option.
The ERCC reference was based on the DNA Sequence Library SRM2374 from NIST, the FASTA sequence was corrected according to differences found in (Jiang et al. 2011, PMID: 21816910). The ERCC-00085 was re-annotated as Subpool C.
Unique alignments were created by keeping only reads that aligned to a single location (NH:i:1) using grep (v2.20). HTseq v0.6.1p1 (Anders et al., 2014. PMID: 25260700) was used to create gene level read counts with default options except (-s reverse) was used to get strand specific read counts.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GeneBank assembly accession: GCA_000001215.4)
Supplementary_files_format_and_content: Tab delimited file containing gene level read counts from HTseq.

source_name: Heads

growth_protocol: Mated parental flies, reared on standard banana food (https://stockcenter.ucsd.edu/info/food_banana_Opuntia.php) were allowed to oviposit in embryo chambers with agar 0.5% for 24 h. First instar larvae (n=40) were collected and allowed to develop in vials with the particular diets at 25C and a 12L:12D light regime.

extract_protocol:
Heads were dissected in RNAlater (Qiagen, Valencia, CA. Cat. No. 1018087), pooled and stored at -20ºC until RNA extractions. Total RNA was extracted using Direct-zol RNA MiniPrep (Zymo, Irvine, CA. Cat. No. R2050) following manufacturers protocol.
Libraries were prepared using the Truseq PolyA+ stranded mRNA kit (Illumina, San Diego, CA. Cat. No. RS-122-2101), following the manufacturer’s protocol. We used a half reaction size with 100ng total RNA as input for all samples. External RNA Control Consortium (ERCC) spike-ins transcribed from a certified plasmid collection (SRM2374) were added to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used the previously described RNAs from Pool 78A for DMSO treated flies and 78B for control flies (20pg /sample)  (Zook et al., 2012. PMID: 22859977).  Libraries were multiplexed using 12 differently barcoded adapters from TruSeq (Illumina, San Diego, CA). Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad, CA), and pooled for multiplexed sequencing. We sequenced in an Illumina HiSeq2500, to produce single-end, 75 bp reads.  (Illumina, San Diego, CA.).

treatment_protocol: The diets were composed of sucrose (VWR, Randor, PA.), active dry yeast (Genesee, San Diego, CA.), yellow cornmeal (Genesee, San Diego, CA.) and agar (Genesee, San Diego, CA.) (Table1). Ingredients were mixed and boiled and an antifungal composed of methyl paraben (Genesee, San Diego, CA.) dissolved in ethanol was added once the food was cooled (Matzkin et al., 2011, PMID: 21525254). HPS diet had a protein/carbohydrate ratio of 0.43 while LPS diet had a protein/ carbohydrate ratio of 0.1. Immediately after preparation, the food was pipetted in 10-mL aliquots to 8-dram vials. Ten vials with 40 larvae each were set up per combination of diet and strain levels.

tag: tissue

value: head

tag: Sex

value: female

tag: diet

value: Low Protein high sugar

tag: developmental stage

value: 2-6 h post-eclosion flies


title: C12_151020_run0437_female_LPS_6


title: T47D-E2-Y537S-rep2


title: C9_151020_run0437_male_LPS_6

value: male


title: C8_151020_run0437_male_LPS_3


title: D1_160225_run0465_male_LPS_2


title: C7_151020_run0437_male_LPS_2


title: C6_151020_run0437_female_HPS_6

value: High Protein low sugar


title: T47D-veh-Y537S-rep4


title: C4_151020_run0437_female_HPS_2


title: C5_151020_run0437_female_HPS_3


title: C1_160225_run0465_male_HPS_2


title: C3_151020_run0437_male_HPS_6


title: T47D-veh-Y537S-rep2


title: T47D-veh-WT-rep1


title: C2_151020_run0437_male_HPS_3


title: Day 14S Mouse 3

status: Public on Jun 02 2017

city: Boston

first: Driss

last: Zoukhri

state: MA

address: 1 Kneeland st. DHS635

department: Comprehensive Care

institute: Tufts University

description:
D14SM3
rawExprData.xlsx

data_processing:
Samples were sequenced on an Illumina HiSeq 2500
All sequencing reads were processed using the ArrayStudio suite (OmicSoft)
Reads were mapped to the mm10 whole genome OmicSoft Aligner Version 4 (OSA4)
Abundance measurements were performed using the ArrayStudio implementation of the RSEM algorithm
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of DESeq2 normalized expression values for each sample

source_name: Lacrimal Gland

extract_protocol:
Lacrimal glands were excised and total RNA was extracted using miRNeasy isolation kit (Qiagen, Valencia, CA), according to the manufacturer’s protocol.
Sequencing libraries were constructed using Illumina's TruSeq Stranded mRNA HT sample prep kit according to the manufacturers protocol

treatment_protocol: Lacrimal glands were treated with 1ug IL-1α, saline, or left un-treated followed by RNA extraction 1, 2, 3, 4, 5, 7, or 14 days post treatment.

value: BALB/c

value: Lacrimal Gland

tag: age

value: 8-10 weeks

tag: time point

value: 14 day post saline injection (secondary control)


title: Day 14S Mouse 2

description:
D14SM2
rawExprData.xlsx


title: Day 14S Mouse 1

description:
D14SM1
rawExprData.xlsx


title: Day 14 Mouse 3

description:
D14M3
rawExprData.xlsx

value: 14 day post IL-1[alpha] injury


title: Day 7 Mouse 1

description:
D7M1
rawExprData.xlsx

value: 7 day post IL-1[alpha] injury


title: Day 14 Mouse 1

description:
D14M1
rawExprData.xlsx


title: Day 14 Mouse 2

description:
D14M2
rawExprData.xlsx


title: Day 7 Mouse 3

description:
D7M3
rawExprData.xlsx


title: Day 5 Mouse 1

description:
D5M1
rawExprData.xlsx

value: 5 day post IL-1[alpha] injury


title: C10_151020_run0437_female_LPS_2


title: Day 7 Mouse 2

description:
D7M2
rawExprData.xlsx

value: Wild type


title: Day 4 Mouse 3

description:
D4M3
rawExprData.xlsx

value: 4 day post IL-1[alpha] injury


title: Day 4 Mouse 1

description:
D4M1
rawExprData.xlsx


title: Day 3 Mouse 2

description:
D3M2
rawExprData.xlsx

value: 3 day post IL-1[alpha] injury


title: Day 4 Mouse 2

description:
D4M2
rawExprData.xlsx


title: Day 5 Mouse 2

description:
D5M2
rawExprData.xlsx


title: Day 3 Mouse 3

description:
D3M3
rawExprData.xlsx


title: Day 3 Mouse 1

description:
D3M1
rawExprData.xlsx


title: Day 2 Mouse 3

description:
D2M3
rawExprData.xlsx

value: 2 day post IL-1[alpha] injury


title: Day 2 Mouse 2

description:
D2M2
rawExprData.xlsx


title: Day 1 Mouse 3

description:
D1M3
rawExprData.xlsx

value: 1 day post IL-1[alpha] injury


title: Day 1 Mouse 2

description:
D1M2
rawExprData.xlsx


title: Day 0 Mouse 3

description:
D0M3
rawExprData.xlsx

value: Un-injured (control)


title: Day 0 Mouse 2

description:
D0M2
rawExprData.xlsx


title: Day 5 Mouse 3

description:
D5M3
rawExprData.xlsx


title: Day 0 Mouse 1

description:
D0M1
rawExprData.xlsx


title: BV2-EZHi-LPS-2

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

description: mRNA

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
Quality controlled FASTQ files were alignment to Mus musculus UCSC mm10 reference genome sequence using the STAR (version 2.5.1) aligner software. To measure differential gene expression, DESeq2 was used.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: BV2 cells

growth_protocol: PM were isolated from 3-day-old ICR mice as previously described with minor modifications. All experimental protocols were performed in accordance with Institutional Animal Care and Use Committee (IACUC) guidelines and approved by the IACUC committee of Hanyang University (HY-IACUC-2014-0164A and HY-IACUC-2015-0075). Briefly, whole brains of neonatal mice were dissected out of the skull, and blood vessels and meninges were carefully removed. Then, the tissues from whole brains obtained from 12 mice were pooled together, finely minced, and digested using a Neural Tissue Dissociation Kit-Postnatal Neurons (Miltenyi Biotec, Germany, 130-094-802). Next, the digested cells were passed through a 70-µm nylon cell strainer (BD Bioscience, Franklin Lakes, NJ) and seeded in poly-L-lysine coated T-75 flasks in DMEM/nutrient mixture F-12 (DMEM/F12, 1:1) containing 20% FBS (catalog # 26140; Gibco, Waltham, MA), 100 IU/ml penicillin and 10 µg/ml streptomycin (catalog # 15140) obtained from Invitrogen (Waltham, MA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C. The medium was changed every 2-3 days. After two weeks in culture, the mixed glial cell cultures were shaken at 110 rpm at 37°C for 55 min, and the glial cell suspensions were collected from each flask and seeded on poly-L-lysine coated cell culture plates. Microglial cells were sub-plated and used for further experiments. More than 92 % of cells obtained were PM microglia as quantified by CD11b (rat monoclonal immunoglobulin G2b (IgG2b), clone: M1/70.15.11.5, Miltenyi Biotec Germany) FACS analysis (Figure 1C). Mouse microglial BV2 microglial cell lines were grown in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (catalog # 26140; Gibco, Waltham, MA), 100 IU/ml penicillin, and 10 µg/ml streptomycin (catalog # 15140; Invitrogen, Waltham, MA). The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. Medium containing the appropriate agents was replaced every other day. The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. Medium containing the appropriate agents was replaced every other day. The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2500 (101 cycles PE lane).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine microglial PM and BV2 cells were reated with EPZ-6438 (10 uM) and LPS (10 ng/ml) for 4 hrs

tag: cell type

value: microglia cell line

value: treated with EPZ-6438 (10 uM) and LPS (10 ng/ml) for 4 hrs


title: BV2-EZHi-LPS-1

description: mRNA

tag: treatment


title: BV2-EZHi-1

description: mRNA

value: treated with EPZ-6438 (10 uM) for 4 hrs


title: BV2-EZHi-2

description: mRNA


title: PMG-EZHi-LPS-2

description: mRNA

source_name: primary microglia cells

value: primary microglia cells


title: PMG-EZHi-LPS-3

description: mRNA


title: PMG-EZHi-LPS-1

description: mRNA


title: PMG-EZHi-2

description: mRNA


title: PMG-EZHi-3

description: mRNA


title: PMG-EZHi-1

description: mRNA


title: Day 1 Mouse 1

description:
D1M1
rawExprData.xlsx

value: BALB/c


title: Day 2 Mouse 1

description:
D2M1
rawExprData.xlsx

value: Lacrimal Gland


title: dpse_WB_m_r2

description: mixed-species [D. melanogaster (w1118), D. pseudoobscura, and D. virilis] RNA preparation

data_processing:
De-multiplexed reads (Chastity > 0.6) were generated by Illumina CASAVA (v.1.8.2) as fastq files.  For the single-species samples (i.e., D. melanogaster genitalia samples), we provided the raw de-multiplexed fastq files without processing.  For the multi-species samples, we first made merged genome and annotation of appropriate Drosophila species plus corrected ERCC standards (Lee et al., Journal of Genomics, 2016, PMID 27512518).  Additionally, we added a four-letter prefix for each chromosome or scaffold in the merged genome or annotation (e.g., 2L => dmel_2L).  ERCC names were unchanged due to their specific prefix.  The de-multiplexed reads from the multi-species samples were then mapped to the appropriate merged genome and annotation using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with default parameters.  We used an in-house python script to fetch the prefix of read names in the bam alignments, and obtained all uniquely-mapped and multi-hit (2-10 hits) reads (in bam format) that were mapped exclusively to a single species or exclusively to ERCC.  We converted the bam reads to fastq reads by BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).  After this step, reads of each multi-species sample were split into five categories – species 1, species 2, species 3, ERCC, and leftover, which includes unmapped reads and reads mapped to multiple species (or multiple species plus ERCC).  For multi-species samples, the original fastq file can be restored by merging the reads of appropriate three species as well as the ERCC and leftover reads.
We provide both STAR (SRR5639* and SRR6181*) and HiSAT2 (SRR724*) fastq and associated matrices of raw gene-level read counts in this GEO entry. For STAR read count files, we used the FlyBase (FB) annotations (version 2017_03). For HiSAT2 read count files, we used both FB and updated (YO) annotations (data in Supplementary Files of this GEO). For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level Jaccard index overlap between our YO annotation gene IDs and FlyBase ones. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.
Supplementary_files_format_and_content: counts

organism: Drosophila pseudoobscura

source_name: whole body

growth_protocol: D. melanogaster stocks were obtained from the Drosophila Stock Center (Bloomington IN, NIH P40OD018537, http://fly.bio.indiana.edu), and were reared at the NIH (Bethesda MD).  Fly food for D. melanogaster was a medium of water (8.5 L), agar (79 g), torumel yeast (275 g), cornmeal (520 g), granulated sugar (1,100 g), p-hydroxy-benzoic acid methyl ester (23.8 g), and 95% ethanol (91.8 mL) (LabExpress, Ann Arbor MI).  All non-melanogaster flies were reared and dissected at the Drosophila Species Stock Center (San Diego CA, NSF CSBR 1351502, https://stockcenter.ucsd.edu).  D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, and D. virilis were grown on a medium of de-ionized water (28 L), agar (300 g), soy flour (700 g), cornmeal (2,940 g), molasses (2,230 g), yeast (860 g), propionate (135 g), and nipogen (200 g) (https://stockcenter.ucsd.edu/info/food_cornmeal.php).  D. persimilis and D. mojavensis were grown on a medium of agar (85 g), yeast (165 g), methylparaben (13.4 g), blended bananas (825 g), syrup (570 g), liquid malt extract (180 g), and 100% ethanol (134 mL) (https://stockcenter.ucsd.edu/info/food_banana_Opuntia.php).  All flies were reared at 23-25 oC.

extract_protocol:
Flies were anesthetized using CO2, and all samples were dissected in phosphate buffered saline solution (PH 7.4, Life Technologies, Carlsbad CA) and transferred to 56 or 112 μL of RNAlater (Life Technologies, Carlsbad CA) in 96-well 1.5 mL plates at room temperature after being macerated with forceps.  Plates were stored at -80 oC at the NIH after dissection (melanogaster samples) or after dissection and shipping (non-melanogaster samples).  For RNA extraction, we added 20-30 1.0 mm glass beads (BioSpec Products, Bartlesville OK) to each sample and added RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to 712 μL (final volume).  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK).  Extraction of total RNA was performed using the RNeasy 96 kit (spin version), except that we used 712 μL of 70% ethanol due to the increased volumes of RNAlater/RLT mixture.  RNA was quantified using Quant-iT RiboGreen (Life Technologies, Carlsbad CA).  We spot checked RNA integrity by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA) and found that the rRNA bands were distinct.  We used 33 ng aliquots of RNA of three genetically distant species for each library, except for thorax, where we used 17 ng due to lower yield.  The mixing of RNA was performed using a pipetting robot (Andrew Alliance, Vernier CH).  RNA from D. melanogaster genitalia was not mixed with tissues of the other species.
We used 100 ng of total RNA as input (except thorax samples: 50 ng), and followed the TruSeq PolyA+ stranded mRNA kit protocol with half volume reactions (Illumina, San Diego CA).  For each sample, we also added 10 pg Standard Reference Material 2374 beta (Pool 78A or 78B) ERCC spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used 96-plex molecular barcoding (Kozarewa and Turner, Methods in Molecular Biology, 2011, PMID 21431778) from the Illumina TruSeq kit for all samples.  Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA).  For each sample, we conducted RNA-seq for the three libraries with the highest DNA concentration out of four libraries.  The quality (i.e., no overt primer dimers or low complexity) of all selected libraries were confirmed by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA).  We performed single-end 76 bp PolyA+ sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA).

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: adult

value: whole body

value: Male

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: TCCGGAGA-TATAGCCT

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: dpse_WB_m_r1

value: ATTACTCG-TATAGCCT


title: dpse_WB_f_r2

value: Female

value: GAATTCGT-TATAGCCT


title: dpse_WB_m_r3

value: CGCTCATT-TATAGCCT


title: dpse_WB_f_r3

value: TAATGCGC-TATAGCCT


title: dpse_TX_m_r1

source_name: thorax without digestive system

value: thorax without digestive system

value: ATTACTCG-CCTATCCT


title: dpse_TX_f_r2

value: CTGAAGCT-CCTATCCT


title: dpse_TX_f_r3

value: TAATGCGC-CCTATCCT


title: dpse_WB_f_r1

value: ATTCAGAA-TATAGCCT


title: dpse_TX_f_r1

value: GAATTCGT-CCTATCCT


title: dpse_TX_m_r3

value: GAGATTCC-CCTATCCT


title: dpse_RE_m_r3

source_name: reproductive system without gonad

value: adult

value: reproductive system without gonad

value: CGCTCATT-TAATCTTA


title: dpse_RE_f_r2

value: CTGAAGCT-TAATCTTA


title: dpse_RE_f_r3

value: TAATGCGC-TAATCTTA

value: without ERCC


title: dpse_RE_f_r1

value: Female

value: ATTCAGAA-TAATCTTA


title: dpse_RE_m_r2

value: Male

value: TCCGGAGA-TAATCTTA


title: dpse_HD_m_r3

source_name: head

value: head

value: GAGATTCC-ATAGAGGC


title: dpse_HD_f_r3

value: TAATGCGC-ATAGAGGC


title: dpse_RE_m_r1

value: ATTACTCG-TAATCTTA


title: dpse_HD_m_r2

value: CGCTCATT-ATAGAGGC


title: dpse_HD_f_r1

value: ATTCAGAA-ATAGAGGC


title: dpse_GO_m_r3

source_name: gonad

value: gonad

value: GAGATTCC-AGGCGAAG


title: dpse_TX_m_r2

value: adult

value: thorax without digestive system

value: CGCTCATT-CCTATCCT


title: dpse_GO_m_r2

value: CGCTCATT-AGGCGAAG


title: dpse_GO_f_r3

value: TAATGCGC-AGGCGAAG

value: without ERCC


title: dpse_GO_f_r1

value: Female

value: ATTCAGAA-AGGCGAAG


title: dpse_GO_f_r2

value: CTGAAGCT-AGGCGAAG


title: dpse_DG_f_r3

source_name: digestive plus excretory system

value: digestive plus excretory system

value: TAATGCGC-GTACTGAC


title: dpse_DG_m_r2

value: Male

value: TCCGGAGA-GTACTGAC


title: dpse_AC_m_r3

source_name: abdomen without digestive or reproductive system

value: GAGATTCC-GGCTCTGA


title: dpse_DG_m_r1

value: ATTACTCG-GTACTGAC


title: dpse_HD_m_r1

value: head

value: TCCGGAGA-ATAGAGGC


title: dpse_DG_m_r3

value: adult

value: CGCTCATT-GTACTGAC


title: dpse_AC_f_r1

value: abdomen without digestive or reproductive system

value: ATTCAGAA-GGCTCTGA


title: dpse_AC_f_r2

value: GAATTCGT-GGCTCTGA


title: dpse_GO_m_r1

value: gonad

value: TCCGGAGA-AGGCGAAG

value: without ERCC


title: dpse_AC_m_r1

value: ATTACTCG-GGCTCTGA


title: dpse_AC_f_r3

value: Female

value: CTGAAGCT-GGCTCTGA


title: dpse_HD_f_r2

value: CTGAAGCT-ATAGAGGC


title: LIN-41_Lysate

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: processed data file: File_S3_v2.xlsx

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters:ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the WBcel235/ce11 build of the C. elegans genome with STAR (version STAR_2.4.2a_modified)
Mapped reads were indexed and sorted with samtools 1.0
Gene quantification and deferential expression was performed using the GenomicAlignments (1.8.4) and DESeq2 (1.12.3) packages in Bioconductor.
Genome_build: WBcel235/ce11

organism: Caenorhabditis elegans

source_name: Cell Lysate

growth_protocol: Worms were grown at 15°C on peptone-enriched plates seeded with bacterial strain NA22. Embryos were isolated by alkaline hypochlorite treatment (20% bleach and 0.5 N NaOH), washed in M9 buffer, and allowed to hatch overnight in the absence of food at 25°C (hatch rates were typically >90%). 30,000 L1-stage animals were cultured on each 150 x 15 mm petri dish on peptone-enriched medium with NA22 as a food source (lysate preparation utilized 65-70 petri dishes per experiment).  Animals were refed as needed with concentrated NA22 and collected for lysate preparation as young adults, approximately 48 hours after being placed on food at 25°C.

extract_protocol:
RNAeasy Micro Kit (Qiagen) was used to prepare RNA from the samples described above.
TruSeq (Illumina) RNA libraries were prepared from the recovered RNA.

tag: strain

tag: genotype/variation

tag: antibody

tag: rna enrichment


title: dana_WB_f_r1

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

organism: Drosophila ananassae

tag: developmental stage

tag: tissue

value: whole body

tag: Sex

value: CGGCTATG-TATAGCCT


title: dana_WB_m_r1

value: Male


title: dana_WB_f_r2

value: TCCGCGAA-TATAGCCT


title: dana_WB_m_r2


title: dana_TX_m_r2

value: thorax without digestive system

value: TCTCGCGC-GGCTCTGA


title: dana_TX_f_r2

value: adult

value: TCCGCGAA-GGCTCTGA


title: dana_WB_m_r3

value: TCTCGCGC-TATAGCCT


title: dana_TX_m_r3

value: AGCGATAG-GGCTCTGA


title: dpse_AC_m_r2

value: abdomen without digestive or reproductive system

value: CGCTCATT-GGCTCTGA


title: dana_TX_f_r1

value: CGGCTATG-GGCTCTGA

value: without ERCC


title: dpse_DG_f_r1

value: digestive plus excretory system

value: Female

value: GAATTCGT-GTACTGAC


title: LIN-41_LysateRZ

description: processed data file: File_S3_v2.xlsx

source_name: Ribosomally Depleted Cell Lysate

value: RiboZero Kit (Illumina)


title: dana_TX_f_r3


title: dana_RE_m_r3

value: reproductive system without gonad

value: AGCGATAG-CAGGACGT


title: LIN-41_IP-2

description: processed data file: File_S3_v2.xlsx

source_name: Immunoprecipitated LIN-41 RNP

value: 1:1 mixture of 12A6 and 4C9 (Sanchez et al. 2014)


title: dana_RE_m_r2

value: Male

value: TCTCGCGC-CAGGACGT


title: dana_WB_f_r3

value: adult

value: whole body

value: AGCGATAG-TATAGCCT


title: LIN-41_IP-1

description: processed data file: File_S3_v2.xlsx


title: dana_TX_m_r1

value: thorax without digestive system


title: OMA-1_Lysate

description: processed data file: File_S3_v2.xlsx


title: OMA-1_LysateRZ

description: processed data file: File_S3_v2.xlsx


title: dana_RE_m_r1

value: TCCGCGAA-CAGGACGT


title: dana_RE_f_r3


title: OMA-1_IP-2

description: processed data file: File_S3_v2.xlsx

source_name: Immunoprecipitated OMA-1 RNP


title: OMA-1_IP-1

description: processed data file: File_S3_v2.xlsx


title: dana_RE_f_r1

value: CGGCTATG-CAGGACGT


title: dana_HD_m_r3

value: head

value: AGCGATAG-ATAGAGGC


title: dana_HD_m_r1

value: CGGCTATG-ATAGAGGC

value: without ERCC


title: dana_HD_f_r2

value: Female

value: TCCGCGAA-ATAGAGGC


title: dana_GO_m_r3

value: gonad

value: AGCGATAG-TAATCTTA


title: w1118_dpse_dvir_WB_m_r2.ERCC

description: ERCC SetA

organism: synthetic construct

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)

value: not applicable

value: TCCGGAGA-TATAGCCT

value: ERCC SetA


title: w1118_dpse_dvir_WB_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-TATAGCCT


title: w1118_dpse_dvir_WB_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-TATAGCCT

value: ERCC SetB


title: w1118_dpse_dvir_WB_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-TATAGCCT


title: w1118_dpse_dvir_WB_f_r2.ERCC

description: ERCC SetA

value: GAATTCGT-TATAGCCT


title: dana_GO_m_r2

value: adult

value: Male

value: TCCGCGAA-TAATCTTA


title: w1118_dpse_dvir_TX_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-CCTATCCT


title: dana_HD_f_r1

value: head

value: CGGCTATG-ATAGAGGC

value: without ERCC


title: w1118_dpse_dvir_TX_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-CCTATCCT


title: w1118_dpse_dvir_TX_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-CCTATCCT


title: dana_GO_m_r1

value: gonad

value: CGGCTATG-TAATCTTA


title: dana_RE_f_r2

value: reproductive system without gonad

value: Female

value: TCTCGCGC-CAGGACGT


title: w1118_dpse_dvir_TX_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-CCTATCCT

value: ERCC SetB


title: dana_GO_f_r3

value: adult

value: AGCGATAG-TAATCTTA


title: w1118_dpse_dvir_WB_m_r3.ERCC

description: ERCC SetB

value: CGCTCATT-TATAGCCT


title: dana_HD_m_r2

value: Male

value: TCCGCGAA-ATAGAGGC


title: w1118_dpse_dvir_RE_m_r3.ERCC

description: ERCC SetB

value: CGCTCATT-TAATCTTA


title: w1118_dpse_dvir_TX_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-CCTATCCT


title: dana_DG_m_r3

value: digestive plus excretory system

value: AGCGATAG-GTACTGAC

value: without ERCC


title: dana_HD_f_r3

value: head

value: AGCGATAG-ATAGAGGC


title: dana_GO_f_r1

value: gonad

value: Female

value: CGGCTATG-TAATCTTA


title: w1118_dpse_dvir_RE_m_r2.ERCC

description: ERCC SetA

value: not applicable

value: TCCGGAGA-TAATCTTA

value: ERCC SetA


title: w1118_dpse_dvir_RE_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-TAATCTTA


title: dana_DG_m_r1

value: adult

value: CGGCTATG-GTACTGAC


title: w1118_dpse_dvir_TX_f_r1.ERCC

description: ERCC SetA

value: GAATTCGT-CCTATCCT


title: dana_DG_m_r2

value: Male

value: TCTCGCGC-GTACTGAC


title: w1118_dpse_dvir_RE_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-TAATCTTA


title: dana_DG_f_r3

value: digestive plus excretory system

value: AGCGATAG-GTACTGAC


title: w1118_dpse_dvir_RE_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-TAATCTTA

value: ERCC SetB


title: w1118_dpse_dvir_RE_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-TAATCTTA


title: dana_DG_f_r2

value: Female

value: without ERCC


title: w1118_dpse_dvir_HD_m_r2.ERCC

description: ERCC SetB

value: not applicable

value: CGCTCATT-ATAGAGGC


title: w1118_dpse_dvir_HD_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-ATAGAGGC


title: dana_DG_f_r1


title: dana_AC_m_r3

value: abdomen without digestive or reproductive system

value: AGCGATAG-AGGCGAAG


title: w1118_dpse_dvir_HD_m_r1.ERCC

description: ERCC SetA

value: TCCGGAGA-ATAGAGGC

value: ERCC SetA


title: w1118_dpse_dvir_HD_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-ATAGAGGC


title: dana_AC_f_r2

value: adult

value: TCCGCGAA-AGGCGAAG


title: dana_AC_m_r2

value: Male


title: dana_AC_f_r3


title: w1118_dpse_dvir_HD_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-ATAGAGGC


title: dana_AC_m_r1

value: CGGCTATG-AGGCGAAG


title: dana_AC_f_r1


title: w1118_dpse_dvir_GO_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-AGGCGAAG

value: ERCC SetB


title: w1118_dpse_dvir_HD_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-ATAGAGGC


title: w1118_dpse_dvir_GO_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-AGGCGAAG


title: dmoj_WB_m_r2

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

organism: Drosophila mojavensis

value: whole body

value: TCCGGAGA-TATAGCCT

value: without ERCC


title: dmoj_WB_m_r3

value: GAGATTCC-TATAGCCT


title: w1118_dpse_dvir_GO_m_r1.ERCC

description: ERCC SetA

value: not applicable

value: TCCGGAGA-AGGCGAAG


title: dmoj_WB_m_r1

value: ATTACTCG-TATAGCCT


title: dana_GO_f_r2

value: gonad

value: Female

value: TCTCGCGC-TAATCTTA


title: dmoj_WB_f_r3

value: adult

value: TAATGCGC-TATAGCCT


title: dmoj_WB_f_r2

value: CTGAAGCT-TATAGCCT


title: w1118_dpse_dvir_GO_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-AGGCGAAG

value: ERCC SetA


title: w1118_dpse_dvir_GO_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-AGGCGAAG

value: ERCC SetB


title: dmoj_WB_f_r1

value: whole body

value: ATTCAGAA-TATAGCCT


title: w1118_dpse_dvir_DG_m_r3.ERCC

description: ERCC SetB

value: CGCTCATT-GTACTGAC


title: w1118_dpse_dvir_DG_m_r2.ERCC

description: ERCC SetA

value: TCCGGAGA-GTACTGAC


title: w1118_dpse_dvir_GO_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-AGGCGAAG


title: dmoj_TX_m_r3

value: thorax without digestive system

value: Male

value: GAGATTCC-CCTATCCT

value: without ERCC


title: dmoj_TX_m_r2

value: adult

value: CGCTCATT-CCTATCCT


title: dmoj_TX_f_r3

value: Female

value: TAATGCGC-CCTATCCT


title: w1118_dpse_dvir_DG_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-GTACTGAC

value: ERCC SetA


title: w1118_dpse_dvir_DG_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-GTACTGAC

value: ERCC SetB


title: w1118_dpse_dvir_DG_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-GTACTGAC


title: dmoj_RE_m_r3

value: reproductive system without gonad

value: GAGATTCC-TAATCTTA


title: dmoj_TX_f_r1

value: ATTCAGAA-CCTATCCT


title: w1118_dpse_dvir_DG_f_r1.ERCC

description: ERCC SetA

value: not applicable

value: GAATTCGT-GTACTGAC


title: dmoj_RE_m_r2

value: Male

value: CGCTCATT-TAATCTTA


title: w1118_dpse_dvir_AC_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-GGCTCTGA


title: w1118_dpse_dvir_AC_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-GGCTCTGA


title: dmoj_RE_f_r3

value: adult

value: TAATGCGC-TAATCTTA

value: without ERCC


title: dmoj_RE_m_r1

value: ATTACTCG-TAATCTTA


title: dmoj_RE_f_r2

value: Female

value: GAATTCGT-TAATCTTA


title: dmoj_RE_f_r1

value: ATTCAGAA-TAATCTTA


title: w1118_dpse_dvir_AC_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-GGCTCTGA

value: ERCC SetA


title: dmoj_TX_f_r2

value: thorax without digestive system

value: CTGAAGCT-CCTATCCT


title: w1118_dpse_dvir_AC_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: CTGAAGCT-GGCTCTGA

value: ERCC SetB


title: w1118_dpse_dvir_AC_f_r2.ERCC

description: ERCC SetA

value: GAATTCGT-GGCTCTGA


title: dmoj_HD_m_r3

value: head

value: Male

value: GAGATTCC-ATAGAGGC


title: dmoj_HD_m_r2

value: adult

value: CGCTCATT-ATAGAGGC


title: dmoj_TX_m_r1

value: TCCGGAGA-CCTATCCT

value: without ERCC


title: dmoj_HD_m_r1

value: ATTACTCG-ATAGAGGC


title: w1118_dpse_dvir_AC_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-GGCTCTGA


title: orgR_dmoj_dper_WB_m_r3.ERCC

description: ERCC SetB

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila mojavensis; Drosophila persimilis)

value: GAGATTCC-TATAGCCT


title: dmoj_HD_f_r3

value: Female

value: CTGAAGCT-ATAGAGGC


title: orgR_dmoj_dper_WB_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-TATAGCCT

value: ERCC SetA


title: dmoj_HD_f_r2

value: GAATTCGT-ATAGAGGC


title: dmoj_HD_f_r1

value: ATTCAGAA-ATAGAGGC


title: orgR_dmoj_dper_WB_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-TATAGCCT

value: ERCC SetB


title: orgR_dmoj_dper_WB_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-TATAGCCT


title: orgR_dmoj_dper_WB_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-TATAGCCT


title: orgR_dmoj_dper_TX_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-CCTATCCT


title: orgR_dmoj_dper_TX_m_r1.ERCC

description: ERCC SetA

value: TCCGGAGA-CCTATCCT


title: orgR_dmoj_dper_TX_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-CCTATCCT


title: dmoj_GO_m_r2

value: adult

value: gonad

value: Male

value: CGCTCATT-AGGCGAAG

value: without ERCC


title: dmoj_GO_m_r1

value: TCCGGAGA-AGGCGAAG


title: dmoj_GO_f_r2

value: Female

value: GAATTCGT-AGGCGAAG


title: dmoj_GO_m_r3

value: GAGATTCC-AGGCGAAG


title: orgR_dmoj_dper_TX_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-CCTATCCT


title: dmoj_GO_f_r1

value: ATTCAGAA-AGGCGAAG


title: orgR_dmoj_dper_TX_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-CCTATCCT

value: ERCC SetA


title: dmoj_DG_m_r3

value: digestive plus excretory system

value: GAGATTCC-GTACTGAC


title: dmoj_DG_m_r2

value: CGCTCATT-GTACTGAC


title: orgR_dmoj_dper_WB_m_r2.ERCC

description: ERCC SetA

value: TCCGGAGA-TATAGCCT


title: dmoj_DG_f_r2

value: adult

value: GAATTCGT-GTACTGAC


title: orgR_dmoj_dper_RE_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-TAATCTTA

value: ERCC SetB


title: orgR_dmoj_dper_RE_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-TAATCTTA


title: dmoj_GO_f_r3

value: gonad

value: Female

value: TAATGCGC-AGGCGAAG

value: without ERCC


title: orgR_dmoj_dper_RE_m_r2.ERCC

description: ERCC SetB

value: not applicable

value: CGCTCATT-TAATCTTA


title: orgR_dmoj_dper_RE_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-TAATCTTA


title: orgR_dmoj_dper_RE_f_r2.ERCC

description: ERCC SetA

value: GAATTCGT-TAATCTTA

value: ERCC SetA


title: dmoj_AC_m_r2

value: abdomen without digestive or reproductive system

value: Male

value: CGCTCATT-GGCTCTGA


title: dmoj_AC_m_r3

value: adult

value: GAGATTCC-GGCTCTGA


title: orgR_dmoj_dper_RE_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-TAATCTTA


title: dpse_DG_f_r2

value: digestive plus excretory system

value: CTGAAGCT-GTACTGAC


title: orgR_dmoj_dper_HD_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-ATAGAGGC

value: ERCC SetB


title: orgR_dmoj_dper_HD_m_r3.ERCC

description: ERCC SetB

value: GAGATTCC-ATAGAGGC


title: orgR_dmoj_dper_TX_f_r2.ERCC

description: ERCC SetB

value: CTGAAGCT-CCTATCCT


title: orgR_dmoj_dper_HD_f_r3.ERCC

description: ERCC SetB

value: not applicable

value: CTGAAGCT-ATAGAGGC


title: dmoj_AC_m_r1

value: ATTACTCG-GGCTCTGA

value: without ERCC


title: dmoj_AC_f_r3

value: Female

value: TAATGCGC-GGCTCTGA


title: dmoj_AC_f_r2

value: abdomen without digestive or reproductive system

value: CTGAAGCT-GGCTCTGA


title: orgR_dmoj_dper_HD_f_r2.ERCC

description: ERCC SetA

value: GAATTCGT-ATAGAGGC

value: ERCC SetA


title: orgR_dmoj_dper_HD_m_r1.ERCC

description: ERCC SetA

value: ATTACTCG-ATAGAGGC


title: orgR_dmoj_dper_HD_f_r1.ERCC

description: ERCC SetA

value: ATTCAGAA-ATAGAGGC


title: dmoj_DG_f_r3

value: adult

value: digestive plus excretory system

value: TAATGCGC-GTACTGAC


title: dmoj_DG_m_r1

value: Male

value: TCCGGAGA-GTACTGAC


title: dmoj_DG_f_r1

value: ATTCAGAA-GTACTGAC


title: orgR_dmoj_dper_GO_m_r3.ERCC

description: ERCC SetB

value: not applicable

value: GAGATTCC-AGGCGAAG

value: ERCC SetB


title: orgR_dmoj_dper_GO_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-AGGCGAAG


title: orgR_dmoj_dper_GO_m_r1.ERCC

description: ERCC SetA

value: TCCGGAGA-AGGCGAAG


title: orgR_dmoj_dper_GO_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-AGGCGAAG


title: LWT GR1 3

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

data_processing:
Illumina RTA software v 1.13.48.0
Illumina2bam v:0.03
SamToFastq.jar v1.86
Reads were pre-processed with Cutadapt 1.2.1, To remove TruSeq adaptor.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And genome, Using RSEM v1.2.3 and Bowtie2 v2.0.6.
Data were normalized using TMM with the Bioconductor package EdgeR
Data were batch corrected with Bioconductor package ComBat.R
Differential expression were tested using GLM with the Bioconductor package EdgeR
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids, TMM-Normalized counts per million for each sample.

source_name: Lyzs cre mice treated with ab Ly6G fed with MCD_mix3_Liver

growth_protocol: Conplastic strains were obtained after 10 generations of backcrossing to create a new line harboring the nuclear genome of one strain and the mtDNA of another (C57BL/6 and NZB were purchased from Harlan Laboratories).

extract_protocol:
Twelve 10-week-old males per genotype were fed with MCD diet for 3 weeks.  Liver tissue was dissected and immediately frozen in liquid nitrogen. Total RNA was extracted with QIAzol Lysis Reagent and then purified on RNeasy spin columns (Qiagen). RNA integrity (RNA Integrity Score ≥ 7) and quantity were determined on the Agilent 2100 Bioanalyzer. RNA samples from different animals were mixed in equal proportion at two samples per pool, and four pools per genotype were analyzed in the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mitochondria

value: NZB

value: liver

tag: genotype

value: Lyzs cre

tag: diet


title: LWT GR1 4

source_name: Lyzs cre mice treated with ab Ly6G fed with MCD_mix4_Liver


title: L34 3

source_name: Lyzs p38g/d KO fed with MCD_mix3_Liver

value: Lyzs cre p38g/d


title: L34 4

source_name: Lyzs p38g/d KO fed with MCD_mix4_Liver


title: LWT GR1 2

source_name: Lyzs cre mice treated with ab Ly6G fed with MCD_mix2_Liver


title: LWT GR1 1

source_name: Lyzs cre mice treated with ab Ly6G fed with MCD_mix1_Liver


title: orgR_dmoj_dper_GO_f_r1.ERCC

description: ERCC SetA

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: ATTCAGAA-AGGCGAAG

value: ERCC SetA


title: LWT4

source_name: Lyzs cre mice fed with MCD_mix4_Liver


title: orgR_dmoj_dper_DG_m_r1.ERCC

description: ERCC SetA

tag: age post eclosion (days)

tag: fly culture temperature (oc)


title: LWT3

source_name: Lyzs cre mice fed with MCD_mix3_Liver


title: L34 1

source_name: Lyzs p38g/d KO fed with MCD_mix1_Liver


title: orgR_dmoj_dper_DG_m_r2.ERCC

description: ERCC SetB

tag: replicate

tag: illumina barcode

value: CGCTCATT-GTACTGAC


title: orgR_dmoj_dper_DG_f_r3.ERCC

description: ERCC SetB

value: TAATGCGC-GTACTGAC

tag: plate and well id

tag: ercc infomation


title: LWT2

source_name: Lyzs cre mice fed with MCD_mix2_Liver

tag: strain


title: orgR_dmoj_dper_DG_f_r2.ERCC

description: ERCC SetA

value: GAATTCGT-GTACTGAC


title: LWT1

source_name: Lyzs cre mice fed with MCD_mix1_Liver


title: orgR_dmoj_dper_DG_f_r1.ERCC

description: ERCC SetA


title: dmoj_AC_f_r1

source_name: abdomen without digestive or reproductive system

value: adult

value: Female

value: ATTCAGAA-GGCTCTGA

value: without ERCC


title: orgR_dmoj_dper_AC_m_r3.ERCC

description: ERCC SetB

value: not applicable

value: GAGATTCC-GGCTCTGA

value: ERCC SetB


title: LOXBR_BIBR1532-1

city: Philadelphia

first: Tian

last: Tian

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

description: biological replicate 1

data_processing:
RNA-seq reads were aligned to reference hg19 by STAR 2-pass alignment steps
Put through the usual Picard processing steps: Adding read group information, sorting, marking duplicates and indexing
Split'N'Trim and reassign mapping qualities, indel realignment and base recalibration were performed by GATK
Read summarization was performed by featureCounts v1.5.1
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: melanoma cells

growth_protocol: Melanoma cells were grown in 6-well plates at the density of 25,000 cells/well.

extract_protocol:
RNA was purified with TRIzol reagent (Ambion).
Libraries were prepared according to the Tru-Seq Non-Strand Specific Kit (Illumina).

treatment_protocol: Melanoma cells were treated with the control, 6-Thio-dG at 5uM and BIBR 1532 at 25uM, respectively.

tag: cell type

value: human metastatic melanoma cell line

tag: cell line

value: LOX-IMVI BR

tag: treatment


title: orgR_dmoj_dper_GO_f_r2.ERCC

description: ERCC SetA

tag: developmental stage

tag: tissue

value: GAATTCGT-AGGCGAAG


title: orgR_dmoj_dper_AC_m_r1.ERCC

description: ERCC SetA

tag: Sex

value: ATTACTCG-GGCTCTGA


title: LOXBR_6-thio-dG-2

description: biological replicate 2


title: orgR_dmoj_dper_AC_m_r2.ERCC

description: ERCC SetB

value: CGCTCATT-GGCTCTGA


title: LOXBR_CTRL-2

description: biological replicate 2

value: control


title: A375_BIBR1532-1

description: biological replicate 1


title: LOXBR_6-thio-dG-1

description: biological replicate 1


title: L34 2

source_name: Lyzs p38g/d KO fed with MCD_mix2_Liver

tag: mitochondria

value: liver

tag: genotype

value: Lyzs cre p38g/d


title: LOXBR_CTRL-1

description: biological replicate 1


title: orgR_dmoj_dper_AC_f_r1.ERCC

description: ERCC SetA

tag: flybase species id

value: ERCC SetA


title: orgR_dmoj_dper_AC_f_r2.ERCC

description: ERCC SetB

tag: strain (strain name or flybase id or drosophila species stock center id)

value: CTGAAGCT-GGCTCTGA


title: A375_BIBR1532-2

description: biological replicate 2


title: dwil_dana_dyak_WB_m_r3.ERCC

description: ERCC SetB

source_name: ERCC that merged to the multi-species sample (Drosophila willistoni; Drosophila ananassae; Drosophila yakuba)

tag: age post eclosion (days)

value: TCTCGCGC-TATAGCCT


title: orgR_dmoj_dper_AC_f_r3.ERCC

description: ERCC SetB

tag: fly culture temperature (oc)

value: TAATGCGC-GGCTCTGA


title: A375_6-thio-dG-2

description: biological replicate 2


title: A375_CTRL-2

description: biological replicate 2


title: dwil_dana_dyak_WB_m_r2.ERCC

description: ERCC SetA

tag: replicate

value: TCCGCGAA-TATAGCCT


title: A375_6-thio-dG-1

description: biological replicate 1


title: A375_CTRL-1

description: biological replicate 1


title: LOXBR_BIBR1532-2

description: biological replicate 2


title: dwil_dana_dyak_WB_f_r3.ERCC

description: ERCC SetB

tag: illumina barcode

value: AGCGATAG-TATAGCCT


title: Resistance Cells Input

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

data_processing:
Basecalls, demultiplexing and fastq generation was carried out using CASAVA v 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using BWA (Burrough Wheel Aligner). PCR duplicate and reads corresponding to adaptor Seq were excluded
MACS (Model based analysis of ChIP-seq) package was used to call peaks.
Peaks were called using bandwidth 300 bp; mfold, 30; P-value of 1.00e-04
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated.

source_name: HCC827 cells _ Lung cancer

growth_protocol: The NSCLC cell lines HCC827 and H3255 were grown in DMEM media (Invitrogen) containing 1% of dialyzed fetal bovine serum (Invitrogen) and 13C-lysine (100 mg/L) or 12C -lysine (100 mg/L) for six passages according the standard SILAC protocol. Incorporation of 13C-lysine exceeded 95% of the total protein lysine content. Debris were removed by centrifugation at 5,000 x g and then by filtration through a 0.22-μm filter.

extract_protocol:
Chromatin Immunopricipitation was performed using EZ-Chip kit (Millipore Catalog# 17-371). For controls, Normal Mouse IgG and Anti-RNA Polymerase II antibodies were provided by the kit, for C-Jun Santa Cruz catalog# SC-1694X was used. Standard end-point PCR was performed with GAPDH primers to verify that Chip controls have worked properly.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters.  After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq  following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

treatment_protocol: HCC827 cells were maintained on 15-cm plates until 80-90% confluent. Cells were fixed using 1% formaldehyde. Cells were lysed using SDS lysis buffer and Protease Inhibitor Cocktail provided by EZ-CHIP.  Sonication conditions were optimized on Covaris S2 sonicator to yield sheared crosslinked DNA between 200-1000 base pairs in length.

value: Resistance HCC827 ZDR3  Cells

tag: antibody

value: Mouse IgG


title: dwil_dana_dyak_WB_f_r2.ERCC

description: ERCC SetA

value: not applicable

tag: plate and well id

tag: ercc infomation


title: orgR_dmoj_dper_DG_m_r3.ERCC

description: ERCC SetB

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila mojavensis; Drosophila persimilis)

value: GAGATTCC-GTACTGAC

value: ERCC SetB


title: Resistance Cells ChIP_Seq

value: C-Jun Santa Cruz catalog# SC-1694X


title: dwil_dana_dyak_TX_m_r2.ERCC

description: ERCC SetB

value: TCTCGCGC-GGCTCTGA


title: dwil_dana_dyak_TX_m_r3.ERCC

description: ERCC SetB

value: AGCGATAG-GGCTCTGA


title: dwil_dana_dyak_TX_m_r1.ERCC

description: ERCC SetA

value: CGGCTATG-GGCTCTGA


title: Parental Cells ChIP_Seq

value: Parental HCC827 cells


title: Parental Cells Input


title: dwil_dana_dyak_TX_f_r3.ERCC

description: ERCC SetB


title: Resistance cells

data_processing:
Illumina Casava1.7 software (illumina)  used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg9 whole genome using  TopHat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Differential expression was calculated at a significance of p<0.05 after Benjamini and Hochberg correction using a null model.
Genome_build: hg9
Supplementary_files_format_and_content: TXT file (File1 Vasu_Normalized RPKM values_ RNAseq_Agus .txt) include RPKM values for each Sample.

source_name: cell line

extract_protocol: RNA extracted from cells was polyA+ labelled and used to generate libraries  following the manufacturer’s protocols (Illumina).  The modified cDNA molecules were subjected to sequencing by Illumina Hiseq 2000 system

treatment_protocol: HCC827 cells were co-cultured in 10 nM gefitinib for 1 month. The concentration of gefitinib was increased threefold every month. At 1 micro M gefitinib, the cells maintained growth with kinetics equal to that of the parental line. Three individual colonies from the HCC827


title: dwil_dana_dyak_TX_f_r2.ERCC

description: ERCC SetA

value: TCCGCGAA-GGCTCTGA


title: dwil_dana_dyak_RE_m_r3.ERCC

description: ERCC SetB

value: AGCGATAG-CAGGACGT


title: dwil_dana_dyak_RE_f_r3.ERCC

description: ERCC SetB


title: dwil_dana_dyak_RE_m_r1.ERCC

description: ERCC SetA

value: TCCGCGAA-CAGGACGT

value: ERCC SetA


title: NuGEN QIAGEN 18 cycles

city: Roanoke

first: Shannon

last: Farris

state: VA

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech

data_processing:
Reads were trimmed using Sickle and only paired reads with a quality score >20 and a minimum length of 20 bp were aligned to the GENCODE (M9) gene models and the mm10 mouse genome assembly index using STAR (v 2.4.1d) with the recommended ENCODE RNAseq parameters.
Transcript abundance was quantified using FeatureCounts given GENCODE (M9) gene models.
Samples were normalized with DESeq2 using total read counts mapped to annotated exons.
Genome_build: mm10
Supplementary_files_format_and_content: excel files of DESeq2 normalized counts for each sample

source_name: hippocampal CA2 neurons

extract_protocol:
RNA was extracted using either the QIAGEN RNeasy® Micro kit (cat #74004) or the Picopure® RNA isolation kit (Thermo Fisher Scientific, cat #KIT0204) according to the manufacturer's instructions. All samples were subjected to on-column DNase-treatment (Qiagen, cat#79254).
Libraries were generating using either the NuGEN Ovation Universal RNA-Seq Systems 1-16 for Model Organisms (mouse, cat# 0348) or Clontech SMARTer Stranded RNA-Seq Kit (cat# 634837) with the Clontech RiboGone mammalian kit (cat# 634847) according to the manufacturer's instructions.

treatment_protocol: Naive mice were deeply anesthetized with Fatal Plus (50mg/kg) before decapitation and swift removal of the brain (<3 min). Brains were bisected in the sagittal plane and individually flash frozen in 22 x 22mm disposable cryomold (Polysciences, Inc.) filled with Tissue-Tek Optimal Cutting Temperature (O.C.T., Sakura Finetek) compound and submerged in isopentane cooled to -20°C in a dry ice and ethanol slurry.

tag: strain

value: Amigo2-GFP C57BL/6

value: brain

tag: age

value: 6 weeks

value: male

tag: rna extraction kit

value: QIAGEN

tag: library generation kit

value: NuGEN

tag: pcr cycles


title: NuGEN QIAGEN 20 cycles

tag: tissue

tag: Sex


title: dwil_dana_dyak_WB_f_r1.ERCC

description: ERCC SetA

value: not applicable

tag: developmental stage

value: CGGCTATG-TATAGCCT


title: NuGEN QIAGEN 16 cycles


title: dwil_dana_dyak_HD_m_r3.ERCC

description: ERCC SetB

tag: flybase species id

value: AGCGATAG-ATAGAGGC

value: ERCC SetB


title: dwil_dana_dyak_RE_m_r2.ERCC

description: ERCC SetB

tag: strain (strain name or flybase id or drosophila species stock center id)

value: TCTCGCGC-CAGGACGT


title: dwil_dana_dyak_RE_f_r2.ERCC

description: ERCC SetB

tag: age post eclosion (days)


title: dwil_dana_dyak_HD_m_r2.ERCC

description: ERCC SetA

tag: fly culture temperature (oc)

value: TCCGCGAA-ATAGAGGC


title: SMARTer CA2 LCM Pico

description: NuGEN_vs_SMARTer_Exon_countMatrix.xlsx, NuGEN_vs_SMARTer_gene_countMatrix.xlsx

value: PicoPure

value: Clontech


title: NuGEN CA2 LCM QIAGEN