title: DA-4

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

description: Apoptotic superntant from human Jurkat Lymphoma that express a uncleavable dominant-negative Panx1 (Panx1-DN)

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GCF_000223135.1_CriGri_1.0_genomic
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

source_name: Fibroblast

growth_protocol: alpha-MEM + 1% BSA + 1% PSQ + 10mM HEPES

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform

treatment_protocol: Jurkat lymphoma cells were UV C treated at 1500mJ then cultured for 4h prior supernatant collection for treatment with phagocytes

tag: cell line

value: Apoptotic Supernatant (Panx1-DN)


title: Root, M-81E-salt3

status: Public on Mar 19 2020

type: SRA

city: Jinan

last: Sui

state: Shandong

address: Wenhua East Road

department: College of Life Sciences

country: China

institute: Shandong normal university

library_source: transcriptomic

data_processing:
Generally, after total RNA is extracted from the whole transcriptome, two sequencing libraries are constructed: a small RNA library smaller than 50 nt and a de-rRNA strand specific library larger than 200 nt. The first library uses the SE50 on-boarding strategy, and the second library uses the 150PE on-boarding strategy.
Small RNA libraries smaller than 50 nt were single-ended sequenced on Illumina Hiseq 2500 on LC-BIO (Hangzhou, China), and de-rRNA strand-specific libraries larger than 200 nt were paired-end sequenced on Illumina Hiseq 4000 (lc-bio, China) .
First, Cutadapt was used to remove reads containing linker contamination, low quality bases, and undetermined bases. We used Bowtie2 and Tophat2 to map the reads to the genome of sweet sorghum, and used StringTie to assemble the mapped reads for each sample. Then, merge using a perl script to build a complete transcriptome.
After the final transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts.
Genome_build: sorghum bicolor Ensembl release58
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Sorghum bicolor

source_name: Root

extract_protocol:
Sweet sorghum in the three-leaf stage was subjected to salt treatment for 24 hours, and then RNA was harvested using Trizol reagent. The TruSeq Small RNA Sample Preparation Kit (Illumina, San Diego, USA) was used with 1 ug total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: three-leaf phase

tag: tissue

value: root

tag: stress

value: salt


title: Root, M-81E-CK1

value: control


title: DA-3

city: New York

state: New York

country: USA

organism: Cricetulus griseus

tag: treatment


title: Metastatic gastric cancer sample 1

type: RNA

city: Shenyang

first: Yong

last: Zhou

state: Liaoning

address: 4 Chongshan Road

institute: the Fourth Affiliated Hospital of China Medical University

description: Test

data_processing:
LncRNA array analysis was conducted by GeneStudy_1.0.030.1023 according to the manufacturer’s instruction.
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

organism: Homo sapiens

source_name: Fresh gastric cancer specimen

label_protocol: 250 ng RNA was reverse transcribed to cDNA in 20 μl system by Reverse Transcription Reaction kit (Thermo Fisher Scientific). Real-time PCR was performed using the Mx3000P system (Thermo Fisher Scientific). PCR was conducted as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s, and 72 °C for 20s.

growth_protocol: The primary cancer tissues and the synchronous lymph node metastasis were collected and stored in liquid nitrogen immediately. Subsequently, samples were reviewed by independent pathologists.

extract_protocol: Total RNA was extracted by the RNA mini kit (GE Healthcare, Chicago, IL, US) according to the manufacturer’s protocol.

tag: sample type

value: Metastatic gastric cancer


title: Metastatic gastric cancer sample 3

description: Test


title: Metastatic gastric cancer sample 2

description: Test


title: Reference spike ins

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Human Jurkat cells, mouse 32D cells (spike-ins)

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.1.0).
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: Human: GRCh38/h38, Mouse: mm10
Supplementary_files_format_and_content: Matrices: corrected transcript per million (TPM) matrices. Data in mtx format, row names (genes), and column names (barcodes)
Supplementary_files_format_and_content: CellAnnotation_final.tsv; Annotation of cell types to barcodes

organism:
Homo sapiens
Mus musculus

source_name: Human Jurkat cells, mouse 32D cells

growth_protocol: Human islets were extracted cadaveric donors and shipped using the Islet Integrated Distribution Program (IIDP) Mouse islets were extracted and shipped from the Collombat laboratory. Both human and mouse islets were cultured in CMRL media supplemented with 10% FBS and 1X Glutamax, and mantained in culture at 37 C in a 5% CO2 humidified atmosphere.

extract_protocol:
Islet dissociation was performed by incubating the islets in accutase for 20 min at room temperature. Reaction was stopped by adding CMRL media with 10% FBS. The dissociated islets were filtered through a 40 µm filter to obtain a single-cell suspension.
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Islets were treated with 10muM Artemether, 100 muM GABA, 10 muM FoxO inhibitor and DMSO as control for 36 and 72 hours.

value: Human Jurkat cells, mouse 32D cells

tag: treatment time

tag: replicate


title: HX17_CB1

city: Changsha

first: Xin

last: He

state: Hunan

address: No. 1 Nongda Road, Furong district, Changsha, China

institute: Hunan Agricultural University

description:
Rapeseed variety HX17
HX17 treated with 4℃ replicate 1.
processed data file: gene.description_fin.txt

data_processing:
Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data/reads were obtained by removing reads containing adapter or reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content for the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http://www.genoscope.cns.fr/brassicanapus/data/) directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end reads were aligned to the reference genome using Hisat2 v2.0.4. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thus providing better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to the gene. FPKM considers the combined effects of sequencing depth and gene length for the read counts, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Brassica napus “Aarmor-bzh”; Genoscope Brassica_napus_v4.1.chromosomes.fa, Brassica_napus.annotation_v5.gff3, Brassica_napus.annotation_v5.cds.fa, Brassica_napus.annotation_v5.pep.fa files.
Supplementary_files_format_and_content: gene.description_fin.txt: Tab-delimited text file includes read counts and FPKM values for all samples.

organism: Brassica napus

source_name: leaves

extract_protocol:
Samples were collected and flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions.

tag: variety

value: leaves

value: 4 degree Celsius


title: Localized gastric cancer sample 3

description: Control

value: Localized gastric cancer


title: HX17_CB2

description:
Rapeseed variety HX17
HX17 treated with 4℃ replicate 2.
processed data file: gene.description_fin.txt


title: Localized gastric cancer sample 2

description: Control


title: HX17_MA3

description:
Rapeseed variety HX17
HX17 control A replicate 3.
processed data file: gene.description_fin.txt

value: Control


title: DA-2


title: WT-Rituximab-Day8_rep1

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was accomplished using STAR (Dobin et al. 2013) against the CHO genome (GCF_000419365.1_C_griseus_v1.0) with default parameters.
HTSeq (Anders et al. 2015) was used to quantify the expression of each gene. We performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: C_griseus_v1.0 (GCF_000419365.1)
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

source_name: Ovary

growth_protocol: Batch cultivation was performed in 250 mL shake flasks containing 60-80 mL CD-CHO medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 8 mM L-glutamine (Life Technologies) and 0.2% anti-clumping reagent (Life Technologies). Prior to inoculation into fed-batch bioreactors, cells were adapted from CD-CHO medium to FortiCHO (Gibco, Carlsbad, CA, USA), OptiCHO (Gibco), or ActiPro (GE Healthcare, Chicago, IL, USA) medium during three passages. All media were supplemented with 1% Anti-Anti (Life Technologies), 0.1% anti-clumping agent (Life Technologies) and 8 mM L-glutamine (Lonza, Basel, Switzerland).

extract_protocol:
Cell cultures were resuspended in RLT buffer (Qiagen) and kept at -80°C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion. RNA was eluted in 40µl of nuclease free water (RNAse/DNAse free); concentration was measured on Qubit and the purity was checked on Fragment Analyzer. Complementary DNA synthesis was obtained from 1 μg of RNA using the High capacity cDNA RT kit (Thermo Fisher scientific) as per manufacturer’s instructions.
Samples were diluted to 60ng/µL in 50µL and library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: 20020595), according to manufacturer’s protocol.

value: CHO-S

value: Ovary

tag: time point

value: Day 8


title: Localized gastric cancer sample 1

description: Control


title: DA-1


title: ACE2 library sorted for low binding to the RBD of S protein from SARS-CoV-2 (Replicate 2; PCR fragments A and B)

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description:
ACE2 nCoV-S-Low Replicate 2 (AB)
processed data file: ACE2_deep_mutagenesis.xlsx

data_processing:
Data was analyzed using python scripts in the Enrich package: http://depts.washington.edu/sfields/software/enrich/
Fuser command (Fragment A):
python Paired_read_fuser.py --path directory_A/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq tccaccattgaggaacaggccaagacatttttggacaagtttaaccacgaagccgaagacctgttctatcaaagttcacttgcttcttggaattataacaccaatattactgaagagaatgtccaaaacatgaataatgctggggacaaatggtctgcctttttaaag --read1_overlap_start 49 --read1_overlap_end 217 --read2_overlap_start 61 --read2_overlap_end 229 --mode B
Fuser command (Fragment B):
python Paired_read_fuser.py --path directory_B/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq cttgcttcttggaattataacaccaatattactgaagagaatgtccaaaacatgaataatgctggggacaaatggtctgcctttttaaaggaacagtccacacttgcccaaatgtatccactacaagaaattcagaatctcacagtcaagcttcagctgcaggctcttcagcaa --read1_overlap_start 28 --read1_overlap_end 202 --read2_overlap_start 53 --read2_overlap_end 227 --mode B
Fuser command (Fragment C):
python Paired_read_fuser.py --path directory_C/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq agattttggacaaatctgtactctttgacagttccctttggacagaaaccaaacatagatgttactgatgcaatggtggaccaggcctgggatgcacagagaatattcaaggaggccgagaagttctttgtatctgttggtcttcctaatatgactcaaggattctgggaaaat --read1_overlap_start 31 --read1_overlap_end 205 --read2_overlap_start 48 --read2_overlap_end 222 --mode B
Fuser command (Fragment D):
python Paired_read_fuser.py --path directory_D/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq gtctgccatcccacagcttgggacctggggaagggcgacttcaggatccttatgtgcacaaaggtgacaatggacgacttcctgacagctcatcatgagatggggcatatccagtatgatatggcatatgctgcacaaccttttctgctaagaaatggagctaatgaaggattccatgaagctgttggggaaatcatgtca --read1_overlap_start 25 --read1_overlap_end 226 --read2_overlap_start 30 --read2_overlap_end 231 --mode B
Fuser command (Fragment E Read 1):
python Paired_read_fuser.py --path directory_E1/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq ttcctgctcaaacaagcactcacgatt --read1_overlap_start 49 --read1_overlap_end 76 --read2_overlap_start 26 --read2_overlap_end 212 --mode R1
Fuser command (Fragment E Read 2):
python Paired_read_fuser.py --path directory_E2/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq --read2 sample_R2.fastq --wtseq ttccatgtttctaatgattactcattcattcgatattacacaagg --read1_overlap_start 49 --read1_overlap_end 235 --read2_overlap_start 161 --read2_overlap_end 206 --mode R2
Aligner command (Fragment A):
python2.7 Fused_read_aligner.py --path directory_A/ --infile sample_R1.fast_B_qc1 --referenceDNA tccaccattgaggaacaggccaagacatttttggacaagtttaaccacgaagccgaagacctgttctatcaaagttcacttgcttcttggaattataacaccaatattactgaagagaatgtccaaaacatgaataatgctggggacaaatggtctgcctttttaaag --referenceAA STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLK --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment B):
python2.7 Fused_read_aligner.py --path directory_B/ --infile sample_R1.fast_B_qc1 --referenceDNA cttgcttcttggaattataacaccaatattactgaagagaatgtccaaaacatgaataatgctggggacaaatggtctgcctttttaaaggaacagtccacacttgcccaaatgtatccactacaagaaattcagaatctcacagtcaagcttcagctgcaggctcttcagcaa --referenceAA LASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQ --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment C):
python2.7 Fused_read_aligner.py --path directory_C/ --infile sample_R1.fast_B_qc1 --referenceDNA agattttggacaaatctgtactctttgacagttccctttggacagaaaccaaacatagatgttactgatgcaatggtggaccaggcctgggatgcacagagaatattcaaggaggccgagaagttctttgtatctgttggtcttcctaatatgactcaaggattctgggaaaat --referenceAA RFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWEN --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment D):
python2.7 Fused_read_aligner.py --path directory_D/ --infile sample_R1.fast_B_qc1 --referenceDNA gtctgccatcccacagcttgggacctggggaagggcgacttcaggatccttatgtgcacaaaggtgacaatggacgacttcctgacagctcatcatgagatggggcatatccagtatgatatggcatatgctgcacaaccttttctgctaagaaatggagctaatgaaggattccatgaagctgttggggaaatcatgtca --referenceAA VCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMS --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment E Read 1):
python2.7 Fused_read_aligner.py --path directory_E1/ --infile sample_R1.fast_R1_qc1 --referenceDNA ttcctgctcaaacaagcactcacgatt --referenceAA FLLKQALTI --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode R1
Aligner command (Fragment E Read 2):
python2.7 Fused_read_aligner.py --path directory_E2/ --infile sample_R1.fast_R2_qc1 --referenceDNA ttccatgtttctaatgattactcattcattcgatattacacaagg --referenceAA FHVSNDYSFIRYYTR --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode R2
MapCounts command: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios command Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts command: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues_in_fragment
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution. Also includes the total reads for each mutation in the naive plasmid library.

source_name: Synthetic coding sequences

extract_protocol:
Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from one of two gene-specific primers. The ACE2 cDNA was PCR amplified as five separate fragments that together fully cover the diversified regions of ACE2 present in the SSM library. The PCR fragments were amplified for Illumina sequencing in two rounds. In the first round, primer overhangs added sequences for annealing to the Illumina sequencing primers. In the second round, primer overhangs added unique barcodes and Illumina adaptors. To determine the frequencies of mutations in the naive library, the library plasmid DNA was also used as a template for PCR amplification and Illumina sequencing.
Gene-specific primers for reverse transcription with Accuscript were: ACE2_RevTrans_411R (CAGTACTGTAGATGGTGCTC) for fragments A and B, and ACE2_RevTrans_1685R (CAGTTTCTGTCCAGCTTCTG) for fragments C, D and E.
Primer pair for 1st round of PCR (Fragment A):
MiSeq_CCR5_myctag_F (TCTTTCCCTACACGACGCTCTTCCGATCTCGAGCAAAAGCTGATCTCAG) and Illumina_ACE2_286_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTGGGCAAGTGTGGACTGT)
Primer pair for 1st round of PCR (Fragment B):
Illumina_ACE2_147_for (TCTTTCCCTACACGACGCTCTTCCGATCTAGCCGAAGACCTGTTCTATC) and Illumina_ACE2_354_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTGAGAGCACTGAAGAC)
Primer pair for 1st round of PCR (Fragment C):
Illumina_ACE2_827_for (TCTTTCCCTACACGACGCTCTTCCGATCtccctgctcatttgcttggt) and Illumina_ACE2_1044_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAACATTTCCTGGGTCC)
Primer pair for 1st round of PCR (Fragment D):
Illumina_ACE2_1044_for (TCTTTCCCTACACGACGCTCTTCCGATCTggacccaggaaatgttcaga) and Illumina_ACE2_1270_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTAGGTGTGGCTGCAGAAAG)
Primer pair for 1st round of PCR (Fragment E):
Illumina_ACE2_1304_for (TCTTTCCCTACACGACGCTCTTCCGATCttggtcttctgtcacccgat) and Illumina_ACE2_1621_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCTGCTTGACAAAGTGCTTC)
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors):
MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a NovaSeq 6000 using a 2x250 nt paired end protocol.

treatment_protocol: Expi293F cells were transfected using expifectamine (ThermoFisher) with a pCEP4 episomal plasmid-based library encoding variants of myc-tagged ACE2 diluted with a 1500-fold excess of carrier DNA; these transfection conditions ensure that most cells express no more than a single ACE2 sequence variant, thereby linking genotype to phenotype. Cells were harvested 24 h post-transfection and co-incubated with anti-myc-Alexa 647 and cleared medium from cells secreting RBD-sfGFP. For independent replicates 1 and 2, the RBD-sfGFP-containing medium was diluted 1/40- and 1/20-fold, respectively. Cells were washed and sorted by FACS. Gates were drawn for the main population of viable cells using forward and side scatter properties and exclusion of the fluorescent viability dye DAPI. The top 67% of ACE2-positive cells based on Alexa 647 fluorescence were further gated to collect the top 15% and bottom 20% of cells for bound RBD-sfGFP relative to ACE2 expression.

tag: cell type

tag: protein

tag: sort gate

value: Bottom 20% of cells for bound RBD-sfGFP relative to surface ACE2 expression


title: HX17_MA2

description:
Rapeseed variety HX17
HX17 control A replicate 2.
processed data file: gene.description_fin.txt


title: ACE2 library sorted for low binding to the RBD of S protein from SARS-CoV-2 (Replicate 2; PCR fragments C, D and E)

description:
ACE2 nCoV-S-Low Replicate 2 (CDE)
processed data file: ACE2_deep_mutagenesis.xlsx


title: HX17_MA1

description:
Rapeseed variety HX17
HX17 control A replicate 1.
processed data file: gene.description_fin.txt


title: ACE2 library sorted for low binding to the RBD of S protein from SARS-CoV-2 (Replicate 1; PCR fragments C, D and E)

description:
ACE2 nCoV-S-Low Replicate 1 (CDE)
processed data file: ACE2_deep_mutagenesis.xlsx


title: FA-4

description: Apoptotic superntant from human Jurkat Lymphoma

value: Apoptotic Supernatant


title: Ler (Cy5) vs cuc1 cuc2 (Cy3)

city: Kumamoto

first: Mitsuhiro

last: Aida

address: 2-39-1 Kurokami, Chuo-ku

country: Japan

institute: Kumamoto University

description: Technical replicate 1 of 2

hyb_protocol: Labeled cRNAs were mixed with control targets and applied on microarray after fragmentation. Hybridization was carried out at 60°C for 17 hrs. Slides were washed with 6xSSC, 0.005% Triton X-102 at room temperature for 10 min and then with 0.1xSSC, 0.005% Triton X-102 at 4°C for 5 min. Slides were dried with N2.

scan_protocol: Slides were scanned with Agilent Technologies Microarray Scanner at 10 μm resolution.

data_processing: Agilent Feature Extraction Software was used for background subtraction and Linear & LOWESS normalization.

organism: Arabidopsis

source_name: Cy3-cuc1 cuc2

label_protocol: cDNA synthesis and labeling of cRNA were carried out using Low RNA Fluorescent Linear Amplification Kit (Agilent Technologies). Labeled cRNA was purified using RNeasy mini spin columns (QIAGEN).

growth_protocol: Parent plants (cuc1-1 cuc2-1/+) were grown on soil at 23°C under continuous light.

extract_protocol: Embryos (approx. 100 embryos/sample) were excised in 6% glucose and fixed overnight in Ethanol:Acetic acid solution (3:1, vol:vol) at 4°C. Fixed embryos were washed with ethanol and homogenized using a pestle in a 1.5 ml tube. Total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: No treatment.

tag: genotype

value: cuc1 cuc2

tag: tissue and developmental stage

value: torpedo stage embryo

tag: test or reference

value: test

growth_protocol: Parent plants (Ler) were grown on soil at 23°C under continuous light.

value: Ler

value: reference


title: 2-Carboxyanthraquinone treatment group rep1

city: shenzhen

first: song

last: zhiman

address: Shenzhen Guangdong

department: college of life sciences and oceanography

institute: shenzhen university

description:
E1_8_1
24h mature static biofilm bacteria treated by 100 μg/mL of  2-Carboxyanthraquinone for another 8h static cultivate

data_processing:
Raw data were converted into Fastq format. The number of transcripts in each sample was calculated based on the number of fragments per kilobase of transcript per million fragments mapped (FPKM)
Cuffnorm software was used to calculate the FPKM value for each sample, and the values were log2 transformed. DESeq software was used to calculate the differential gene transcripts between different samples.
Genome_build: Staphylococcus aureus A9754 (ensembl version 44)
Supplementary_files_format_and_content: tab-delimited text file includes all genes expression

organism: Staphylococcus aureus

source_name: bacteria

growth_protocol: The biofilm was grow in LB broth with 0.5% glucose for 24h to get the mature biofilm, and then  rinsed twice by 1×PBS, followed by adding fresh LB broth with 0.5% glucose and  compounds or DMSO respectively

extract_protocol: Trizol reagent

treatment_protocol: three were negative congtrol in DMSO, three were treated by 100ug/ml  2-Carboxyanthraquinone  and  three were treated by 100ug/ml Rhein.

tag: phenotype

value: methicillin-resistant


title: 2-Carboxyanthraquinone treatment group rep3

description:
E1_8_3
24h mature static biofilm bacteria treated by 100 μg/mL of  2-Carboxyanthraquinone for another 8h static cultivate

tag: strain


title: FA-3

tag: cell line


title: 2-Carboxyanthraquinone treatment group rep2

description:
E1_8_2
24h mature static biofilm bacteria treated by 100 μg/mL of  2-Carboxyanthraquinone for another 8h static cultivate


title: ACE2 library sorted for low binding to the RBD of S protein from SARS-CoV-2 (Replicate 1; PCR fragments A and B)

description:
ACE2 nCoV-S-Low Replicate 1 (AB)
processed data file: ACE2_deep_mutagenesis.xlsx


title: Ler (Cy3) vs cuc1 cuc2 (Cy5)

description: Technical replicate 2 of 2

source_name: Cy5-cuc1 cuc2


title: HX17_FA2

description:
Rapeseed variety HX17
HX17 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 2.
processed data file: gene.description_fin.txt

tag: tissue

value: -4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: FA-1


title: ACE2 library sorted for high binding to the RBD of S protein from SARS-CoV-2 (Replicate 2; PCR fragments C, D and E)

description:
ACE2 nCoV-S-High Replicate 2 (CDE)
processed data file: ACE2_deep_mutagenesis.xlsx

value: Top 15% of cells for bound RBD-sfGFP relative to surface ACE2 expression


title: HX17_FA3

description:
Rapeseed variety HX17
HX17 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 3.
processed data file: gene.description_fin.txt

value: leaves


title: FA-2


title: Rhein treatment group rep2

description:
D1_8_2
24h mature static biofilm bacteria treated by 100 μg/mL of Rhein for another 8h static cultivate

value: Rhein


title: HX17_FA1

description:
Rapeseed variety HX17
HX17 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 1.
processed data file: gene.description_fin.txt


title: ACE2 library sorted for high binding to the RBD of S protein from SARS-CoV-2 (Replicate 2; PCR fragments A and B)

description:
ACE2 nCoV-S-High Replicate 2 (AB)
processed data file: ACE2_deep_mutagenesis.xlsx


title: HX17_CA3

description:
Rapeseed variety HX17
HX17 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 3.
processed data file: gene.description_fin.txt

value: 4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: ACE2 library sorted for high binding to the RBD of S protein from SARS-CoV-2 (Replicate 1; PCR fragments C, D and E)

description:
ACE2 nCoV-S-High Replicate 1 (CDE)
processed data file: ACE2_deep_mutagenesis.xlsx


title: FL-3

description: Live cell supernatant from humanJurkat Lymphoma

value: Live Supernatant


title: ACE2 library sorted for high binding to the RBD of S protein from SARS-CoV-2 (Replicate 1; PCR fragments A and B)

description:
ACE2 nCoV-S-High Replicate 1 (AB)
processed data file: ACE2_deep_mutagenesis.xlsx


title: HX17_CA2

description:
Rapeseed variety HX17
HX17 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 2.
processed data file: gene.description_fin.txt


title: Control rep2

description:
C1_8_2
24h mature static biofilm bacteria treated by DMSO for another 8h static cultivate

value: Control


title: FL-2


title: FL-4


title: Rhein treatment group rep1

description:
D1_8_1
24h mature static biofilm bacteria treated by 100 μg/mL of Rhein for another 8h static cultivate


title: HX17_CA1

description:
Rapeseed variety HX17
HX17 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 1.
processed data file: gene.description_fin.txt


title: Control rep1

description:
C1_8_1
24h mature static biofilm bacteria treated by DMSO for another 8h static cultivate


title: Library of ACE2 variants (PCR fragments A and B)

description:
ACE2 Naive (Fragments AB)
Plasmid DNA
processed data file: ACE2_deep_mutagenesis.xlsx


title: Library of ACE2 variants (PCR fragments C, D and E)

description:
ACE2 Naive (Fragments CDE)
Plasmid DNA
processed data file: ACE2_deep_mutagenesis.xlsx


title: Rhein treatment group rep3

description:
D1_8_3
24h mature static biofilm bacteria treated by 100 μg/mL of Rhein for another 8h static cultivate


title: Control rep3

description:
C1_8_3
24h mature static biofilm bacteria treated by DMSO for another 8h static cultivate


title: FL-1


title: sample_51b_neurons

status: Public on Mar 18 2020

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description:
Bisulfite-converted DNA
Sample 51a and 51b were bioinformatically pooled for downstream analysis
see ample_51_neurons_diff_cpg_level.txt

library_source: genomic

data_processing:
Basecalls was performed using CASAVA
After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark with paired end mode and default setting . For ACCEL-NGS Methyl-Seq DNA Library, as recommended by the manufacturer, 15 bp were trimmed on 5' and 3' of both reads.
Duplicate reads were removed using Picard tools and reads with more than 10% unconverted CHG or CHH cytosines were filtered out
SNP calling was performed with BisSNP using default settings, except for the maximum coverage filter set at 200. Heterozygous SNPs with less than 5 reads per allele were filtered out. In addition, SNP with multiple mapping positions were filtered out, as well as SNPs with more than one minor allele with allele frequency>0.05. or deviating significantly from Hardy-Weinberg equilibrium based on exact tests corrected for multiple tests. C/T and G/A SNPs were assessed after filtering out reads mapping to the C/T strand.
ASM calling was performed after separating the SNP-containing reads by allele using R. After Bismark methylation extractor is applied, CpG methylation calls by allele are retrieved using allele tagged read IDs. Paired reads with ambiguous SNP calling (i.e., called as REF allele on one paired end and ALT allele on the other) were discarded.
genome build: GRCh37
processed data files format and content: Processed files per sample contain difference in methylation percentage at the CpG level between the alternate and reference alleles for each SNPs associated with high confidence ASM (observed in >2 biological samples) if the given sample was informative. The columns include chromosome, start and end of the CpG (reported on positive strand), difference in methylayion percentage and SNP ID. The unique identifier in these files is the CpG coordinate AND SNP ID.

molecule: genomic DNA

source_name: neurons

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
For Nextera transposase-based library approach, genomic DNA was first tagmented using Nextera XT transposome and end repair was performed using 5mC. After bisulfite conversion, Illumina adapters and custom bisulfite converted adapters are attached by limited cycle PCR. Illumina TruSeq DNA Methylation Kit and ACCEL-NGS Methyl-Seq DNA Library kit were used according to the manufacturer’s instructions.

tag: subject id

tag: cancer status

value: non-cancer

tag: organ

value: brain

tag: library

value: Nextera transposase-based library


title: sample_68_T_cells

description: Bisulfite-converted DNA

source_name: T cells

value: blood


title: sample_52_neurons

description: Bisulfite-converted DNA


title: sample_53_neurons

description: Bisulfite-converted DNA


title: sample_48_glial_cells

description: Bisulfite-converted DNA

source_name: glial cells


title: sample_47_glial_cells

description: Bisulfite-converted DNA


title: sample_54_neurons

description: Bisulfite-converted DNA


title: sample_78_T_cells

description: Bisulfite-converted DNA


title: HCT116_3

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FASTQ files containing the raw sequence reads from polyA-seq were de-barcoded by allowing up to 2 mismatches between the first 6 bases and one of 4 barcodes. Reads with more than 2 mismatches from a barcode used in the experiment were discarded. The next 6 bases were designed to contain a random hexamer for de-duplication of PCR duplicates. This sequence was removed from the read and annotated into the read name. These de-barcoded FASTQ files, one per individual sample/replicate, are provided in this record.
Next, sequenced polyA tails were removed from the reads by detecting the first instance of 4 consecutive As with no more than 1 non-A base in the following 6 base pairs. The remaining sequences were aligned to the hg19 genome build using bowtie 2.2.5. Uniquely mapping alignments were retained by requiring a mapping quality (MAPQ) score > 20. PCR duplicates were removed by collapsing all alignments with identical random hexamer annotations and the same alignment position into a single alignment. Reads due to predicted internal priming of genomic A were removed by filtering all alignments with at least 7 of 10 or 6 consecutive downstream A bases. Processing regions were computed by merging all regions with a coverage of at least 10 reads in one experiment within 10 bp of each other into contiguous genomic ranges.
Genome_build: hg19
Supplementary_files_format_and_content: A text file is provided that contains the genomic coordinates for each processing region (PR) and the un-normalized count of the number of overlapping reads forming the PR. There is one column for each sample, named the same as the samples in this record.

molecule: polyA RNA

source_name: HCT116 colon cancer cell line

growth_protocol: HCT116 and DKO cells were grown in McCoy's 5A (Modified) Medium (Thermo Fisher Scientific) with 10% FBS (Atlanta Biologicals) at 37°C and 5% CO2. Cells were harvested at 75-95% confluence by PBS wash, scraping into PBS, pelleting at 500g for 2 minutes, and storage of cell pellet at -80°C.

extract_protocol:
Total cellular RNA was prepared from 4 x 10 cm plates of each cell type using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instructions. Poly(A)+ RNA was selected from 10 ug of total cellular RNA using oligo(dT)25 Dynabeads (Thermo Fisher Scientific) according to manufacturer’s instructions.
This poly(A) site sequencing technique was derived by modification of an existing technique for ribosome footprinting (Ingolia et al., Science, 2009, PMID: 19213877). Poly(A)+ RNA was fragmented by addition of 2X fragmentation buffer to 1X final concentration (6 mM Na2CO3, 44 mM NaHCO3, 1 mM EDTA) and incubation at 95°C for 40 minutes. Fragmentation was stopped on ice, and then RNA was precipitated with 300 mM NaOAc, pellet paint, and isopropanol. After resuspension in stop solution/PAGE loading buffer (Affymetrix), RNA fragments were separated on 15% PAGE/urea gels then 50-100 nt RNA was purified by excision and maceration of gel fragments followed by elution of RNA into diffusion buffer (20 mM Tris pH=7.5, 250 mM NaOAc, 1 mM EDTA, 0.25% SDS) at 37°C for 45 min with shaking. cDNA copies of poly(A)+ RNA fragments were made using SuperScript III (Thermo Fisher Scientific), and 1 of 4 anchored oligo(dT) primers (/5Phos/NNNNNNXXXXXXCCGCATCGTCCTCCCTCCCTATAGTGACTCGTATTA/iSp18/CACTCA/iSp18/CCGCTGGAAGTGACTGACACTTTTTTTTTTTTTTTTTTTTVN; N=degenerate bases; XXXXXX=4 different sample barcodes TGACCA, GCCAAT, CTTGTA, or AAGTGC ; V=C, G, or T) at 48°C for 30 minutes according to manufacturer’s instructions. Residual RNA was degraded by addition of NaOH to 0.1 M and incubation at 98°C for 15 minutes. 2X stop solution/PAGE loading buffer (Affymetrix) was added and cDNA was separated from unextended oligo(dT) primer on 10% PAGE/urea gels then 120-170 nt cDNA was purified by excision and maceration of gel fragments and elution of cDNA into diffusion buffer (20 mM Tris pH=7.5, 250 mM NaOAc, 1 mM EDTA, 0.25% SDS) at 50°C for 45 min with shaking. cDNA was precipitated using 300 mM NaOAc, pellet paint, and isopropanol, then circularized using CircLigase (Epicentre) according to manufacturer’s instructions. Circularization causes primer sequences for amplification to face each other, allowing cDNA libraries of poly(A) sites to be amplified for sequencing using primers that contain machine adaptors (AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG; CAAGCAGAAGACGGCATACGACCGCTGGAAGTGACTGACAC). PCR was carried out using Phusion DNA polymerase (Thermo Fisher Scientific) according to manufacturer’s instructions (initial denaturation 98°C 30 sec; cycle at 98°C 10 sec, 58°C 30 sec, 72°C 30 sec). Optimum cycle number was empirically determined using a small aliquot of cDNA library, then the rest of each cDNA library was amplified using this cycle number. Amplified libraries (150-200 bp) were gel purified on 2% agarose gels using a Gel Purification Kit (Qiagen), slightly altering manufacturer’s instructions. Briefly, gel slices were dissolved in buffer QG at room temperature instead of 50°C and all optional washes were carried out for 5 minutes each as recommended for sensitive applications. Final libraries were sequenced using a custom primer (CTATGGATACTTAGTCAGGGAGGACGATGCGG) on Illumina HiSeq 2000 at Genome Quebec.

tag: dna methylation

value: methylation competent


title: HCT116_4


title: DKO_4

source_name: Double knock out of DNMT1(-/-) and DNMT3b(-/-) derived from HCT116 cells

value: methylation defective


title: DKO_3


title: HCT116_2


title: HCT116_1


title: DKO_2


title: DKO_1


title: KO_1

city: Daejun

first: Bo-Ran

last: Choi

address: E22 3F 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute of Basic Science

data_processing:
Paired-end reads, 50 bp in length, were generated on an Illumina HiSeq 2500 system. To analyze the RNA-seq data, reads were quality checked and trimmed using the programs fastqc and fqtrim. Reads were then mapped to the mouse genome mm10 using the spliced alignment program Tophat2 v2.1.1, and assembled into transcripts using Cufflinks v2.2.1. Transcript assemblies across all samples were merged with Cuffcompare v.2.2.1, using GENCODE v.M5 as reference, to create a set of gene and transcript annotations that was later used in the differential analyses. Lastly, Cuffdiff v2.2.1 was run on each pairwise comparison to determine statistically significant differentially expressed genes (significance cutoffs: p-value <= 0.05, q-value <= 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: gtf

organism: Mus musculus

source_name: Gde2KO_spinal cord

extract_protocol:
poly-adenylated mRNA was extracted using a Qiagen RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: age

value: 5 weeks

value: spinal cord

tag: region of tissue

value: Lumbar


title: WT_1

source_name: WT_spinal cord

value: WT


title: WT_2


title: KO_3


title: WT_3


title: KO_2


title: C4

city: Yayoi, Bunkyo

first: Shoko

last: Kobayashi

state: Tokyo

institute: Univ. of Tokyo

hyb_protocol: Hybridization mixture containing 15 ug of cRNA fragment was injected into the DNA chip and hybridized at 45 °C for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After washing and staining, the arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by Factor Analysis for Robust Microarray Summarization (FARMS) method using R2.10.1.

label: biotin

source_name: control

label_protocol: Streptavidin labeled with phycoerythrin was bound to the biotinylated cRNA from 250 ng total RNA.

extract_protocol: Total RNA was isolated from the hippocampus using the NucleoSpin RNA Kit (Macherey-Nagel, Betheleham, PA, USA) according to the manufacturer's instructions.

value: hippocampus

value: 10 month old


title: R4

source_name: dose


title: R3


title: C1


title: C2


title: R2


title: C3


title: R1


title: OT01_P3_H04

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
Reads were aligned to the reference mouse genome (mm10) using the Hisat 2 aligner
Transcript abundances were estimated using CuffNorm against the mouse GENCODE reference transcriptome (vM8)
Relative abundances were converted to absolute estimates of gene expression using the Monocle2 CENSUS approach and used as input for the dpFeature workflow.
Genome_build: mm10
Supplementary_files_format_and_content:
expression_matrix.tsv - Tab-separated matrix of monocle2 CENSUS estimates of mRNA copies per cell.
cellAnnotation.tsv - Tab-separated dataframe of cellular phenotype annotations
featureAnnotation.tsv - Tab-separated dataframe of feature (gene) annotations

source_name: OT-2A-Flp::fdGFP+ sorted oxytocinergic neuron_P23_Magnocellular_FG-negative

growth_protocol: Experiments were conducted in 3 - 7 week-old male mice. Flp-dependent GFP reporter mice (Stock # 32038) were obtained from the Mutant Mouse Resource Center. Transgenic mice were bred in-house and weaned at 3 weeks of age. Oxytocin-2A-Flp-optimized (OT-2A-Flp) knock-in mice were generated by Cyagen Biosciences (Santa Clara, CA). The stop codon in exon 3 of the endogenous OT gene was replaced with a 2A-Flp-optimized (FlpO) construct. All mice were maintained on a on a 12:12h natural light dark cycle, starting at 7:30am with food and water ad libitum. All procedures were conducted in accordance with protocols approved by the Johns Hopkins Animal Care and Use Committee.

extract_protocol:
OT-2A-Flp::fdGFP mice were weaned at P21 and given i.v. injections of FluoroGold on that and the following day. At P23 mice were sacrificed. Brains were rapidly removed and 250 µm thick coronal slices (n = 7 mice) containing the paraventricular nucleus of the hypothalamus were sectioned using a Leica VT-1200s vibrating microtome in ice-cold ACSF solution containing the following (in mM): 124 NaCl; 2.5 KCl; 1.2 NaH2PO4; 24 NaHCO3; 5 HEPES; 13 glucose; 2 MgSO4’; 2 CaCl2, oxygenated with carbogen gas (95% O2 and 5% CO2) to pH 7.3 - 7.4. To microdissect the PVN, slices were placed in a petri-dish containing ice-cold, oxygenated ACSF solution and the PVN was identified using the 3rd ventricle and other structural markers. Following dissection, tissue was placed into 2.6 mL equilibrated Papain DNase-I solution. The dissociation protocol was similar to Chevée et al., 2018, itself an adaptation from the trehalose-enhanced neuronal isolation protocol using the Worthington Papain Dissociation System (Worthington Biochemical Corporation). The following modifications from Chevée et al., 2018 were made: a single low speed centrifugation (300xg for 5 min) was performed after dissociation, and the pellet was resuspended in 250 µL media (DMEM, 5% trehalose (w/v), 25 µM AP-V, 0.4 mM kynurenic acid, 6 µL of 40 U/µl RNase inhibitor) and 250 uL of EBSS#2 (EBSS, 25 mM AP-V, 100 mM Kynurenic acid, ovomucoid protease inhibitor with BSA, DNase-I, 5% w/v Trehalose, 40 U/µl RNase inhibitor) at room temperature. Following resuspension, single-cell suspensions were introduced into a FACS machine (Beckman Coulter MoFlo Cell Sorter).     Neurons were sorted based on fluorescence (GFP+/FG- or GFP+/FG+) directly into individual wells of a 96-well plate containing 2 µL Smart-Seq2 lysis buffer + RNAase inhibitor, 1µL oligo-dT primer, and 1 µL dNTPs(48). Three plates were collected across 2 separate dates (Plate 1: n = 1 mouse, 32 GFP+/FG- neurons and 47 GFP+/FG+ neurons; Plate 2: n = 1 mouse, 32 GFP+/FG- neurons and 33 GFP+/FG+ neurons; Plate 3: n = 5 mice, 25 GFP+/FG- neurons and 48 GFP+/FG+ neurons). Following the sort, plates were briefly spun-down in a table-top microcentrifuge and immediately placed on dry ice. Single-cell lysates were kept at -80°C until cDNA library preparation.
Library preparation and amplification of single-cell samples was performed using a modified version of the Smart-Seq2 protocol as described in Cheveé et. al 2018. Individual libraries were quality controlled, pooled, and sequenced on two lanes of an Illumina HiSeq 2500 sequencer to an average depth of 1,424,499 ±77,731 paired-end 50bp reads per neuron.

treatment_protocol: Stereotaxic injections into the nucleus accumbens (NAc; distance from bregma: anterior +1.54 mm; lateral ±1.065 mm; ventral - 4.1 mm)) were performed under general ketamine-medetomidine anesthesia using a stereotaxic instrument. For i.v. labeling of magnocellular OT neurons with FG, 1 or 2 tail-vein injections of 15 µl 4% FG (Fluorochrome) diluted in sterile saline were performed using a syringe and 25-gauge needle at least 24 hours prior to sacrifice. To facilitate i.v. injections, mice were placed under a warm lamp for 3-5 min and were briefly restrained using a tail vein restrainer (TV-150; Braintree Scientific).

tag: ot subtype

value: Magnocellular

tag: fluorogold staining


title: OT01_P3_G08

source_name: OT-2A-Flp::fdGFP+ sorted oxytocinergic neuron_P23_Magnocellular_FG-positive


title: OT01_P3_H03

source_name: OT-2A-Flp::fdGFP+ sorted oxytocinergic neuron_P23_Parvocellular_FG-negative

value: Parvocellular


title: OT01_P3_H10


title: OT01_P3_H08


title: OT01_P3_G07


title: OT01_P3_H12


title: OT01_P3_H05


title: OT01_P3_F07


title: OT01_P3_F12


title: OT01_P3_H09


title: OT01_P3_E11


title: jejunum_CTL_2

city: Sherbrooke

first: François

last: Boudreau

address: 3201, rue Jean-Mignault

country: Canada

institute: Université de Sherbrooke

description:
Gene expression data from adult mice fed a HFD
2141 JD

hyb_protocol: The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours). After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

scan_protocol: Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody Vector Laboratories). The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples.

data_processing:
Transcriptome Analysis Console (TAC) software (4.0.2.15)
RMA

source_name: Raw jejunum

label_protocol: Total RNA has been isolated by Ambion ToTALLY RNA kit from total jejunum biopsies

growth_protocol: Mice were maintained in pathogen free environnement.

extract_protocol: Total RNA with Ambion Totally RNA

treatment_protocol: Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice

tag: genotype

value: jejunum


title: jejunum_KO_1

description:
Gene expression data from adult mice fed a HFD
2121 JD

value: hnf4alpha mutant


title: jejunum_CTL_3

description:
Gene expression data from adult mice fed a HFD
2186 JD

value: Control


title: jejunum_CTL_1

description:
Gene expression data from adult mice fed a HFD
2109 JD


title: OT01_P3_E10


title: jejunum_KO_3

description:
Gene expression data from adult mice fed a HFD
2125 JD


title: jejunum_KO_2

description:
Gene expression data from adult mice fed a HFD
2122 JD


title: OT01_P3_E04


title: OT01_P3_E07


title: OT01_P3_E02


title: OT01_P3_E08


title: OT01_P3_G04


title: OT01_P3_F10


title: OT01_P3_G01


title: OT01_P3_E01


title: OT01_P3_G05


title: OT01_P3_E06


title: OT01_P3_D12


title: OT01_P3_D09


title: OT01_P3_C06


title: OT01_P3_C05


title: OT01_P3_C10


title: OT01_P3_C04


title: OT01_P3_C03


title: OT01_P3_C12


title: OT01_P3_C11


title: OT01_P3_D08


title: OT01_P3_C02


title: OT01_P3_B07


title: OT01_P3_B11


title: OT01_P3_B09


title: OT01_P3_B10


title: OT01_P3_B12


title: OT01_P3_A12


title: OT01_P3_A09


title: OT01_P3_A07


title: OT01_P3_A11


title: OT01_P3_A06


title: OT01_P3_D11


title: OT01_P3_D10


title: OT01_P3_A01


title: OT01_P3_A02


title: OT01_P2_F11


title: OT01_P3_A03


title: OT01_P2_F10


title: OT01_P2_F09


title: OT01_P3_B08


title: OT01_P3_A08


title: OT01_P2_F08


title: OT01_P2_F07


title: OT01_P2_F06


title: OT01_P2_F05


title: OT01_P2_E09


title: OT01_P2_E07


title: OT01_P2_E05


title: OT01_P2_E06


title: OT01_P2_E04


title: OT01_P2_D11


title: OT01_P2_E02


title: OT01_P2_D12


title: OT01_P2_E03


title: OT01_P2_E10


title: OT01_P2_D10


title: OT01_P2_D08


title: OT01_P2_D04


title: OT01_P2_D02


title: OT01_P2_D07


title: OT01_P2_D06


title: OT01_P2_D05


title: OT01_P2_D03


title: OT01_P2_D01


title: OT01_P2_E11


title: OT01_P2_C06


title: OT01_P2_C07


title: OT01_P2_E01


title: OT01_P2_D09


title: OT01_P2_F04


title: OT01_P2_C05


title: OT01_P2_C02


title: OT01_P2_B08


title: OT01_P2_B07


title: OT01_P2_B05


title: OT01_P2_B06


title: OT01_P2_A06


title: OT01_P2_B04


title: OT01_P2_A07


title: OT01_P2_B03


title: OT01_P2_A11


title: OT01_P1_G11


title: OT01_P2_A05


title: OT01_P1_G09


title: OT01_P1_G10


title: OT01_P2_C03


title: OT01_P1_G06


title: OT01_P1_G08


title: OT01_P1_G07


title: OT01_P2_B01


title: OT01_P1_G04


title: OT01_P1_G05


title: OT01_P1_G02


title: OT01_P1_G03


title: OT01_P1_F07


title: OT01_P2_A04


title: OT01_P1_F06


title: OT01_P1_F03


title: OT01_P1_F05


title: OT01_P1_F02


title: OT01_P1_E07


title: OT01_P1_E05


title: OT01_P1_E02


title: OT01_P1_E03


title: OT01_P1_E01


title: OT01_P1_D12


title: OT01_P1_D10


title: OT01_P1_D09


title: OT01_P1_D11


title: TNBC T097

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Arrays were scanned on an Affymetrix GeneChip 3000 7G scanner according to the manufacturer’s instructions.

data_processing: We normalized gene expression data using GCRMA and log2 transformation.

source_name: Primary triple negative breast cancer tissue

label_protocol: Approximately two micrograms of purified total RNA was used in the One-Cycle Eukaryotic Target Labeling Assay.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

tag: subject status

value: triple negative breast cancer (TNBC) patient

tag: ajcc stage

tag: vital status

value: Alive

tag: follow-up time (month)

tag: suv

value: tumor tissue


title: TNBC T098

tag: tissue


title: TNBC T100


title: OT01_P1_D08

tag: strain


title: OT01_P1_D04


title: TNBC T099


title: OT01_P1_D05


title: TNBC T096


title: TNBC T094


title: TNBC T093


title: TNBC T091


title: TNBC T095


title: TNBC T090


title: OT01_P1_E06


title: TNBC T087


title: TNBC T089


title: TNBC T088


title: TNBC T092


title: TNBC T085


title: TNBC T086


title: TNBC T081


title: TNBC T084


title: TNBC T077


title: TNBC T073


title: OT01_P1_D06


title: OT01_P1_C03


title: OT01_P1_C02


title: OT01_P1_D03


title: OT01_P1_D02


title: OT01_P1_C09


title: OT01_P1_B07


title: OT01_P1_B05


title: OT01_P1_B12


title: OT01_P1_C08


title: TNBC T078


title: TNBC T071

value: Dead


title: TNBC T076


title: OT01_P1_B04


title: TNBC T079


title: OT01_P1_C05


title: OT01_P1_A12


title: TNBC T069


title: OT01_P1_B06


title: OT01_P1_B01


title: OT01_P1_B02


title: OT01_P1_A10


title: OT01_P1_A03


title: KP_T1_25

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
KP_T1_IGO_10027_25_S25
KP LUAD cells (untransduced parental population).
SE-76

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a).
Genome-wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table.
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: FSR_RNAseq.featureCounts.cnt.csv: Comma-separated text file includes raw count values for each sample.

source_name: Murine KrasG12D/+;Trp53-/- (KP) lung adenocarcinoma (LUAD) cells

growth_protocol: All cells were maintained in a humidified incubator at 37°C with 5% CO2, and grown in DMEM supplemented with 10% FBS and 100 IU/ml penicillin/streptomycin. Cells sampled here were cultured for 120hrs post-transduction, at which point RNA was harvested.

extract_protocol:
RNeasy Mini Kit (Qiagen)
Poly-A RNA-Seq / Single-end 76

treatment_protocol: 1 million KP LUAD cells were seeded in 10cm plates and immediately transduced with retroviral supernatants and 8ug/mL polybrene. Cells were grown for 48hrs before purifying using fluorescence activated cell sorting (FACS). All transductions were done in triplicate. Following transduction, stable GFP+ populations were purified by FACS on a FACSAria (BD Biosciences). 120 hours post-transduction, total RNA was isolated using the RNeasy Mini Kit (Qiagen) following standard manufacturer protocols.

tag: cell type

value: KP LUAD cells

tag: oncotype

tag: stably transduced

value: Untransduced parental population

tag: time point

value: 120 hours post-transduction

tag: sorting strategy

value: GFP+


title: R277K_E282K_B_23

description:
696_B_IGO_10027_23_S23
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate B.
SE-76

tag: genotype/variation

tag: replicate

value: B


title: TNBC T063

tag: age


title: TNBC T072


title: TNBC T066


title: TNBC T070


title: TNBC T062


title: TNBC T067


title: TNBC T060


title: TNBC T068


title: TNBC T061


title: TNBC T059


title: R277K_E282K_A_22

description:
696_A_IGO_10027_22_S22
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate A.
SE-76

value: A


title: TNBC T065


title: TNBC T055


title: TNBC T054


title: TNBC T058


title: OT01_P1_A08

tag: ot subtype

tag: fluorogold staining


title: OT01_P1_A07


title: E284D_B_17

description:
206_B_IGO_10027_17_S17
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate B.
SE-76


title: E284D_A_16

description:
206_A_IGO_10027_16_S16
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate A.
SE-76


title: R277T_E284D_B_20

description:
691_B_IGO_10027_20_S20
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate B.
SE-76


title: E284D_C_18

description:
206_C_IGO_10027_18_S18
KP LUAD cells stably transduced with pMIG-p53-E284D Replicate C.
SE-76

value: C


title: R277K_E282K_C_24

description:
696_C_IGO_10027_24_S24
KP LUAD cells stably transduced with pMIG-p53-R277K-E282K Replicate C.
SE-76


title: R277T_C_12

description:
41_C_IGO_10027_12_S12
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate C.
SE-76


title: R277K_C_15

description:
51_C_IGO_10027_15_S15
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate C.
SE-76


title: R277T_E284D_C_21

description:
691_C_IGO_10027_21_S21
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate C.
SE-76


title: R277T_A_10

description:
41_A_IGO_10027_10_S10
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate A.
SE-76


title: TNBC T057

tag: subject status


title: TNBC T056

tag: ajcc stage


title: TNBC T049

tag: vital status


title: TNBC T045

tag: follow-up time (month)


title: TNBC T053

tag: suv


title: TNBC T044

tag: tissue


title: TNBC T042


title: TNBC T046


title: TNBC T052


title: TNBC T047


title: E282K_B_8

description:
12_B_IGO_10027_8_S8
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate B.
SE-76


title: R277K_A_13

description:
51_A_IGO_10027_13_S13
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate A.
SE-76


title: E282K_A_7

description:
12_A_IGO_10027_7_S7
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate A.
SE-76


title: WT_C_6

description:
WT_C_IGO_10027_6_S6
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate C.
SE-76


title: R277T_B_11

description:
41_B_IGO_10027_11_S11
KP LUAD cells stably transduced with pMIG-p53-R277T Replicate B.
SE-76


title: R277T_E284D_A_19

description:
691_A_IGO_10027_19_S19
KP LUAD cells stably transduced with pMIG-p53-R277T-E284D Replicate A.
SE-76


title: TNBC T048


title: TNBC T051


title: E282K_C_9

description:
12_C_IGO_10027_9_S9
KP LUAD cells stably transduced with pMIG-p53-E282K Replicate C.
SE-76


title: TNBC T041


title: TNBC T043


title: TNBC T040


title: E_A_1

description:
E_A_IGO_10027_1_S1
KP LUAD cells stably transduced with pMIG-Empty - Replicate A.
SE-76

value: pMIG-Empty


title: TNBC T050


title: TNBC T037


title: E_B_2

description:
E_B_IGO_10027_2_S2
KP LUAD cells stably transduced with pMIG-Empty - Replicate B.
SE-76


title: WT_B_5

description:
WT_B_IGO_10027_5_S5
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate B.
SE-76


title: TNBC T038


title: TNBC T039


title: R277K_B_14

description:
51_B_IGO_10027_14_S14
KP LUAD cells stably transduced with pMIG-p53-R277K Replicate B.
SE-76


title: TNBC T034


title: WT_A_4

description:
WT_A_IGO_10027_4_S4
KP LUAD cells stably transduced with pMIG-WT-p53- Replicate A.
SE-76


title: E_C_3

description:
E_C_IGO_10027_3_S3
KP LUAD cells stably transduced with pMIG-Empty - Replicate C.
SE-76


title: vWAT, 20 weeks, H3K4me1, high fat diet, rep 2

city: Lausanne

first: Federica

last: Gilardi

state: Vaud

address: Lausanne 1015

department: CIG - Center of Integrative Genomics

country: Switzerland

institute: University of Lausanne

data_processing:
Basecalls performed using CASAVA version 1.82
ChIP-seq 100 bases Single-ended reads were aligned to mouse genome Ensemble GRCm38 (mm10) by Elandv2e
Tags were filtered by the threshold of 5 mismatchs and ambiguous mapping
ChiP-Cor (https://ccg.vital-it.ch/chipseq/chip_cor.php) was used to analyze the correlation between 5’ and 3’ tags position and determined the average ChIP fragment length for each sample
The mm10 genome was divided into 500 bases long consecutive, non-overlapping bins to calculate the ChIP signal. For each bin, each sample has its own value of tag density which is the AUC (area under the curve) created by the tags pilled-up , strand-shifted by half of the fragment length produced by ChIP-Cor. The bin values were scaled by the total tags for each sample and 30 pseudo-counts were added to stabilize the variance of low scores. The same quantifications were done for all the INPUT samples. All the values were then log2 converted.
The log2 scaled bin values of each ChIP sample and of the corresponding time-tissue-treatment INPUT sample were used to compute ratio-mean distribution. This distribution was sectioned into 200 step-wise proportions along the mean axis. Smoothing function lowess with smoother-span 0.2 was applied for only the negative-ratio bin population of each step-wise proportion. From the predicted distribution of smooth function, the mirrored bins were selected on the positive-ratio population. Distribution function was applied for this positive-ratio population with the  mean and standard deviation derived from smooth function. The p-values were adjusted for false discovery rate (Benjamini–Hochberg). All bins with adjusted p-value less than 0.05 were considered significant. Comparison was done for each replicates of ChIP sample over each replicate of INPUT sample, reapeated with shifted of half bin size (250 bases).
The significant bins in both replicates and both bin sets (non-shift and 250-shifted) were pooled into consistency analysis. A bin was considered consistently significant if it was found in both replicates, either in the same or shifted position. The final bin set was determined for each sample. All the collected bins for all time points, tissues, diet treatments and IP treatments were pooled and merged with maximum distant of 250–two bins separated by 250 bases would be merged–into significant regions.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from remaining tags and scaled by the total tag number for each sample

source_name: visceral adipose tissue

growth_protocol: C57/BL6 male, 4-wk-old (at time of sacrifice), mice were housed in  a 12 h light/12 h dark (LD) regimen  with water and food available ad libitum. All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age they were either shifted to a high fat diet containing 60% in fat (D12492, Research Diet) or kept in control diet for 1, 8 and 20 weeks.  At each time time point, 20 mice were sacrified using CO2. Subcutaneous and viceral adipose tissue were immediately collected, snap-frozen in liquid nitrogen and kept at −80°C for RNA extraction and chromatin preparation. For chromatin preparation, aliquats of 4 grams of adipose tissue were homogenized on dry ice and immediately crosslinked in 45ml of PBS containing 0.5% formaldehyde. All animal care and handling was performed according to the Swiss law for animal protection

extract_protocol:
The chromatin samples collected from different mice at the same time point were pooled, frozen in liquid nitrogen and stored at -80˚C. Chromatin was subjected to immunoprecipitation with an anti-POLR2B (Santa Cruz Biotechnology, H-201) antibody as described (Le Martelot et al. 2012). Immuno-precipitated complexes were collected by adsorption to ten µl of protein-A-Sepharose beads that had been pre-blocked with 10 µg/ml of salmon sperm DNA and BSA at 4˚C overnight. The beads were washed with dialysis buffer and ChIP wash buffer, as described. The immuno-precipitated complexes were eluted with 50 mM NaHCO3, 1% SDS, 1mM EDTA and 50 mM of Tris pH8 at 65°C, adjusted to 125 mM NaCl, and incubated at 65°C overnight to reverse the cross-links. After successive treatments with 10 µg/ml of RNase A and 20 µg/ml of proteinase-K, the samples were extracted with a NucleoSpin® Kit (Machery Nagel). The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen).  5-10 ng of DNA was used for the preparation of the library.  Libraries for ultra-high throughput sequencing were prepared   using Diagenode kit (C05010013) according to the manufacturer’s instruction and subjected PE sequencing in a HiSeq 2500.
Libraries for ultra-high throughput sequencing were prepared with the using Diagenode kit (C05010013) according to the manufacturer’s instruction.

treatment_protocol: All mice were fed  with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age a total of 170 and 180 mice were put on HFD (D12492, Research Diet) and chow diet (D12450J, Research Diet, respectively. Mice were sacrified after 1, 8 or 20 week of diet.

tag: strain

value: visceral (epididymal) white adipose tissue (VWAT)

value: 26 weeks old

tag: diet

value: High fat diet (D12492)

tag: time

value: 20 weeks

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: vWAT, 20 weeks, RNAPol-II, high fat diet, rep 1

value: RNAPol-II (Santa-Cruz, SC-67318)


title: vWAT, 20 weeks, RNAPol-II,control, rep 2

value: Control chow diet (D12450J)


title: vWAT, 20 weeks, RNAPol-II, high fat diet, rep 2


title: vWAT, 20 weeks, H3K4me1, high fat diet, rep 1


title: vWAT, 20 weeks, H3K27ac, high fat diet, rep 2

value: H3K27ac (Abcam, ab4729)


title: vWAT, 20 weeks, H3K4me1, control, rep 1


title: vWAT, 20 weeks, H3K4me1, control, rep 2


title: vWAT, 20 weeks, H3K27ac, high fat diet, rep 1


title: vWAT, 20 weeks, H3K27ac, control, rep 2


title: TNBC T035

value: triple negative breast cancer (TNBC) patient

value: Alive

value: tumor tissue


title: TNBC T036


title: TNBC T029


title: TNBC T024


title: TNBC T026


title: TNBC T025


title: TNBC T028


title: TNBC T031


title: TNBC T023

value: Dead


title: TNBC T018


title: TNBC T020


title: TNBC T015


title: TNBC T017


title: TNBC T019


title: TNBC T016


title: TNBC T021


title: vWAT, 20 weeks, DNA input, high fat diet, rep 2


title: vWAT, 20 weeks, H3K27ac, control, rep 1


title: vWAT, 20 weeks, DNA input, high fat diet, rep 1


title: scWAT, 20 weeks, RNAPol-II, high fat diet, rep 2

source_name: subcutaneous adipose tissue

value: subcutaneous (inguinal) white adipose tissue (scWAT)


title: vWAT, 20 weeks, DNA input, control, rep 2


title: vWAT, 20 weeks, DNA input, control, rep 1


title: scWAT, 20 weeks, RNAPol-II, high fat diet, rep 1


title: scWAT, 20 weeks, RNAPol-II,control, rep 2


title: scWAT, 20 weeks, RNAPol-II,control, rep 1


title: scWAT, 20 weeks, H3K4me1, control, rep 2


title: scWAT, 20 weeks, H3K27ac, high fat diet, rep 2


title: TNBC T014


title: scWAT, 20 weeks, H3K27ac, high fat diet, rep 1


title: scWAT, 20 weeks, H3K4me1, high fat diet, rep 2


title: TNBC T011


title: TNBC T002


title: Breast cancer BRC461

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver.3 of the Illumina HT-12 expression BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data were obtained from Illumina GenomeStudio software. We normalized gene expression data using Quantile normalization and log2 transformation.

source_name: Primary breast cancer

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

tag: disease status

value: Breast cancer

value: Primary breast cancer tumor


title: scWAT, 20 weeks, H3K4me1, high fat diet, rep 1


title: TNBC T001


title: Breast cancer BRC457P


title: TNBC T006


title: TNBC T013


title: Breast cancer BRC458


title: TNBC T003


title: TNBC T012


title: scWAT, 20 weeks, H3K4me1, control, rep 1


title: scWAT, 20 weeks, H3K27ac, control, rep 1


title: Breast cancer BRC459P


title: scWAT, 20 weeks, DNA input, high fat diet, rep 2


title: vWAT, 20 weeks, RNAPol-II,control, rep 1


title: scWAT, 20 weeks, DNA input, high fat diet, rep 1


title: scWAT, 20 weeks, H3K27ac, control, rep 2


title: scWAT, 20 weeks, DNA input, control, rep 2


title: scWAT, 20 weeks, DNA input, control, rep 1


title: vWAT, 8 weeks, RNAPol-II, high fat diet, rep 2

value: 14 weeks old

value: 8 weeks


title: vWAT, 8 weeks, RNAPol-II, high fat diet, rep 1

value: visceral (epididymal) white adipose tissue (VWAT)


title: vWAT, 8 weeks, RNAPol-II,control, rep 2


title: Breast cancer BRC455


title: Breast cancer BRC454P


title: vWAT, 8 weeks, RNAPol-II,control, rep 1


title: Breast cancer BRC456P


title: Breast cancer BRC460


title: vWAT, 8 weeks, H3K4me1, high fat diet, rep 2


title: vWAT, 8 weeks, H3K4me1, control, rep 2


title: Breast cancer BRC451


title: Breast cancer BRC453N


title: Breast cancer BRC452P


title: vWAT, 8 weeks, H3K4me1, high fat diet, rep 1


title: Breast cancer BRC449P


title: Breast cancer BRC436


title: Breast cancer BRC448


title: vWAT, 8 weeks, H3K27ac, high fat diet, rep 2


title: Breast cancer BRC450P


title: Breast cancer BRC433


title: vWAT, 8 weeks, H3K27ac, control, rep 2


title: vWAT, 8 weeks, H3K27ac, high fat diet, rep 1


title: Breast cancer BRC432


title: Breast cancer BRC441


title: vWAT, 8 weeks, DNA input, high fat diet, rep 1


title: vWAT, 8 weeks, H3K27ac, control, rep 1


title: vWAT, 8 weeks, H3K4me1, control, rep 1


title: vWAT, 8 weeks, DNA input, control, rep 2


title: scWAT, 8 weeks, H3K4me1, high fat diet, rep 2


title: Breast cancer BRC425


title: TNBC T009


title: Breast cancer BRC428


title: vWAT, 8 weeks, DNA input, control, rep 1


title: scWAT, 8 weeks, H3K4me1, high fat diet, rep 1


title: Breast cancer BRC423E


title: Breast cancer BRC430


title: Breast cancer BRC422


title: Breast cancer BRC424


title: Breast cancer BRC416


title: scWAT, 8 weeks, RNAPol-II, high fat diet, rep 2


title: Breast cancer BRC419


title: scWAT, 8 weeks, RNAPol-II,control, rep 2


title: scWAT, 8 weeks, RNAPol-II, high fat diet, rep 1


title: Breast cancer BRC421


title: Breast cancer BRC420


title: scWAT, 8 weeks, H3K4me1, control, rep 1


title: scWAT, 8 weeks, H3K27ac, high fat diet, rep 2


title: vWAT, 8 weeks, DNA input, high fat diet, rep 2


title: scWAT, 8 weeks, RNAPol-II,control, rep 1


title: scWAT, 8 weeks, H3K4me1, control, rep 2


title: Breast cancer BRC413


title: Breast cancer BRC412


title: scWAT, 8 weeks, H3K27ac, high fat diet, rep 1


title: Breast cancer BRC418


title: scWAT, 8 weeks, H3K27ac, control, rep 2


title: Breast cancer BRC411


title: Breast cancer BRC417


title: Breast cancer BRC415


title: scWAT, 8 weeks, H3K27ac, control, rep 1


title: vWAT, 1 week, RNAPol-II, high fat diet, rep 2

value: 7 week old

value: 1 week


title: scWAT, 8 weeks, DNA input, high fat diet, rep 2

value: High fat diet (D12492)


title: scWAT, 8 weeks, DNA input, high fat diet, rep 1


title: Breast cancer BRC414


title: Breast cancer BRC410


title: Breast cancer BRC407


title: Breast cancer BRC405


title: Breast cancer BRC408


title: scWAT, 8 weeks, DNA input, control, rep 2


title: scWAT, 8 weeks, DNA input, control, rep 1


title: vWAT, 1 week, RNAPol-II, high fat diet, rep 1


title: vWAT, 1 week, RNAPol-II,control, rep 2


title: vWAT, 1 week, RNAPol-II,control, rep 1


title: vWAT, 1 week, H3K4me1, high fat diet, rep 2

value: H3K4me1 (Abcam, ab8895)


title: vWAT, 1 week, H3K4me1, high fat diet, rep 1


title: vWAT, 1 week, H3K4me1, control, rep 2


title: vWAT, 1 week, H3K4me1, control, rep 1


title: vWAT, 1 week, H3K27ac, high fat diet, rep 2


title: vWAT, 1 week, H3K27ac, high fat diet, rep 1


title: Breast cancer BRC403


title: Breast cancer BRC387E


title: Breast cancer BRC398


title: Breast cancer BRC399


title: Breast cancer BRC400E


title: vWAT, 1 week, H3K27ac, control, rep 2


title: vWAT, 1 week, H3K27ac, control, rep 1


title: Breast cancer BRC379


title: vWAT, 1 week, DNA input, high fat diet, rep 1


title: Breast cancer BRC404


title: Breast cancer BRC383


title: Breast cancer BRC375


title: Breast cancer BRC374


title: Breast cancer BRC377


title: Breast cancer BRC378


title: Breast cancer BRC376


title: Breast cancer BRC372


title: Breast cancer BRC371


title: vWAT, 1 week, DNA input, control, rep 1


title: Breast cancer BRC402


title: scWAT, 1 week, RNAPol-II, high fat diet, rep 2

value: RNAPol-II (Santa-Cruz, SC-67318)


title: vWAT, 1 week, DNA input, high fat diet, rep 2


title: vWAT, 1 week, DNA input, control, rep 2

value: Control chow diet (D12450J)


title: scWAT, 1 week, RNAPol-II, high fat diet, rep 1


title: scWAT, 1 week, H3K4me1, high fat diet, rep 2


title: scWAT, 1 week, RNAPol-II,control, rep 1


title: scWAT, 1 week, H3K4me1, control, rep 2


title: scWAT, 1 week, H3K4me1, control, rep 1


title: scWAT, 1 week, RNAPol-II,control, rep 2


title: scWAT, 1 week, H3K27ac, high fat diet, rep 2

value: H3K27ac (Abcam, ab4729)


title: Breast cancer BRC368


title: Breast cancer BRC373


title: scWAT, 1 week, H3K4me1, high fat diet, rep 1


title: Breast cancer BRC370


title: Breast cancer BRC365


title: Breast cancer BRC363


title: scWAT, 1 week, H3K27ac, control, rep 1


title: Breast cancer BRC382


title: scWAT, 1 week, DNA input, high fat diet, rep 2


title: scWAT, 1 week, H3K27ac, high fat diet, rep 1


title: scWAT, 1 week, H3K27ac, control, rep 2


title: Breast cancer BRC362


title: Breast cancer BRC364


title: Breast cancer BRC352


title: Breast cancer BRC367


title: Breast cancer BRC357


title: Breast cancer BRC355


title: Breast cancer BRC359


title: Breast cancer BRC369E


title: Breast cancer BRC360


title: Breast cancer BRC361


title: Breast cancer BRC356


title: LacZ

city: Rome

first: Julie

last: Martone

address: P.le Aldo Moro 5

country: Italy

institute: "Sapienza" University

description:
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold
LacZ_pull-down_peaks.bed

data_processing:
Base-Calling with Casava.
Reads were pre-processed using Trimmomatic software which removed adapter sequences and poor quality bases, filtering out those reads whose length after trimming was less than 30 nucleotides. Then, Bowtie 2 was used to identify and discard reads mapping to rRNAs and tRNAs.
In order to calculate the distribution of the inner distance between mate pairs, reads from depletion experiment were aligned to a non-redundant set of murine RNA sequences derived from Ensembl 77 mouse annotation using BWA software. We estimated mean and variance of the inner distance distribution from aligned read pairs whose inner distance was within interval [Q1-2(Q3-Q1),Q3+2(Q3-Q1)] (Q1=first quartile, Q3=third quartile). TopHat2 was employed to align reads to GRCm38 mouse genome and Ensembl 77 transcriptome using parameters -i 50 -r 40 --mate-std-dev 80 --library-type fr-firststrand. Reads mapping to mithocondrial genome were filtered out using bamtools.
We used Htseq-count software in intersection-strict mode to count reads mapping to Ensembl 77 genes. RPKM values were calculated using edgeR rpkm function.
Genome_build: GRCm38
Supplementary_files_format_and_content: text file containing per sample gene RPKMs
Base-Calling with Casava.
Reads were pre-processed using Trimmomatic software which removed adapter sequences and poor quality bases, filtering out those reads whose length after trimming was less than 30 nucleotides. Then, Bowtie 2 was used to identify and discard reads mapping to rRNAs and tRNAs.
TopHat2 was employed to align reads to GRCm38 mouse genome and Ensembl 77 transcriptome using parameters -i 50 --library-type fr-firststrand. Reads mapping to mithocondrial genome were filtered out using bamtools. Aligned reads were further processed using Picard MarkDuplicates to remove duplicate reads and bamtools to filter out reads mapping to multiple positions.
Piranha tool was used to call peaks for lnc-SMaRT pull-down and LacZ pull-down reads, using Input reads as a covariate; bin size was set to 200.
Genome_build: GRCm38
Supplementary_files_format_and_content: bed files containing genomic coordinates and p-values of lnc-SMaRT and LacZ pull-down enriched read clusters.
Supplementary_files_format_and_content: ----
Supplementary_files_format_and_content: rpkm_RNA-Seq.tsv: text file containing per sample gene RPKMs
Supplementary_files_format_and_content: lnc-SMaRT_pull-down_peaks.bed: bed file containing genomic coordinates and p-values of lnc-SMaRT pull-down enriched read clusters.
Supplementary_files_format_and_content: LacZ_pull-down_peaks.bed: bed file containing genomic coordinates and p-values of LacZ pull-down enriched read clusters.

source_name: LacZ sample from C2C12 RNA pull down

growth_protocol: Mantainance of C2C12 cells is described in this study.

extract_protocol:
Total RNA was extracted Qiazol reagent and miRNEasy spin columns according to the manufacturer’s specifications (QIAGEN).
See SAMPLES section

treatment_protocol: siRNA treatment is described n this study; while the pull down was performed as described Dimartino et al., 2018

tag: cell type

value: C2C12 murine myoblasts


title: scWAT, 1 week, DNA input, control, rep 2


title: lnc-SmaRT_Pull-Down

description:
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold
lnc-SMaRT_pull-down_peaks.bed

source_name: Sample from C2C12 lnc-Smart  pull down (set#1)


title: scWAT, 1 week, DNA input, control, rep 1


title: INPUT

description: TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

source_name: INPUT from C2C12 RNA pull down


title: Breast cancer BRC384

value: Alive


title: si-SMaRT_1.2

description:
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold
rpkm_RNA-Seq.tsv

source_name: C2C12 (DM2) treated with si-SMaRT_1.2


title: si-SMaRT_1.1

source_name: C2C12 (DM2) treated with si-SMaRT_1.1


title: siSCR_1.2

source_name: C2C12 (DM2) treated with si-scr-1.2


title: siSCR_1.1

source_name: C2C12 (DM2)  treated with si-scr-1.1


title: Breast cancer BRC347


title: Breast cancer BRC358


title: Breast cancer BRC349


title: Breast cancer BRC348


title: scWAT, 1 week, DNA input, high fat diet, rep 1


title: Breast cancer BRC350


title: Breast cancer BRC351


title: Breast cancer BRC344


title: Breast cancer BRC343


title: Breast cancer BRC341


title: Breast cancer BRC345


title: Breast cancer BRC346


title: Breast cancer BRC337


title: Breast cancer BRC338


title: Breast cancer BRC340


title: Breast cancer BRC336


title: Breast cancer BRC333


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_12H_REP1

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

country: France

institute: Institut Pasteur

hyb_protocol: Hybridization cocktail of fragmented and labeled ss-cDNA were incubated 16hr, 60rpm at 45°C on the Human Transcriptome Arrays 2.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip® Expression Wash, Stain, and Scan User Manual for Cartridge Arrays (PN 702731)

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix HTA 2.0 array intensity data were analyzed using open-source Bioconductor packages on R. Internal control probe sets were removed and average expression deciles over time-points were then defined independently for each treatment. Probes whose average expression was lower than the 4th expression decile in both conditions were removed for subsequent analyses.
To remove sources of unwanted variation and consider batch effects, data were finally corrected with the sva package. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to check for consistency between biological replicates and experimental conditions at each step of the pre-processing.

source_name: WI38, RAF OIS, 12h

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: WI-38 fibroblasts  were cultured in DMEM with 4.5g/L glucose and 10% FBS at 37˚C in the presence of 5% CO2 and 3% O2.

extract_protocol: RNA was extracted using the QIAGEN Rneasy Plus kit according to the manufacturer's instructions.

treatment_protocol: Replicative senescent cells were generated by proliferative exhaustion under 21% O2. RAF OIS  was induced with 100ng/ml doxycycline.

tag: cell line

tag: treatment

value: RAF induced senescence

tag: timepoint


title: Breast cancer BRC334

tag: age


title: Breast cancer BRC339


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_48H_REP2

source_name: WI38, RAF OIS, 48h


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_72H_REP1

source_name: WI38, RAF OIS, 72h


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_48H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_24H_REP2

source_name: WI38, RAF OIS, 24h


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_24H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_96H_REP1

source_name: WI38, RAF OIS, 96h


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_12H_REP2


title: Breast cancer BRC332


title: Breast cancer BRC335E


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_72H_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_96H_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_T0_REP1

source_name: WI38, RAF OIS, T0


title: Breast cancer BRC330


title: Breast cancer BRC329


title: Breast cancer BRC328


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_144H_REP1

value: Replicative senescence


title: WI38_SENESCENCE_TRANSCRIPTOME_RAF_T0_REP2


title: Breast cancer BRC327


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_144H_REP2


title: Breast cancer BRC326


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_264H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_264H_REP2


title: Breast cancer BRC323


title: Breast cancer BRC325E

value: Dead


title: Breast cancer BRC319E

value: Breast cancer


title: Breast cancer BRC313E

value: Primary breast cancer tumor


title: Breast cancer BRC322


title: Breast cancer BRC321


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_624H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_432H_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_792H_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_624H_REP2


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_432H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_1368H_REP2


title: Breast cancer BRC309


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_1008H_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_2112H_REP2


title: Breast cancer BRC308


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T0_REP2

source_name: WI38, RS, T0


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_792H_REP1


title: Breast cancer BRC312


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_T0_REP1


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_1368H_REP1


title: Breast cancer BRC304


title: Breast cancer BRC303


title: CL2treated_H3KMe3

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

institute: Lunenfeld- Tanenbaum Research Institute

data_processing:
library strategy: Cut&Run
Reads aligned to mm10 usingHisat2 (2.1.0) with parameters --no-spliced-alignment and --no-unal
Duplicate reads removed with Picard; Non-uniquely aligned reads removed (hisat flag ZS:i), Remove reads aligned to ambiguous chromosomes; remove reads in mm10 blacklist regions (https://www.nature.com/articles/s41598-019-45839-z)
Normalizaed bedgraphs using bedtools genomecov with -scale x (spike in)
Headmap generated using deepTools 3.3.0 (computeMatrix + plotHeatmap)
Genome_build: mm10
Supplementary_files_format_and_content: signal file in BigWig format

source_name: Brain Tumor Cells_hypoxia

extract_protocol:
Zymoresearch DNA purification kit
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells grown in 1% or 21% oxygen tension

value: Posterior Fossa A, primary brain tumor cells

tag: antibody

tag: antibody vendor

value: Diagenode

tag: antibody catalog #

tag: antibody lot/batch #

value: hypoxia


title: CL5WT_H3KMe3

source_name: Brain Tumor Cells_normaxia

value: normaxia


title: CL2WT_H3KMe3


title: CL5treated_H3KMe3


title: Breast cancer BRC300

source_name: Primary breast cancer

tag: ajcc stage

tag: vital status

tag: follow-up time (month)


title: DKO_TotalRNAPol2

description:
TotalRNAPol2 binding to DKO
DKO_TrPol2_vs_HCT116_TrPol2_all_Mavalues.xls

data_processing:
ChIP-seq reads were processed by ENCODE ChIP-seq pipeline (BWA/MAC2) developed by Kundaje lab (https://github.com/kundajelab/chipseq_pipeline). Differential binding sites are called by MANorm.
Genome_build: hg19
Supplementary_files_format_and_content: differential binding sites between ChIP-seq HCT116 and DKO in TSV file format

source_name: Colorectal carcinoma cell line

growth_protocol: HCT116 and DKO cells were cultured in McCoy’s 5A medium with 10% FBS at 37°C and 5% CO2.

extract_protocol:
Cultured cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with G (for Pol2-Ser2 and Pol2-Ser5) or A (for CTCF, RAD21, SMC1, and H3K27) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against each of the protein. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: Colon

value: Pol2Ser5 (Active Motif #61086)


title: HCT116_TotalRNAPol2

description:
TotalRNAPol2 binding to HCT116
DKO_TrPol2_vs_HCT116_TrPol2_all_Mavalues.xls


title: Breast cancer BRC305

tag: tissue


title: DKO_Input

description:
Input control ChIP-Seq for DKO
none
38_030K_00CWCCF_DKO_AHT_Input_hs_i85

data_processing:
ChIP-seq reads were processed by ENCODE ChIP-seq pipeline (BWA/MACS2) developed by Kundaje lab (https://github.com/kundajelab/chipseq_pipeline). Differential binding sites are called by MANorm.
Genome_build: hg19
Supplementary_files_format_and_content: differential binding sites between ChIP-seq HCT116 and DKO in TSV file format

value: DKO

tag: tissue source

value: Colorectal carcinoma cell line

value: none; Input


title: Breast cancer BRC307


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_2112H_REP1


title: Breast cancer BRC318


title: Breast cancer BRC306


title: DKO_Pol2Ser2

description:
Pol2Ser2 binding to DKO
processed data file:
DKO_Pol2Ser2_vs_HCT116_Pol2Ser2_all_Mavalues.txt
32_031G_00CWCCF_DKO_AHT_Pol2Ser2_hs_i94

value: Pol2Ser2 (Active Motif #61084)


title: DKO_H3K27Ac

description:
H3K27Ac binding to DKO
processed data file:
DKO_H3K27Ac_vs_HCT116_H3K27Ac_all_Mavalues.txt
20_030C_00CWCCF_DKO_AHT_H3K27Ac_hs_i80

value: H3K27Ac (Active Motif #39133)


title: DKO_RAD21

description:
RAD21 binding to DKO
processed data file:
DKO_RAD21_vs_HCT116_RAD21_all_Mavalues.txt
14_031O_00CWCCF_DKO_AHT_RAD21_hs_i73

value: RAD21 (Santa Cruz #sc98784)


title: WI38_SENESCENCE_TRANSCRIPTOME_REPLICATIVE_1008H_REP2


title: DKO_SMC1

description:
SMC1 binding to DKO
processed data file:
DKO_SMC1_vs_HCT116_SMC1_all_Mavalues.txt
08_030Q_00CWCCF_DKO_AHT_SMC1_hs_i87

value: SMC1 (Bethyl #A300-005A)


title: HCT116_Pol2Ser5

description:
Pol2Ser5 binding to HCT116
processed data file:
DKO_Pol2Ser5_vs_HCT116_Pol2Ser5_all_Mavalues.txt
25_031J_00CWCCF_HCT116_AHT_Pol2Ser5_hs_i68


title: HCT116_Input

description:
Input control ChIP-Seq for HCT116
none
37_030J_00CWCCF_HCT116_AHT_Input_hs_i84


title: HCT116_Pol2Ser2

description:
Pol2Ser2 binding to HCT116
processed data file:
DKO_Pol2Ser2_vs_HCT116_Pol2Ser2_all_Mavalues.txt
31_031F_00CWCCF_HCT116_AHT_Pol2Ser2_hs_i93


title: Breast cancer BRC298E

value: Alive


title: Breast cancer BRC301


title: Breast cancer BRC297E


title: HCT116_H3K27Ac

description:
H3K27Ac binding to HCT116
processed data file:
DKO_H3K27Ac_vs_HCT116_H3K27Ac_all_Mavalues.txt
19_030B_00CWCCF_HCT116_AHT_H3K27Ac_hs_i79


title: Breast cancer BRC296


title: HCT116_RAD21

description:
RAD21 binding to HCT116
processed data file:
DKO_RAD21_vs_HCT116_RAD21_all_Mavalues.txt
13_031N_00CWCCF_HCT116_AHT_RAD21_hs_i72


title: Breast cancer BRC294


title: DKO_Pol2Ser5

description:
Pol2Ser5 binding to DKO
processed data file:
DKO_Pol2Ser5_vs_HCT116_Pol2Ser5_all_Mavalues.txt
26_031K_00CWCCF_DKO_AHT_Pol2Ser5_hs_i69


title: Breast cancer BRC293


title: Breast cancer BRC288

value: Dead


title: DKO_CTCF

description:
CTCF binding to DKO
processed data file:
DKO_CTCF_vs_HCT116_CTCF_all_Mavalues.txt
02_0308_00CWCCF_DKO_AHT_CTCF_hs_i73

value: CTCF (Active Motif #61311)


title: Breast cancer BRC291

value: Breast cancer

value: Primary breast cancer tumor


title: Breast cancer BRC292


title: Breast cancer BRC295


title: 16-877_RNA-seq

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg38). The reference genome index and reads mapping of tissue samples were performed using the STAR software (ver. 2.5.3a).
The read counts per
million fragments mapped (CPM) of each sample was used to estimate the expression level of each gene. The CPM data were normalized by the quantile method and log2-transformed.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text format with log2 transformed CPM values of transcripts

source_name: diffuse type gastric cancer

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

value: gastric cancer

tag: cancer type

value: diffuse type

tag: gender

value: M

tag: histologic type

value: poorly differentiated


title: 17-247_RNA-seq


title: 16-338_RNA-seq

value: poorly cohesive carcinoma


title: 16-451_RNA-seq

value: F


title: 16-265_RNA-seq


title: Breast cancer BRC279E

tag: disease status


title: Breast cancer BRC283


title: Breast cancer BRC281


title: HCT116_SMC1

description:
SMC1 binding to HCT116
processed data file:
DKO_SMC1_vs_HCT116_SMC1_all_Mavalues.txt
07_030P_00CWCCF_HCT116_AHT_SMC1_hs_i86

tag: cell line

value: Colon

tag: cell type

value: Colorectal carcinoma cell line

tag: chip antibody


title: HCT116_CTCF

description:
CTCF binding to HCT116
processed data file:
DKO_CTCF_vs_HCT116_CTCF_all_Mavalues.txt
01_0307_00CWCCF_HCT116_AHT_CTCF_hs_i72


title: Breast cancer BRC282

tag: age


title: Breast cancer BRC275


title: Breast cancer BRC271


title: Breast cancer BRC270


title: Breast cancer BRC276


title: Breast cancer BRC289


title: 16-579_RNA-seq


title: Breast cancer BRC266


title: Breast cancer BRC280


title: 16-2099_RNA-seq


title: Breast cancer BRC278


title: Breast cancer BRC268


title: Breast cancer BRC269


title: Breast cancer BRC263


title: 16-1807_RNA-seq


title: 16-195_RNA-seq


title: 16-1648_RNA-seq


title: 16-1992_RNA-seq


title: 16-1597_RNA-seq


title: 16-147_RNA-seq


title: 16-1378_RNA-seq


title: 16-1034_RNA-seq


title: Breast cancer BRC262


title: 16-1014_RNA-seq


title: Breast cancer BRC260E


title: 15-968_RNA-seq


title: 15-696_RNA-seq


title: 15-720_RNA-seq


title: 15-547_RNA-seq


title: Breast cancer BRC259


title: Breast cancer BRC255


title: Breast cancer BRC257


title: Breast cancer BRC251


title: 15-250_RNA-seq


title: Breast cancer BRC249


title: Breast cancer BRC246E


title: 15-213_RNA-seq


title: 15-2017_RNA-seq


title: 16-2133_RNA-seq


title: Breast cancer BRC247


title: 15-1873_RNA-seq


title: Breast cancer BRC254


title: 15-680_RNA-seq


title: Breast cancer BRC250


title: Breast cancer BRC253


title: 15-1350_RNA-seq


title: 15-1464_RNA-seq


title: 14-952_RNA-seq


title: 14-853_RNA-seq


title: Breast cancer BRC241E


title: Breast cancer BRC242


title: Breast cancer BRC244


title: 14-464_RNA-seq


title: Breast cancer BRC245


title: Breast cancer BRC236


title: Breast cancer BRC239


title: Breast cancer BRC237


title: Breast cancer BRC240E


title: Breast cancer BRC243E


title: 17-99_RNA-seq


title: 14-769_RNA-seq


title: Breast cancer BRC238


title: Breast cancer BRC233


title: Breast cancer BRC232E


title: Breast cancer BRC234E


title: 14-438_RNA-seq


title: 15-108_RNA-seq


title: 15-1049_RNA-seq


title: 14-377_RNA-seq

value: mucinous adenocarcinoma


title: 14-207_RNA-seq


title: 14-165_RNA-seq


title: 14-162_RNA-seq


title: 14-428_RNA-seq


title: 14-1020_RNA-seq


title: 14-1280_RNA-seq


title: 13-991_RNA-seq


title: 13-803_RNA-seq


title: Breast cancer BRC228


title: Breast cancer BRC231E


title: Breast cancer BRC227


title: Breast cancer BRC229


title: Breast cancer BRC226


title: Breast cancer BRC224


title: 13-888_RNA-seq


title: Breast cancer BRC230


title: 13-791_RNA-seq


title: Breast cancer BRC225


title: Breast cancer BRC220


title: Breast cancer BRC214


title: Breast cancer BRC212


title: Breast cancer BRC223


title: 13-852_RNA-seq


title: 13-1401_RNA-seq


title: 13-1458_RNA-seq


title: 13-662_RNA-seq


title: 13-1176_RNA-seq


title: 12-1144_RNA-seq


title: 12-1010_RNA-seq


title: Breast cancer BRC204


title: 10-691_RNA-seq


title: Breast cancer BRC210


title: Breast cancer BRC205


title: 10-876_RNA-seq


title: 04796590T_RNA-seq

source_name: intestinal type gastric cancer

value: intestinal type


title: Breast cancer BRC199


title: Breast cancer BRC201


title: Breast cancer BRC198


title: Breast cancer BRC202


title: Breast cancer BRC209


title: 13-1113_RNA-seq


title: 09-833_RNA-seq


title: 09-813_RNA-seq


title: 04779308T_RNA-seq


title: 04793833T_RNA-seq


title: Breast cancer BRC197


title: 04782633T_RNA-seq


title: Breast cancer BRC195


title: 04773965T_RNA-seq


title: Breast cancer BRC186


title: Breast cancer BRC192


title: Breast cancer BRC190


title: Breast cancer BRC188


title: Breast cancer BRC194


title: 04768632T_RNA-seq


title: Breast cancer BRC189


title: Breast cancer BRC211


title: Breast cancer BRC179


title: Breast cancer BRC185


title: Breast cancer BRC178


title: Breast cancer BRC177


title: 04718872T_RNA-seq

value: papillary adenocarcinoma


title: 04721895N_RNA-seq

source_name: Normal mucosae

value: normal intestinal mucosae


title: 04669224T_RNA-seq


title: 04683938T_RNA-seq


title: 04651200T_RNA-seq


title: 04651200N_RNA-seq


title: 04721895T_RNA-seq


title: 04639545T_RNA-seq


title: Breast cancer BRC176


title: Breast cancer BRC174

value: Alive


title: Breast cancer BRC171

value: Dead


title: 04594894T_RNA-seq


title: Breast cancer BRC169


title: 04558340T_RNA-seq


title: Breast cancer BRC264


title: Breast cancer BRC168


title: 04541076T_RNA-seq


title: 04552910T_RNA-seq


title: Breast cancer BRC161


title: 04540586T_RNA-seq

value: invasive ductal carcinoma


title: 04538456T_RNA-seq


title: Breast cancer BRC170

value: Breast cancer


title: Breast cancer BRC175

value: Primary breast cancer tumor


title: 04525849N_RNA-seq


title: 04525849T_RNA-seq

value: gastric cancer


title: 04522350T_RNA-seq


title: Breast cancer BRC160


title: 04509021T_RNA-seq

value: diffuse type


title: Breast cancer BRC151


title: Breast cancer BRC152E


title: Breast cancer BRC154


title: Breast cancer BRC146


title: Breast cancer BRC140


title: Breast cancer BRC155


title: 04508565T_RNA-seq


title: Breast cancer BRC149


title: Breast cancer BRC167


title: 04508805T_RNA-seq


title: 04507614T_RNA-seq

value: M


title: 04507912T_RNA-seq


title: 04507462T_RNA-seq


title: 04508204T_RNA-seq


title: 04505833T_RNA-seq


title: 04508919T_RNA-seq


title: Breast cancer BRC136


title: Breast cancer BRC132


title: 04507457T_RNA-seq


title: Breast cancer BRC138


title: 04522350N_RNA-seq


title: 04505498N_RNA-seq


title: Breast cancer BRC130


title: Breast cancer BRC129


title: Breast cancer BRC127


title: Breast cancer BRC125


title: 04505048T_RNA-seq