title: MB002 CPD mut Dox 8h

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

description:
MB002 Sox9-T236/240A treated with 100 ng/ml doxycycline in triplicates for 8h.
Processed data file: Expression_data_MB002_dox.tsv

data_processing:
All RNA sequence reads were mapped against the human genome assembly GRCh37/hg19 using STAR v2.4.0 in a two-step approach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016.
Unmapped reads were realigned using Bowtie2 v2.2 and default parameters.
Duplicate reads were removed with Piccard v1.127 and default parameters.
The transcriptome were assembled and the expression profile quantified with Cufflinks v2.2.1 and default parameters.
Comparison of transcriptomes and their expression levels were performed using Cuffcompare and Cuffdiff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Expression_data_MB002_dox.tsv: A tab-delimited text file with FPKM values for each sample.

source_name: MB002 medulloblastoma cells, Sox9-T236/240A

growth_protocol: MB002 were maintained in culture media made up of 1:1 (v/v) DMEM/F-12 (Gibco) and Neurobasal -A media (Gibco, #10888-022) supplemented with HEPES, sodium pyruvate, non-essential amino acid, L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, Heparin, and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer's recommendations.
RNA-Seq libraries were prepared for sequencing using standard Ion-Torrent protocols.

treatment_protocol: MB002 were treated with 100 ng/mL doxycycline in the regular propagation culture medium (described above) for 8 hours prior to being collected for extraction.

value: Medulloblastoma cell line

tag: transduction


title: MB002 EV Dox 8h

status: Public on Sep 13 2016

type: SRA

country: Sweden

description:
MB002 Empty Vector treated with 100 ng/ml doxycycline in triplicates for 8h.
Processed data file: Expression_data_MB002_dox.tsv

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: MB002 medulloblastoma cells, empty vector

tag: cell line

tag: cell type

value: Empty vector


title: MB002 Sox9 Dox 8h

description:
MB002 Sox9 wild type treated with 100 ng/ml doxycycline in triplicates for 8h.
Processed data file: Expression_data_MB002_dox.tsv

source_name: MB002 medulloblastoma cells, Sox9 WT

value: Sox9 wild type


title: 9267X13_tumor

status: Public on Sep 12 2016

city: Salt Lake City

first: Rodney

last: Stewart

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

country: USA

institute: University of Utah

data_processing:
USeq’s MakeTranscriptome (v8.8.8) application was used to create all possible splice junction sequences using ensemble transcript annotations.
A novoalign (v2.08.01) index was created using the combination of the splice junction sequences and zv10 genomic sequence.
Reads were aligned to the reference using Novoalign, allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.
The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application, which counts the number of alignments to each gene
Differential expression analysis was generated on the count data with DESeq2 using default settings
Genome_build: zv10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts, FPKM values, log2FC and FDR values

organism: Danio rerio

source_name: brain tumor

growth_protocol: Control and tumor-bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit.
Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA-Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.

treatment_protocol: Normal brain and brain tumors were dissected from zebrafish, briefly submerged in RNAlater, snap frozen in liquid nitrogen, and stored at -80C. To extract RNA, samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.

tag: tissue

value: brain tumor


title: 9267X8_tumor


title: 9267X6_tumor


title: 9267X7_tumor


title: 9267X15_control

source_name: whole zebrafish brain

value: normal brain


title: 9267X5_tumor


title: 9267X10_control


title: 9267X9_control


title: 9267X11_control


title: DSG_sup-1 [S. pombe]

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

library_source: genomic

data_processing:
Library strategy: Micro-C XL
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to reference genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate contact matrix.
Genome_build: S288C (sacCer3) or S. pombe 972h- (ASM294v2)
Supplementary_files_format_and_content: Interaction_density.xlsx

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Yeast

growth_protocol: The 100mL yeast cultures were grown to midlog phase ~OD 0.55 in indicated media at 30 C.

extract_protocol:
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~10-13 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina Nextseq 500 paired end sequencing with 40 x 40 bp reads.

treatment_protocol: 1) Protocol for formaldehyde only: Yeast cells were fixed with 3% formaldehyde for 15 min and quenched with 125 mM glycine for 5 min. Cells were pelleted, spheroplasted with Zymolyase, and treated with a level of MNase yielding >95% mononucleosomes. 2) Protocol for long crosslinking: Yeast cells were fixed with 3% formaldehyde for 10 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted and spheroplasted with Zymolyase. The spheroplasts were washed by PBS, subjected to long-crosslinker fixation for 40min, and quenched with 250 mM glycine for 5 min. Cells were pelleted again, washed with PBS, and treated with a level of MNase yielding >95% mononucleosomes. After stopping MNase, chromatin pellet and supernatant was dephosphorylated using rSAP separately. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Chromatin was diluted into 2.5 mL and treated with T4 DNA ligase. Ligated products were treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated at 65 C overnight.

tag: strain

tag: media

value: Compromised Media

tag: first fixation

value: 1% Formaldehyde for 10 min

tag: second fixation

value: 3mM DSG for 40min


title: 9267X4_control


title: 9267X3_control


title: 9267X2_control


title: 9267X1_control


title: MCF7controlcell

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

data_processing: Each library was indexed in order to multiplex four samples per sequencing run on the Illumina MiSeq platform using MiSeq 50 cycle Reagent Kits v2. A minimum of 17 million 50bp sequencing reads were collected from each sample and data were analyzed using Genesifter software (formerly Geospiza) (PerkinElmer, Santa Clara CA). Raw data for each sample were aligned to the most recent mirBASE database (mirBase.org [17]) with remaining reads aligned to the most recent human genome (hg18 build [18]) build in order to identify previously unknown regions that may encode for unique miRNAs. Pairwise comparison of the alignment results was done using Genesifter for identification of miRNAs that are differentially expressed at a significant level, i.e. up- or down-regulated.

source_name: MCF7 breast cancer cells

growth_protocol: The human mammary epithelial cell line MCF10A, and breast cancer cell lines MCF7 and MDA-MB-231 were obtained from the American Type Culture Collection (Manassas, VA). MCF10A cells were cultured in DMEM/F12 medium supplemented with 5% exosome-depleted horse serum, 20ng/ml epithelial growth factor, 0.5mg/ml hydrocortisone, 100ng/ml cholera toxin, 10 μg/ml insulin, 100 IU/mL penicillin and 100 μg/mL streptomycin. MCF7 and MDA-MB-231 cells were cultivated in DMEM medium supplemented with 10% exosome-depleted fetal bovine serum (FBS), 100 IU/mL penicillin and 100 μg/mL streptomycin (Corning/Mediatech, Inc. Manassas, VA). Exosome-depleted FBS and horse serum were prepared by pelleting the serum exosomes by ultracentrifugation at 100,000 x g for 2 h at 4°C, and the resulting supernatant was filtered through a 0.2 μm pore filter. Cells were routinely maintained in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
Exosomes were isolated utilizing a combination of centrifugation, ultracentrifugation, and filtration as we have previously described [16] or with the Exoquick-TC reagent (System Biosciences, Mountain View, CA) following the manufacturer’s protocol. For ultracentrifugation isolation, conditioned cell culture media was collected and centrifuged at 10,000 x g for 30 min at 4°C, to remove cells and large debris. The supernatant was filtered using a 0.22-μm pore filter and the exosomes were pelleted at 100,000 x g for 1 h at 4°C. The exosome pellet was washed with 10 ml of 1X PBS and pelleted again by centrifugation at 100,000 x g for 1 h at 4°C. The resulting pellet was either suspended in 1X PBS for whole exosome applications or further processed for RNA or protein extraction. Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).
Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.

value: breast cancer


title: MCF7controlexosome


title: MDA-MB-231-control-exosome

source_name: MDA-MB-231 breast cancer cells


title: MDA-MB-231control-cell


title: MCF10controlcell

source_name: MCF10A cells

value: normal mammary epithelial


title: 9267X14_tumor


title: MCF10controlexosome


title: 9267X12_tumor


title: Males rep2

city: Tempe

first: R. Taylor

last: Raborn

state: AZ

address: 727 E Tyler St

department: Center for Mechanisms of Evolution

institute: Arizona State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and de-multiplexed using the FASTX Toolkit (fastx_barcode_splitter.pl; http://hannonlab.cshl.edu/fastx_toolkit/). Reads from each sample were iteratively mapped to the D. pulex Dappu1 nuclear genome assembly using bwa aln 0.6.2-r126 with parameters -t16 -B 3 -n 3 followed by bwa samse. Barcodes (3nt) were removed from reads prior to upload using the FASTX Toolkit (fastx_trimmer).
Ribosomal RNA reads (28S, 18S and 5S) were removed by rRNAdust (fantom.gsc.riken.jp/5/suppl/rRNAdust/).
CAGE-dectected TSSs (CTSSs) from each sample were normalized by fitting the data to a power-law distribution (Balwierz et al.,2009) using CAGEr (Haberle et al., 2015).
Abundance measurments of CTSSs in raw counts and tags per million (tpm) from each sample were made using CAGEr (Haberle et al., 2015).
Genome_build: Dappu1 (http://genome.jgi.doe.gov/Dappu1/Dappu1.home.html)
Supplementary_files_format_and_content: tab-delimited abundance files include the coordinates of CTSSs and their normalized abundance in tags per million (tpm)

organism: Daphnia pulex

source_name: Males_whole carcass

growth_protocol: Females were maintained in 3L containers containing COMBO media diluted 1:1 with H2O at 20C. All females were fed Scenedesmus at approximately 100,000 cells/mL. New offspring were removed from the containers daily and transferred to new containers. Males, asexual females and sexual females were isolated from culture seperately using differentially-sized strainers and visual identification under a dissecting microscope.

extract_protocol:
Collections of whole D. pulex individuals (~50-75) were homogenized using a small pestle in microcentrifuge tubes containing lysis buffer. Total RNA was isolated using solid phase extraction (Bioline, Inc.). Each sample was then snap-frozen in liquid nitrogen and stored at -80C.
Library construction utilized the nAnT-iCAGE protocol (Murata et al., 2014). Briefly, first-strand reverse transcription was performed with total RNA from each sample using a random primer (N6 plus 3). The 5' m7G cap was oxidized (with sodium peroxide) and biotinylated using biotin (long arm) hydrazide. Biotinylated RNA/cDNA hybrid molecules were pulled down using magnetic streptavadin beads. After RNase-treatment of captured hybrids, a barcoded linker oligo was ligated to the 5' end of the cDNA molecules, follwed by ligation of a 3' linker. Second-strand synthesis was completed using primers that anneal to the 5' linker and anchor primer, creating the final dsDNA product.

tag: clone

tag: developmental stage

value: Adult males

tag: age

value: 8 days (±1)

value: Whole carcass


title: Males rep1


title: Sexual Females rep1

source_name: Sexual Females_whole carcass

value: Pre-ephipial females


title: Sexual Females rep2


title: esiRNA Targeting PNLDC1 2

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description: rRNA an small RNA(<200nt) depleted Total RNA

data_processing:
Fastq files converted to Sanger format
Fastq files in Sanger format converted to Fasta
The reads were aligned on the whole sequence of mouse genome  using TopHat
Changes in gene expression profiles were determined using  Cuffdiff
Genome_build: Mus musculus: mm10 GRCm38.p4

organism: Mus musculus

source_name: E14 embryonic stem cells

growth_protocol: Mouse E14 ESC cells were cultured in GMEM BHK–12 (Gibco) supplemented with 10% ES Cell Qualified FBS, 2 mM GlutaMAX, MEM nonessential amino acids, βME (Gibco), tylosin,  1% Pen/Strep (Gibco)  and 100 U/mL Leukemia Inhibitory Factor (LIF; ESGRO, Chemicon) on 0.2% gelatin–coated dishes (Gibco). Cells were maintained at 37 °C in a humidified atmosphere of 5% CO2

extract_protocol:
Total RNA was extracted using the RNAqueous-4PCR Kit (Ambion)
Library construction was performed using the using the Ion OneTouch 200 template kit v2

treatment_protocol: Lipofectamine® RNAiMAX Transfection Reagent (Invitrogen) was used to transfect the cells with the esiRNAs targeting PNLDC1 or LUC according to the manufacturer’s instructions


title: Sexual Females rep3


title: esiRNA Targeting Luc 2


title: esiRNA Targeting PNLDC1 1


title: Asexual Females rep3

source_name: Asexual Females_whole carcass


title: esiRNA Targeting Luc 1


title: Asexual Females rep2


title: Asexual Females rep1


title: MonkeyPeripheralRetina-2 27

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

description:
Isolated retina mRNA
Monkey_PeripheralRetina-2

data_processing:
Prepared libraries of Macaca fasicularis were sequenced by paired-end sequencing with the Illumina Genome Analyzer IIx or HiScan SQ. Data for Macaca fasicularis were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA) rhesus (rheMac3) genome assembly and transcript annotations, respectively, using the Genomic Short-read Nucleotide Alignment Program (GSNAP), manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation of RPKM statistics by gene.
Genome_build: rheMac3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

organism: Macaca fascicularis

source_name: WT Monkey Peripheral Retina 2

extract_protocol: Library preparation for isolated eye and retinal tissue in RNALater, obtained macaque species, was performed similarly to that used for rodent tissues except for the larger scale homogenization required. Macaque samples were each prepared from one eye. Biological replicates were prepared for Macaca fasicularis eye and retina samples.

value: WT

value: Peripheral Retina

tag: genotype

value: Wild Type


title: MonkeyCentralRetina-4 23

description:
Isolated retina mRNA
Monkey_CentralRetina-4

source_name: WT Monkey Central Retina 4

value: Central Retina


title: ChIPSeq-nullMUT-L1-STAT5A

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

description: ChIP-seq

data_processing:
ChIP-seq signals were trimmed using trimmomatic (Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014)) to filter low-quality reads.
ChIP-seq reads were aligned to the mm10 genome assembly using the Bowtie aligner with -m 1 parameter (Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25).
BedGraph files were generated using Homer (Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010)).
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files

source_name: Mammary

growth_protocol: Wild type (Stat5+/+), heterozygous for the Stat5 locus (Stat5+/-), homozygous for the Stat5 enhancer mutation (Stat5∆E/∆E) and carrying one Stat5-null allele and one mutant allele (Stat5∆E/-) were generated by crossing mixed background (B6, 129 and FVN/N). Genotyping was confirmed by PCR followed by the DNA sequencing using genomic DNAs from a tail snip. All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Disaeses Animal Care and Use Committee.

extract_protocol:
Frozen-stored mammary tissues were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors).  Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), H3K27ac (Abcam, Ab4729), STAT3 (Santa Cruz, sc-482) were used for ChIP-seq.
Libraries were prepared for sequencing using standard Illumina protocols.

value: mixed

value: Mammary gland

tag: state

value: lactation day one

value: one Stat5-null allele and one mutant allele (Stat5deltaE/-)

tag: chip antibody

value: STAT5A (Santa Cruz, sc-1081x)


title: MonkeyPeripheralRetina-1 25

description:
Isolated retina mRNA
Monkey_PeripheralRetina-1

source_name: WT Monkey Peripheral Retina 1


title: ChIPSeq-nullMUT-L1-H3K27ac

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: MonkeyPeripheralRetina-3 29

description:
Isolated retina mRNA
Monkey_PeripheralRetina-3

source_name: WT Monkey Peripheral Retina 3


title: ChIPSeq-MUT-I24-H3K27ac-rep2

description: ChIP-seq

value: involution 24 hours

value: homozygous for the Stat5 enhancer mutation (Stat5deltaE/deltaE)


title: MonkeyCentralRetina-3 21

description:
Isolated retina mRNA
Monkey_CentralRetina-3

source_name: WT Monkey Central Retina 3


title: GEK124

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Vernicia fordii

source_name: mature seed

growth_protocol: fruits from V. fordii plants growth in an open environment were collected at 80-120 (mature seeds) days after flower opening (DAF). Seeds were dissected from fruits and immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing by Illumina HiSeq2000. Three libraries were generated from immature, intermediate and mature seeds. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: pool

tag: daf

value: seeds


title: MonkeyRetina-2 15

description:
Isolated retina mRNA
Monkey_Retina-2

source_name: WT Monkey Retina 2

value: Whole Retina


title: MonkeyCentralRetina-2 19

description:
Isolated retina mRNA
Monkey_CentralRetina-2

source_name: WT Monkey Central Retina 2


title: ChIPSeq-MUT-I12-H3K27ac-rep2

description: ChIP-seq

value: involution 12 hours


title: ChIPSeq-MUT-I24-H3K27ac-rep1

description: ChIP-seq


title: ChIPSeq-MUT-I12-H3K27ac-rep1

description: ChIP-seq


title: MonkeyCentralRetina-1 17

description:
Isolated retina mRNA
Monkey_CentralRetina-1

source_name: WT Monkey Central Retina 1


title: ChIPSeq-MUT-I24-STAT5A-rep2

description: ChIP-seq


title: ChIPSeq-MUT-L1-H3K27ac-rep1

description: ChIP-seq


title: MonkeyRetina-2 13

description:
Isolated retina mRNA
Monkey_Retina-2


title: ChIPSeq-MUT-L1-H3K27ac-rep2

description: ChIP-seq


title: MonkeyRetina-1 11

description:
Isolated retina mRNA
Monkey_Retina-1

source_name: WT Monkey Retina 1


title: ChIPSeq-MUT-I24-STAT5A-rep1

description: ChIP-seq


title: ChIPSeq-MUT-I12-STAT5A-rep1

description: ChIP-seq


title: MonkeyEye-2 7

description:
Isolated eye mRNA
Monkey_Eye-2

source_name: WT Monkey Eye 2

value: Eye


title: MonkeyEye-1 1

description:
Isolated eye mRNA
Monkey_Eye-1

source_name: WT Monkey Eye 1

value: WT


title: ChIPSeq-MUT-I12-STAT5A-rep2

description: ChIP-seq


title: MonkeyEye-2 5

description:
Isolated eye mRNA
Monkey_Eye-2


title: p300 ChIP-Seq in MLL3-/-;MLL4flox/flox D4EB

first: Kai

last: Ge

address: 50 South Dr Rm 4154

data_processing:
Base calling and alignment were performed using Illumina's CASAVA package v1.8.2 with default parameters
Conversion to BED format by bedtools v2.16
Peak-calling by SICER v1.1. For p300 ChIP-Seq, Window size 50bps, Gap size 50bps, FDR<1e-3.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files of identified enriched regions generated by SICER v1.1.

source_name: mouse embryonic stem cell

growth_protocol: ESCs were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)).

extract_protocol:
For ChIP-Seq, suspended 10 x 106 ESCs (feeder removed) and EBs are fixed with 1% formaldehyde in culture medium, followed by ChIP assay. For RNA-Seq, total RNA are collected using Trizol extraction followed by mRNA purification using Dynabeads® mRNA DIRECT™ Kit (invitrogen).
Libraries were prepared according to Illumina TruSeq RNA and DNA sample preparation Kit

treatment_protocol: To differentiate ESCs, 1 x 106 ES cells re-suspended in 10 ml LIF-free ES medium were transferred onto a 10-cm bacteriological petri dish. EBs were kept in suspension in LIF-free ES medium for 4 days. Medium was changed at day2.

tag: antibody

value: Differentiated embryoid body at day 4


title: p300 ChIP-Seq in MLL3-/-;MLL4-/- ESCs

value: embryonic stem cell


title: ChIPSeq-het-L1-STAT5A

description: ChIP-seq

value: heterozygous for Stat5 (Stat5+/-)


title: ChIPSeq-WT-I24-STAT3-rep2

description: ChIP-seq

value: mixed

value: wild type

value: STAT3 (Santa Cruz, sc-482)


title: ChIPSeq-MUT-L1-STAT5A-rep2

description: ChIP-seq

value: Mammary gland

value: lactation day one


title: MonkeyEye-1 3

description:
Isolated eye mRNA
Monkey_Eye-1

value: Wild Type


title: p300 ChIP-Seq in MLL3-/-;MLL4-/- D4EB


title: p300 ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs


title: ChIPSeq-het-L1-H3K27ac

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: MonkeyRetina-1 9

description:
Isolated retina mRNA
Monkey_Retina-1


title: ChIPSeq-WT-I24-STAT3-rep1

description: ChIP-seq

value: involution 24 hours


title: ChIPSeq-WT-I12-STAT3-rep2

description: ChIP-seq


title: ChIPSeq-WT-L1-STAT3-rep1

description: ChIP-seq


title: ChIPSeq-WT-I24-H3K27ac-rep2

description: ChIP-seq


title: Warm challenge 1 Input

city: San Francisco

first: Chan Lek

last: Tan

state: California

address: 1550 Fourth St. Room 346

department: Physiology

institute: University of California

description:
Total RNA
Antibody for PhosphoTRAP experiments: Anti- phosphoS6(244/247) (Invitrogen #44923G)

data_processing:
Sequenced reads were trimmed for adaptor sequences and index sequences.
Mapping to annotated mRNA and abundance calculations done using ArrayStar software (DNA star)
Genes with RPKM<0.1 are excluded
Genome_build: mm9
Supplementary_files_format_and_content: read count and RPKM values

source_name: Preoptic neurons

extract_protocol:
Detailed protocol and buffer recipes are described previously(Knight et al., 2012). Briefly, mice were rapidly sacrificed by cervical dislocation and brains were removed, rinsed briefly with cold dissection buffer and place in a cold sectioning matrix. 0.5 mm sections were obtained and the anterior hypothalamus was removed under a dissecting microscope.
Amplified cDNA was prepared using Ovation RNA-Seq System V2, and sequencing library was prepared using the Ovation Ultralow DR Multiplex system and sequenced on an Illumina HiSeq2500 platform

value: Preoptic neurons


title: Warm challenge 1 Immunoppt

description:
phosphoRPS6 associated RNA
Antibody for PhosphoTRAP experiments: Anti- phosphoS6(244/247) (Invitrogen #44923G)


title: Warm challenge 2 Immunoppt


title: Warm challenge 2 Input


title: Warm challenge 3  Input


title: Warm challenge 3 Immunoppt


title: ChIPSeq-MUT-L1-STAT5A-rep1

description: ChIP-seq

value: homozygous for the Stat5 enhancer mutation (Stat5deltaE/deltaE)

value: STAT5A (Santa Cruz, sc-1081x)


title: ChIPSeq-WT-I24-H3K27ac-rep1

description: ChIP-seq


title: ChIPSeq-WT-I12-H3K27ac-rep1

description: ChIP-seq

value: involution 12 hours


title: ChIPSeq-WT-L1-H3K27ac-rep1

description: ChIP-seq


title: ChIPSeq-WT-I24-GR-rep2

description: ChIP-seq

value: GR (Thermo Scientific, PA1-511A)


title: ChIPSeq-WT-L1-H3K27ac-rep2

description: ChIP-seq


title: RNA-Seq in MLL3-/-;MLL4flox/flox MEFs

data_processing:
Base calling and alignment were performed using Illumina's CASAVA package v1.8.2 with default parameters
Reads/Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the script from the SICER package. In short, reads located on exons as annotated in NCBI RefSeq for assembly mm9 are collected, and reads per kilobase per million for each gene as measure of expression level.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene

source_name: mouse embryonic fibroblasts

growth_protocol:
MEFs were cultured in DMEM medium supplemented with 10% FBS.
ESCs were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)).
MEFs were cultured in DMEM medium supplemented with 10% FBS.

treatment_protocol:
To induce the reprogramming of MEFs,MEFs are infected with lenti-viral Oct4,Sox,Klf4 and c-MYC. Two days after infection, medium are replaced with ES medium. Medium are changed every 2 days.
To diiferentiate ESCs, 1 x 106 ES cells re-suspended in 10 ml LIF-free ES medium were transferred onto a 10-cm bacteriological petri dish. EBs were kept in suspension in LIF-free ES medium for 4 days. Medium was changed at day2.
To induce the reprogramming of MEFs,MEFs are infected with lenti-viral Oct4,Sox,Klf4 and c-MYC. Two days after infection, medium are replaced with ES medium. Medium are changed every 2 days.

value: embryonic fibroblasts


title: RNA-Seq in MLL3-/-;MLL4-/- D20 iPSC

value: Reprogrammed fibroblasts at day20


title: ChIPSeq-WT-I12-STAT3-rep1

description: ChIP-seq


title: RNA-Seq in MLL3-/-;MLL4flox/flox D4EB_rp

growth_protocol:
ESCs were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)).
ESCs were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)).
MEFs were cultured in DMEM medium supplemented with 10% FBS.

treatment_protocol:
To diiferentiate ESCs, 1 x 106 ES cells re-suspended in 10 ml LIF-free ES medium were transferred onto a 10-cm bacteriological petri dish. EBs were kept in suspension in LIF-free ES medium for 4 days. Medium was changed at day2.
To diiferentiate ESCs, 1 x 106 ES cells re-suspended in 10 ml LIF-free ES medium were transferred onto a 10-cm bacteriological petri dish. EBs were kept in suspension in LIF-free ES medium for 4 days. Medium was changed at day2.
To induce the reprogramming of MEFs,MEFs are infected with lenti-viral Oct4,Sox,Klf4 and c-MYC. Two days after infection, medium are replaced with ES medium. Medium are changed every 2 days.

value: Differentiated embryoid body at day 4


title: RNA-Seq in MLL3-/-;MLL4-/- MEFs


title: ChIPSeq-WT-I12-GR-rep1

description: ChIP-seq


title: ChIPSeq-WT-I24-GR-rep1

description: ChIP-seq


title: ChIPSeq-WT-I12-GR-rep2

description: ChIP-seq


title: RNA-Seq in MLL3-/-;MLL4flox/flox ESCs_rp

value: embryonic stem cell


title: RNA-Seq in MLL3-/-;MLL4-/- ESCs_rp


title: ChIPSeq-WT-L1-GR-rep2

description: ChIP-seq

value: mixed


title: Rat Retina-tech replicate 2

description:
Isolated retina mRNA
Rat_Retina.txt

data_processing:
Libraries of Rattus norvegicus were sequenced by single-end sequencing with the Illumina Genome Analyzer IIx or HiScan SQ. Data for Rattus norvegicus were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA) rat (rn4) genome assembly and transcript annotations, using the Genomic Short-read Nucleotide Alignment Program (GSNAP), manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation of RPKM statistics by gene.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

organism: Rattus norvegicus

source_name: Retina tissue

extract_protocol: Each rodent species-specific library preparation was pooled from multiple RNA samples: 5 rats for Rattus norvegicus.

value: Long Evans

value: Retina


title: ChIPSeq-WT-L1-GR-rep1

description: ChIP-seq

value: Mammary gland

value: wild type


title: ChIPSeq-WT-I12-H3K27ac-rep2

description: ChIP-seq


title: Rat Retina-tech replicate 1

description:
Isolated retina mRNA
Rat_Retina.txt

value: Wild Type


title: ChIPSeq-WT-I12-STAT5A-rep2

description: ChIP-seq


title: RNAseq_IFNg+_rep2

city: New York

first: Lionel

last: Ivashkiv

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalls performed using CASAVA version 1.7
RNA-seq reads were aligned to the hg19 genome assembly using TopHat
Gene expression analysis was done using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM measurement.

source_name: human primary monocytes isolated from PBMC of healthy donors

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood

value: monocytes


title: ChIPSeq-WT-I24-STAT5A-rep1

description: ChIP-seq

value: involution 24 hours


title: RNAseq_IFNg-_rep2


title: ChIPSeq-WT-I24-STAT5A-rep2

description: ChIP-seq


title: RNA-Seq in MLL3-/-;MLL4flox/flox D20 iPSC


title: ChIPSeq-WT-I12-STAT5A-rep1

description: ChIP-seq


title: ChIPSeq-WT-L1-STAT5A-rep2

description: ChIP-seq

value: lactation day one


title: ChIPSeq-WT-L1-STAT5A-rep1

description: ChIP-seq

value: STAT5A (Santa Cruz, sc-1081x)


title: RNAseq_IFNg+_rep1


title: Rat Eye-tech replicate 2

description:
Isolated retina mRNA
Rat_Eye.txt

source_name: Eye tissue

value: Eye


title: RNA-Seq in MLL3-/-;MLL4-/- D4EB_rp


title: RNAseq_IFNg-_rep1


title: H3K27me3_IFNg+_rep1

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.1
Reads have passed Illumina filters, and been trimmed using Sickle using quality threshold >20
Peaks were called using ChIPseeqer with the following setting: p < 10~-15, FDR <0.02)
Annotation and downstream analysis was done using ChIPseeqer
Genome_build: hg19
Supplementary_files_format_and_content: text file with peak data. Sample_K27me3_A represents IFNg- and Sample_K27me3_B represents IFNg+

extract_protocol:
ChIP assay
DNA libraries were prepared for sequencing using standard Illumina protocols


title: H3K27me3_IFNg-_rep2


title: H3K27me3_IFNg-_rep1


title: input in MLL3-/-;MLL4flox/flox D4EB

data_processing:
Base-calling and alignment performed by Illumina Analysis Pipeline
Conversion to BED format by bedtools v2.16
For ChIP-Seq, Peak-calling by SICER v1.1. For MLL4, Window size 50bps, Gap size 50bps, FDR<1e-3. For H3K4me1/2/3 and H3K27ac, Window size 200bps, Gap size 200bps, FDR <1e-3.
For RNA-Seq, Read-counting and RPKM calculation on exonic regions by SICER v1.1
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-Seq, Wig files of identified enriched regions generated by SICER v1.1. For RNA-Seq, Txt files of calculated RPKMs by SICER v1.1.

extract_protocol:
For ChIP-Seq, suspended 10 x 106 ESCs (feeder removed) and EBs are fixed with 1% formaldehyde in culture medium, followed by ChIP assay. For RNA-Seq,  total RNA are collected using Trizol extraction followed by mRNA purification using Dynabeads® mRNA DIRECT™ Kit (invitrogen).
Libraries were prepared according to Illumina TruSeq RNA and DNA sample preparation Kit

treatment_protocol: To diiferentiate ESCs, 1 x 106 ES cells re-suspended in 10 ml LIF-free ES medium were transferred onto a 10-cm bacteriological petri dish. EBs were kept in suspension in LIF-free ES medium for 4 days. Medium was changed at day2.

value: input

tag: genetic background

value: C57BL/6 and SV/129


title: input in MLL3-/-;MLL4-/- ESCs


title: input in MLL3-/-;MLL4flox/flox ESCs


title: input in MLL3-/-;MLL4-/- D4EB


title: CRISPR p53-KO/si-SET #2

first: Wei

last: Gu

address: 1130 Saint Nicholas Ave

department: ICG

institute: Columbia University

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped to a reference genome (Human: NCBI/build37.2) using Tophat (version 2.0.4)
Relative abundance of genes and splice isoforms were determined using cufflinks (version 2.0.2) with default settings
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: Data were present as .csv format files, including tracking_id, gene_id, FPKM etc.

source_name: U2OS cell line

growth_protocol: Cells were maintained in routine DMEM medium with 10% FBS complement.

extract_protocol:
Total RNA was extracted by Trozol as the routine protocol.
Library was prepared by using Illumina TruSeq RNA prep kit according to the protocol.

treatment_protocol: Control siRNA or SET-specific siRNA were transfected into cells for 96 hours.

tag: cell line

value: U2OS-derived cell line

tag: sample information

value: p53 KO, SET knocking-down

tag: biological replicates


title: CRISPR p53-KO/si-SET #1


title: CRISPR p53-KO/si-Ctr #2

value: p53 KO


title: RNA-Seq in MLL3-/-;MLL4-/- D4EB

tag: cell type

value: Differentiated embryoid body at day 4


title: RNA-Seq in MLL3-/-;MLL4flox/flox D4EB


title: Rat Eye-tech replicate 1

description:
Isolated retina mRNA
Rat_Eye.txt

tag: strain

value: Long Evans

tag: tissue


title: MLL4 ChIP-Seq in MLL3-/-;MLL4flox/flox D4EB


title: CRISPR p53-KO/si-Ctr #1


title: CRISPR Ctr/si-SET #2

value: p53 WT, SET knocking-down


title: H3K27ac ChIP-Seq in MLL3-/-;MLL4-/- D4EB


title: CRISPR Ctr/si-SET #3


title: H3K4me1 ChIP-Seq in MLL3-/-;MLL4-/- D4EB


title: H3K4me1 ChIP-Seq in MLL3-/-;MLL4flox/flox D4EB


title: CRISPR Ctr/si-SET #1


title: H3K27ac ChIP-Seq in MLL3-/-;MLL4flox/flox D4EB


title: CRISPR Ctr/si-Ctr #3

value: p53 WT


title: RNA-Seq in MLL3-/-;MLL4-/- ESCs

value: embryonic stem cell


title: H3K27me3_IFNg+_rep2


title: CRISPR Ctr/si-Ctr #1


title: RNA-Seq in MLL3-/-;MLL4flox/flox ESCs


title: CRISPR Ctr/si-Ctr #2


title: MLL4 ChIP-Seq in MLL3-/-;MLL4-/- ESCs


title: H3K27ac ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs


title: H3K27ac ChIP-Seq in MLL3-/-;MLL4-/- ESCs


title: MLL4 ChIP-Seq in MLL3-/-;MLL4-/- D4EB


title: H3K4me3 ChIP-Seq in MLL3-/-;MLL4-/- ESCs


title: H3K4me1 ChIP-Seq in MLL3-/-;MLL4-/- ESCs


title: H3K4me2 ChIP-Seq in MLL3-/-;MLL4-/- ESCs


title: H3K4me1 ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs


title: Human_Retina 1

description: Isolated retina mRNA

data_processing:
Libraries of Homo sapiens were sequenced by single-end sequencing with the Illumina Genome Analyzer IIx or HiScan SQ. Data for Homo sapiens were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA)  human (hg19) genome assembly and transcript annotations, respectively, using the Genomic Short-read Nucleotide Alignment Program (GSNAP), manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation of RPKM statistics by gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

source_name: Retina tissue-Human

extract_protocol: Library preparation for isolated eye and retinal tissue in RNALater, obtained from human and macaque species, was performed similarly to that used for rodent tissues except for the larger scale homogenization required. Human and macaque samples were each prepared from one eye.

value: Normal tissue

value: Retina

value: Wild Type


title: Human_Retina 2

description: Isolated retina mRNA


title: RHO KO Mouse eye bioreplicate 3

description:
Isolated whole eye mRNA
RhoKO-3.txt

data_processing:
Libraries Mus musculus were sequenced by single-end sequencing with the Illumina Genome Analyzer IIx or HiScan SQ. Data for Mus musculus were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA) mouse (mm9) genome asembly and transcript annotations, respectively, using the Genomic Short-read Nucleotide Alignment Program (GSNAP), manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation of RPKM statistics by gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

source_name: Eye tissue-RHO KO3

extract_protocol: Each rodent species-specific library preparation was pooled from multiple RNA samples: 5 mice for Mus musculus. Biological replicates were prepared for both Mus musculus eye and retina samples.

value: C57BL6/J RHO KO

value: Whole Eye

value: Rhodopsin Knockout


title: WT Mouse retina bio replicate 3-tech replicate 2

description:
Isolated retina mRNA
B6-retina-3.txt

source_name: Retina tissue-WT3


title: EGS_pellet-2 [S. pombe]

data_processing:
Library strategy: Micro-C XL
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to reference genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate contact matrix.
Genome_build: S288C (sacCer3) or S. pombe 972h- (ASM294v2)
Supplementary_files_format_and_content: Interaction_density.xlsx

source_name: Yeast

tag: media

value: Compromised Media

tag: first fixation

value: 1% Formaldehyde for 10 min

tag: second fixation

value: 3mM EGS for 40min


title: WT Mouse retina bio replicate 1-tech replicate 2

description:
Isolated retina mRNA
B6-retina-1.txt

source_name: Retina tissue-WT2


title: WT Mouse retina bio replicate 2-tech replicate 2

description:
Isolated retina mRNA
B6-retina-2.txt

source_name: Retina tissue-WT1


title: WT Mouse retina bio replicate 2-tech replicate 1

description:
Isolated retina mRNA
B6-retina-2.txt


title: WT Mouse retina bio replicate 3-tech replicate 1

description:
Isolated retina mRNA
B6-retina-3.txt


title: WT Mouse retina bio replicate 1-tech replicate 1

description:
Isolated retina mRNA
B6-retina-1.txt


title: E9.5 spine DR/+

city: Ithaca

first: Paul

last: Soloway

address: 237 Tower Road

institute: Cornell

data_processing:
Galaxy (usegalaxy.org version 1.0.0) FASTQ Groomer (version 1.0.4) was used to clean up raw formatting.
Galaxy (usegalaxy.org version 1.0.0) Trimmer (version 0.0.1) was used to reduce reads to 250bp.
Galaxy (usegalaxy.org version 1.0.0) Filter by quality tool (version 1.0.0) was used to pick only high quality reads.
Galaxy (usegalaxy.org version 1.0.0) FASTQ to FASTA converter (version 1.0.0) was used in preparation for bisulfite analysis.
Large files were truncated in linux command line to 10MB to limit analysis time.
A local installation of QUMA (http://quma.cdb.riken.jp/) was run with default input parameters and file type 3 output.
Supplementary_files_format_and_content: tab deliminated text files with summary methylation results

source_name: Spine

extract_protocol:
Genomic tail DNA was isolated by standard procedures (Laird, P.W. et al. Nucleic Acids Res. 1991, 19:4293). Genomic sperm DNA was isolated by standard procedures (Griffin J. Methods Mol Biol. 2013, 927:379-384.). Genomic oocyte DNA was isolated by standard procedures (Smallwood, S.A. et al. Nat. Methods 2014, 11:817-820). DNA from tail and sperm were phenol chlorform extracted before bisulfite treatment.
75ng of purified BS-PCR product was end polished (End-IT kit #ER0720) for 45 minutes, A-tailed (NEB Klenow exo- # M0212L) for 50 minutes, and ligated with TruSeq adapters. This product was subjected to 10 rounds of amplification with barcode-specific primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA) and gel purified before sequencing. Ampure beads (Agencourt #A63880) were used to clean up between steps.

value: Spine

value: DR/+

tag: developmental stage


title: E9.5 organs +/DR

source_name: Visceral organs

value: Visceral organs

tag: genotype

value: +/DR


title: E9.5 head DR/+

source_name: Head

value: Head


title: E9.5 EE DR/+

source_name: Extraembryonic tissue

value: Extraembryonic tissue


title: MLL4 ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs

source_name: mouse embryonic stem cell

value: C57BL/6 and SV/129


title: E9.5 organs DR/+


title: H3K4me3 ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs

value: embryonic stem cell


title: E9.5 spine +/DR


title: H3K4me2 ChIP-Seq in MLL3-/-;MLL4flox/flox ESCs


title: 35670 supernatant

source_name: Sperm

value: Sperm


title: 35670 pellet


title: 35669 supernatant


title: 35669 pellet


title: E9.5 head +/DR


title: 31819 F4 A

source_name: Tail

value: Tail


title: RHO KO Mouse eye bio replicate 2

description:
Isolated whole eye mRNA
RhoKO-2.txt

source_name: Eye tissue-RHO KO2


title: BDNF GFP Input 2

description:
Total RNA
Antibody for TRAP seq experiments : Anti-EGFP, equal mixture of clones 19C8 and 19F7 from Monoclonal Antibody Core Facility at Memorial Sloan-Kettering cancer center.

data_processing:
Sequenced reads were trimmed for adaptor sequences and index sequences.
Mapping to annotated mRNA and abundance calculations done using ArrayStar software (DNA star)
Genes with read count =0 are excluded.
Genes with both match input and immunoprecipitated RPKM value<1 are excluded
Genome_build: mm9
Supplementary_files_format_and_content: read count and RPKM values

source_name: Preoptic neurons

extract_protocol:
Detailed protocol and buffer recipes are described previously(Knight et al., 2012). Briefly, mice were rapidly sacrificed by cervical dislocation and brains were removed, rinsed briefly with cold dissection buffer and place in a cold sectioning matrix. 0.5 mm sections were obtained and the anterior hypothalamus was removed under a dissecting microscope.
Amplified cDNA was prepared using Ovation RNA-Seq System V2, and sequencing library was prepared using the Ovation Ultralow DR Multiplex system and sequenced on an Illumina HiSeq4000 platform

value: Preoptic neurons BDNF+


title: RHO KO Mouse eye bio replicate 1

description:
Isolated whole eye mRNA
RhoKO-1.txt

source_name: Eye tissue-RHO KO1

value: C57BL6/J RHO KO


title: 31508 F4 A


title: BDNF GFP Immunoprecipitated 1

description:
GFP-L10a associated RNA
Antibody for TRAP seq experiments : Anti-EGFP, equal mixture of clones 19C8 and 19F7 from Monoclonal Antibody Core Facility at Memorial Sloan-Kettering cancer center.


title: Oocyte pool 1

source_name: oocytes

value: Oocytes

value: DR/DR


title: 35090 Sperm


title: Oocyte pool 2


title: 35084 Sperm


title: PACAP GFP Immunoprecipitated 2

value: Preoptic neurons PACAP+


title: mESC input

city: Montpellier

first: Claude

last: Sardet

address: 208 rue des Apothicaires

department: Inserm U1194 - Université de Montpellier - Institut Régional du Cancer de Montpellier (ICM)

country: France

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

data_processing:
Basecalls performed using Illumina software RTA (Bustard).
Alignment performed using CASAVA version 1.7 for Illumina GAIIx runs (elandv2).
10 millions of mm9 uniquely mapped tags were randomly sampled from each sequencing run. Redundant reads occurrence's is adjusted to one, chromosome Y and M are removed. Input tags distribution is analyzed with hts_windowsummaryv2.exe hts_peakdetectorv2.exe (cisgenomeV2) to identify artifactual reads aggregates. False positive tag enriched regions are then removed from IP and input files prior peak calling.
E4F1 peak calling is done with CisgenomeV2 (Seqpeak) and Qeseq V0.2.2 with the following parameters. Seqpeak -b 50 -w 1 -e 150 -ts 1 -c 3 -maxgap 50 -minlen 100 -br 1 -bar 1 -dat 1 - bw 5 -lpois 1 -lpwin 10000 -lpcut 1e-5 and QESEQ -s 150 -v 1 -p 0.01 -c 20. Genomic regions identified by both algorithms (intersection) were retained as E4F1-bound genomic regions. All pre and post data processing were done with R and Galaxy.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: bed file contains the intersection of detected peaks by cisgenomeV2 and Qeseq V0.2.2.
Supplementary_files_format_and_content: bar files contain the tag density.

source_name: mESC, input

growth_protocol: mESc (129Sv/J) were grown at 37°C in Knock-out DMEM optimized for ES cells supplemented with SVF ES, penicilline-streptomycine, MEM-NEAA, L-glutamine, 2beta-mercaptoethanol and mLIF under 5% CO2, 100% saturated H2O incubator. Two days before crosslinking, cells were plated without feeders on gelatinized plates.

extract_protocol: Input and immunoprecipitated DNA were purified and prepared for Illumina/Solexa sequencing following their standard protocol.

treatment_protocol: Cells were trypsinized, counted and crosslinked with 1% formaldehyde for 8 minutes. Nuclei were then isolated and lysed. Chromatin was sheared by sonication to fragments below 500 nucleotides. Sonicated chromatin of mESC was immunoprecipitated with an in-house rabbit polyclonal antibody raised against full-length E4F1 protein.

tag: strain/background

value: embryo

value: embryonic stem cells


title: E4F1 ChIP in mESC

source_name: mESC, E4F1 ChIP

tag: chip antibody

value: rabbit polyclonal anti-E4F1


title: PACAP GFP Immunoprecipitated 1


title: 32530 F6 A


title: 32529 F6 A


title: PACAP GFP Input 2


title: E9.5 EE +/DR


title: 32339 F6 A


title: BDNF GFP Immunoprecipitated 2


title: WGBS PreC_3

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: primary cell culture of prostate epithelial cells

data_processing:
Bisulfite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulfite_tools. Briefly, adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters. Bismark v0.8.3 [PMID: 21493656] was then used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”. PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file containing counts of methylated (C) and coverage (cov, methylated Cs + unmethylated Ts) at each CpG site assayed

source_name: PrEC

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. LNCaP cells were used at passage 73 and PrEC cell at passage 6.

extract_protocol:
Genomic DNA for both cell lines was extracted using QIAamp DNA Mini and Blood Mini kit following the manufacturer’s protocol for cultured cells (Qiagen).
Whole genome bisulfite sequencing libraries were prepared using the Illumina Paired-end DNA Sample Prep Kit (Illumina). Briefly, DNA (1ug), was spiked with 0.5% unmethylated lambda DNA (Promega) in a final volume of 50-65ul.  DNA was sheared to 150-300bp by sonication with a Covaris S2. Library preparation was performed according to the manufacturer’s protocol - fragments were end-repaired and adenylated before ligation of Illumina Truseq adaptors.  Gel size selection (260-330bp) was used to purify and size select the ligated DNA, using Qiagen Gel extraction kit (Qiagen, part #28704) and DNA was eluted in 20ul H2O.  Bisulphite treatment was then carried out as previously described [PMID: 17406479], with the bisuphite reaction being performed for 4 hrs at 55°C. After bisulphite cleanup the DNA pellet was resuspended in 50 ul H2O. The adaptor-ligated bisulfite-treated DNA was enriched by performing 5 independent PCR reactions for 10 cycles using PfuTurboCx Hotstart DNA polymerase (Stratagene) in a volume of 50ul per PCR reaction.  The 5 independent PCRs were pooled together, cleaned up using the MinElute PCR purification kit and eluted in 20ul Qiagen EB buffer. Library quality was assessed with the Agilent 2100 Bioanalyzer using the High-sensitivity DNA kit (Agilent, CA, USA). DNA was quantified using the KAPA Library Quantification kit by quantitative PCR (KAPA Biosystems). Paired-end 100bp sequencing was performed for each library on the Illumina HiSeq 2500 platform using Truseq v3 cluster kits and SBS kits.

value: primary prostate epithelial cells (PrEC)

tag: gender

value: Male


title: WGBS PreC_2


title: 32802 F6 P

value: +/DR


title: WGBS PreC_1


title: 32804 F6 M

value: DR/+


title: PACAP GFP Input 1


title: 32803 F6 M


title: WGBS LNCaP_5

description: transformed prostate cancer cell line

source_name: LNCAP

value: prostate cancer cell line (LNCaP)


title: 32181 F5 A


title: 32178 F5 A


title: WGBS PreC_4


title: BDNF GFP Input 1


title: 32415 F5 P


title: WGBS LNCaP_4

description: transformed prostate cancer cell line


title: 31544 F3 A


title: WGBS LNCaP_3

description: transformed prostate cancer cell line


title: WGBS LNCaP_2

description: transformed prostate cancer cell line


title: 31289 F3 A


title: 31078 F2 A


title: 30999 F1 P


title: 31075 F2 M


title: 31071 F2 M


title: 31153 F1 P


title: 31150 F1 P


title: Mock Brain

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
Total RNA isolated from Brain
Pigtailedmacaque_BrainTemporallobe_9_C2AFCACXX.6.ID06

data_processing:
Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Genome_build: Ensembl; build, Mmul_1
Supplementary_files_format_and_content: We then mapped all the remaining reads to the rhesus macaque reference genome (source, Ensembl; build, Mmul_1) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.

organism: Macaca nemestrina

source_name: Brain

growth_protocol: Whole Animal

extract_protocol:
Brain tissues used for whole transcriptome sequencing were excised from dam and fetus at necropsy (day 43 post-inoculation) and immediately immersed in RNALater (Ambion) for 24h at 4°C. Tissues were subsequently homogenized in TRIzol® Reagent (Life Technologies) and total RNA was isolated using the QIAGEN miRNeasy Kit.
KAPA Stranded RNA-Seq with RiboErase workflow for Total RNA-Seq libraries (KAPA Biosystems).
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: Subcutaneous inoculation and mock infected

value: Downloaded from NHPRTR.org


title: Dam Brain

description:
Total RNA isolated from Brain
F2_RNA_Total_S4

value: FSS13025 genome (Accession no. KU955593)


title: 31092 F1 P


title: Fetal Brain

description:
Total RNA isolated from Brain
D12_RNA_Total_S12


title: Ground Squirrel Retina 5

description:
Isolated retina mRNA
GSq_retina_expression_with_topblast

data_processing:
Transcriptomes of Arivacanthis niloticus and Ictidomys tridecemlineatus were assembled de novo. The processed reads were assembled using velvet, oases, and Trinity with multiple k-mers ranging from 21 to 67 with an increment of 2 whereas reads assembled with ABYSS and trans-ABYSS were done with multiple k-mers ranging from 40 to 78 with an increment of 2. The assemblies were combined and the duplicated transcripts were collapsed together to remove redundancy. Transcriptome annotation was done by first searching against the SWISS-PROT database using the BLASTx algorithm and an E value cutoff of 1e-5. Transcripts with the best matches to proteins from viruses and bacteria were considered as potential contaminants and thus were removed from further analysis. The resulting filtered BLASTx results were then used for Gene Ontology analysis with the blast2GO program. Protein domains were predicted for all such transcripts by searching the PFAM database with the HMMER program. The expression value for each transcript was calculated by aligning the original Illumina reads to the transcriptome using the Bowtie program, with all mapping reads reported. The expression value for each transcript was calculated as RPKM using a customized Perl script.
Genome_build: de novo assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

organism: Ictidomys tridecemlineatus

source_name: Ground Squirrel Retina tissue

extract_protocol: Each rodent species-specific library preparation was pooled from multiple RNA samples: 4 ground squirrels for Ictidomys tridecemlineatus.

value: WT

value: Retina

value: Wild Type


title: Nile Rat Eye 9

description: Isolated eye mRNA

organism: Arvicanthis niloticus

source_name: Nile rat eye tissue

extract_protocol: Each rodent species-specific library preparation was pooled from multiple RNA samples: 5 Nile rats for Arivacanthis niloticus.

value: Eye


title: Nile Rat Eye 5

description: Isolated eye mRNA


title: Nile Rat Eye 1

description: Isolated eye mRNA


title: Nile Rat Eye 7

description: Isolated eye mRNA


title: Ground Squirrel Eye 3

description:
Isolated eye mRNA
GSq_eye_expression_with_topblast

source_name: Ground Squirrel Eye tissue


title: Ground Squirrel Eye 5


title: C120h

status: Public on Sep 11 2016

city: wuhan

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

data_processing:
RNA-Seq reads of each sample were firstly mapped to S. lemnae MAC genome assembly (http://stylo.ciliate.org/index.php/home/downloads) using TopHat2 allowing two edit distances (including mismatch and indel). Differential expressed genes (predicted gene models) were analyzed using the Cufflinks program [16], and FPKM (Fragments Per Kilobase of exon per Million mapped reads) were used to measure the gene expression level. Differential expressed genes were determined by 1.5 fold changes of FPKM. (http://www.broadinstitute.org/annotation/genome/Tetrahymena/MultiHome.html) using TopHat allowing  2 edit distances (including mismatch and indels). To assemble the transcripts, the mapping results of all the samples were independently assembled in both strands using the Cufflinks program, and then merged the assemblies using cuffmerge.
Genome_build: Stylonychia lemnae MAC genome assembly (http://stylo.ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: Expression level (FPKM) matrix table

organism: Stylonychia lemnae

source_name: S. lemnae_control_120hrs

growth_protocol: Stylonychia lemnae (a gift from Prof. Dieter Ammermann, Zoologisches Institut der Universität Tübingen, Abteilung Zellbiologie) was cultivated axenically at 25°C in distilled water using Chlorogonium elongatum cells as food source. The initial concentration of cell density we used was 30 cells/ml each 24-well plate. For the treatment, human EGF (hEGF) was added with the final concentration 10μg/ml. Triplicates were performed for both the control and EGF treatment. Cells were mixed well and counted using hemacytometer like in Tetrahymena.

extract_protocol:
Chlorogonium elongatum cells (d = 5-25μm) were filtered using 30μm filter, comparing to the S. lemnae (200×50μm). Cells were kept using the RNeasy Protect Cell Mini Kit (Qiagen, Valencia, CA), then RNA was extracted using the RNeasy Plus Mini Kit (Qiagen,Valencia, CA) according to the protocol used for Tetrahymena in TetraFGD (http://tfgd.ihb.ac.cn/index/smphelp).
The concentration and RNA integrity of the samples was then determined by e-Spect ES-2 (Malcom, Japan). For each time point, equal amounts of RNA from 3 replicates was pooled for standard RNA-seq library construction. RNA-seq libraries were sequenced using Illumina HiSeq2000 platform with paired-end mode.

tag: genotype/variation

value: wild type

tag: treated with

value: none for 120hrs (control)


title: E120h

source_name: S. lemnae_EGF_120hrs

value: 10μg/ml human epidermal growth factor (hEGF) for 120hrs


title: E96h

source_name: S. lemnae_EGF_96hrs

value: 10μg/ml human epidermal growth factor (hEGF) for 96hrs


title: C108h

source_name: S. lemnae_control_108hrs

value: none for 108hrs (control)


title: E108h

source_name: S. lemnae_EGF_108hrs

value: 10μg/ml human epidermal growth factor (hEGF) for 108hrs


title: WGBS LNCaP_1

description: transformed prostate cancer cell line


title: C96h

source_name: S. lemnae_control_96hrs

value: none for 96hrs (control)


title: INO80-Replicate2 [MNase-Seq] [PSU56201]

status: Public on Sep 10 2016

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

description:
INO80 Mnase-Seq Replicate number 2
PSU56201
MNase-Seq

data_processing:
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads
MNase-Seq reads were aligned to the sg7(R55) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads
Custom python script used to extract only 5' end position
Genome_build: R55 (SGD)
Supplementary_files_format_and_content: tab delimeted; enriched 5'end position

organism: Saccharomyces cerevisiae

source_name: in vitro

growth_protocol: InVitro

extract_protocol:
InVitro DNA extraction
MNase-Seq libraries were prepared for sequencing using NEBNext standard Illumina protocols

treatment_protocol: For MNase-Seq, cells were not crosslinked.

tag: genomic dna strain

value: GRF88, MATa his4-38, S288C background

tag: histone source

value: Drosophila embryo


title: Ground Squirrel Retina 3


title: Nile Rat Eye 3

description: Isolated eye mRNA


title: RL(+)_rep1

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.32) tool: (1) removing the reads with adaptor contamination; (2) filtering the low-quality reads with ambiguous sequences ‘N’; (3) removing the low-quality bases (quality score < Q30).
All downstream analyses were based on clean, high quality data. The TopHat-cufflink-cuffmerge-cuffcompare-cuffdiff pipeline was used to discover novel transcripts and to identify differentially expressed genes. TopHat (v2.0.5) was used to align reads to the C. merolae 10D reference genome. Following TopHat alignment, Qualimap software (v2.1) was used to evaluate the coverage of the alignment data and a Pearson’s correlation analysis was conducted to obtain the transcript-level R2 value between replicates
We used the q-value < 0.01 (FDR) and the absolute value of |Fold change| ≥ 2 as the threshold to judge the significant differences of gene expression.
Genome_build: ASM9120v1
Supplementary_files_format_and_content: Microsoft Office Open XML Spreadsheet (RNA-seq abundance measurements in FPKM values across samples)

organism: Cyanidioschyzon merolae

growth_protocol: C. merolae 10D cells were grown in 2× Allen’s medium (2×MA) at pH 2.3. Fifty-mL flasks containing C. merolae cultures were shaken under continuous light (100 µmole m-2s-1) at 42 °C.

extract_protocol:
Total RNA was extracted from OD750=0.6, 5 ml cell culture by using TRIzol reagent according to the manufacturer’s instructions.
After quality and quantity measurements by using 2100 BioAnalyzer, the total RNA was treated with RNase-free DNase I at a concentration of 1 U/µg to remove residual genomic DNA. Next, mRNAs were purified from 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer with the TruSeq mRNA Sample Preparation Kit according to manufacturer's instructions. The cleaved short RNA fragments were used for the first-strand cDNA synthesis using random hexamer-primer, and then the second strand was synthesized by using DNA polymerase I and RNase H. The double strand cDNAs were purified with AMPure XP beads and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. Paired-end sequencing was performed for the two cDNA libraries (two biological replicates) for each condition using the Illumina MiSeq sequencing platform.  All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.

treatment_protocol: For the blue light (BL) experiments, exponentially growing cells were sub-cultured to OD750=0.6 (3×10^7 cells/ml) in 50 mL of 2×MA and then placed into complete darkness for 36 hours by covering the tubes with aluminum foil. Then, the cells were exposed to BL (15 µmole m-2s-1) for 30 minutes. BL intensity was measured with a UVX Digital Radiometer at 365 nm. For red light (RL) experiments, dark kept cells were exposed to RL for 30 minutes. RL intensity was measured by Thorlabs PM100 console system at 630 nm. To assess the effect of reactive oxygen species, cells grown under complete darkness were treated with 600 µM hydrogen peroxide for 45 minutes.


title: RL(+)_rep2


title: RL(-)_rep2


title: RL(-)_rep1


title: BL(+)_rep2


title: Ground Squirrel Retina 1


title: BL(+)_rep1


title: BL(-)_rep2


title: BL(-)_rep1


title: Pele_Mar

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

description:
total RNA globin-depleted by RNase H assay prior to library construction and sequencing
For differential expression analysis, only those genes with PPDE >= 1 - FDR are significantly differentially expressed.

data_processing:
Data processing steps for DQH_blood_CuffLinks_Genome_data.xls:

The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
Reads were mapped to the Ensembl Tursiops truncatus genome, turTru1 v76.1, using Tophat2 v 2.3.13 with bowtie2 v 2.2.4 as the alignment engine on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.
Read counts as FPKM (fragments per kilobase of trnascript per million mapped reads) were generated using Cufflinks v 2.2.0 with the genome as a reference on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.
Genome_build: Ensembl turTru1 v76.1
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column "Gene ID" contains the gene ID from the Ensembl genome.  The second column "Gene Symbol" contains the gene symbol, if assigned, from the Ensembl turTru1 v76.1 annotation. The remaining colums contain the FPKM values for each sample as generated by Cufflinks.  A FPKM > 0 in at least half the samples and and average FPKM ≥ 1 across all samples was required for all further data analysis.  Only genes meeting these requirements are included in the processed data table.

Data processing steps for DQH_blood_RSEM_Genome_data.xls:

The Illumina BCL output files were converted to fastq-sanger file format and sequence quality trimming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
Reads were mapped to the Ensembl Tursiops truncatus genome, turTru1 v76.1, using RSEM v 1.2.18 with bowtie2 as the alignment engine and read counts were generated as FPKM (fragments per kilobase of transcript per million mapped reads) at the gene level.
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column "Gene ID" contains the gene ID from the Ensembl genome.  The second column "Gene Symbol" contains the gene symbol, if assigned, from the Ensembl turTru1 v76.1 annotation. The remaining columns contain the FPKM values for each sample as generated by RSEM.  A FPKM > 0 in at least half the samples and an average FPKM >= 1 across all samples was required for all further data analysis.  Only genes meeting these requirements are included in the processed data table.

Data processing steps for DQH_blood_RSEM_Trinity_data.xls:

The Illumina BCL output files were converted to fastq-sanger file format and sequence quality trimming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
The read files from one summer and one winter globin-depleted sample from each animal (n=8; Hua: Feb and Sept, Kainalu: Feb and Aug, Keo: Feb and Aug, Pele: Feb and Sept) were concatenated into a single fastq file for assembly using a minimum K-mer coverage of 1, a minimum overlap value of 25 and a minimum contig length of 400 nucleotides on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications.  Annotation of the de novo assembly was obtained by BLASTx searches of the human subset of the uniprot_swissprot database.  Reads were mapped to the de novo Trinity assembly, using RSEM v 1.2.18 with bowtie2 as the alignment engine and read counts were generated as FPKM (fragments per kilobase of transcript per million mapped reads) at the gene level.
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Accession Number" contains the uniprot_swissprot accession number, if assigned, from BLASTx searches. The FASTA file with the sequences is available on the series record. The remaining columns contain the FPKM values for each sample as generated by RSEM.  A FPKM > 0 in at least half the samples and an average FPKM >= 1 across all samples was required for all further data analysis.  Only genes meeting these requirements are included in the processed data table.

Data processing steps for Female_v_Male_FC.xlsx:

FPKM values generated by RSEM were used to calculate fold change values, at the gene level, in EBSeq between female (n=16, all samples from Keo and Pele) and male (n=16, all samples from Hua and Kainalu) samples.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Log2 Fold Change" contains the Log2(fold change) value calculated by EBSeq.  Positive Log2(fold change) values are more highly expressed in females.   The third column "PPDE" is the EBSeq calculated posterior probability that a gene is differentially expressed.  With the hard-threshold method used to control FDR, only those genes with PPDE >= 1 - FDR are significantly differentially expressed.

Data processing steps for Sum_v_Win_FC.xlsx:

FPKM values generated by RSEM were used to calculate fold change values, at the gene level, in EBSeq between summer (n=8, Hua: July and August, Kainalu: July and September, Keo: August, Pele: July, August, and September) and winter (n=8, Hua: December and February, Kainalu: December and February, Keo: December and February, Pele: December and February) samples.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Log2 Fold Change" contains the Log2(fold change) value calculated by EBSeq.  Positive Log2(fold change) values are more highly expressed in warmer months.   The third column "PPDE" is the EBSeq calculated posterior probability that a gene is differentially expressed.  With the hard-threshold method used to control FDR, only those genes with PPDE >= 1 - FDR are significantly differentially expressed.

Data processing steps for Sum_v_Win_Male_FC.xlsx:

FPKM values generated by RSEM were used to calculate fold change values, at the gene level, in EBSeq between summer (n=4, Hua: July and August, Kainalu: July and September) and winter (n=4, Hua: December and February, Kainalu: December and February) in samples from male animals.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Log2 Fold Change" contains the Log2(fold change) value calculated by EBSeq.  Positive Log2(fold change) values are more highly expressed in warmer months.   The third column "PPDE" is the EBSeq calculated posterior probability that a gene is differentially expressed.  With the hard-threshold method used to control FDR, only those genes with PPDE >= 1 - FDR are significantly differentially expressed.

Data processing steps for Sum_v_Win_Female_FC.xlsx:
FPKM values generated by RSEM were used to calculate fold change values, at the gene level, in EBSeq between summer (n=4, Keo: August, Pele: July, August, and September) and winter (n=4, Keo: December and February, Pele: December and February) samples.  The first column "Gene ID" contains the gene ID from the de novo Trinity assembly.  The second column "Log2 Fold Change" contains the Log2(fold change) value calculated by EBSeq.  Positive Log2(fold change) values are more highly expressed in warmer months.   The third column "PPDE" is the EBSeq calculated posterior probability that a gene is differentially expressed.

organism: Tursiops truncatus

source_name: blood

extract_protocol:
Whole blood RNA was extracted using a PAXgene Blood RNA Kit (Qiagen).  Total RNA samples were globin-reduced using an Rnase H assay targeting HBA, HBB, and HBM transcripts.
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

value: blood

tag: Sex

value: Female

tag: age (years)

tag: sampling date


title: Pele_Dec


title: Pele_Aug


title: Pele_Sep


title: Pele_May


title: Keo_May


title: Keo_Aug


title: Keo_Dec


title: Keo_Jun


title: Keo_Nov


title: Keo_Apr


title: Pele_Jul


title: Keo_Feb


title: Pele_Feb


title: Kai_Dec

value: Male


title: Keo_Oct


title: Kai_Sep


title: Keo_Mar


title: Hua_Dec


title: Kai_Jun


title: Hua_Oct


title: Kai_Apr


title: Kai_Jul


title: Hua_Jul


title: Hua_Aug


title: Kai_May


title: Hua_Mar


title: Hua_May


title: Hua_Feb


title: ASF1B Donor-9

city: Madison

first: Pradyut

middle: K

last: Paul

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
alignment: bowtie
quantification: RSEM
normalization: median-by-ratio
Genome_build: hg19
Supplementary_files_format_and_content: Paul et all Supplementary Table ASF1B Overexpression RNA-Seq All and DE Genes.xlsx
Raw Data: The values for each gene in this worksheet are FPKMs (Fragments Per Kilobase of Transcript per Million mapped reads). These values were used to generate the data in other worksheet.
Sorted_PP_DE_Nonrounding: The data on this worksheet contains processed reads based on which genes that were differentially expressed (DE) were identified and sorted based on posterior probability (PP). Copy number data on this worksheet was nonrounded.

source_name: Donor-derived human pancreatic Islets

extract_protocol: Total RNA was isolated from human islets using RNeasy spin columns according to the manufacturer’s directions (Qiagen). RNA quantity was determined using a Nanodrop (Thermo Scientific) and the quality assessed by a Bioanalyzer (Agilent). Total mouse RNA was used for RNA-sequencing on an Illumina HiSeq 2000.

value: Donor-derived human pancreatic Islets

tag: transduction


title: GFP Donor-10

description: GFP

tag: tissue

value: GFP


title: ASF1B Donor-5


title: ASF1B Donor-1


title: ASF1B Donor-6 (1)


title: ASF1B Donor-10


title: ASF1B Donor-6 (2)


title: ASF1B Donor-8


title: ASF1B Donor-4


title: ASF1B Donor-3


title: GFP Donor-9

description: GFP


title: GFP Donor-6 (2)

description: GFP


title: GFP Donor-6 (1)

description: GFP


title: GFP Donor-4

description: GFP


title: GFP Donor-5

description: GFP


title: GFP Donor-8

description: GFP


title: Kai_Feb


title: GFP Donor-3

description: GFP


title: Hua_Apr


title: GFP Donor-2

description: GFP


title: GFP Donor-1

description: GFP


title: RNA-Seq CHD8_KD11_new

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description:
RNA-Seq CHD8_KD2_new
processed data file: RNASEQ_fpkm_new.txt

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat2. The TopHat2 program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). Differential expression test between different groups was performed with Cuffdiff module, and genes with both fold change > 1.2 and  p-value < 0.05 were selected as differentially expressed genes. The GTF annotation file for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM table format for RNA-Seq

source_name: E13-E15 cortex

growth_protocol: GFP transfected cells, either with control or Chd8 shRNA, from E15 cortices electroporated at E13 were FAC sorted.

extract_protocol:
Total RNA was extracted using Rneasy Plus Kit (Qiagen).
RNASEQ library was constructed using Clontech Low Input Prep Kit.

value: brain cortex

tag: treatment

value: CHD8 knockdown


title: RNA-Seq CTRL11_new

description:
RNA-Seq CTRL2_new
processed data file: RNASEQ_fpkm_new.txt

value: control


title: RNA-Seq CHD8_KD10_new

description:
RNA-Seq CHD8_KD1_new
processed data file: RNASEQ_fpkm_new.txt


title: RNA-Seq CTRL12_new

description:
RNA-Seq CTRL3_new
processed data file: RNASEQ_fpkm_new.txt


title: RNA-Seq CTRL10_new

description:
RNA-Seq CTRL1_new
processed data file: RNASEQ_fpkm_new.txt


title: ASF1B Donor-2


title: RNA-Seq CHD8_KD12_new

description:
RNA-Seq CHD8_KD3_new
processed data file: RNASEQ_fpkm_new.txt


title: si con plus SB431524  rep3

city: Leiden

first: Peter

last: ten Dijke

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description: sample 15

data_processing:
RNAseq reads (50bp single end) were generated by Illumina-HiSeq2000/2500 platform at BGI.
Raw RNAseq reads are trimmed with low quality bases using sickle ( version 1.33 with settings “se -t sanger”) before aligned to mm10 using gsnap (version 2014-12-23 with settings “--novelsplicing 1 –npaths 1 --quiet-if-excessive”).
Aligned reads were counted to their associated genes based on UCSC Refseq gene annotation (created on 11-09-2015 for mm10) using htseq-count (version 0.6.1p1)
RPKM counts are calculated further from the raw read count table generated by htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: TSV, raw reads counts and RPKM counts

source_name: inner cell mass

growth_protocol: the mESCs were cultured in a serum-free DMEM medium comprises N2 and B27 supplements, 1% nonessential amino acids, 2 mM L-glutamine, and 0.1 mM b-mercaptoethanol (Sigma).

extract_protocol:
The NucleoSpin RNA II kit (BIOKE) was used to isolate RNA, and cDNA was obtained by reverse transcription-PCR (RevertAid First Strand cDNA Synthesis Kits, Fermentas).
RNA-Seq Quantification Library

treatment_protocol: mESCs were treated with or without 25ng/ml Activin A during differentiation.

tag: cell type

value: embryonic stem cell

tag: strain

tag: passages

value: less than 20


title: si Vprbp plus ActivinA rep3

description: sample 14


title: si con  rep3

description: sample 11


title: si Vprbp plus ActivinA rep2

description: sample 9


title: si Vprbp  rep3

description: sample 12


title: si con plus SB431524  rep2

description: sample 10


title: si con plus Activin A rep3

description: sample 13


title: si con plus SB431524  rep1

description: sample 5


title: si con  rep1

description: sample 1


title: si Vprbp  rep2

description: sample 7


title: si con  rep2

description: sample 6


title: si Vprbp  rep1

description: sample 2


title: si Vprbp plus ActivinA rep1

description: sample 4


title: si con plus Activin A rep1

description: sample 3


title: Scr 1

first: Michał

last: Pasternak

state: - None -

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Illumina OLB(off-line Basecaller) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bwa with parameters GenomeBwaOptions_PE = -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
The mapped read counts for each gene were normalized for RNA length and for the total read number in each lane using the fragments per kilobase per million (FPKM) method.We used a strict algorithm to identify differentially expressed genes (DEGs) based on comparing the exposed with unexposed group to generate the DEGs.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Control oocytes

growth_protocol: Ovaries were dissected from two to five 10-12 day old (C57BL x CBA) F1 females. To obtain individual follicles, the ovaries were incubated in modified MEM-alpha medium optimized for in vitro culture of follicles (MEM-alpha (Gibco 12000-014) supplemented with 0.026M NaHCO3 (Sigma), 5678U/100 ml Penicillin G (Sigma) and 8265U/100ml Streptomycin (Sigma), 1x ITS (Insulin/Transferrin/Selenium Solution; Sigma; Stock is 100x), 5% FBS (Fetal Bovine Serum; Gibco 16000044) and 0.01 µg/ml FSH (Follicle Stimulating Hormone; National Hormone and Peptide Program, NDDK-oFSH-20) that was supplemented with 2 mg/ml collagenase (Roche) for about 30-40 minutes total. During incubation with collagenase, the ovaries were pipetted up and down every 10 minutes to facilitate dissociation and then washed through several droplets of follicle culture medium without collagenase and were cultured at 37°C in 5% CO2 on membrane inserts in 6 well or 12 well culture dishes filled with follicle culture medium (see above). After 8-10 days of culture the oocytes were isolated in M2 medium supplemented with 10% FBS and matured until reached metaphase of the second meiotic division (MII).

extract_protocol:
NucleoSpin RNA XS (Macherey-Nagel)
A cDNA library was prepared using SMARTer® Ultra™Low Input RNA for Sequencing (Clonetech Laboratories) and the samples were processed by BGI Tech Solutions. The cDNA product was synthesized and amplified using SMARTer PCR cDNA Synthesis Kit (Clontech) from the total RNA (10 ng) of sample. The cDNA was fragment by Covaris E210 (Covaris) and the median insert length was about 200bp.

treatment_protocol: injections with siRNAs

value: (C57BL x CBA) F1

tag: developmental stage

value: Metaphase II


title: Scr 3


title: Scr 2


title: Btg4 3

source_name: Btg4-depleted oocytes


title: RNA-Seq CHD8_KD1

description: processed data file: RNASEQ_fpkm.txt


title: RNA-Seq CTRL2

description: processed data file: RNASEQ_fpkm.txt


title: Btg4 2


title: RNA-Seq CTRL1

description: processed data file: RNASEQ_fpkm.txt


title: Btg4 1


title: RNA-Seq CHD8_KD2

description: processed data file: RNASEQ_fpkm.txt


title: si con plus Activin A rep2

description: sample 8


title: HBEC2MBT_DAC

status: Public on Sep 09 2016

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

data_processing:
Multiplexing performed with CASAVA version 1.4
Adapter trimming performed with fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
miRNA reads aligned to human genome build using Bowtie v0.12.7 with parameters (Bowtie -a --best --strata -v 3  -m 10 -q -t)
Counts per mature miRNA from aligned reads computed using Bedtools and list of genomic features from miRBase v17
Counts were normalized to rpm (total # reads aligned per sample) and log2 transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file including separate tabs for raw counts and RPM values

source_name: Lung

growth_protocol: cultured using ATCC method and suggested media

extract_protocol:
total RNA was isolated with TRIzol following manual instructions
Small molecular weight fraction (<200 bp) RNA was size fractioned using the Ambion (Life Technologies) flashPAGE fractionator to obtain small RNAs of 10-40nts. Small RNA sequencing libraries were created using SOLiD Small RNA Expression Kit (Ambion) starting with 200 ng of the size-fractionated material following the manufacturer’s instructions.  Libraries were sequenced on an Applied Biosystems (Life Technologies) SOLiD System to obtain 36bp reads.

treatment_protocol: DAC treated cell lines were treated daily with vehicle or 5-aza-2’deoxycytidine (500 nM) for four days

tag: cell line

value: vehicle


title: HBEC2MBT


title: SmartSeq2B_H9

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: Library preparations were performed using the Smart-seq2 protocol, as described in Picelli et al., Nature Methods 2013

data_processing:
base-calls were performed with Illumina bcl2fastq
all cDNA reads were aligned with Star v2.4.0
SCRB-seq and Drop-seq protocol reads were tagged with its mate-pair UMI and cell barcode; unique reads were obtained; more information see README file
Smart-seq and Smart-seq2 reads were assigned to genes using Rsubread
only cells were considered with at least 1,000,000 reads; doublets discarded and failed libraries filtered by low nearest-neighbor correlation coefficients
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with unique gene-wise counts of cells considered for final analysis: ziegenhain_complete_data.txt

source_name: mouse embryonic cell line

growth_protocol: J1 mESC were cultured in ground pluripotency states by 2i/LIF culture as described previously.

extract_protocol: single-cell lysate

tag: library preparation


title: SmartSeqB_H12

description: Library preparation was performed with the Fluidigm C1 platform as per manufacturers' protocol.

value: Smart-seq / C1


title: SmartSeqB_H9


title: SmartSeqB_H6


title: SmartSeq2B_H7


title: SmartSeqB_H5


title: SmartSeqB_H7


title: SmartSeq2B_H6


title: SmartSeqB_H4


title: SmartSeq2B_H8


title: SmartSeqB_H1


title: SmartSeqB_G11


title: SmartSeqB_G9


title: SmartSeqB_G12


title: SmartSeq2B_H4


title: SmartSeq2B_H3


title: SmartSeqB_G3


title: SmartSeqB_H10


title: SmartSeqB_G2


title: SmartSeqB_G1


title: SmartSeq2B_H2


title: SmartSeq2B_H10


title: SmartSeqB_F11


title: SmartSeqB_F6


title: SmartSeq2B_H1


title: SmartSeq2B_H11


title: SmartSeq2B_H5


title: SmartSeqB_F4


title: SmartSeqB_F2


title: SmartSeq2B_G9


title: SmartSeqB_E10


title: SmartSeq2B_G7


title: SmartSeq2B_G8


title: SmartSeqB_E8


title: SmartSeq2B_G2


title: SmartSeq2B_G4


title: SmartSeqB_F5


title: SmartSeq2B_G5


title: SmartSeq2B_G6


title: SmartSeq2B_G11


title: SmartSeqB_E11


title: SmartSeqB_E6


title: SmartSeqB_E7


title: SmartSeqB_E4


title: SmartSeq2B_G3


title: SmartSeq2B_G1


title: SmartSeq2B_G10


title: SmartSeqB_D10


title: SmartSeqB_D9


title: SmartSeq2B_F9


title: SmartSeqB_D8


title: SmartSeq2B_F8


title: SmartSeq2B_F7


title: SmartSeqB_D5


title: SmartSeq2B_F6


title: SmartSeq2B_F4


title: SmartSeqB_D3


title: SmartSeq2B_F3


title: SmartSeqB_D1


title: SmartSeq2B_F5


title: SmartSeqB_C12


title: SmartSeqB_C9


title: SmartSeq2B_F2


title: SmartSeqB_C7


title: SmartSeq2B_E7


title: SmartSeqB_C6


title: SmartSeqB_C10


title: SmartSeq2B_E8


title: SmartSeq2B_E6


title: SmartSeq2B_E5


title: SmartSeqB_C5


title: SmartSeqB_C4


title: SmartSeq2B_E4


title: SmartSeqB_D7


title: SmartSeqB_C3


title: SmartSeq2B_E3


title: SmartSeqB_C11


title: SmartSeqB_D11


title: SmartSeq2B_E2


title: SmartSeqB_C2


title: SmartSeqB_C1


title: SmartSeq2B_E11


title: SmartSeq2B_F1


title: SmartSeq2B_E9


title: SmartSeq2B_E1


title: SmartSeq2B_E10


title: SmartSeqB_B8


title: SmartSeq2B_D9


title: SmartSeq2B_D8


title: SmartSeq2B_D6


title: SmartSeqB_B4


title: SmartSeqB_B5


title: SmartSeq2B_D7


title: SmartSeq2B_D5


title: SmartSeq2B_D4


title: SmartSeqB_B1


title: SmartSeqB_B2


title: SmartSeq2B_D2


title: SmartSeqB_B3


title: SmartSeqB_A10


title: SmartSeq2B_D3


title: SmartSeq2B_D1


title: SmartSeq2B_D10


title: SmartSeqB_A8


title: SmartSeqB_A7


title: SmartSeqB_B12


title: SmartSeqB_A9


title: SmartSeq2B_C9


title: SmartSeq2B_C8


title: SmartSeq2B_C7


title: SmartSeqB_B10


title: SmartSeqB_A5


title: SmartSeqB_A4


title: SmartSeqB_B9


title: SmartSeqB_B7


title: SmartSeq2B_C6


title: SmartSeqB_A1


title: SmartSeq2B_C5


title: SmartSeqA_H5


title: SmartSeqA_H7


title: SmartSeq2B_C2


title: SmartSeq2B_C4


title: SmartSeqA_H8


title: SmartSeq2B_C11


title: SmartSeqA_H4


title: SmartSeq2B_C10


title: SmartSeq2B_B9


title: SmartSeqA_H12


title: SmartSeqA_H2


title: SmartSeqA_H11


title: SmartSeq2B_B11


title: SmartSeqA_G8


title: SmartSeq2B_B2


title: SmartSeq2B_A8


title: SmartSeqA_G6


title: SmartSeqA_G5


title: SmartSeq2B_A7


title: SmartSeq2B_B10


title: SmartSeq2B_A6


title: SmartSeqA_G3


title: SmartSeqA_G2


title: SmartSeq2B_A5


title: SmartSeqA_G1


title: SmartSeqA_G12


title: SmartSeqA_G11


title: SmartSeq2B_B4


title: SmartSeqA_H3


title: SmartSeq2B_A2


title: SmartSeqA_F9


title: SmartSeq2B_A11


title: SmartSeq2B_B3


title: SmartSeqA_F6


title: SmartSeqA_F5


title: SmartSeq2B_A10


title: PMG-LPS-4H-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.36)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the TopHat (version 2.0.10) software based on reference genome sequence (Mus musculus UCSC mm10) and the differential gene expressed values of each sample were calculated by Cufflinks(v2.2.1)
the number of reads mapped to gene ID features were counted using HTSeq v0.6.1.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: primary microglia cells

growth_protocol: PM were seeded in poly-L-lysine-coated T-75 flask in DMEM/nutrient mixture F-12 (DMEM/F12, 1:1) containing 20% FBS (catalog # 26140), 100 IU/ml penicillin and 10 µg/ml streptomycin (catalog # 15140) from Invitrogen (CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C. The medium was changed every 2-3 days. After two weeks in culture, mixed glial cell cultures are shaken at 150 rpm at 37°C for 45 min, and the glial cell suspension was collected from each flask and seeded on poly-L-lysine coated cell culture plate. PM were sub-plated and used for further experiments.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine microglial PM, were treated with LPS (10ng/ml) for 2hrs or 4 hrs.

value: primary microglia cells

value: treated with LPS (10ng/ml) for 4 hrs


title: SmartSeqA_F3


title: SmartSeqA_F12


title: SmartSeqA_F10


title: SmartSeqA_F1


title: SmartSeq2B_A4


title: SmartSeqA_F8


title: PMG-LPS-4H-1


title: SmartSeq2B_A12


title: PMG-LPS-2H-3

value: treated with LPS (10ng/ml) for 2 hrs


title: PMG-LPS-2H-1


title: PMG-LPS-2H-2


title: PMG-Cont-3


title: SmartSeqA_F2


title: SmartSeq2B_A1


title: SmartSeqA_E5


title: SmartSeqA_E9


title: SmartSeqA_E7


title: PMG-Cont-1 (2)


title: SmartSeqA_F11


title: SmartSeqA_F4


title: PMG-LPS-4H-2


title: BV2-LPS-GSKJ4-3

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the TopHat (version 2.0.10) software based on reference genome sequence (Mus musculus UCSC mm10) and the differential gene expressed values of each sample were calculated by Cufflinks(v2.2.1)
the number of reads mapped to gene ID features were counted using HTSeq v0.6.1.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: BV2 cells

growth_protocol: Murine microglia BV-2 cells were grown in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) (catalogue # 26140), 100 IU/ml penicillin, and 10 µg/ml streptomycin (catalogue # 15140) from Invitrogen (CA, USA). Cells were maintained in a humidified incubator with 95% air, 5% CO2 atmosphere at 37°C.

treatment_protocol: Murine microglial BV-2 cells, were treated with LPS (10ng/ml) or GSK-J4 (10 μM) then stimulated with LPS (10 ng/ml) and GSK-J4 (10 μM) for 4 hrs.

value: treated with LPS (10 ng/ml) and GSK-J4 (10 μM) for 4 hrs

value: microglia


title: SmartSeqA_E4


title: SmartSeqA_E3


title: SmartSeqA_E2


title: BV2-LPS-GSKJ4-2


title: BV2-LPS-2H-1

treatment_protocol: Murine microglial BV-2 cells, were treated with LPS (10ng/ml) or GSK-J4 (10 μM) then stimulated with LPS (10 ng/ml) and GSK-J4 (10 μM) for 2hr and 4 hrs.


title: BV2-LPS-2H-3

tag: agent

value: LPS (10ng/ml) for 2 hrs


title: BV2-LPS-GSKJ4-1


title: SmartSeqA_E8


title: BV2-GSKJ4-3

value: treated with GSK-J4 (10 μM) for 4 hrs


title: SmartSeqA_E6


title: SmartSeqA_E12


title: SmartSeqA_E1


title: SmartSeqA_E11


title: BV2-LPS-2H-2


title: BV2-GSKJ4-1


title: SmartSeqA_D7


title: BV2-LPS-2


title: SmartSeqA_D9


title: SmartSeqA_E10


title: SmartSeqA_D6


title: BV2-Cont-3


title: BV2-Cont-2


title: SmartSeqA_D5


title: BV2-LPS-3


title: BV2-LPS-1


title: BV2-GSKJ4-2


title: SmartSeqA_D4


title: PMG-Cont-2 (2)


title: BV2-Cont-1


title: SmartSeqA_D3


title: RiboMin-TotalRNA-wt-AL

city: Rotterdam

first: Akos

last: Gyenis

address: Wytemaweg 80

department: Genetics

institute: ERASMUS MC

description: Ribosomal RNA depleted

data_processing:
Basecalling is performed by using NARWAL
Raw FASTQ files
FPKM values from separated long reads were calculated using Cufflinks2
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: TXT files with FPKM values

source_name: Liver

extract_protocol:
Total RNA from flash frozen liver was extracted by using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN). Ribosomal RNA species were removed by using RiboMinus kit (Ambion).
Illumina TruSeq v3 protocol

value: Liver

tag: background strain

tag: genotype

value: wildtype

tag: diet

value: Ad libidum diet

tag: age

value: 16 weeks


title: SmartSeqA_D2


title: RiboMin-TotalRNA-Ercc1-DR

description: Ribosomal RNA depleted

value: Ercc1 delta/-

value: Diet restriction


title: SmartSeqA_D10