title: S2 UNTR IP REP3

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

description: smRNA-seq

data_processing:
Image analysis and base-calling were performed with OLBv1.8 software.
Fastx toolkit was used to clip adapter sequence
Sequenced tags were aligned to the mouse genome using STAR
featureCounts was used to count reads mapped to exons
differential expression by edgeR
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: raw count matrix (MECP2_RIP_countmatrix.tsv)

source_name: mouse primary cortical cells

growth_protocol: Isolated cortical neurons from 15 day C57BL/6 mice were seeded at a density of 2 x 10^7 cells onto poly-D-lysine treated T75 flasks and maintained in a humidified 37 C incubator with 5% CO 2 . Cells were maintained in plating medium for 2 h before replacing medium with serum-free growth media consisting of neurobasal media containing B27 supplements, gentamicin and glutamine. Cultures were allowed to mature for 6 days in vitro (DIV) before harvesting for experiments.

extract_protocol:
Preparation of soluble chromatin fractions using micrococcal nuclease (MNase) digestion. Briefly, the primary cortical neurons were scraped off the bottom of the flask in 1 mM EDTA in PBS -/- (Ca 2+ and Mg 2+ free) and centrifuged to pellet. Cell pellet was re-suspended and incubated in 600 mL nucleus isolation buffer [15 mM Tris-HCL pH 7.5, 60 mM KCl, 0.5 M sucrose, 0.25 mM EDTA, 0.125 mM EGTA, 1 mM DTT, 0.5 mM PMSF, 0.15 mM spermidine, 0.15 mM spermine, 0.2% NP-40, 1 x complete proteinase inhibitor (PI) (Roche)] for 5 min at 48C with rotation then centrifuged for 3 min at 5000 g. The precipitate, containing cell nuclei and the supernatant, containing cytosolic fraction were recovered. The precipitate was re-suspended in 400 mL of MNase digestion buffer [20 mM Tris-HCl, 70 mM NaCl, 20 mM KCl, 5 mM MgCl, 3 mM CaCl, 0.5 mM PMSF, 1 x complete PI (Roche)] and 250 units of micrococcal nuclease (Worthington) were added. The MNase digestion was performed for 12 min. Digestion was stopped by addition of 16 mL MNase stop solution (125 mM EDTA, 125 mM EGTA). The digest was centrifuged (5 min, 5000 g, 48C) and S1 chromatin fraction (first supernatant) was collected. The pellet was lysed in 400 mL of MNase lysis buffer (2 mM EDTA with PI) for 15 min at 48C by rotation and lysed material was centrifuged for 5 min at 5000 g at 4oC. Second supernatant S2 was recovered and the pellet (P fraction) was resuspended in nuclear isolation buffer with PI. MNase digestion produced two distinct chromatin fractions designated as S1 chromatin fraction (micrococcal nuclease sensitive and mononucleosomal enriched) and S2 chromatin fraction (micrococcal nuclease resistant and oligonucleosomal enriched) as described previously. 26 MNase digestion of chromatin and the purity of the preparation was assessed by analyzing length of DNA fragments in each chromatin fraction by gel electrophoresis.  Chromatin Immunoprecipitation on MNase digested chromatin fractions. Chromatin immunoprecipitation was performed on MNase digested chromatin fractions S1 and S2 using anti-MeCP2  antibody (M9317, Sigma). To avoid RNA degradation while performing RIP, RNase free tubes and RNase inhibitor RNase-OUT reagent (Invitrogen) were used. RNA was purified from immunopurified chromatin and sequenced with massive parallel sequencing for the discovery of small ncRNAs bound by MeCP2. Briefly, 1 mg of quantified DNA in chromatin was retained as input material. To each tube, 5 mg of chromatin diluted in ChIP dilution buffer was added, along with 20 mL of protein A Dynabeads (Invitrogen) for pre-clearing. An additional equal number of tubes were set up in parallel containing 475 mL ChIP dilution buffer and 20 mL of protein A Dynabeads, with either 3 mg of anti-MeCP2 antibody (Sigma) or Rabbit IgG (non-specific antibody). All tubes were placed at 48C with rotation for 1 h for pre-clearing and pre-binding. Precleared chromatin was separated from beads using a magnetic rack (Invitrogen) and was transferred to a parallel set of tubes containing beads pre-bound to antibodies. RNaseOUT reagent was added to the tubes and incubated overnight at 48C with rotation in order to precipitate chromatin. The next day, chromatin-bound beads were washed twice consecutively with 0.5 mL of the following buffers, in order: low salt buffer, high salt buffer, LiCl buffer, and TE buffer. RNaseOUT was added to all wash buffers. After washes, ChIP elution buffer was added to the retained input material and to antibody and no-antibody or IgG controls and sample pooled together into anti-MeCP2 antibody bound, No antibody or IgG-bound control, and Input. RNA was purified using Trizol and mirVana miRNAs isolation kit (Ambion).
Deep sequencing of the immunopurified small ncRNAs. We performed deep sequencing of the immunopurified small ncRNAs from active and silent chromatin. Small RNAs were converted into cDNA and sequenced using the Illumina high-throughput sequencing. A cDNA library was prepared according to the Illumina Small RNA v1.5 protocol. Briefly, adapters were ligated at 3’ and 5’ ends of the RNA and RNA was then reverse transcribed to cDNA, after which cDNA was amplified for 14 or 18 cycles of PCR. Complimentary DNA libraries were size-selected on an agarose gel. The quality and quantity of the 200 library was evaluated using the Shimadzu MultiNA. Sequencing was performed for 51 cycles using the Genome Analyzer IIx, according to the manufacturer’s protocols. Image analysis and base calling were performed using the software supplied with the Genome Analyzer instrument.

value: primary cortical neurons

value: untreated

tag: ip antibody

value: anti-MeCP2 antibody (M9317, Sigma)

tag: enrichment

value: MeCP2 immunoprecipitation

tag: chromatin fraction

value: S2 (closed chromatin)


title: 102cell_siCtrl

status: Public on May 23 2018

type: SRA

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Number of transcripts per million reads mapped (TPM) were computed using kallisto (http://pachterlab.github.io/kallisto/)
Fold changes based on Kallisto TPM were computed using R (added 1 to all TPM values to avoid zero/infinite ratios)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample (VKMJ-STAT3_kallisto_abundance.txt) and transcript-based fold changes for 102siCtrl vs. 103siCtrl (VKMJ-STAT3_fold_changes.txt)

molecule: total RNA

organism: Homo sapiens

source_name: angiolipoma cells from LAM patient

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc., San Diego, CA)

treatment_protocol: For the rapamycin condition, cells were treated with 100 nM rapamycin for 18 hr in serum-free condition (DMEM supplemented with 0.1% BSA).  For downregulation of STAT3, 20mM siSTAT3 or NT (non targeting) siRNA was added to the cells in complete medium and incubated for 24 hours.  Medium was changed to DMEM containing 0.1% BSA, and cells were incubated overnight.

tag: cell type

value: angiolipoma

tag: disease

value: Lymphangioleiomyomatosis

tag: treatment

value: siCtrl

tag: cell line genotype


title: Brain Mirror-Seq Negative Control

status: Public on May 22 2018

city: Irvine

first: Xueguang

last: Sun

state: CA

address: 17062 Murphy Ave

institute: zymo research corp

library_source: genomic

data_processing:
Using this method, the 5hmC levels of various human tissues and paired tumor liver tissues were mapped genome-wide.
Genome_build: hg19
Supplementary_files_format_and_content: big bed file

molecule: genomic DNA

source_name: Brain Tissue

extract_protocol:
Genomic DNA from the source was purified via phenol::chloroform extraction
RRBS-derived
Mirror-seq library

tag: tissue

value: Brain Tissue


title: S1 UNTR IP REP3

country: Australia

description: smRNA-seq

organism: Mus musculus

tag: strain

value: S1 (open chromatin)


title: S2 UNTR INPUT REP1

description: smRNA-seq

value: input background control


title: S2 UNTR IP REP1

description: smRNA-seq


title: S2 UNTR INPUT REP2

description: smRNA-seq


title: S2 UNTR IP REP2

description: smRNA-seq


title: Brain


title: treated 2 (SC3_b10nM)

city: Orbassano

first: Elio

last: Grazio

address: Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10

country: Italy

institute: University of Turin

data_processing: Reads were mapped to the Rattus norvegicus rn5 reference assembly using TopHat v2.0.10 (D. Kim et al., 2013) ts were generated using htseq and the refseq transcriptome.  Genes with RPKM > 1 in all 3 replicates were considered expressed in each condition.

organism: Rattus norvegicus

source_name: Schwann cells

growth_protocol:
Primary Schwann cells were routinely cultured on poly-L-lysine (PLL, Sigma)-coated plate, in complete medium consisting of DMEM (Sigma #D5671) supplemented with 10% heat-inactivated foetal bovine serum (FBS, Invitrogen), 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, 63 ng/mL glial growth factor (GGF, #369-HB, R&D Systems) and 10 µM forskolin (Sigma) and incubated at 37°C in 5% CO2.
Confluent Schwann cells were starved overnight (18 hours) in "starving medium" consisting in: DMEM (Sigma #D5671) supplemented with 2% heat-inactivated foetal bovine serum, 100 units/mL penicillin, 0.1 mg/mL streptomycin, 1 mM sodium pyruvate, 2 mM L-glutamine, and 10 µM forskolin

extract_protocol: Deep RNA sequencing was performed on three mock samples and three stimulated samples obtained in three independent experiments. RNA quality was assessed on an Agilent 2100 Bioanalyzer. All samples had RIN ≥ 9. For RNA-Seq library preparation, approximately 2 μg of total RNA were subjected to poly(A) selection and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.

treatment_protocol: Starved Schwann cells were stimulated for 6 hours in "starving medium" containing  10 nM recombinant soluble NRG1β1 (#396-HB), purchased from R&D systems. Control mock samples were stimulated with the same volume of ligand resuspension buffer (PBS containing 1% bovine serum albumin, BSA, Sigma).

value: Wistar

tag: age

value: adult

value: Schwann cells


title: S2 UNTR INPUT REP3

description: smRNA-seq


title: S1 UNTR IP REP2

description: smRNA-seq


title: S1 UNTR IP REP1

description: smRNA-seq


title: S1 UNTR INPUT REP3

description: smRNA-seq


title: S1 UNTR INPUT REP1

description: smRNA-seq


title: S1 UNTR INPUT REP2

description: smRNA-seq


title: F

status: Public on May 21 2018

city: Beijing

first: Yimian

last: Ma

address: No. 151 Malianwa North Road, Haidian District

country: China

institute: The Institute of Medicinal Plant Development (IMPLAD)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and did the quality control with custom perl script
assembled transcriptome using trinity version Trinityrnaseq_r20131110 with parameters --output  --seqType fq --JM 350G --left  --right  --min_contig_length 200 --CPU 40
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
differentially expressed genes selected using custom R v3.1.0 script
Supplementary_files_format_and_content: Excel file include RPKM values for three samples

organism: Epimedium pseudowushanense

source_name: Epimedium pseudowushanense seed

extract_protocol:
Total RNA was extracted from seeds using TRIzol Reagent (Invitrogen, Carlsbad, CA). RNA pellets were dissolved in RNAse-free water, quantified by Nano-Drop ND-2000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE). RNA quality was checked by 2% agarose gel electrophoresis.
The cDNA library was constructed by using a TruSeq PE Cluster Kit for Illumina,  the quality of retrieved cDNA was checked using the Agilent 2100 Bioanalyzer (RNA Nano Chip, Agilent), and it was sequenced using an Illumina HiSeq 2500 paired-end sequencing system

tag: developmental stage

value: At the stage of seed germinating

value: seeds


title: 400B


title: X3_4_1

value: At the stage of seed embryo growed to more than 1/2 length of the seeds


title: YYH_3

value: At the stage of seed embryo started to grow


title: A234T6_BC

city: Taipei City

first: Shau-Ping

last: Lin

address: No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description: strand-specific

data_processing:
Adapter trimmed RNAs are aligned to gga5 genome assembly using tophat2, with options: -G galGal5.refseq.gtf --library-type fr-firststrand
Reference guided sequence assembly on RNA-seq samples using Cufflinks (v2.2.1), with options: --GTF-guide galGal5.refseq.gtf --frag-bias-correct galGal5.fa --multi-read-correct --library-type fr-firststrand --max-mle-iterations 500 --no-effective-length-correction --min-isoform-fraction 0.4 --pre-mrna-fraction 0.4 --min-frags-per-transfrag 100 --min-intron-length 20 --max-multiread-fraction 0.3 --3-overhang-tolerance 0 --intron-overhang-tolerance 0
Cuffmerge assemble the Cufflinks results of each RNA-seq samples, with option: --min-isoform-fraction 0.7
Cuffnorm for gene and novel transcript expression calculation on the RNA-seq samples, with reference to Cuffmerge results, with options:  --library-type fr-firststrand
Supplementary_files_format_and_content: Cuffnorm normalized transcript expressions, for RNA-seq samples

organism: Gallus gallus

source_name: Blastodermal cells

growth_protocol: Fertilized eggs incubated at 37oC at 60% humidity to desired date

extract_protocol:
Total RNA samples are extracted via TRIzol reagent according to according to manufacturers’ instructions.
Strand-specific library was constructed following Illumina TruSeq stranded total RNA sample preparation kit according to manufacture's instruction

tag: breed

value: Blastodermal cells

value: fresh fertilized eggs


title: A234T4_E14G

description: strand-specific

source_name: E14 male gonads

value: Male gonads


title: A234T5_BC

description: strand-specific


title: A234T1_E11G

description: strand-specific

source_name: E11 male gonads


title: A234T3_E14G

description: strand-specific


title: A234T2_E11G

description: strand-specific


title: E14G rep2

description: periodate oxidation treated

data_processing:
Base-calling via real time analysis in Illumina HiSeq 2000 systems
adapter trimmed small RNAs are aligned to gga4 genome assembly using tophat2, with options: -g 1 -N 0 --read-gap-length 0 --read-edit-dist 0 --read-realign-edit-dist 0 --max-insertion-length 0 --max-deletion-length 0
filtering out potential rRNA/tRNA based on Rfam record, and filtering out potential miRNA based on miRBase record, using bowtie v1.2.0 with options: --norc -v 0; piRNA candidates are selected at range of 24nt to 34nt
piRNA cluster prediction via proTRAC v2.0.5, with options: -pdens 0.05 -1Tor10A 0.01 -1Tand10A 0.01 -distr 1-90 -clsize 3000 -clsplit 0.2 -pimin 24 -pimax 34 -rpm -nh -nr -noimage -nofaspi; the proTRAC v2.0.5 was slightly modfied for identifying dual-strand piRNA clusters
Genome_build: gga5
Supplementary_files_format_and_content: proTRAC output that list piRNA clusters identified in each sample

extract_protocol:
Samples are homogenized and small RNAs are collected via miRNeasy Mini Kit (Qiagen, CA, USA) according to manufacturers’ instructions
Sodium periodate oxidation treatment on small RNA samples, followed by library preparation using Illumina TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA, USA) accordint to manufactures' iinstruction

value: Leghorn


title: E11G rep2

description: periodate oxidation treated


title: E7PGC rep2

description: periodate oxidation treated

source_name: E7 cultured male PGC

value: Arbor Acres broiler


title: E7PGC rep1

description: periodate oxidation treated


title: UM-SCC6

city: dalian

first: Xiaojie

last: Li

address: No. 9 of Lvshun South Road

institute: Dalian Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts. In this step, clean datas(clean reads) were obtained by  removing reads containing poly-N, with 5’ adapter contaminants, without 3’  adapter or the insert tag, containing ploy A or T or G or C and low quality reads  from raw data. At the same time, Q20, Q30, and GC-content of the raw datas  were calculated. Then, chose a certain range of length from clean reads to do all  the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et  al., 2009) without mismatch to analyze their expression and distribution on the  reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0  was used as reference, modified software mirdeep2(Friedlander et al., 2011) and  srna-tools-cli were used to obtain the potential miRNA and draw the secondary  structures. Custom scripts were used to obtain the miRNA counts as well as base  bias on the first position of identified miRNA with certain length and on each  position of all identified miRNA respectively. miRNA expression levels were estimated by transcript per million (TPM) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*106.
Genome_build: mirBase 20.0
Supplementary_files_format_and_content: text file with normalized expression values and statistics.

source_name: UM-SCC６cells_parental line

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Takara, Dalian, China) according to the manufacturer’s instructions.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® EB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: Cells that invaded through the matrix channel from the cell culture channel and spread into the stimulation channel were termed as the invasion front cells in our study. These invasion front cells were harvested by trypsinization and transferred into a culture dish. When reaching confluence, cells were collected and used to generate the second round invasion front cells in the microfluidic chip by repeating the above steps. The third round invasion front cells of UM-SCC6 were obtained in the microfluidic chip and named as UM-SCC6-M.

value: oral squamous cell carcinoma

tag: cell line


title: UM-SCC6-M

description: UM-SCC6-M cells were obtained by three rounds of isolation of invasion front UM-SCC6 cells on the microfluidic chip.  UM-SCC6-M cells exhibit some mesenchymal cell characteristics and have high invasion ability.

source_name: UM-SCC６cells_invasion front cells


title: BC rep2

description: periodate oxidation treated


title: GRO-seq_231ERαLQ_45min_rep4

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
library strategy: GRO-seq
FastQC
Adaptor trimming using Cutadapt
Alignment to the human reference genome (hg19) and one complete copy of an rDNA repeat (GenBank ID: U13369.1) using the BWA aligner. The replicates 1, 2 are biological replicates and replicates 3, 4 are technical replicates of replicates 1,2 respectively. The technical replicates (1,3 & 2,4)  were merged to consider as a single replicate after confirming positive correlation between them and used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization

growth_protocol: MDA-MB-231 cells obtained from ATCC were transduced with ERα wile-type or L540Q mutant by lentivirus-mediated transduction and maintained in phenol red-free Dulbecco’s modified Eagle’s medium/nutrient mixture F-12 Ham (DMEM/F-12; Sigma, D2906) supplemented with 10% charcoal-dextran treated calf serum.

extract_protocol:
Approximately 2 x 106 cells were seeded on a 15 cm2 plate and grown to ~80% confluence.  The cells were washed twice with ice-cold PBS and collected by scraping in Swelling Buffer [10 mM Tris•HCl pH 8.0, 2 mM MgOAc, 3 mM CaCl2, 0.5 mM DTT, 1x complete protease inhibitor cocktail, and SUPERase•In (Ambion)] on ice.  The cells were pelleted by centrifugation, resuspended in Lysis Buffer [10 mM Tris•HCl pH 8.0, 2 mM MgOAc, 3 mM CaCl2, 10 mM NaCl, 0.5% NP-40, 300 mM sucrose, 0.5 mM DTT, 1x complete protease inhibitor cocktail, and SUPERase•In (Ambion)].  To isolate the nuclei, the swollen cells were lysed by pipetting up and down 60 times using P1000 pipet tips.  The nuclei were pelleted by brief centrifugation, equilibrated and dispersed in Freezing Buffer to 5 x 106 nuclei/100 μL [50 mM Tris•HCl pH 8.3, 5 mM MgCl2, 40% glycerol, 0.1 mM EDTA, and SUPERase•In (Ambion)], aliquoted, and stored at -80°C.
The nuclei were incubated in the presence of 5’-bromo-UTP and α-32P radiolabeled-CTP for 5 min., with subsequent quenching by the addition of RQ-1 DNase (Promega, M6101).  RNA was isolated from the run-on reaction mixture and hydrolyzed by incubating with 0.2 N NaOH on ice for 15 min.  The fragmented RNA was treated with T4 PNK (NEB, M0201S) in the absence of ATP to dephosphorylate the 3’-terminus.  Nascent transcripts were isolated from the total RNA with two rounds of affinity purification using anti-BrdU antibody-conjugated agarose beads (Santa Cruz Biotechnology, sc-32323).  PolyA tails were added to the nascent transcripts using 1 mM ATP and 0.5 U/μL E. coli Poly(A) Polymerase (NEB, M0276S) at 37°C for 8 min.  cDNA was generated using the oNTI223HIseq primer (custom synthesized by IDT, HPLC purified) (Ingolia, 2009)  and purified on an 8% polyacrylamide TBE-urea gel.  The purified cDNA was then circularized using CircLigase (Epicentre, CL4111K), relinerized using APE1 (NEB, M0282S), and amplified using TruSeq small RNA-seq PCR primers (custom synthesized by IDT, HPLC purified) to generate the GRO-seq library.  The library quality was assessed using a D1000 ScreenTape (Agilent, 5067-5582) on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851).  The libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina HiSeq 2000 (single-end, 50 bp reads) for ~18 million raw reads per biological replicate.

treatment_protocol: Cells were treated with vehicle (EtOH) for 45 min or 100 nM E2 for 20 or 45 min.

tag: cell line background

tag: transduced with

value: ERα L540Q

tag: treated with

tag: molecule subtype

value: nascent RNA


title: BC rep1

description: periodate oxidation treated


title: GRO-seq_231ERαLQ_45min_rep1


title: GRO-seq_231ERαLQ_20min_rep4


title: GRO-seq_231ERαLQ_45min_rep2


title: GRO-seq_231ERαLQ_20min_rep3


title: GRO-seq_231ERαLQ_0min_rep3


title: GRO-seq_231ERαLQ_0min_rep4


title: GRO-seq_231ERαLQ_20min_rep1


title: GRO-seq_231ERαLQ_20min_rep2


title: MKOC_Untreated

data_processing:
Number of transcripts per million reads mapped (TPM) were computed using kallisto (http://pachterlab.github.io/kallisto/)
Fold changes based on Kallisto TPM were computed using R (added 1 to all TPM values to avoid zero/infinite ratios)
Genome_build: mm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values (VKMJ-TSC2Effects_kallisto_abundance.txt) and transcript-based fold changes for MEF_TSC2_neg vs. MEF_TSC2_plus (VKMJ-TSC2Effects_fold_changes.txt).

source_name: Tsc2-null mouse kidney epithelial cells

treatment_protocol: Cells were treated with diluent or 100 nM rapamycin for 18 hr in serum-free condition (DMEM supplemented with 0.1% BSA).

value: kidney epithelial cells

tag: genotype


title: GRO-seq_231ERαLQ_0min_rep1


title: GRO-seq_231ERαLQ_0min_rep2


title: GRO-seq_231ERαWT_45min_rep4

value: ERα wt


title: GRO-seq_231ERαWT_45min_rep3


title: GRO-seq_231ERαWT_45min_rep2


title: GRO-seq_231ERαWT_20min_rep4


title: GRO-seq_231ERαWT_45min_rep1


title: GRO-seq_231ERαLQ_45min_rep3


title: GRO-seq_231ERαWT_0min_rep3


title: GRO-seq_231ERαWT_20min_rep2


title: GRO-seq_231ERαWT_20min_rep3


title: GRO-seq_231ERαWT_20min_rep1


title: H3K27ac_ChIP-seq_231ERαLQ_45min_rep2

data_processing:
FastQC
Alignment using BOWTIE (version 0.12.7) with the default parameters.
ERα peak calling was performed using MACS software (version 1.4.2) using the default p-value and input condition as a control. Peak calling for ERα wild-type (Wt) and L540Q mutant was performed separately. The peak calling was done separately for each sequencing run and the peak calls of the two runs were compared to get a set of common peaks among the sequencing runs (i.e. replicates 1&2, 3&4 were combined respectively and the two peak universes were compared to get final set of peaks for Wt and LQ).  The replicates were combined and bigwig files were generated for combined replicates to visualize on genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization

extract_protocol:
Cells were grown to ~80% confluence and were crosslinked with 1% formaldehyde in PBS at 37°C for 10 min.  The crosslinking reaction was quenched by adding glycine to a final concentration of 125 mM.  The cells were collected by scraping in 1x PBS containing 1x complete protease inhibitor cocktail (Roche, 11697498001).  The cells were pelleted by brief centrifugation in a microcentrifuge and lysed by pipetting in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1x complete protease inhibitor cocktail).  The nuclei were collected by brief centrifugation in a microcentrifuge and resuspended in SDS Lysis Buffer (Tris•HCl pH 7.9, 1% SDS, 10 mM EDTA, 50 mM, 1 mM DTT, 1x complete protease inhibitor cocktail) by pipetting and incubation on ice for 10 min.  The chromatin was then sheared to ~200-500 bp DNA fragments by sonication using a Bioruptor Plus sonicator (Diagenode) for 25-30 cycles of 30 seconds on and 30 seconds off.  The solubilized sonicated chromatin was precleared with Protein A or Protein G Dynabeads (Invitrogen, 10001D and 10003D, respectively) and incubated overnight with 8 μL of polyclonal antiserum or 2.5 to 5.0 μg of commercial antibody. The immune complexes from the ChIP were precipitated by the addition of Protein A or Protein G Dynabeads (depending on the antibody used) and washed once with each of the following wash buffer in sequence: (1) Low Salt Wash Buffer (20 mM Tris•HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1x complete protease inhibitor cocktail); (2) High Salt Wash Buffer (20 mM Tris•HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1x complete protease inhibitor cocktail); (3) LiCl Wash Buffer (10 mM Tris•HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1x complete protease inhibitor cocktail); and (4) 1x Tris-EDTA (TE) containing 1x complete protease inhibitor cocktail.  The precipitated immune complexes were transferred to a new tube in 1x TE/complete protease inhibitor cocktail before elution of the genomic DNA fragments in Elution Buffer [40 mM Tris•HCl pH 7.9, 10 mM EDTA, 100 mM NaCl, 100 mM NaHCO3, 1% SDS, and 50 μg Proteinase K (Life Technologies, 2542)] for 2 hours at 55°C.  The crosslinks were reversed by incubating overnight at 65 °C, and the genomic DNA was purified using phenol:chloroform:isoamyl acid extraction (Sigma, P2069) followed by ethanol precipitation.
Input DNA or ChIPed DNA was subjected to additional purification using Agencourt AMPure XP beads (Beckman Coulter, A63881).  Two and a half to 10 ng of purified genomic DNA was subjected to end repair using an end-repair mix (Enzymatics, Y9140-LC-L) and 0.1 mM dNTPs.  A single dA base was added to the end repaired DNA using Klenow 35 Exo-minus (Enzymatics, P7010-HC-L), 1x Blue Buffer (Enzymatics, B0110), and 0.2 mM dATP to facilitate adaptor ligation.  TruSeq DNA Sample Prep Kit adaptors (custom synthesized by IDT, HPLC purified) were partially annealed to form double-stranded adaptors on one terminus, and annealed to insert DNA through double strand DNA-DNA ligation using T4 DNA ligase (Enzymatics, L6030-HC-L) in DNA Rapid Ligase Buffer (Enzymatics, B1010).  The adaptor-ligated DNA was amplified by PCR for 6 - 11 cycles and purified by electrophoresis on a 1% agarose gel containing SYBR Gold (Invitrogen, S11494).  The DNA was excised from the agarose gel and eluted using a QIAquick Gel Extraction Kit (Qiagen, 28706).  The quality of the library was assessed using a D1000 ScreenTape (Agilent, 5067-5582) on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851).  The libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina HiSeq 2000 (single-end, 50 base reads).

treatment_protocol: Cells were treated with vehicle (EtOH) or 100 nM E2 for 45 min.


title: H3K27ac_ChIP-seq_231ERαLQ_45min_rep1


title: GRO-seq_231ERαWT_0min_rep1


title: H3K27ac_ChIP-seq_231ERαLQ_0min_rep1


title: H3K27ac_ChIP-seq_231ERαLQ_0min_rep2


title: H3K27ac_ChIP-seq_231ERαWT_0min_rep1


title: H3K27ac_ChIP-seq_231ERαWT_45min_rep1


title: H3K27ac_ChIP-seq_231ERαWT_0min_rep2


title: SRC_ChIP-seq_231ERαLQ_0min_rep1


title: SRC_ChIP-seq_231ERαLQ_45min_rep1


title: SRC_ChIP-seq_231ERαLQ_45min_rep2


title: SRC_ChIP-seq_231ERαWT_45min_rep2


title: Med1_ChIP-seq_231ERαLQ_45min_rep1


title: Med1_ChIP-seq_231ERαLQ_45min_rep2


title: SRC_ChIP-seq_231ERαWT_0min_rep1


title: SRC_ChIP-seq_231ERαWT_0min_rep2


title: SRC_ChIP-seq_231ERαWT_45min_rep1


title: Med1_ChIP-seq_231ERαLQ_0min_rep2


title: SRC_ChIP-seq_231ERαLQ_0min_rep2


title: GRO-seq_231ERαWT_0min_rep4


title: GRO-seq_231ERαWT_0min_rep2


title: Med1_ChIP-seq_231ERαLQ_0min_rep1


title: ERα_ChIP-seq_231ERαLQ_45min_rep3


title: Med1_ChIP-seq_231ERαWT_45min_rep1


title: Med1_ChIP-seq_231ERαWT_45min_rep2


title: Med1_ChIP-seq_231ERαWT_0min_rep2


title: Med1_ChIP-seq_231ERαWT_0min_rep1


title: ERα_ChIP-seq_231ERαLQ_45min_rep4


title: H3K27ac_ChIP-seq_231ERαWT_45min_rep2


title: ERα_ChIP-seq_231ERαLQ_0min_rep1


title: ERα_ChIP-seq_231ERαLQ_45min_rep2


title: ERα_ChIP-seq_231ERαLQ_0min_rep4


title: ERα_ChIP-seq_231ERαLQ_45min_rep1


title: ERα_ChIP-seq_231ERαLQ_0min_rep2


title: ERα_ChIP-seq_231ERαWT_45min_rep2


title: ERα_ChIP-seq_231ERαWT_0min_rep2


title: ERα_ChIP-seq_231ERαLQ_0min_rep3


title: ERα_ChIP-seq_231ERαWT_45min_rep4


title: ERα_ChIP-seq_231ERαWT_45min_rep3


title: ERα_ChIP-seq_231ERαWT_0min_rep3


title: ERα_ChIP-seq_231ERαWT_45min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_0min_rep4


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_45min_rep4


title: ERα_ChIP-seq_231ERαWT_0min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_45min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_45min_rep3


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_45min_rep2


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_0min_rep2


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_0min_rep3


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαLQ_0min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_45min_rep3


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_45min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_45min_rep2


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_0min_rep2


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_0min_rep4


title: ERα_ChIP-seq_231ERαWT_0min_rep4


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_0min_rep1


title: p300_ChIP-seq_231ERαLQ_20min_rep2

data_processing:
FastQC
Alignment using BOWTIE (version 0.12.7) with the default parameters.
ERalpha peak calling was performed using MACS software (version 1.4.2) using the default p-value and input condition as a control. Peak calling for ERalpha wild-type (Wt) and L540Q mutant was performed separately. The peak calling was done separately for each sequencing run and the peak calls of the two runs were compared to get a set of common peaks among the sequencing runs (i.e. replicates 1&2, 3&4 were combined respectively and the two peak universes were compared to get final set of peaks for Wt and LQ). The replicates were combined and bigwig files were generated for combined replicates to visualize on genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization

value: ERalpha L540Q


title: p300_ChIP-seq_231ERαWT_20min_rep2

value: ERalpha wt


title: p300_ChIP-seq_231ERαLQ_20min_rep1


title: Input_ChIP-seq_231ERαLQ_20min_rep1


title: E14G rep1

description: periodate oxidation treated

value: Cobb 500


title: p300_ChIP-seq_231ERαWT_20min_rep1


title: Input_ChIP-seq_231ERαWT_20min_rep2


title: p300_ChIP-seq_231ERαLQ_45min_rep2


title: p300_ChIP-seq_231ERαLQ_0min_rep2


title: E11G rep1

description: periodate oxidation treated


title: p300_ChIP-seq_231ERαLQ_45min_rep1


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_45min_rep4


title: hda108-PMeA_R1

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adaptor removal with Trimmomatic 0.33
contaminant rRNA removal with ERNE_FILTER version 1.2
mapping with Tophat 2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000
BAM filtering using Samtools to remove alignments with MAPQ smaller than 1
Differential expression analysis usign Cufflinks/Cuffdiff version 2.2.1; parameters: --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv3; Zea_mays.AGPv3.31.gtf transcript annotation
Supplementary_files_format_and_content: tab-delimited matrix with normalized FPKM values

organism: Zea mays

source_name: post-meiotic anthers

growth_protocol: Maize plants grown in the field during spring/summer season

extract_protocol:
Total RNA was extracted from frozen tissue using the RNeasy Plant Mini Kit (QiAgen) and subjected to on-column DNase treatment (QiAgen).
TruSeq® Stranded Total RNA Library Preparation Kit with Ribo-Zero™ Plant (Illumina); sequenced on Illumina HiSeq2500, multiplex level of 6

value: hda108/hda108 mutant

value: anthers at post-meiotic stage


title: hda108-MiA_R1

source_name: mitotic anthers

value: anthers at mitotic stage


title: hda108-MiA_R2


title: Input_for_ERα_Med1_H3K27ac_SRC_ChIP-seq_231ERαWT_0min_rep3


title: hda108-PMeA_R2


title: p300_ChIP-seq_231ERαWT_0min_rep1


title: p300_ChIP-seq_231ERαWT_0min_rep2


title: p300_ChIP-seq_231ERαWT_45min_rep1


title: wt-MiA_R1

value: wild-type


title: Input_for_p300_ChIP-seq_231ERαLQ_45min_rep1


title: Input_for_p300_ChIP-seq_231ERαLQ_45min_rep2


title: wt-PMeA_R2


title: wt-MiA_R2


title: Input_for_p300_ChIP-seq_231ERαLQ_0min_rep2


title: wt-PMeA_R1


title: hda108-Leaves_R3

source_name: hda108_11th wrapped leaf from V8 stage plants

growth_protocol: Maize plants were grown in greenhouse until V8 leaf stage during spring/summer season

extract_protocol:
Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), and subjected to On-Column DNase Digestion (SIGMA).
TruSeq® Stranded Total RNA Library Preparation Kit with Ribo-Zero™ Plant (Illumina);  sequenced on Illumina HiSeq2500, multiplex level of 6

tag: genotype/variation

value: V8 plants

value: developing 11th leaf


title: Input_for_p300_ChIP-seq_231ERαLQ_0min_rep1


title: hda108-Leaves_R2


title: Input_for_p300_ChIP-seq_231ERαWT_45min_rep2


title: hda108-Leaves_R1


title: Input_for_p300_ChIP-seq_231ERαWT_0min_rep2


title: Input_for_p300_ChIP-seq_231ERαWT_45min_rep1


title: Input_ChIP-seq_231ERαWT_20min_rep1


title: p300_ChIP-seq_231ERαLQ_0min_rep1


title: Input_for_p300_ChIP-seq_231ERαWT_0min_rep1


title: wt-Leaves_R3

source_name: WT_11th wrapped leaf from V8 stage plants


title: wt-Leaves_R2


title: shCTCF2

city: Seoul

first: Shim

last: Kyuwon

address: 1, Gwanak-ro,Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the mouse genome reference mm10 using RSEM (version 1.2.28). Uniquely and properly mapped read pairs were used for further analysis.
TPM (Transcript per million) measure were calculated using the read counts of each genes annotated in ENSEMBL release 82
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: CTCF knockdown, replicate2

extract_protocol:
Total RNA from cultured cortical neurons were extracted using TRIzol (Invitrogen).
The standard illumina protocol was used to make sequencing libraries for RNA-Seq. Using gel electrophoresis, ~300 bp fragments were isolated and amplified by PCR and sequenced using the illumina HiSeq 2000 in the paired-end sequencing mode (2X101 bp)

treatment_protocol: Both CTCF and lacZ knockdown were induced individually in primary mouse cortical culture using adeno-associated virus

value: CTCF knockdown

tag: sample type

value: Experiment


title: wt-Leaves_R1


title: shLAC2

source_name: lacZ knockdown, replicate2

value: lacZ knockdown

value: Control


title: shCTCF1

source_name: CTCF knockdown, replicate1


title: W1

status: Public on May 20 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10

source_name: bone marrow derived macrophage

extract_protocol:
RNA isolation was performed by the miRNA Isolation kit.
Library preparation was performed using a SureSelect Strand-Specific RNA library kit (Agilent) according to the manufacturer’s instructions.

value: 7 weeks

value: macrophage


title: KO_non

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 platform in a 50-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm9) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm9

source_name: Bone marrow derived macrophage

growth_protocol: M-CSF induced bone marrow derived macrophage

extract_protocol: 1x10^6 bone marrow derived macrophages were stimulated by LPS for 4 hrs, and RNA was harvested using Trizol reagent. Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: 100 ng/ml LPS stimulation for 4 hours

value: bone marrow


title: W2


title: WT_non

value: wild type


title: K1


title: KO_LPS


title: Mouse BM_4

status: Public on May 18 2018

city: hangzhou

first: guoji

last: guo

state: zhejiang

address: yuhangtang road 388

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

data_processing:
Cellular barcode and unique molecular index were extracted from read 1. We discarded the read pairs within which base quality of any one base of barcode was below 10, since sequencing error and low quality may produce spurious barcodes. After tagging of cellular barcode and molecular barcode, we used read 2 as input for alignment. We used STAR-2.5.1b with default parameters for mapping.Reads from CD34+, CD34- and transferred CD34+ cells were aligned to GRCh38 human genome. Reads from ckit+ and mouse bone marrow cells were aligned to GRCm38 mouse genome reference. Reads from zebrafish cells were aligned to GRCz10 zebrafish genome reference.  All multi-aligned reads were removed and GTF annotation files from Gencode were used to tag aligned read that overlaps the exon of a gene with the relative gene symbol. For UMI calculation, molecular barcodes that have one base distance were merged to one in case of spurious UMI.
Genome_build: GRCh38, GRCm38,GRCz10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample. Column headers are named by the cellular barcodes that represent one single cell; rows represent gene symbols

molecule: polyA RNA

source_name: Mouse  bone marrow cells

extract_protocol:
Human CD34+ mobilized peripheral blood cells were isolated by human CD34 MicroBead Kit (MiltenyiBiotec), according to the manufacturer's protocol after collecting red cells by Ficoll-Paque PLUS (GE). MPP cells (CD34+CD38-Thy1-CD45RA-CD49f-) were isolated from Human CD34+ mobilized peripheral blood cells by flow cytometry sorting using CD34, CD38, Thy, CD45RA and CD49f antibodies.
RNA libraries were prepared for sequencing using TruePrep DNA Library Prep Kit V2 for Illumina ( Vazyme, cat # TD513).

tag: cell type

value: Mouse  bone marrow cells


title: L08_26d

status: Public on May 19 2018

city: Hangzhou

first: Fei

last: Xu

address: 198 Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then assembled by Trinity software with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: non-reference
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Brassica napus

source_name: 26-day-old seeds

growth_protocol: grown at natural field condition at Hangzhou, P. R. China

extract_protocol:
Whole seeds were isolated from selique, flash frozen on dry ice, ground in liquid nitrogen and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: seeds

value: 26 days after flowering

tag: seed coat colour

value: yellow


title: Mouse BM_5


title: Mouse BM_1


title: Mouse BM_3


title: ckit+ _b3

source_name: Mouse ckit+ bone marrow stem cells

value: Mouse ckit positive cells


title: ckit+ _b1

description: Sample 14


title: WT_LPS


title: p300_ChIP-seq_231ERαWT_45min_rep2

value: ERα wt


title: ckit+ _b2


title: Mouse BM_2


title: shLAC1

source_name: lacZ knockdown, replicate1


title: TON3

city: Saint Louis

first: Michael

last: Hughes

state: MO

address: 425 South Euclid Avenue

department: Internal Medicine

institute: Washington University

data_processing:
RUM (Grant et al. 2011) was used to align raw reads to the reference genomes and transcriptomes using the following parameters:  “--strand-specific --variable-length-reads --bowtie-nu-limit 10 --nu-limit 10”.
Genome_build: mm10 and rn5
Supplementary_files_format_and_content: plain text files: normalized read counts for all features (transcripts, exons & introns).
Supplementary_files_format_and_content: bed files: contain information about the reads that aligned to known and unknown junctions in their respective sample.

source_name: Tongue

growth_protocol: Ten week old male C57/B6 mice (n=18: Charles River Labs) were entrained to 12L:12D for 4 weeks and normal chow ad libitum. At 14 weeks of age,  mice were sacrificed two hours after lights-on, and muscle tissues were rapidly dissected and frozen in liquid nitrogen. Six total biological replicates will be collected, and tissue from three mice will be pooled  together for each biological replicate.

extract_protocol:
All tissues were collected between ZT3 and ZT7, immediately frozen in liquid nitrogen, then stored at -80 degrees Celcius.  RNA was harvested using Trizol reagent. Strand-specific sequencing libraries were prepared using 200 nanograms of RNA as starting material and the TruSeq Stranded mRNA LT kit (Illumina cat# RS-122-2101).
Standard Illumina protocol & twelve cycles of PCR were performed for each sample.

tag: Sex

value: male


title: TON5


title: TON1


title: TON4


title: TON2


title: TAN4

source_name: Tibialis anterior


title: TAN6


title: K2


title: L07_26d

value: brown


title: TA5

source_name: Thoracic aorta


title: TAN2


title: TA6


title: TAN1


title: TA3


title: TA2


title: SOL6

source_name: Soleus


title: TON6


title: SOL3


title: SOL5


title: SOL2


title: SOL4


title: SOL1


title: TAN3


title: TAN5


title: TA1


title: QUAD6

source_name: Quadricep


title: QUAD4


title: QUAD2


title: TA4


title: QUAD3


title: PLA6

source_name: Plantaris


title: RV1

source_name: Right ventricle


title: QUAD5


title: RV6


title: PLA5


title: PLA3


title: PLA4


title: QUAD1


title: PLA1


title: PLA2


title: RV4


title: MAS6

source_name: Masseter


title: RV5


title: RV3


title: MAS3


title: MAS4


title: MAS5


title: MAS1


title: MAS2


title: LV5

source_name: Left ventricle


title: LV6


title: LV3


title: LV4


title: GAS6

source_name: Gastrocnemius


title: LV2


title: LV1


title: GAS5


title: FDB4

source_name: Flexor digitorum brevis


title: GAS1


title: RV2


title: GAS2


title: GAS4


title: FDB3


title: FDB6


title: FDB1


title: FDB5


title: GAS3


title: DIA6

source_name: Diaphragm


title: DIA5


title: DIA4


title: DIA2


title: DIA3


title: DIA1


title: EYE4

source_name: Extraocular eye


title: EYE5


title: EYE6


title: EYE3


title: EYE1


title: Sample_6053_C14

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

description: FFPE

data_processing:
Basecalls were performed using Illumina's CASAVA vesrsion 1.8.2
quality of the sequenced reads were assessd using FastQC from Babraham Bioinformatics
reads were aligned to Human Genome Consortium's reference human genome (hg19) using TopHat2
data normalization and differential expression were calculated using the Cufflinks2 Suite; the UCSC transcriptome (hg19) was used as annotation reference
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited, log 10 fold change, tumor vs. normal differential expression as a function of race

source_name: tumor 15

extract_protocol:
Total RNA was isolated from the formalin-fixed paraffin-embeded (FFPE) specimens using the RecoverAll kit for FFPE with extended proteinase K and DNAse treatement (Life Technologies Inc., Carlsband, CA)
Double stranded cDNA preparation and library construction was done with the Ovation Human FFPE RNA-sequencing Multiplex System (NuGEN, San Carlos, CA) using 200ng total RNA.

value: prostate tumor

tag: ethnicity

value: European Americans


title: Sample_3365_B17

description: FFPE

source_name: normal tissue matched to tumor 13

tag: tissue

value: normal prostate


title: Sample_3869_B22

description: FFPE

source_name: tumor 14


title: Sample_3869_B12

description: FFPE

source_name: normal tissue matched to tumor 14


title: Sample_6053_C13

description: FFPE

source_name: normal tissue matched to tumor 15


title: Sample_8047_C36

description: FFPE

source_name: normal tissue matched to tumor 16

value: African Americans


title: Sample_3309_22

description: FFPE

source_name: normal tissue matched to tumor 12


title: Sample_3139_18

description: FFPE

source_name: normal tissue matched to tumor 11


title: EDL4

source_name: Extensor digitorum longus

tag: strain


title: EDL6


title: Sample_3309_40

description: FFPE

source_name: tumor 12


title: EYE2


title: EDL5


title: EDL3


title: EDL2


title: Sample_3139_12

description: FFPE

source_name: tumor 11


title: Sample_2249_25

description: FFPE

source_name: normal tissue matched to tumor 10


title: Sample_2249_14

description: FFPE

source_name: tumor 10


title: Sample_8047_C11

description: FFPE

source_name: tumor 16


title: ATR6

source_name: Atria


title: Sample_1193_C15

description: FFPE

source_name: normal tissue matched to tumor 9


title: EDL1


title: Sample_1193_C12

description: FFPE

source_name: tumor 9


title: ATR5


title: Sample_1136_20

description: FFPE

source_name: tumor 8


title: ATR4


title: ATR3


title: FDB2

source_name: Flexor digitorum brevis


title: Sample_1014_C17

description: FFPE

source_name: normal tissue matched to tumor 7


title: Sample_1014_C9

description: FFPE

source_name: tumor 7


title: Sample_881_826

description: FFPE

source_name: normal tissue matched to tumor 6


title: Sample_1136_11

description: FFPE

source_name: normal tissue matched to tumor 8


title: Sample_3365_B5

description: FFPE

source_name: tumor 13


title: AOR6

source_name: Total Aorta


title: Sample_647_A20

description: FFPE

source_name: normal tissue matched to tumor 5


title: AOR5


title: Sample_647_A7

description: FFPE

source_name: tumor 5


title: AOR2


title: AOR3


title: AOR4


title: AA6

source_name: Abdominal Aorta


title: Sample_881_819

description: FFPE

source_name: tumor 6


title: Sample_487_33

description: FFPE

source_name: tumor 4


title: Sample_487_31

description: FFPE

source_name: normal tissue matched to tumor 4


title: Sample_376_9

description: FFPE

source_name: normal tissue matched to tumor 2


title: Sample_413_15

description: FFPE

source_name: tumor 3


title: AA4


title: AA5


title: Sample_334_A24

description: FFPE

source_name: normal tissue matched to tumor 1


title: AA3


title: Sample_376_8

description: FFPE

source_name: tumor 2


title: ATR2

source_name: Atria


title: ATR1


title: CD45RA+ CD25+ nTreg Donor3

city: Amsterdam

first: Eloy

last: Cuadrado

address: Plesmalaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin

data_processing:
Reads were aligned using Tophat version 2.0.12 with bowtie 1. Tophat was guided by using a transcriptome index version 77 From Ensemble
Additional parameters used by Tophat were --prefilter-multihits -- no-coverage-search --library-type fr-firststrand
Gene expression data was generated using a custom script that follows the criteria of HTSeq-count. Genes that have zero expression across all samples were removed from the dataset.
Genome_build: hg38
Supplementary_files_format_and_content: readcounts.txt contains the counts per gene for each of the samples

source_name: Human CD4+ T cells

extract_protocol:
Total RNA was extracted from 1×106 cells using TRIzol reagent (15596-018, Ambion Life Technologies) according to the manufacturer’s protocol. The total RNA pellet was air-dried for 8 minutes and dissolved in an appropriate volume of nuclease free water (AM9937, Ambion Life Technologies) followed by a total RNA quantification using the Nanodrop UV-VIS Spectrophotometer (Thermo Scientific). The total RNA was further purified using the MinElute Cleanup Kit (74204, Qiagen) according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA). Total RNA samples having RNA Integrity Number (RIN)>8 were subjected to library generation
RNA libraries were prepared for sequencing using standard Illumina protocols for stranded RNA sequencing on a hiseq2500 machine

tag: cell population

value: CD45RA+ CD25+ nTreg


title: Sample_334_A7

description: FFPE

source_name: tumor 1


title: CD45RA- CD25- mTconv Donor3

value: CD45RA- CD25- mTconv


title: CD45RA+ CD25- nTconv Donor3

value: CD45RA+ CD25- nTconv


title: CD45RA- CD25hi eTreg Donor2

value: CD45RA- CD25hi eTreg


title: CD45RA+ CD25+ nTreg Donor2


title: AOR1


title: CD45RA- CD25- mTconv Donor2


title: CD45RA- CD25hi eTreg Donor1


title: CD45RA- CD25+ Fr.III Donor2

value: CD45RA- CD25+ Fr.III


title: CD45RA+ CD25- nTconv Donor1


title: CD45RA+ CD25+ nTreg Donor1


title: CD45RA- CD25+ Fr.III Donor1


title: RAT_SOL_F6

source_name: Soleus

growth_protocol: Rats (9-10 weeks of age, Sprague Dawleys, half male/ half female) were entrained to a 12 h light/12 h dark (12L:12D) cycle for 2 weeks and then placed in total darkness for 30 h prior to the start of the tissue collection to remove any light cues. Tissues were collected in darkness with red light.

value: Sprague Dawleys

value: female


title: AA2


title: RAT_SOL_F5


title: transferred CD34+ cells

description:
Sample 13
mPB CD34+ cells were transplanted into sublethally irradiated NCG (NOD-Prkdcem26Cd52Il2rgem26Cd22/Nju, Nanjing Biomedical Research Institute of Nanjing University) mice via an injection into the femur cavity (approximately, 1X105 cells per mouse). Two months after transplantation, hCD45+CD34+ cells (mouse-transferred CD34+ cells) were sorted from mice bone marrow cells collected from the femur and tibia.

source_name: Human CD34+ mobilized peripheral blood stem cells (PBSCs)

value: transferred cells


title: RAT_SOL_F3


title: AA1


title: RAT_SOL_F4


title: RAT_SOL_F1


title: RAT_SOL_F2


title: RAT_SOL_M6


title: CD45RA- CD25+ Fr.III Donor3


title: MCF7-TRC_H7MNYALXX_L5

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

institute: Yunnan university of Chinese Medicine

data_processing:
STAR_2.4.2a_modified was used to mapping reads to reference genome
featureCounts Version 1.4.6-p5 was used to calculate raw counts

source_name: MCF7 breast cancer cell line

growth_protocol: ERα positive breast cancer cell line MCF-7 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin, and 1% streptomycin at 37˚C in a humidified atmosphere of 5% carbon dioxide.

extract_protocol: Total RNA was extracted from cell lines using TRIzol (Invitrogen, Carlsbad, CA, USA), and 2 μg of total RNA was reverse transcribed into first-strand cDNA using the TaKaRa reverse transcription reagent kit according to the manufacturer's protocol.

treatment_protocol: MCF7 cells  were  seeded  at  1x105  cells/well  into  a  24-wells  plate respectively  and  grown  until  the  culture  was  ~75% confluent. Lentivirus expressing shRNA against XIST or TurboTRC (sh control) were produced and used to infect the cells at multiplicity of infection (MOI) 5. After overnight infection, cells were washed, given fresh medium and cultured for 48 hours. Cells were treated with medium (control), cisplatin or carboplatin for 24 hours after which they were washed.

value: MCF7 breast cancer cell line


title: RAT_SOL_M4


title: RAT_SOL_M5


title: RAT_SOL_M3


title: MCF7-TRC_H7MNYALXX_L7


title: MCF7-4_HFKKJALXX_L3


title: MCF7-4_HFKKJALXX_L5


title: RAT_SOL_M1


title: CD45RA- CD25- mTconv Donor1


title: MCF7-2_HFKKJALXX_L5


title: RAT_SOL_M2


title: MCF7-2_H7MNYALXX_L7


title: RAT_EDL_F3

source_name: Extensor digitorum longus


title: RAT_EDL_F5


title: Sample_413_24

description: FFPE

source_name: normal tissue matched to tumor 3


title: RAT_EDL_F4


title: RAT_EDL_F1


title: RAT_EDL_M5


title: RAT_EDL_F2


title: RAT_EDL_M4


title: CD34+_b7

description: Sample 7

data_processing:
Cellular barcode and unique molecular index were extracted from read 1. We discarded the read pairs within which base quality of any one base of barcode was below 10, since sequencing error and low quality may produce spurious barcodes. After tagging of cellular barcode and molecular barcode, we used read 2 as input for alignment. We used STAR-2.5.1b with default parameters for mapping. Reads from human mouse contamination test were aligned to a merged hg19-mm10 genome reference. Reads from CD34+, CD34- and MPP cells were aligned to GRCh38 human genome. All multi-aligned reads were removed and GTF annotation files from Gencode were used to tag aligned read that overlaps the exon of a gene with the relative gene symbol. For UMI calculation, molecular barcodes that have one base distance were merged to one in case of spurious UMI.
See README.pdf
Genome_build: GRCh38, hg19, mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample. Column headers are named by the cellular barcodes that represent one single cell; rows represent gene symbols

extract_protocol:
Human CD34+mobilized peripheral blood cells were isolated by human CD34 MicroBead Kit (MiltenyiBiotec), according to the manufacturer's protocol after collecting red cells by Ficoll-Paque PLUS (GE). MPP cells (CD34+CD38-Thy1-CD45RA-CD49f-) were isolated from Human CD34+ mobilized peripheral blood cells by flow cytometry sorting using CD34, CD38, Thy, CD45RA and CD49f antibodies.
RNA libraries were prepared for sequencing using TruePrep DNA Library Prep Kit V2 for Illumina ( Vazyme, cat # TD513).

value: Human CD34 positive cells

value: peripheral blood


title: CD34-_2

description: Sample 9

source_name: Human CD34- mobilized peripheral blood stem cells (PBSCs)

value: Human CD34 negative cells


title: CD34-_1

description: Sample 8


title: CD34+_thawed_l7

description: Sample 11


title: CD34+_thawed_l6

description: Sample 10


title: RAT_EDL_M3

value: male


title: CD45RA- CD25hi eTreg Donor3


title: CD34+_b2

description: Sample 2


title: CD34+_b3

description: Sample 3


title: RAT_EDL_M1


title: RAT_EDL_M2


title: RAT_EDL_F6


title: CD34+_b4

description: Sample 4


title: CD34+_b6

description: Sample 6


title: WT2-2_nRNA

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

description: nuclear, non-polyadenylated RNA

data_processing:
Fastq files were filtered for quality with the FASTQC toolkit (FASTX Toolkit version 0.0.13) and mapped to the genome with Tophat2 (version 2.0.12) (Kim et al., 2013) using the following settings: fastq_quality_filter -Q 33 -q 20 -p 90; tophat2 -p 5 -i 30 -I 900 –g 1 -N 2 -G <Spombe_EF2> –segment-length 25 –library-type fr-firststrand –minanchor-length 8 –splice-mismatches 0 –min-coverage-intron 30 –max-coverageintron 900 –min-segment-intron 30 –max-segment-intron 900. For indexing, file conversion and analysis samtools version 1.1 (Li et al., 2009) and bedtools version 2.20.1 (Quinlan & Hall, 2010) were used. Sequencing data were visualized using the IGV genome browser (Robinson et al., 2011; Thorvaldsdóttir, Robinson, & Mesirov, 2013). Coverage data (bedgraph-format) were obtained using the samtools view and depth function to first extract mapped reads per DNA strand and then converting them into coverage data (wig-format). Wig-files were converted with awk into the bedgraph-format.
RNA-seq coverage was adjusted for library size, excluding reads mapped to rDNA regions. rDNA region coordinates are: III: 1-24713, III: 2439224-2452883. Non-rDNA counts per position were summed and divided by the read length to determine the mapped library size. Library sizes were weighted using the R-package edgeR (calcNormFactors without additional parameters) and multiplied by 10^-6. Counts per position were divided by this scaling factor to yield RPM (Reads Per Million).
Genome_build: S. pombe EF2
Supplementary_files_format_and_content: mapped and normalized data in bedGraph-format

organism: Schizosaccharomyces pombe

source_name: cells in exponential growth in complete media at 30C

growth_protocol: Cell cultures originating from single colonies were grown in complete media (YES) at 30°C and 250 rpm. Cells were harvested in exponential growth at an OD (595nm) of 0.5-1.

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction. PolyA- RNA was obtained using oligo-dT coated magnetic beads binding to polyA+ RNA (Dynabeads mRNA DIRECT Micro Purification Kit, Life technologies). rRNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Yeast, Epicenter/Illumina) from ~5 μg RNA. For cytoplasmic mRNA analysis, total RNA was extracted from the cytoplasmic fraction during the nascent RNA isolation protocol and enriched for polyA+ RNA using oligo-dT coated magnetic beads binding to polyA+ RNA (Dynabeads mRNA DIRECT Micro Purification Kit, Life technologies).
Random hexamer primed libraries were prepared with standard Illumina library protocols. Single-end sequencing with 76 bp read length was done. Samples were sequenced in biological triplicates for mock- and caffeine-treatment and in duplicate for wild-type strain SP286.

treatment_protocol: To induce global gene expression changes three replicate cultures were treated with 10mM Caffeine for 15minutes and harvested subsequently. The three reference cultures were mock-treated with water. No treatment was performed for WT2 cultures. For nascent RNA extraction, 1l of cells was pelleted, washed with ice-cold PBS, quick-frozen in liquid nitrogen in 6 aliquots and kept at -80°C.


title: nRNA_37C_prp2-1

description: nuclear, non-polyadenylated RNA

data_processing:
PacBio SMRT Analysis v2.3.0 software was used to obtain CCS reads (reads of inserts protocol).  Fastq files were filtered and trimmed for the 3’ end DNA adaptor and downstream Clontech adaptor sequences with cutadapt 1.8 (-a CTGTAGGCACCATCAAT -n 1 -O 17 -e 0.1 –match-read-wildcards –discard-untrimmed -m 15). Also the reverse-complement adaptor was trimmed (-g ATTGATGGTGCCTACAG) and the read was reverse-complemented. Demultiplexing prp2-1 and WT37 data was done similarly using the sample identifier and its reverse-complement identifier. Trimmed fastq-files were catenated and PCR duplicates were removed using custom scripts. The remaining 5 nt random 3’ barcode was removed using the FASTX toolkit (fastx_trimmer -Q 33 -t 5, version 0.0.13). Processed fastq-data were mapped to the genome version S. pombe EF2 using gmap 2013-05-09 (-d <genome_index> –min-intronlength=30 –intronlength=850 –localsplicedist=850 –totallength=850 –trimendexons=0 –microexon-spliceprob=0.5 –direction=auto –find-shifted-canonical –allow-close-indels=2 –npaths=1 –nofails –fails-as-input –mapboth -A –format=samse).
Genome_build: S. pombe EF2
Supplementary_files_format_and_content: mapped data in bed-format

source_name: cells in exponential growth in complete media at 37C for 2hours

growth_protocol: Wild-type cell cultures originating from single colonies were grown in complete media (YES) at 30°C and 250 rpm. Cells were harvested in exponential growth at an OD (595nm) of 0.5-1. For prp2-1 splicing analysis YES cultures originating from single prp2-1 S. pombe and 972h- S. pombe cell colonies were grown at 26°C to an OD (595nm) 0.4, then shifted to 37°C for 2 hours and harvested subsequently.

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction. PolyA- RNA was obtained using oligo-dT coated magnetic beads binding to polyA+ RNA (Dynabeads mRNA DIRECT Micro Purification Kit, Life technologies). rRNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Yeast, Epicenter/Illumina) from ~5 μg RNA. Nascent RNA was 3’ end ligated to the DNA adaptor (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) and reverse transcribed into cDNA with a slight modification of the SMARTer PCR cDNA Synthesis Kit (Clontech). A custom primer reverse-complement to the 3’ end adaptor was used (AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG). Maximal 1 µg of RNA was used per reaction. The subsequent low cycle PCR was carried out with the Advantage 2 PCR Kit according to the instructions provided by the kit. Double-stranded cDNA was further used for Pacific Biosciences library preparation and sequencing with standard protocols and kit from Pacific Biosciences (SMRTbell™ Template Prep Kit 1.0).
SMRTbell™ Template Prep Kit 1.0

treatment_protocol: For nascent RNA extraction, 1l of cells was pelleted, washed with ice-cold PBS, quick-frozen in liquid nitrogen in 6 aliquots and kept at -80°C.


title: WT2-1_nRNA

description: nuclear, non-polyadenylated RNA


title: WT1-3_nRNA_water

description: nuclear, non-polyadenylated RNA

value: Wild-type h-


title: nRNA_37C_WT

description: nuclear, non-polyadenylated RNA


title: WT1-3_nRNA_caffeine

description: nuclear, non-polyadenylated RNA


title: MPP

description: Sample 12

value: CD34+CD38-Thy1-CD45RA-CD49f- MPP cells


title: nRNA_30C_2

description: nuclear, non-polyadenylated RNA

value: prp5::KanMx-prp5-WT, h+


title: CD34+_b5

description: Sample 5


title: CD34+_b1

description: Sample 1


title: WT1-3_mRNA_caffeine

description: cytoplasmic, polyadenylated RNA


title: WT1-2_nRNA_caffeine

description: nuclear, non-polyadenylated RNA


title: WT1-2_nRNA_water

description: nuclear, non-polyadenylated RNA


title: WT1-2_mRNA_caffeine

description: cytoplasmic, polyadenylated RNA


title: WT1-1_mRNA_water

description: cytoplasmic, polyadenylated RNA


title: WT1-3_mRNA_water

description: cytoplasmic, polyadenylated RNA


title: WT1-1_mRNA_caffeine

description: cytoplasmic, polyadenylated RNA


title: Kinsella Composite-RNAseq-20

status: Public on May 17 2018

city: Edmonton

first: Changxi

state: Alberta

address: Agriculture/Forestry Centre

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

description:
K451B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.15

data_processing:
Basecalls performed using bcl2fastq v1.8.3
Sequence reads were assessed for sequencing quality using FASTQC ( Version 0.11.5)
RNAseq reads were aligned to UMD3.1 reference genome using Tophat2 with default alignment parameters
Raw read sequences uniquily aligned and mapped to each annotated gene in the bovine reference genome were counted using  using HTSEQ-count (0.6.1) with default parameters.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt files; First colunm contains the ENSEMBL gene IDs and second column contains the number of  the raw reads that were aligned and mapped to each gene

organism: Bos taurus

source_name: Liver

extract_protocol:
Total RNA was then extracted from  pulverised liver tissue using a Qiagen RNeasy Plus Universal Kit .
cDNA libraries for mRNA were constructed using SuperScript II cDNA kit (Thermo Scientific) for the first strand and the Illumina TruSeq RNA Sample Prep Kit v2 for the second strand,

value: Kinsella Composite

value: Liver

tag: finishing diet

value: 75% barley grain, 20% barley silage, 5% rumensin pellets

tag: sire

tag: rfi group

value: high-RFI


title: Kinsella Composite-RNAseq-19

description:
K433B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.97

tag: breed


title: Kinsella Composite-RNAseq-18

description:
K401B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.14


title: nRNA_30C_1

description: nuclear, non-polyadenylated RNA


title: Kinsella Composite-RNAseq-17

description:
K397B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.96

value: low-RFI


title: Kinsella Composite-RNAseq-12

description:
K183B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.63


title: Kinsella Composite-RNAseq-16

description:
K387B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.01


title: Kinsella Composite-RNAseq-15

description:
K339B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.16


title: Kinsella Composite-RNAseq-11

description:
K165B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.77


title: Kinsella Composite-RNAseq-10

description:
K111B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.93


title: Kinsella Composite-RNAseq-14

description:
K277B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.95


title: Kinsella Composite-RNAseq-13

description:
K261B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.78


title: Kinsella Composite-RNAseq-8

description:
K091B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.98


title: Kinsella Composite-RNAseq-6

description:
K067B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.77


title: Kinsella Composite-RNAseq-5

description:
K059B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.73


title: WT1-1_nRNA_water

description: nuclear, non-polyadenylated RNA


title: WT1-2_mRNA_water

description: cytoplasmic, polyadenylated RNA


title: Kinsella Composite-RNAseq-3

description:
K021B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.66


title: Kinsella Composite-RNAseq-4

description:
K047B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.09


title: Kinsella Composite-RNAseq-1

description:
K003B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.77


title: Kinsella Composite-RNAseq-2

description:
K007B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.18


title: Kinsella Composite-RNAseq-7

description:
K087B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.69


title: WT1-1_nRNA_caffeine

description: nuclear, non-polyadenylated RNA


title: Kinsella Composite-RNAseq-9

description:
K103B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.14


title: Charolais-RNAseq-20

description:
C637B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.05

value: Charolais


title: Charolais-RNAseq-18

description:
C631B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.75


title: Charolais-RNAseq-14

description:
C587B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.26


title: Charolais-RNAseq-17

description:
C617B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.83


title: Charolais-RNAseq-15

description:
C607B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.24


title: Charolais-RNAseq-19

description:
C633B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.05


title: Charolais-RNAseq-16

description:
C611B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.27


title: Charolais-RNAseq-11

description:
C579B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.165


title: Charolais-RNAseq-10

description:
C577B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.82


title: Charolais-RNAseq-7

description:
C549B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.06


title: Charolais-RNAseq-5

description:
C541B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.07


title: Charolais-RNAseq-6

description:
C543B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.23


title: Charolais-RNAseq-8

description:
C551B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.06


title: Charolais-RNAseq-4

description:
C539B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.8


title: Charolais-RNAseq-2

description:
C531B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.89


title: Charolais-RNAseq-1

description:
C515B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.78


title: Angus-RNAseq-20

description:
A913B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.7

value: Angus


title: Angus-RNAseq-16

description:
A897B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.87


title: Angus-RNAseq-15

description:
A891B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.69


title: Angus-RNAseq-14

description:
A889B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.81


title: Angus-RNAseq-17

description:
A899B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.83


title: Charolais-RNAseq-13

description:
C585B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 36.28


title: Angus-RNAseq-13

description:
A877B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.72


title: Angus-RNAseq-12

description:
A863B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.74


title: Angus-RNAseq-07

description:
A821B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.82


title: CD45RA+ CD25- nTconv Donor2

value: CD45RA+ CD25- nTconv


title: Angus-RNAseq-11

description:
A843B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.65


title: Angus-RNAseq-08

description:
A825B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.71


title: Charolais-RNAseq-12

description:
C583B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.91


title: Angus-RNAseq-09

description:
A827B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.73


title: Angus-RNAseq-19

description:
A909B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.7


title: Angus-RNAseq-06

description:
A809B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.73


title: Charolais-RNAseq-9

description:
C563B
Illumina HiSeq 2500
Rapid-Run Mode
fastq average Phred score: 34.92


title: Angus-RNAseq-02

description:
A781B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.8


title: Angus-RNAseq-01

description:
A773B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.78


title: Angus-RNAseq-03

description:
A785B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.74


title: Angus-RNAseq-04

description:
A787B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.68


title: Charolais-RNAseq-3

description:
C537B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 36.05


title: N2_PolyA-2

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
Supplementary_files_format_and_content: DESeq2 results for gene expression analysis between N2 and HPL-2(tm1489)
HPL2_PolyA_DESeq2results.xlsx
N2_HPL-2_rawCounts.txt

data_processing:
Basecalls performed using CASAVA software from Illumina
Analysis of library complexity and per-base sequence quality (i.e. q > 30) was assessed using FastQC (v0.11.2) software. Low quality bases (q < 10) were trimmed from the 3’ end of reads.
Reads were aligned to the C. elegans WS220 genome using TopHat2 (v2.0.14) --b2-very-sensitive -i 30 -I 5000 --read-edit-dist 3 -N 3 - -read-realign-edit-dist 0 -p 10 --segment-length 25 --segment-mismatches 2 --no- coverage-search --min-coverage-intron 30 --max-coverage-intron 5000 --min-segment-intron 30 --max-segment-intron 5000
(RNAseq) For poly-A selected RNA-Seq reads, uniquely mapped reads were used as input to obtain gene counts using the WS220 annotation with Rsubread (v 1.18.0). Differential expression of genes was determined using DESeq2 (v1.14.1)
(ChIPseq) Reads were uniquely mapped to the WS220 genome with Bowtie1 allowing 2 mismatches in a 45bp seed. Total genomic DNA control libraries were processed and mapped in an identical manner. MACS version 1.4.2 (47) was used to identify significant peaks (p<0.05, FDR<10%) and total genomic sequencing of DNA from wild type and tdp-1(ok803) worms respectively were used as the control datasets to normalize HPL-2 ChIP-seq peaks. Diffbind (version 1.10.2) was used to call differentially represented peaks between wild type and tdp-1(ok803). HPL-2 ChIP-seq and respective total genomic sequencing for each sample was used for normalization. A p-value cut off of P<0.05 and FDR<10% was used.
Genome_build: ws220
Supplementary_files_format_and_content: (RNA-Seq) abundance measurements and differential expression of genes
(ChIPseq) bigwig files

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown at on agarose plates and harvested as young adults

extract_protocol:
(RNAseq) Worms were broken by bead beating (Minibead Beater; Biospec Products) in homogenization buffer [10 mM KCl/1.5/1 mM DTT/10 mM Tris·HCl (pH 8.0)/50 mM Sucrose/0.05% Nonidet P-40/1 mM complete protease inhibitors (Sigma #P2714) at a 1:1 ratio of 0.1mm glass beads to packed worm volume for 3 cycles of 30 secs at 5,000 rpm. Extracts were used immediately for immunoprecipitations and equal concentration of extract as determined by protein quantification was added to each IP
(ChIPseq) All worms were maintained and grown on op50 seeded NGM plates and harvested in water. The worms were washed three times in water, and the bacteria were cleared by sucrose flotation. The worms were then frozen in liquid nitrogen and ground to a powder with a mortar and pestle. The resulting worm powder was transferred into cross-linking buffer (1 mM phenylmethylsulfonyl fluoride [PMSF], 1 mM EDTA, 1 mM EGTA, 1% formaldehyde, phosphate-buffered saline [PBS]) for 10 min at room temperature. The reaction was quenched for 5 min at room temperature by the addition of glycine to the mixture to a final concentration of 125 mM and sedimented at 4,000 × g. Pellets were washed three times with FA buffer plus 0.1% SDS (50 mM HEPES [pH 7.5], 1 mM EDTA, 1% Triton, 0.1% deoxycholic acid, 150 mM NaCl, 0.1% SDS) containing protease inhibitors. Each wash mixture was incubated for 5 min at 4°C and then sedimented at 4,000 × g. The pellets were then divided into 500-μl aliquots and stored at −80°C. Each aliquot was resuspended in 1.5 ml of FA buffer plus 0.3% SDS containing protease (Complete cocktail tablets, catalog number 11697498001; Roche) and phosphatase inhibitors (catalog number 786-450; GBiosciences). The samples were sonicated with a Virsonic digital 600 sonicator using a microtip (20 pulses of 11 s each at 30% amplitude with bursts of 0.9 s on and 0.5 s off) to generate DNA fragments of approximately 500 bp, as determined experimentally. Samples were sedimented at 13,000 × g for 15 min at 4°C, and the supernatant was transferred into a new tube, which was then diluted to 4.5 ml with FA buffer containing protein and phosphatase inhibitors.
Total RNA sequencing libraries was extracted from whole animals by TRIzol extraction. Genomic DNA was removed using TURBO DNase (Invitrogen). Poly-A selected, single-ended, 125 bp strand-specific libraries were prepared by the UCCC Genomics Core (Aurora, CO) using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For the J2-IP analyses, RNA recovered by immunoprecipitation with the J2 antibody (three biologically independent lysates) of young adult worms as well as input material (as a loading control) was converted into strand‐specific total RNA libraries using V2 Scriptseq (Epicenter #SSV21106) kits following manufacturer's instructions, except reverse transcription was done with SuperScript III (Invitrogen #18080‐044) using incrementally increasing temperatures from 42 to 59°C to allow for transcription though structured RNAs. rRNA was not removed from J2‐IP RNA samples. Immunoprecipitated DNA from ChIP samples were converted into sequencing libraries using ChIP‐Seq DNA Sample Prep Kit (IP‐102– 1001). Cluster generation and sequencing were performed on the Illumina HiSeq 2500 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina.

treatment_protocol: hpl-2(tm1489)  and tdp-1(ok803) mutants strains were compared to WT (N2 Bristol) worms.

tag: Stage

value: young adult

value: N2 (Bristol)

tag: temperature


title: N2_PolyA-1


title: Angus-RNAseq-10

description:
A835B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.8


title: Hpl2_J2IP-3

description:
total RNA (J2IP)
Supplementary_files_format_and_content: Deseq results for the comparison between N2_J2IP replicates and HPL_J2IP replicates. All J2IP samples were normalized by the Input control.
N2_HPL2_J2IP_DESeqresults.xlsx

tag: ip antibody

value: J2 antibody, English & Scientific Consulting, Lot J2-1102 and J2-1103


title: Hpl2_InputRNA-1

description:
Supplementary_files_format_and_content: Deseq results for the comparison between N2_J2IP replicates and HPL_J2IP replicates. All J2IP samples were normalized by the Input control.
N2_HPL2_J2IP_DESeqresults.xlsx


title: Hpl2_J2IP-2


title: Hpl2_J2IP-1


title: Hpl2_InputRNA-2


title: HPL2_polyA-1

growth_protocol: Worms were grown at on agarose plates and harvested as L4's


title: HPL2_polyA-2


title: N2_Hpl2-1_ChIP

description:
genomic DNA (Hpl-2 IP)
Supplementary_files_format_and_content: Processed data file "N21_Hpl2_ChIP.bw" is an RPKM normalized bigwig and "N2-1_HPL2Chip_subtractedControl.bw" has been normalized by RPKM and by the N2 genomic control via subtraction using DeepTools compare function.
HPL2_ChIP_consensusPeaks.xlsx
tdp1ChIP-1_subtractedControl.bw
tdp1ChIP-2_subtractedControl.bw
HPL2_SigDiffPeaks_overlapWith_TDP1ChIP.xlsx
TDP-1_Chip_control.bw
TDP-1_Chip_rep1.bw
TDP-1_Chip_rep2.bw

value: HPL-2 antibody, Research antibody provided by the Palladino lab


title: HPL2_polyA-3

growth_protocol: Worms were grown at on agarose plates and harvested as L4s


title: N2_Hpl2-2_ChIP

description:
genomic DNA (Hpl-2 IP)
Supplementary_files_format_and_content: Processed data file "N22_Hpl2_ChIP.bw" is an RPKM normalized bigwig and "N2-2_HPL2Chip_subtractedControl.bw" has been normalized by RPKM and by the N2 genomic control via subtraction using DeepTools compare function.
HPL2_ChIP_consensusPeaks.xlsx
tdp1ChIP-1_subtractedControl.bw
tdp1ChIP-2_subtractedControl.bw
HPL2_SigDiffPeaks_overlapWith_TDP1ChIP.xlsx
TDP-1_Chip_control.bw
TDP-1_Chip_rep1.bw
TDP-1_Chip_rep2.bw


title: Pv9-1

middle: Fang

last: Zeng

state: Beijing

address: Yuanmingyuan West Road No. 2 Haidian district

department: college of veterinary medicine

institute: China Agriculture University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sus scrofa whole genome using Tophat2 v2.0.10 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

organism: Sus scrofa

source_name: primary pulmonary alveolar macrophages

growth_protocol: Pulmonary alveolar macrophages (PAMs) were isolated from a 6-week-old specific-pathogen-free (SPF) piglets that were free of PRRSV, porcine circovirus type 2, classical swine fever virus, porcine parvovirus, pseudorabies virus, swine influenza virus and Mycoplasma hyopneumoniae infections

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Epicentre Ribo-Zero rRNA Removal Kit was used with 1 ug of total RNA for removing rRNA.  Illumina TruSeq Stranded Total RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prior to infection, PAMs were thawed and cultured for 48h in plate at a density of 5*107 cells/plate. After gently washed with 1 × phosphate-buffered saline (PBS), the cells were infected with PRRSV strain JXwn06 at a multiplicity of infection (MOI) of 10 or mock infected with DMEM. After 1h of incubation, the inoculums was removed and the cells were washed once again and then supplemented with fresh RPMI 1640 medium containing 5% FBS. The cells were collected using TRIzol (Invitrogen) at different time points (6h, 9h and 12h, 24h post-infection). / Prior to IFN stimulation, PAMs were thawed and cultured for 48h as described previously. After stimulation with pig-IFN-α for 6 and 12 hours, respectively, the cells were processed with TRIzol (Invitrogen) and preserved in liquid nitrogen for further transcriptomic analysis. Each experiment was performed in duplicate.

value: primary pulmonary alveolar macrophages

tag: agent

value: porcine reproductive and respiratory syndrome virus

tag: viral strain

tag: viral passages

tag: ifn


title: PI12-2

value: Recombinant porcine interferon alpha protein (R&D)


title: Pv9-2


title: PI12-1


title: Pv12-1


title: Angus-RNAseq-05

description:
A789B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.7

value: male


title: Pv6-1


title: PI6-1


title: Pv12-2


title: PI6-2


title: Angus-RNAseq-18

description:
A903B
Illumina HiSeq 2500
High-Output Mode
fastq average Phred score: 35.74


title: P0-2


title: P0-1


title: JS.actin

city: Houston

first: Jason

last: Shohet

address: One Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Reads were mapped using BWA to the human genome build UCSC hg19/NCBI 37. The MACS2 software was used to identify enriched regions (peaks).
Genome_build: UCSC hg19/NCBI 37
Supplementary_files_format_and_content: BED files with peaks

source_name: MYCN3 cells

growth_protocol: Human neuroblastoma cell line SHEP was stably transduced with Tet-inducible human MYCN gene and stable single clone was selected and named as MYCN3 (SHEP-MYCN-TET) and was routinely maintained and cultured. Treatment with doxycycline for 16 h induce MYCN levels.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Chromatin immunoprecipitated DNA was prepared for sequencing following a modified version of Illumina's Genomic DNA protocol. Sheared DNA fragments undergo end repair by T4 DNA polymerase to fill in 5′ overhangs, Klenow polymerase to remove 3′ overhangs, and T4PNK to phosphorylate the 5′-OH. For Illumina adapter ligation, a single adenine nucleotide overhang must be added to the polished DNA. A 1:30 dilution of the Adaptor Oligo Mix (20) was used in the ligation step. The resulting adapted constructs are amplified by 18 cycles of PCR enriching the DNA fragments with adapters flanking each end. The amplified product was quantified using a spectrophotometer at 260 nm (Nanodrop) then a portion of final sample is size separated on a 6% TBE (Invitrogen) to verify correct target range amplification. The validated DNA library is submitted at a 10 nmol/L concentration for sequencing. All protocols for Illumina library sequence preparation, sequencing, and quality control are provided by Illumina.

treatment_protocol: The samples are A) ChIP with Actin Antibody as control B) ChIP with MYCN antibody, C) ChIP with MYCN antibody on cells treated with doxycycline for 16 h to induce MYCN high conditions

tag: cell type

value: Neuroblastoma cell line with inducible MYCN expression

tag: cell line

value: MYCN3 (SHEP-MYCN-TET)

tag: antibody

value: Actin

tag: condition

value: control


title: JS.mycn-high

value: MYCN

value: mycn-high


title: JS.mycn-low

value: mycn-low


title: HFD-Only.23

city: Philadelphia

first: Isaac

middle: J

last: Perron

address: 125 S 31st St, Auite 2100

department: Medicine

institute: University of Pennsylvania

description: 2 brain punches pooled

data_processing:
The pooled samples were run thrice. Fastq and BAM files were merged using Picard Tools (v2.7.1). Alignment of fastq files to the mouse reference genome  was conducted with STAR (v2.5.1b) using gene models from Ensembl v67 genome annotation.
Data was normalized using Pipeline Of RNA-Seq Transformations (PORT - v0.8.1-beta). Briefly, PORT recognizes potential confounding factors (e.g., ribosomal RNA and mitochondrial DNA) and omits these reads from the normalization process. Importantly, our samples had normal ranges and distributions of both ribosomal RNA (2.28 – 6.05%) and mitochondrial DNA (0.5 – 1.8%). Next, PORT identifies the input sample with the fewest number of gene-mapping reads and randomly re-samples each of the other datasets down to this minimum read count. This re-sampling approach accounts for batch effects and differences in sequencing depth between the samples, and allows for direct comparison between samples.
Genome_build: mm9
Supplementary_files_format_and_content: txt file contains PORT-normalized and quantified read counts for each gene in each sample

source_name: Circumventricular Hypothalamus (CVH)

growth_protocol: Twelve- to fourteen- week old male C57/B6J mice were acquired from Jackson Labs. Mice were assigned to one of four dietary conditions (RC only, RC -> HFD, HFD -> RC, HFD only)

extract_protocol:
Mice were sacrificed and whole brains were dissected and snap-frozen in dry-ice cold isopentane. CVH punches were conducted in a cryostat on RNAse-free microscope slides. RNA was extracted using the Qiagen Rneasy Mini Kit, according to manufacturers’ protocols (using RLT buffer).
CVH punches from two animals of the same condition wereequally pooled (300 ng total) to reduce technical variability. The TruSeq Stranded mRNA Sample Preparation Kit was used to prepare samples for Illumina sequencing according to the manufacturer’s protocol for polyA enrichement (n=6 per condition).  Following preparation, library quality was assessed using a Qubit, Bioanalyzer, and Kapa; 3 samples did not meet QC standards and were omitted from sequencing. Libraries from samples which passed QC (21 samples)whereequimolarly pooled together and sequenced using an Illumina HiSeq 4000 (100 bp single-end reads).

treatment_protocol: Mice were sleep deprived by novel objects for 3 hours prior to tissue collection. Mice were sacrificed by cervical dislocation during the middle of the light phase (ZT6).

tag: strain

tag: tissue

value: Brain

tag: dietary condition

value: HFD Only


title: HFD-Only.20

description: 2 brain punches pooled


title: HFD-Only.24

description: 2 brain punches pooled


title: HFD-Only.21

description: 2 brain punches pooled


title: HFD-Only.19

description: 2 brain punches pooled


title: Hpl2_InputRNA-3

value: young adult


title: Donor2_CD33_CAR

city: Memphis

first: Lance

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Paired-end reads were aligned to the following 4 database files using BWA (0.5.10) aligner: (1) the human GRCh37-lite reference sequence; (2) RefSeq; (3) a sequence file representing all possible combinations of non-sequential pairs in RefSeq exons; (4) AceView database flat file downloaded from UCSC representing transcripts constructed from human ESTs. The mapping results from (2) and (4) were aligned to human reference genome coordinates. In addition, reads were aligned using STAR 2.3.0 to the human GRCh 37-lite reference sequence without annotations. The final BAM file was constructed by selecting the best alignment among the five mappings
Gene counts were obtained using htseq-count version 0.6.1 with Gencode vM5 level 1 and 2 gene annotations.
Within R, gene counts were normalized using voom, and then differential analysis expression were performed with the limma packagepackage using the lmFIt and eBayes functions with default parameters.
P-value adjustments were done with false discovery rate (FDR) correction.
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: tab-delimited text files containing gene and count generated by htseq-count

source_name: CD33 CAR T-cells

growth_protocol: Transduced human primary T cells were sorted and expanded in culture for 5-7 days, supplementing with fresh IL-2 every 2 days.

extract_protocol:
Total RNA was extracted from three samples of CD33 CAR or control T cells from three different donors, 12 days after initial stimulation by CD3/CD28, using TRIzol reagent (Life Technologies).
Method: Stranded Total; Vendor Kit: Illumina Stranded Total RNA; Description: Hybridization based rRNA reduction with strand information; Application: expression levels, splice variants, with strand information. Tolerant of somewhat degraded RNA; Input: >250ng total RNA.

treatment_protocol: human T cells were isolated and stimulated with anti-human CD3 and CD28 antibodies for 24h prior to transduction of either anti-CD33CAR or empty vector. GFP positive transduced T cells were sorted 5 days post initial activation and expanded in culture for 7 days, supplementing with fresh IL-2 every 2 days. Then cells were used to extract RNA.

value: blood

tag: source

value: apheresis ring from healthy donors


title: Donor3_Control

source_name: Control T-cells


title: HFD-RC.17

description: 2 brain punches pooled

value: HFD --> RC


title: Donor2_Control


title: Donor3_CD33_CAR


title: RAT_EDL_M6

value: Sprague Dawleys

tag: Sex


title: Pv6-2

city: Beijing

value: primary pulmonary alveolar macrophages

value: porcine reproductive and respiratory syndrome virus


title: HFD-RC.15

description: 2 brain punches pooled


title: Donor1_CD33_CAR


title: HFD-RC.14

description: 2 brain punches pooled


title: Donor1_Control


title: RC-HFD.11

description: 2 brain punches pooled

value: RC --> HFD


title: RC-HFD.10

description: 2 brain punches pooled


title: RC-HFD.12

description: 2 brain punches pooled


title: RC-HFD.9

description: 2 brain punches pooled


title: RC-HFD.8

description: 2 brain punches pooled


title: SA33558

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: UCSC mm10/NCBI 38
Supplementary_files_format_and_content: tab-delimited text file include normalized FPKM values for each Sample

growth_protocol: Human neuroblastoma cell line SHEP was stably transduced with Tet-inducible human MYCN gene and stable single clone was selected and named as MYCN3 (SHEP-MYCN-TET) and was routinely maintained and cultured.

extract_protocol:
RNA was extracted from neuroblastoma cells using Arcturus PicoPure RNA isolation kit (Applied Biosystems Inc., Carlsbad, CA) according to the manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples are: A) untreated, B) treated with nutlin3a for 8 h, C) treated with doxycycline for 16 h, D) treated with doxycycline for 16 h followed by nutlin3a for 8 h

tag: protocol


title: SA33621

value: nutlin3a for 8 h


title: SA33620

value: MYCN3 (SHEP-MYCN-TET)

value: doxycycline for 16 h


title: SA33564

value: doxycycline for 16 h followed by nutlin3a for 8 h


title: SA33556


title: HFD-RC.16

description: 2 brain punches pooled


title: RC-Only.6

description: 2 brain punches pooled

value: RC Only


title: RC-HFD.7

description: 2 brain punches pooled


title: SA33561

value: untreated


title: SA33552


title: RC-Only.5

description: 2 brain punches pooled


title: HFD-RC.13

description: 2 brain punches pooled


title: RC-Only.2

description: 2 brain punches pooled


title: RC-Only.3

description: 2 brain punches pooled


title: RC-Only.1

description: 2 brain punches pooled