title: Myotubes_Day7 Biological Replicate 1

data_processing:
Sequenced RNA reads had Phred Quality scores ≥ 24 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimming wasn’t necessary. Genes that were differentially expressed were identified using TopHat (TopHat v2.0.9) (http://tophat.cbcb.umd.edu/) and Cuffinks (cufflinks v2.1.1)(Trapnell et al. 2010). Paired RNA reads were aligned to a reference genome (UCSC-mm10.fa) and the splice sites of the genes identified by providing a reference transcriptome (UCSC-mm10.gtf file) in tophat (with parameters -r 200 -p 32). Approximately 92% of the reads aligned to the reference genome concordantly as a pair. Significant differentially expressed genes for the pair of biological replicates and the three stages of muscle cell differentiation (MyoblastsàMyotubes(Day3)àMyotubes(Day7+AraC)) were identified using the Cuffdiff function of the Cufflinks package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample averaged across both Biological replicates  and pairwise comparison statistics for the three different types of samples, C1-Myoblasts, C2-Myotubes_Day3, C3-Myotubes_Day7

growth_protocol: Myoblasts from the skeletal muscle-derived C2C12 cell line were obtained from American Type Culture Collection (ATCC® CRL1772™). C2C12 myoblasts were propagated at 37 ˚C, 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) (high glucose, +pyruvate, +phenol red, +L-Glutamine) (Gibco® 11995-073) supplemented with 10% fetal bovine serum (FBS; Gibco®) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco®). All experiments were performed using cells at passage 3. Myoblasts were plated at a low cellular density of 5 × 103/cm2 (to achieve sub-confluent myoblast cultures) or a high cellular density of 2.5 × 104/cm2 (to allow cell crowding and myogenic differentiation to occur). Cells from the same source culture were plated in parallel at the appropriate cell density into T-75 tissue culture flasks (Greiner bio-one, 658175) (75 cm2 growth surface, 20 mL media volume, (for HiC extraction) and 12W Multiwell Plates (Greiner bio-one, 665180)  (3.9 cm2/well growth surface, 1 mL/well media volume) (for RNA extraction and cellular fixation). Six replicate T75 culture flasks were plated for each experimental condition in order to achieve estimated cell numbers required for analysis. Following 72 hours proliferation, cells which were plated at the low density were harvested as sub-confluent myoblast cultures (Myoblasts). At the same time (D0), high density cultures were switched to differentiation media (DMEM (Gibco® 11995-073) supplemented with 2% horse serum (HS, Gibco®  16050-122)) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco® 15140-122)) to induce myotube formation. Following 3 days of differentiation myotube cultures were either harvested (Myotubes(Day3)), or switched to differentiation media supplemented with 10 µg/mL Cytosine β-D-arabinofuranoside (AraC, Sigma, C1768) in order to kill/eliminate remaining myoblasts and obtain more purified myotube cultures. On day 5, AraC media was replenished and AraC purified myotube cultures were harvested on day 7 (Myotubes(Day7+AraC)). The experimental procedure was repeated on an independent occasion using a second stock C2C12 source vial. If Myotubes(Day3) and Myotubes(Day7+AraC) are not exclusively specified, the terms Myotubes refers collectively to Myotubes(Day3) and Myotubes(Day7+AraC) further in the text.

extract_protocol:
RNA was extracted using a procedure that combined Trizol (Invitrogen) and the RNAeasy Mini Kit (Qiagen). Myoblasts, Myotubes(Day3) and Myotubes(Day7+AraC) grown on 12 well plates in two Biological Replicates were used for RNA extraction. Media from nine different wells per plate was removed. The cells in each well were treated immediately with 390 μl Trizol (Invitrogen) (5 min, RT). The cell content was then homogenized by pipetting to permit complete dissociation of the nucleoprotein complexes, before transferring the content from each well to a new 1.5 mL microfuge tube. Homogenized RNA samples were stored at -80°C and the RNA extracted within one month of the date of storage. RNA extraction continued with addition of 58 μl chloroform to each tube. The mixture was inverted several times and incubated at RT for 2 min. To separate the RNA from the DNA and proteins, the mixture was centrifuged (12000x g, 15 min, 4°C). The upper aqueous layer (~150 μl) was transferred to a new tube, and 150 μl 70% ethanol (in DEPC-treated water) was added. Samples were mixed by inversion to prevent the formation of any visible white precipitate. The extraction was continued using the RNAeasy Mini Kit (Qiagen) spin columns. Samples were transferred to a Spin Cartridge Column (with a Collection Tube) and centrifuged (12000x g, 30 sec, RT). The flow-through was discarded. Wash Buffer I (350 μl) was added to the Spin Cartridge Column containing the bound RNA and the samples were centrifuged (12000x g, 30 sec, RT). RNase-Free DNase Set (Qiagen; 80 μl) was added to the center of the Spin Cartridge Column and the samples incubated (15 min at RT). Wash Buffer RW I (350 μl) was added to the Spin Cartridge Column and the samples were centrifuged twice (12000x g, 30 sec, RT). Another 700 μl Wash Buffer RW I was added and samples were spun three times (12000x g, 30 sec, RT) consecutively. Finally, the Spin Cartridge Column was washed twice with Elusion buffer (500 μl 12000x g, 30 sec, RT) and dried with a final spin (12000x g, 30 sec, RT). For the RNA elution 2 x 15 μl RNAase-free water was added to the center of the Spin Cartridge Column and incubated (1 min, RT) before the RNA was retrieved by a final centrifugation (12000x g, 30 sec, RT). The purity of the extracted RNA was evaluated by determining the 260/280 and 260/230 ratio of the samples using a NanoDrop (ND-1000 Spectrophotometer). To account for variations between wells, equal RNA amounts extracted from three separate wells were combined to constitute a representative RNA sample of 5 μg. Before sending RNA samples for Transcriptome sequencing, the integrity of the RNA was determined using an Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer Instrument. The RNA integrity number (RIN) of the RNA samples was between 9.4 and 10, which indicated high quality of the RNA samples.
Library construction protocol not provided.

tag: collection stage

value: harvested as myotubes after 7 Days in DM


title: ElodeaValcea1

status: Public on Apr 07 2017

type: SRA

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description:
Sample name: EV1
Sample 1_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB2_vs_EV_FC2_FDR5.xlsx

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using BWA v.0.7.10 to a de novo Elodea nuttalii transcriptome.
The reads were mapped with TopHat v.2.0.11 on the Chlamydomonas renhardtii 236 genome.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis were performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2.
Genome_build: de novo transcriptome Elodea nuttallii (Nicole Regier, Rebecca Beauvais-Flück, Vera I. Slaveykova, Claudia Cosio. Mercury exposure under enhanced ultraviolet radiation in Elodea nuttallii: effects on bioaccumulation, transcriptome, pigment content and oxidative stress endpoints. Aquatic toxicology under review.)
Genome_build: Chlamydomonas reinhardtii 236 (Phytozome v.9.1)
Supplementary_files_format_and_content: normalized*: Excel file with normalized counts in cpm (count per million) for each Sample.
Supplementary_files_format_and_content: DEG*: Excel file with significantly differentially expressed genes with a fold change 2 threshold and FRD 5% correction.
Supplementary_files_format_and_content: Elodea_muttallii.fasta: FASTA file of the de novo Elodea nuttallii transcriptome assembly.

molecule: total RNA

organism: Elodea nuttallii

source_name: ElodeaValcea1 shoots

growth_protocol: Collected in situ in clean site.

extract_protocol:
TRI-Reagent
The libraries were prepared with 300 ng of total RNA as starting material and processed with the Illumina TruSeq mRNA stranded kit according to the manufacturer instructions.

treatment_protocol: 2h in situ exposure in the River Olt.

tag: tissue

value: shoots

tag: section

value: 10cm of top with apex


title: Myotubes Day7, Biological Replicate 1

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Myotubes_Day7_Interaction_Matrix_Corr_500kb.txt

library_source: genomic

data_processing:
We used HiCUP (hicup_v0.5.3) (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) pipeline to analyse the HiC libraries. The pipeline was fed with the forward and the reverse reads generated from the sequencing for each of the six libraries. Sequencing reads were mapped to the reference genome (Mus_musculus_GRCh38) using bowtie aligner to generate BAM files. BAM files obtained this way have the corresponding forward and reverse reads of a sequenced DNA fragment mapped to the reference genome as a pair (di-tag). The choice to use HiCUP software for HiC data mapping was motivated by the ability of the pipeline to execute a variety of filtering steps.
We employed the HOMER HiC software pipeline (http://biowhat.ucsd.edu/homer/)(Heinz et al., 2011) to generate interaction matrices, to perform identification of A and B compartments and to determine significant interactions. Briefly, paired-end (i.e. di-tags) reads outputted from HiCUP were checked for GC content (“-checkGC”) and reads originating from regions with unusually high tag density “5 fold higher” (‘‘-removeSpikes 10000 5’’) were removed. Next, only read pairs where both ends mapped near restriction sites for HindIII “AAGCTT” (e.g. maximum distance from restriction site is 1.5x of the insert fragment size) were retained specifying (‘‘-both’’) option. Further, normalized interaction matrices for each biological replicate were generated using 500kb bin size resolution. Normalization is based on the generation of a background model using the entire genome which calculates the number of expected reads between any two loci accounting both for linear distance and sequencing depth. Generally, the normalized interaction matrices output the ratio of observed to expected interactions. When the normalized matrices were generated the “-corr” function was specified which replaces the number of interactions with a Pearson Correlation Coefficient representing how each region interacts with  any other region.
Genome_build: mm10
Supplementary_files_format_and_content: Intreaction matrices generated at 500kb resolution using the information from two Biological replicates for each condition

molecule: genomic DNA

organism: Mus musculus

source_name: myotubes differentiated in vitro from myoblasts cultured from the thigh muscle of C3H mice after a crush injury

growth_protocol: Myoblasts from the skeletal muscle-derived C2C12 cell line were obtained from American Type Culture Collection (ATCC® CRL1772™). C2C12 myoblasts were propagated at 37 ˚C, 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) (high glucose, +pyruvate, +phenol red, +L-Glutamine) (Gibco® 11995-073) supplemented with 10% fetal bovine serum (FBS; Gibco®) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco®). All experiments were performed using cells at passage 3. Myoblasts were plated at a low cellular density of 5 × 103/cm2 (to achieve sub-confluent myoblast cultures) or a high cellular density of 2.5 × 104/cm2 (to allow cell crowding and myogenic differentiation to occur). Cells from the same source culture were plated in parallel at the appropriate cell density into T-75 tissue culture flasks (Greiner bio-one, 658175) (75 cm2 growth surface, 20 mL media volume, (for HiC extraction) and 12W Multiwell Plates (Greiner bio-one, 665180)  (3.9 cm2/well growth surface, 1 mL/well media volume) (for RNA extraction and cellular fixation). Six replicate T75 culture flasks were plated for each experimental condition in order to achieve estimated cell numbers required for analysis. Following 72 hours proliferation, cells which were plated at the low density were harvested as sub-confluent myoblast cultures (Myoblasts). At the same time (D0), high density cultures were switched to differentiation media (DMEM (Gibco® 11995-073) supplemented with 2% horse serum (HS, Gibco®  16050-122)) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco® 15140-122)) to induce myotube formation. Following 3 days of differentiation myotube cultures were either harvested (Myotubes(Day3)), or switched to differentiation media supplemented with 10 µg/mL Cytosine β-D-arabinofuranoside (AraC, Sigma, C1768) in order to kill/eliminate remaining myoblasts and obtain more purified myotube cultures. On day 5, AraC media was replenished and AraC purified myotube cultures were harvested on day 7 (Myotubes(Day7+AraC)). The experimental procedure was repeated on an independent occasion using a second stock C2C12 source vial.

extract_protocol: HiC libraries were prepared as described previously (Lieberman-Aiden et al. 2009), with minor modifications. Cells were cross-linked with formaldehyde and lysed in lysis buffer before the chromatin was digested with HindIII. Following digestion the restriction sites were filled in and marked by incorporating biotinylated dCTP. The ligation of the filled in blunt DNA ends was performed in dilute condition to promote ligation between DNA fragments residing within the same cross-links. Cross-links were then reversed and DNA purified. After the removal of the biotin from unligated ends using the action of T4 DNA polymerase, the DNA libraries were sheared by sonication and the DNA ends were repaired using the combined action of T4 DNA polymerase, T4 polynucleotide kinase and Klenow DNA polymerase. An 'A' was added to the 3' ends of the end repaired blunt DNA fragments using Klenow (exo-) to prevent the ends from ligating to one another during adapter ligation. Further the DNA was electrophoresed on 1.5% agarose gel and DNA between 300 and 650 base pairs was excised and purified. Paired-end adapters for sequencing (Truseq nano DNA LT kit ) were attached to the HiC libraries. For the amplification of the HiC libraries, 2 PCR reactions for all replicates and samples were used with the exception of Myoblasts Replicate 2 and Myotubes(Day7+AraC) Replicate 1 where 4 PCR reactions were used with total volume of 50 μl (22.5 μl template [2.5 μl Streptavidin beads and 20 μl 1XNEBbuffer] + 22.5 μl Enhanced PCR mix + 5 μl Primer cocktail), were performed to amplify sufficient PCR products (~ 1 μg) for sequencing. The temperature profile was 95°C (3 min) followed by 15 cycles ( 98°C, 20 s; 60°C, 15 s; 72°C, 30 s) and a final extension (72°C, 5 min). The PCR products from each HiC library were purified by mixing with 1x volume Ampure beads (Truseq nano DNA LT kit; Illumina).

tag: treatment

value: treated with AraC between Day 3 and Day 7 in DM

tag: cell line

tag: protocol

value: "diluted" HiC


title: Myotubes Day3, Biological Replicate 1

description: Myotubes_Day3_Interaction_Matrix_Corr_500kb.txt

value: not treated with AraC


title: Myotubes_Day7 Biological Reaplicate 2


title: Myoblasts, Biological Replicate 2

description: Myoblasts_Interaction_Matrix_Corr_500kb.txt

source_name: myoblasts cultured from the thigh muscle of C3H mice after a crush injury


title: Myoblasts, Biological Replicate 1


title: Myotubes_Day3 Biological Replicate 2

value: harvested as myotubes after 3 Days in DM


title: Myoblasts Biological Replicate 1

value: harvested as proliferating myoblasts prior reaching confluence


title: Myotubes_Day3 Biological Replicate 1


title: MT_48h_rep2

city: Beijing

first: Chunhua

last: Zhao

address: No.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CP009273.1 whole genome using bowtie2
Quantification of gene expression and analysis of gene differential expression were performed using Fragment Per Kilo bases per Million reads (FPKM) value based rsem software version 1.2.4 and edgeR version 3.4.2 (Bioconductor), respectively
Genome_build: CP009273.1
Supplementary_files_format_and_content: Excel file include FPKM values of different genes for each sample

organism: Escherichia coli

source_name: Bacteria cells

extract_protocol:
Total RNAs were isolated using TRIzol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: product

value: Butanol


title: Myoblasts Biological Replicate 2


title: FR016

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

description:
FR.cts.txt
FR016_TGACCA_L002_R1

data_processing:
PLATE-Seq data are comprised of sets of two paired-end reads. The first read contains an 8-base barcode sequence that identifies the well from which a given sample originates. The second read contains a sequence that typically maps strand-specifically to the 3’-end of an mRNA transcript. We first record the barcode sequence associated with each read. The barcode sequences are designed so that a single error can be corrected, and so we allow an edit distance of one from the actual barcode sequences. Next, we use the bwa-mem aligner to map the set of second reads to a pre-assembled human transcriptome (hg19, UCSC known genes). We then demultiplex the resulting alignments and count the number of uniquely mapped reads associated with each gene. We define a read as uniquely mapped if the maximum alignment score among alignments that map to the correct strand is associated with a single gene.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are formatted as tab-delimited text and contain the number of uniquely mapped reads for each gene in each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: BT20 cell line

growth_protocol: BT20 cells: BT20 epithelial breast carcinoma cells were cultured in white 96-well tissue culture-treated plates (Greiner 655083) at a starting density of 8,000 cells per well in 100 uL of Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. U87 cells: Cells were maintained in EMEM medium (Corning cat no. 10-009) containing 10% fetal bovine serum, 100 u/ml Penicillin Streptomycin (Thermo Fisher Scientific cat no. 15140122), in 37℃ incubator with 5% CO2 and 95% humidity control.  LnCAP cells: LnCAP cells were grown in RPMI1640 with 10% FBS at 37C, 5% CO2, and 95% humidity.

extract_protocol:
PLATE-Seq: Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 uL of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 uL of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295xg for 1 minute to eliminate air bubbles followed by incubation for 90 minutes at room temperature with shaking at 200 rpm. Lystate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 uL of Elution Buffer (nuclease-free water supplemented with 0.4 U/uL SUPERaseIN (ThermoFisher)), incubation at 65°C for five minutes, and incubation at room temperature for 5 minutes. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 uL tips on the Hamilton STAR.
To anneal primers for reverse transcription, 3 uL of 100 uM adapter-linked oligo(dT) primers are added to each well along with 10 uL of 5x ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 uL channel pipetting system. The plate is then heated to 94°C for two minutes and placed immediately on ice for 5 minutes. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 uL per well. The plate is then centrifuged at 295xg for 1 minute and incubated at 42°C for 2 hours. At this point, the samples can optionally be frozen at -80°C.
To remove excess primer, 1 uL of a four-fold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25°C for one hour. To hydrolyze the RNA, we add 20 uL of a 1:1 mixture of 1M sodium hydroxide and 0.5M EDTA to each well and incubate at 65°C for 15 minutes. The wells are then pooled together into a single tube to which 80 uL of 12 M hydrochloric acid are added to neutralize the sample.  At this point, the pooled sample can optionally be frozen at -80°C.
The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer?s instructions, and pooled cDNA is eluted in 15 uL of nuclease-free water. For second-strand synthesis, 1 uL of 10 mM dNTP mixture and 1 uL of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70°C for two minutes and immediately placed on ice for five minutes. Next, 2 uL of NEB Buffer 2 (New England BioLabs) and 1 uL of Klenow Large Fragment DNA Polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 minutes. The reaction is then stopped by addition of EDTA to a final concentration of 50 uM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs) with 0.5 uM Illumina RP1 primer and Illumina RPIx primer (where x is a number indicating the Illumina index). The thermocycling protocol begins with 98°C for 30 seconds followed by 10-12 cycles of 98°C for 15 seconds, 62°C for 15 seconds, and 72°C for 60 seconds followed by a seven-minute incubation at 72°C.
TruSeq: To compare PLATE-Seq and conventional RNA-Seq, we conducted a small-scale screen in a single 96-well plate.  We treated each well containing cultured BT20 cells with one of seven compounds or DMSO (vehicle) including mitoxantrone, crizotinib, albendazole, idarubicin, aprepitant, gemcitabine, and bortezomib with 12 replicate wells for each condition.  Half of the material in each well was allocated to PLATE-Seq, and 96 libraries were constructed using the automated, pooled procedure described above.  For the other half, we pooled two sets of six wells for each condition to generate 16 samples in total (two replicates for each condition). We then extracted total RNA from each pool using an RNeasy column (Qiagen) and subjected the total RNA to Illumina TruSeq poly(A)+ RNA-Seq library construction according to the manufacturer?s instructions.
RNA-Seq using PLATE-Seq or Illumina TruSeq

treatment_protocol: BT20 and U87 cells: After 24 hours of incubation, the plates were treated with drugs. Each drug was dosed at the concentration at which the cells were 80% viable after 48 hours of treatment. After 6 hours of treatment (BT20) or 24 hours of treatment (U87), the medium was replaced with 100 mL of FBS supplemented with 10% DMSO and the plates were frozen at -80C prior to PLATE-Seq. After thawing for PLATE-Seq, cells were washed twice with phosphate-buffered saline (PBS) prior to lysis.

tag: drug

value: DMSO

tag: concentration (um)

tag: library construction

value: Illumina TruSeq RNA-Seq


title: eIF5Ad.2HS

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description: Ribosome Protected mRNA (15-34 nt)

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (CTGTAGGCACCATCAAT) removed with CutAdapt v.1.4.2
Low quality reads removed by fastx toolkit
Reads mapping to ncRNA were removed (mapped with Bowtie 1.1.0 using parameters "-v 2 –y –a –m 1 –best –strata –S –p 4")
Reads were mapped to yeast genome (mapped with Bowtie 1.1.0 using parameters "-v 2 –y –a –m 1 –best –strata –S –p 4")
Coverage across genome computed as reads per million using 3' end mapping
Genome_build: SacCer3 R64-1-1
Supplementary_files_format_and_content: Fixed-step WIG density files for mapped reads at every nucleotide

organism: Saccharomyces cerevisiae

source_name: eIF5A depletion profiling after high salt wash

growth_protocol: Cells were grown to an OD of 0.5 in YPD media containing 0.5mM auxin

extract_protocol:
Lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, IDT miRNA Cloning Linker 1 was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

value: eIF5Ad (yCW33)

value: Whole Cells


title: Eed -/- 2

city: Ann Arbor

first: Emily

last: Maclary

state: MI

address: 1241 Catherine St., 3710 Med Sci-II

department: Human Genetics

institute: University of Michigan

data_processing:
Basecalls were performed using CASAVA 1.8.2 (Samples 1-3) or bcl2Fastq 1.8.4 (Samples 4-7) software.
Polymorphism data was obtained from the Wellcome Trust Sanger Institute Mouse Genomes Project FTP site  (129S1/SvImJ) and the NIG Mouse Genome Database (JF1/Ms). Polymorphisms were substituted in to the mm9 reference genome using VCFtools to create in silico strain-specific references
Reads were mapped separately to strain-specific references using STAR v. 2.3.0e using options --outFilterMismatchNmax 0 --outFilterMultimapNmax 1
Mapped reads overlapping annotated SNP sites differing between the 129 and JF1 strains were identified using Bedtools
129-specific and JF1-specific reads were quantified for each polymorphic site. To obtain gene-level allele-specific expression results, the percent of JF1 allelic reads were averaged across all exonic SNPs within a gene.
Reads mapping to annotated genes were quantified using HTSeq-count, and differential expression analysis performed with DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files for each sample include tab-delimited text file listing SNP-containing reads and separate bedgraphs of RNA-seq coverage for the minus strand and the plus strand

source_name: Eed -/-_TS cell line

growth_protocol: Blastocysts were dissected out of pregnant mice 3.5 dpc and plated in 4 well dishes pre-seeded with mouse embryonic fibroblasts. Hatched embryos were cultured in standard TS medium (RPMI with 20% ES-grade FBS, 1 mM Sodium Pyruvate, 100 uM beta-mercaptoethanol, and 2 mM L-glutamine) supplemented with 37.5 ng/ml FGF4 and  1.5 ug/ml Heparin for 4-5 days until blastocyst outgrowths were of ideal size. Blastocysts were then trypsinized in 0.05% Trypsin-EDTA, neutralized, and cultured in 96 well dishes. Established cell lines were maintained in culture in standard TS media supplemented with 25 ng/ml FGF4 and 1 ug/ml Heparin.

extract_protocol:
RNA was extracted from cells using TRIZOL reagent
PolyA RNA was selected and strand-specific libraries constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit

tag: strain background

tag: genotype/variation

value: Eed -/-

tag: cell type

value: Trophoblast stem (TS) cell


title: Eed fl/fl

source_name: Eed fl/fl_TS cell line

value: Eed fl/fl


title: Eed -/- 1


title: Eed +/+ 2

source_name: Eed +/+_TS cell line

value: Eed +/+


title: MT_48h_rep1


title: FR015

description:
FR.cts.txt
FR015_TTAGGC_L002_R1


title: MT_24h_rep2


title: Eed +/+ 3


title: FR013

description:
FR.cts.txt
FR013_ATCACG_L002_R1

value: Bortezomib (Velcade)


title: WT.2HS

description: Ribosome Protected mRNA (15-34 nt)

source_name: Wild-Type profiling after high salt wash

value: Wild-Type (yCW30)


title: FR014

description:
FR.cts.txt
FR014_CGATGT_L002_R1


title: FR012

description:
FR.cts.txt
FR012_ATTCCT_L002_R1

value: Gemcitabine HCl (Gemzar)


title: MT_24h_rep1


title: eIF5Ad.1HS

description: Ribosome Protected mRNA (15-34 nt)

extract_protocol:
For ribosome footprint profiling, lysates were clarified and monosomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform. For RNA-Seq, total RNA was extracted from lysates by using SDS/hot phenol/chloroform.
For ribosome footprint profiling, fragments ranging from 15-34 nt were gel purified and rRNA was depleted from this pool through Ribo-Zero Gold (Yeast) treatment. Upon dephosphorylation of sample RNA, IDT miRNA Cloning Linker 1 was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing. For RNA-Seq, rRNA was depleted through Ribo-Zero Gold (Yeast) treatment and the remaining RNA was randomly fragmented with light base treatment. Fragments of 40-60 nt were prepared using the above protocol.

treatment_protocol: Cells were harvested by vacuum filtration and flash frozen. Profiling samples were homogenized and lysed with lysis buffer using a freezer mill. Total RNA for RNA-Seq was extraced from whole cell lysates.


title: MT_12h_rep1


title: Eed -/- 3


title: Eed +/+ 1


title: MT_12h_rep2


title: eIF5Ad.1

description: Ribosome Protected mRNA (15-34 nt)

source_name: eIF5A depletion profiling


title: MT_6h_rep2


title: eIF5Ad.2

description: Ribosome Protected mRNA (15-34 nt)

source_name: eIF5A depletion profiling (Replicate)


title: FR011

description:
FR.cts.txt
FR011_ACTGAT_L002_R1


title: WT.2

description: Ribosome Protected mRNA (15-34 nt)

source_name: Wild-Type profiling (Replicate)


title: FR009

description:
FR.cts.txt
FR009_CGTACG_L001_R1

value: Aprepitant (MK - 0869)


title: WT.1

description: Ribosome Protected mRNA (15-34 nt)

source_name: Wild-Type profiling


title: WT_48h_rep2


title: WT_48h_rep1


title: Bactin_RNASeq_Nuclear_26hpf_2

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: Bactin promoter driving biotin ligase.

data_processing:
ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes.
RNA-seq reads were mapped using STAR (v.2.4.2a).
BAM files incorporating reads belonging to either DNA strand were generated using custom python script.
Genome_build: danRer7 (Zv9)
Supplementary_files_format_and_content: bigWig files

organism: Danio rerio

extract_protocol:
Nuclei isolation using biotin-tagged outer nuclear envelope, adapted from INTACT procedure. Polyribosome isolation using biotin-tagged Rpl10 protein, adapted from TRAP procedure. FACS procedure using cell-specific fluorescent marker, following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al., 2013, adapted for FACS-sorted embryonic cells.
RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non-directional sequencing libraries after polyA-selection of RNA transcripts (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB) were built using NEBnext Ultra RNA library kit for Illumina (NEB). Following ribodepletion using Ribo-ZeroTM Magnetic Kit (Epicentre), directional RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (KAPABiosystems).

tag: strain/background

value: AB/TU

value: embryonic structure

tag: assay

value: RNA-seq stranded

value: nuclear

tag: ribodepleted

value: ribodepleted

value: InVivoBiotinylatedNuclei

tag: strand

value: reverse


title: FR010

description:
FR.cts.txt
FR010_GAGTGG_L002_R1

value: Illumina TruSeq RNA-Seq


title: MT_6h_rep1

value: Butanol


title: WT.1HS

description: Ribosome Protected mRNA (15-34 nt)

tag: tissue

value: Whole Cells


title: FR008

description:
FR.cts.txt
FR008_GTTTCG_L001_R1

value: Idarubicin HCl


title: FR006

description:
FR.cts.txt
FR006_GTGAAA_L001_R1

value: Albendazole (Albenza)


title: WT_24h_rep1


title: Bactin_RNASeq_Nuclear_26hpf_1

description: Bactin promoter driving biotin ligase.


title: WT_24h_rep2


title: WT_12h_rep2


title: FR004

description:
FR.cts.txt
FR004_CCGTCC_L001_R1

value: Crizotinib


title: FR005

description:
FR.cts.txt
FR005_GTCCGC_L001_R1


title: Bactin_RNASeq_Nuclear_16ss_2

description: Bactin promoter driving biotin ligase.


title: Sox10_RNASeq_Ribo_16ss_1

description: Sox10 BAC driving biotin ligase.

value: neural crest and otic

value: polyribosome-associated

value: InVivoBiotinylatedPolysomes


title: FR007

description:
FR.cts.txt
FR007_GTGGCC_L001_R1


title: WT_12h_rep1


title: FR003

description:
FR.cts.txt
FR003_ATGTCA_L001_R1


title: WT_6h_rep2


title: Sox10_RNASeq_Nuclear_PolyA_2

description: Sox10 promoter driving biotin ligase.

value: RNA-seq

value: polyA

value: unstranded


title: WT_6h_rep1


title: K100Q rep 3

status: Public on Apr 06 2017

city: Maywood

first: Alan

middle: J

last: Wolfe

state: Illinois

department: Microbiology and Immunology

institute: Loyola University - Chicago

description:
BD_09
replicate 3

data_processing:
Base calls were made using MiSeq Reporter v. 2.6.2.1
Low quality reads were trimmed with CutAdapt
Adpater sequences were clipped with CutAdapt
The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand
Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10
Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1)
Genome_build: Escherichia coli str. K-12 substr. MG1655
Supplementary_files_format_and_content: text files containing gene counts output by htseq-count
Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made

growth_protocol: Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8.

extract_protocol:
Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent).
rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina)
ScriptSeq v2 Complete Kit (EpiCentre)

tag: media

value: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose

tag: growth phase

value: Late exponential/Early stationary (OD ~1.8)


title: Sox10_RNASeq_Nuclear_PolyA_1

description: Sox10 promoter driving biotin ligase.

value: AB/TU

value: neural crest

value: nuclear


title: FR002

description:
FR.cts.txt
FR002_AGTTCC_L001_R1

value: Mitoxantrone Hydrochloride

value: Illumina TruSeq RNA-Seq


title: Sox10_RNASeq_Nuclear_16ss_2

description: Sox10 BAC driving biotin ligase.

value: RNA-seq stranded

value: ribodepleted

value: InVivoBiotinylatedNuclei

value: reverse


title: FR001

description:
FR.cts.txt
FR001_AGTCAA_L001_R1


title: Bactin_RNASeq_Nuclear_16ss_1

description: Bactin promoter driving biotin ligase.

value: embryonic structure


title: K100R rep 2

description:
BD_11
replicate 2


title: AR1-/AR2- rep 2

description:
BD_02
replicate 2


title: WT rep 1

description:
BD_04
replicate 1

source_name: WT

value: WT


title: AR1-/AR2- rep 3

description:
BD_03
replicate 3


title: K100R rep 1

description:
BD_10
replicate 1


title: WT rep 2

description:
BD_05
replicate 2


title: WT rep 3

description:
BD_06
replicate 3


title: AR1-/AR2- rep 1

description:
BD_01
replicate 1


title: K100R rep 3

description:
BD_12
replicate 3


title: SAM24315063 WT microglia 2

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: SAM24315063 WT microglia 2

data_processing:
Bioinformatic analyses were performed using custom scripts written in the R programming language (http://r-project.org), using packages from the Bioconductor project (http://bioconductor.org).
Demultiplexed RNA sequencing reads were processed using the HTSeqGenie package (version 3.14.2). Reads were aligned to the reference mouse genome sequence (NCBI Build 37) using the GSNAP algorithm (version 2013-10-10). Uniquely aligned read pairs that fell within exons were tallied to estimate gene expression levels.
To determine differential expression of genes, we used the DESeq2 algorithm, using the default parameters. To control for multiple testing, P-values were adjusted using the Benjamini-Hochberg method.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: Brain

growth_protocol: NRROS -/- , Nox2 -/- , NRROS -/- Nox2 -/- , NRROS conditional (NRROS fl/fl ) and NRROS fl/fl LysM-Cre mice have been previously described. NRROS fl/fl mice were crossed to Vav-Cre mice to generate hematopoietic-specific knockout mice. All animals were housed under specific pathogen-free conditions. The Genentech Institutional Animal Care and Use Committee approved all animal studies.

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen). The quantity and quality of total RNA extracted were determined prior to the processing by RNA-seq. The concentration of total RNA samples was determined using NanoDrop 8000 (Thermo Scientific). The integrity of RNA samples was determined using 2100 Bioanalyzer (Agilent Technologies).
< 0.5 mg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads.

tag: inventory sample name

value: WT microglia 2

tag: primary tissue

value: Brain

tag: genotype

value: Wild Type

value: microglia


title: SAM24315065 WT pvm 1

description: SAM24315065 WT pvm 1

value: WT pvm 1

value: perivascular macrophages


title: SAM24315068 KO pvm 1

description: SAM24315068 KO pvm 1

value: KO pvm 1

value: NRROS KO


title: SAM24315070 KO pvm 3

description: SAM24315070 KO pvm 3

value: KO pvm 3


title: SAM24315066 WT pvm 2

description: SAM24315066 WT pvm 2

value: WT pvm 2


title: SAM24315062 WT microglia 1

description: SAM24315062 WT microglia 1

value: WT microglia 1


title: SAM24315064 WT microglia 3

description: SAM24315064 WT microglia 3

value: WT microglia 3


title: K100Q rep 2

description:
BD_08
replicate 2

tag: strain

value: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose

value: Late exponential/Early stationary (OD ~1.8)


title: Mouse_input

first: Hongkui

last: Deng

address: this is for reviewer only

institute: Peking University

description: mc2i and mc6-1 cells are F1 hybrids between STOCK Tg(Sox2-cre)1Amc/J and B6.Cg-Gt(ROSA)26Sortm14(CAG-Tdtomato)Hze/J, which were purchased from Jackson Laboratory.

data_processing:
Human and mouse ChIP-seq reads were aligned to the human genome build hg19 and mouse genome build mm9, respectively, using the bwa (v0.7.12) software.
Duplicate PCR reads were removed using Picard (version 2.6) from the aligned sequences.
MACS (version 2.1.0) was used to identify regions of histone marks enrichment over background with the "—broad" option.
Genome_build: hg19 (GRCh37) for human samples; mm9 (MGSCv37) for mouse samples.
Supplementary_files_format_and_content: broadPeak files contain enriched peaks detected by MACS version 2.1.0.

source_name: Mouse ESCs and mouse extended PSCs, input

growth_protocol:
Human primed pluripotent stem cells were maintained in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells in conventional human embryonic stem cell medium. Human extended pluripotent stem cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells.
Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq library was prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina according to the manufacturer's instructions.

tag: cell line

value: mc2i, mc6-1

value: Mouse embryonic stem cells and mouse extended pluripotent stem cells

tag: chip antibody


title: mc6-1_H3K27me3

source_name: Mouse extended PSCs, H3K27me3 ChIP

value: Mouse extended pluripotent stem cells

value: anti-H3K27me3 (Millipore, cat. no. 07-449, lot# 2194165)


title: mc2i_H3K4me3

source_name: Mouse ESCs, H3K4me3 ChIP

value: Mouse embryonic stem cells

value: anti-H3K4me3 (Millipore, cat. no. 07-473, lot# 2152225)


title: K100Q rep 1

description:
BD_07
replicate 1


title: mc2i_H3K27me3

source_name: Mouse ESCs, H3K27me3 ChIP


title: SAM24315069 KO pvm 2

description: SAM24315069 KO pvm 2

value: KO pvm 2

value: Brain


title: mc6-1_H3K4me3

source_name: Mouse extended PSCs, H3K4me3 ChIP


title: SAM24315067 WT pvm 3

description: SAM24315067 WT pvm 3

value: WT pvm 3

value: Wild Type

value: perivascular macrophages


title: SAM19770264 NRROS KO bulk CD11b+ cells 1

description:
SAM19770264 NRROS KO microglia CD11b+ 1
PolyA RNA

data_processing:
Bioinformatic analyses were performed using custom scripts written in the R programming language (http://r-project.org), using packages from the Bioconductor project (http://bioconductor.org).
Demultiplexed RNA sequencing reads were processed using the HTSeqGenie package (version 3.14.2). Reads were aligned to the reference mouse genome sequence (mm9) using the GSNAP algorithm (version 2013-10-10). Uniquely aligned read pairs that fell within exons were tallied to estimate gene expression levels.
To determine differential expression of genes, we used the DESeq2 algorithm, using the default parameters. To control for multiple testing, P-values were adjusted using the Benjamini-Hochberg method.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: Entrez Gene IDs, gene exonic counts, gene length, and RPKM values.

source_name: KO Microglia CD11b+

growth_protocol: NRROS -/-, Nox2 -/-, NRROS -/- Nox2 -/-, NRROS conditional (NRROS fl/fl) and NRROS fl/fl LysM-Cre mice have been previously described (PMID 24739962). NRROS fl/fl mice were crossed to Vav-Cre mice to generate hematopoietic-specific knockout mice. All animals were housed under specific pathogen-free conditions. The Genentech Institutional Animal Care and Use Committee approved all animal studies.

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen). The quantity and quality of total RNA extracted were determined prior to the processing by RNA-seq. The concentration of total RNA samples was determined using NanoDrop 8000 (Thermo Scientific). The integrity of RNA samples was determined using 2100 Bioanalyzer (Agilent Technologies).
<0.5 mg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR-based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq 2500 (Illumina) to generate 30M of single-end 50-base-pair reads.

value: KO microglia CD11b+ 1

value: Microglia

value: NRROS KO


title: SAM19770263 WT bulk CD11b+ cells 5

description:
SAM19770263 WT microglia CD11b+ 5
PolyA RNA

source_name: WT Microglia CD11b+

value: WT microglia CD11b+ 5

value: WT


title: SAM19770268 NRROS KO bulk CD11b+ cells 5

description:
SAM19770268 NRROS KO microglia CD11b+ 5
PolyA RNA

value: KO microglia CD11b+ 5


title: SAM19770266 NRROS KO bulk CD11b+ cells 3

description:
SAM19770266 NRROS KO microglia CD11b+ 3
PolyA RNA

value: KO microglia CD11b+ 3


title: SAM19770265 NRROS KO bulk CD11b+ cells 2

description:
SAM19770265 NRROS KO microglia CD11b+ 2
PolyA RNA

value: KO microglia CD11b+ 2


title: SAM19770267 NRROS KO bulk CD11b+ cells 4

description:
SAM19770267 NRROS KO microglia CD11b+ 4
PolyA RNA

value: KO microglia CD11b+ 4


title: SAM19770262 WT bulk CD11b+ cells 4

description:
SAM19770262 WT microglia CD11b+ 4
PolyA RNA

value: WT microglia CD11b+ 4


title: SAM19770260 WT bulk CD11b+ cells 2

description:
SAM19770260 WT microglia CD11b+ 2
PolyA RNA

value: WT microglia CD11b+ 2


title: SAM19186752 NRROS KO brain 5

description:
SAM19186752 NRROS KO brain 5
PolyA RNA

source_name: KO Brain

value: KO brain 5


title: SAM19186751 NRROS KO brain 4

description:
SAM19186751 NRROS KO brain 4
PolyA RNA

value: KO brain 4


title: SAM19770261 WT bulk CD11b+ cells 3

description:
SAM19770261 WT microglia CD11b+ 3
PolyA RNA

value: WT microglia CD11b+ 3


title: SAM19186750 NRROS KO brain 3

description:
SAM19186750 NRROS KO brain 3
PolyA RNA

value: KO brain 3

value: Brain


title: SAM19186749 NRROS KO brain 2

description:
SAM19186749 NRROS KO brain 2
PolyA RNA

value: KO brain 2


title: SAM19186746 WT brain 4

description:
SAM19186746 WT brain 4
PolyA RNA

source_name: WT Brain

value: WT brain 4


title: SAM19186748 NRROS KO brain 1

description:
SAM19186748 NRROS KO brain 1
PolyA RNA

value: KO brain 1


title: SAM19186747 WT brain 5

description:
SAM19186747 WT brain 5
PolyA RNA

value: WT brain 5


title: SAM19186745 WT brain 3

description:
SAM19186745 WT brain 3
PolyA RNA

value: WT brain 3


title: sAML.1uM.OTX.2

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

description: Processed data file: sAML_RNASeq_coding.qn.txt

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SET2_RNASeq_coding.qn.txt: Tab-delimited text file includes quantile normalized FPKM values for each Sample.
Supplementary_files_format_and_content: sAML_RNASeq_coding.qn.txt: Tab-delimited text file includes quantile normalized FPKM values for each Sample.

source_name: CD34+ sAML progenitor cells, OTX015

growth_protocol: SET2 cells were grown in RPMI-1640 media supplemented with 20% FBS.

extract_protocol:
Total RNA was isolated utilizing a Pure Link RNA mini isolation kit following the manufacturer's protocol. RNA were eluted in 40 uL (primary PD sample) or 50 uL (SET2 cells).
Illumina mRNA-Seq kit.

treatment_protocol: Cultured sAML SET2 or patient-derived CD34+ sAML were treated with BET inhibitor OTX-015 or BET-PROTAC for 4 hrs (SET2 cells) or 8 hours (patient-derived CD34+ sAML cells). Cells were pelleted and snap frozen in liquid nitrogen until processing for RNA extraction.

value: patient-derived CD34+ sAML progenitor cells

tag: treatment


title: sAML.Control.1

source_name: CD34+ sAML progenitor cells, control

value: Control


title: sAML.Control.2


title: sAML.1uM.OTX.1


title: sAML.1uM.ARV.2

source_name: CD34+ sAML progenitor cells, ARV-825


title: SAM19770259 WT bulk CD11b+ cells 1

description:
SAM19770259 WT microglia CD11b+ 1
PolyA RNA

value: WT microglia CD11b+ 1

value: Microglia

value: WT


title: sAML.1uM.ARV.1


title: SET2.Control.3

description: Processed data file: SET2_RNASeq_coding.qn.txt

source_name: Cultured secondary AML cell line, control

value: cultured sAML cells


title: SET2.Control.2


title: SET2.1uM.OTX015.3

source_name: Cultured secondary AML cell line, OTX015


title: SET2.Control.1


title: SET2.1uM.ARV.1

source_name: Cultured secondary AML cell line, ARV-825


title: SET2.1uM.ARV.3


title: SET2.1uM.ARV.2


title: G1S-CAS9-P2-S6

city: Lafayette

first: Matthew

last: Perkett

state: CO

address: 2650 Crescent Drive Suite 100

institute: Dharmacon, GE Healthcare

data_processing:
Read trimming for Illumina adapters using Trimmomatic v0.32
Read quality report from FastQC v0.11.2
Read mapping to human reference transcriptome using Tophat2 v2.0.13 and Bowtie2 v2.2.3
FPKM values using Cufflinks v2.2.1
Genome_build: Grch38
Supplementary_files_format_and_content: Excel files with two worksheets corresponding to the Cufflinks output files "genes.fpkm_tracking" and "isoforms.fpkm_tracking".  Columns include gene ID/transcript accession, genomic locus, and FPKM values.

source_name: recombinant U2OS cell line

growth_protocol: G1S-CCMP-Cas9 U2OS cells were cultured at 37 °C/5% CO2 in McCOYS 5A medium (GE Healthcare HyClone, Cat #SH.30200.01) with 10% fetal bovine serum, 1% L-Glutamine and 500 µg/mL Genetecin (Gibco, Ref 10131-027).

extract_protocol:
Total RNA from one million G1S-CCPM-Cas9 cells was collected using the RNeasy Mini Kit (Qiagen, #74106).
RNA-seq libraries were prepared from the total RNA collected using the NEXTflex™ Rapid Directional mRNA-Seq Kit Bundle with RNA-Seq Barcodes and poly(A) beads (Bioo Scientific, #5138-10, 5138-11).

treatment_protocol: Untreated

value: G1S-CCMP-Cas9 U2OS cells

value: bone osteosarcoma


title: G1S-CAS9-P1-S5


title: Tip60KD_ATACseq_Rep1

city: Worcester

first: Thomas

last: Fazzio

state: MA

address: 364 Plantation street

institute: UMMS

data_processing:
Library strategy: ATAC-seq
TopHat2 was used to map the RNAseq reads to the mouse genome (mm10). The bam files from the Tophat output were used for downstream analysis using HOMER. DESeq2 was used to identify the differentially expressed genes. Heatmaps were generated using Java TreeView. K-means clustering was performed using Cluster 3.0.
For ATACseq: Paired-end 75 bp reads were trimmed to 24 bases and reads were then aligned to mm10 using Bowtie2 with the parameter -X 2000 to ensure that fragments up to 2 kb were allowed to align. Duplicates were then removed using Picard. Reads with low quality score (MAPQ < 10) and reads mapping to the mitochondrial genome were removed. Reads were separated into size classes, and only nucleosome free reads (less than 100 bp) were used for subsequent analyses. These reads were processed in HOMER. Genome browser tracks were generated from mapped reads using the “makeUCSCfile” command. Peaks were individually called from replicate datasets using the “findPeaks” command and those peaks enriched in both replicates were retained. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each bin. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, and high quality (peak score > 6) Tip60 peaks called from (Raven et al 2015). After anchoring mapped reads over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2. During differentiation, ESCs were cultured without LIF.

extract_protocol:
RNA was isolated using TRIzol and further purified on RNA Clean and Concentrator columns for RNAseq
For ATACseq, cells were treated with lysis buffer containing non-ionic detergent to generate nuclei
Two independent ATAC reactions per biological replicate were performed, using 35,000 and 70,000 ESCs each. After library preparation (Buenrostro:2013, Buenrostro:2015), the two reactions were found to have indistinguishable distributions of fragment sizes, and were therefore combined for sequencing. (Therefore, each biological replicate consisted of two ATAC reactions).
Strand specific library construction and RNAseq were performed by Applied Biological Materials, Inc. and the UCLA Clinical Microarray Core for ESCs and differentiating ESCs, respectively

treatment_protocol: Lentivirus sepcific to Tip60 is used for Tip60KD.

tag: passage

value: lentivirus for the Tip60 knockdown

value: Tip60fl/+ ES cells


title: Tip60ciMut_ATACseq_Mut2

value: untreated

tag: genotype/variation

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity


title: WT_ATACseq_Rep2


title: Tip60ciMut_ATACseq_Mut1


title: SAM19186743 WT brain 1

description:
SAM19186743 WT brain 1
PolyA RNA

value: WT brain 1

value: Brain


title: SAM19186744 WT brain 2

description:
SAM19186744 WT brain 2
PolyA RNA

value: WT brain 2


title: Neu-24h-siPU Rep2 ATAC-seq

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

data_processing:
Library strategy: ATAC-seq
ATAC-seq reads were mapped to the hg38 reference genome using bowtie (Langmead et al., 2009). Using parameters (bowtie -S --trim3 7 --chunkmbs 3000 -p 32 -m 3 -v 2 --best --strata -X 3000)
BAM was generated from SAM file using samtools/0.1.18
BedTools genomeCoverageBed was used to convert BAM to bedGraph with hg38 chromosome sizes.
bedGraphToBigWig from UCSC was used to generate bigWig files.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Neutrophil

growth_protocol: HL-60 cells (ATCC) were grown in Modified Dulbecco's Medium in a final concentration of 20% FBS with penicillin antibiotics (1%). Cells were routinely cultured at a density of 1x10^6 cells/ml.

extract_protocol:
Approximately 50,000 HL-60 and differentiated cells were collected for ATAC-seq. ATAC-seq was performed as previously described (Buenrostro et al., 2013) with one amendment. DNA size exclusion was utilized after library generation to enrich for accessible chromatin ranging from 100-400bp.
ATAC-seq libraries as paired-end 43bp reads on the Nextseq 500 Illumina platform.

treatment_protocol: Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. Briefly, 1x10e6 undifferentiated HL-60 cells were washed in 1X PBS and transfected with the Lonza nucleofector cocktail, 1μg of GFP plasmid and human PU.1 siRNA (Dharmacon Inc, E-010537-00-0005). HL-60 and differentiated myeloid cells were harvested 24 hours post-nucleofection. Cell viability was determined using trypan blue staining and counted using a hemocytometer prior to RNA isolation.

tag: induction

value: DMSO/ATRA

tag: time

value: 24 hr

value: siRNA PU.1


title: Neu-24h-siPU Rep1 ATAC-seq


title: Mon-24h-siPU Rep2 ATAC-seq

source_name: Monocyte

value: Vitamin D3


title: Mac-24h-siPU Rep1 ATAC-seq

source_name: Macrophage

value: PMA


title: Mon-24h-siPU Rep1 ATAC-seq


title: Mac-24h-siPU Rep2 ATAC-seq


title: HL60-siPU1 Rep1 ATAC-seq


title: HL60-siPU1 Rep2 ATAC-seq


title: Neu-24h-siPU Rep2 RNA-seq

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 20 gene annotations using Cufflinks (Trapnell et al., 2010).
FPKM and counts were normalized for batch effects using Combat (Johnson et al., 2007).
Genome_build: hg38
Supplementary_files_format_and_content: FPKM

extract_protocol:
RNA quality was evaluated for all samples using an Agilent 2100 Bioanalyzer. Samples with a RIN > 9 were used to build RNA-seq libraries from 50,000 cells using the Smart-seq2 protocol (Picelli et al., 2013).
Reads were sequenced as 40 bp paired-end dual indexed reads using Illumina’s NextSeq 500

treatment_protocol: Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. Briefly, 1x10e6 undifferentiated HL-60 cells were washed in 1X PBS and transfected with the Lonza nucleofector cocktail, 1μg of GFP plasmid and either a human non-targeting siRNA (Dharmacon Inc, D-001206-13-05) or human PU.1 siRNA (Dharmacon Inc, E-010537-00-0005). HL-60 and differentiated myeloid cells were harvested 24 hours post-nucleofection. Cell viability was determined using trypan blue staining and counted using a hemocytometer prior to RNA isolation.


title: Neu-24h-siPU Rep1 RNA-seq


title: Neu-24h-siCon Rep2 RNA-seq

value: siRNA Control


title: Mon-24h-siPU Rep1 RNA-seq


title: Mon-24h-siCon Rep2 RNA-seq


title: SET2.1uM.OTX015.1

tag: cell type


title: Tip60KD_ATACseq_Rep2


title: Neu-24h-siCon Rep1 RNA-seq


title: WT_ATACseq_Rep1


title: Mon-24h-siCon Rep1 RNA-seq


title: E60 rep3

first: Yingying

last: Su

address: Tian Tan Xi Li No.4

institute: Capital Medical University School of Stomatology

data_processing:
After the completion of sequencing run, raw data was processed by the Illumina base-calling pipeline.
Raw sequencing data were first processed to filter out low-quality reads that containing more than 5 ‘N’s or over 50% of the sequence with low quality value (Phred score < 5).
The MeDIP-seq data were aligned to the UCSC pig reference genome (Sscrofa9.2, ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/), allowing up to two mismatches using SOAP2 (Version 2.21)
Methylation peaks were obtained using MACS1.4.0.
Genome_build: Sscrofa9.2
Supplementary_files_format_and_content: Wig files include peak distribution in all chromosomes of E50 and E60 tooth germ

organism: Sus scrofa

source_name: tooth germ

extract_protocol:
The last deciduous mandibular molar germs at embryonic day 50 (E50) and E60 were isolated under a microscope
MeDIP DNA libraries were constructed following the protocol

tag: developmental stage


title: Mac-24h-siCon Rep2 RNA-seq


title: Mac-24h-siPU Rep1 RNA-seq


title: E60 rep2


title: Mac-24h-siCon Rep1 RNA-seq


title: E50 rep3


title: E50 rep2


title: HL60-siCon Rep2 RNA-seq


title: HL60-siPU1 Rep1 RNA-seq


title: HL60-siPU1 Rep2 RNA-seq


title: E60 rep1


title: Mon-24h-siPU Rep2 RNA-seq


title: HL60-siCon Rep1 RNA-seq


title: Mac-24h-siPU Rep2 RNA-seq


title: 168h Monocyte-derived Mac PMA Rep2 RNA-seq

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 20 gene annotations using Cufflinks (Trapnell et al., 2010).
FPKM values were normalized for batch effects using Combat (Johnson et al., 2007).
Genome_build: hg38

source_name: Monocyte-derived Macrophage

extract_protocol: Approximately ~1-2 million HL-60 and differentiated cells were collected for RNA-seq. Briefly, cells were assessed for cell viability, counted and washed with PBS.  RNA-seq was performed as previously described (Mortazavi et al., 2008).

treatment_protocol: Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. LPS stimulation at 48, 120, and 168 hours for specific cell-types was induced at a final concentration of 100ng/ml for ~3h, immediately followed by expression analysis.


title: 144h Monocyte-derived Mac PMA Rep1 RNA-seq


title: 168h Monocyte-derived Mac PMA LPS-Rep2 RNA-seq

value: PMA+LPS


title: 168h Monocyte-derived Mac PMA Rep1 RNA-seq


title: 168h Monocyte-derived Mac PMA LPS-Rep1 RNA-seq


title: 168h Monocyte-derived Mac PMA Rep3 RNA-seq


title: 144h Monocyte-derived Mac PMA Rep2 RNA-seq


title: 132h Monocyte-derived Mac PMA Rep3 RNA-seq


title: 132h Monocyte-derived Mac PMA Rep1 RNA-seq


title: 126h Monocyte-derived Mac PMA Rep3 RNA-seq


title: 168h Monocyte-derived Mac PMA LPS-Rep3 RNA-seq


title: 144h Monocyte-derived Mac PMA Rep3 RNA-seq


title: 126h Monocyte-derived Mac PMA Rep2 RNA-seq


title: 132h Monocyte-derived Mac PMA Rep2 RNA-seq


title: 126h Monocyte-derived Mac PMA Rep1 RNA-seq


title: 123h Monocyte-derived Mac PMA Rep3 RNA-seq


title: 123h Monocyte-derived Mac PMA Rep2 RNA-seq


title: 123h Monocyte-derived Mac PMA Rep1 RNA-seq


title: 120h Monocyte LPS Rep1 RNA-seq

value: Vitamin D3+LPS


title: 120h Monocyte Rep2 RNA-seq


title: 120h Monocyte Rep3 RNA-seq


title: 120h Monocyte LPS Rep2 RNA-seq


title: 48h Monocyte Rep3 RNA-seq

value: 48 hr


title: 96h Monocyte Rep3 RNA-seq

value: 96 hr


title: 96h Monocyte Rep2 RNA-seq


title: 120h Monocyte Rep1 RNA-seq


title: 24h Monocyte Rep3 RNA-seq


title: 48h Monocyte Rep2 RNA-seq


title: 48h Monocyte Rep1 RNA-seq


title: 12h Monocyte Rep3 RNA-seq

value: 12 hr


title: 6h Monocyte Rep3 RNA-seq

value: 6 hr


title: 6h Monocyte Rep2 RNA-seq


title: 12h Monocyte Rep1 RNA-seq


title: 96h Monocyte Rep1 RNA-seq


title: 24h Monocyte Rep2 RNA-seq


title: 3h Monocyte Rep1 RNA-seq

value: 3 hr


title: 120h Neutrophil LPS Rep3 RNA-seq

value: DMSO/ATRA+LPS


title: 24h Monocyte Rep1 RNA-seq


title: 3h Monocyte Rep2 RNA-seq


title: 6h Monocyte Rep1 RNA-seq


title: E50 rep1


title: 120h Neutrophil LPS Rep2 RNA-seq


title: 120h Neutrophil  Rep3 RNA-seq


title: 96h Neutrophil  Rep2 RNA-seq


title: 120h Neutrophil LPS Rep1 RNA-seq


title: 120h Neutrophil  Rep1 RNA-seq


title: 96h Neutrophil  Rep3 RNA-seq


title: 48h Neutrophil  Rep3 RNA-seq


title: 3h Monocyte Rep3 RNA-seq


title: Human_input

source_name: Human primed PSCs and human extended PSCs, input

value: H1, H1-EPS

value: Human primed pluripotent stem cells and human extended pluripotent stem cells


title: 48h Neutrophil  Rep2 RNA-seq


title: 12h Monocyte Rep2 RNA-seq


title: H1-EPS_H3K4me3

source_name: Human extended PSCs, H3K4me3 ChIP

value: Human extended pluripotent stem cells

value: anti-H3K4me3 (Millipore, cat. no. 07-473, lot# 2152225)


title: 48h Neutrophil  Rep1 RNA-seq

value: DMSO/ATRA


title: H1-EPS_H3K27me3

source_name: Human extended PSCs, H3K27me3 ChIP

value: anti-H3K27me3 (Millipore, cat. no. 07-449, lot# 2194165)


title: 24h Neutrophil  Rep3 RNA-seq

value: 24 hr


title: 24h Neutrophil  Rep2 RNA-seq


title: H1_H3K4me3

source_name: Human primed PSCs, H3K4me3 ChIP

value: Human primed pluripotent stem cells


title: 24h Neutrophil  Rep1 RNA-seq


title: 12h Neutrophil  Rep3 RNA-seq


title: 12h Neutrophil  Rep2 RNA-seq


title: H1_H3K27me3

source_name: Human primed PSCs, H3K27me3 ChIP


title: ES1-EPS-2

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using RPKM for mouse samples and FPKM for human samples respectively.
Genome_build: hg19 for human and GRCm38/mm10 for mouse
Supplementary_files_format_and_content: Excel files include the expression values for each sample

source_name: Human extended pluripotent stem cells

growth_protocol: Human primed pluripotent stem cells were maintained in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells in conventional human embryonic stem cell medium.Human extended pluripotent stem cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or or Matrigel-coated plates.

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: ES1-EPS-1


title: 120h Neutrophil  Rep2 RNA-seq


title: 6h Neutrophil  Rep2 RNA-seq


title: 6h Neutrophil  Rep3 RNA-seq


title: 12h Neutrophil  Rep1 RNA-seq


title: 3h Neutrophil  Rep3 RNA-seq


title: 6h Neutrophil  Rep1 RNA-seq


title: 3h Neutrophil  Rep2 RNA-seq


title: 3h Neutrophil  Rep1 RNA-seq


title: 120h MacLPS-Rep3 RNA-seq


title: 120h Macrophage Rep2 RNA-seq

value: PMA


title: 120h Macrophage Rep1 RNA-seq


title: 120h Macrophage Rep3 RNA-seq


title: 120h MacLPS-Rep1 RNA-seq

value: PMA+LPS


title: 96h Macrophage Rep3 RNA-seq


title: SAM19447996

description: Mouse ID: 372; Tissue: Kidney; Treatment: Cytoxan

data_processing:
The libraries were multiplexed (five per lane) and sequenced on Illumina HiSeq2500 (Illumina) to generate 30 million of single end 50 base pair reads for each sample.
50bp Illumina single end reads were processed using the HTSeqGenie Bioconductor package (Pau and Reeder, 2014). RNA-sequencing reads were aligned to release 37 of the reference mouse genome (MGSCv37) using GSNAP (Genomic Short-read Nucleotide Alignment Program) version '2013-10-10' (Wu and Nacu, 2010). QC of RNA-seq samples after alignment resulted in removal of one naïve spleen sample and one sample treated with P505-15.
We filtered out genes with low expression, retaining genes that had at least 10 reads in at least 4 of the samples.
The Bioconductor package, DESeq2 (version 1.4.5) (Love et al., 2014), was used to normalize expression across samples and identify genes that were significantly differentially expressed using the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: Mouse 372 Kidney Cytoxan

extract_protocol:
The spleen and kidney tissues were disrupted in RLT buffer using a tissue lyser and RNA was extracted using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion. Blood RNA was isolated using Paxgene RNA isolation kit from Qiagen as per manufacturer’s instructions. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of total RNA samples was determined using NanoDrop 8000 (Thermo Scientific). The integrity of RNA samples was tested using Fragment Analyzer and High Sensitivity RNA kit (Advanced Analytical).
1ug of total RNA was input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Generated libraries were amplified with 8 cycles of PCR. Size of the libraries was confirmed using Fragment Analyzer and High Sensitivity DNA NGS kit (Advanced Analytical) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were first multiplexed (five per lane) and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30 million of single end 50 base pair reads for each sample.

treatment_protocol: The mice were treated with vehicle or Btk SMI G7744 SMI, Syk SMI, G955 SMI, anti-ragweed IgG2a, mBR3-IgG2a and cytoxan in 100ul saline for eight weeks.

value: pre-clinical mouse lupus model (NZB/W F1)

tag: mouse id

value: Kidney

tag: treatment name

value: Cytoxan


title: SAM19447971

description: Mouse ID: 398; Tissue: Kidney; Treatment: Vehicle HPMC in citrate

source_name: Mouse 398 Kidney Vehicle HPMC in citrate

value: Vehicle HPMC in citrate


title: SAM19447985

description: Mouse ID: 379; Tissue: Kidney; Treatment: Anti ragweed IgG2a

source_name: Mouse 379 Kidney Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: SAM19447935

description: Mouse ID: 381; Tissue: Spleen; Treatment: Btki

source_name: Mouse 381 Spleen Btki

value: Spleen

value: Btki


title: SAM19447951

description: Mouse ID: 373; Tissue: Spleen; Treatment: mBR3 IgG2a

source_name: Mouse 373 Spleen mBR3 IgG2a

value: mBR3 IgG2a


title: SAM19447925

description: Mouse ID: 274; Tissue: Spleen; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 274 Spleen Ad5 IFNa TD day 21

value: Ad5 IFNa TD day 21


title: SAM19447978

description: Mouse ID: 251; Tissue: Kidney; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 251 Kidney SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: SAM19447954

description: Mouse ID: 365; Tissue: Spleen; Treatment: Cytoxan

source_name: Mouse 365 Spleen Cytoxan


title: SAM19447962

description: Mouse ID: 440; Tissue: Kidney; Treatment: Naive

source_name: Mouse 440 Kidney Naive

value: Naive


title: 96h Macrophage Rep1 RNA-seq

source_name: Macrophage

value: 96 hr


title: 96h Macrophage Rep2 RNA-seq


title: SAM19447948

description: Mouse ID: 255; Tissue: Spleen; Treatment: mBR3 IgG2a

source_name: Mouse 255 Spleen mBR3 IgG2a


title: SAM19447927

description: Mouse ID: 359; Tissue: Spleen; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 359 Spleen Ad5 IFNa TD day 21


title: SAM19447968

description: Mouse ID: 267; Tissue: Kidney; Treatment: Vehicle HPMC in citrate

source_name: Mouse 267 Kidney Vehicle HPMC in citrate


title: 48h Macrophage LPS Rep3 RNA-seq

value: 48 hr


title: 48h Macrophage LPS Rep2 RNA-seq


title: 48h Macrophage LPS Rep1 RNA-seq


title: 120h MacLPS-Rep2 RNA-seq


title: SAM19447989

description: Mouse ID: 364; Tissue: Kidney; Treatment: mBR3 IgG2a

source_name: Mouse 364 Kidney mBR3 IgG2a


title: 96h Neutrophil  Rep1 RNA-seq

source_name: Neutrophil

value: DMSO/ATRA


title: SAM19447924

description: Mouse ID: 371; Tissue: Spleen; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 371 Spleen Ad5 IFNa TD day 21


title: ESCdiff_RNAseq_Day6_Mut1

data_processing:
TopHat2 was used to map the RNAseq reads to the mouse genome (mm10). The bam files from the Tophat output were used for downstream analysis using HOMER. DESeq2 was used to identify the differentially expressed genes. Heatmaps were generated using Java TreeView. K-means clustering was performed using Cluster 3.0.
For ATACseq: Paired-end 75 bp reads were trimmed to 24 bases and reads were then aligned to mm10 using Bowtie2 with the parameter -X 2000 to ensure that fragments up to 2 kb were allowed to align. Duplicates were then removed using Picard. Reads with low quality score (MAPQ < 10) and reads mapping to the mitochondrial genome were removed. Reads were separated into size classes, and only nucleosome free reads (less than 100 bp) were used for subsequent analyses. These reads were processed in HOMER. Genome browser tracks were generated from mapped reads using the “makeUCSCfile” command. Peaks were individually called from replicate datasets using the “findPeaks” command and those peaks enriched in both replicates were retained. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each bin. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, and high quality (peak score > 6) Tip60 peaks called from (Raven et al 2015). After anchoring mapped reads over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

value: untreated

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity  at day6 during differentiation


title: ESCdiff_RNAseq_Day4_Mut2

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity  at day4 during differentiation


title: SAM19447939

description: Mouse ID: 252; Tissue: Spleen; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 252 Spleen SYK SMI G955 60 mg/kg

value: pre-clinical mouse lupus model (NZB/W F1)


title: SAM19447966

description: Mouse ID: 357; Tissue: Kidney; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 357 Kidney Ad5 IFNa TD day 21

value: Kidney


title: 48h Macrophage Rep3 RNA-seq

value: PMA


title: SAM19447997

description: Mouse ID: 411; Tissue: Kidney; Treatment: Cytoxan

source_name: Mouse 411 Kidney Cytoxan

value: Cytoxan


title: 48h Macrophage Rep2 RNA-seq


title: ESCdiff_RNAseq_Day6_Mut2


title: 48h Macrophage Rep1 RNA-seq


title: SAM19447995

description: Mouse ID: 369; Tissue: Kidney; Treatment: Cytoxan

source_name: Mouse 369 Kidney Cytoxan


title: ESCdiff_RNAseq_Day0_Mut2

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity  at day0 during differentiation


title: 24h Macrophage Rep2 RNA-seq

value: 24 hr


title: 12h Macrophage Rep3 RNA-seq

value: 12 hr


title: 24h Macrophage Rep3 RNA-seq


title: ESCdiff_RNAseq_Day2_Mut2

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity  at day2 during differentiation


title: ESCdiff_RNAseq_Day4_Mut1


title: SAM19447994

description: Mouse ID: 365; Tissue: Kidney; Treatment: Cytoxan

source_name: Mouse 365 Kidney Cytoxan


title: SAM19447979

description: Mouse ID: 252; Tissue: Kidney; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 252 Kidney SYK SMI G955 60 mg/kg


title: 12h Macrophage Rep1 RNA-seq


title: 24h Macrophage Rep1 RNA-seq


title: SAM19447933

description: Mouse ID: 363; Tissue: Spleen; Treatment: Btki

source_name: Mouse 363 Spleen Btki

value: Spleen

value: Btki


title: ESCdiff_RNAseq_Day0_Mut1


title: ESCdiff_RNAseq_Day4_Rep2

value: E14 ES cells at day4 during differentiation


title: ESCdiff_RNAseq_Day6_Rep2

value: E14 ES cells at day6 during differentiation


title: SAM19447945

description: Mouse ID: 379; Tissue: Spleen; Treatment: Anti ragweed IgG2a

source_name: Mouse 379 Spleen Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: 12h Macrophage Rep2 RNA-seq


title: ESCdiff_RNAseq_Day6_Rep1


title: ESCdiff_RNAseq_Day2_Mut1


title: 6h Macrophage Rep3 RNA-seq

value: 6 hr


title: ESCdiff_RNAseq_Day4_Rep1

value: untreated


title: SAM19447946

description: Mouse ID: 382; Tissue: Spleen; Treatment: Anti ragweed IgG2a

source_name: Mouse 382 Spleen Anti ragweed IgG2a


title: ESCdiff_RNAseq_Day2_Rep2

value: E14 ES cells at day2 during differentiation


title: 6h Macrophage Rep2 RNA-seq

source_name: Macrophage


title: 3h Macrophage Rep3 RNA-seq

value: 3 hr


title: ESCdiff_RNAseq_Day2_Rep1


title: SAM19447982

description: Mouse ID: 374; Tissue: Kidney; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 374 Kidney SYK SMI G955 60 mg/kg

value: pre-clinical mouse lupus model (NZB/W F1)

value: SYK SMI G955 60 mg/kg


title: 3h Macrophage Rep2 RNA-seq

value: PMA


title: SAM19447943

description: Mouse ID: 272; Tissue: Spleen; Treatment: Anti ragweed IgG2a

source_name: Mouse 272 Spleen Anti ragweed IgG2a


title: SAM19447949

description: Mouse ID: 364; Tissue: Spleen; Treatment: mBR3 IgG2a

source_name: Mouse 364 Spleen mBR3 IgG2a

value: mBR3 IgG2a


title: SAM19447987

description: Mouse ID: 428; Tissue: Kidney; Treatment: Anti ragweed IgG2a

source_name: Mouse 428 Kidney Anti ragweed IgG2a

value: Kidney


title: ESCdiff_RNAseq_Day0_Rep2

value: E14 ES cells at day0 during differentiation


title: 6h Macrophage Rep1 RNA-seq


title: ESCdiff_RNAseq_Day0_Rep1


title: 3h Macrophage Rep1 RNA-seq


title: SAM19447986

description: Mouse ID: 382; Tissue: Kidney; Treatment: Anti ragweed IgG2a

source_name: Mouse 382 Kidney Anti ragweed IgG2a


title: HL60 Rep3 RNA-seq

value: 0 hr


title: HL60 Rep2 RNA-seq


title: SAM19447969

description: Mouse ID: 377; Tissue: Kidney; Treatment: Vehicle HPMC in citrate

source_name: Mouse 377 Kidney Vehicle HPMC in citrate

value: Vehicle HPMC in citrate


title: SAM19447942

description: Mouse ID: 374; Tissue: Spleen; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 374 Spleen SYK SMI G955 60 mg/kg

value: Spleen


title: Tip60ciEp400ciMut_RNAseq_Mut1

source_name: murine embryonic stem cells

value: Tip60 and Ep400 double mutant lacking KAT and ATPase activity


title: HL60 Rep1 RNA-seq


title: 120h Monocyte LPS Rep3 RNA-seq

source_name: Monocyte

value: Vitamin D3+LPS


title: SAM19447922

description: Mouse ID: 440; Tissue: Spleen; Treatment: Naive

source_name: Mouse 440 Spleen Naive

value: Naive


title: SAM19447955

description: Mouse ID: 369; Tissue: Spleen; Treatment: Cytoxan

source_name: Mouse 369 Spleen Cytoxan

value: Cytoxan


title: Ep400ciMut_RNAseq_Mut3

value: Ep400 mutant lacking catalytic activity


title: Tip60ciEp400ciMut_RNAseq_Mut2

value: untreated


title: Ep400ciMut_RNAseq_Mut2


title: SAM19447923

description: Mouse ID: 253; Tissue: Spleen; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 253 Spleen Ad5 IFNa TD day 21

value: Ad5 IFNa TD day 21


title: 168h Monocyte-derived Mac PMA-LPS Rep 2 ATAC-seq

data_processing:
Library strategy: ATAC-seq
ATAC-seq reads were mapped to the hg38 reference genome using bowtie (Langmead et al., 2009). Using parameters (bowtie -S --trim3 7 --chunkmbs 3000 -p 32 -m 3 -v 2 --best --strata -X 3000)
[bed]
HOMER was used to call ATAC-seq peaks. Using parameters (findPeaks Mapp.dir -size 500 -minDist 50 -fdr 0.01) and findPeaks Mapp.dir -minDist 50 -fdr 0.01 -style factor). ‘Narrow’ and ‘broad’ regions were then merged into a single bed file for each replicate.
Counts were normalized for batch effects using Combat (Johnson et al., 2007).
[bigWig]
BAM was generated from SAM file using samtools/0.1.18
BedTools genomeCoverageBed was used to convert BAM to bedGraph with hg38 chromosome sizes.
bedGraphToBigWig from UCSC was used to generate bigWig files.
Genome_build: hg38
Supplementary_files_format_and_content: bed, bigWig

source_name: Monocyte-derived Macrophage

extract_protocol: Approximately 50,000 HL-60 and differentiated cells were collected for ATAC-seq. ATAC-seq was performed as previously described (Buenrostro et al., 2013) with one amendment. DNA size exclusion was utilized after library generation to enrich for accessible chromatin ranging from 100-400bp.

value: PMA+LPS


title: 168h Monocyte-derived Mac PMA-LPS Rep 3 ATAC-seq


title: SAM19447958

description: Mouse ID: 436; Tissue: Kidney; Treatment: Naive

source_name: Mouse 436 Kidney Naive

value: pre-clinical mouse lupus model (NZB/W F1)


title: SAM19447991

description: Mouse ID: 373; Tissue: Kidney; Treatment: mBR3 IgG2a

source_name: Mouse 373 Kidney mBR3 IgG2a


title: Ep400ciMut_RNAseq_Mut1


title: Ep400hypo_RNAseq_Rep2

value: Ep400 mutant lacking ATPase domain


title: 168h Monocyte-derived Mac PMA-LPS Rep 1 ATAC-seq


title: 168h Monocyte-derived Mac PMA Rep 2 ATAC-seq

value: PMA


title: SAM19447953

description: Mouse ID: 358; Tissue: Spleen; Treatment: Cytoxan

source_name: Mouse 358 Spleen Cytoxan


title: 168h Monocyte-derived Mac PMA Rep 3 ATAC-seq


title: Ep400hypo_RNAseq_Rep1


title: SAM19447983

description: Mouse ID: 272; Tissue: Kidney; Treatment: Anti ragweed IgG2a

source_name: Mouse 272 Kidney Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: Tip60ciEp400ciMut_RNAseq_Mut3


title: WT_RNAseq_Rep2

value: E14 ES cells


title: Tip60ciMut_RNAseq_Mut1

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity


title: 144h Monocyte-derived Mac PMA Rep 2 ATAC-seq


title: SAM19447928

description: Mouse ID: 267; Tissue: Spleen; Treatment: Vehicle HPMC in citrate

source_name: Mouse 267 Spleen Vehicle HPMC in citrate


title: WT_RNAseq_Rep1


title: Tip60fl/+_RNAseq_Rep2

value: Tip60fl/+ ES cells


title: 132h Monocyte-derived Mac PMA Rep 3 ATAC-seq


title: 168h Monocyte-derived Mac PMA Rep 1 ATAC-seq


title: SAM19447975

description: Mouse ID: 381; Tissue: Kidney; Treatment: Btki

source_name: Mouse 381 Kidney Btki

value: Kidney

value: Btki


title: SAM19447974

description: Mouse ID: 376; Tissue: Kidney; Treatment: Btki

source_name: Mouse 376 Kidney Btki


title: 144h Monocyte-derived Mac PMA Rep 1 ATAC-seq


title: SAM19447972

description: Mouse ID: 399; Tissue: Kidney; Treatment: Vehicle HPMC in citrate

source_name: Mouse 399 Kidney Vehicle HPMC in citrate

value: Vehicle HPMC in citrate


title: Tip60KD_RNAseq_Rep2

value: lentivirus for the Tip60 knockdown


title: SAM19447947

description: Mouse ID: 428; Tissue: Spleen; Treatment: Anti ragweed IgG2a

source_name: Mouse 428 Spleen Anti ragweed IgG2a

value: Spleen


title: 132h Monocyte-derived Mac PMA Rep 2 ATAC-seq


title: 132h Monocyte-derived Mac PMA Rep 1 ATAC-seq


title: Tip60fl/+_Tip60ciRNAseq_Rep1


title: Tip60KD_RNAseq_Rep1


title: SAM19447938

description: Mouse ID: 251; Tissue: Spleen; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 251 Spleen SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: SAM19447957

description: Mouse ID: 411; Tissue: Spleen; Treatment: Cytoxan

source_name: Mouse 411 Spleen Cytoxan

value: Cytoxan


title: 126h Monocyte-derived Mac PMA Rep 3 ATAC-seq


title: Tip60ciMut_RNAseq_Mut2

source_name: murine embryonic stem cells

value: untreated


title: EGFPKD_RNAseq_Rep2

value: lentivirus for the contol knockdown


title: SAM19447988

description: Mouse ID: 255; Tissue: Kidney; Treatment: mBR3 IgG2a

source_name: Mouse 255 Kidney mBR3 IgG2a

value: mBR3 IgG2a


title: SAM19447930

description: Mouse ID: 391; Tissue: Spleen; Treatment: Vehicle HPMC in citrate

source_name: Mouse 391 Spleen Vehicle HPMC in citrate

value: pre-clinical mouse lupus model (NZB/W F1)


title: 144h Monocyte-derived Mac PMA Rep 3 ATAC-seq


title: EGFPKD_RNAseq_Rep1


title: 126h Monocyte-derived Mac PMA Rep 1 ATAC-seq


title: SAM19447973

description: Mouse ID: 363; Tissue: Kidney; Treatment: Btki

source_name: Mouse 363 Kidney Btki


title: 123h Monocyte-derived Mac PMA Rep 2 ATAC-seq


title: SAM19447952

description: Mouse ID: 386; Tissue: Spleen; Treatment: mBR3 IgG2a

source_name: Mouse 386 Spleen mBR3 IgG2a


title: 123h Monocyte-derived Mac PMA Rep 3 ATAC-seq

source_name: Monocyte-derived Macrophage


title: SAM19447964

description: Mouse ID: 371; Tissue: Kidney; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 371 Kidney Ad5 IFNa TD day 21

value: Ad5 IFNa TD day 21


title: SAM19447959

description: Mouse ID: 437; Tissue: Kidney; Treatment: Naive

source_name: Mouse 437 Kidney Naive

value: Naive


title: SAM19447993

description: Mouse ID: 358; Tissue: Kidney; Treatment: Cytoxan

source_name: Mouse 358 Kidney Cytoxan


title: 123h Monocyte-derived Mac PMA Rep 1 ATAC-seq

value: PMA


title: SAM19447936

description: Mouse ID: 389; Tissue: Spleen; Treatment: Btki

source_name: Mouse 389 Spleen Btki


title: 120h Monocyte LPS Rep 1 ATAC-seq

source_name: Monocyte

value: Vitamin D3+LPS


title: SAM19447990

description: Mouse ID: 367; Tissue: Kidney; Treatment: mBR3 IgG2a

source_name: Mouse 367 Kidney mBR3 IgG2a


title: 120h Monocyte LPS Rep 3 ATAC-seq


title: 120h Monocyte LPS Rep 2 ATAC-seq


title: SAM19447980

description: Mouse ID: 268; Tissue: Kidney; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 268 Kidney SYK SMI G955 60 mg/kg


title: SAM19447981

description: Mouse ID: 356; Tissue: Kidney; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 356 Kidney SYK SMI G955 60 mg/kg


title: 120h Monocyte Rep 2 ATAC-seq

value: Vitamin D3


title: 126h Monocyte-derived Mac PMA Rep 2 ATAC-seq


title: SAM19447992

description: Mouse ID: 386; Tissue: Kidney; Treatment: mBR3 IgG2a

source_name: Mouse 386 Kidney mBR3 IgG2a


title: SAM19447921

description: Mouse ID: 439; Tissue: Spleen; Treatment: Naive

source_name: Mouse 439 Spleen Naive


title: 120h Monocyte Rep 1 ATAC-seq


title: 96h Monocyte Rep 3 ATAC-seq

value: 96 hr


title: SAM19447965

description: Mouse ID: 274; Tissue: Kidney; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 274 Kidney Ad5 IFNa TD day 21

value: Kidney


title: 96h Monocyte Rep 1 ATAC-seq


title: 48h Monocyte Rep 3 ATAC-seq

value: 48 hr


title: SAM19447931

description: Mouse ID: 398; Tissue: Spleen; Treatment: Vehicle HPMC in citrate

source_name: Mouse 398 Spleen Vehicle HPMC in citrate

value: Vehicle HPMC in citrate


title: 96h Monocyte Rep 2 ATAC-seq


title: 48h Monocyte Rep 2 ATAC-seq


title: 48h Monocyte Rep 1 ATAC-seq


title: 24h Monocyte Rep 3 ATAC-seq

value: 24 hr


title: SAM19447920

description: Mouse ID: 438; Tissue: Spleen; Treatment: Naive

source_name: Mouse 438 Spleen Naive

value: Spleen


title: SAM19447932

description: Mouse ID: 399; Tissue: Spleen; Treatment: Vehicle HPMC in citrate

source_name: Mouse 399 Spleen Vehicle HPMC in citrate


title: 24h Monocyte Rep 1 ATAC-seq


title: SAM19447976

description: Mouse ID: 389; Tissue: Kidney; Treatment: Btki

source_name: Mouse 389 Kidney Btki

value: Btki


title: 12h Monocyte Rep 3 ATAC-seq

value: 12 hr


title: 120h Monocyte Rep 3 ATAC-seq


title: SAM19447929

description: Mouse ID: 377; Tissue: Spleen; Treatment: Vehicle HPMC in citrate

source_name: Mouse 377 Spleen Vehicle HPMC in citrate


title: 12h Monocyte Rep 1 ATAC-seq


title: SAM19447960

description: Mouse ID: 438; Tissue: Kidney; Treatment: Naive

source_name: Mouse 438 Kidney Naive


title: 6h Monocyte Rep 3 ATAC-seq

value: 6 hr


title: SAM19447977

description: Mouse ID: 414; Tissue: Kidney; Treatment: Btki

source_name: Mouse 414 Kidney Btki


title: 6h Monocyte Rep 2 ATAC-seq


title: SAM19447963

description: Mouse ID: 253; Tissue: Kidney; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 253 Kidney Ad5 IFNa TD day 21


title: 6h Monocyte Rep 1 ATAC-seq


title: SAM19447956

description: Mouse ID: 372; Tissue: Spleen; Treatment: Cytoxan

source_name: Mouse 372 Spleen Cytoxan

value: Cytoxan


title: SAM19447967

description: Mouse ID: 359; Tissue: Kidney; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 359 Kidney Ad5 IFNa TD day 21


title: SAM19447926

description: Mouse ID: 357; Tissue: Spleen; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 357 Spleen Ad5 IFNa TD day 21


title: SAM19447919

description: Mouse ID: 437; Tissue: Spleen; Treatment: Naive

source_name: Mouse 437 Spleen Naive


title: 3h Monocyte Rep 3 ATAC-seq

source_name: Monocyte

value: 3 hr


title: SAM19447950

description: Mouse ID: 367; Tissue: Spleen; Treatment: mBR3 IgG2a

source_name: Mouse 367 Spleen mBR3 IgG2a

value: pre-clinical mouse lupus model (NZB/W F1)

value: mBR3 IgG2a


title: 3h Monocyte Rep 2 ATAC-seq


title: SAM19447984

description: Mouse ID: 273; Tissue: Kidney; Treatment: Anti ragweed IgG2a

source_name: Mouse 273 Kidney Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: 3h Monocyte Rep 1 ATAC-seq


title: SAM19447934

description: Mouse ID: 376; Tissue: Spleen; Treatment: Btki

source_name: Mouse 376 Spleen Btki


title: 12h Monocyte Rep 2 ATAC-seq


title: DLYM-1118_PD01_valspodar_Pre

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v0.33) with the optional "--qualitycontrol" option; 3bp sliding-window trimming from 3' end requiring minimum Q16).
A HISAT2 index for the canine reference genome  (canFam3) was used for mapping sequences with the HISAT2 aligner (2.0.2-beta) using default parameters. After mapping each bam file was sorted and indexed.
Insert size metrics calculated for each sample usng Picard.
Abundance files were generated with Cuffquant (Cufflinks (v2.2.1)).
Cuffnorm used to generate a table of FPKM expression data using the classic-fpkm normalization method.
Genome_build: canFam3
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

organism: Canis lupus familiaris

source_name: lymphoma

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits

treatment_protocol: Lymph node biopsy samples were obtained from dogs newly diagnosed with diffuse large B-cell lymphoma. Dogs were then randomized to receive oral valspodar(7.5 mg/kg) or placebo twice a day for 4 days, at which time lymph node biopsies were obtained again prior to initiation of doxorubicin chemotherapy. The goal was to determine potential effects of ABC transporter inhibition on overall gene expression by lymphoma cells, and specifically on the possibility to detect alterations in gene expression of rare CD34+/CD117+ lymphoid progenitor cells.

tag: treatment group

value: valspodar

tag: time of sample

value: pre-treatment

tag: breed

value: English Bulldog

tag: gender (neuter status)

value: F(S)

tag: age (yr)

tag: duration of remission (days)

value: NR

tag: overall surival (days)


title: DLYM-1118_PD01_valspodar_Post

value: post-treatment


title: 120h Neutrophil LPS Rep 3 ATAC-seq

source_name: Neutrophil

value: DMSO/ATRA+LPS


title: DLYM-1121_MN05_placebo_Pre

value: placebo

value: Vizsla


title: 24h Monocyte Rep 2 ATAC-seq

value: Vitamin D3

value: 24 hr


title: SAM19447970

description: Mouse ID: 391; Tissue: Kidney; Treatment: Vehicle HPMC in citrate

source_name: Mouse 391 Kidney Vehicle HPMC in citrate

tag: strain

tag: primary tissue

value: Kidney

value: Vehicle HPMC in citrate


title: SAM19447944

description: Mouse ID: 273; Tissue: Spleen; Treatment: Anti ragweed IgG2a

source_name: Mouse 273 Spleen Anti ragweed IgG2a

value: Spleen


title: SAM19447941

description: Mouse ID: 356; Tissue: Spleen; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 356 Spleen SYK SMI G955 60 mg/kg

value: pre-clinical mouse lupus model (NZB/W F1)

value: SYK SMI G955 60 mg/kg


title: 120h Neutrophil LPS Rep 2 ATAC-seq


title: 120h Neutrophil LPS Rep 1 ATAC-seq


title: SAM19447937

description: Mouse ID: 414; Tissue: Spleen; Treatment: Btki

source_name: Mouse 414 Spleen Btki

value: Btki


title: SAM19447961

description: Mouse ID: 439; Tissue: Kidney; Treatment: Naive

source_name: Mouse 439 Kidney Naive

value: Naive


title: DLYM-1115_PENN03_valspodar_Post

value: valspodar

value: Labrador Retriver

value: M(N)


title: 120h Neutrophil Rep 3 ATAC-seq

value: DMSO/ATRA


title: 96h Neutrophil Rep 3 ATAC-seq

value: 96 hr


title: DLYM-1121_MN05_placebo_Post

value: post-treatment

value: F(S)


title: SAM19448036

description: Mouse ID: 372; Tissue: Blood; Treatment: Cytoxan

source_name: Mouse 372 Blood Cytoxan

value: Blood

value: Cytoxan


title: DLYM-1115_PENN03_valspodar_Pre

value: pre-treatment


title: 96h Neutrophil Rep 1 ATAC-seq


title: 120h Neutrophil Rep 2 ATAC-seq


title: SAM19448037

description: Mouse ID: 411; Tissue: Blood; Treatment: Cytoxan

source_name: Mouse 411 Blood Cytoxan


title: SAM19448027

description: Mouse ID: 428; Tissue: Blood; Treatment: Anti ragweed IgG2a

source_name: Mouse 428 Blood Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: DLYM-1109_MN06_valspodar_Pre

value: Golden Retriever


title: 48h Neutrophil Rep 3 ATAC-seq

value: 48 hr


title: SAM19448008

description: Mouse ID: 267; Tissue: Blood; Treatment: Vehicle HPMC in citrate

source_name: Mouse 267 Blood Vehicle HPMC in citrate

value: pre-clinical mouse lupus model (NZB/W F1)

value: Vehicle HPMC in citrate


title: SAM19448018

description: Mouse ID: 251; Tissue: Blood; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 251 Blood SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: SAM19448016

description: Mouse ID: 389; Tissue: Blood; Treatment: Btki

source_name: Mouse 389 Blood Btki

value: Btki


title: SAM19448006

description: Mouse ID: 357; Tissue: Blood; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 357 Blood Ad5 IFNa TD day 21

value: Ad5 IFNa TD day 21


title: SAM19575180

description: Mouse ID: 360; Tissue: Blood; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 360 Blood Ad5 IFNa TD day 21


title: SAM19575187

description: Mouse ID: 417; Tissue: Blood; Treatment: Vehicle HPMC in citrate

source_name: Mouse 417 Blood Vehicle HPMC in citrate


title: DLYM-1120_PENN05_placebo_Pre

value: placebo

value: Vizsla

value: M(I)


title: 120h Neutrophil Rep 1 ATAC-seq

value: DMSO/ATRA


title: 24h Neutrophil Rep 3 ATAC-seq

value: 24 hr


title: DLYM-1109_MN06_valspodar_Post

value: valspodar

value: post-treatment

value: M(N)


title: 24h Neutrophil Rep 2 ATAC-seq


title: 48h Neutrophil Rep 2 ATAC-seq


title: DLYM-1108_MN02_valspodar_Post


title: DLYM-1203_MN07_valspodar_Pre

value: pre-treatment

value: F(S)


title: SAM19575189

description: Mouse ID: 432; Tissue: Blood; Treatment: Vehicle HPMC in citrate

source_name: Mouse 432 Blood Vehicle HPMC in citrate

value: Blood


title: 96h Neutrophil Rep 2 ATAC-seq

value: 96 hr


title: SAM19575188

description: Mouse ID: 418; Tissue: Blood; Treatment: Vehicle HPMC in citrate

source_name: Mouse 418 Blood Vehicle HPMC in citrate

value: pre-clinical mouse lupus model (NZB/W F1)


title: SAM19448007

description: Mouse ID: 359; Tissue: Blood; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 359 Blood Ad5 IFNa TD day 21


title: DLYM-1203_MN07_valspodar_Post

source_name: lymphoma

value: Golden Retriever


title: SAM19448028

description: Mouse ID: 255; Tissue: Blood; Treatment: mBR3 IgG2a

source_name: Mouse 255 Blood mBR3 IgG2a

value: mBR3 IgG2a


title: DLYM-1116_MN03_valspodar_Pre

value: Labrador Retriver


title: 12h Neutrophil Rep 3 ATAC-seq

source_name: Neutrophil

value: 12 hr


title: 12h Neutrophil Rep 2 ATAC-seq


title: SAM19448022

description: Mouse ID: 374; Tissue: Blood; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 374 Blood SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: DLYM-1108_MN02_valspodar_Pre

value: Vizsla


title: SAM19447998

description: Mouse ID: 436; Tissue: Blood; Treatment: Naive

source_name: Mouse 436 Blood Naive

value: Naive


title: DLYM-1116_MN03_valspodar_Post


title: DLYM-1208_MN09_placebo_Pre

value: placebo


title: DLYM-1208_MN09_placebo_Post


title: 6h Neutrophil Rep 3 ATAC-seq

value: DMSO/ATRA

value: 6 hr


title: DLYM-1206_PD03_valspodar_Pre

value: valspodar


title: 48h Neutrophil Rep 1 ATAC-seq

value: 48 hr


title: DLYM-1120_PENN05_placebo_Post

value: post-treatment

value: M(I)


title: 12h Neutrophil Rep 1 ATAC-seq


title: DLYM-1206_PD03_valspodar_Post

value: F(S)


title: 6h Neutrophil Rep 2 ATAC-seq


title: 6h Neutrophil Rep 1 ATAC-seq


title: 24h Neutrophil Rep 1 ATAC-seq

value: 24 hr


title: SAM19448033

description: Mouse ID: 358; Tissue: Blood; Treatment: Cytoxan

source_name: Mouse 358 Blood Cytoxan

value: pre-clinical mouse lupus model (NZB/W F1)

value: Blood

value: Cytoxan


title: DLYM-1209_MN10_valspodar_Pre

value: pre-treatment

value: Standard Poodle

value: M(N)


title: 3h Neutrophil Rep 3 ATAC-seq

value: 3 hr


title: SAM19448002

description: Mouse ID: 440; Tissue: Blood; Treatment: Naive

source_name: Mouse 440 Blood Naive

value: Naive


title: SAM19448020

description: Mouse ID: 268; Tissue: Blood; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 268 Blood SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: 3h Neutrophil Rep 1 ATAC-seq

value: DMSO/ATRA


title: DLYM-1209_MN10_valspodar_Post


title: 3h Neutrophil Rep 2 ATAC-seq