title: non-metastatic line YCU-OR891

city: YOKOHAMA

last: Hyakusoku

state: KANAGAWA

department: ENT

institute: Yokohama City University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2545A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data were analyzed with GeneSpring 11.5 using Agilent default analysis settings and global scaling as normalization method.

source_name: HNSCC cells

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: RNA was prepared using the Rneasy mini kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: The cells were maintained on monolayer plastic and incubated with RPMI or DMEM with 10% fetal bovine serum  at 37°C and 5% CO2

tag: origin

value: oral floor

value: non-cervical lymph node metastases


title: non-metastatic line YCU-MS861

status: Public on Mar 22 2019

type: RNA

first: Hiroshi

country: Japan

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: maxillary sinus

tag: cell type


title: high metastatic line Detroit562

value: pleural effusion

value: high cervical lymph node metastases


title: synovium, CAIA, biological rep3

city: Atsugi

first: Kyoko

last: Shimazu

state: Kanagawa

address: 5-1-3 Midorigaoka

department: Innovation Center

institute: Nippon Flour Mills Co., Ltd.

description: Gene expression data from synovium in CAIA mouse

hyb_protocol: The biotinylated cRNA was then fragmented and hybridized to a GeneChip Mouse genome 430 2.0 Array (Thermo Fisher Scientific) at 45°C for 16 h.

scan_protocol: The array was washed and stained using a GeneChip Fluidics Station 450 (Thermo Fisher Scientific). Fluorescence signals were scanned using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The Affymetrix GeneChip Command Console program (Thermo Fisher Scientific) was used to convert the array images into intensity values for each probe (CEL files).The CEL files were normalized using the distribution free weighted method (DFW) in the statistical packages R (version 3.2.1 or 3.2.2) and Bioconductor (version 3.2) . A total of 5044 probe sets with NetAffx (ver. 2014/10) annotation grade E or R were excluded from the subsequent analyses.

label: biotin

organism: Mus musculus

source_name: synovium, CAIA

label_protocol: The cDNA was synthesized from 100 ng of purified total RNA, and biotinylated cRNA was transcribed using T7 RNA polymerase and purified using the GeneChip 3’IVT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Five-week-old male DBA/1J mice were housed under conventional conditions (24°C ± 1°C, 50% ± 10% relative humidity with a 12 h light/dark cycle). The mice were fed the AIN-93G diet, where fat is provided by corn instead of soy, and were provided ad libitum access to the diet and water for 24 h.

extract_protocol: The left hind legs were collected, treated with RNAlater solution (Thermo Fisher Scientific Inc., Waltham, MA, USA), stored at 4°C overnight, and then removed from the reagent and stored at -80°C. Synoviums were collected from the legs by cleaning of the surrounding muscle and skin, and total RNA was isolated using Isogen reagent (Nippon Gene Co., Ltd., Tokyo, Japan) and then purified using the RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan)

treatment_protocol: After a week of acclimatization, the mice were divided into three groups: untreated (CT), CAIA (CA), and CAIA plus MA treatment (CA + MA). MA was suspended in corn oil and orally administered to CA + MA mice daily at a dose of 200 mg/kg of body weight. The other two groups were administrated corn oil instead of MA. CAIA was induced by intraperitoneal injection with 1 mg of a type II collagen mAb (Chondrex, Inc., Redmond, WA, USA) on day 8 and 25 µg of LPS (Chondrex) on day 11. Mice were sacrificed on day 12.

tag: gender

value: male

tag: strain

tag: tissue

value: synovium

tag: age

value: 8 weeks


title: high metastatic line FaDu

value: FaDu

value: hypopharynx


title: synovium, CAIA, biological rep2


title: synovium, CAIA+MA, biological rep1

description: Gene expression data from synovium in CAIA mouse administrated Maslinic acid.

source_name: synovium, CAIA+MA


title: ChIPseq of paf1+ ade6+, replicate 2, H3 total

type: SRA

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
smallRNA-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
Genome_build: Spombe.ASM294v2.24
Supplementary_files_format_and_content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures was grown exponentially in YES media at 30 degrees celsius

extract_protocol:
Exponentially growing S. pombe cell culture (50ml YES, OD = 1) was fixed with 1% formaldehyde and lysed. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol. For chromatin immunoprecipitation (ChIP), histone H3-specific rabbit polyclonal antibody from Abcam (ab1791) was used. For a detailed protocol, see Kowalik et al., 2015.
For multiplex ChIP sequencing, samples were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L) and NEBNext Multiplex Oligos for Illumina (E7600S).

tag: genotype


title: white matter sample from CD47 null mice

city: Maebashi

last: Ohnishi

state: Gunma

address: 3-39-22 Showa-machi

department: Department of Laboratory Sciences

institute: Gunma University Graduate School of Health Sciences

description: Gene expression data from CD47 null mouse white matter

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on the GeneChip Mouse Genome 430 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: brain white matter

label_protocol: Total RNAs from four (wild-type) and five (CD47 knockout) different genotype-matched animals were pooled and labelled. Biotinylated cRNA were synthesized by GeneChip 3' IVT Expression Kit（Affymetrix) from 250 ng of the pooled total RNA sample according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Mice were housed in an air-conditioned room under specific pathogen–free conditions with a 12-h-light, 12-h-dark cycle.

extract_protocol: Total RNAs were prepared from the tissues by the use of Sepasol RNA I (Nacalai Tesque) and an RNeasy Mini kit (Qiagen, Hilden, Germany). Extraction and purification of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues were dissected from genotype-matched male mice euthanised by cervical dislocation after deep anaesthesia. Tissues were rinsed with PBS, frozen in liquid nitorgen, and then stored in deep freezer (-80°C ) until the RNA extraction.

value: optic nerve and optic tract

value: CD47 null

value: 12-15 weeks of age


title: single quiescent vs single reactivating pair 3

city: Plymouth

first: Claudia

last: Barros

state: Devon

address: The John Bull Building, Plymouth Science Park, 16 Research Way

department: School of Medicine

country: United Kingdom

institute: University of Plymouth

description: single quiescent vs single reactivating pair. Biological replicate 3

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Only gene spots are included in the analysis. Also gene probes are removed which have intensity below 150 or are flagged RR, RS, SR in more than 2 samples (remaining 2455 probes). Raw data are then loaded into limma (Bioconductor) and quantile normalised. The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

label_protocol: For cDNA PCR amplification, 2μl of nested primer (5’- AAGCAGTGGTATCAACGCAGAGT-3’), 2μl dNTPs (10mM), 5μl Roche buffer, 0.5μl Roche Long Expand polymerase and 34.5μl of ultrapure water were added. PCR program: one cycle (95oC 3min, 50oC 5min, 68oC 15min) followed by 25 cycles (95oC 20s, 60oC 1min, 68oC 7min). 3 pairs of NSC quiescent/ reactivating samples showing clear banding patterns on agarose gels were used for microarray analysis. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: Individual quiescent and reactivating neural stem cells (NSCs) expressing CD8-GFP driven by grh-Gal4 were manually harvested from 17h after larval hatching live CNSs

extract_protocol: Each single cell was expelled in its own Eppendorf tube containing annealing mix: 0.3μl anchored polyT primer (5’- AAGCAGTGGTATCAACGCAGAGTACT(26)VN-3’, 10pM), 0.3μl SM primer (5’-AAGCAGTGGTATCAACGCAGAGTACGCrGrGrG-3’, 10pM), 0.4μl RNase inhibitor (Superase, Ambion) and 2μl Lysis Mix (10% Nonidet P-40, 0.1M DTT in DEPC-treated ultrapure water), and processed in less than 20 min. Each sample was spun (14000rpm, 1min, 4oC), primers annealed (3min, 70oC) and snap-frozen in dry ice/ isopropanol. 1.5μl of mix 1 (1μl Invitrogen first strand buffer, 0.5μl 10mM dNTPs) and 0.5μl of mix 2 (3μl Invitrogen Superscript II reverse transcriptase, 0.5μl Ambion Superase RNase inhibitor) were added per sample. Samples were thawed during centrifugation (14000rpm, 1 min, 4oC) and reverse transcribed (37oC, 90min), followed by enzyme thermal inactivation (65oC, 10 min). RNA was digested in 2μl digestion mix (0.7μl Roche RNase H buffer, 0.5μl Roche RNase H, 0.8μl ultrapure water) for 20min at 37oC, followed by enzyme thermal inactivation (65oC, 15 min).

value: Quiescent NSC

value: grainyhead-GaL4, UAS-mCD8-GFP

value: CNS

value: 17h after larval hatching

value: Reactivating NSC


title: single quiescent vs single reactivating pair 2

description: single quiescent vs single reactivating pair. Biological replicate 2


title: sRNAseq of F11, paf1+ rdp1D, replicate 3

description:
F11_rdp1_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT

library_source: transcriptomic

data_processing:
Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
smallRNA-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17. Illumina or Qiagen 3' adaptors were trimmed using cutadapt with parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie 1.0.0 with parameters -M 1 -v 0 --best --strata. Bowtie sam out put was converted to bam using samtools (v1.3.1). Bam files were converted to bed using bedtools bamtobed (v2.25.0), Bed files were used to calculate strand-specific coverage using bedtools genomecov (v2.25.0) and resulting bedgraph files were normalized to 1 million genome mapping reads (RPM) and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data was demultiplexed and converted to fastq format using bcl2fastq2 v1.17 and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation by bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities), non-aligned reads and muli-mapping reads were discarded and read coverage was normalized to 1 million genome mapping reads (RPM).
Genome_build: Spombe.ASM294v2.24
Supplementary_files_format_and_content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV.

extract_protocol:
Total RNA was extracted with the MasterPure RNA Purification Kit from epicenter (MCR85102).
Small RNA libraries were prepared with the QIAseq miRNA Library Kit (331505) according to manufacturer’s instructions.

value: h- leu1-32 ura4-D18 ade6-M210/704 trp1+::ade6+  rdp1D::natMX


title: SW48_bi_rep3

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

institute: University Hospital Bern

hyb_protocol: 1500 ng of biotin labeled, intact cRNA was hybridized to Sentrix HumanWG6 v3 Expression BeadChips (Illumina) according to the manufacturer’s protocol. Replicates were randomly distributed among slides and positions. Bead arrays were washed and stained using FluoroLink Cy3 Streptavidin (GE Healthcare Life Sciences).

scan_protocol: Fluorescent signal data was collected using a high-resolution scanner system (Illumina iScan) using factory settings for whole genome expression arrays.

data_processing: The data was processed with Illumina genome studio software (gene expression module 1.0.6) with no background correction or normalization. VST (variance stabilization) transformation 'lumiT()', quantile normalization 'lumiN(, method = quantile)' and statistical analysis were performed with R (2.14.0) / Bioconductor using the package lumi (2.6.0).

label_protocol: Starting with 500 ng / sample of total RNA, total RNAs were transcribed and labeled with Illumina(r) TotalPrep RNA Amplification Kit (Ambion). cRNA was quantified with QuantIT (Invitrogen) against ribosomal RNA standard (Invitrogen).

growth_protocol: The human microsatellite-instable CRC cell line SW48 was cultured in Dulbecco’s Modified Eagle Medium (DMEM; Sigma, Hamburg, Germany) supplemented with 10% fetal calf serum (FCS), 2 mM L-Glutamine (Sigma), 60 U/ml Penicillin (Sigma) and 10 µg/ml Streptomycin (Sigma)

extract_protocol: The cells were harvested and total RNA were extracted with TRI REAGENT (Sigma)

treatment_protocol: For pharmacological DNA demethylation SW48 cells were incubated with 5'-Aza-cytidine (DNA methyltransferase inhibitor) and/or Trichostatin A (TSA, Histone deacetylase inhibitor). After 24 h of culture the normal medium was replaced by medium containing 1 μM 5´-Aza-C and/or 0.5 μM TSA and incubated for five and two days, respectively. The medium was renewed every 24 h. For the double treatment, cells were first treated with 5-Aza‑cytidine followed by an exposure to TSA.

tag: treatment

value: 5'-Aza-cytidine + Trichostatin A


title: sRNAseq of F11, paf1+ rdp1D, replicate 2

description:
F11_rdp1_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: single quiescent vs single reactivating pair 1

description: single quiescent vs single reactivating pair. Biological replicate 1


title: sRNAseq of F11, paf1+ rdp1D, replicate 1

description:
F11_rdp1_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: SW48_aza_rep3


title: SW48_aza_rep2


title: WT_H1792_BT_1

city: Dallas

first: Neal

last: Alto

state: TX

address: 6000 Harry Hines Blvd, NL3.108

country: USA

institute: UT Southwestern Medical Center

data_processing:
Basecalls performed using bcl2fastq/1.8.4
Reads were trimmed using fastq-mcf (ea-utils/1.1.2-806)
Trimmed reads were mapped using TopHat 2 (2.0.12)
Raw reads were counted using featureCounts (subread/1.4.6) or Cufflinks 2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files

source_name: H1792 NSCLCs

growth_protocol: Cells were drown in RPMI supplemented with 10% FBS and 1×NEAA.

extract_protocol:
Total RNA purification was performed according to RNAeasy mini kit instruction (QIAGEN, 74104), with DNA digestion step according to the kit instruction
RNA concentration was determined with a Qubit fluorimeter prior to library prep.  4μg of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. In brief, polyadenylated RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA was A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer.

treatment_protocol: For identification of NIK-stimulated genes and SIX2 downregulated NIK-stimulated genes, we transduced WT STAT1-deficient fibroblasts with indicated lenti-virus. For comparision of gene transcription profiles induced by BV6/TNF, indicated genotypes H1792 cells were treated with 5 μM BV6 along with 25 ng/ml TNF for 24 hours.

value: NSCLC cells

value: WT

tag: treated with


title: sRNAseq of F11, paf1+ clr4F449Y, replicate 3

description:
F11_clr4F449Y_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: SW48_con_rep3

value: non-treated


title: SW48_con_rep2


title: SW48_tsa_rep3

value: Trichostatin A


title: WT_H1792_2

value: DMSO


title: sRNAseq of F11, paf1+ clr4F449Y, replicate 2

description:
F11_clr4F449Y_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: WT_H1792_1


title: SW48_bi_rep2


title: sRNAseq of F11, paf1+ clr4F449Y, replicate 1

description:
F11_clr4F449Y_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: SIX1_SIX2_KO_BT_H1792_2


title: sRNAseq of F11, paf1+ ade6+imp, replicate 5

description:
F11_ade6si3_r5
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ade6+imp, replicate 9

description:
F11_ade6si3_r9
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: SIX1_SIX2_KO_BT_H1792_1


title: SW48_tsa_rep2


title: SW48_bi_rep1


title: WT_H1792_BT_2


title: sRNAseq of F11, paf1+ ade6+imp, replicate 7

description:
F11_ade6si3_r7
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: SIX1_SIX2_KO_H1792_2


title: SIX1_SIX2_KO_H1792_1


title: SW48_tsa_rep1


title: sRNAseq of F11, paf1+ ade6+imp, replicate 6

description:
F11_ade6si3_r6
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: NIK_SIX2_STAT1-deficient fibroblasts_2

source_name: STAT1-deficient fibroblasts

value: STAT1-deficient fibroblasts

tag: transduction


title: SW48_con_rep1


title: SW48_aza_rep1


title: NIK_SIX2_STAT1-deficient fibroblasts_1


title: NIK_Fluc_B_STAT1-deficient fibroblasts_2


title: NIK_Fluc_B_STAT1-deficient fibroblasts_1


title: sRNAseq of F11, paf1+ clr4D, replicate 1

description:
F11_clr4D_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT

value: h- leu1-32 ura4-D18 ade6-M210/704 trp1+::ade6+  clr4D::hphMX


title: sRNAseq of F11, paf1+ ade6+imp, replicate 8

description:
F11_ade6si3_r8
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ dcr1D, replicate 3

description:
F11_dcr1D_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT

value: h- leu1-32 ura4-D18 ade6-M210/704 trp1+::ade6+  dcr1D::hphMX


title: NIK_STAT1-deficient fibroblasts_1

value: NIK


title: sRNAseq of F11, paf1+ dcr1D, replicate 2

description:
F11_dcr1D_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ago1D, replicate 3

description:
F11_ago1D_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT

value: h- leu1-32 ura4-D18 ade6-M210/704 trp1+::ade6+  ago1D::hphMX


title: sRNAseq of F11, paf1+ ago1D, replicate 1

description:
F11_ago1D_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ clr4D, replicate 2

description:
F11_clr4D_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: NIK_STAT1-deficient fibroblasts_2


title: sRNAseq of F11, paf1+ dcr1D, replicate 1

description:
F11_dcr1D_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ade6+imp, replicate 4

description:
F11_ade6si3_r4
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: Fluc_RB_STAT1-deficient fibroblasts_2


title: Fluc_R_SIX2_STAT1-deficient fibroblasts_2


title: sRNAseq of F11, paf1+ clr4D, replicate 3

description:
F11_clr4D_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: Fluc_STAT1-deficient fibroblasts_1

value: Fluc


title: Fluc_STAT1-deficient fibroblasts_2


title: Fluc_R_SIX2_STAT1-deficient fibroblasts_1


title: Fluc_RB_STAT1-deficient fibroblasts_1


title: sRNAseq of F11, paf1+ ago1D, replicate 2

description:
F11_ago1D_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: MED1_siERG _HUVEC

city: London

first: Graeme

middle: Miles

last: Birdsey

address: Hammersmith Hospital, Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

data_processing:
ChIP sequence reads were identified by the Sequencing Service (using Illumina’s NextSeq 500).
ChIP-seq reads were aligned using the BWA algorithm to the hg19 reference genome.
Only tags that map uniquely, with no more than 2 mismatches and pass quality control filtering are used subsequently.
Bigwig generated using bedGraphToBigWig from UCSC.
Peak calls were performed with MACS2 with default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: bigWig files.

source_name: human umbilical vein endothelial cells

growth_protocol: Cells were seeded in pre-coated culture dishes with 1% gelatin and cultured in commercial EGM2 media from Lonza.

extract_protocol:
Chromatin samples were prepared by Active Motif Services.
Libraries were prepared by Active Motif Services.

treatment_protocol: siRNA was synthesized by Qiagen and 20nM was transfected with Atufect transfection reagent (Silence Therapeutics).

value: Pooled HUVEC

tag: passage

value: 4 to 6

value: ERG siRNA treated

tag: chip antibody

value: MED1 (A300-793A, Bethyl Laboratories)


title: sRNAseq of F11, paf1+ ade6+imp, replicate 1

description:
F11_ade6si3_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ade6+imp, replicate 2

description:
F11_ade6si3_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: Input_siRNA_HUVEC

value: control


title: MED1_siCTL_HUVEC

value: control siRNA treated


title: H3K27ac_siERG _HUVEC

value: H3K27ac (cat no. 39133, Active Motif)


title: sRNAseq of F11, paf1+ ade6+, replicate 4

description:
F11_r4
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: H3K27ac_siCTL _HUVEC


title: sRNAseq of F11, paf1+ ade6+, replicate 2

description:
F11_r2
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ade6+, replicate 3

description:
F11_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: sRNAseq of F11, paf1+ ade6+, replicate 1

description:
F11_r1
3'_adapter_sequence: AACTGTAGGCACCATCAAT


title: 181_cell

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit (Qiagen) as per manufacturer’s instructions.

tag: patient number

tag: sample group

value: cell

tag: Sex

value: m

tag: diagnosis

tag: patient id

tag: btic id

tag: subtype

value: Classical

tag: parental tumor subtype

tag: sample plate

tag: sentrix id

tag: sentrix position


title: Triple-LB-3d2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
We used Edge-Pro for mapping and quantification and qualimap for quality control
Noiseq was used for data normalization
Genome_build: ASM96383v1 (P. chlororaphis) and ASM34474v1 (B. subtilis)
Supplementary_files_format_and_content: tab-delimited excel files include Log2FC of the comparison of strains in interaction vs single colonies, with p-value and padj values

organism: Bacillus subtilis

source_name: Triple mut_LB

extract_protocol:
Single colonies of P. chlororaphis and B. subtilis were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 2 ul were spotted on an LB solid medium at 0.7 cm of distance. Cultures were grown for 72h.  Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gentoype/variation

value: Triple mut


title: Triple-LB-3d1


title: 73_xeno

label: Cy5 and Cy6

value: xeno

tag: age

value: gbm

value: Mesenchymal


title: 194_cell


title: sRNAseq of F11, paf1+ ade6+imp, replicate 3

description:
F11_ade6si3_r3
3'_adapter_sequence: AACTGTAGGCACCATCAAT

tag: strain

tag: genotype


title: 143_xeno

label: Cy5 and Cy4

value: f


title: 284_tumor

value: tumor


title: 53_xeno

label: Cy5 and Cy5

value: Proneural


title: 181_tumor


title: 238_tumor


title: 198_tumor


title: 50_tumor

value: Unknown


title: 246_cell


title: 147_xeno


title: D538G WM_+E2_R1

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ17
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

data_processing:
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and v2.2.1 and a normalized RPKM matrix was generated using the cufflinks v2.2.1
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.7
Genome_build: Hg19
Supplementary_files_format_and_content:
[Processed_data_read_Counts.CSV]: Count Matrix File
[RPKM_counts.csv]: RPKM Matrix File_filtered to include the top 1,000 most variable genes
[RPKM_counts_full.csv]: RPKM Matrix_including all genes

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% CSS.

extract_protocol:
RNA was extracted using Qiagen RNAeasy kits
RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Cells were either maintaned in white medium or treated with estadiol x24 hrs.

tag: cell line

tag: mutation

value: D538G ESR1 mutation

tag: medium conditions

value: white medium + estrogen


title: 198_cell

tag: patient number

tag: sample group


title: 248_tumor

tag: Sex

tag: diagnosis


title: 245_tumor

tag: patient id


title: D538G WM_no E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ15
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

value: white medium


title: D538G WM_+E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ18
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: 280_cell

tag: btic id

tag: subtype


title: HEK.WT.1 repl4

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
Trim Galore! v0.4.0 with parameters "--stringency 3 -e 0.2 -a TGGAATTCTCGGGTGCCAAGGA" was used to remove sequencing adapters.
Bismark v0.14.4 with parameters "-n 2 -l 50 --un --ambiguous --bowtie1 --chunkmbs 2048" was used to align the reads to the hg38 reference genome.
Seqtk with parameters "-e 3" was used to remove last three bases from unaligned and ambigous reads followed by re-alignment by Bismark.
Ngsutils v0.5.9 in the "junction" mode was used to extract splice junctions; unaligned reads from the previous alignment attempt were aligned to them using Bismark. The aligned reads were coverted back to genomic coordinates using bamutils in "convertregion" mode. 'N' in the cigar string was replaced with 'D' for compatibility with bismark_methylation_extractor.
Samtools merge was used to combine aligned reads from all steps. Reads with >1/3 methylated cytosines were discarded.
bismark_methylation_extractor with the "--bedGraph --counts --CX_context" options was used to extract methylated cytosines.
Genome_build: hg38
Supplementary_files_format_and_content: The bismark coverage reports are tab delimited and contain methylation level at each covered cytosine in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: HEK cells

growth_protocol: H9 cells were grown on matrigel coated plates in essential 8 medium, passaged as clumps after dissociation using EDTA in PBS, HEK293 cells were grown in DMEM media completed with 10% fetal bovine serum and glutamax.

extract_protocol:
15 μg of total RNA was extracted using Trizol (ThermoFisher) and DNase (Ambion) then Ribo‐Zero (Illumina) treated (3 times treatment of 5 ug and then pooled). The remaining RNA fraction was bisulfite‐treated according to Pollex, T., Hanna, K., & Schaefer, M. (2010). Detection of cytosine methylation in RNA using bisulfite sequencing. Cold Spring Harbor Protocols, 2010(10). Briefly, ribosomal depleted RNA was mixed with 42.5 μl of 40% sodium bisulfite pH 5.0 and 17.5 μl of DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for three cycles of 5 min at 70°C followed by 1 h at 60°C and then desalted with Micro Bio‐spin 6 chromatography columns (Bio‐Rad). RNA was desulphonated by adding an equal volume of 1 M Tris (pH 9.0) to the reaction mixture and incubated for 1 h at 37°C, followed by ethanol precipitation. Bisulfite converted RNA was treated with T4 PNK (New England Biolabs) to repair both 5’ and 3’ ends for library preparation. Repaired RNA quality and concentration was measured on a Bioanalyzer 2100 RNA nano‐chip (Agilent).
About 100 ng of RNA was used to generate Bisulfite‐seq libraries. Libraries were performed according to TruSeq Small RNA preparation kit (Illumina). RNA adapters were then ligated, reverse‐transcribed followed by 18‐cycle PCR amplification before sequencing.

tag: cell type

value: human embryonic kidney 239 cells

tag: genotype/variation

value: wildtype

tag: batch


title: Parental WM_+E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ3
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

value: WT ESR1


title: 246_tumor

tag: parental tumor subtype

tag: sample plate

tag: sentrix id

tag: sentrix position


title: 238_cell

value: cell

tag: age


title: 248_cell


title: 245_cell

value: m


title: HEK.WT.1 repl3

tag: cell line


title: 194_tumor

value: Classical


title: 206_cell


title: 126_cell


title: 126_tumor


title: 220_cell


title: 143_cell


title: 191_cell


title: 167_tumor


title: 100_cell_rep


title: HEK.WT.rescue2 repl3

value: HEK.KO.2 carrying insertions of a piggybac vector coding for a flagged version of NSUN6, puromycin selection,clonal


title: HEK.WT.1 repl1


title: 206_tumor


title: Parental WM_+ E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ4
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

tag: mutation

tag: medium conditions


title: E380Q 2 WM_+E2 R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ15
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

value: E380Q ESR1 mutation


title: 140_cell

tag: patient number

tag: sample group

value: gbm


title: 73_tumor

tag: Sex

tag: diagnosis

value: Mesenchymal


title: Parental WM_no E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ1
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: HEK.WT.1 repl2


title: Parental WM_no E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ2
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: HEK.WT.rescue2 repl2


title: E380Q 2 WM_+E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ14
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: D538G WM_no E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
FRJ16
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: 156_tumor

tag: patient id


title: E380Q 2 WM_no E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ13
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: E380Q 2 WM_no E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ12
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: 89_cell

value: f

tag: btic id

tag: subtype


title: HEK.WT.rescue2 repl1

tag: cell type

tag: genotype/variation


title: HEK.WT.rescue1 repl4

value: HEK.KO.1 carrying insertions of a piggybac vector coding for a flagged version of NSUN6, puromycin selection,clonal

tag: batch


title: HEK.WT.rescue2 repl4


title: 100_tumor

value: tumor

tag: parental tumor subtype

tag: sample plate


title: HEK.WT.rescue1 repl3


title: Y537S WM_+ E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ9
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

value: Y537S ESR1 mutation


title: Y537S WM_+ E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ10
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: 280_tumor

tag: sentrix id

tag: sentrix position


title: Y537S WM_no E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ7
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

tag: cell line


title: 284_cell

tag: age


title: 53_tumor

value: Proneural


title: 41_tumor


title: HEK.KO.2 repl4

value: Crispr /Cas9 mediated (NHEJ) InDel of exon2 of NSUN6 (deletion causes frameshift and premature stop), clone2


title: HEK.WT.rescue1 repl2


title: HEK.KO.2 repl3


title: 127_cell

value: Unknown


title: E380Q 1 WM_+ E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ4
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

tag: mutation

tag: medium conditions

value: white medium + estrogen


title: E380Q 1 WM_+E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ3
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: E380Q 1 WM_no E2_R1

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ1
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination

value: white medium


title: E380Q 1 WM_no E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ2
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: HEK.WT.rescue1 repl1

value: human embryonic kidney 239 cells


title: HEK.KO.2 repl2


title: Y537S WM_no E2_R2

description:
Processed_data_read_Counts.CSV
RPKM_counts.csv
ERJ8
Parental MCF7 cells that were derived from a clonal selection and MCF7 cells  knocked-in with ESR1 mutations using TALEN technology and homologous recombination


title: HEK.KO.2 repl1


title: HEK.KO.1 repl4

value: Crispr /Cas9 mediated (NHEJ) InDel of exon2 of NSUN6 (deletion causes frameshift and premature stop), clone1


title: HEK.KO.1 repl3


title: WTSM3

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Base-calling: Illumina RTA v2
Alignment: Hisat2 was used to align reads to the human genome.
Mixture-of-isoforms (MISO) was used to quantify splicing regulation.
Gene expression quantitation: Kallisto was used to quantify gene expression. Cyclic Loess (R code) was used to normalize gene expression values.
Genome_build: mm10
Supplementary_files_format_and_content: nonUTRevents_psiTable.txt: Tab-delimited file summarizing inclusion levels of exons. Includes chromosomal location of regulated exon (Event), gene symbol (Symb), and psi values.
Supplementary_files_format_and_content: kallisto.txt:  Tab-delimited file including gene names and estimated transcripts per million.

source_name: Mouse tibialis anterior muscle

extract_protocol:
Total RNA was isolated from tissue by Trizol.
RNAseq libraries were generated using the NEB Ultra II Directdional RNAseq prep kit with rRNA depletion.

treatment_protocol: Mice were treated by IP injection.

value: WT

tag: treatment

value: small molecule


title: WTSM2


title: HEK.KO.1 repl2


title: 84_tumor

tag: patient number

tag: sample group

tag: Sex

value: m


title: HEK.KO.1 repl1


title: 172_cell

value: cell

tag: diagnosis

tag: patient id

tag: btic id

value: Classical


title: WTSM1

tag: genotype/variation


title: H9.WT.EV2 repl3

source_name: H9 cells

tag: cell type

value: human embryonic stem cells

value: WT H9 carrying insertions of a piggybac vector coding for puromycin selection, clone 2

tag: batch


title: WTPBS3

value: PBS


title: WTPBS1


title: H9.WT.EV2 repl4


title: WTPBS2


title: 220_tumor

value: tumor

value: gbm

tag: subtype

tag: parental tumor subtype

tag: sample plate


title: SM759

value: HSALR


title: H9.WT.EV2 repl2

tag: cell line


title: 73_cell

tag: age

value: Mesenchymal

tag: sentrix id

tag: sentrix position


title: WT2

tag: treatment

value: Untreated


title: H9.WT.EV1 repl4

value: WT H9 carrying insertions of a piggybac vector coding for puromycin selection, clone 1


title: 208_cell

tag: patient number

value: Unknown


title: 67_tumor

tag: sample group


title: WT3


title: 85_tumor

tag: Sex


title: H9.WT.EV2 repl1


title: 69_tumor

tag: diagnosis


title: 167_cell

tag: patient id


title: H9.WT.EV1 repl3


title: SM788


title: PBS784


title: H9.WT.EV1 repl1


title: 75_tumor

value: Proneural


title: PBS764


title: H9.WT.crispr repl4

value: H9 cells with unsuccesful crispr cutting, carrying WT NSUN6, clonal


title: H9.WT.crispr repl3


title: Luminal Input

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: LUM-Input

data_processing:
Reads were aligned to the mouse genome by Rsubread version 1.22.2.
Reads mapped to putative gene promoter regions (from 3kbp upstream to 2kbp downstream of the TSS) of NCBI Entrez Genes were counted using Rsubread's featureCounts function.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file; columns represent Entrez Gene ID and the number of reads mapped to the putative promoter region of that gene.

source_name: Luminal Input

extract_protocol:
The ChIP assay was carried out as per the manufacturer’s protocol (Millipore #17-371).
The ChIP DNA samples were prepared and indexed for Ilumina sequencing using the TruSeq DNA sample Prep Kit (Ilumina) as per manufacturer’s instructions. The indexed libraries were then prepared for single-end 75-85 bp sequencing on an Illumina NextSeq 500 using the 150 cycle kit v2 chemistry (Ilumina) as per the manufacturer’s instructions.

tag: strain

value: FBV/N

tag: tissue

value: Mammary epithelium

value: Luminal epithelial cell

tag: chip antibody


title: 94_cell

value: cell

value: f

tag: btic id


title: 50_cell

value: m

tag: subtype

value: Classical


title: PBS758

tag: genotype/variation

value: PBS


title: H9.WT.crispr repl2

tag: cell type

value: human embryonic stem cells

tag: batch


title: Luminal Foxp1 ChIP

source_name: Luminal Foxp1 ChIP


title: H9.WT.EV1 repl2

tag: cell line


title: 147_tumor

value: tumor

tag: age

tag: parental tumor subtype

tag: sample plate

tag: sentrix id


title: H9.WT.crispr repl1


title: 156_cell

tag: patient number

tag: sample group

tag: sentrix position


title: Basal Input

description: DP-Input

source_name: Basal Input

value: Basal epithelial cell


title: H9.WT.1 repl4

value: WT H9 cell line


title: 89_tumor

tag: Sex

tag: diagnosis

value: gbm

tag: patient id

value: Mesenchymal


title: SM790

value: HSALR

tag: treatment

value: small molecule


title: Basal Foxp1 ChIP

source_name: Basal Foxp1 ChIP

tag: strain

tag: tissue

tag: chip antibody


title: H9.WT.1 repl3

tag: cell type

tag: genotype/variation


title: H9.WT.1 repl2

tag: cell line

tag: batch


title: 140_tumor

tag: age

tag: subtype

value: Proneural

tag: parental tumor subtype


title: DM_HYP_B_H3K27me3_ChIPSeq

first: William

middle: G

last: Kaelin

state: MA

address: M457, 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls
For ChIP-Seq: sonicated DNA (~5ng) was ligated with the Rubicon Thruplex adapter and used to prep library using the Illumina Nextera prep method. Reads were aligned using bowtie, followed by peak calling using MACS. Aligned reads were analyzed using the ChiLin pipeline {Qin Q. etal (2016) BMC Bioinformatics 17: 404}
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-Seq: the .csv file contains the normalized RPKM values. For ChIP-Seq: bigwig files are attached.

source_name: C2C12 cells

growth_protocol:
C2C12 cells were cultured in DMEM+10%FBS+1XPenn-Strep. Cells were typically split every 3 days at 1:20. Cells were never allowed to get confluent.
C2C12 cells (seeded at 200,000 cells/well of a six well plate) were differentiated by culturing in DMEM+2% Horse Serum+1X ITS for days with media changes on Day 2, Day 3, and Day 4.

extract_protocol:
RNA was extracted using Trizol, as per the manufacturer's instructions. Histone-DNA complexes for ChIP-Seq were recovered by immunoprecipitation using cell lysates from clarified sonicated nuclei.
Libraries were constructed as per the manufacturers instructions. For RNASeq: 500 ng RNA was used with the Illumina stranded total RNASeq protocol; whereas, for ChIP-Seq the Illumina Nextera protocol was used.

value: C2C12 cells


title: DM_HYP_B_input DNA


title: DM_HYP_B_RNASeq

data_processing:
Basecalls
For RNA-Seq: gene counts were done using STAR (v2.5.1b) {Dobin A., etal (2013), Bioinformatics 29: 15.} and normalized gene counts (RPKM) were calculated using Cufflinks (v2.2.1) {Trapnell C., etal (2010), Nat. Biotech. 28: 511.}. Analysis was performed using the VIPER snakemake pipeline {Cornwell M., etal (2018), BMC Bioinformatics 19: 135.}
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-Seq: the .csv file contains the normalized RPKM values. For ChIP-Seq: bigwig files are attached.


title: H9.WT.1 repl1


title: H9.OEX.2 repl4

value: WT H9 carrying insertions of a piggybac vector coding for a flagged version of NSUN6, puromycin selection, clonal


title: 119_tumor

tag: patient number

tag: sample plate

tag: sentrix id


title: DM_HYP_A_RNASeq


title: H9.OEX.2 repl3


title: 208_tumor

tag: sample group

tag: Sex

value: Unknown

tag: sentrix position


title: DM_HYP_A_input DNA


title: 67_cell

value: cell

tag: diagnosis

tag: patient id

tag: btic id


title: H9.OEX.2 repl2


title: EGN265_nonCU-SGA

city: Salt

first: Judit

last: Bassols

address: C/ Dr. Castany s/n

institute: IDIBGI

description: test

data_processing:
The amplification efficiency was calculated using algorithms similar to the LinReg software. All assays were inspected for distinct melting curves and the Tm was checked to be within known specifications for the assay. Furthermore assays must be detected with 5 Cqs less than the negative control, and with Cq<37 to be included in the data analysis. Data that did not pass these criteria were omitted from any further analysis. Cq was calculated as the 2nd derivative.
Using NormFinder the best normalizer was found to be the average of assays detected in all samples. All data was normalized to the average of assays detected in all samples. The formula used to calculate the normalized Cq values are: Normalized Cq = average Cq (n=15) - assay Cq (sample)

label: SYBR green

source_name: umbilical cord

label_protocol: RNA was reverse transcribed in 50 μl reactions using the miRCURY LNA™ Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). cDNA was diluted 100 x and assayed in 10 ul PCR reactions according to the protocol for miRCURY LNA™ Universal RT microRNA PCR; each microRNA was assayed once by qPCR on the microRNA Ready-to-Use PCR, Human panel I+II using ExiLENT SYBR® Green master mix.The amplification was performed in a LightCycler® 480 Real-Time PCR System (Roche) and data was analyzed with the Roche LC software.

extract_protocol: Total RNA was extracted from umbilical cord tissue using the Qiagen miRNeasy® Mini Kit.

tag: condition

value: nonCU-SGA

tag: gender

value: female

tag: gestational age (wk)

tag: birth weight (g)

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)

tag: tissue

value: umbilical cord


title: 119_cell

tag: patient number

tag: age

value: f

tag: subtype

value: Classical

tag: parental tumor subtype


title: 147_cell

tag: sample group

tag: Sex

value: m

tag: sample plate

tag: sentrix id


title: DM_HYP_A_H3K27me3_ChIPSeq


title: EGN347_CU-SGA

description: test

value: CU-SGA

value: male


title: DM_NOR_B_RNASeq


title: DM_NOR_B_input DNA


title: H9.OEX.1 repl4

tag: cell type

value: human embryonic stem cells

tag: genotype/variation

tag: cell line

tag: batch


title: H9.OEX.1 repl3


title: 41_cell

tag: diagnosis

tag: patient id

tag: btic id

tag: sentrix position


title: EGN434_CU-SGA

description: test

tag: condition

tag: gender

tag: gestational age (wk)

tag: birth weight (g)

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)

tag: tissue


title: DM_NOR_B_H3K27me3_ChIPSeq


title: H9.OEX.1 repl2


title: 161_cell

tag: patient number

tag: sample group

tag: age

tag: Sex

value: gbm

tag: subtype

tag: parental tumor subtype

tag: sample plate

tag: sentrix id


title: H9.OEX.2 repl1

tag: cell type

tag: genotype/variation

tag: cell line

tag: batch


title: DM_NOR_A_RNASeq


title: 85_cell

tag: diagnosis

tag: patient id

tag: btic id

value: Mesenchymal

tag: sentrix position


title: 53_cell


title: 75_cell


title: EGN525_AGA

description: control

tag: condition

value: AGA

tag: gender

tag: gestational age (wk)

tag: birth weight (g)

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)

tag: tissue


title: 84_cell

tag: patient number

tag: sample group

tag: age

tag: Sex

tag: subtype

value: Proneural

tag: parental tumor subtype

tag: sample plate

tag: sentrix id


title: 69_cell

tag: diagnosis

tag: patient id

tag: btic id

tag: sentrix position


title: EGN563_AGA

description: control

tag: condition

tag: gender

tag: gestational age (wk)

tag: birth weight (g)


title: DM_NOR_A_H3K27me3_ChIPSeq

tag: tissue

value: C2C12 cells


title: EGN716_CU-SGA

description: test

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)


title: H9.OEX.1 repl1

tag: cell type

tag: genotype/variation

value: WT H9 carrying insertions of a piggybac vector coding for a flagged version of NSUN6, puromycin selection, clonal

tag: cell line

tag: batch


title: H9.KO.3 repl4

value: Crispr /Cas9 mediated (NHEJ) InDel of exon9 of NSUN6 (deletion of 7nt on allele1 and 50 nt on allele 2 causes framshift and premature stop), clonal


title: DM_NOR_A_input DNA


title: 94_tumor

tag: patient number

tag: sample group

value: tumor

tag: age

tag: Sex

tag: subtype

tag: parental tumor subtype

tag: sample plate

tag: sentrix id


title: GM_HYP_B_input DNA


title: 127_tumor

tag: diagnosis

tag: patient id

value: Unknown

tag: sentrix position


title: 172_tumor


title: H9.KO.3 repl1


title: GM_HYP_B_RNASeq

tag: tissue


title: EGN862_AGA

description: control

tag: condition

tag: gender

tag: gestational age (wk)

tag: birth weight (g)

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)


title: EGN454_nonCU-SGA

description: test

value: nonCU-SGA


title: EPG034_CU-SGA

description: test

value: female

value: umbilical cord


title: H9.KO.2 repl4

tag: cell type

tag: genotype/variation

value: Crispr /Cas9 mediated (HDR) deletion of EXON 2 of NSUN6, clone 2, puromycin selection

tag: cell line

tag: batch


title: GM_HYP_A_RNASeq


title: GM_HYP_B_H3K27me3_ChIPSeq


title: EGN839_nonCU-SGA

description: test


title: H9.KO.2 repl3


title: GM_HYP_A_input DNA


title: EGN368_CU-SGA

description: test


title: H9.KO.2 repl2


title: GM_NOR_B_RNASeq


title: EPG236_AGA

description: control


title: H9.KO.2 repl1


title: EPG582_nonCU-SGA

description: test


title: H9.KO.1 repl4

value: Crispr /Cas9 mediated (HDR) deletion of EXON 2 of NSUN6, clone 1 puromycin selection


title: H9.KO.1 repl3


title: GM_NOR_B_input DNA


title: 161_tumor

tag: patient number

tag: sample group

tag: age

tag: Sex

value: f

tag: subtype

value: Classical

tag: parental tumor subtype

tag: sample plate


title: H9.KO.1 repl2

value: human embryonic stem cells


title: treatment rep7

city: GAINESVILLE

first: FAHONG

last: YU

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the sequencing platform were cleaned with the Cutadapt program (Martin 2011) to trim off sequencing adaptors, low quality bases, and potential errors introduced during sequencing or library preparation. Reads with a quality Phred-like score < 20 and read length < 40 bases were excluded from RNAseq analysis.
The transcripts of Bos taurus (80,896 sequences) retrieved from the NCBI RefSeq database were used as reference sequences for RNAseq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the bowtie2 mapper (v. 2.2.3) with a ‘3 mismatches a read’ allowance (Langmead & Salzberg 2012). The mapping results were processed with the samtools and scripts developed in house at the University of Florida ICBR to remove potential PCR duplicates and choose uniquely mapped reads for gene expression analysis. Gene expression between the control and treatment group was assessed by counting the number of mapped reads for each transcript (Yao & Yu 2011).
Pathway analysis was performed using Ingenuity Pathway Analysis (Qiagen). Differentially expressed genes with a P-value ≤ 0.05 and log2 FC < -2 or > 2 were used for analysis. Represented canonical pathways with a -log P-value > 1.3 were determined with corresponding z-scores to describe predicted activation status. Represented gene networks were determined by assessing the number of differentially expressed genes in a given gene network. Upstream regulators of specific gene networks and upstream regulators of differentially expressed genes were predicted using IPA algorithms.
Genome_build: btaurus_ref
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Bos taurus

source_name: blood

extract_protocol:
Granulosa cells were thawed and resuspended in RLT buffer for RNA extraction using the RNeasy Micro kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Total RNA concentration was determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Total RNA with a 28S to 18S ratio > 1 and RNA integrity number (RIN) ≥ 7 were used for RNAseq library construction.
To produce RNAseq libraries, 200 ng of total RNA was used to isolate mRNA using NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Ipswich, MA, USA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions. Briefly, extracted mRNA was fragmented in NEBNext first strand synthesis buffer by heating at 94°C, followed by first strand cDNA synthesis using reverse transcriptase and random primers. Synthesis of double-stranded cDNA was performed using the 2nd strand master mix provided with the kit. The resulting double-stranded cDNA was end-repaired, dA-tailing and ligated with NEBNext adaptors. Finally, libraries were enriched by 12 cycles of amplification and purified by Meg-Bind RxnPure Plus beads (Omega Biotek, Norcross, GA, USA).

treatment_protocol: The dominant follicle was sampled 63 ± 3 d post partum following a caudal epidural injection of 60 mg of lidocaine hydrochloride 2% (Aspen Veterinary Resources, Greely, CO, USA). The perineum and vulva were cleaned and disinfected with povidone iodine followed by 70% ethanol. Vagina lavage with 100 mL of 0.2% chlorohexidine was followed by two washes with 100 mL sterile 0.9% saline. An oocyte pick-up instrument including a 7.5 MHz convex ultrasound probe (Choice Medical, South Pasadena, FL, USA) was covered in a sanitary sleeve (IMV Technologies, Normandy, France) and introduced into the vagina with sterile lubricant. The ovary was visualized by ultrasound (Aloka SSD-500, Hitachi Healthcare Americas, Twinsburg, OH, USA), and the internal diameter of the dominant follicle was measured based on the average of two measurements at 90° angle of the diameters from the larger cross sectional area of the follicle. An 18 gauge needle attached to a tygon tube connected to a vacuum pump was introduced into the oocyte pick-up instrument and the dominant follicle aspirated into collection medium (Medium 199 with Earle’s Salts, 0.5% BSA, 20 mM HEPES, 2 mM sodium pyruvate, 10 IU/mL heparin 100 U/mL penicillin and 100 μg/mL streptomycin; all Fisher Scientific, Hampton NH). The needle was maintained inside the follicle and 10 mL of collection medium was infused through the needle to flush the follicle. The volume of aspirate was recorded prior to centrifugation at 300 ₓ g for 10 min to separate the follicular fluid from granulosa cells, which were washed twice in sterile PBS. The follicular fluid and granulosa cells were stored at -80°C.

tag: tissue

value: blood

tag: location

value: University of Florida Dairy Unit

value: lactation, female


title: H9.KO.3 repl2


title: GM_HYP_A_H3K27me3_ChIPSeq


title: EPG350_AGA

description: control

tag: condition

value: AGA

tag: gender

tag: gestational age (wk)

tag: birth weight (g)


title: GM_NOR_B_H3K27me3_ChIPSeq

value: C2C12 cells


title: GM_NOR_A_RNASeq


title: GM_NOR_A_input DNA


title: H9.KO.1 repl1

tag: cell type


title: treatment rep6


title: treatment rep3


title: 191_tumor

tag: diagnosis

value: gbm

tag: patient id

value: Mesenchymal

tag: sentrix id

tag: sentrix position


title: treatment rep4


title: treatment rep2


title: 143_tumor

tag: patient number

tag: sample group

value: tumor


title: Patient1_Malignant

city: Iowa City

first: Ali

last: Jabbari

state: Iowa

address: 200 Hawkins Drive

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x Data was processed with the Cell Ranger pipeline, version 2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Malignant (CD3+CD4+CD5brightSSChi) and nonmalignant CD4 (CD3+CD4+CD5intSSCint) T cell populations were flow sorted in parallel. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sezary Syndrome T Cells


title: treatment rep5

tag: age


title: Patient1_Nonmalignant

value: Normal PBMC T Cells


title: EPG250_nonCU-SGA

description: test

value: nonCU-SGA

value: female

tag: birth height (cm)

tag: weight 12 mo (kg)

tag: height 12 mo (cm)


title: GM_NOR_A_H3K27me3_ChIPSeq

tag: tissue


title: treatment rep1

tag: location


title: control rep9


title: control rep8


title: Differentiated keratinocytes, replicate 5

source_name: human keratinocytes

extract_protocol:
Total RNA of about 4 μg was extracted using Trizol (ThermoFisher) and DNase (Ambion) then Ribo‐Zero (Illumina) treated. The remaining RNA fraction was bisulfite‐treated according to manufacturer's guidelines. Briefly, ribosomal depleted RNA was mixed with 70 μl of 40% sodium bisulfite pH 5.0 and DNA protection buffer (EpiTect Bisulfite Kit, Qiagen). The reaction mixture was incubated for three cycles of 5 min at 70°C followed by 1 h at 60°C and then desalted with Micro Bio‐spin 6 chromatography columns (Bio‐Rad). RNA was desulphonated by adding an equal volume of 1 M Tris (pH 9.0) to the reaction mixture and incubated for 1 h at 37°C, followed by ethanol precipitation. Bisulfite converted RNA was treated with T4 PNK (New England Biolabs) to repair both 5’ and 3’ ends for library preparation. Repaired RNA quality and concentration was measured on a Bioanalyzer 2100 RNA nano‐chip (Agilent).
About 100 ng of RNA was used to generate Bisulfite‐seq libraries. Libraries were performed according to TruSeq Small RNA preparation kit (Illumina). RNA adapters were then ligated, reverse‐transcribed followed by 18‐cycle PCR amplification before sequenced.

treatment_protocol: Undifferentiated: Keratinocytes were cultured in low Ca++ KBMGold media for 4 days then collected for RNA isolation. Differentiated: After 2 days of culturing keratinocytes in low Ca++ GBMGold + factors, differentiation was started by chaning low Ca++ KBMGold medium to high Ca++ KBMGold medium. Media was changed every other day and differentiation was terminated at day 8 of differentiation.

tag: culture condition

value: 1.2mM Ca++ KBMGold+factors


title: Differentiated keratinocytes, replicate 4


title: Differentiated keratinocytes, replicate 3


title: Differentiated keratinocytes, replicate 2


title: control rep7


title: Differentiated keratinocytes, replicate 1


title: Undifferentiated keratinocytes, replicate 5

value: 0.06mM Ca++ KBMGold+factors


title: SDK_Polysome_RNA_Sample_B

city: Bengaluru

first: Sandeep

last: Eswarappa

state: Karnataka

address: C V Raman Avenue, Devasandra layout

department: Biochemistry

country: India

institute: Indian Institute of Science

data_processing:
Sequencing data quality was assessed using FastQC and MultiQC programs
Trim Galore was used to remove adapter sequences and low quality bases
Mitochondrial genome was removed from the reference genome while building the index. The processed reads were mapped to reference genome (GRCh38) using STAR 2 aligner
Number of reads mapped per gene was obtained using featureCounts program
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) values were calculated using R statistical program
Supplementary_files_format_and_content: Excel sheets with RPKM values

source_name: Erythrocytes

extract_protocol:
Red blood cells were isolated from whole blood. CD71 negative mature erythrocytes were isolated using CD71 magnetic beads based depletion. The cells were lysed using lysis buffer. RNA from this lysate was isolated using GeneJet RNA purification kit (Thermo Fisher Scientific) and corresponds to "Total RNA". For Polysome RNA, Toal erythrocytes were lysed using polysome buffer containing 2mM Dithiothreitol, 100μg/mL Cycloheximide, and 1% Triton X-100. The lysate was loaded on a sucrose gradient (10%-50%) and ultracentrifuged at 29000 RPM for 4 hours. The RNA from heavier fractions were isolated using the same kit as mentioned above and this RNA corresponds to "Polysome RNA".
The RNA library was prepared according to the protocol for Illumina sequencing

value: Whole Blood

value: Erythrocytes


title: Undifferentiated keratinocytes, replicate 4


title: Patient 3 C5

city: Changsha

first: Yeping

last: Dong

country: China

institute: Xiangya Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, circRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed circRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed circRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: NSCLC lung samples

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: NSCLC lung samples

tag: Sex

value: Female

value: 59 years


title: Patient 3 B5

source_name: normal lung samples

value: normal lung samples


title: Patient 2 C4


title: Patient 1 C3

value: 46 years


title: Patient 2 B4

value: 57 years


title: SDK_Total_RNA_Sample_B


title: control rep4

value: blood

value: University of Florida Dairy Unit

value: lactation, female


title: Undifferentiated keratinocytes, replicate 3


title: Undifferentiated keratinocytes, replicate 2


title: control rep5


title: control rep3


title: Patient 1 B3


title: control rep2


title: SDK_Total_RNA_Sample_A


title: SDK_Polysome_RNA_Sample_A


title: Undifferentiated keratinocytes, replicate 1


title: Intermediate_LB-3d2

organism:
Bacillus subtilis
Pseudomonas chlororaphis

source_name: PCL1606-Triple mut_LB

tag: gentoype/variation

value: PCL1606-Triple mut


title: control rep6


title: U87_N5C

city: Geneva

first: Ariel

last: Ruiz i Altaba

address: 1 rue Michel Servet

department: GEDEV

institute: University of Geneva Medical School

data_processing:
The sequencing reads were checked for quality using FastQC and were found to be of good quality. The reads were mapped to human genome hg38 using STAR aligner (STAR_2.5.2b) with gencode gtf annotation (gencode.v25.GRCh38.gtf) provided as guide.
The differential expression analyses were performed separately for U251 and U87 cell lines using DESeq2 software (DESeq2_1.20.0). A minimal filtering was applied before the differential analysis: only those genes were kept that are present with at least 1 reads in at least one of the control or cases samples. Significant differentially expressed genes were filtered using the criterion: adjusted p.value (padj) < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: nanep-rnaseq-diffExp-U87.tab : Differential Expression Results from DESeq2 for U87 cell line
Supplementary_files_format_and_content: nanep-rnaseq-diffExp-U251.tab : Differential Expression Results from DESeq2 for U251 cell line

source_name: U87 cell line

growth_protocol: Adherent culture in EMEM media supplemented with 10%FBS and 1xP/S

extract_protocol:
Total RNA extraction using Trizol.
Illimina TruSeq protocol

tag: cell line

value: glioblastoma

tag: grade

value: IV

value: brain


title: control rep1


title: Intermediate_LB-3d1


title: Sample 4_ETS2_Input_F

city: Berkeley

first: Richard

last: Harland

state: CA

address: Life Sciences Addition #3200

institute: University of California, Berkeley

description:
processed data file:
RHRK_F_S56
ChIPETS_CF_M2_treat_pileup.bw
ChIPETS_CF_M2_peaks.bed
Ets_common_peaks.bed

data_processing:
ChIP-seq reads were aligned to the Xenopus laevis genome version 9.1 assembly using bowtie 2.2.3.
Peaks were called using MACS2 using defalt settings
File with common peaks between replicate samples was created by R package ChipPeakAnno
bigwig files were created by first removing scaffolds from bedgraph files generated by MACS2, then with command, bedGraphToBigWig
Genome_build: http://www.xenbase.org/common/displayJBrowse.do?data=data/xl9_1
Supplementary_files_format_and_content:
ChIPETS_AD_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3.  Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_CF_M2_treat_pileup.bw: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4.  Bigwig was made by first removing scaffolds from bedgraph files generated by MACS2, then converted with nedGraphToBigWig command
ChIPETS_AD_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 1 and Input Control is Sample 3.
ChIPETS_CF_M2_peaks.bed: Peaks were called using MACS2 using default setings. ChIP sample is Sample 3 and Input Control is Sample 4.
Ets_common_peaks.bed: Common peaks were the intersect of peaks from Proccessed samples ChIPETS_AD_M2_peaks.bed and ChIPETS_CF_M2_peaks.bed using the ChIPpeakAnno R package.

organism: Xenopus laevis

growth_protocol: Embryos were cultured in 1/3MR until stage 11.5

extract_protocol:
Lysates were clarified from sonicated DNA and ETS2-tripple-FLAG bound DNA complexes were isolated with antibody.
Illumina TruSeq ChIP kit. Libraries were made by the UC Berkeley Functional Genomics Laboratory.

treatment_protocol: Embryos were injected with 750pg tripple-FLAG tagged ETS2 mRNA and collected mid-gastrulation (stage 11.5)

value: embryo

tag: injected with

value: tripple-FLAG tagged ETS2 mRNA

tag: time point

value: mid-gastrulation (stage 11.5)

tag: antibody


title: Sample 3_ETS2_Input_D

description:
processed data file:
RHRK_D_S54
ChIPETS_AD_M2_treat_pileup.bw
ChIPETS_AD_M2_peaks.bed
Ets_common_peaks.bed


title: U87_N5A


title: Sample 2_ETS2_ChIPseq_C

description:
processed data file:
RHRK_C_S53
ChIPETS_CF_M2_treat_pileup.bw
ChIPETS_CF_M2_peaks.bed
Ets_common_peaks.bed

value: FLAG, SIGMA F3165, Lot # SLBN8915V


title: U87_CT3


title: Sample 1_ETS2_ChIPseq_A

description:
processed data file:
RHRK_A_S51
ChIPETS_AD_M2_treat_pileup.bw
ChIPETS_AD_M2_peaks.bed
Ets_common_peaks.bed


title: la_p_cluster_3

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

data_processing:
Adapter Removal, Cutadapt v.1.11, Default parameters
Trimming, ERNE-filter v.1.4.6, default parameters
Alignment to Transcriptome Reference, TopHat V.2.0.5, default parameters
Transcript Quantification, Cufflinks V2.0.2, default parameters
Differential Expression analysis, Cuffdiff V2.0.2, default parameters
Genome_build: Transcriptome Build LAGI02, available as supplementary data at https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-230
Supplementary_files_format_and_content: We provide as processed data file the cuffdiff output of differential expression analysis

organism: Lupinus albus

extract_protocol:
Total RNA was extracted from three biological replicates of 12 root samples apices for control plants  and apices and cluster root for Pi and Fe deficient plants using the Spectrum™ Plant Total RNA Kit (Sigma Aldrich ).
cDNA library preparation and sequencing reactions were performed by IGA Technology Services s.r.l. (Udine, Italy). An amount of 2 μg of total RNA was used for library preparation following the Illumina protocol TrueSeq 2.0. Briefly, RNA was fragmented into fragment with an average of 500 bp. Then, mRNA was purified using poly-T beads. The first- and second-strand cDNAs were synthesized and end repaired. Adaptors were ligated after adenylation at the 3’ ends and cDNA templates were enriched by PCR. The 50 bp single end reads were obtained using an Illumina Hiseq2000 platform.

tag: group

value: Root Clusters of P Deprived Roots


title: U87_CT2


title: la_p_cluster_2


title: U87_CT1


title: la_fe_cluster_3

value: Root Clusters of Fe Deprived Roots


title: U251_N5B

source_name: U251 cell line

value: III-IV


title: U251_N5C


title: H9.KO.3 repl3

tag: cell type

value: human embryonic stem cells

tag: genotype/variation

value: Crispr /Cas9 mediated (NHEJ) InDel of exon9 of NSUN6 (deletion of 7nt on allele1 and 50 nt on allele 2 causes framshift and premature stop), clonal

tag: batch


title: la_fe_cluster_2


title: MpGL3ox#2-3

city: Noda-shi

first: Kengo

last: Morohashi

state: Chiba

address: 2641 Yamazaki, Morohashi Lab 3rd Floor at 6-go-kan

department: Applied Biological Science

institute: Tokyo University of Science

data_processing:
Sequence data was mapped onto the genome by bowtie2 and the number of fragments stuck with HTseq was measured.
The number of fragments stuck with Cuffdiff (version 2.2.1 ) was counted and the magnitude of the expression fluctuation was calculated.
Genome_build: JGI_3.1.fasta (http://marchantia.info/download/download/JGI_3.1.fasta.gz)
Supplementary_files_format_and_content: integrated replicates for calculation  "average FPKM" of each gene

organism: Marchantia polymorpha

source_name: MpGL3ox#2_Thallus at 3-week-old

growth_protocol: Marchantia polymorpha plants (ecotype Tak-1) were grown at 22°C and under the continuous light conditions on half-strength Gamborg's B5 medium. A total of nine pieces of the thalli (approximately 5 mm x 5 mm size) were cut out and collected at 3 weeks.

extract_protocol:
Three independent biological replicates were done. Total RNA was extracted using the Nucleo Spin® RNA Plant (MACHEREY-NAGEL).
According to manufactor's instruction (Illumina TruSeq RNA kit Part # 15008136 Rev. A)

treatment_protocol: no treatment

tag: ecotype

value: MpGL3 ectopic expression line #2

tag: age

value: 3 week old

value: Thallus


title: la_fe_apex_3

value: Root Apices of Fe Deprived Roots


title: MpGL3ox#3-1

source_name: MpGL3ox#3_Thallus at 3-week-old

value: MpGL3 ectopic expression line #3


title: la_fe_cluster_1


title: U251_N5A

value: glioblastoma


title: MoGL3ox#3-2


title: la_fe_apex_2


title: U251_CT3


title: la_fe_apex_1


title: U87_N5B

value: IV


title: U251_CT2

value: brain


title: MoGL3ox#3-3


title: Tak-1-3

source_name: WT_Thallus at 3-week-old

value: Wild type


title: la_controll_3

value: Control Plants


title: la_p_cluster_1


title: MpGL3ox#2-1


title: Tak-1-2


title: U251_CT1


title: la_controll_2


title: 1606-LB-3d2

organism: Pseudomonas chlororaphis


title: MoGL3ox#2-2


title: la_controll_1


title: 1606-LB-3d1


title: Tak-1-1


title: FL2_SWED-015.1_6R04C02

status: Public on Mar 21 2019

city: Uppsala

first: Lars

last: Feuk

address: Husargatan 3

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio 2011.1
Average Beta and Unmethylated and methylated signal intensities are in Series supplementary files

source_name: genomic DNA from frontal cortex post-mortem brain tissue

extract_protocol: genomic DNA was extracted using the QIAmp DNA Mini Kit (Qiagen, cat no./ID: 51306)

value: frontal cortex

tag: gender

value: M

tag: disease state

value: schizophrenic


title: CEP_C1.7_10R05C02

tag: tissue

value: X

value: CHECK


title: FL2_A161/00.1_6R06C02

value: control


title: FL2_A008/97.1_6R05C01

value: F


title: CEP_C1.7_10R06C02


title: FL2_SWED-022.1_6R06C01


title: FL2_A271/93.1_3R06C02


title: FL2_AN08082.1_6R04C01


title: FL2_SD033/10.1_6R05C02


title: FL2_SWED-009.1_3R05C02


title: FL2_A292/09.1_3R06C01


title: FL2_SWED-002.1_3R05C01


title: FL2_A321/94.1_3R04C02


title: FL2_SD029/11.1_3R04C01


title: shRNAseq_pool2_LS_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description:
PCR-product (from genomic DNA)
shRNAseq_counttable_pool2_represented_only.csv

data_processing:
Library strategy: shRNA screen
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For shRNA screen analysis, pre-normalized fastq files were mapped to a custom generated reference database containing all shRNA sequences that were used in the shRNA screen. Mapping was done using Bowtie v1.1.1 not allowing any mismatches.
Reads per reference database entry (= unique combination of shRNA-sequence ID and Ensemble gene ID of the targeted gene) were counted. Rawcounts for all replicates and conditions were combined in a count-table. Based on the counts, relevant fold-changes were calculated and a Z-score statistic was applied in order to compare results from the two separately screened shRNA pools and to determine cut-offs for hit selection.
genome_build: N/A
Supplementary_files_format_and_content: Count matrix containing an identifier  (= unique combination of shRNA-sequence ID and Ensemble gene ID of the targeted gene) and the counts for all sufficiently represented shRNAs of all samples. Two separate counttables were generated. One for each of the two separately screened shRNA library pools.

source_name: SH-EP-NMYCER

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
Genomic DNA was extracted from harvested cells using DNAzol reagent (Invitrogen) following the suppliers manual.
To retrieve shRNA sequences that have previously been integrated into the genomic host DNA via lentiviral transduction, custom PCR-primers were used that spcifically bind to pGIPZ vector sequences flanking the shRNA hairpin sequence. A PCR (24 cycles) was done for with the genomic DNA as template to amplify the shRNA sequences. PCR products were gel-purified and finally libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).

treatment_protocol: SH-EP-NMYCER cells were treated with 200nM 4-OHT or EtOH for 3h. Lentiviruses expressing a shRNA targeting BRCA1 were produced by transfection of pGIPZ plasmid together with the packaging plasmid psPAX.2, and the envelope plasmid pMD2.G into HEK293TN cells. Virus-containing supernatant was harvested 24 h and 48 h after transfection. SH-EP cells were infected with lentiviral supernatants in the presence of 4ug ml   1 polybrene (Sigma-Aldrich) for 24 h. Cells were selected for two days with puromycin (2 ug ml-1) and afterwards plated for the experiment. Where indicated, cells were treated with 10nM flavopiridol or 5uM etoposide for 2 h. shRNA sequences against BRCA1 (#1: TTCGCGTTGAAGAAGTACAAAA, #2: GCAGATAGTTCTACCAGTAAAA, SCR: GTGAGCGATCTCGCTTGGGCG) were taken from Fellmann et al., 2013. For the shRNA screen, SH-EP-NMYCER cells were lentivirally infected with either of two pGIPZ-based shRNA library pools. Following puromycin-selection, the cells were treated with 100 nM 4-OHT or EtOH continuously for 2 weeks.

value: SH-EP-NMYCER

tag: treatment

tag: shRNA


title: znf_mut_10x

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

description: 10x single cell transcriptomes

data_processing:
Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics.
Raw BCL files from Illumina nextseq were demultiplexed into paired end, gzip-compressed FASTQ files using cellranger mkgastq.
Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read.
Reads were aligned to a zebrafish reference transcriptome(ENSEMBL Zv10, release 82 reference transcriptome) and transcript counts quantified for each annotated gene.
10bp UMI on th eleft read was used to collapse PCR duplicates.
Genome_build: GRCz10
Supplementary_files_format_and_content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene.

organism: Danio rerio

source_name: zebrafish brain

extract_protocol:
Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium
10x chromium

value: Forebrain

tag: developmental stage

value: znf mutant


title: znf_wt_10x

description: 10x single cell transcriptomes

value: znf wild type


title: fetalOvary_Input-rep2

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description: input ChIP-seq on pools of E14.5 mouse ovaries

data_processing:
Sequenced reads were filtered to retain only those with average base quality score >20.
Filtered reads were mapped against the mm10 reference genome via bowtie v1.2 with parameter "-m 1".
Alignments were deduplicated with MarkDuplicates.jar from the Picard tools suite v1.110.
For visualization of read depth, each uniquely-mapped non-duplicate read was extended to a length of 200nt.  Depth tracks were  generated via BEDTools genomeCoverageBed v2.24.0, normalized to 10 million reads, then converted to bigWig format with UCSC utility bedGraphToBigWig .
Peak were identified by HOMER v4.9 with parameters "-style factor -fdr 0.00001 -tbp 0 -inputtbp 0" using merged replicates.  Peaks were then re-defined as 300mers centered on the called peak midpoint.
Genome_build: mm10
Supplementary_files_format_and_content: Depth tracks in bigWig format.
Supplementary_files_format_and_content: Peaks in BED format.

source_name: E14.5 XX gonads

extract_protocol:
Ovaries from E14.5 CD1 embryos were separated from the mesonephros, snap-frozen, and stored at -80°C. Two independent ChIP-seq experiments were performed by Active Motif Inc. using 20-30 ug of shared chromatin from different pools of embryonic ovaries (n=80-100 ovaries/ChIP), and 4 ug of FOXL2 antibody (Novus, NB100-1277).
Libraries were prepared by Active Motif Inc.

treatment_protocol: CD1 mice were time-mated overnight and checked for a vaginal plug the next morning. Noon of the day when the vaginal plug was detected was considered as embryonic day E0.5. Pregnant females were euthanized at E14.5 and embryos were collected

tag: strain

value: ovaries


title: FL2_AN01235.1_3R03C02


title: fetalOvary_FOXL2-rep2

description:
FOXL2 ChIP-seq on pools of E14.5 mouse ovaries
FOXL2_ChIP.peaks.bed.gz


title: shRNAseq_pool2_LS_rep1

tag: cell line


title: fetalOvary_FOXL2-rep1


title: fetalOvary_Input-rep1


title: FL2_SWED-014.1_3R03C01


title: FL2_A016/93.1_3R02C02


title: shRNAseq_pool2_LU_rep1

value: EtOH


title: FL2_AN05874.1_3R02C01


title: shRNAseq_pool2_EU_rep2


title: shRNAseq_pool2_EU_rep1


title: FL2_A046/94.1_2R06C01


title: FL2_AN12916.1_3R01C01


title: FL2_A278/96.1_2R05C02


title: shRNAseq_pool1_LS_rep2

description:
PCR-product (from genomic DNA)
shRNAseq_counttable_pool1_represented_only.csv


title: FL2_A033/11.1_2R04C02


title: shRNAseq_pool1_LU_rep2


title: shRNAseq_pool1_LS_rep1


title: shRNAseq_pool1_EU_rep2


title: shRNAseq_pool1_EU_rep1


title: FL2_AN03389.1_3R01C02


title: FL2_A218/93.2_2R06C02


title: shRNAseq_pool1_LU_rep1


title: shRNAseq_pool2_LU_rep2


title: FL2_SWED-013.1_2R04C01


title: ChIP-Rxseq_2_plusOHT_shSCR_RNAPII

description: ChIP-Rx-seq

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-Rx-seq, reads were mapped independently to the human hg19 and murine mm10 (spike-in) genome and a spike-in normalization factor was calculated by dividing the number of mapped reads of the spike-in of the smallest sample by the number of mapped reads of the spike-in for each sample. For each sample, this factor was multiplied by the number of reads that map to the human genome and all bam files were adjusted to this read count.
.bedgraph files were generated using bedtools genomecov.
Genome_build: hg19
Supplementary_files_format_and_content: spike-in-normalized .bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

extract_protocol:
Cells were mixed with 10% murine KPC cells and treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

value: shSCR

value: RNAPII (A10, Santa Cruz, sc-17798)


title: FL2_A077/00.1_2R03C01


title: FL2_A032/95.1_2R03C02


title: FL2_SWED-001.1_2R02C02


title: ChIP-Rxseq_2_plusOHT_shBRCA1#1_RNAPII

description: ChIP-Rx-seq


title: FL2_A048/09.1_2R05C01


title: FL2_A063/12.1_2R02C01


title: ChIP-Rxseq_2_minusOHT_shBRCA1#1_RNAPII

description: ChIP-Rx-seq


title: ChIP-Rxseq_2_plusOHT_shSCR_input

description:
ChIP-Rxseq_2_spikeNorm_input.bedgraph.gz
ChIP-Rx-seq


title: ChIP-Rxseq_2_minusOHT_shSCR_input


title: ChIP-Rxseq_2_minusOHT_shBRCA1#1_input


title: FL2_A150/01.1_2R01C02


title: FL2_A282/96.1_2R01C01


title: pancreatic islets, Tlr2/Tlr4 DKO, 7 months HFD intervention, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.40.1).

source_name: Pancreatic islets, isolated from a Tlr2/Tlr4 double knockout mouse, fed a high-fat diet for 7 months

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Tlr2/Tlr4 double knockout (DKO) mice on a C57BL/6 background and wildtype C57BL/6 mice were bred, reared, and housed in a specific pathogen-free facility. Mice were fed a high-fat diet (60% fat, 20% carbohydrate, and 20% protein, D12492 Research Diets Inc.) starting at 6 weeks of age for either 5 weeks or 7 months. Throughout the experiment animals had free access to water and feed.

extract_protocol: Total RNA was extracted using Trizol and RNA miniprep kit (Sigma RTN350) with DNaseI digestion (Roche).

treatment_protocol: At the indicated  time points, i.e.  5 weeks or 7 months after being fed with the HFD, wildtype C57BL/6 mice and Tlr2/Tlr4 DKO mice were sedated, pancreatic islets were collected, and snap-frozen in liquid nitrogen until RNA isolation.

value: Pancreatic islets

tag: genotype

value: Tlr2/Tlr4 double knockout

tag: time of hfd intervention

value: 7 months


title: ChIP-Rxseq_plusOHT_shSCR_NMYC

tag: antibody

value: NMYC (B8.4.B, Santa Cruz, sc-53993)


title: pancreatic islets, Tlr2/Tlr4 DKO, 7 months HFD intervention, replicate 2


title: ChIP-Rxseq_2_minusOHT_shSCR_RNAPII

description: ChIP-Rx-seq


title: ChIP-Rxseq_plusOHT_shBRCA1#1_NMYC


title: FL2_A042/01.1_8R06C01

value: frontal cortex


title: ChIP-Rxseq_minusOHT_shSCR_input

description: Processed data for input samples are available on GSM3477899.


title: ChIP-Rxseq_plusOHT_shSCR_input


title: ChIP-Rxseq_plusOHT_shBRCA1#1_input


title: pancreatic islets, Tlr2/Tlr4 DKO, 7 months HFD intervention, replicate 1


title: ChIP-Rxseq_minusOHT_shBRCA1#1_input


title: pancreatic islets, wild type, 7 months HFD intervention, replicate 3

source_name: Pancreatic islets, isolated from a wild type (C57BL/6) mouse, fed a high-fat diet for 7 months

value: wild type


title: pancreatic islets, Tlr2/Tlr4 DKO, 7 months HFD intervention, replicate 4


title: ChIP-Rxseq_2_plusOHT_shBRCA1#1_input


title: FL2_SWED-012.1_8R05C01

value: M

value: schizophrenic


title: pancreatic islets, wild type, 7 months HFD intervention, replicate 4


title: pancreatic islets, wild type, 7 months HFD intervention, replicate 2


title: pancreatic islets, Tlr2/Tlr4 DKO, 5 wks HFD intervention, replicate 2

source_name: Pancreatic islets, isolated from a Tlr2/Tlr4 double knockout mouse, fed a high-fat diet for 5 wks

value: 5 wks


title: ChIPseq_pRRL-NMYC_input

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Peak calling was done with MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6 (BRCA1) and 1e-11 (NMYC) and keep-dup parameter = 5. bedgraph files were generated using bedtools genomecov.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

source_name: SH-EP

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <500 bp using a Branson sonifier. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Biorad Experion system. The amount of library DNA was quantified using a picogreen assay

value: SH-EP

value: pRRL-NMYC


title: ChIPseq_pRRL-NMYC_NMYC


title: pancreatic islets, Tlr2/Tlr4 DKO, 5 wks HFD intervention, replicate 1


title: FL2_SWED-006.1_8R06C02


title: ChIP-Rxseq_minusOHT_shSCR_NMYC

value: SH-EP-NMYCER


title: ChIP-Rxseq_minusOHT_shBRCA1#1_NMYC


title: FL2_SWED-027.1_8R04C02


title: ChIPseq_3_input

value: shSCR, shBRCA1#1


title: ChIPseq_3_plusOHT_shBRCA1#1_DCP1A

value: DCP1A (Santa Cruz, sc-100706)


title: FL2_A268/93.1_8R04C01

value: control


title: FL2_A124/94.1_8R05C02

value: F


title: FL2_SWED-021.1_8R03C02


title: ChIPseq_3_plusOHT_shSCR_DCP1A

value: shSCR


title: pancreatic islets, wild type, 5 wks HFD intervention, replicate 4

source_name: Pancreatic islets, isolated from a wild type (C57BL/6) mouse, fed a high-fat diet for 5 wks

value: Pancreatic islets


title: ChIPseq_3_minusOHT_shBRCA1#1_DCP1A

value: EtOH


title: ChIPseq_2_input

value: etoposide,flavopiridol


title: pancreatic islets, wild type, 7 months HFD intervention, replicate 1

value: 7 months


title: pancreatic islets, wild type, 5 wks HFD intervention, replicate 2


title: pancreatic islets, wild type, 5 wks HFD intervention, replicate 3


title: pancreatic islets, wild type, 5 wks HFD intervention, replicate 1


title: ChIPseq_2_plusOHT_BRCA1

value: BRCA1 (Bethyl, A300-000A)


title: FL2_A066/95.1_8R03C01

value: frontal cortex


title: FL2_A324/94.1_8R02C02


title: ChIPseq_2_plusOHT_flavopiridol_BRCA1

value: flavopiridol


title: FL2_AN02738.1_8R02C01

value: schizophrenic


title: ChIPseq_3_minusOHT_shSCR_DCP1A


title: ChIPseq_2_plusOHT_etoposide_BRCA1

value: etoposide