title: Med1 fl/fl K27ac ChIP

value: Med1 fl/fl


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 8

status: Public on Oct 30 2019

type: RNA

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from bone marrow leukemic cells from Pax5+/- mice treated with a cocktail of antibiotics during 8 weeks.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion).

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens. All the animals are females.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were given a cocktail of antibiotics (ampicillin, 1 g/L, Ratiopharm; vancomycin, 500 mg/L, Cell Pharm; ciprofloxacin, 200 mg/L, Bayer Vital; imipenem, 250 mg/L, MSD; metronidazole, 1 g/L, Fresenius) added to the drinking water ad libitum for a period of eight weeks.

tag: genotype/variation

tag: Sex

value: Female

tag: tissue

value: Total Bone marrow

tag: treatment

value: Antibiotics


title: Bone Marrow proB and preB cells from WT mouse, biological replicate 4

description: Gene expression data from WT bone marrow proB and preB cells.

source_name: WT 23

value: WT

value: Bone marrow proB and preB


title: MCF7 Cas9 4-hydroxytamoxifen rep 2

type: SRA

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3243_MCF7_None_Tam_B_CRI01_1

library_source: transcriptomic

data_processing:
library strategy: CRISPR gRNA-seq
Short reads were depleted from low-quality sequences and aligned to human gRNA sequence library (GRC_h37) using BLAT v. 34
Exact-matching reads were counted and treated as a measurement of gRNA abundance.
MAGecK was performed to rank the genes and DESeq2 was used to get log2 fold changes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files with counts for each sample.

organism: Homo sapiens

source_name: MCF7 Cas9 4-hydroxytamoxifen gRNA-seq

growth_protocol: MCF7-Cas9 expressing cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate with blasticidin.

extract_protocol:
Qiagen Blood and Cell culture Maxi kit was used to extract genomic DNA. Viral vector covering DNA were amplified with Illumina adapters containing primers.
Viral vector covering DNA were amplified with Illumina adapters containing primers. Libraries were made using Illumina Truseq HT and Thruplex dual indices.

treatment_protocol: Cells were infected with pooled gRNA libraries for 9 days and treated with drugs for 26 days.

tag: cell line

value: MCF7 Cas9 expressing cells

tag: cell type

value: ER+  Breast Cancer Cell Line

tag: passages

tag: time point

value: 4-hydroxy tamoxifen treated for 26 days after 9 days of infection


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 9


title: Med1 fl/fl K27me3 ChIP

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
Raw sequences reads were pre-processed using TrimGalore and aligned to the mm10 mouse reference genome with Bowtie with at most 2 mismathes. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication.
BigWig files were generated from the coverage for visualization purposes.
Gzip compressed Fastq files were split into multiple files if more than 1.25GB in size to aid customer downloading.
ChIP-seq peaks were dertermined using EaSeq software v1.05 (easeq.net; Lerdrup M, et al. Nat Struct Mol Biol. 2016;23:349–357) using default settings with minor modification. Peaks were identified using adaptive local thresholding with the most abundant DNA-fragment size determined according to the Phantom Peak Coefficient method.
Thresholds from the input control was scaled according with the NCIS normalization factor to define border regions. Shoulders were excluded at values below µ + 2SD.
After border refinement and peak-merging, peaks were positively selected for a FDR value of 1E-05 or better and minimum a NCIS normalized log2 fold difference of two.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for peak visualization in a genomic browser

molecule: genomic DNA

source_name: cardiac tissue

growth_protocol: Med1 fl/fl mice backrossed into C57Bl6 were crossed with Med1 fl/+ mice expressing Cre from the Myh6 promoter to generate cardiac specific Med1 KO mice and control littermates

extract_protocol:
Hearts from euthanized three-week-old male mice were rapidly harvested, rinsed in cold phosphate buffered saline, and snap frozen in liquid nitrogen. Genomic DNA was extracted from frozen tissue using the Zymo-Spin ChIP Kit according to manufacturer's directions.
Chromatin was immunoprecipitated in triplicate using antibodies against RNA Pol-II (Bethyl Laboratories #9201012), H3K27ac (Abcam #ab4729), H3K27me3 (Abcam #ab6002), and normal mouse IgG (Diagenode #C15410206 and Millipore #12-371B).
Libraries were prepared from pooled ChIP DNA and constructed by Zymo Research using EpiQuest services and proprietary methods.

value: cardiac tissue

tag: antibody

value: tri-metylated H3K27

tag: developmental stage

value: post natal day 21

tag: strain

tag: genotype

tag: gender

value: male


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 6


title: Bone Marrow proB and preB cells from WT mouse, biological replicate 2

source_name: WT 21


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 7


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 4


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 5


title: PV_rpl22_G2

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the mouse reference genome (mm10) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: The mouse reference genome was indexed using the Ensembl annotations (v84) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene abundance. The raw count from rsem-calculate-expression is used.

extract_protocol:
Centrifuge the brain tissue sample to prepare supernatant and mix with Qiazol aliquot. This is total RNA sample usied for immunoprecipitation.
Ribosome-associated mRNA libraries were prepared using TruSeq® Stranded Total RNA Library Prep (Illumina # RS-122-2201) following the manufacturer protocol. In brief, 0.5ug of total RNA was treated with Ribo-zero rRNA removal and cleaned with RNACleanXP. Both cDNA strands were synthesized, Adenylation of 3' end was done and indexing adapters were ligated. Libraries were amplified and the final product was purified using Agencourt AMPure XP (Beckman Coulter, #A63881). Libraries were validated using High sensitivity DNA bioanalyzer (Agilent).

tag: strain background

tag: condition

value: PV RiboTag IP

value: RiboTag

value: Whole brain

tag: molecule subtype


title: PV_rpl22_G3


title: Med1 fl/fl Pol-II ChIP

value: RNA Pol-II


title: MCF7 Cas9 JQ1 rep 3

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3241_MCF7_None_JQ1_C_CRI01_1

source_name: MCF7 Cas9 JQ1 gRNA-seq

value: JQ1 treated for 26 days after 9 days of infection


title: MCF7 Cas9 4-hydroxytamoxifen rep 3

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3244_MCF7_None_Tam_C_CRI01_1


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 3

value: Female


title: MCF7 Cas9 4-hydroxytamoxifen rep 1

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3242_MCF7_None_Tam_A_CRI01_1


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 2

value: Total Bone marrow


title: MCF7 Cas9 JQ1 rep 2

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3240_MCF7_None_JQ1_B_CRI01_1


title: Gad_rpl22_B3

value: Gad2 RiboTag IP


title: CD4+ T cells: Tfh-like (Tox2) - ATACseq

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

country: China

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were aligned to mm10 by Bowtie2 with default parameters
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a fdr value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file with quantitative data for each Sample

source_name: CD4+ T cells

growth_protocol: For in vivo-generated Tfh group, NP-Keyhole limpet hemocyanin (NP-KLH, 2mg/ml, Sigma) were mixed well with Complete Freund’s adjuvant (CFA, 2mg/ml) in a ratio of 1:1 and administrate subcutaneously in the base of the tail.

extract_protocol:
After 7 days, in vivo-generated Tfh (CD4+CD44hiCXCR5hiBcl6-RFPhiFoxp3-GFP-) cells were sorted using BD FACSAria Cell Sorter.
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.

treatment_protocol: For sample 1 to 7, naive CD4+ T cells were activated and infected with retrovirus under neutral condition,  after which GFP+ cells were sorted and cultured in Th0 or Tfh-like conditions.

value: Spleen+Lymph nodes

tag: age

value: wild type


title: CD4+ T cells: Tfh - ATACseq

value: Draining Lymph nodes


title: CD4+ T cells: Tfh-like (Bcl6) - ATACseq


title: MCF7 Cas9 DMSO_ Day26 rep 3

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3239_MCF7_None_D26_C_CRI01_1

source_name: MCF7 Cas9 DMSO_Day26 gRNA-seq

value: MCF7 Cas9 expressing cells

value: ER+  Breast Cancer Cell Line

value: Vehicle-DMSO treated for 26 days after 9 days of infection


title: CD4+ T cells: Tfh-like (GFP) - ATACseq


title: Gad_rpl22_B2

tag: genotype/variation


title: 293_pCW57_PNUTSW401A_pDox_BruSeq

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description: Bru-seq

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: BigWig

source_name: HEK293+pCW57 bla Avi-PNUTS W401A

growth_protocol: DMEM 10% FCS,  +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
BrU-labeled RNA was isolated by IP
20-100 ng of RNA was used with the KAPA RNA HyperPrep Kit (KR1350)

tag: growth conditions

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: Mouse B44 anti-BrU

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: CD4+ T cells: Th0 (Bcl6) - ATACseq

tag: tissue


title: anti-Xrn2_ChIP_pCW57_PNUTSW401A_Dox_Xrn2

description: anti Xrn2 ChIP

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor or Covaris Ultrasonicator
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

treatment_protocol: PNUTS  W401A expression was induced with 2ug/ml doxycycline for 24 hrs,

value: rabbit anti-Xrn2 (aa402-537, affinity pure Brannan et al Mol Cell  46, 311-324, 2012 )


title: anti-Xrn2_ChIP_HEK293_pCW57_PNUTS_WT_Dox

description: anti Xrn2 ChIP

treatment_protocol: PNUTS  WT expression was induced with 2ug/ml doxycycline for 24 hrs,


title: MCF7 Cas9 DMSO_ Day26 rep 1

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3237_MCF7_None_D26_A_CRI01_1


title: 293_pCW57_PNUTSW401A_mDox_BruSeq

description: Bru-seq

value: DMEM 10% FCS,  +blasticidin

tag: treatment

value: control without doxycycline induction


title: CD4+ T cells: Th0 (Tox2) - ATACseq


title: MCF7 Cas9 DMSO_ Day26 rep 2

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3238_MCF7_None_D26_B_CRI01_1

tag: cell line


title: Gad_rpl22_B1

value: RiboTag

value: Whole brain


title: VGluT2_3_MeDIP

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the mouse reference genome (mm10) using Bowtie (v2.0.2) with default parameters allowing for 2 mismatches using seed alignment. Subsequently, aligned reads were filtered for high quality uniquely and multi-mapped reads (MAPQ ! = {0, 2, 3, 4}).
Genome_build: mm10
Supplementary_files_format_and_content: For the analysis of differentially methylated regions (DMRs) the R package MEDIPS (v1.16.0) was used with BSgenome=BSgenome.Mmusculus.UCSC.mm10, extend=250, shift=0, uniq=TRUE, window_size=700 and minRowSum=35. An adjusted p value < 0.1 using the Benjamini–Hochberg method for controlling the false discovery rate was set as significant in order to detect small methylation changes.

source_name: FACS-sorted brain nuclei

extract_protocol:
Fixed nuclei for FACS using mKate2 fluorescence
DNA was isolated from FACS sorted nuclei and sheared using Bioruptor plus (Diagenode # B01020001) sonication device and purified using SureClean plus (Bioline, #BIO-37048) as described in (Halder et al.,2015). 100ng of DNA samples were end-repaired and ligated with NEB adapters (NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645) and cleaned up using Agencourt AMPure XP (Beckman Coulter, #A63881). MeDIP reaction was performed using Methylated DNA IP kit (Zymo Research #D5101) according to manufacturer protocol.

value: vGluT2 Tagger

value: NucTag

tag: sample type

value: FACS-sorted brain nuclei


title: 293_pCW57_PNUTSW401A_Dox_Ser2

description: Ser2-PO4 ChIP-seq

value: rat monoclonal anti-Ser2-P 3E10 (Chromotek)


title: VGluT2_2_MeDIP


title: MCF7 Cas9 Day 0 rep 2

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3235_MCF7_None_D0_B_CRI01_1

source_name: MCF7 Cas9 Day 0 gRNA-seq

tag: cell type

tag: passages

value: Day 9 of Infection with pooled gRNA library


title: 293_pCW57_PNUTS_WT_Dox_Ser2

description: Ser2-PO4 ChIP-seq

source_name: HEK293+pCW57 bla Avi-PNUTS WT

tag: antibody

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: VGluT2_1_MeDIP


title: Gad_rpl22_B4

value: Gad2 RiboTag IP


title: MCF7 Cas9 Day 0 rep 3

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3236_MCF7_None_D0_C_CRI01_1

value: MCF7 Cas9 expressing cells

value: ER+  Breast Cancer Cell Line

tag: time point


title: CD4+ T cells: Th0 (GFP) - ATACseq

tag: strain

value: Spleen+Lymph nodes

value: wild type


title: CD4+ T cells: CM - ATACseq

tag: genotype


title: MCF7 Cas9 Day 0 rep 1

description:
processed data file:
mcf7_cas9_counts2.tsv
jc3234_MCF7_None_D0_A_CRI01_1


title: 293_pCW57_PNUTSW401A_Dox_AviTag

description: Avitag-PNUTS W401A ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: Rabbit anti-avi-tag (GenScript A00674)

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: MCF7_Cas9_1C3_Plasmid library  rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4337_MCF7_Cas9_1C3_Plasmid_Plasmid

source_name: Plasmid library gRNA-seq

value: Pooled gRNA library without infecting cells


title: Gad2_1_MeDIP

value: Gad2 Tagger


title: MCF7_Cas9_1C3_Plasmid library  rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4336_MCF7_Cas9_1C3_Plasmid_Plasmid


title: Gad2_3_MeDIP


title: 293_pCW57_PNUTSW401A_Dox_DRB_5_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline+DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MCF7 Cas9 Day 20 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4355_MCF7_Cas9_1C3_Day_20_Day_20

source_name: MCF7 Cas9 Day 20 gRNA-seq

value: Day 20 of Infection with pooled gRNA library


title: Patient S7 0 days post treatment

city: Rockville

first: Brandon

middle: W

last: Higgs

state: Maryland

address: 2273 Research Blvd Suite 220

institute: Immunocore, Ltd

hyb_protocol: Each RNA sample was diluted in RNase free water (Qiagen) and hybridized using the PanCancer Immune Profiling Panel CodeSet (NanoString Technologies), and hybridization buffer (NanoString Technologies). Following overnight hybridization, the hybridized samples were loaded onto an nCounter SPRINT Profiler cartridge (NanoString Technologies), along with negative (RNAse free water); positive (Universal Human Reference) control samples.

scan_protocol: NanoString data was collected and processed using the nCounter SPRINT profiler software version 2.0.1.8 on an nCounter SPRINT profiler system using the nSolver software.

data_processing: Data was normalised according to the manufacture’s guidelines using positive control and housekeeping gene probes.

label: NanoStrings

source_name: melanoma

label_protocol: Multiplex gene expression analysis of RNA samples was carried out using nCounter PanCancer Immune Profiling Panel (Nanostring, Cat. no. 115000131). All kit components were used  in accordance with the supplier’s recommendations and internal SOPs.

extract_protocol: Tumor biopsy samples were collected in RNALater and stored at -80°C (nominal) until processed. RNA was extracted using RNeasy fibrous tissue mini kit (Qiagen Cat# 74704) in accordance with the supplier’s recommendations. Quantitation was carried out using the NanoDrop 2000 Software version 1.6 on a NanoDrop 2000 instrument. Assessment of RNA quality was performed using the 2200 TapeStation Controller Software version A.01.04, and processed using the 2200 TapeStation Analysis Software version A.01.04 on a 2200 TapeStation instrument.

tag: tag

value: tumor

tag: time (days post treatment)

tag: disease

value: NON-UVEAL

tag: response

value: PD


title: Patient S5 5 days post treatment

value: PR


title: Patient S5 26 days post treatment


title: Patient S5 0 days post treatment


title: 293_pCW57_PNUTSW401A_Dox_DRB_PolII_Rep2

description: Pol II ChIP-seq


title: PvGR_I3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data was analyzed using Oasis 2. In brief, FASTQC quality control tool was used for the assessment of raw reads quality. After adapter trimming (TGGAATTCTCGGGTGCCAAGG), reads were filtered for a minimum length of 15 and maximum length of 32bp. Subsequently, the left over reads were first aligned to mm10 transcripts including known miRNAs, novel miRNAs, piRNAs, snoRNAs, snRNAs, rRNAs, and their families using STAR aligner with no mismatches for reads of length 15–19 nucleotides and allowing for 1 mismatch for the reads of length 20–32 nucleotides.
Genome_build: mm10
Supplementary_files_format_and_content: Expression (counts) of these sRNAs served as the basis for differential expression analysis with DESeq2 package (v1.16.1) using Oasis 2 pipeline.

source_name: PV Input RNA

extract_protocol:
Brain tissue lysates were centrifuged and the supernatant was mixed with Qiazol aliquot and purified using miRNeasy micro kit (Qiagen). This is total RNA sample used for immunoprecipitation.
Ribosome-associated mRNA libraries were prepared using TruSeq® Stranded Total RNA Library Prep (Illumina # RS-122-2201) following the manufacturer protocol. In brief, 0.5ug of total RNA was treated with Ribo-zero rRNA removal and cleaned with RNACleanXP. Both cDNA strands were synthesized, Adenylation of 3' end was done and indexing adapters were ligated. Libraries were amplified and the final product was purified using Agencourt AMPure XP (Beckman Coulter, #A63881). Libraries were validated using High sensitivity DNA bioanalyzer kit (Agilent).

tag: strain background

value: Whole brain

tag: condition

value: PV Input RNA

value: cytoplasmic RNA


title: 293_pCW57_PNUTS_WT_Dox_DRB_15_PolII_Rep2

description: Pol II ChIP-seq

tag: growth conditions

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 355_50: WT-SPL-KEP

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on May 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 normalized counts for each Sample.

source_name: Spleen

growth_protocol: The generation and characterization of K14cre;Cdh1F/F;Trp53F/F mice have been previously described in detail. The mice were backcrossed onto the FVB/N background  and genotype was confirmed by PCR. MMTV-NeuT mice on a Balb/c background were purchased from Charles River Laboratories  and were bred in house. Female K14cre;Cdh1F/F;Trp53F/F and MMTV-NeuT mice were monitored twice every week for the onset of mammary tumor formation by caliper and palpation measurement starting at 2 or 4 months of age, respectively. Mice were kept in open cages with food and water provided ad libitum at a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Mini and Micro Kits (Qiagen)
Ovation RNA-Seq system V2 and Encore Rapid library systems protocols (NuGEN)
50 bp single-end run was performed on a HiSeq1500

treatment_protocol: Mammary glands or mammary tumors (size±225mm2), spleen and bone marrow were harvested from 4 month old K14cre;Cdh1F/F;Trp53F/F female mice containing early lesions, 8 months old tumor-bearing K14cre;Cdh1F/F;Trp53F/F, 4 month old tumor-bearing MMTV-NeuT female mice and age- and sex-matched FVB/N and Balb/c mice. Tumors and mammary glands were mechanically chopped with a McIlwain Tissue Chopper (Ted Pella, Inc, CA, USA) and were enzymatically digested for 1 hour at 37°C with 3 mg/ml collagenase type A (Roche) and 1.5 mg/ml porcine pancreatic trypsin (BD Biosciences) in serum-free DMEM medium. Digestion was stopped by the addition of DMEM supplemented with 8% FBS and the suspension was disaggregated through a 70 μm cell strainer. Spleens and bone marrow cells from tibiae and femora were harvested and disaggregated through a 70 μm cell strainer. Splenic suspensions were subsequently treated twice with NH4Cl erythrocyte lysis buffer for 3 min at room temperature. All single-cell suspensions were stained for 20 min at 4°C in the dark with anti-mouse F4/80 (1:200; BM8; eBioscience) and anti-mouse CD11b (1:200; M1/70; eBioscience) in IMDM supplemented with 2% FBS, 0.5% beta-mercaptoethanol, 0.5mM EDTA, Pen/Strep. Cells were then washed and incubated with magnetic anti-APC MicroBeads (Miltenyi Biotec) following the manufacturer’s guidelines. Isolation of F4/80+ cells from the CD11b+-enriched fraction was performed on a BD FACS ARIA II sorter with Diva software (BD Biosciences).

value: FVB

value: WT

tag: tissue

value: Spleen


title: MCF7 Cas9 Day 20 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4353_MCF7_Cas9_1C3_Day_20_Day_20

value: MCF7 Cas9 expressing cells

value: ER+  Breast Cancer Cell Line


title: MCF7 Cas9 Day 15 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4352_MCF7_Cas9_1C3_Day_15_Day_15

source_name: MCF7 Cas9 Day 15 gRNA-seq

value: Day 15 of Infection with pooled gRNA library


title: 293_pCW57_PNUTS_WT_Dox_AviTag

description: Avitag-PNUTS WT ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: Rabbit anti-avi-tag (GenScript A00674)

tag: treatment


title: MCF7 Cas9 Day 15 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4351_MCF7_Cas9_1C3_Day_15_Day_15

tag: cell line


title: MCF7 Cas9 Day 20 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4354_MCF7_Cas9_1C3_Day_20_Day_20

value: Day 20 of Infection with pooled gRNA library


title: Gad2_2_MeDIP

value: Gad2 Tagger

tag: genotype/variation

value: NucTag

tag: sample type

value: FACS-sorted brain nuclei


title: 293_pCW57_PNUTS_WT_Dox_DRB_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline+DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: MCF7-ARID1A_DCDT_Vehicle rep 3

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

source_name: ARID1A ChIP-seq DCDT Vehicle

growth_protocol: MCF7 cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate

extract_protocol:
Nuclear lysates were prepared and antibody-bound chromatin was purified using appropriate antibodies. Antibodies used: ARID1A HPA005456, BRG1 ab215998, SNF5 Bethyl A301-087A, ERα ab3575 and Merck Millipore 06-935 antibody mix, H3K27ac Diagenode C15410196 Premium, HDAC1 Diagenode Premium C15410325, ARID2 Bethyl A302-229A, BRD4 from Cheng Ming Chiang's lab.
DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated, without any serum deprivation, for 6 hours with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen, 250 nM JQ1 and 10 nM Fulvestrant. For estrogen treatment, cells were treated with media containing double times charcoal stripped serum (DCDT) for 72 hours prior to Vehicle or b-estradiol treatment for 6 hours.

tag: cell type

tag: passages

value: Charcoal stripped serum for 72 hours - vehicle

tag: chip antibody

value: ARID1A HPA005456


title: 293_pCW57_PNUTSW401A_Dox_DRB_10_PolII_Rep2

description: Pol II ChIP-seq

tag: antibody

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: Patient S12 0 days post treatment

value: tumor

value: NON-UVEAL

value: PD


title: MCF7_Cas9_1C3_Plasmid library  rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4335_MCF7_Cas9_1C3_Plasmid_Plasmid

value: MCF7 Cas9 expressing cells

tag: time point

value: Pooled gRNA library without infecting cells


title: PvGR_I4

value: Whole brain

value: PV Input RNA

value: cytoplasmic RNA


title: 293_pCW57_PNUTSW401A_Dox_DRB_10_PolII_Rep1

description: Pol II ChIP-seq


title: 293_pCW57_PNUTSW401A_Dox_DRB_15_PolII_Rep2

description: Pol II ChIP-seq


title: Patient S7 5 days post treatment

tag: tag


title: MCF7 Cas9 Day 12 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4348_MCF7_Cas9_1C3_Day_12_Day_12

source_name: MCF7 Cas9 Day 12 gRNA-seq

value: ER+  Breast Cancer Cell Line

value: Day 12 of Infection with pooled gRNA library


title: vGlut2GR_E5

value: vGluT2 Input RNA


title: Patient S12 3 days post treatment

tag: time (days post treatment)


title: PvGR_I2


title: Patient S12 52 days post treatment

tag: disease


title: MCF7 Cas9 Day 12 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4349_MCF7_Cas9_1C3_Day_12_Day_12


title: Patient S7 26 days post treatment

tag: response


title: PvGR_I1

tag: strain background


title: Patient S3 0 days post treatment


title: 293_pCW57_PNUTS_WT_Dox_DRB_10_PolII_Rep2

description: Pol II ChIP-seq

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: MCF7-ARID1A_Vehicle rep 3

source_name: ARID1A ChIP-seq Vehicle

value: Vehicle


title: 293_pCW57_PNUTS_WT_Dox_DRB_15_PolII_Rep1

description: Pol II ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline+DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: WT-miRNA-F1

source_name: WT Input RNA

tag: condition

value: WT Input RNA


title: MCF7 Cas9 Day 9 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4345_MCF7_Cas9_1C3_Day_9_Day_9

source_name: MCF7 Cas9 Day 9 gRNA-seq

value: Day 9 of Infection with pooled gRNA library


title: 293_pCW57_PNUTS_WT_Dox_DRB_5_PolII_Rep2

description: Pol II ChIP-seq

tag: growth conditions


title: Patient S9 3 days post treatment

value: tumor


title: Patient S3 52 days post treatment

value: NON-UVEAL


title: MCF7 Cas9 Day 15 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4350_MCF7_Cas9_1C3_Day_15_Day_15

value: Day 15 of Infection with pooled gRNA library


title: vGlut2GR_E4

tag: tissue


title: vGlut2GR_Ago2_C5

value: AgoTag

value: vGluT2 AgoTag IP

value: Ago2 RNA IP


title: Patient S3 3 days post treatment

value: PD


title: 293_pCW57_PNUTS_WT_Dox_DRB_10_PolII_Rep1

description: Pol II ChIP-seq

tag: treatment


title: 293_pCW57_PNUTSW401A_Dox_DRB_15_PolII_Rep1

description: Pol II ChIP-seq

tag: cell line

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 293_pCW57_PNUTS_WT_Dox_DRB_5_PolII_Rep1

description: Pol II ChIP-seq


title: Patient S10 0 days post treatment


title: vGlut2GR_E3

tag: genotype/variation

value: Whole brain

value: cytoplasmic RNA


title: 293_pCW57_PNUTSW401A_Dox_DRB_PolII_Rep1

description: Pol II ChIP-seq


title: vGlut2GR_Ago2_C1


title: vGlut2GR_E2

value: vGluT2 Input RNA


title: Patient S9 52 days post treatment


title: MCF7 Cas9 Day 9 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4346_MCF7_Cas9_1C3_Day_9_Day_9

value: MCF7 Cas9 expressing cells

value: ER+  Breast Cancer Cell Line


title: MCF7 Cas9 Day 12 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4347_MCF7_Cas9_1C3_Day_12_Day_12

value: Day 12 of Infection with pooled gRNA library


title: vGlut2GR_Ago2_C4


title: 293_pCW57_PNUTSW401A_Dox_DRB_5_PolII_Rep1

description: Pol II ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline+DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: Patient S9 0 days post treatment


title: 293_pCW57_PNUTS_WT_Dox_DRB_PolII_Rep1

description: Pol II ChIP-seq

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: MCF7 Cas9 Day 9 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4344_MCF7_Cas9_1C3_Day_9_Day_9

value: Day 9 of Infection with pooled gRNA library


title: vGlut2GR_Ago2_C2


title: vGlut2GR_Ago2_C3


title: MCF7 Cas9 Day 7 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4342_MCF7_Cas9_1C3_Day_7_Day_7

source_name: MCF7 Cas9 Day 7 gRNA-seq

value: Day 7 of Infection with pooled gRNA library


title: MCF7 Cas9 Day 7 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4343_MCF7_Cas9_1C3_Day_7_Day_7


title: PvGR_Ago2_H3

value: PV AgoTag IP


title: Patient S8 0 days post treatment

value: tumor

value: NON-UVEAL


title: Patient S10 11 days post treatment


title: MCF7 Cas9 Day 7 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4341_MCF7_Cas9_1C3_Day_7_Day_7


title: PvGR_Ago2_H2

value: AgoTag

value: Ago2 RNA IP


title: 293_pCW57_PNUTSW401A_Dox_Spt5_Rep2

description: Spt5 ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: MCF7 Cas9 Day 3 rep 3

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4340_MCF7_Cas9_1C3_Day_3_Day_3

source_name: MCF7 Cas9 Day 3 gRNA-seq

value: Day 3 of Infection with pooled gRNA library


title: 293_pCW57_PNUTSW401A_Dox_Spt5PO4_Rep2

description: Spt5-PO4 ChIP-seq

source_name: HEK293+pCW57 bla Avi-PNUTS W401A

value: rabbit anti phospho-Spt5 this work


title: MCF7 Cas9 Day 3 rep 2

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4339_MCF7_Cas9_1C3_Day_3_Day_3

value: MCF7 Cas9 expressing cells

value: ER+  Breast Cancer Cell Line


title: PvGR_Ago2_H1

value: Whole brain


title: 293_pCW57_PNUTS_WT_Dox_Spt5PO4_Rep2

description: Spt5-PO4 ChIP-seq


title: Patient S8 3 days post treatment

value: PD


title: Patient S19 0 days post treatment

value: UVEAL

value: PR


title: Gad2GR_Ago2_A4

value: Gad2 AgoTag IP


title: MCF7 Cas9 Day 3 rep 1

description:
processed data file:
mcf7_cas9_counts1.tsv
jc4338_MCF7_Cas9_1C3_Day_3_Day_3


title: HFF1- input

city: Illkirch

first: Farrah

last: El-Saafin

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg38 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: purified DNA from the control fibroblasts

growth_protocol: A biopsy was taken from the patient which was used to establish a fibroblast cell line (LR14). Control fibroblasts were HFF1 fibroblasts (ATCC). Fibroblasts were cultured on 15cm2 plates in standard fibroblast medium (DMEM/F12 with GLUTAMAX, 10% FCS, 15mM HEPES and pen/strep) at 37 oC. Drosophila S2 cells, used for ChIP spike-in were cultured in standard medium (Schneider, 10% heat inactivated FCS and 0.5% pen/strep) at 28oC with no CO2.

extract_protocol:
phenol-chloroform
SQ00/SIL-01-SR library preparation kit for ChIP-seq was used according to manufacturer's instructions

treatment_protocol: For each ChIP experiment, a minimum of 20 x 15 cm2 plates were used per genotype. Approximately 2 x 10^6 fibroblast cells were seeded onto each 15 cm^2 plate, then the following day the fibroblasts were fixed in 1% PFA for 10 minutes at room temperature, then the PFA was quenched with glycine at a final concentration of 125mM for 5 minutes at room temperature. After 2 washes in cold PBS, fibroblasts were scraped, and pelleted. Nuclei were isolated by incubating cells with nuclear isolation buffer (50mM Tris-HCl pH 8.0, 2mM EDTA pH 8.0, 0.5% NP40, 10% glycerol, and 1x protease inhibitors) for 10 minutes at 4 degree C with gentle agitation, followed by centrifugation at 13K RPM to pellet the nuclei. Nuclei were resuspended in sonication buffer (0.1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and 1x protease inhibitors) then chromatin was sheared with the Covaris E220 sonicator and chromatin concentration was measured with the Qubit 3.0 (ThermoFischer). A minimum of 50ug of chromatin was used for each IP, which was diluted in ChIP dilution buffer (0.5% NP40, 16.7mM Tris-HCl pH8.0, 1.2mM EDTA, 167mM NaCl and 1x protease inhibitor) and each sample was spiked with 1/10 amount of Drosophila sheared chromatin for normalization. Antibody used for the ChIP-seq was the anti-pol II CTD (1PB 7G5), which was incubated with the chromatin overnight with gentle agitation at 4 degrees C. The following day, magnetic beads were isolated and washed for 5 minutes at 4 degrees C, once with low salt wash buffer (0.1% SDS, 0.5% NP40, 2mM EDTA, 150mM NaCl, 20mM and Tris-HCl pH8.0), high salt wash buffer (0.1% SDS, 0.5% NP40, 2mM EDTA, 500mM NaCl, 20mM and Tris-HCl pH8.0), and LiCl wash buffer (0.2M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH8.0), then twice with TE buffer, then the beads were incubated in freshly prepared elution buffer (1% SDS, 0.1M NaHCO3) at 65 degrees C with shaking to elute complexes. Crosslinks were reversed with by adding NaCl at a final concentration of 0.2M overnight as well as 50ug/ml RNase A at 65 degrees C and the following day the samples were treated with Protinase K Tris-HCl pH7.9 and EDTA.


title: Patient S19 17 days post treatment


title: PvGR_Ago2_H4

value: PV AgoTag IP


title: Gad2GR_Ago2_A3


title: 293_pCW57_PNUTS_WT_Dox_PolII_Rep2

description: Pol II ChIP-seq

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: LR14 -IP

source_name: human fibroblasts (and 1/10 spiked in drosophila DNA)

value: anti-pol II CTD (1PB 7G5)


title: Patient S17 0 days post treatment

value: tumor

value: NON-UVEAL


title: Patient S17 52 days post treatment


title: Gad2GR_Ago2_A2

value: AgoTag

value: Ago2 RNA IP


title: 293_pCW57_PNUTSW401A_Dox_Spt5_Rep1

description: Spt5-PO4 ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 293_pCW57_PNUTSW401A_Dox_PolII_Rep2

description: Pol II ChIP-seq


title: Patient S8 52 days post treatment


title: Tumor-bearing bone marrow cells from Pax5+/- mouse treated with antibiotics, biological replicate 1

description: Gene expression data from bone marrow leukemic cells from Pax5+/- mice treated with a cocktail of antibiotics during 8 weeks.

tag: Sex

value: Female

value: Total Bone marrow

value: Antibiotics


title: HFF1 - IP


title: Sample 18: SigB Dark 3

city: Galway

first: Amber

middle: Louise

last: Dorey

state: Galway

address: University Road

department: Microbiology

country: Ireland

institute: National University of Ireland Galway

data_processing:
Reads were mapped to the complete sequenced genome of reference strains EGDe (ENSEMBL ASM19603v1) using Bowtie 2 v 2.2.4 with standard parameters and --sensitive-local (Langmead and Salzberg 2012).
BAM alignment files were used as input for read counting using htseq-count (HTSeq version 0.6.0) (Anders et al. 2015).
Differential expression analyses were performed using DESeq2 in R v 3.2.2 (Love et al. 2014).
The differential expression was reported as log2 fold changes, wtih p-values adjusted by the DESeq2 default Benjamini-Hochberg (BH) adjustment method and genes with a >2-fold change in expression and a p-value < 0.05 were considered as DE.
Supplementary_files_format_and_content: Comma separated text files.

organism: Listeria monocytogenes

source_name: SigB Dark

growth_protocol: Cells were cultured in BHI broth at 30°C to OD600 ~0.2

extract_protocol:
Samples were stabilised in RNAlater and RNA was extracted using Rneasy mini prep kit (Qiagen).  The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (Illumina) was used to prepare the cDNA fragment libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultures were divided in two in darkness, with one aliquot kept in darkness and the other exposed to 0.6 mW cm2 470 nm light for 20 min.

tag: strain

value: EGDe {delta}sigB

tag: growth condition

value: Dark


title: Sample 17: SigB Dark 2


title: 293_pCW57_PNUTSW401A_Dox_PolII_Rep1

description: Pol II ChIP-seq


title: Patient S17 3 days post treatment

value: PD


title: 293_pCW57_PNUTS_WT_Dox_Spt5_Rep2

description: Spt5 ChIP-seq

source_name: HEK293+pCW57 bla Avi-PNUTS WT

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)


title: Sample 16: SigB Dark 1


title: 293_pCW57_PNUTS_WT_Dox_Spt5PO4_Rep1

description: Spt5-PO4 ChIP-seq

value: rabbit anti phospho-Spt5 this work


title: 293_pCW57_PNUTS_WT_Dox_Spt5_Rep1

description: Spt5 ChIP-seq


title: Sample 15: SigB Light 3

source_name: SigB Light

value: Light


title: FH-rep2

city: Shanghai

first: Wenlin

last: Li

address: 800 Xiangyin Road

institute: Second Military Medical University

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values

source_name: Liver

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

tag: cell type

value: freshly isolated hepatocytes


title: LBDXL 3W-rep2

value: LBDXL hepatocytes at 3 weeks


title: LBDXL 3W-rep1


title: FH-rep1


title: Sample 14: SigB Light 2


title: PEX100 Control 2

type: protein

city: St Louis

first: Jing

last: Hughes

state: Missouri

address: 660 S Euclid

institute: Washington University

description: Signal Ratio is determined using average signal intensity of replicate spots for each pair of site-specific and phospho site-specific antibody,

hyb_protocol: Array slides were blocked with dry milk and blocking solution for 2 hours at room temp, then rinsed with sterile water x 10 times. Coupling reaction was performed according to manufacturer's instructions for 2 hours at room temp with orbital shaking. Slides were rinsed with water 10 times, then developed with Cy3-Streptavidin at 0.5mg/mL x 20 minutes, washed 3 x 10 minutes in wsh solution, then rinsed 10x in water, and spun dry.

scan_protocol: Slides were returned to FullMoonBio for scanning and image analysis services.

data_processing:
Slides were scanned and interpreted by FullMoonBio. Data include 1) signal intensity for each spot, 2) average signal intensity for replicates, 3) coefficient of variation for replicates, 4) ratio of phospho vs site-specific antibody signal, 5) fold change between control and treated sample.
Normalized data = Average Signal Intensity of Replicate Spots / Median Signal. Fold change = Treatment Sample / Control Sample. Ratio analysis = (Signal Intensity of Phospho Site-Specific Antibody) / (Signal Intensity of Site-Specific Antibody)

molecule: protein

source_name: Pancreatic islet

label_protocol: 200ug total protein per sample were conjugated with biotin and DMF for 2 hours at room temp.

growth_protocol: Homozygous INS1-Cre x IFT88-Flox (KO) or INS1-CreERT2 x IFT88-Flox (Control WT) mice were weaned at age 3 weeks and maintained on standard rodent chow diet. Animals were 10 weeks of age at time of sacrifice.

extract_protocol: 240 size-matched islets were selected from each sample. Islets were hand-picked into eppendorf tubes, washed once in HBSS buffer, then lysed in extraction buffer containing protease inhibitors and metal beads. Cells were vortexed every 10 minutes x 5 times, centrifuged 10000g x 5 minutes, transferred to new tube and centrifuged again to obtain cleared lysates. Samples were quantified and QC'ed on a DeNovix machine to obtain an A260/280 ratio of 0.57-0.60.

treatment_protocol: Whole pancreata were digested with collagenase at 34C x 10 minutes with shaking, then centrifuged 1000rpm x 2 minutes and washed twice in HBSS buffer. Islets were hand-picked into 11mM glucose RPMI media containing 10% FBS and 1% PS. After overnight incubation, islets were hand-picked into collection tubes for protein extraction.

value: IFT88 fl/fl mice

tag: age

tag: gender

value: male


title: PEX100 IFT88 KO 2


title: PEX100 IFT88 KO 1


title: FH YAP-/--rep2

value: freshly isloaded YAP-/- hepatocytes


title: Sample 13: SigB Light 1


title: 293FlpIN_pcDNA5_NS1A_pDox_Spt5PO4_Rep2

description: Spt5-PO4 ChIP-seq

source_name: HEK293 Flp-in T-REx pcDNA5 HA-NS1A

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

tag: antibody

value: NS1A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: FH YAP-/--rep1


title: Sample 12: C56A Dark 3

source_name: C56A Dark

value: EGDe Lmo0799 C56A


title: 293_pCW57_PNUTSW401A_Dox_Spt5PO4_Rep1

description: Spt5 ChIP-seq

value: DMEM 10% FCS,  +blasticidin, +doxycycline

value: PNUTS W401A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: PEX100 Control 1


title: BM 3W YAP-/--rep2

value: BM YAP-/- hepatocytes at 3 weeks


title: 293FlpIN_pcDNA5_NS1A_mDox_Spt5PO4_Rep2

description: Spt5-PO4 ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin

value: control without doxycycline induction


title: Sample 11: C56A Dark 2

value: Dark


title: BM 3W YAP-/--rep1


title: Sample 10: C56A Dark 1


title: Synovial tissue_ACLT_rep4

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

hyb_protocol: After purification, cRNA was hybridized overnight to a rat microarray slide (Rat miRNA Microarray, Release 21.0, 8×15K; Agilent Technologies) at 20 rpm at 55°C.

scan_protocol: Fluorescent images of the microarray slide were scanned using a DNA Microarray Scanner (G2505C; Agilent Technologies).

data_processing: The fluorescent intensity of each spot was quantified using Feature Extraction software (Agilent Technologies).

organism: Rattus norvegicus

source_name: Synovial tissue, ACLT, replicate 4

label_protocol: Cy3-labelled cRNA was prepared from total RNA (50 ng) using the Low Input Quick Amp Labeling Kit according to the manufacturer’s protocol (Agilent Technologies, CA, USA).

extract_protocol: Total RNA was isolated using an RNAiso plus kit (Takara Bio, Shiga, Japan).

treatment_protocol: The anterior cruciate ligament transection (ACLT) procedure for producing an OA model was slightly modified from the protocol described previously. Briefly, the left medial parapatellar skin was incised to perform medial arthrotomy. The ACL was exposed by dislocating the patella laterally and then transected. Adequacy of the section was confirmed by positive anterior draw sign. After relocation of the patella, the capsule and skin were closed with 4-0 silk thread (Matsudaika Kogyo, Tokyo, Japan). For the sham operation, the ACL was exposed but not transected. Synovial tissue from the opposite side of the incision made by the ACLT procedure was collected from the left knee 2 weeks after ACLT or sham operation.

value: Sprague-Dawley

value: Synovial tissue

tag: protocol

value: ACLT


title: 293FlpIN_pcDNA5_NS1A_pDox_Spt5_Rep2

description: Spt5 ChIP-seq

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)


title: Synovial tissue_ACLT_rep3

source_name: Synovial tissue, ACLT, replicate 3


title: Synovial tissue_Sham surgery_rep3

source_name: Synovial tissue, Sham surgery, replicate 3

value: Sham surgery


title: 293FlpIN_pcDNA5_NS1A_mDox_Spt5_Rep2

description: Spt5 ChIP-seq


title: BM 3W-rep2

value: BM hepatocytes at 3 weeks


title: Sample 9: C56A Light 3

source_name: C56A Light

value: Light


title: 293_pCW57_PNUTS_WT_Dox_PolII_Rep1

description: Pol II ChIP-seq

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: PNUTS  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 293FlpIN_pcDNA5_NS1A_pDox_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

value: NS1A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: Sample 8: C56A Light 2

value: EGDe Lmo0799 C56A


title: Sample 7: C56A Light 1


title: Hap1_PSMG1_pA-MT_PolII_Rep2

description: Pol II ChIP-seq

growth_protocol: IMDM 10% FCS,

value: IMDM 10% FCS,

value: no treatment


title: 293FlpIN_pcDNA5_NS1A_mDox_PolII_Rep1

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin


title: Synovial tissue_ACLT_rep2

source_name: Synovial tissue, ACLT, replicate 2


title: Sample 6: Wild-Type Dark 3

source_name: Wild-Type Dark

value: EGDe


title: Synovial tissue_Sham surgery_rep4

source_name: Synovial tissue, Sham surgery, replicate 4


title: Synovial tissue_Sham surgery_rep2

source_name: Synovial tissue, Sham surgery, replicate 2


title: BM 3D-rep1

value: BM hepatocytes at 3 days


title: BM 1D-rep2

value: BM hepatocytes at 1 day


title: Hap1_PolII_Rep2

description: Pol II ChIP-seq


title: CD4+ T cells: Input - ChIPseq

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were aligned to mm10 by Bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.01
The uniquely mapped reads were used to call peak with MACS2 using a q value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each RNAseq Sample and bigwig file with quantitative data for Chip Sample

source_name: CD4+ T cells

extract_protocol:
The ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: Naive CD4+ T cells were activated and infected with retrovirus Tox2:HA-RV-GFP under neutral condition, after which GFP+ cells were sorted and cultured in Tfh-like conditions.

value: Spleen+Lymph nodes

tag: genotype

value: wild type


title: BM 1D-rep1


title: Synovial tissue_ACLT_rep1

source_name: Synovial tissue, ACLT, replicate 1

value: Sprague-Dawley

value: Synovial tissue

value: ACLT


title: CD4+ T cells: Tox2:HA - ChIPseq


title: Sample 4: Wild-Type Dark 1

value: Dark


title: HLA-A2 surface expression replicate 1

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description: HLA-A*02:01 library sorted for high surface expression (replicate 1)

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script (Fragment A Read 1): python Paired_read_fuser.py --path directory/ --read1 sample_R1.fastq --read2 sample_R1.fastq --wtseq TCTCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGC --read1_overlap_start 62 --read1_overlap_end 173 --mode R1
Fuser script (Fragment A Read 2): python Paired_read_fuser.py --path directory/ --read1 sample_R2.fastq --read2 sample_R2.fastq --wtseq GAGGGTCCGGAGTATTGGGACGGGGAGACACGGAAAGTGAAGGCCCACTCACAGACTCACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCGTCCAGAGGATGTATGGCTGCGACGTGGGGTCGGACTGGCGCTTCCTCCGCGGGTACCACCAGTACGCCTACGACGGC --read2_overlap_start 32 --read2_overlap_end 230 --mode R2
Fuser script (Fragment B Read 1): python Paired_read_fuser.py --path directory/ --read1 sample_R1.fastq --read2 sample_R1.fastq --wtseq AGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGTCCGGAGTATTGGGACGGGGAGACACGGAAAGTGAAGGCCCACTCACAGACTCACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCGTCCAGAGGATGTATGGCTGCGACGTGGGGTCGGACTGG --read1_overlap_start 18 --read1_overlap_end 228 --mode R1
Fuser script (Fragment B Read 2): python Paired_read_fuser.py --path directory/ --read1 sample_R2.fastq --read2 sample_R2.fastq --wtseq AAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCGGCCCATGTGGCGGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGT --read2_overlap_start 29 --read2_overlap_end 212 --mode R2
Aligner script (Fragment A Read 1): python Fused_read_aligner.py --path directory/ --infile sample_R1.fast_R1_qc1 --referenceDNA TCTCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGC --referenceAA SHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDS --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script (Fragment A Read 2): python Fused_read_aligner.py --path directory/ --infile sample_R2.fast_R2_qc1 --referenceDNA GAGGGTCCGGAGTATTGGGACGGGGAGACACGGAAAGTGAAGGCCCACTCACAGACTCACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCGTCCAGAGGATGTATGGCTGCGACGTGGGGTCGGACTGGCGCTTCCTCCGCGGGTACCACCAGTACGCCTACGACGGC --referenceAA EGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script (Fragment B Read 1): python Fused_read_aligner.py --path directory/ --infile sample_R1.fast_R1_qc1 --referenceDNA AGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGTCCGGAGTATTGGGACGGGGAGACACGGAAAGTGAAGGCCCACTCACAGACTCACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTTCTCACACCGTCCAGAGGATGTATGGCTGCGACGTGGGGTCGGACTGG --referenceAA SDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDW --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script (Fragment B Read 2): python Fused_read_aligner.py --path directory/ --infile sample_R2.fast_R2_qc1 --referenceDNA AAGGATTACATCGCCCTGAAAGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCAGCTCAGACCACCAAGCACAAGTGGGAGGCGGCCCATGTGGCGGAGCAGTTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGT --referenceAA KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQR --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: python mapCounts.py --path directory/ --infile filename
MapRatios script: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: 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 Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.  Data was then assembled from the different fragments/reads to span the full sequence.  Maximum depletion was set to log(base2) enrichment ratio = -5.
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 frequency of each mutation in the naive plasmid library.

source_name: Synthetic coding sequence

growth_protocol: Expi293F cells were cultured in Expi293 Expression Medium (Life Technologies) in 8% CO2 at 37 deg C and 125 rpm.

extract_protocol:
Total RNA was extracted from the collected cells, and cDNA was reverse transcribed using high-fidelity Accuscript primed with VN-internal-rev1 (5’-GAACTTGTGGCCGTTTACGT-3’), which anneals to the VN moiety and thereby avoids endogenous HLA-A2 transcripts. The diversified regions of interest in both the naive plasmid library and in the cDNA samples were amplified by PCR for deep sequencing.  Two rounds of PCR amplification were applied using primers containing overhanging sequences; the first round added bases for annealing to the Illumina sequencing primers, and the second round added unique barcodes and Illumina adaptors.
Primer pairs for 1st round of PCR (Fragment A): Illumina_A02_47_for (TCTTTCCCTACACGACGCTCTTCCGATCTCCGAGCAGAAATTGATCAGC) and Illumina_A02_468_rev (TGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTCAGGGCGATGTAATCC).
Primer pairs for 1st round of PCR (Fragment B): Illumina_A02_199_for (TCTTTCCCTACACGACGCTCTTCCGATCTcagttcgtgcggttcgac) and Illumina_A02_667_rev (TGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACAGCGTGGTGAGTCATATG).
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 SP using a 2x250 nt paired end protocol.

treatment_protocol: HLA-A2 was expressed from the pCEP4 (Invitrogen) episomal plasmid.  Cells were transiently transfected using Expifectamine (Life Technologies), with the plasmid library diluted by a large excess of carrier DNA to minimize the number of coding sequences acquired per cell.  Cells were harvested 24-25 hours post-transfection.  For analyzing surface HLA-A2 expression in wild-type Expi293F, cells were stained with anti-myc Alexa 647 (clone 9B11, Cell Signaling Technology).  For analyzing BiFC in cells stably expressing VC-fused TAPBPR-TM, cells were unstained.  Highly fluorescent cells were sorted on a BD FACSAria II after first gating for single cell events (based on FSC/SSC properties) and excluding propidium iodide-positive dead cells.

tag: protein

tag: collected cells

tag: sort gate

value: Top 0.5% of the total population for Alexa 647 fluorescence

tag: molecule subtype


title: HLA-A2 surface expression replicate 2

description: HLA-A*02:01 library sorted for high surface expression (replicate 2)


title: CD4+ T cells: Th0 (Tox2) - RNAseq

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: Naive CD4+ T cells were activated and infected with retrovirus under neutral condition, after which GFP+ cells were sorted and cultured in Th0 or Tfh-like conditions.

tag: tissue


title: BM 3W-rep1

value: BM hepatocytes at 3 weeks


title: Sample 3: Wild-Type Light 3

source_name: Wild-Type Light

value: Light


title: HLA-A2 BiFC replicate 2

description: HLA-A*02:01 library sorted for high BiFC with TAPBPR-TM (replicate 2)

value: Top 20% of Venus-positive cells (1.0% of the total population)


title: CD4+ T cells: Tfh-like (Tox2) - RNAseq


title: Sample 2: Wild-Type Light 2


title: BM 3D-rep2


title: HLA-A2 BiFC replicate 1

description: HLA-A*02:01 library sorted for high BiFC with TAPBPR-TM (replicate 1)


title: Synovial tissue_Sham surgery_rep1

source_name: Synovial tissue, Sham surgery, replicate 1

value: Sham surgery


title: Sample 1: Wild-Type Light 1


title: CD4+ T cells: Tfh-like (GFP) - RNAseq


title: Naive HLA-A*02:01 library

description: HLA-A*02:01 naive single site-saturation mutagenesis library

value: plasmid DNA


title: Sample 5: Wild-Type Dark 2


title: SET100 IFT88 KO 2

description: Normalized signal is calculated from average intensity of replicate spots / median signal.

data_processing: Slides were scanned and interpreted by FullMoonBio. Data include 1) signal intensity for each spot, 2) average signal intensity for replicates, 3) coefficient of variation for replicates, 4) normalized average/median signal, 5) fold change between control and treated sample.

growth_protocol: Homozygous INS1-Cre x IFT88-Flox (KO) or INS1-CreERT2 x IFT88-Flox (Control WT) mice were weaned at age 3 weeks and maintained on standard rodent chow diet. Animals were 8 weeks of age at time of sacrifice.

extract_protocol: 250 size-matched islets were selected from each sample. Islets were hand-picked into eppendorf tubes, washed once in HBSS buffer, then lysed in extraction buffer containing protease inhibitors and metal beads. Cells were vortexed every 10 minutes x 5 times, centrifuged 10000g x 5 minutes, transferred to new tube and centrifuged again to obtain cleared lysates. Samples were quantified and QC'ed on a DeNovix machine to obtain an A260/280 ratio of 0.57-0.60.

value: male


title: SET100 Control 2

value: IFT88 fl/fl


title: CD4+ T cells: Th0 (GFP) - RNAseq


title: SET100 Control 1


title: WT15and16PC

status: Public on Oct 29 2019

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina Real Time Analysis software (RTA) software was used for base calling.
Sequencing data were demultiplexed using the bcl2fastq Conversion Software (v. 2.20, Illumina; San Diego, California, USA).
Reads were mapped to mm10 with bowtie2 using end-to-end sensitive -k 20 parameters (HTSstation, David et al, 2014).
Reads Per Kilobase per Million reads (RPKM) were calculated from the raw counts with program rnacounter 1.5.2 (https://pypi.python.org/pypi/rnacounter).
Normalisation and differential analysis were done with the R packages limma and voom. Only genes with a minimum count of 50 in at least one a the compared samples were considered.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts with Ensembl gene ID, tab separated RPKM with Ensembl gene ID

molecule: polyA RNA

source_name: Blood monocytes

growth_protocol: Apcfl/fl mice (Shibata, Science 1997, a kind gift of Tatiana Petrova, University of Lausanne, Switzerland) were crossed to Cdx2CreERT2 mice (The Jackson Laboratory, Charles River, L'Arbresle, France).

extract_protocol:
Total RNA was prepared from 2E5 -5E5 cells and collected in quadruplicates using PicoPure RNA isolation kit (Arcturus).
Illumina TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, California, USA) was used for library preparation

treatment_protocol: CreERT2 recombinase was activated at age of 8 to 10 weeks by a single i.p. injection of 25mg/kg body weight Tamoxifen (Sigma) in corn oil.

tag: disease

value: Healthy

tag: transgene

value: No

tag: agent

value: Blood

value: monocyte

tag: group

tag: replicate


title: WtaCN

source_name: Colon stromal cells

tag: strain

value: Colon

value: stromal cells


title: WT6CN

tag: cell type


title: WT18CE

source_name: Colon epithelial cells

value: epithelial cells


title: WT15PG

source_name: Blood neutrophils

value: neutrophils


title: WT1CN


title: WT16PG


title: WtaCE


title: SET100 IFT88 KO 1

source_name: Pancreatic islet

tag: genotype/variation

tag: age


title: WT13PG


title: WT11and12PC


title: WT11CE


title: WT10PC


title: T9PC

value: Tumor bearing

value: Cdx2CreERT2 - Apc fl/fl

value: Tamoxifen


title: T9PG


title: T8and10PG


title: T8PC


title: T5PG


title: WT8CN


title: T5CG

source_name: Colon tumor neutrophils

value: Colon tumor


title: LX2_TGFb1+CM272_R1

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

institute: CIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized, independently for each cell line, with Bioconductor software using RMA algorithm.

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: LX2 cells were cultured as described by Xu, L., Hui, A.Y., Albanis, E., Arthur, M.J., O'Byrne, S.M., Blaner, W.S., Mukherjee, P., Friedman, S.L., and Eng, F.J. (2005). Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut 54, 142-151

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: LX-2 cells were pretreated with CM272 (400nM) or vehicle (0.01%DMSO) for 24 hours followed by incubation of TGFβ1 (5ng/ml) for another 24 hours.


title: LX2_TGFb1_R2


title: WT17CE


title: T5CC

source_name: Colon tumor monocytes

value: monocytes


title: LX2_TGFb1_R1


title: LX2_TGFb1+CM272_R2


title: T4CG


title: WT14PG


title: WT13and14PC


title: T3CG


title: T1CE

source_name: Colon tumor epithelial cells


title: T1CN

source_name: Colon tumor stromal cells


title: T2CN


title: T4CE


title: T18CN


title: T1CG


title: T3CC


title: T18PC


title: T17PG


title: T4CC


title: T17CN


title: T17CC


title: T5CE


title: T2CE


title: STZ Rep #4_small RNA

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
small RNA
Streptozotocin-induced diabetic model
obob_STZ_RPMMM_all.csv
Sample name:
STZ04_GGCTAC_L008_R1_001

data_processing:
Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9, rn6, and hg19 for mouse, rat, and monkey small RNA-seq, mm10 and rn6 for mouse and rat RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.

source_name: liver

extract_protocol:
RNA extraction protocol not provided.
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: liver


title: STZ Rep #2_small RNA

description:
small RNA
Streptozotocin-induced diabetic model
obob_STZ_RPMMM_all.csv
Sample name:
STZ02_ACAGTG_L007_R1_001


title: STZ Rep #5_small RNA

description:
small RNA
Streptozotocin-induced diabetic model
obob_STZ_RPMMM_all.csv
Sample name:
STZ05_CTTGTA_L008_R1_001


title: STZ Rep #1_small RNA

description:
small RNA
Streptozotocin-induced diabetic model
obob_STZ_RPMMM_all.csv
Sample name:
STZ01_TGACCA_L007_R1_001


title: ob/ob Rep #4_small RNA

description:
small RNA
Obese mouse with mutation in the leptin receptor
obob_STZ_RPMMM_all.csv
Sample name:
OBOB4_AGTTCC_L008_R1_001


title: ob/ob Rep #3_small RNA

description:
small RNA
Obese mouse with mutation in the leptin receptor
obob_STZ_RPMMM_all.csv
Sample name:
OBOB3_AGTCAA_L008_R1_001


title: ob/ob Rep #2_small RNA

description:
small RNA
Obese mouse with mutation in the leptin receptor
obob_STZ_RPMMM_all.csv
Sample name:
OBOB2_ACTTGA_L007_R1_001


title: ob/ob and STZ control Rep #5_small RNA

description:
small RNA
Control mouse for the ob/ob and STZ treatments
obob_STZ_RPMMM_all.csv
Sample name:
LEAN5_TAGCTT_L008_R1_001


title: ob/ob and STZ control Rep #4_small RNA

description:
small RNA
Control mouse for the ob/ob and STZ treatments
obob_STZ_RPMMM_all.csv
Sample name:
LEAN4_GATCAG_L008_R1_001


title: ob/ob and STZ control Rep #3_small RNA

description:
small RNA
Control mouse for the ob/ob and STZ treatments
obob_STZ_RPMMM_all.csv
Sample name:
LEAN3_TTAGGC_L007_R1_001


title: ob/ob Rep #1_small RNA

description:
small RNA
Obese mouse with mutation in the leptin receptor
obob_STZ_RPMMM_all.csv
Sample name:
OBOB1_CAGATC_L007_R1_001


title: ob/ob and STZ control Rep #2_small RNA

description:
small RNA
Control mouse for the ob/ob and STZ treatments
obob_STZ_RPMMM_all.csv
Sample name:
LEAN2_CGATGT_L007_R1_001


title: ob/ob and STZ control Rep #1_small RNA

description:
small RNA
Control mouse for the ob/ob and STZ treatments
obob_STZ_RPMMM_all.csv
Sample name:
LEAN1_ATCACG_L007_R1_001


title: 6dpp male gonad rep-3

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Testies

growth_protocol: Timed matings were performed by placing a male mouse with two females in a cage

extract_protocol:
Gonads were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The cDNA library was constructed with a SMARTer® Ultra Low Input RNA for lllumina® Sequencing kit (Clontech Laboratories) and sequenced on an Illumina HiSeq 2500.

treatment_protocol: Females were checked for the presence of vaginal plugs the next morning. Noon of the day when the mating plug was observed was designated 0.5 dpc. On the relevant days of gestation (12.5, 13.5 and 16.5 dpc), pregnant females were euthanized with carbon dioxide. Embryonic gonads were dissected free of the mesonephros, snap frozen in liquid nitrogen, and stored at −80°C. The gonads of 6 dpp mice were also collected, immediately frozen in liquid nitrogen and stored at −80°C.

value: Testies

value: 6 dpp

value: wild type


title: T17PC


title: 16.5dpc male gonad rep-3

source_name: Gonad

value: Gonad


title: 13.5dpc male gonad rep-1


title: 6dpp male gonad rep-1


title: 13.5dpc male gonad rep-3


title: 13.5dpc male gonad rep-2


title: 12.5dpc male gonad rep-3


title: 16.5dpc male gonad rep-1


title: ob/ob Rep #5_small RNA

description:
small RNA
Obese mouse with mutation in the leptin receptor
obob_STZ_RPMMM_all.csv
Sample name:
OBOB5_ATGTCA_L008_R1_001


title: 6dpp male gonad rep-2


title: 16.5dpc male gonad rep-2


title: 16.5dpc female gonad rep-1


title: 16.5dpc female gonad rep-3


title: 16.5dpc female gonad rep-2


title: 6dpp female gonad rep-1

source_name: Ovary

value: Ovary


title: 13.5dpc female gonad rep-3


title: 6dpp female gonad rep-3


title: 6dpp female gonad rep-2


title: 12.5dpc male gonad rep-1


title: 12.5dpc female gonad rep-3


title: 13.5dpc female gonad rep-2


title: 12.5dpc female gonad rep-2


title: 13.5dpc female gonad rep-1


title: 12.5dpc female gonad rep-1


title: 12.5dpc male gonad rep-2


title: liver_Ad-Ctrl_rep1

city: shanghai

first: chao

last: sun

state: shanghai

address: 320 Yueyang Road, Xuhui District, Shanghai, China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy ofSciences

description: Gene expression after adenovirus injection 2 weeks in the mouse liver

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

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

growth_protocol: Eight-week-old male mice were injected with adenovirus 1x10^9 PFU, and liver tissue was collected two weeks later.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The corresponding adenovirus was injected into the tail vein, and the liver was taken two weeks later.

tag: gender

value: male


title: liver_Ad-378_rep1 (miR-378 overexpression)

department: Shanghai Institutes for Biological Sciences

description: Gene expression after adenovirus injection 3 weeks in the mouse liver


title: WT_I_14_R2

city: Vienna

first: Michael

last: Tscherner

address: Dr. Bohr Gasse 9/2

department: Max F. Perutz Laboratories, Department for Medical Biochemistry

country: Austria

institute: Medical University of Vienna

description: Gene expression after 14 days C. glabrata infection

hyb_protocol: Isolated, labeled cRNAs were hybridized to Agilent Whole Mouse Genome Microarrays (SurePrint G3 Mouse GE 8x60K ) and microarray slides were washed according to the standard protocol of the manufacturer.

scan_protocol: Microarray slides were scanned after washing on an Agilent Scanner G2505C using one color scan setting for SurePrint G3 Mouse GE 8x60K array slides according to the standard protocol of the manufacturer.

data_processing: Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v10.7.3. Further analyses were performed using R Bioconductor. The raw intensities were imported into Bioconductor using spot weighting and further processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. To reduce the effects of outlier arrays, arrays were weighted using the arrayWeights function of limma. Normalization between arrays was performed using the quantile method and a linear model was fitted. P-values were adjusted for multiple testing using the Benjamini & Hochberg method. Log2 intensities for IFNAR-/- and WT samples were normalized to uninfected controls first and subsequently differentially expressed genes in IFNAR-/- versus WT samples were determined for each day.

source_name: WT mouse spleen_14 day post infection

label_protocol: The Low Input Quick Amp Labeling Kit (one-color) (Agilent) was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using SV Total RNA Isolation System (Promega).

extract_protocol: For RNA isolation, the SV Total RNA Isolation System (Promega) was used according to the manufacturer’s instructions. RNA quality was checked on RNA 6000 Nano chips (Agilent) using a Bioanalyzer 2100 (Agilent).

treatment_protocol: Wild-type (C57BL/6J) and Ifnar1-/- mice (8-12 weeks old) were infected intravenously (i.v.) with 5 x 10^7 colony-forming units (CFUs) of C. glabrata (ATCC2001) (in 100 μl) per 21.5 g mouse weight. On day 1, 3, 7 and 14 post-infection, spleens were collected and stored in RNAlaterTM Stabilization Solution (Thermo Fisher Scientific). Organs were homogenized in 1.5 ml RNA lysis buffer (Promega) with occasional cooling on ice by using an Ika T10 basic Ultra-Turrax homogenizer (IKA).

tag: strain background

tag: treatment/time point

value: after 14 days C. glabrata infection

value: spleen


title: WT_PBS_14_R4

description: Gene expression uninfected

source_name: WT mouse spleen_uninfected control

value: uninfected


title: WT_I_7_R2

description: Gene expression after 7 days C. glabrata infection

source_name: WT mouse spleen_7 day post infection

value: after 7 days C. glabrata infection


title: WT_I_3_R3

description: Gene expression after 3 days C. glabrata infection

source_name: WT mouse spleen_3 day post infection

value: after 3 days C. glabrata infection


title: WT_I_3_R1


title: WT_I_3_R2


title: WT_I_1_R2

description: Gene expression after 1 day C. glabrata infection

source_name: WT mouse spleen_1 day post infection

value: after 1 day C. glabrata infection


title: IF_I_14_R1

source_name: Ifnar1-/- mouse spleen_14 days post infection


title: WT_I_1_R3


title: WT_I_1_R1


title: IF_I_14_R3


title: IF_I_7_R3

source_name: Ifnar1-/- mouse spleen_7 days post infection


title: IF_I_7_R2


title: WT_I_7_R1


title: WT_PBS_14_R2

description: Gene expression uninfected


title: IF_PBS_14_R3

description: Gene expression uninfected

source_name: Ifnar1-/- mouse spleen_uninfected control


title: IF_I_14_R2


title: IF_I_7_R1


title: IF_PBS_14_R1

description: Gene expression uninfected


title: IF_PBS_14_R2

description: Gene expression uninfected


title: WT_PBS_14_R1

description: Gene expression uninfected


title: WT_I_14_R3


title: IF_I_3_R3

source_name: Ifnar1-/- mouse spleen_3 days post infection


title: WT_I_14_R1


title: WT_PBS_14_R3

description: Gene expression uninfected


title: WT_I_7_R3


title: IF_I_3_R2


title: primary colorectal cancer AMC-R98

city: Daejeon

first: Seon-Kyu

last: Kim

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

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data for Homo sapiens were obtained from the National Center for Biotechnology Information (NCBI) genome database (assembly ID: GRCh38).
Kallisto was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 0.43.0).To estimate gene expression levels, transcripts per million (TPM) mapped reads values were calculated for each sample. The TPM data were normalised using quantile normalisation in the R language environment (version 3.2.5).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text format with log2 transformed TPM values of transcripts

source_name: primary colorectal cancer

extract_protocol:
Total RNA was isolated using an 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.
The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR.

tag: systemic recurrence

value: Yes


title: primary colorectal cancer AMC-R95

value: No


title: IF_PBS_14_R4

description: Gene expression uninfected


title: primary colorectal cancer AMC-R99

value: female


title: primary colorectal cancer AMC-R97


title: GM8

city: Tirupati

first: Guruprasad

middle: Ramarao

last: Medigeshi

state: Andhra Pradesh

address: Panguru (G.P.), Yerpedu Mandal

department: Biology

country: India

institute: Indian Institute of Science Education and Research Tirupati

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg38 genome assembly using Tophat2 version 2.1.0
Data were filtered and assembly was build using cufflinks and cuffmerge
Processed data is submitted as an Excel file with FPKM values. Differentially expressed transcripts between Control and Treated samples were identified by CuffDiff data analysis pipeline using a fold-change threshold of absolute fold-change >=1.5 and a statistically significant Student's t-test P value threshold adjusted for false discovery rate of less than 0.001. Statistically significantly enriched functional classes with a P value adjusted for false discovery rate of less than 0.05 derived using the hypergeometric distribution test corresponding to differentially expressed genes were determined using Student's t-test with Benjamini Hocheberg FDR test.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM; GROUP 3 is DMSO and GROUP 4 is TPEN

growth_protocol: Caco-2 cells were seeded in a 24-well plate at the cell density of 100,000 cells per well. On day 2 post-seeding, cells were washed twice with PBS and serum-free DMEM containing DMSO and TPEN (0.5 mM) were added to respective wells and cultured for 4 h. After 4 hours of treatment, media was removed and cells were washed twice with PBS. Cells were collected in 300 µl RNA lysis buffer (RNA prep kit-Zymo-R1051).

extract_protocol:
RNA was prepared according to the manufacturer's instructions (RNA prep kit-Zymo-R1051) and eluted in 20 µl nuclease-free water.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation, after end-repair and the addition of an ‘A’ base and SPRI cleanup. The prepared cDNA library was amplified using PCR for the enrichment of the adapter-ligated fragments. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. . The individual libraries were quantified using a NanoDrop spectrophotometer (Thermo Scientific) and validated for quality with a Bioanalyzer (Agilent Technologies). Adapter-ligated fragments are then PCR amplified and gel purified.

tag: cell line

value: Caco-2 (ATCC HTB-37)

value: Colon Adenocarcinoma cell line

tag: treatment

value: 0.5 micromolar TPEN


title: GM7


title: GM5

value: DMSO


title: primary colorectal cancer AMC-R92


title: GM6


title: primary colorectal cancer AMC-R94


title: primary colorectal cancer AMC-R91


title: primary colorectal cancer AMC-R90


title: IF_I_1_R1

source_name: Ifnar1-/- mouse spleen_1 day post infection


title: IF_I_1_R2


title: primary colorectal cancer AMC-R88


title: primary colorectal cancer AMC-R86


title: IF_I_1_R3


title: primary colorectal cancer AMC-R57


title: primary colorectal cancer AMC-R54


title: primary colorectal cancer AMC-R52


title: primary colorectal cancer AMC-R8


title: primary colorectal cancer AMC-R85


title: primary colorectal cancer AMC-R75


title: primary colorectal cancer AMC-R87


title: primary colorectal cancer AMC-R50


title: STZ Rep #3_small RNA

description:
small RNA
Streptozotocin-induced diabetic model
obob_STZ_RPMMM_all.csv
Sample name:
STZ03_GCCAAT_L007_R1_001

value: liver


title: primary colorectal cancer AMC-R49


title: primary colorectal cancer AMC-R93


title: primary colorectal cancer AMC-R295


title: primary colorectal cancer AMC-R4


title: primary colorectal cancer AMC-R39


title: primary colorectal cancer AMC-R289


title: primary colorectal cancer AMC-R34


title: primary colorectal cancer AMC-R278


title: primary colorectal cancer AMC-R290


title: primary colorectal cancer AMC-R284


title: primary colorectal cancer AMC-R270


title: primary colorectal cancer AMC-R262


title: primary colorectal cancer AMC-R258


title: primary colorectal cancer AMC-R265


title: primary colorectal cancer AMC-R25


title: primary colorectal cancer AMC-R256


title: primary colorectal cancer AMC-R245


title: primary colorectal cancer AMC-R241


title: primary colorectal cancer AMC-R261


title: primary colorectal cancer AMC-R235


title: primary colorectal cancer AMC-R243


title: primary colorectal cancer AMC-R249


title: primary colorectal cancer AMC-R232


title: primary colorectal cancer AMC-R246


title: primary colorectal cancer AMC-R233


title: primary colorectal cancer AMC-R253


title: primary colorectal cancer AMC-R293


title: primary colorectal cancer AMC-R248


title: primary colorectal cancer AMC-R231


title: primary colorectal cancer AMC-R230


title: primary colorectal cancer AMC-R229


title: primary colorectal cancer AMC-R267


title: IF_I_3_R1


title: primary colorectal cancer AMC-R225


title: primary colorectal cancer AMC-R223


title: primary colorectal cancer AMC-R2


title: primary colorectal cancer AMC-R212


title: primary colorectal cancer AMC-R168


title: primary colorectal cancer AMC-R259


title: primary colorectal cancer AMC-R183


title: primary colorectal cancer AMC-R170


title: primary colorectal cancer AMC-R162


title: primary colorectal cancer AMC-R161


title: primary colorectal cancer AMC-R167


title: primary colorectal cancer AMC-R160


title: primary colorectal cancer AMC-R158


title: primary colorectal cancer AMC-R157


title: primary colorectal cancer AMC-R156


title: primary colorectal cancer AMC-R159


title: primary colorectal cancer AMC-R155


title: primary colorectal cancer AMC-R150


title: primary colorectal cancer AMC-R146


title: primary colorectal cancer AMC-R148


title: primary colorectal cancer AMC-R143


title: primary colorectal cancer AMC-R142


title: primary colorectal cancer AMC-R23


title: primary colorectal cancer AMC-R141


title: primary colorectal cancer AMC-R147


title: primary colorectal cancer AMC-R140


title: primary colorectal cancer AMC-R138


title: primary colorectal cancer AMC-R137


title: primary colorectal cancer AMC-R135


title: primary colorectal cancer AMC-R133


title: primary colorectal cancer AMC-R136


title: primary colorectal cancer AMC-R139


title: primary colorectal cancer AMC-R128


title: primary colorectal cancer AMC-R129


title: primary colorectal cancer AMC-R125


title: primary colorectal cancer AMC-R127


title: primary colorectal cancer AMC-R134


title: primary colorectal cancer AMC-R126


title: primary colorectal cancer AMC-R123


title: primary colorectal cancer AMC-R124


title: primary colorectal cancer AMC-R12


title: primary colorectal cancer AMC-R122


title: primary colorectal cancer AMC-R121


title: primary colorectal cancer AMC-R120


title: primary colorectal cancer AMC-R117


title: primary colorectal cancer AMC-R116


title: primary colorectal cancer AMC-R113


title: primary colorectal cancer AMC-R114


title: primary colorectal cancer AMC-R111


title: primary colorectal cancer AMC-R112


title: primary colorectal cancer AMC-R109


title: primary colorectal cancer AMC-R110


title: primary colorectal cancer AMC-R132


title: primary colorectal cancer AMC-R103


title: primary colorectal cancer AMC-R102


title: primary colorectal cancer AMC-R131


title: primary colorectal cancer AMC-R101


title: myc2_MYC2:MYC2_FLAG_untreated

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Sample 2

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600),  FDR (0.01)
Genome_build: TAIR10
Supplementary_files_format_and_content: 110316_6-W200-G600-FDR0.01-islandfiltered-normalized.wig contains SICER comparison Sample 3 vs Sample 2 (FLAG_25 minute touch vs FLAG_untreated)

organism: Arabidopsis thaliana

source_name: leaves, whole rosette

growth_protocol: Seedlings were grown on soil

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment or 25 min touch treatment

value: rosette leaves

tag: genotype

value: myc2 MYC2::MYC2-FLAG

tag: antibodies

value: FLAG (Millipore Sigma, F1804)


title: primary colorectal cancer AMC-R1

value: male


title: myc2_MYC2:MYC2_FLAG_25_min_touch

description: Sample 3

tag: tissue


title: Col-0_IgG

description: Sample 1

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: primary colorectal cancer AMC-R100


title: primary colorectal cancer AMC-R104


title: p34: Pca_Sample34_Prognosis_bad

type: genomic

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

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

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

data_processing: The methylation data was processed using the RnBeads R package (Assenov et al, 2014). Probes with SNPs (dbSNP 144) overlapping with the C nucleotide of the CG site and having MAF>0.01 (28722 probes) were excluded. Probes with high likelihood of false hybridization (28736 probes, as defined in RnBeads) were also removed. Quality filtering was performed using the Greedycut algorithm, which removed 21040 probes and 11 samples. Additional 969 non-CpG probes and 9229 probes located on the sex chromosomes were removed. No normalization or background correction was used. The top 10000 most variable CpG sites showing differences based on the souce of tissue (fresh frozen vs. formalin-fixed, paraffin embedded) were removed. These probes were identified using prinipal component analysis.

label: Standard Illumina labelling (Cy5, Cy3)

source_name: prostate tumor

label_protocol: Standard Illumina Protocol

extract_protocol: AllPrep® DNA/RNA FFPE kit (Qiagen)

tag: diagnosis

value: prostate cancer

value: prostate tumor

tag: prognosis

value: bad


title: p38: Pca_Sample38_Prognosis_bad


title: p17: Pca_Sample17_Prognosis_bad


title: p43: Pca_Sample43_Prognosis_bad


title: p48: Pca_Sample48_Prognosis_bad


title: p11: Pca_Sample11_Prognosis_bad


title: p08: Pca_Sample08_Prognosis_bad


title: p20: Pca_Sample20_Prognosis_bad


title: p35: Pca_Sample35_Prognosis_bad


title: p42: Pca_Sample42_Prognosis_bad


title: p23: Pca_Sample23_Prognosis_bad


title: p29: Pca_Sample29_Prognosis_bad


title: p26: Pca_Sample26_Prognosis_bad


title: p33: Pca_Sample33_Prognosis_bad


title: p27: Pca_Sample27_Prognosis_bad


title: p18: Pca_Sample18_Prognosis_bad


title: p31: Pca_Sample31_Prognosis_bad


title: p45: Pca_Sample45_Prognosis_bad


title: p10: Pca_Sample10_Prognosis_bad


title: p49: Pca_Sample49_Prognosis_bad


title: p22: Pca_Sample22_Prognosis_bad


title: p15: Pca_Sample15_Prognosis_bad


title: p16: Pca_Sample16_Prognosis_bad


title: p09: Pca_Sample09_Prognosis_bad


title: p14: Pca_Sample14_Prognosis_bad


title: p30: Pca_Sample30_Prognosis_bad


title: p39: Pca_Sample39_Prognosis_bad


title: p40: Pca_Sample40_Prognosis_bad


title: p19: Pca_Sample19_Prognosis_bad


title: p28: Pca_Sample28_Prognosis_bad


title: p02: Pca_Sample02_Prognosis_bad


title: g48: Pca_Sample48_Prognosis_good

value: good


title: p07: Pca_Sample07_Prognosis_bad


title: g49: Pca_Sample49_Prognosis_good


title: g45: Pca_Sample45_Prognosis_good


title: g47: Pca_Sample47_Prognosis_good


title: g40: Pca_Sample40_Prognosis_good


title: g34: Pca_Sample34_Prognosis_good


title: g38: Pca_Sample38_Prognosis_good


title: g37: Pca_Sample37_Prognosis_good


title: g25: Pca_Sample25_Prognosis_good


title: g30: Pca_Sample30_Prognosis_good


title: g24: Pca_Sample24_Prognosis_good


title: g28: Pca_Sample28_Prognosis_good


title: g35: Pca_Sample35_Prognosis_good


title: p04: Pca_Sample04_Prognosis_bad


title: g23: Pca_Sample23_Prognosis_good


title: g43: Pca_Sample43_Prognosis_good


title: g36: Pca_Sample36_Prognosis_good


title: g21: Pca_Sample21_Prognosis_good


title: g42: Pca_Sample42_Prognosis_good


title: g19: Pca_Sample19_Prognosis_good


title: g26: Pca_Sample26_Prognosis_good


title: g27: Pca_Sample27_Prognosis_good


title: g44: Pca_Sample44_Prognosis_good


title: g18: Pca_Sample18_Prognosis_good


title: p05: Pca_Sample05_Prognosis_bad


title: p03: Pca_Sample03_Prognosis_bad


title: g41: Pca_Sample41_Prognosis_good


title: g20: Pca_Sample20_Prognosis_good


title: p53R248W/+ H3K27me3 ChIP-seq

city: Chicago

first: Yan

last: Liu

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

data_processing:
For ChIP-seq: sequence reads were aligned to mouse reference genome mm10 using BWA with default settings. Mouse alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. H3K27me3 enriched regions were identified using the SICER algorithm with a MaxGap parameter setting of 600 bp. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
For RNA-seq:  sequence reads were aligned to mouse reference genome mm10 with STAR-2.5.2b. featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“–Q 10")
For RNA-seq: differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq: bigwig file; for RNA-seq: tab-delimited file includes raw counts, log2 fold change values, p-values and FDR for all samples

source_name: p53R248W/+_Lin-Kit+ cells

extract_protocol:
Lin-Kit+ 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..
For ChIP-seq, 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). Clontech SMART-Seq v4 Ultra Low Input RNA Kit  was used for preparing the RNA-seq libraries.

value: Hematopoietic stem and progenitor cells

tag: cell subtype

value: Lin-Kit+ cells

tag: chip antibody

value: H3K27me3 (clone:39155, Active Motif)


title: TSS-Seq in WT cold - rep2

city: Frederiksberg C

first: Quentin

middle: Angelo Pierre

last: Thomas

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

description: TSS-Seq

data_processing:
Adapter and UMI-trimmed with cutadaptv1.18
PolyA tails removed with cutadapt and filtered with AfterQC v0.9.7
Aligned using STAR v2.6.1c (--alignEndsType EndToEnd – alignMatesGapMax 15000)
Deduplicated with UMI-tools and filtered for multi-aligned reads with SAMtools
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files of TIF-Seq clusters calculated with a clustering custom script in relation with the method. Bedgraph for TSS-Seq files calculated with BEDTools genomecov

source_name: seedlings

growth_protocol: Sterilized Arabidopsis thaliana seeds were grown on plates containing 1/2 Murashige and Skoog (MS) medium containing 1% sucrose and supplemented with 1% Microagar. Plates were grown in climate chambers with a long day photoperiod (16h light/8h dark cycle) at 22°C/18 °C for 14 days

extract_protocol:
total Arabidopsis RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (Thermo Fisher Scientific) according to manufacturers’ instructions
libraries were prepared according to the publication protocol for TIF-Seq. For TSS-Seq the protocol was as in Nielsen et al,2019

treatment_protocol: For cold treatment, seedlings were grown in control conditions for two weeks and subsequently transferred to a cold room (4 °C) for three hours before harvesting. For others seedling were frozen in liquid nitrogen immediately

value: seedlings

value: Col-0 wild type

value: 4C cold treatment for 3h

tag: developmental stage

value: 14 days seedlings