title: MstTg rep5

description: rRNA depleted RNA


title: wt rep1

status: Public on Aug 29 2019

type: SRA

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

description: rRNA depleted RNA

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.19.1.403 pipeline was used to generate the sequence data.
FastX Toolkit was used to trim low quality bases from the 5’ end of reads using a minimum phred threshold of 20 and minimum length of 18 using (Hannon 2009).
Reads were mapped with STAR (Dobin et al, 2013) to the mouse genome downloaded from Ensembl (GRCm38).
FeatureCounts (Liao et al, 2014) was used to count reads mapped to gene exons on the correct strand with a minimum mapping quality of 20 using Ensembl genome annotation (Mus musculus.GRCm38.85.gtf).
Genes with fewer than 10 reads per sample on average were excluded from downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression

molecule: total RNA

organism: Mus musculus

source_name: wt, left ventricle

growth_protocol: Standard mouse housing conditions

extract_protocol:
Left ventricle RNA was isolated from Trizol homogenates using the Direct-zol™ RNA MiniPrep Kit (Zymo Research).
RNA quality was assessed by Multi-NA bioanalyzer (Shimadzu Japan). 200 ng of total RNA underwent ribosomal RNA depletion using the NEBNext® rRNA Depletion Kit followed by library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs).

tag: background strain

tag: genotype

value: Wild type

tag: tissue

value: Left ventricle


title: E8_ant_Pharynx_1

city: Vienna

first: Alison

middle: G

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0117

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: nanus_anchored_Vs2
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

organism: Acrobeloides nanus

source_name: embryo

extract_protocol:
Egg shells were removed from a A. nanus embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

tag: developmental stage

value: stage E8

tag: cell type

value: embryonic cell


title: E8_ant_epithelia_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0118


title: E8_post_Abp_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0116


title: 13_MS_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0113

value: 13 cell


title: 13_D4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0114


title: 13_C2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0112


title: 13_c_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0111


title: WT P2 H3K4me3 rep1

city: Shinjuku-ku

first: Haruhiko

last: Siomi

state: Tokyo

address: Shinanomachi 35

department: Department of Molecular Biology

country: Japan

institute: Keio University, School of Medicine

library_source: genomic

data_processing:
Basecalled performed using Illumina RTA software in sequencer
adaptor was trimmed with cutadapt tool with the following setting -m 20.
Reads were alignedto the mm10 genome assembly using bowtie with the following setting -m 1.
dupicate reads were removed with picard tool
Genome_build: mm10
Supplementary_files_format_and_content: wig

molecule: genomic DNA

source_name: WT P2 H3K4me3

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with corresponding anti-body
Libraries were prepared according to QIAGEN's instructions accompanying the QIAseq Ultralow Input Library Kit (Part# 180492). In the adaptor ligation step, the original adaptor reagent was diluted to 100 times. After adapter ligation DNA was PCR amplified with Illumina primers for 13~16 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified with AMPure XP beads(Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

tag: strain

value: gonocyte

tag: chip antibody

value: MBL (MABI0304)

tag: age


title: WT P2 H3K4me3 rep2


title: 13_E+P4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0110


title: WT E19.5 H3K4me3 rep2

source_name: WT E19.5 H3K4me3


title: 13_P4d_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0109


title: WT E19.5 H3K4me3 rep1


title: 13_E_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0107


title: DLD-1-HMGA2-2

type: RNA

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

hyb_protocol: OneArray Plus Hybridization Protocol

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Homo sapiens

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000; pass criteria for CyDye incorporation efficiency at > 15 dye molecular/1000nt.

growth_protocol: DLD-1-Vector and DLD-1-HMGA2 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1 mM sodium pyruvate, 1% L-glutamine, 1% antibiotic-antimycotic solution, 0.5 mg/mL G418, and incubated at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: RNA was prepared using the GENEzol TriRNA Pure Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Stable HMGA2-overexpressing DLD-1 (DLD-1-HMGA2) and the corresponding vector-overexpressing (DLD-1-Vector) cell lines were established by transfecting tGFP-tagged pCMV6-HMGA2 and pCMV6-AC-GFP plasmids, respectively, and then stable clones were selected with 1 mg/mL G418. Stable cells were maintained in medium containing 0.5 mg/mL G418. Total RNA from untreated cells were prepared form microarray analysis.

tag: cell line

tag: genotype/variation

value: Stable HMGA2-overexpression


title: WT E17.5 H3K4me3 rep2

source_name: WT E17.5 H3K4me3


title: WT E17.5 H3K4me3 rep1


title: 13_AB3_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0108


title: DLD-1-Vector-1

source_name: DLD-1-Vector, control

value: control


title: DLD-1-HMGA2-1


title: 13_P4_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0106


title: WT E13.5 H3K4me3 rep2

source_name: WT E13.5 H3K4me3


title: Comma_posterior_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0105

value: comma stage


title: Comma_posterior_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0104


title: WT E13.5 H3K4me3 rep1


title: E8_post_E_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0115


title: Comma_posterior_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0103


title: Comma_anterior_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0102


title: Comma_anterior_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0100


title: Comma_middle_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0099


title: Comma_middle_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0098


title: Comma_middle_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0097


title: input genome, NMuMG, TGF-beta treated, 1.5 h

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: input genome

data_processing:
Unfiltered 36-bp sequence reads were aligned against the mouse reference genome (mm9) using Bowtie2 with default parameters.
Peaks were called using CisGenome v2 (two-sample analysis (anti-Smad2/3 ChIP vs input genome) with a FDR cutoff of 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: bed and wig files were generated using CisGenome v2.0.

source_name: NMuMG

growth_protocol: NMuMG cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS), 50 units/ml penicillin, 50 ug/ml streptomycin, and insulin (10 ug/ml).

extract_protocol:
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). Smad2/3-DNA complexes were isolated with anti-Smad2/3 antibody (610843, BD, Franklin Lakes, NJ, USA, lot number not available).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h in the presence of 10% FBS.

tag: histology

value: mammary gland epithelial cells

tag: tgfb treatment


title: VE_posterior_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0096


title: VE_middle_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0095


title: LE_E6c_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0091


title: VE_ant_pharynx_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0093


title: Comma_anterior_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0101


title: VE_middle_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0094


title: LA1-55n_shGLDC99c

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

country: USA

institute: University of Alabama at Birmingham

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

label: biotin

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: LA1-55n_teton-shGFP and -shGLDC99 cells were cultured in RPMI 1640 (HyClone SH30027, Thermo Fisher Scientific) supplemented with 10% FBS (Atlanta Biologicals S11050).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: LA1-55n_teton-shGFP and -shGLDC99 cells were cultured n the presence of 0.5µg/ml doxycycline for 7 days

value: Neuroblastoma


title: DLD-1-Vector-2


title: LE_2c_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0090


title: LA1-55n_shGLDC99b

description: RNA expression value


title: VE_ant_pharynx_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0092


title: LA1-55n_shGFPb

description: RNA expression value


title: 4_c_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0184

value: 4 cell


title: SAM24325568 Hyperplasia Epidermal Irf6KO

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: RNA from kinase dead skin from E15.5

extract_protocol: Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.

value: Hyperplasia Epidermal


title: LA1-55n_shGLDC99a

description: RNA expression value


title: LA1-55n_shGFPa

description: RNA expression value


title: liver tissue, Clonorchis sinensis infection, 4 weeks, replicate 2

city: Jinju

first: Byoung-Kuk

state: Gyeongnam

address: Jinjudaero 816

department: Department of Parasitology and Tropical Medicine, and Institute of Health Sciences

country: South Korea

institute: Gyeongsang National University

description: Gene expression after 4 weeks in the livers of Clonorchis sinensis-infected rats

hyb_protocol: The labeled 1.5 ug of each cRNA sample was then hybridized on Agilent 4x44K whole rat genome arrays (Agilent Design #028282) at 65 ̊C for 17 hr with rotation in the dark. Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies, Inc.) following the manufacturer's instructions.

scan_protocol: After washing in GE washing buffer, the slides were scanned with an Agilent Microarray Scanner (G2505C). Feature extraction software (version 10.5.1.1) employing defaults for all parameters was used to convert the images into gene expression data.

data_processing: All intensities were normalized using 'agilent' option of Babelomics v5 (www.babelomics.org) according to the recommentation of Agilent and log-transformed.

organism: Rattus norvegicus

source_name: liver tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: For the detailed information, see the reference: Comparative biochemical and functional properties of two leucine aminopeptidases of Clonorchis sinensis. Mol Biochem Parasitol. 2012 Mar;182(1-2):17–26. PMID: 22155540

value: Sprague-Dawley

value: liver

tag: infection

value: Clonorchis sinensis infection


title: liver tissue, no infection, replicate 1

description: Gene expression in the liver of normal rat


title: LA1-55n_shGFPc

description: RNA expression value


title: liver tissue, Clonorchis sinensis infection, 2 weeks, replicate 1

description: Gene expression after 2 weeks in the livers of Clonorchis sinensis-infected rats


title: P9V5

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

data_processing:
sequencing: Illumina HIseq 2000: 75 cycle flow cell (catalog#: FC-404-2005) with approximately 4-8 million reads per sample
Base-calling: Illumina-base caller (Base space)
Trim, quality filter: Trimmomatic software (v0.32) and bbduk.sh script (Bbmap suite)
Alignment: STAR (v2.5.2b) and the Gencode (v28, Ensembl release 92) annotation as the reference for splice junctions.
Samples were then quantified with HT_seq  and DGE was obtained using paired samples with DESeq2 - Here are the versions of the computational tools used A number of open source code was used to analyze this data as well as custom code.   open source code includes:   FastQC 0.11.5  samtools 1.8   Rstudio and R (both versions 3.2, 3.4 and 3.5 used - since some packages are specific to a certain version)   on R, we have used: Diffbind (3.9), Deseq2 (1.18.0 and 1.2.0), ggplot2 (3.1.0).  HT-seq 0.6  UCSC toolkit (no version available)
Genome_build: hg38
Supplementary_files_format_and_content: Lavery_CTLvTRT_DESeq2_filter_paired_15-6-2018.txt is differential gene expression using 12 CTL and 12 NR treated samples, analysis was paired (based on patient). Also provided is a text file with normalized reads (Lavery_Normalised_counts_Deseq2.txt)

source_name: Muscle biopsy_Placebo

growth_protocol: not applicable - samples were collected and frozen from patients

extract_protocol:
Manufacturer's instructions using TruPure RNA extraction.
Library prep using 2x Lexogen QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD), 24 preps (catalog#: 015.24.)

treatment_protocol: Subjects were given NR for 3weeks, 1g/day or placebo. Following a 3 week break, the treatment was reversed. Muscle biopsies were collected from leg muscle.

tag: treatment

value: Placebo

value: Muscle biopsy (vastus lateralis)


title: P9V3

source_name: Muscle biopsy_Treatment

value: Treatment


title: LE_3c2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0089

value: embryonic cell


title: P9V2

source_name: Muscle biopsy_CTL

value: CTL


title: liver tissue, Clonorchis sinensis infection, 2 weeks, replicate 2


title: anti-Smad2/3 ChIP-seq, NMuMG, TGF-beta treated, 1.5 h

description: anti-Smad2/3 ChIP sample


title: liver tissue, Clonorchis sinensis infection, 4 weeks, replicate 1


title: liver tissue, no infection, replicate 2


title: P8V3


title: LE_3c_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0086


title: P8V2


title: P7V3


title: E4_E4_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0081

value: stage E4


title: P6V5


title: LE_ant_pharynx_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0084


title: E4_C_MB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0083


title: E4_CM6_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0079


title: P6V3


title: E4_E2M_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0080


title: P6V2


title: E4_E46_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0082


title: LE_ant_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0087


title: LE_6 cells_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0088


title: P8V5


title: P5V5


title: E4_MIDb_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0077


title: E4_M6_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0078


title: P5V2


title: E2_E2_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0073

value: stage E2


title: P5V3


title: P4V5


title: E2_E2MB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0074


title: P4V3


title: LE_p4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0085


title: P7V5


title: P7V2


title: E2_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0072


title: P4V2


title: P3V5


title: E2_AB2_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0071


title: P3V3


title: P3V2


title: 13_P4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0069

value: 13 cell


title: P2V5


title: E4_P4D_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0070


title: 13_CDP4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0068


title: E4_AB6_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0076


title: E4_ANT_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0075


title: P2V3


title: 13_MS2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0067


title: 13_AB2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0066


title: 13_AB_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0065


title: P2V2


title: 3_P2_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0064

value: 3 cell


title: 4_P3_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0063


title: P1V5


title: 4_P3_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0062


title: 5_EMS_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0061

value: 5 cell


title: P1V3


title: 4_AB_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0060


title: 329_SB939

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

data_processing:
Data was analyzed using MAPRSeq version 3.0.0, which is an integrated RNA-Seq analysis pipeline developed at Mayo Clinic (Kalari et al., 2014).
As part of the MAPRSeq pipeline, reads were aligned to the hg38 (GRCh38) build of the human reference genome using STAR with default parameter setting (Dobin et al., 2013).
The aligned reads were then used for Ensembl (v78) gene and exon expression quantification using featureCounts from the Subread package to obtain raw counts as well as normalized (RPKM – Reads Per Kilobase of exon per Million mapped reads) expression values (Liao et al., 2013).
Extensive quality control analysis of the aligned RNA-Seq reads was performed using the RSeQC package to assess metrics such as insert size, gene body coverage, and junction saturation (Wang et al., 2012).
Genome_build: hg38
Supplementary_files_format_and_content: text file containing RPKMs for all samples

source_name: isolated from IPF lung tissue

growth_protocol: Human lung fibroblasts were grown on tissue culture plastic in standard growth media. For this experiment, fibroblasts were in 0.1% FBS in EMEM.

extract_protocol: mRNA was isolated using RNeasy mini kit (Qiagen, Valencia, CA, USA); concentration of mRNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA quality was determined using the Fragment Analyzer (Agilent, Santa Clara, California, USA). RNA samples that had RQN values ≥ 6 were approved for library prep and sequencing. RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA), employing poly-A mRNA enrichment using oligo dT magnetic beads. The final adapter-modified cDNA fragments were enriched by 12 cycles of PCR using Illumina TruSeq PCR primers.  The concentration and size distribution of the completed libraries were determined using a Fragment Analyzer (Agilent, Santa Clara, CA, USA) and Qubit fluorometry (Invitrogen, Carlsbad, CA, USA). Libraries were sequenced as 100 x 2 paired end reads on an Illumina HiSeq 4000, following Illumina’s standard protocol with the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit, which yielded approximately 43-65 million reads per sample. Base-calling was performed using Illumina’s RTA version 2.7.3. Data was analyzed using MAPRSeq version 3.0.0, which is an integrated RNA-Seq analysis pipeline developed at Mayo Clinic (Kalari et al., 2014). As part of the MAPRSeq pipeline, reads were aligned to the hg38 (GRCh38) build of the human reference genome using STAR with default parameter setting (Dobin et al., 2013). The aligned reads were then used for Ensembl (v78) gene and exon expression quantification using featureCounts from the Subread package to obtain raw counts as well as normalized (RPKM – Reads Per Kilobase of exon per Million mapped reads) expression values (Liao et al., 2013). Extensive quality control analysis of the aligned RNA-Seq reads was performed using the RSeQC package to assess metrics such as insert size, gene body coverage, and junction saturation (Wang et al., 2012).

treatment_protocol: Fibroblasts were treated with TGFbeta (2ng/mL) and/or pracinostat (SB939) (1uM)

value: lung fibroblasts

value: pracinostat (SB939)


title: 329_TGFB__plus__SB939

value: treatment TGFbeta + pracinostat (SB939)


title: 4_C_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0059

value: 4 cell


title: P12V5


title: 329_TGFB

value: TGFbeta


title: 3_AB_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0057


title: 3_AB_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0056


title: 3_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0058


title: P12V3


title: 329_DMSO

value: DMSO (control)


title: 3_P2_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0055


title: 293_TGFB__plus__SB939


title: P12V2


title: 2_AB_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0053

value: 2 cell


title: P11V5


title: 3_EMS_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0054


title: 2_P1_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0051


title: 293_SB939


title: P11V3

value: Placebo


title: 293_TGFB


title: 2_P1_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0050


title: 2_AB_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0052


title: E4_E4_2c_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0049


title: P1V2

value: Muscle biopsy (vastus lateralis)


title: P11V2


title: E4_MIDa_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0048


title: 293_DMSO


title: E4_AB_POST_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0046


title: P10V5

value: Treatment


title: 16_unkn_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0045

value: 16 cell

value: embryonic cell


title: 292_TGFB__plus__SB939


title: P10V3


title: 16_MS

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0043


title: 292_SB939


title: 16_unkn_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0044


title: E_E_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0042

value: gastrula


title: 292_TGFB


title: P10V2

value: CTL


title: 6_P4D_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0041

value: 6 cell


title: 16_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0040


title: 292_DMSO


title: 16_AB_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0038


title: 6_DP4_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0039


title: 6_unkn_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0037


title: 6_EMS_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0036


title: A673 7 R2: hairpin7 (iLSD2-7a) replicate 2

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
STAR 2.5.2b two pass approach was used to align the sequences to hg19
featureCounts from subread 1.6.2 package was run to count features. GRCh37.75.gtf was used for annotation
DESeq2 was run to perform differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: TestVsRef.complete.txt contains results from DESeq2 for all the features. Columns descriptions.docx contains descriptions of each column in the txt file.

source_name: A673 cells

growth_protocol: A673 Ewing sarcoma cells were grown as described previously (Lessnick et al., 2002)

extract_protocol: Cells were trypsinized, counted, and 5 million cells were washed with PBS, pelleted, and flash-frozen. RNA was extracted using an Rneasy kit with on-column DNA digestion per kit instructions (Qiagen). 2.5 ug of total RNA was used for library prep.

treatment_protocol: A673 cells were stably infected with retroviral vector pMSCV-puro expressing Luciferase shRNA (iLuc) or KDM1B shRNA (iLSD2-3a and iLSD2-7a) and selected for 4 days, followed by total RNA extraction.

value: Ewing sarcoma

tag: shRNA

value: LSD2 (KDM1B)


title: A673 3 R2: hairpin 3 (iLSD2-3a) replicate 2


title: 5_C_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0033

value: 5 cell


title: 5_C_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0032


title: A673 iLUC R2: iLuc replicate 2

value: Luciferase


title: 6_AB_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0035


title: E4_AB_ANT_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0047

value: stage E4


title: A673 7 R1: hairpin7 (iLSD2-7a) replicate1


title: 5_EMS_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0031


title: 5_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0030


title: 5_P4_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0034


title: A673 3 R1: hairpin3 (iLSD2-3a) replicate1


title: 4_P3_ 4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0029

value: 4 cell


title: 4_C_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0028


title: 4_EMS_5

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0027


title: 10dag_PORIxrpt2a_2

city: DAEGU

first: JAE

middle: HO

last: LEE

address: 333, Techno jungang-daero, Hyeonpung-myeon, Dalseong-gun

department: NewBiology

institute: DGIST

description: rpt2a mutant

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling
Quality control and preprocessing of metagenomic data were performed using FastQC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and performed the alignment of the read sequences by pRNASeqTools pipeline. (https://github.com/grubbybio/pRNASeqTools).
Adapters trimmed the adapter sequence (“AGATCGGAAGAGCACACGTCT”) from the reads by using cutadapt v1.9.1 (Martin, 2011). , and alignment was performed using the Arabidopsis TAIR10 genome (ENSEMBL annotation) and ShortStack v3.4 (Johnson et al., 2016).
The reads mapped to the annotated miRNA loci (no mismatches and at most 1 nt shift allowed) were identified as miRNA reads.
A differential gene expression analysis was performed using DESeq2 (Love et al., 2014). P-values were adjusted via the Benjamini–Hochberg method (Benjamini and Hochberg, 1995), and differentially expressed genes with false discovery rates (FDR) < 0.05 were considered significant.
Genome_build: Arabidopsis_thaliana.TAIR10
Supplementary_files_format_and_content: Tab-delimited count file including read counts processed by HTSeq-count. The meaning of the 9 columns in the '.count' file is the 18-26 nucleotide size.

organism: Arabidopsis thaliana

source_name: PORI rpt2a seedlings

growth_protocol: Plants were grown on 1/2 Murashige and Skoog (MS) media or soil at 22°C under long-day condition (16-h light/8h dark condition).

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Invitrogen) and purified with the Quick-RNA Miniprep Kit (Zymo Research).
The RNA integrity number (RIN) of each sample was measured using the Agilent Technologies 2100 BioAnalyzer, and RINs for all the samples were larger than 8. After gel electrophoresis of total RNA by TBE-urea PAGE, small RNAs were purified from the excised gel slices. Small RNA samples were converted to DNA libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, MA, USA), following the manufacturer’s protocol.

value: PORI rpt2a

value: seedlings

value: 10 days after germination


title: 3_EMS_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0024

value: 3 cell


title: 10dag_PORIxrpt2a_1

description: rpt2a mutant


title: 3_P2_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0025


title: 10dag_PORI_2

description: control

source_name: PORI seedlings

value: PORI


title: 3_AB_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0023


title: rtt109∆ NET-seq S90 rep2

city: Worcester

first: Salih

last: Topal

state: MA

address: 373 Plantation Street

institute: UMass Medical School

data_processing:
library strategy: NET-seq
The adapter sequence was (ATCTCGTATGCCGTCTTCTGCTTG) removed and the random hexamer sequence was removed from the 5’ end. The 3’ ends of the reads were then trimmed for quality using FASTQ Quality Timmer by sliding window (Blankenberg et al., 2010) with a window size of 10 and a step size of 5. The reads were trimmed until the aggregate score was ≥ 21.
Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and S. pombe rRNA, tRNA, and RDN sequences to remove contaminating reads.
Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and the S. pombe genome (ASM294v.2, PomBase) with TopHat2, allowing up to three mismatches.
reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads. This scaling factor was then used to scale the uniquely mapped S. cerevisiae reads. the pombe-scaled WT S. cerevisiae read counts were then scaled to 1 M reads, and this additional scaling factor was included to scale the sample reads
Only the 5’ end of the sequencing read, which corresponds to the 3’ end of the nascent RNA was recorded and used for downstream analyses.
Genome_build: SacCer3, ASM294v.2
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: rtt109∆ NET-seq S90

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
Cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
RNA Pol II IP, RNA purification, and library construction was carried out as described previously (Churchman and Weissman, 2011; Mayer et al., 2015). 3’ end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol: Rapamycin was added for 1 hour prior to harvest (for anchor-away strains). S. pombe cells containing a flag-tagged Rpb3 were added in a 1:10 ratio at time of harvest for library spike-in

tag: growth phase

value: log phase

tag: protocol

value: Native elongating transcript sequencing (NET-seq)

tag: molecule subtype

value: nascent RNA


title: 3_P2_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0022

source_name: embryo

value: embryonic cell


title: rtt109∆ NET-seq S90 rep1


title: 10dag_PORI_1

description: control

tag: genotype


title: 3_EMS_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0021


title: rtt109∆ NET-seq S60 rep2

source_name: rtt109∆ NET-seq S60


title: 2_P1_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0019

value: 2 cell


title: rtt109∆ NET-seq S60 rep1


title: 2_AB_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0016


title: 3_P2_7

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0014


title: rtt109∆ NET-seq S30 rep1

source_name: rtt109∆ NET-seq S30


title: 3_AB_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0020


title: 2_P1_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0017


title: 3_AB_7

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0012


title: 2_AB_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0018


title: 3_EMS_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0010


title: WT NET-seq S90 rep2

source_name: WT NET-seq S90

value: WT

value: Nascent RNA


title: 3_P2_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0011


title: 4_AB_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0026


title: A673 iLUC R1: iLuc replicate 1

value: Ewing sarcoma


title: WT NET-seq S60 rep2

source_name: WT NET-seq S60


title: 1_P0_3

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0015

value: 1 cell


title: rtt109∆ NET-seq S30 rep2


title: rtt109∆ NET-seq G1 rep3

source_name: rtt109∆ NET-seq G1


title: 2_P1_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0008


title: 2_AB_8

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0007


title: WT Net-seq S30 rep2

source_name: WT Net-seq S30


title: rtt109∆ 4sU-seq rep2

data_processing:
NET-seq: The adapter sequence was (ATCTCGTATGCCGTCTTCTGCTTG) removed and the random hexamer sequence was removed from the 5’ end. The 3’ ends of the reads were then trimmed for quality using FASTQ Quality Timmer by sliding window (Blankenberg et al., 2010) with a window size of 10 and a step size of 5. The reads were trimmed until the aggregate score was ≥ 21.
NET-seq: Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and S. pombe rRNA, tRNA, and RDN sequences to remove contaminating reads.
NET-seq: Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and the S. pombe genome (ASM294v.2, PomBase) with TopHat2, allowing up to three mismatches.
NET-seq: reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
NET-seq: libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads. This scaling factor was then used to scale the uniquely mapped S. cerevisiae reads. the pombe-scaled WT S. cerevisiae read counts were then scaled to 1 M reads, and this additional scaling factor was included to scale the sample reads
NET-seq: Only the 5’ end of the sequencing read, which corresponds to the 3’ end of the nascent RNA was recorded and used for downstream analyses.
Genome_build: SacCer3, ASM294v.2
RNA-seq: FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
RNA-seq: Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and ERCC spike-in sequences to remove contaminating reads.
RNA-seq: Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and ERCC sequences with TopHat2, allowing up to two mismatches.
RNA-seq: reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
RNA-seq: For visualization in USCS genome browser, libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads.
RNA-seq: To compare RNA expression between samples, HTseq 0.9.1 was used to count the number of reads that aligned to each annotated gene.
RNA-seq: Normalized S. cerevisiae read counts were generated by scaling ERCC read counts (derived from DeSeq) relative to WT biological replicate 1 to determine scaling factors for S. cerevisiae read counts
TT-seq: FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
TT-seq: Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and ERCC spike-in sequences to remove contaminating reads.
TT-seq: Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and ERCC sequences with TopHat2, allowing up to two mismatches.
TT-seq: reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
TT-seq: For visualization in USCS genome browser, libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads.
TT-seq: To compare RNA expression between samples, HTseq 0.9.1 was used to count the number of reads that aligned to each annotated gene.
TT-seq: Normalized S. cerevisiae read counts were generated by scaling ERCC read counts (derived from DeSeq) relative to WT biological replicate 1 to determine scaling factors for S. cerevisiae read counts
4SU-seq: FASTQ files from paired end libraries were collapsed by barcode and the Illumina adapter sequence was trimmed from the 3’ end.
4SU-seq: Reads were first aligned using Bowtie2 to a combined FASTA file of S. cerevisiae and ERCC spike-in sequences to remove contaminating reads.
4SU-seq: Reads were then aligned to a combined version of the S. cerevisiae genome (SacCer3, SGD) and ERCC sequences with TopHat2, allowing up to two mismatches.
4SU-seq: reads were separated by their respective genomes with SAMtools, and only uniquely mapped reads were used for further analyses
4SU-seq: For visualization in USCS genome browser, libraries were normalized by scaling the uniquely mapped S. pombe reads to 100,000 reads.
4SU-seq: To compare RNA expression between samples, HTseq 0.9.1 was used to count the number of reads that aligned to each annotated gene.
4SU-seq: Normalized S. cerevisiae read counts were generated by scaling ERCC read counts (derived from DeSeq) relative to WT biological replicate 1 to determine scaling factors for S. cerevisiae read counts
Supplementary_files_format_and_content: bigwig, abundance measurements

source_name: rtt109∆ 4sU-seq

growth_protocol:
NET-seq: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.
RNA-seq: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.
TT-seq: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.
4sU-seq: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
NET-seq: Cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
NET-seq: RNA Pol II IP, RNA purification, and library construction was carried out as described previously (Churchman and Weissman, 2011; Mayer et al., 2015). 3’ end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.
RNA-seq: Total RNA was purified by hot-phenol extraction and ethanol precipitation
RNA-seq: Libraries were then prepared as in (Zhang et al., 2012), and paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.
TT-seq: Total RNA was purified by hot-phenol extraction and ethanol precipitation
TT-seq: Libraries were then prepared as in (Zhang et al., 2012), and paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.
4sU-seqTotal RNA was purified by hot-phenol extraction and ethanol precipitation
4sU-seqLibraries were then prepared as in (Zhang et al., 2012), and paired-end sequencing was performed on an Illumina NextSeq 500 with a read length of 75 bp.

treatment_protocol:
NET-seq: Rapamycin was added for 1 hour prior to harvest (for anchor-away strains). S. pombe cells containing a flag-tagged Rpb3 were added in a 1:10 ratio at time of harvest for library spike-in
RNA-seq:  ERCC spike-ins were added for library spike-in accordingly (Schwalb et al., 2016)
TT-seq: 2.5 mM 4-thiouracil was added for 10 min prior harvest. ERCC spike-ins were added for library spike-in accordingly (Schwalb et al., 2016)
4sU-seq2.5 mM 4-thiouracil was added for 10 min prior harvest. ERCC spike-ins were added for library spike-in accordingly (Schwalb et al., 2016)


title: 2_AB_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0003


title: rtt109∆ 4sU-seq rep1


title: 2_P1_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0006


title: 3_EMS_7

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0013


title: 2_AB_6

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0005


title: 1_P0_2

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0002


title: WT 4sU-seq rep2

source_name: WT 4sU-seq


title: 3_AB_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0009


title: 100x_4r40_1

description: sample name: 350

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: PRJNA186477
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules

organism: Panagrellus redivivus

extract_protocol:
Egg shells were removed from a Panagrellus redivivus embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.

value: late gastrula


title: 100x_4r38_1

description: sample name: 348


title: 100x_4r39_1

description: sample name: 349


title: 100x_4r35_1

description: sample name: 345


title: 100x_r36_1

description: sample name: 346


title: 100x_3r34_1

description: sample name: 344


title: rtt109∆ TT-seq rep1

source_name: rtt109∆ TT-seq

value: TT-seq


title: 100x_4r37_1

description: sample name: 347


title: WT 4sU-seq rep1


title: rtt109∆ TT-seq rep2


title: 1_P0_1

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0001


title: WT TT-seq rep2

source_name: WT TT-seq


title: 100x_4r32_1

description: sample name: 342


title: 100x_2r33_1

description: sample name: 343


title: 2_P1_4

description: sample name: Alison_nanusblastomeres_A.nanus_sample_0004


title: WT TT-seq rep1


title: 100x_4r31_1

description: sample name: 341


title: Ileal Uninvolved 208

city: new york

first: Mamta

last: Giri

state: new york

address: 1470 madison ave

department: Institute of Personalized medicine

institute: Mount Sinai hospital

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grch38 human
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 800 UMIs from the “Raw” output UMI matrices of CellRanger
Epithelial cells, Red blood cells and cell-barcodess associated with high mitochondrial mRNA content were excluded by "in-silico" gating precedure which computes that fractoin of UMIs assocated with each gene signature. Thresholds and genes lists are detailed in the manuscripts.
Genome_build: Grch38

source_name: Surgical resection

extract_protocol:
10X genomics V1 or V2 protocol following manufacturer recommendations
10x Genomics Library Kits

treatment_protocol: Lamina prorpia single cell suspensions were prepared from surgically resected inflamed or uninflamed ileum from Crohn's disease patients. Fifteen to twenty mucosal biopsies sampled all along the resected specimens using a biopsy forceps (EndoChoice, Alpharetta, GA). Epithelial cells were dissociated by incubating the biopsies in an EDTA-enriched dissociation medium (HBSS w/o Ca2+ Mg2+ (Life Technologies, Carlsbad, CA) - HEPES 10mM (Life Technologies) - EDTA 5mM (Life Technologies)) at +37oC under 100 rpm agitation for two cycles of 15 minutes. After each cycle, biopsies were hand-shaken for 30s and then vortexed vigorously for another 30s. Biopsies were then washed in complete RPMI media previously put at RT, and transferred in digestion medium (HBSS with Ca2+ Mg2+ - FCS 2% - DNase I 0.5mg/ml (Sigma-Aldrich, St. Louis, MO) – Collagenase IV 0.5mg/ml (Sigma-Aldrich)) for 40 minutes at +37oC under 100 rpm agitation. After digestion, the cell suspension was filtered through a 70mm cell strainer, washed in DBPS/ 2% FCS/ 1mM EDTA and spun down at 400g for 10 minutes. After red blood cell lysis (BioLegend, San Diego, CA), cells were washed as before. Dead cells were depleted from the suspension using the dead cell depletion kit (Miltenyi Biotec, Bergisch Gladbach, Germany), following manufacturer’s recommendations. Viability of the final cell suspension was calculated using a hemocytometer and Trypan blue (Corning) exclusion and was routinely > 85%.

tag: tissue

value: ileal

tag: status

value: Uninvolved

tag: 10x chemistry


title: Ileal Uninvolved 195


title: Ileal Involved 209

value: Involved


title: Ileal Involved 196


title: 100x_4r30_1

description: sample name: 340

tag: developmental stage

tag: cell type


title: 100x_4r29_1

description: sample name: 339


title: rtt109∆ RNAseq rep2

source_name: rtt109∆ RNAseq

value: RNA-seq


title: 100x_4r27_1

description: sample name: 337


title: 100x_4r28_1

description: sample name: 338


title: Ileal Involved 190


title: rtt109∆ RNAseq rep1


title: WT RNAseq rep1

source_name: WT RNAseq


title: Ileal Involved 193


title: Ileal Involved 187


title: Ileal Uninvolved 186


title: 100x_6r25_1

description: sample name: 335


title: H3K56R NET-seq rep2

source_name: H3K56R NET-seq


title: 100x_2r23_1

description: sample name: 333


title: Ileal Involved 181


title: 100x_2r19_1

description: sample name: 329


title: 100x_2r20_1

description: sample name: 330


title: H3K56R NET-seq rep1


title: 100x_r18_1

description: sample name: 328


title: Ileal Uninvolved 192


title: Slow Pol II NET-seq rep2

source_name: Slow Pol II NET-seq


title: 100x_r17_1

description: sample name: 327


title: Ileal Uninvolved 159


title: 100x_r16_1

description: sample name: 326


title: Ileal Uninvolved 180


title: 100x_r15_1

description: sample name: 325


title: 100x_r14_1

description: sample name: 324


title: 100x_6r26_1

description: sample name: 336


title: Ileal Uninvolved 189


title: 100x_r13_1

description: sample name: 323


title: WT RNAseq rep2


title: 100x_2r24_1

description: sample name: 334


title: Slow Pol II NET-seq rep1


title: 100x_2r21_1

description: sample name: 331


title: 100x_r12_1

description: sample name: 322


title: WT NET-seq S60


title: 100x_r11_1

description: sample name: 321


title: Ileal Involved 138


title: 100x_r10_1

description: sample name: 320


title: Ileal Uninvolved 135


title: WT NET-seq S30

source_name: WT NET-seq S30


title: 100x_r8_1

description: sample name: 318

source_name: embryo


title: 100x_2r22_1

description: sample name: 332


title: cac1∆ rtt06∆ NET-Seq S90

source_name: cac1∆ rtt06∆ NET-Seq S90

value: cac1{delta} rtt106{delta}


title: 100x_r7_1

description: sample name: 317


title: Ileal Involved 128


title: 100x_r9_1

description: sample name: 319


title: 100x_r6_1

description: sample name: 316


title: cac1∆ rtt06∆ NET-Seq S60

source_name: cac1∆ rtt06∆ NET-Seq S60


title: 100x_r5_1

description: sample name: 315


title: WT NET-seq S90

source_name: WT NET-seq S90


title: Ileal Uninvolved 123


title: 100x_r4_1

description: sample name: 314


title: Ileal Uninvolved 129


title: Ileal Involved 122


title: 100x_r2_1

description: sample name: 312


title: 100x_r3_1

description: sample name: 313


title: 40x_r33_1

description: sample name: 310

value: early gastrula


title: Ileal Involved 158


title: cac1∆ rtt06∆ NET-Seq G1-arrested

source_name: cac1∆ rtt06∆ NET-Seq G1-arrested

value: log phase


title: 100x_r1_1

description: sample name: 311


title: Ileal Uninvolved 68


title: ASF1-AA NET-Seq S90

source_name: ASF1-AA NET-Seq S90

value: Native elongating transcript sequencing (NET-seq)


title: 40x_r32_1

description: sample name: 309


title: 40x_r31_1

description: sample name: 308


title: 40x_r30_1

description: sample name: 307


title: 40x_r26_1

description: sample name: 303


title: 40x_r28_1

description: sample name: 305


title: 40x_r29_1

description: sample name: 306


title: cac1∆ rtt06∆ NET-Seq S30

source_name: cac1∆ rtt06∆ NET-Seq S30


title: 40x_r25_1

description: sample name: 302


title: ASF1-AA NET-seq G1-arrested

source_name: ASF1-AA NET-seq G1-arrested


title: ASF1-AA NET-Seq S60

source_name: ASF1-AA NET-Seq S60


title: 40x_r24_1

description: sample name: 301


title: 40x_r27_1

description: sample name: 304


title: HeLa_siTriple-3: Cyclin F / E2F7/8 triple knockdown #3

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

country: Netherlands

institute: Utrecht University

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality of the raw sequencing was checked with FastQC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR version 2.4.2a with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were counted using HTSeq version 0.6.1 in union mode. Processed data are provided as raw count tables
Genome_build: hs38
Supplementary_files_format_and_content: tab-delimited text files include raw transcript counts for each sample

source_name: HeLa cells

extract_protocol:
RNA was extracted from the HeLa cells using Qiagen Rneasy kits
Truseq stranded PolyA

value: HeLa


title: HeLa_siTriple-2: Cyclin F / E2F7/8 triple knockdown #2


title: 40x_r23_1

description: sample name: 300

value: embryonic cell


title: HeLa_siTriple-4: Cyclin F / E2F7/8 triple knockdown #4


title: 40x_r21_1

description: sample name: 298


title: 40x_r22_1

description: sample name: 299


title: rtt109∆ NET-seq rep2

source_name: rtt109∆ NET-seq


title: WT NET-seq rep2

source_name: WT NET-seq


title: 40x_r20_1

description: sample name: 297


title: HeLa_siE2F78-4: E2F7/8 double knockdown #4


title: rtt109∆ NET-seq rep1


title: Ileal Involved 69

source_name: Surgical resection


title: 40x_r19_1

description: sample name: 296


title: WT NET-seq rep1


title: ASF1-AA NET-Seq S30

source_name: ASF1-AA NET-Seq S30


title: 40x_r18_1

description: sample name: 295


title: 40x_r17_1

description: sample name: 294


title: HeLa_siE2F78-2: E2F7/8 double knockdown #2


title: HeLa_siTriple-1: Cyclin F / E2F7/8 triple knockdown #1


title: HeLa_siE2F78-1: E2F7/8 double knockdown #1


title: 40x_r15_1

description: sample name: 292


title: 40x_r13_1

description: sample name: 290


title: HeLa_siCCNF-4: Cyclin F knockdown #4


title: 40x_r14_1

description: sample name: 291


title: S12_ATAC-Seq

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

department: Genetics Section

institute: University of Chicago

data_processing:
The FASTQ files were processed using the MUGQIC ChIP-Seq pipeline v.2.2.1 to obtain narrow peaks.
The pipeline pools the replicates for each condition and was adapted to retain reads longer than 37 bp for subsequent processing.
Sequencing adaptors were trimmed using Trimmomatic v0.36 before aligning to the hg19 human reference with BWA v0.7.12.
Unique reads were filtered by mapping quality using Samtools v1.3.1 and duplicates were marked with Picard v2.0.1.
Narrow peaks were called with MACS2 v2.1.0, using profiles from non-infected cells as background (input) to obtain differentially accessible peaks.
All software indicated was run using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: The processed peak file tabs correspond to the standard NarrowPeak file format: chrom, chromStart, chromEnd, name, score, strand, signalValue, qValue, peak

source_name: Macrophages

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation. Monocytes were purified from peripheral blood mononuclear cells by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech) using the autoMACS Pro Separator. The purity of the isolated monocytes was verified using an antibody against CD14 (BD Biosciences) and only samples showing > 90% purity were used to differentiate into macrophages. Monocytes were then cultured for 7 days in RPMI-1640 (Fisher) supplemented with 10% heat-inactivated FBS (FBS premium, US origin, Wisent), L-glutamine (Fisher) and M-CSF (20ng/mL; R&D systems). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned. Before infection, we checked the differentiation/activation status of the monocyte-derived macrophages by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR (BD Biosciences). Only samples presenting the expected phenotype for non-activated macrophages (CD1a+, CD14+, CD83, and HLA-DRlow) were used in downstream experiments.

extract_protocol:
DNA from infected and non-infected macrophages was extracted using the PureGene DNA extraction kit (Gentra Systems).
ATAC-seq libraries were generated from 100,000 cells, as previously described in (Buenrostro et al., 2013) and sequenced on an Illumina HiSeq 2500 using 100-bp paired-end reads. We found high concordance between the ATAC-seq signals for the two biological replicates sequenced for each of the conditions (Spearman r > 0.80), which allowed us to merge them for downstream footprint analyses.

treatment_protocol: We infected macrophages with two bacteria, Salmonella typhimurium and Listeria monocytogenes. The day prior to infection, aliquots of Salmonella typhimurium and Listeria monocytogenes were thawed and bacteria were grown overnight in Tryptic Soy Broth (TSB) media. Bacterial culture was diluted to mid-log phase prior to infection and supernatants density was checked at OD600. Monocyte-derived macrophages were infected at a multiplicity of infection (MOI) of 10:1 for Salmonella typhimurium and an MOI of 5:1 for Listeria monocytogenes for 2h at 37°C. A control group of non-infected macrophages was treated the same way but with only medium without bacteria. After 2 hr in contact with the bacteria, macrophages were washed and cultured for another hour in the presence of 50 ug/mL gentamycin in order to kill all extracellular bacteria present in the medium. The cells were then washed a second time and cultured in complete medium with 3 ug/mL gentamycin for an additional 2h. A control group of non-infected macrophages was treated the same way but with only medium without bacteria.

value: Infected with Salmonella typhimurium

tag: time

value: 12 hours post infection


title: L12_ATAC-Seq

value: Infected with Listeria monocytogenes


title: 40x_r12_1

description: sample name: 289


title: HeLa_siCCNF-3: Cyclin F knockdown #3

tag: cell line


title: AK49_ZC3-2

data_processing:
TopHat V2
FeatureCounts
edgeR
hypergeometric gene set enrichment test on the gene ontology + KEGG pathway
Genome_build: hg19

source_name: ovarian cancer

growth_protocol: The OVCAR-8 cells were cultured in RPMI-1640 medium (Corning) supplemented with 8% fetal bovine serum (Millipore).

extract_protocol: Total RNA was extracted from frozen cells using the miRNeasy mini kit (Qiagen) following the supplier’s instructions. Libraries were prepared using Illumina TruSeq mRNA v2.

treatment_protocol: RNA-seq was performed  48 h after siRNA transfection.

value: ovarian cancer cell line

value: OVCAR-8 cells

tag: genotype/variation


title: NI_ATAC-Seq

value: Non-infected


title: HeLa_siE2F78-3: E2F7/8 double knockdown #3


title: 40x_r9_1

description: sample name: 286


title: AK49_ZC3-1


title: 40x_r8_1

description: sample name: 285


title: 40x_r10_1

description: sample name: 287


title: 40x_r7_1

description: sample name: 284


title: HeLa_siCCNF-1: Cyclin F knockdown #1


title: AK41_ZC3-2


title: HeLa_con-4: control (scrambled siRNA) #4


title: 40x_r6_1

description: sample name: 283


title: 40x_r4_1

description: sample name: 281


title: 40x_r5_1

description: sample name: 282


title: HeLa_con-3: control (scrambled siRNA) #3


title: AK41_ZC3-1


title: 40x_r3_1

description: sample name: 280


title: 40x_r16_1

description: sample name: 293


title: 40x_r2_1

description: sample name: 279


title: 40x_r11_1

description: sample name: 288


title: HeLa_con-2: control (scrambled siRNA) #2


title: 20_3r17_1

description: sample name: 277

value: 20 cell


title: HeLa_con-1: control (scrambled siRNA) #1


title: AK49_Luc

value: control


title: HeLa_siCCNF-2: Cyclin F knockdown #2


title: 40x_r1_1

description: sample name: 278


title: AK39_ZC3-2


title: AK39_ZC3-1


title: 20_r15_1

description: sample name: 275


title: 20_r14_1

description: sample name: 274


title: 20_r16_1

description: sample name: 276


title: 20_r13_1

description: sample name: 273


title: endogenous_circGFP_rep1

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive

department: Dermatology

institute: Stanford University School of Medicine

data_processing:
Library strategy: CLIP-seq
FASTQ files first demultiplexed by sample, PCR duplicates removed, and all adaptor sequences trimmed as previously described (PMID: 25411354).
Processed sequencing reads were mapped to human genome indices, RT stop positions extracted, and replicate experiments intersected to obtain highly reproducible binding sites for further analysis as per FAST-iCLIP (PMID: 25411354).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig and text files containing RT stops of m6A-irCLIP datasets mapped to hg38 build of human genome, and mapped to circGFP sequence.

source_name: HeLa

growth_protocol: DMEM 10% FBS 1% P-S.

extract_protocol:
Total RNA was isolated from HeLa cells using Qiagen RNeasy columns. RNA was ribo-/polyA- selected and treated with RNase R to remove linear RNA. Circular RNA was then fragmented to ~30-60 nts, and m6A residues were isolated by crosslinking anti-m6A antibody to fragmented RNA.
RNA ligation for library construction was performed on affinity beads and RNA was subsequently transformed into dsRNA libraries using RT, cDNA circularization, and PCR amplification.

tag: circrna generation

value: endogenous splicing


title: AK39_Luc


title: 20_r11_1

description: sample name: 271

source_name: embryo


title: endogenous_circGFP_rep3


title: 20_r12_1

description: sample name: 272


title: AK41_Luc


title: 20_r9_1

description: sample name: 269


title: SHI1_R3

city: Boston

first: Andrew

last: Lane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Data were analyzed using the Broad Picard Pipeline which includes de-multiplexing and data aggregation. RNA-seq reads were aligned to the B37 version of human genome using TopHat version 1.4. Gene level read count values and FPKM were determined using the RNA-SeQC pipeline
Genome_build: NCBI human genome build 37
Supplementary_files_format_and_content: Matrix of RPKM values determined using the RNA-SeQC pipeline

source_name: SHI1 cell line

growth_protocol: Cells grown in RPMI plus 10% fetal bovine serum plus L-glutamine plus penicillin/streptomycin

extract_protocol:
Trizol RNA preparation
Total RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit and normalized to 5 ng/µl. 200 ng of each sample was transferred into library preparation which was an automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample. It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using indexed adapters for multiplexing. After enrichment the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly. The entire process was in 96-well format and all pipetting was done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2 nM and denatured using 0.1 N NaOH prior to sequencing.

treatment_protocol: Cells were treated with vehicle or tagraxofusp, repeatedly over 2-4 weeks, to generate tagraxofusp resistant cells

value: tagraxofusp

tag: phenotype

value: Resistant cells


title: 20_r10_1

city: Vienna

first: Alison

address: Djerassiplatz 1

institute: University of Vienna

description: sample name: 270


title: SHI1_R2


title: autocatalytic_circGFP_rep3

value: autocatalytic splicing


title: 20_r7_1

description: sample name: 267


title: 20_r8_1

description: sample name: 268


title: autocatalytic_circGFP_rep2


title: SHI1_R1


title: 20_r6_1

description: sample name: 266


title: 20_r5_1

description: sample name: 265


title: 20_r2_1

description: sample name: 262


title: endogenous_circGFP_rep2


title: 20_r1_1

description: sample name: 261


title: SHI1_3

value: vehicle

value: Parental cells


title: SHI1_2


title: 12_r8_2

description: sample name: 258

value: 12 cell


title: 12_r9_2

description: sample name: 259


title: 12_r6_2

description: sample name: 256


title: CAL1_R3

source_name: CAL1 cell line


title: SHI1_1


title: 12_r10_2

description: sample name: 260


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP ERRa sample 4

city: San Francisco

first: Vassily

middle: Igor

last: Kutyavin

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California - San Francisco

data_processing:
Raw sequence data were aligned to the mouse genome (mm10) using Bowtie2 (Langmead et al. 2012). Homer (Heinz et al. 2010) was used to identify and annotate peaks in 4 biological replicates per condition and DESeq2 was used to compare enrichment at each peak in Bcl6f/f and Bcl6f/f Ucp1Cre BAT samples. Differential ERRα enrichment was defined as a fold change ≥1.5 (adjusted p-value ≤0.05). BigWig files were generated with the bedGraphToBigWig program (Kent et al. 2010) and visualized with the UCSC Genome Browser (Kent et al. 2002).
BigWig file for each sample
(see Samples section)
Genome_build: mm10
Supplementary_files_format_and_content: (see Samples section)

source_name: interscapular brown adipose tissue

growth_protocol: Mice were maintained with free access to standard chow under a regular 12h light/12h dark cycle at a constant temperature of 30°C.

extract_protocol:
Interscapular brown adipose tissue was isolated, finely minced with a razor blade, and fixed in 1% formaldehyde in PBS for 20 minutes at room temperature, followed by addition of 125 mM glycine. Fragments were collected in cell lysis buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail) and homogenized in a Dounce homogenizer (15 strokes with type B pestle). Following centrifugation, the nuclear pellet was resuspended in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, protease inhibitor cocktail) and incubated for 20 minutes on ice. Samples were sonicated with an XL-2000 sonicator (QSonica) for 12 rounds of 20 seconds on setting 2, with 60 seconds on ice between rounds, to generate fragments of 150-300 bp. Sonicated samples were centrifuged, and the supernatants were diluted two-fold with Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl, protease inhibitor cocktail) and incubated with 1.5 micrograms of anti-ERRa antibody (Cell Signaling Technology #13826S) overnight at 4 deg C, then with 50 microliters of Protein G Dynabeads (Invitrogen) for 4 hours at 4 deg C. Beads were washed on a magnetic stand twice with Buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), once with Buffer 2 (same as Buffer 1 but with 0.5 M NaCl), once with Buffer 3 (0.25M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), twice with Buffer 4 (1 mM EDTA, 20 mM Tris-HCl, pH 8.0), and resuspended in elution buffer (50 mm Tris (pH 8.0), 10 mm EDTA, 1% SDS). Beads in elution buffer were incubated at 65 deg C for 10 minutes, and the supernatant collected. Elution was repeated a second time and the combined eluates were incubated at 65 deg C overnight to reverse crosslinks. Samples were treated with RNAse A (1 hour at 37 deg C), Proteinase K (2 hours at 65 deg C), and DNA was isolated with a Qiaquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions. DNA concentrations were measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
For construction of ChIP-Seq libraries, 10 ng of ChIP DNA was treated with end repair enzymes (Fisher Scientific) before proceeding to the 3' adenylation and adapter ligation steps of the TruSeq Stranded mRNA Library Prep Kit (Illumina) protocol. Subsequently, samples were resolved on a 2% agarose gel containing SYBR Gold Stain, visualized by ultraviolet illumination, and gel sections containing 250-500 bp fragments were excised and DNA extracted with a Gel DNA Recovery Kit (Zymoclean). Libraries were then amplified by PCR (15 cycles) and a library size of 250-500 bp was verified by agarose gel electrophoresis. Library concentration was measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
Libraries were pooled, denatured with NaOH, diluted to 1.8 pM, and sequenced on a NextSeq 500 Sequencing System (Illumina) with a NextSeq 500/550 High Output v2 kit (75 cycles) in single-read mode.

tag: strain

value: BCL6-floxed (C57BL/6J)

value: interscapular brown adipose tissue

tag: Sex

value: male


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP ERRa sample 2


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP ERRa sample 3


title: CAL1_R2

tag: treatment


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP ERRa sample 1


title: CAL1_R1


title: BCL6ff Cre- BAT 30 deg C ChIP ERRa sample 3


title: 12_r5_2

last: Cole

description: sample name: 255

value: embryonic cell


title: 12_r4_2

description: sample name: 254


title: 12_r2_2

description: sample name: 252


title: 20_r4_1

description: sample name: 264


title: autocatalytic_circGFP_rep1

value: HeLa


title: 20_r3_1

description: sample name: 263


title: CAL1_3


title: 12_r1_2

description: sample name: 251


title: 10_r9_1

description: sample name: 249

value: 10 cell


title: 10_r10_1

description: sample name: 250


title: BCL6ff Cre- BAT 30 deg C ChIP ERRa sample 2


title: CAL1_2


title: 10_r8_1

description: sample name: 248


title: 12_r7_2

description: sample name: 257


title: BCL6ff Cre- BAT 30 deg C ChIP ERRa sample 1


title: CAL1_1


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP BCL6

data_processing:
Raw sequence data were aligned to the mouse genome (mm10) using Bowtie2 (Langmead et al. 2012). Homer (Heinz et al. 2010) was used to identify and annotate peaks (corresponding to BCL6 binding sites) in pooled BAT samples from Bcl6f/f mice (n=5), with  pooled BAT samples from Bcl6f/f Ucp1Cre mice (n=2) serving as a negative control (default settings). BigWig files were generated with the bedGraphToBigWig program (Kent et al. 2010) and visualized with the UCSC Genome Browser (Kent et al. 2002).
BigWig file for each sample
(see Samples section)
Genome_build: mm10
Supplementary_files_format_and_content: (see Samples section)

extract_protocol:
Interscapular brown adipose tissue was isolated, finely minced with a razor blade, and fixed in 1% formaldehyde in PBS for 20 minutes at room temperature, followed by addition of 125 mM glycine. Fragments were collected in cell lysis buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail) and homogenized in a Dounce homogenizer (15 strokes with type B pestle). Following centrifugation, the nuclear pellet was resuspended in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, protease inhibitor cocktail) and incubated for 20 minutes on ice. Samples were sonicated with an XL-2000 sonicator (QSonica) for 12 rounds of 20 seconds on setting 2, with 60 seconds on ice between rounds, to generate fragments of 150-300 bp. Sonicated samples were centrifuged, and the supernatants were diluted two-fold with Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl, protease inhibitor cocktail) and incubated with 2 micrograms of anti-BCL6 antibody (Cell Signaling Technology #5650) overnight at 4 deg C, then with 50 microliters of Protein G Dynabeads (Invitrogen) for 4 hours at 4 deg C. Beads were washed on a magnetic stand twice with Buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), once with Buffer 2 (same as Buffer 1 but with 0.5 M NaCl), once with Buffer 3 (0.25M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), twice with Buffer 4 (1 mM EDTA, 20 mM Tris-HCl, pH 8.0), and resuspended in elution buffer (50 mm Tris (pH 8.0), 10 mm EDTA, 1% SDS). Beads in elution buffer were incubated at 65 deg C for 10 minutes, and the supernatant collected. Elution was repeated a second time and the combined eluates were incubated at 65 deg C overnight to reverse crosslinks. Samples were treated with RNAse A (1 hour at 37 deg C), Proteinase K (2 hours at 65 deg C), and DNA was isolated with a Qiaquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions. DNA concentrations were measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen). Tissue samples from two different mice were pooled to generate this sample.
For construction of ChIP-Seq libraries, 10 ng of ChIP DNA was treated with end repair enzymes (Fisher Scientific) before proceeding to the 3' adenylation and adapter ligation steps of the TruSeq Stranded mRNA Library Prep Kit (Illumina) protocol. Subsequently, samples were resolved on a 2% agarose gel containing SYBR Gold Stain, visualized by ultraviolet illumination, and gel sections containing 250-500 bp fragments were excised and DNA extracted with a Gel DNA Recovery Kit (Zymoclean). Libraries were then amplified by PCR (15 cycles) and a library size of 250-500 bp was verified by agarose gel electrophoresis. Library concentration was measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
Libraries were pooled, denatured with NaOH, diluted to 1.8 pM, and sequenced on a NextSeq 500 Sequencing System (Illumina) with a NextSeq 500/550 High Output v2 kit (75 cycles) in single-read mode.


title: 10_r6_1

description: sample name: 246


title: 10_r7_1

description: sample name: 247


title: BCL6ff Cre- BAT 30 deg C ChIP BCL6

extract_protocol:
Interscapular brown adipose tissue was isolated, finely minced with a razor blade, and fixed in 1% formaldehyde in PBS for 20 minutes at room temperature, followed by addition of 125 mM glycine. Fragments were collected in cell lysis buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail) and homogenized in a Dounce homogenizer (15 strokes with type B pestle). Following centrifugation, the nuclear pellet was resuspended in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, protease inhibitor cocktail) and incubated for 20 minutes on ice. Samples were sonicated with an XL-2000 sonicator (QSonica) for 12 rounds of 20 seconds on setting 2, with 60 seconds on ice between rounds, to generate fragments of 150-300 bp. Sonicated samples were centrifuged, and the supernatants were diluted two-fold with Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl, protease inhibitor cocktail) and incubated with 2 micrograms of anti-BCL6 antibody (Cell Signaling Technology #5650) overnight at 4 deg C, then with 50 microliters of Protein G Dynabeads (Invitrogen) for 4 hours at 4 deg C. Beads were washed on a magnetic stand twice with Buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), once with Buffer 2 (same as Buffer 1 but with 0.5 M NaCl), once with Buffer 3 (0.25M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), twice with Buffer 4 (1 mM EDTA, 20 mM Tris-HCl, pH 8.0), and resuspended in elution buffer (50 mm Tris (pH 8.0), 10 mm EDTA, 1% SDS). Beads in elution buffer were incubated at 65 deg C for 10 minutes, and the supernatant collected. Elution was repeated a second time and the combined eluates were incubated at 65 deg C overnight to reverse crosslinks. Samples were treated with RNAse A (1 hour at 37 deg C), Proteinase K (2 hours at 65 deg C), and DNA was isolated with a Qiaquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions. DNA concentrations were measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen). Tissue samples from five different mice were pooled to generate this sample.
For construction of ChIP-Seq libraries, 10 ng of ChIP DNA was treated with end repair enzymes (Fisher Scientific) before proceeding to the 3' adenylation and adapter ligation steps of the TruSeq Stranded mRNA Library Prep Kit (Illumina) protocol. Subsequently, samples were resolved on a 2% agarose gel containing SYBR Gold Stain, visualized by ultraviolet illumination, and gel sections containing 250-500 bp fragments were excised and DNA extracted with a Gel DNA Recovery Kit (Zymoclean). Libraries were then amplified by PCR (15 cycles) and a library size of 250-500 bp was verified by agarose gel electrophoresis. Library concentration was measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
Libraries were pooled, denatured with NaOH, diluted to 1.8 pM, and sequenced on a NextSeq 500 Sequencing System (Illumina) with a NextSeq 500/550 High Output v2 kit (75 cycles) in single-read mode.


title: 10_r5_1

description: sample name: 245


title: 10_r2_1

description: sample name: 242


title: 10_r4_1

description: sample name: 244


title: 10_r3_1

description: sample name: 243


title: BCL6ff Cre- BAT 30 deg C ChIP ERRa sample 4


title: Irf6-ko-rep2

data_processing:
Illumina v1.8 software used for basecalling
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ATAC-seq peaks were called for each dataset using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in XLS format

source_name: Skin

extract_protocol:
Skin was collected from WT and Irf6-/- E16.5 mouse embryos (100 mg, n = 2 of each genotype) and placed in L-15 media containing 1X DNase buffer and 200 μl/ml DNase for 20 min at RT. Samples were then cryopreserved by placing them L-15 media containing 10% FBS and 5%  DMSO and freezing them at a slow cooling rate. ATAC-seq was performed by Active Motif. Briefly,  the tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer,  and 100,000 nuclei were tagmented as previously described43, with some modifications44, using  the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was  then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR,  and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was  quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems),  and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

value: lrf6 knockout

value: Skin

tag: background

tag: age

value: E16.5 days


title: TG-KEO8_S8

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

description:
sample name in processed data file:
BALBcJ 3
Ileum.tsv

data_processing:
RNA-Seq reads were aligned to the Mus musculus reference with Ensembl gene annotation (GRCm38) by Kallisto (v0.44.0; default settings) for transcript quantification.
Technical replicates were pooled together and data is treated as additive for analysis purposes.
mRNA expression was quantified at transcript level (transcript per million; TPM) and then summarized into gene level (TPMs summed over all gene transcripts) measurements.
Gene level TPMs were log2 (n+1)-transformed for further analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file of Gene level TPMs for Colon, Ileum and Duodenum/Jejunum samples sequenced from BALB/cJ and C57BL/6J mice

source_name: Ileum

extract_protocol:
RNA extraction was performed using PureLink RNA mini kit (Invitrogen, USA) according to the manufacturer’s instructions.
RNASeq libraries were prepared using Illumina TotalRNA TruSEQ kits (RiboZero 753 depletion).

tag: mouse-id

value: BALBcJ 3

value: Ileum

value: BALB/cJ


title: TG-KEO7_S7

description:
sample name in processed data file:
BALBcJ 3
Colon.tsv

source_name: Colon

value: Colon


title: Irf6-ko-rep1

tag: genotype


title: 12_r3_2

description: sample name: 253


title: TG-KEO6_S6

description:
sample name in processed data file:
BALBcJ 2
Duodenum.tsv

source_name: Duodenum/Jejunum

value: BALBcJ 2

tag: tissue

value: Duodenum/Jejunum


title: 10_r1_1

description: sample name: 241


title: 9_r9_1

description: sample name: 240

value: 9 cell


title: TG-KEO5_S5

description:
sample name in processed data file:
BALBcJ 2
Ileum.tsv


title: 9_r8_1

description: sample name: 239


title: Irf6-wt-rep2

value: wild type


title: TG-KEO4_S4

description:
sample name in processed data file:
BALBcJ 2
Colon.tsv


title: Irf6-wt-rep1


title: 9_r5_1

description: sample name: 236


title: 9_r6_1

description: sample name: 237


title: 9_r3_1

description: sample name: 234


title: 9_r4_1

description: sample name: 235


title: TG-KEO9_S9

description:
sample name in processed data file:
BALBcJ 3
Duodenum.tsv


title: BCL6ff Cre- BAT 30 deg C ChIP Input Control

data_processing:
Raw sequence data were aligned to the mouse genome (mm10) using Bowtie2 (Langmead et al. 2012). Homer (Heinz et al. 2010) was used to identify and annotate peaks in 3 biological replicates per condition (default settings), using an input chromatin sample as a negative control. DESeq2 (Love et al. 2014) was used to compare read abundance at each peak in control and BCL6-deficient samples. BigWig files were generated with the bedGraphToBigWig program (Kent et al. 2010) and visualized with the UCSC Genome Browser (Kent et al. 2002).
Sample_supplementary_files_format_and_content: BigWig file for each sample
Genome_build: mm10

extract_protocol:
Interscapular brown adipose tissue was isolated, finely minced with a razor blade, and fixed in 1% formaldehyde in PBS for 20 minutes at room temperature, followed by addition of 125 mM glycine. Fragments were collected in cell lysis buffer (50 mM Tris (pH 8.0), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail) and homogenized in a Dounce homogenizer (15 strokes with type B pestle). Following centrifugation, the nuclear pellet was resuspended in nuclear lysis buffer (10 mM Tris (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS, protease inhibitor cocktail) and incubated for 20 minutes on ice. Samples were sonicated with an XL-2000 sonicator (QSonica) for 12 rounds of 20 seconds on setting 2, with 60 seconds on ice between rounds, to generate fragments of 150-300 bp. Sonicated samples were centrifuged, and the supernatants were diluted two-fold with Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 8.1), 167 mM NaCl, protease inhibitor cocktail) and incubated with 2 micrograms of anti-H3K27ac antibody (Abcam #ab4729) overnight at 4 deg C, then with 50 microliters of Protein G Dynabeads (Invitrogen) for 4 hours at 4 deg C. Beads were washed on a magnetic stand twice with Buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), once with Buffer 2 (same as Buffer 1 but with 0.5 M NaCl), once with Buffer 3 (0.25M LiCl, 0.5% sodium deoxycholate, 0.5% NP-40, 1 mM EDTA, 20 mM Tris-HCl, pH 8.0), twice with Buffer 4 (1 mM EDTA, 20 mM Tris-HCl, pH 8.0), and resuspended in elution buffer (50 mm Tris (pH 8.0), 10 mm EDTA, 1% SDS). Beads in elution buffer were incubated at 65 deg C for 10 minutes, and the supernatant collected. Elution was repeated a second time and the combined eluates were incubated at 65 deg C overnight to reverse crosslinks. Samples were treated with RNAse A (1 hour at 37 deg C), Proteinase K (2 hours at 65 deg C), and DNA was isolated with a Qiaquick PCR Purification Kit (Qiagen) according to the manufacturer's instructions. DNA concentrations were measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
For construction of ChIP-Seq libraries, 10 ng of ChIP DNA was treated with end repair enzymes (Fisher Scientific) before proceeding to the 3' adenylation and adapter ligation steps of the TruSeq Stranded mRNA Library Prep Kit (Illumina) protocol. Subsequently, samples were resolved on a 2% agarose gel containing SYBR Gold Stain, visualized by ultraviolet illumination, and gel sections containing 250-500 bp fragments were excised and DNA extracted with a Gel DNA Recovery Kit (Zymoclean). Libraries were then amplified by PCR (15 cycles) and a library size of 250-500 bp was verified by agarose gel electrophoresis. Library concentration was measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
Libraries were pooled, denatured with NaOH, diluted to 1.8 pM, and sequenced on a NextSeq 500 Sequencing System (Illumina) with a NextSeq 500/550 High Output v2 kit (75 cycles) in single-read mode.

value: BCL6-floxed (C57BL/6J)

tag: antibody


title: TG-KEO39_S39

description:
sample name in processed data file:
B6 7
Duodenum.tsv


title: TG-KEO38_S38

description:
sample name in processed data file:
B6 7
Ileum.tsv


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP H3K27ac sample 3

value: BCL6-floxed, UCP1Cre (C57BL/6J)

value: interscapular brown adipose tissue


title: 9_r1_1

description: sample name: 232

value: embryonic cell


title: 8_r3_5

description: sample name: 231

value: 8 cell


title: 9_r2_1

description: sample name: 233


title: TG-KEO37_S37

description:
sample name in processed data file:
B6 7
Colon.tsv


title: 8_r2_5

description: sample name: 230


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP H3K27ac sample 1

value: male


title: BCL6ff UCP1Cre+ BAT 30 deg C ChIP H3K27ac sample 2


title: 8_r1_5

description: sample name: 229


title: 6_r4_1

description: sample name: 228

value: 6 cell


title: 9_r7_1

description: sample name: 238


title: TG-KEO35_S35

description:
sample name in processed data file:
B6 6
Ileum.tsv


title: 6_r1_1

description: sample name: 225


title: 8_r7_4

description: sample name: 224


title: TG-KEO34_S34

description:
sample name in processed data file:
B6 6
Colon.tsv


title: BCL6ff Cre- BAT 30 deg C ChIP H3K27ac sample 3


title: 6_r2_1

description: sample name: 226


title: 8_r6_4

description: sample name: 223


title: BCL6ff Cre- BAT 30 deg C ChIP H3K27ac sample 2


title: 8_r4_4

description: sample name: 221


title: 8_r5_4

description: sample name: 222


title: 8_r3_4

description: sample name: 220


title: BCL6ff Cre- BAT 30 deg C ChIP H3K27ac sample 1


title: BCL6ff UCP1Cre+ BAT 22 deg C ChIP H3K27ac sample 3

growth_protocol: Mice were maintained with free access to standard chow under a regular 12h light/12h dark cycle at a constant temperature of 22°C.


title: TG-KEO33_S33

description:
sample name in processed data file:
B6 5
Duodenum.tsv


title: 8_r2_4

description: sample name: 219


title: TG-KEO32_S32

description:
sample name in processed data file:
B6 5
Ileum.tsv


title: 8_r1_4

description: sample name: 218


title: BCL6ff UCP1Cre+ BAT 22 deg C ChIP H3K27ac sample 2


title: TG-KEO36_S36

description:
sample name in processed data file:
B6 6
Duodenum.tsv


title: 6_r3_1

description: sample name: 227


title: TG-KEO31_S31

description:
sample name in processed data file:
B6 5
Colon.tsv


title: 7_r7_1

description: sample name: 217

value: 7 cell


title: 7_r6_1

description: sample name: 216


title: TG-KEO30_S30

description:
sample name in processed data file:
B6 4
Duodenum.tsv


title: 7_r5_1

description: sample name: 215


title: TG-KEO3_S3

description:
sample name in processed data file:
BALBcJ 1
Duodenum.tsv

value: BALBcJ 1


title: BCL6ff UCP1Cre+ BAT 22 deg C ChIP H3K27ac sample 1


title: 7_r4_1

description: sample name: 214


title: BCL6ff Cre- BAT 22 deg C ChIP H3K27ac sample 3


title: BCL6ff Cre- BAT 22 deg C ChIP H3K27ac sample 2


title: TG-KEO29_S29

description:
sample name in processed data file:
B6 4
Ileum.tsv


title: 7_r3_1

description: sample name: 213


title: BCL6ff Cre- BAT 22 deg C ChIP H3K27ac sample 1


title: TG-KEO28_S28

description:
sample name in processed data file:
B6 4
Colon.tsv


title: 7_r2_1

description: sample name: 212


title: 8_r4_3

description: sample name: 210


title: BCL6ff UCP1Cre+ BAT 30 deg C mRNA sample 4

description: RNA_Seq_Processed_data_1._NormalizedCounts.txt

data_processing:
Raw sequence data were pseudoaligned to the mouse transcriptome (mm10, UCSC annotation) using Kallisto (Bray et al. 2016). Differential expression analysis was performed with DESeq2 (Love et al. 2014). A table of normalized read counts for all genes in all samples was generated with DESeq2.
Sample_supplementary_files_format_and_content: Tab-delimited text file containing table of normalized read counts for all samples
Genome_build: mm10

extract_protocol:
Interscapular brown adipose tissue was isolated and placed into tubes containing 1 mL of Trisure (Bioline) and a metal bead, and homogenized in a TissueLyzer II (Qiagen) for 60-120 seconds at 30 Hz. Samples were centrifuged and the Trisure supernatant was collected for RNA isolation according to the manufacturer's instructions. RNA concentration was measured with a Nanodrop 2000 spectrophotometer (Thermo Scientific).
For construction of RNA-Seq libraries, a TruSeq Stranded mRNA Library Prep Kit (Illumina) was used according to the manufacturer's instructions. 2 micrograms of total RNA was used as the starting material. PolyA-containing RNA was purified and fragmented, followed by first and second strand cDNA synthesis, adapter ligation, and PCR amplification (15 cycles). A library size of 200-300 bp was verified by agarose gel electrophoresis and library concentration was measured with a Qubit dsDNA High Sensitivity Assay Kit and a Qubit 2.0 fluorimeter (Invitrogen).
Libraries were pooled, denatured with NaOH, diluted to 1.8 pM, and sequenced on a NextSeq 500 Sequencing System (Illumina) with a NextSeq 500/550 High Output v2 kit (75 cycles) in single-read mode.


title: 7_r1_1

description: sample name: 211


title: 8_r3_3

description: sample name: 209


title: 8_r2_3

description: sample name: 208


title: TG-KEO27_S27

description:
sample name in processed data file:
B6 3
Duodenum.tsv


title: BCL6ff UCP1Cre+ BAT 30 deg C mRNA sample 3


title: 8_r6_2

description: sample name: 206


title: 8_r5_2

description: sample name: 205


title: BCL6ff UCP1Cre+ BAT 30 deg C mRNA sample 2


title: 8_r4_2

description: sample name: 204


title: 8_r3_2

description: sample name: 203


title: BCL6ff UCP1Cre+ BAT 30 deg C mRNA sample 1


title: 8_r2_2

description: sample name: 202


title: TG-KEO25_S25

description:
sample name in processed data file:
B6 3
Colon.tsv


title: TG-KEO24_S24

description:
sample name in processed data file:
B6 2
Duodenum.tsv


title: 8_r1_2

description: sample name: 201


title: TG-KEO23_S23

description:
sample name in processed data file:
B6 2
Ileum.tsv


title: 14_r12_1

description: sample name: 38

value: 14 cell


title: TG-KEO22_S22

description:
sample name in processed data file:
B6 2
Colon.tsv


title: BCL6ff Cre- BAT 30 deg C mRNA sample 3


title: 14_r11_1

description: sample name: 37


title: 14_r10_1

description: sample name: 36


title: 12_r1_1

description: sample name: 39

value: 12 cell


title: 14_r9_1

description: sample name: 35


title: 14_r8_1

description: sample name: 34


title: BCL6ff Cre- BAT 30 deg C mRNA sample 1


title: TG-KEO21_S21

description:
sample name in processed data file:
B6 1
Duodenum.tsv


title: TG-KEO20_S20

description:
sample name in processed data file:
B6 1
Ileum.tsv

value: Ileum


title: 8_r1_3

description: sample name: 207


title: 14_r7_1

description: sample name: 33


title: 14_r6_1

description: sample name: 32


title: TG-KEO26_S26

description:
sample name in processed data file:
B6 3
Ileum.tsv


title: BCL6ff UCP1Cre+ BAT 22 deg C mRNA sample 4


title: 14_r5_1

description: sample name: 31


title: BCL6ff Cre- BAT 30 deg C mRNA sample 2


title: BCL6ff UCP1Cre+ BAT 22 deg C mRNA sample 3


title: TG-KEO2_S2

description:
sample name in processed data file:
BALBcJ 1
Ileum.tsv

value: BALB/cJ


title: 14_r3_1

description: sample name: 29


title: TG-KEO19_S19

description:
sample name in processed data file:
B6 1
Colon.tsv

value: Colon


title: 14_r4_1

description: sample name: 30


title: BCL6ff Cre- BAT 30 deg C mRNA sample 4


title: BCL6ff UCP1Cre+ BAT 22 deg C mRNA sample 2


title: TG-KEO18_S18

description:
sample name in processed data file:
BALBcJ 6
Duodenum.tsv

value: BALBcJ 6

value: Duodenum/Jejunum


title: 14_r2_1

description: sample name: 28


title: BCL6ff UCP1Cre+ BAT 22 deg C mRNA sample 1


title: BCL6ff Cre- BAT 22 deg C mRNA sample 4


title: 14_r1_1

description: sample name: 27


title: TG-KEO17_S17

description:
sample name in processed data file:
BALBcJ 6
Ileum.tsv


title: transgenic line, replicate 2

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C. Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST was solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS. All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

scan_protocol: Scanning was performed on a Axon GenePix 4000A scanner. Laser was set at 33% power.

data_processing: Data extraction was carried out using the GenePix Pro 7 software. The normalization between arrays was performed using the quantile method.

organism: Citrus sinensis x Citrus trifoliata

source_name: root

label_protocol: Six µg of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions

growth_protocol: Three weeks old wild type (WT) and transgenic Carrizo citrange (TCC) plants were grown on MSC agar medium (Caruso et al. 2011) in a controlled growth chamber under a light intensity of 45 µmol m-2 s-1 with a 16/8 h (day/night) photoperiod (27°C, 60% relative humidity).

extract_protocol: Total RNA was extracted from WT and transgenic leaves using TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

treatment_protocol: For the anoxic and recovery experiments, plants were flushed for 24 h at 5 l h-1 with 100% N2 under sterile conditions. After the treatments, WT and TCC plants were transferred into tubes containing fresh MSC agar medium and allowed to recover for two weeks under normoxic conditions in a controlled growth chamber at 27°C.

value: Transgenic Line (Carrizo plus Mybleu)

tag: culture condition

value: normoxia

value: root

value: 3 weeks


title: transgenic line, replicate 3


title: 8_r2_1

description: sample name: 24

tag: developmental stage

value: embryonic cell


title: BCL6ff Cre- BAT 22 deg C mRNA sample 3

value: BCL6-floxed (C57BL/6J)

value: interscapular brown adipose tissue


title: BCL6ff Cre- BAT 22 deg C mRNA sample 2

value: male


title: 8_r3_1

description: sample name: 25

value: 8 cell

tag: cell type


title: 14_P4_1

description: sample name: 26


title: BCL6ff Cre- BAT 22 deg C mRNA sample 1


title: TG-KEO13_S13

description:
sample name in processed data file:
BALBcJ 5
Colon.tsv

value: BALBcJ 5


title: TG-KEO14_S14

description:
sample name in processed data file:
BALBcJ 5
Ileum.tsv


title: transgenic line, anaerobiosis, replicate 3

value: anoxia


title: TG-KEO12_S12

description:
sample name in processed data file:
BALBcJ 4
Duodenum.tsv

value: BALBcJ 4


title: transgenic line, replicate 1