title: GBMX16 BRG1 KD_3

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

hyb_protocol: Nanostring arrays were conducted against the Immunology panels on the nCounter Analysis system

scan_protocol: standard NanoString protocol

data_processing: data was analyzed with nSolver software using a 2-fold cutoff value; mRNA counts were normalized to the geometric means of 40 housekeeping genes

source_name: GBMX16 BRG1 KD

growth_protocol: GBMX16 patient-derived xenoline was maintained as xenografts in immunocompromised mice. Glioma-Initiating Cells  were isolated and maintained in flasks precoated with poly-D-lysine and laminin, and grown in NeuroBasal-A medium (Invitrogen, Carlsbad, CA) containing 2% B27 supplement, 2 mM L-glutamine, 100 units/ml penicillin, 100 g/ml streptomycin, EGF (20 ng/ml), and basic FGF (40 ng/ml).

extract_protocol: Total RNA from GBMX16 and the GBMX16 BRG1 KD cells was extracted using the QIAshredder and RNeasy mini kits

treatment_protocol: pLKO.1 plasmids containing gene-specific or scrambled shRNA (control) were used to knockdown (KD) BRG1 in the GBMX16 patient-derived xenoline.

value: GBMX16 patient-derived xenoline

tag: genotype/variation

value: BRG1 knockdown


title: GBMX16 BRG1 KD_2

status: Public on Jul 03 2018

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: ChAT-eGFP-5

type: SRA

city: Boston

first: Lora

last: Bankova

state: MA

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
Illumina NextSeq500
Each sample’s sequences were aligned utilizing STAR v2.4.2a (Dobin, Davis et al. Bioinformatics 2013) and the following parameters: --twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. Alignments were processed using Picard v1.1073 tools to add read groups and other sequencing information, reorder the BAM file to the reference, and mark duplicate sequences.
The data was assessed for quality using RNA-SeQC (DeLuca, Levin et al.Bioinformatics 2012). TPM were quantified using RSEM v1.2.21 (Li and Dewey BMC Bionformatics 2011) with the paired-end option. Raw counts for differential expression analysis were generated using the FeatureCounts function of Rsubread (Liao, Smyth et al.Nucleic Acids Res 2013)
Differential expression analysis was conducted using the DEseq2 package (Love, Huber et al. Genome Biol 2014). Genes were considered to be significantly differentially regulated based on a fold change in expression of > 4-fold and a false discovery rate of <0.05 based on a Benjamini-Hochberg adjusted p-value to correct for multiple comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized counts from Deseq2 analysis

organism: Mus musculus

source_name: trachea

extract_protocol:
RTracheal epithelial cell suspensions were derived through a 2 step protocol: incubation with high dose dispase followed by papain digestion. Brush cells were identified flow cytometrically as CD45-EpCAM+eGFP+ cells, EpCAM+ cells were identified as CD45−EpCAM+ cells and CD45+ cells were separately sorted using monoclonal antibodies against CD45 and EpCAM, after dead cell exclusion with propidium iodide. Cells were sorted into TCL buffer supplemented with RNAprotect Cell Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: tracheal ChAT-eGFP+ brush cells


title: Saline 4

city: New York

first: Efrain

middle: A

last: Ribeiro

state: New York

address: 1425 Madison Ave, Icahn bldg. Rm 10-24

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
S12
S4_TGACCA
SST-TLG501

data_processing:
STAR
featureCounts from Subread package
Normalized vy weight trimmed mean of M-values
Voom differential expression analysis
Genome_build: Ensembl GRCm38.74
Supplementary_files_format_and_content: logCPM

source_name: saline_FACs isolated nucleus accumbens somatostatin interneuron nuclei

extract_protocol:
FACS
SMARTER Stranded Total RNA-seq kit V2 pico input mammalian (Clontech 063017)
Libraries were made from RNA isolated from ~2000-4000 FACS isolated somatostatin interneuron nuclei. Libraries were pooled across two lanes and both groups were equally balanced.

treatment_protocol: Saline or 7.5mg/kg cocaine

tag: strain background

tag: treatment

value: Saline

tag: number of nuclei

value: 1 Hour

tag: region

value: Nucleus Accumbens


title: ChAT-eGFP-4


title: GBMX16_3

value: scrambled shRNA (control)


title: ChAT-eGFP-3


title: EpCAM-2

value: tracheal EpCAM+ epithelial cells


title: ChAT-eGFP-1


title: GBMX16_1


title: 630Δerm control-2 (wildtype)

city: Leiden

first: Ilse

middle: Michelle

last: Boekhoud

state: Zuid-Holland

address: Albinusdreef 2

department: Medical Microbiology

country: Netherlands

institute: Leiden University Medical Centre

description: Untreated control biological rep 2

data_processing:
Image analysis, base calling, quality check, performed with the Illumina data analysis pipeline RTA vl.18.64 and Bcl2fastq v2.17.
Data normalisation was done by the factorial design statistical method of the RNA-seq analysis R-package EdgeR implemented in the T-Rex pipeline.
Sliding window analysis was performed using the output generated through the T-REX pipeline.
Genome_build: LN614756.1 (Genbank identifier)
Supplementary_files_format_and_content: tab-delimited excel file contains RPKM values for each gene of LN614756,1 (annotated) of each sample (triplicates of wildtype, ACX362E/362E and HPUra). The tab filenames includes the file name of the raw data files and the biological replicate of which sample the data file belongs to.

organism: Clostridioides difficile

source_name: Bacterial culture

growth_protocol: C. difficile 630Δerm was grown for 5h in BHI medium with HPUra (35 µg/mL) or ACX362E (4  µg/mL) starting from an OD600 of 0.05 using an exponentially growing starter culture, after which cells (3mL) were harvested  for RNA isolation

extract_protocol:
RNA isolation was performed with NucleoSpin© RNA kit (Macherey-Nagel). A second rDNAse digestion treatment was performed in solution and RNA was precipitated and recovered by NaAc precipitation to remove residual DNA. Concentration determination and quality control (16S/23S ratio and RNA integrity number [RIN]) was performed with a fragment analyzer (Agilent bio-analyzer), according to the instructions of the manufacturer. Samples with a RIN>9 and 16S/23S ratio >1.4 were submitted for analysis by RNA-seq
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples according to the protocol (NEB #E7420S/L). Ribosomal RNA was selectively removed using Ribo-Zero rRNA Removal Kit for Gram-positive Bacteria. cDNA synthesis was performed after mRNA fragmentation.

tag: pcr ribotype

value: Clostridioides Difficile 630DERM

tag: genbank id

tag: agent

value: Untreated


title: ChAT-eGFP-2


title: GBMX16_2


title: dNS1 infected, hDcr transfected NoDice cells

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Total small RNA (<200nt)

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences (Kozomara and Griffiths-Jones, 2014), Ensembl noncoding RNA database release 70 (Flicek et al., 2014), human functional RNA database version 3.4 (Mituyama et al., 2009), the IAV PR8 sequence (concatenated segment accessions nos. EF190971-EF190978), and finally human genome hg19.  No mismatches were allowed for alignments to the different references except the human genome for which two mismatches were allowed.
Genome_build: IAV PR8 sequence (segment accessions nos. EF190971-EF190978), 8 segments concatenated in order of: PB2-PB1-PA-HA-NP-NA-M-NS
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the PB2 genome segment beginning at 1, ending position of the aligned read, aligned reads per million of total assignable reads (total count of reads that could be aligned to miRbase, Ensembl ncRNA, fRNAdb, PR8 virus, and HG19), and the strand (+ or -) that the read aligns to.

organism:
Homo sapiens
Influenza A virus (A/hvPR8/34(H1N1))

source_name: IAV PR8

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 9% fetal bovine serum and Gentamicin

extract_protocol:
Small RNA were extracted with the miRvana microRNA isolation kit (Thermo Fisher)
Small RNA processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

treatment_protocol: Cells infected with influenza virus for 1 hour, virus replaced with DMEM with 0.01% FBS and 0.35% BSA. Harvested 24 hours post infection.

value: NoDice (clone 4-25)

tag: virus infection

value: Delta-NS1 PR8 mutant

tag: transfected plasmid

value: pK-WT

tag: illumina small rna sequencing index


title: 630Δerm control-3 (wildtype)

description: Untreated control biological rep 3


title: 630Δerm control-1 (wildtype)

description: Untreated control biological rep 1


title: 67NR non-metastatic neoR mCherry+ tumor cells-clone 1-2

city: Heidelberg

first: Richard

middle: P

last: Redvers

state: Victoria

address: 45 Studley Road

department: Translational Breast Cancer Program

country: Australia

institute: ONJCRI

description: Ribominus (Invitrogen) rRNA reduction

data_processing: CEL files were processed for gene level anaysis with the affy package (v1.56.0) in R (v3.4.3) using RMA normalization and the custom chip definition file moex10stmmensg v22 Released on Jun 21, 2017, downloaded from: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/22.0.0/ensg.asp (Dai et al. (2005) Nucleic Acids Res 2005,33:e175.). ID_REF corresponds to ENSEMBL gene ID (Build GRCm38.p5); the_at suffix to signify it corresponds to a custom Affymetrix probeset definition has been removed.

label: biotin

source_name: FACS isolated mammary tumor cells

label_protocol: rRNA-reduced RNA from 2ug starting total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays

growth_protocol: Tumor cells were maintained in a humidified incubator up to 4 weeks with alpha-minimal essential medium/5% fetal calf serum at 37C, 5% CO2. 10^5 cells/20uL Hank's Buffered Salt Solution were injected into the 4th inguinal fat pad of female Balb/c recipients and tumors were resected @ 400-600mm3 (~0.5g) as measured by electronic calipers as calculated with the modified ellipsoidal formula: volume=1/2(length x width2) as per Tomayko (1989)

extract_protocol: Cell pellets were snap-frozen in liquid nitrogen for storage (-80C) and total RNA was isolated with the mirVana miRNA Isolation Kit with phenol (Ambion), DNase-treated (Turbo DNA-free, Ambion) and concentrated with the RNeasy MinElute Kit (Qiagen). rRNA was depleted from 2ug total RNA with the Ribominus Kit (Invitrogen) according to the Affymetrix WT protocol for Exon 1.0 ST arrays. RNA was quantitated with the Quant-iT RNA Broad Range BR Assay Kit on the Qubit fluorometer (Invitrogen) and quality was assessed on the Bioanalyser 2100 with the RNA 6000 Nano Kit (Agilent).

treatment_protocol: Tumors were surgically resected @ ~0.5g, minced with a scalpel and digested with 750U/mL collagenase Type I/10mL DMEM @ 37C with 180rpm shaking for 45 minutes, followed by filtration through 70- and 40-micron strainers, red blood cell lysis and resuspension in alpha-MEM/5%FCS+30nM sytox green viability dye for FACS isolation of mCherry+ tumor cells.

tag: gender

value: female

value: Balb/c

tag: lineage

value: mammary tumor


title: dNS1 infected, hDcr-N1 transfected NoDice cells

description: Total small RNA (<200nt)


title: GBMX16 BRG1 KD_1


title: dNS1 infected, vector transfected NoDice cells

description: Total small RNA (<200nt)

value: pK-Myc


title: PR8 infected, vector transfected NoDice cells

description: Total small RNA (<200nt)


title: 630Δerm + 4 µg/ml ACX362E-1

description: ACX362E treated biological rep 1


title: 67NR non-metastatic neoR mCherry+ tumor cells-clone 1-1

description: Ribominus (Invitrogen) rRNA reduction

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays


title: 4T1 highly metastatic mCherry+ tumor cells-clone 9-2

description: Ribominus (Invitrogen) rRNA reduction

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays


title: 4T1 highly metastatic mCherry+ tumor cells-clone 9-3

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1 highly metastatic mCherry+ tumor cells-clone 9-1

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1BM2 highly metastatic mCherry+ tumor cells-clone 11-3

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1BM2 highly metastatic mCherry+ tumor cells-clone 11-1

description: Ribominus (Invitrogen) rRNA reduction


title: PR8 infected, hDcr-N1 transfected NoDice cells

description: Total small RNA (<200nt)


title: 4T1 highly metastatic neoR mCherry+ tumor cells-clone 2.A5-2

description: Ribominus (Invitrogen) rRNA reduction


title: 67NR non-metastatic neoR mCherry+ tumor cells-clone 1-3

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1 highly metastatic mCherry+ tumor cells-clone 13.5-3

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1 highly metastatic neoR mCherry+ tumor cells-clone 2.A5-1

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1BM2 highly metastatic mCherry+ tumor cells-clone 11-2

description: Ribominus (Invitrogen) rRNA reduction


title: R38A infected 293T

description: Total small RNA (<200nt)

value: NS1-R38A PR8 mutant


title: 630Δerm + 35 µg/ml HPUra-3

description: HPUra treated biological rep 3

value: HPUra


title: 630Δerm + 35 µg/ml HPUra-2

description: HPUra treated biological rep 2


title: PR8 infected, hDcr transfected NoDice cells

description: Total small RNA (<200nt)


title: 630Δerm + 35 µg/ml HPUra-1

description: HPUra treated biological rep 1


title: 630Δerm + 4 µg/ml ACX362E-3

description: ACX362E treated biological rep 3


title: PR8 infected 293T

description: Total small RNA (<200nt)


title: dNS1 infected 293T

description: Total small RNA (<200nt)


title: 4T1 highly metastatic mCherry+ tumor cells-clone 13.5-1

description: Ribominus (Invitrogen) rRNA reduction


title: 4T1 highly metastatic mCherry+ tumor cells-clone 13.5-2

description: Ribominus (Invitrogen) rRNA reduction


title: 630Δerm + 4 µg/ml ACX362E-2

description: ACX362E treated biological rep 2


title: primary NB tumor_nrc8225

status: Public on Jul 02 2018

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

hyb_protocol: Following fragmentation, ~5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Human Exon 1.0 ST Arrays (Affymetrix Part No. 900 651). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update

data_processing:
In order to obtain expression information per gene, exon data was merged by transcript clusters (hg18/core exons). Exon array data was normalized according to the RMA-sketch algorithm using Affymetrix Power Tools (Affymetrix).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
CEL files were rma-sketch normalized using Affymetrix Power Tools (v1.10.0). The resulting data were batch corrected using zscores and rescaled to the largest batch to re-obtain untransformed values.

label: Biotin

source_name: primary untreated neuroblastoma tumor

label_protocol: Biotinylated cDNA was prepared according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 5) from 1000 ng total RNA, including the rRNA reduction step

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

value: no

tag: inss


title: primary NB tumor_nrc8210

value: yes


title: primary NB tumor_nrc8217


title: primary NB tumor_nrc8209


title: primary NB tumor_nrc8212


title: primary NB tumor_nrc8223


title: primary NB tumor_nrc8218


title: primary NB tumor_nrc8206


title: primary NB tumor_nrc8219


title: primary NB tumor_nrc8220


title: primary NB tumor_nrc8203


title: primary NB tumor_nrc8192


title: 4T1 brain metastatic mCherry+ tumor cells-clone 4.2-1

description: Ribominus (Invitrogen) rRNA reduction


title: primary NB tumor_nrc8183


title: 4T1 brain metastatic mCherry+ tumor cells-clone 4.2-2

description: Ribominus (Invitrogen) rRNA reduction


title: primary NB tumor_nrc8204


title: primary NB tumor_nrc8208


title: primary NB tumor_nrc8181


title: primary NB tumor_nrc8175


title: primary NB tumor_nrc8167


title: primary NB tumor_nrc8187


title: 4T1 brain metastatic mCherry+ tumor cells-clone 4.2-3

description: Ribominus (Invitrogen) rRNA reduction


title: primary NB tumor_nrc8180


title: primary NB tumor_nrc8172


title: primary NB tumor_nrc8191


title: primary NB tumor_nrc8205


title: primary NB tumor_nrc8189


title: primary NB tumor_nrc8160


title: primary NB tumor_nrc8173


title: primary NB tumor_nrc8161


title: primary NB tumor_nrc8159


title: primary NB tumor_nrc8153


title: primary NB tumor_nrc8152


title: primary NB tumor_nrc8119


title: primary NB tumor_nrc8151


title: primary NB tumor_nrc8157


title: primary NB tumor_nrc8155


title: primary NB tumor_nrc8145


title: primary NB tumor_nrc8114


title: primary NB tumor_nrc8127


title: primary NB tumor_nrc6109


title: primary NB tumor_nrc6110


title: primary NB tumor_nrc8137


title: primary NB tumor_nrc8142


title: primary NB tumor_nrc6092


title: primary NB tumor_nrc6090


title: primary NB tumor_nrc6102


title: primary NB tumor_nrc6089


title: primary NB tumor_nrc6107


title: primary NB tumor_nrc6098


title: primary NB tumor_nrc6100


title: primary NB tumor_nrc8134


title: primary NB tumor_nrc6103


title: primary NB tumor_nrc6099


title: primary NB tumor_nrc8113


title: primary NB tumor_nrc6091


title: primary NB tumor_nrc6106


title: primary NB tumor_nrc6104


title: primary NB tumor_nrc6088


title: primary NB tumor_nrc8135


title: primary NB tumor_nrc6087


title: primary NB tumor_nrc6085


title: primary NB tumor_nrc6082


title: primary NB tumor_nrc6083


title: primary NB tumor_nrc6079


title: primary NB tumor_nrc6080


title: primary NB tumor_nrc6081


title: primary NB tumor_nrc6086


title: primary NB tumor_nrc6084


title: primary NB tumor_nrc6072


title: primary NB tumor_nrc6074


title: primary NB tumor_nrc6075


title: primary NB tumor_nrc6071


title: primary NB tumor_nrc6068


title: primary NB tumor_nrc6067


title: primary NB tumor_nrc6061


title: primary NB tumor_nrc6073


title: primary NB tumor_nrc6066


title: primary NB tumor_nrc6064


title: primary NB tumor_nrc6069


title: primary NB tumor_nrc6077


title: primary NB tumor_nrc6070


title: primary NB tumor_nrc6078


title: primary NB tumor_nrc4107


title: primary NB tumor_nrc4106


title: primary NB tumor_nrc4108


title: primary NB tumor_nrc6063


title: primary NB tumor_nrc4105


title: primary NB tumor_nrc4109


title: primary NB tumor_nrc6062


title: primary NB tumor_nrc4104


title: primary NB tumor_nrc4101


title: primary NB tumor_nrc4100


title: primary NB tumor_nrc4103


title: primary NB tumor_nrc4097


title: primary NB tumor_nrc4098


title: primary NB tumor_nrc4093


title: primary NB tumor_nrc4094


title: primary NB tumor_nrc4096


title: primary NB tumor_nrc4095


title: primary NB tumor_nrc4088


title: primary NB tumor_nrc4092


title: primary NB tumor_nrc4089


title: primary NB tumor_nrc4090


title: primary NB tumor_nrc4087


title: primary NB tumor_nrc4091


title: primary NB tumor_nrc4083


title: primary NB tumor_nrc4102


title: primary NB tumor_nrc4099


title: primary NB tumor_nrc4081


title: primary NB tumor_nrc4082


title: primary NB tumor_nrc4078


title: primary NB tumor_nrc4079


title: primary NB tumor_nrc4076


title: primary NB tumor_nrc4080


title: primary NB tumor_nrc4077


title: primary NB tumor_nrc4075


title: primary NB tumor_nrc4084


title: primary NB tumor_nrc4074


title: primary NB tumor_nrc4070


title: primary NB tumor_nrc4066


title: primary NB tumor_nrc4072


title: primary NB tumor_nrc4064


title: primary NB tumor_nrc4065


title: primary NB tumor_nrc4071


title: primary NB tumor_nrc4067


title: primary NB tumor_nrc4068


title: primary NB tumor_nrc4061


title: primary NB tumor_nrc4055


title: primary NB tumor_nrc4057


title: primary NB tumor_nrc4063


title: primary NB tumor_nrc4069


title: primary NB tumor_nrc4060


title: primary NB tumor_nrc4056


title: primary NB tumor_nrc4062


title: primary NB tumor_nrc4053


title: primary NB tumor_nrc4046


title: primary NB tumor_nrc4047


title: primary NB tumor_nrc4052


title: primary NB tumor_nrc4054


title: primary NB tumor_nrc4051


title: primary NB tumor_nrc4048


title: primary NB tumor_nrc4045


title: primary NB tumor_nrc4058


title: primary NB tumor_nrc4044


title: primary NB tumor_nrc4059


title: primary NB tumor_nrc4043


title: primary NB tumor_nrc4041


title: primary NB tumor_nrc4042


title: primary NB tumor_nrc4039


title: primary NB tumor_nrc4034


title: primary NB tumor_nrc4038


title: primary NB tumor_nrc4040


title: primary NB tumor_nrc4032


title: primary NB tumor_nrc4037


title: primary NB tumor_nrc4033


title: primary NB tumor_nrc4024


title: primary NB tumor_nrc4027


title: primary NB tumor_nrc4028


title: primary NB tumor_nrc4031


title: primary NB tumor_nrc4029


title: primary NB tumor_nrc4025


title: primary NB tumor_nrc4026


title: primary NB tumor_nrc4030


title: primary NB tumor_nrc4023


title: primary NB tumor_nrc4020


title: primary NB tumor_nrc4019


title: primary NB tumor_nrc4011


title: primary NB tumor_nrc4012


title: primary NB tumor_nrc4036


title: primary NB tumor_nrc4021


title: primary NB tumor_nrc4018


title: primary NB tumor_nrc4006


title: primary NB tumor_nrc4010


title: primary NB tumor_nrc4014


title: primary NB tumor_nrc4015


title: primary NB tumor_nrc4016


title: primary NB tumor_nrc4007


title: primary NB tumor_nrc4022


title: primary NB tumor_nrc4017


title: primary NB tumor_nrc4008


title: primary NB tumor_nrc4013


title: primary NB tumor_nrc4002


title: primary NB tumor_nrc4001


title: primary NB tumor_nrc2558


title: primary NB tumor_nrc2550


title: primary NB tumor_nrc2551


title: primary NB tumor_nrc2555


title: primary NB tumor_nrc4009


title: primary NB tumor_nrc2557


title: primary NB tumor_nrc2556


title: primary NB tumor_nrc2549


title: primary NB tumor_nrc4005


title: primary NB tumor_nrc2546


title: primary NB tumor_nrc2552


title: primary NB tumor_nrc2392


title: primary NB tumor_nrc2390


title: primary NB tumor_nrc2391


title: primary NB tumor_nrc2536


title: primary NB tumor_nrc2542


title: primary NB tumor_nrc2545


title: primary NB tumor_nrc2386


title: primary NB tumor_nrc2538


title: primary NB tumor_nrc2387


title: primary NB tumor_nrc2544


title: primary NB tumor_nrc2385


title: primary NB tumor_nrc2541


title: primary NB tumor_nrc2382


title: primary NB tumor_nrc2383


title: primary NB tumor_nrc2380


title: primary NB tumor_nrc2302


title: primary NB tumor_nrc2284


title: primary NB tumor_nrc2221


title: primary NB tumor_nrc2217


title: primary NB tumor_nrc2219


title: primary NB tumor_nrc2285


title: primary NB tumor_nrc2533


title: primary NB tumor_nrc2288


title: primary NB tumor_nrc2195


title: primary NB tumor_nrc2194


title: primary NB tumor_nrc2193


title: primary NB tumor_nrc2191


title: primary NB tumor_nrc2537


title: primary NB tumor_nrc2198


title: primary NB tumor_nrc2189


title: primary NB tumor_nrc2169


title: primary NB tumor_nrc2155


title: primary NB tumor_nrc2148


title: primary NB tumor_nrc2147


title: primary NB tumor_nrc2172


title: primary NB tumor_nrc2183


title: primary NB tumor_nrc2184


title: primary NB tumor_nrc2181


title: primary NB tumor_nrc2118


title: primary NB tumor_nrc2174


title: primary NB tumor_nrc2150


title: primary NB tumor_nrc2109


title: primary NB tumor_nrc2151


title: primary NB tumor_nrc2175


title: primary NB tumor_nrc2119


title: primary NB tumor_nrc2145


title: primary NB tumor_nrc2130


title: primary NB tumor_nrc2111


title: primary NB tumor_nrc2144


title: primary NB tumor_nrc2114


title: primary NB tumor_nrc2143


title: primary NB tumor_nrc2132


title: primary NB tumor_nrc2101


title: primary NB tumor_nrc2059


title: primary NB tumor_nrc2063


title: primary NB tumor_nrc2056


title: primary NB tumor_nrc2105


title: primary NB tumor_nrc2057


title: primary NB tumor_nrc2107


title: primary NB tumor_nrc2036


title: primary NB tumor_nrc2103


title: primary NB tumor_nrc2041


title: primary NB tumor_nrc2044


title: primary NB tumor_nrc2034


title: primary NB tumor_nrc2050


title: primary NB tumor_nrc2054


title: primary NB tumor_nrc2013


title: primary NB tumor_nrc2032


title: primary NB tumor_nrc2018


title: primary NB tumor_nrc2017


title: primary NB tumor_nrc2020


title: primary NB tumor_nrc2015


title: primary NB tumor_nrc2031


title: primary NB tumor_nrc2022


title: primary NB tumor_nrc2025


title: primary NB tumor_nrc2009


title: primary NB tumor_nrc2021


title: primary NB tumor_nrc2002


title: primary NB tumor_nrc2008


title: primary NB tumor_nrc2026


title: primary NB tumor_nrc0010


title: primary NB tumor_nrc2038


title: primary NB tumor_nrc0009


title: primary NB tumor_nrc0006


title: primary NB tumor_nrc2024


title: primary NB tumor_nrc0007


title: primary NB tumor_nrc0004


title: PW6-H8

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

data_processing:
Kallisto was used for alignment against the human transcriptome
Log2(TPM+1)
Applied threshold of detection, set all Log2(TPM+1) values below threshold to 0.
Applied cell filter, removed all cells with less than 40% of transcripts mapping to the human transcriptome.
Applied gene expression filter, removed all genes expressed in less than 5% of the cells
Performed Quantile normalization with the Preprocesscore package within each experimental plate
Performed Limma batch correction to remove variability associated with experimental plate and donor ID, while protecting BCR isotype and specificity.
Genome_build: HG19
Supplementary_files_format_and_content: normalized abundance measurement

molecule: polyA RNA

source_name: peripheral blood plasmablast

extract_protocol:
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.

tag: donor id

tag: donor gender

tag: isotype

value: IgA

tag: specificity

value: vaccine

tag: experimental batch


title: PW6-H5

value: negative


title: PW6-H6


title: PW6-H7


title: primary NB tumor_nrc0005


title: primary NB tumor_nrc0003


title: PW6-G9

value: male


title: PW6-G6


title: primary NB tumor_nrc2003


title: PW6-G7


title: primary NB tumor_nrc0002


title: PW6-F6

value: IgG


title: PW6-G1


title: PW6-F9


title: PW6-F12


title: PW6-F7


title: PW6-F5


title: PW6-G10


title: PW6-G11


title: PW6-F11


title: PW6-F10


title: PW6-F1


title: PW6-E9


title: PW6-E6


title: PW6-E4


title: PW6-E8


title: PW6-G2


title: PW6-E1


title: PW6-D9


title: PW6-E5


title: PW6-E12


title: PW6-G4


title: PW6-D4


title: PW6-E10


title: PW6-G12


title: PW6-F8


title: PW6-D6


title: PW6-D3


title: PW6-D10


title: PW6-D12


title: PW6-D2


title: PW5-H8


title: PW5-H6


title: PW5-H5


title: PW5-H9


title: PW5-H7


title: PW5-H2


title: PW5-H12


title: PW5-H1


title: PW5-G5


title: PW6-D7


title: PW6-D5


title: PW5-G4


title: PW5-G11


title: PW5-H3


title: PW5-G12


title: PW5-G3


title: PW5-F8


title: PW5-G2


title: PW5-F9


title: PW5-G1


title: PW5-F5


title: PW5-F6


title: PW5-F2


title: PW5-F12


title: PW5-H4


title: PW5-F4


title: PW5-F1


title: PW5-F10


title: PW5-E3


title: PW5-E4


title: PW5-E2


title: PW5-E6


title: PW5-E11


title: PW5-E10


title: PW5-D9


title: PW5-E1


title: PW5-D8


title: CoPRO_MEF_Capped_HS

city: Ithaca

first: Jacob

middle: Michael

last: Tome

address: 416 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

description:
Capped RNAs were selected by treating with Terminator 5’ Phosphate dependent exonuclease (Epicentre, cat. TER51020) to degrade 5’ monophosphate RNA (from terminating polymerase) and CIP to reduce other uncapped RNAs to 5’ hydroxyl, making them incapable of ligating to 5’ adapter.  5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).
CoPRO_HScap_5p_pl.bw
CoPRO_HScap_5p_mn.bw
CoPRO_HScap_3p_pl.bw
CoPRO_HScap_3p_mn.bw
MEF_Rep1_Pooled.Rdata

data_processing:
Library strategy: CoPRO
Adaptors were trimmed using cutadapt 1.16 (-O 1 -m 18).
Reads were aligned to hg19 with bowtie2 v2.2.6 (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal).
Alignments from different sequencing runs were pooled using samtools merge.
After pooling, reads with mappability score less than 30 were removed; the biotin run-on base was trimmed; and reads were weighted to account for the bias of Illumina sequencers using custom R scripts.
Separate bigwig files were generated from weighted 5' and 3' end counts (please note that this does not preserve the single-molecule resolution of the dataset).
All processing code is available at https://github.com/ndt26/CoPRO
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing pooled sequencing runs for each cap state selection treatment (pooling the two replicates and three sequencing runs per library).  For each treatment, two pairs of bigwigs are provided (a pair consists of separate files for reads mapping to the plus and minus strands, minus strand values are negative).  One set contains reads mapped to single baspairs at the 5’ end of the RNA (i.e. reflecting the exact basepair where a Pol II molecule initiated), and the other mapped to the 3’ ends (i.e. the location of the active site of polymerase).  Each library was sequenced in three runs: two by loading cDNA directly (Lane1 and Lane2) and one after amplification (Amplified)
Supplementary_files_format_and_content: Rdata files containing pooled sequencing runs with normalized counts for all treatments. Rdata files are provided for each replicate, and a file that combines data from both replicates.

source_name: Mouse embryonic fibroblasts

growth_protocol: K562 cells were obtained from ATCC and cultured antibiotic-free in accordance with their standards in DMEM, high glucose + HEPES (ThermoFisher cat. 12430054) supplemented with 10% FBS (ThermoFisher 10437028). Cultures were verified to be mycoplasma-free prior to library preparation and sequencing.  Two biological replicates were cultured independently, separated by two passages, with library preparations done separately for technical and biological replicates.  Drosophila S2 cells (grown in M3+BPYE supplemented with 10% FBS) were spiked in at a ratio of 1:1000 during permeabilization.

extract_protocol:
Cell Permeabilization:  Cells are spun down and resuspended in cold 1xPBS, then spun down and resuspended in 5 mL cold Wash Buffer (10 mM Tris-Cl, pH 7.5, 10 mM KCl, 150 mM sucrose, 5 mM MgCl2, 0.5 mM CaCl2, 0.5 mM DTT, 1x Protease Inhibitor (Sigma-Aldrich 11873580001), and 40 units SuperaseIn RNase inhibitor /10 mL (Thermo-Fischer AM2694)).  Cells are spun down and lysed in Permeabilization Buffer (10 mM Tris-Cl, pH 7.5, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.05% Tween-20, 0.1% NP40, 1x Protease Inhibitor, and 40 units SuperaseIn RNase inhibitor /10 mL).  Permeabilized cells are then washed twice in Wash buffer, washed once in Freezing Buffer (50 mM Tris-Cl pH 7.5, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT), snap frozen in Freezing Buffer in liquid nitrogen, and stored at -80°C.
CoPRO-seq library construction: CoPRO is similar to PRO-seq, as described previously (Kwak et al., 2013, Mahat et al, 2016). Briefly, 2×10^7 nuclei per final library were added to 2x Nuclear Run-On reaction mix (10mM Tris-Cl pH 8.0, 5mM MgCl2, 300mM KCl, 1% Sarkosyl, 1mM DTT, 0.05mM each of biotin-11-A/C/G/UTP (PerkinElmer), 0.4 u/µL RNase inhibitor) and incubated for 3 min at 37°C. Total RNA was extracted, nascent RNA was purified using streptavidin beads, and then ligated with reverse 3' RNA adapter (adapter sequence varies for each sample as sample barcodes are added at this step) and biotin-labeled products were enriched by another round of streptavidin bead binding and extraction. At this point, each library was subjected to a series of enzymatic treatments to specifically enrich for different 5’ cap states (each treatment reduces a specific subset of RNAs to 5’ monophosphate to facilitate 5’ adapter ligation, described in the Samples section).  Cap state selected RNA was ligated to reverse 5' RNA adapter (5'- rCrArArGrCrArGrArArGrArCrGrGrCrArUrArCrGrArGrArUrGrUrCrUrCrGrUrGrGrGrCrUrCrGrGrArGrArUrGrUrGrUrArUrArArGrArGrArCrArG-3') before being further purified by a third round of streptavidin bead binding and extraction. RNA was reverse transcribed using the Illumina RP1 primer (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA). Each K562 library was sequenced by loading cDNA on the instrument directly (PCR free, two separate lanes, Lane1 and Lane2), and after PCR amplification (described for each entry in the Samples section).  For PCR amplified samples, cDNA was amplified with the following primers:  CAAGCAGAAGACGGCATACGAGATGTC and CAAGCAGAAGACGGCATACGAGATGTC, after which products greater than 120 bp were PAGE purified and pooled for sequencing.

treatment_protocol: Heat shock was performed exactly as described in Mahat 2016 (PMID 27052732).

tag: cell line

value: MEF HS

tag: 5' end state

value: Capped RNA only

tag: replicate

value: Replicate 1

tag: pcr amplified?

value: Amplified

tag: treatment

value: 60 minutes heat shock at 42 Celsius

tag: 3' ligated rna adapter


title: PW5-D7

value: female


title: PW5-D5


title: PW5-D4


title: PW5-F11


title: PW5-D1


title: CoPRO_K562_CappedAndUncapped_Rep2_Amplified

description:
Capped + Uncapped RNAs were selected by treating with RppH, reducing both capped RNA and pre-capped RNA (5’ triphosphate) to 5’ monophosphate.
CoPRO_AllMerge_CappedAndUncapped_5p_pl.bw
CoPRO_AllMerge_CappedAndUncapped_5p_mn.bw
CoPRO_AllMerge_CappedAndUncapped_3p_pl.bw
CoPRO_AllMerge_CappedAndUncapped_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep2_Pooled.Rdata

source_name: K562 chronic myelogenous leukemia

value: Capped and Uncapped RNA

value: Replicate 2

tag: 3' ligated adapter


title: PW5-D12


title: PW5-C12


title: PW5-D2


title: CoPRO_MEF_Capped_NHS

description:
Capped RNAs were selected by treating with Terminator 5’ Phosphate dependent exonuclease (Epicentre, cat. TER51020) to degrade 5’ monophosphate RNA (from terminating polymerase) and CIP to reduce other uncapped RNAs to 5’ hydroxyl, making them incapable of ligating to 5’ adapter.  5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).
CoPRO_NHScap_5p_pl.bw
CoPRO_NHScap_5p_mn.bw
CoPRO_NHScap_3p_pl.bw
CoPRO_NHScap_3p_mn.bw
MEF_Rep1_Pooled.Rdata

value: MEF NHS

value: Non heat shock


title: PW5-D10


title: CoPRO_K562_Capped_Rep2_Amplified

description:
Capped RNAs were selected by treating with Terminator 5’ Phosphate dependent exonuclease (Epicentre, cat. TER51020) to degrade 5’ monophosphate RNA (from terminating polymerase) and CIP to reduce other uncapped RNAs to 5’ hydroxyl, making them incapable of ligating to 5’ adapter.  5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).
CoPRO_AllMerge_Cap_5p_pl.bw
CoPRO_AllMerge_Cap_5p_mn.bw
CoPRO_AllMerge_Cap_3p_pl.bw
CoPRO_AllMerge_Cap_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep2_Pooled.Rdata


title: CoPRO_K562_Uncapped_Rep2_Amplified

description:
Uncapped RNAs were selected by treating with CIP, Calf Intestinal alkaline Phosphatase (NEB, cat. M0290S) and PNK, T4 Polynucleotide Kinase 3’ phosphatase minus (NEB, cat. M0236S), in order to reduce all uncapped RNAs to 5’ hydroxyl and then add 5’ monophosphate, but without removing the cap from capped RNA.
CoPRO_AllMerge_Uncapped_5p_pl.bw
CoPRO_AllMerge_Uncapped_5p_mn.bw
CoPRO_AllMerge_Uncapped_3p_pl.bw
CoPRO_AllMerge_Uncapped_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep2_Pooled.Rdata

value: Uncapped RNA only


title: PW4-H8


title: CoPRO_K562_Uncapped_Rep2_PCRfree

value: PCRfree


title: CoPRO_K562_CappedAndUncapped_Rep2_PCRfree


title: PW5-E5

value: IgA


title: PW4-H9

value: vaccine


title: CoPRO_K562_Capped_Rep2_PCRfree


title: PW4-H5

value: negative


title: PW4-H4


title: CoPRO_K562_CappedAndUncapped_Rep1_Amplified

description:
Capped + Uncapped RNAs were selected by treating with RppH, reducing both capped RNA and pre-capped RNA (5’ triphosphate) to 5’ monophosphate.
CoPRO_AllMerge_CappedAndUncapped_5p_pl.bw
CoPRO_AllMerge_CappedAndUncapped_5p_mn.bw
CoPRO_AllMerge_CappedAndUncapped_3p_pl.bw
CoPRO_AllMerge_CappedAndUncapped_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep1_Pooled.Rdata


title: CoPRO_K562_Capped_Rep1_Amplified

description:
Capped RNAs were selected by treating with Terminator 5’ Phosphate dependent exonuclease (Epicentre, cat. TER51020) to degrade 5’ monophosphate RNA (from terminating polymerase) and CIP to reduce other uncapped RNAs to 5’ hydroxyl, making them incapable of ligating to 5’ adapter.  5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).
CoPRO_AllMerge_Cap_5p_pl.bw
CoPRO_AllMerge_Cap_5p_mn.bw
CoPRO_AllMerge_Cap_3p_pl.bw
CoPRO_AllMerge_Cap_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep1_Pooled.Rdata


title: CoPRO_K562_Uncapped_Rep1_Amplified

description:
Uncapped RNAs were selected by treating with CIP, Calf Intestinal alkaline Phosphatase (NEB, cat. M0290S) and PNK, T4 Polynucleotide Kinase 3’ phosphatase minus (NEB, cat. M0236S), in order to reduce all uncapped RNAs to 5’ hydroxyl and then add 5’ monophosphate, but without removing the cap from capped RNA.
CoPRO_AllMerge_Uncapped_5p_pl.bw
CoPRO_AllMerge_Uncapped_5p_mn.bw
CoPRO_AllMerge_Uncapped_3p_pl.bw
CoPRO_AllMerge_Uncapped_3p_mn.bw
CoPRO_AllMerge_Pooled.Rdata
CoPRO_Rep1_Pooled.Rdata


title: PW4-H3

value: male


title: CoPRO_K562_CappedAndUncapped_Rep1_PCRfree


title: CoPRO_K562_Capped_Rep1_PCRfree


title: CoPRO_K562_Uncapped_Rep1_PCRfree


title: PW5-D6


title: PW4-H2


title: PW4-H12


title: PW4-H11


title: PJ048

first: Peter

last: Sims

state: NY

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: High grade glioma tissue

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

tag: age

value: Male

tag: location

value: right parietal

tag: diagnosis

value: Glioblastoma, WHO grade IV

tag: idh1 status

value: wt

tag: egfr status

value: not amplified


title: PW4-H10

tag: donor id


title: PW4-G1

tag: donor gender


title: PW4-G12

tag: isotype


title: PW4-F8

value: IgG

tag: specificity


title: PW4-F6

tag: experimental batch


title: PW4-F5


title: PW4-G2


title: CD4 T cell wildtype 48h PolyA-seq rep2

first: Yuheng

last: Lu

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The preprocessing, alignment, peak calling and quantification steps for the PolyA-Seq libraries were performed in the same way as the iCLIP libraries.
Internally primed peaks were removed as previously described.
Read counts were fitted using the DEXSeq model in order to identify cell-specific differences in 3’UTR isoform usage.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format, containing the read coverage profiles on all chromosomes

source_name: CD4 T cell

extract_protocol:
polyadenylated RNA from cells activated for 48 hours (0, 24, and 48 hours for CD4 T cells) was selected by using Sera-Mag oligo-(dT)14 (GE Healthcare), and reverse-transcribed to cDNA using RT primer (RT_1).
The complementary (2nd) strand of cDNA was synthesized using the Klenow fragment (exo-, NEB) and extension primer (Ext_primer_1). Barcoded libraries, amplified by PCR from the double-stranded cDNA pool, were submitted for high throughput sequencing.

tag: strain

tag: genotype

value: wild type

tag: cell type

value: CD4 T cell

value: 48h after stimulation


title: CD4 T cell wildtype 48h PolyA-seq rep3


title: PW4-F3


title: CD4 T cell wildtype 24h PolyA-seq rep3

value: 24h after stimulation


title: PW4-F4


title: CD4 T cell wildtype 24h PolyA-seq rep1


title: PW4-F2


title: PW4-F12


title: PW4-F11


title: CD4 T cell wildtype 0h PolyA-seq rep2

value: naïve


title: CD4 T cell wildtype 48h PolyA-seq rep1


title: PW4-F1


title: PW4-E9


title: CD4 T cell wildtype 0h PolyA-seq rep3


title: Macrophage wildtype PolyA-seq rep3

source_name: Macrophage

value: Macrophage


title: Macrophage wildtype PolyA-seq rep4


title: PW4-H1


title: PW4-E8


title: Macrophage wildtype PolyA-seq rep2


title: PW4-E7


title: Macrophage miR155 KO PolyA-seq rep4

value: miR-155 KO


title: Macrophage wildtype PolyA-seq rep1


title: PW4-E6

value: IgA


title: PW4-E5

value: vaccine


title: CD4 T cell wildtype 24h PolyA-seq rep2


title: Macrophage miR155 KO PolyA-seq rep3


title: PW4-E4

value: negative


title: Macrophage miR155 KO PolyA-seq rep2


title: Dendritic cell wildtype PolyA-seq rep3

source_name: Dendritic cell

value: Dendritic cell


title: PW4-F10

value: male


title: PW4-E10


title: CD4 T cell wildtype 0h PolyA-seq rep1


title: PW4-E3


title: PW4-E1


title: Dendritic cell wildtype PolyA-seq rep2


title: Macrophage miR155 KO PolyA-seq rep1


title: Dendritic cell wildtype PolyA-seq rep1


title: PW4-D6


title: PW4-D7


title: Dendritic cell miR155 KO PolyA-seq rep4


title: Dendritic cell miR155 KO PolyA-seq rep3


title: Dendritic cell miR155 KO PolyA-seq rep2


title: PW4-D5


title: PW4-D4


title: PW4-D3


title: B cell wildtype PolyA-seq rep4

source_name: B cell

value: B cell


title: Dendritic cell miR155 KO PolyA-seq rep1


title: PW4-D12


title: PW4-D2


title: PW4-D11


title: Dendritic cell wildtype PolyA-seq rep4


title: B cell wildtype PolyA-seq rep2


title: PW4-E2


title: B cell wildtype PolyA-seq rep1


title: B cell wildtype PolyA-seq rep3


title: PW4-D10


title: PW4-D1


title: PW4-D9


title: B cell miR155 KO PolyA-seq rep4


title: PW4-C7


title: PW4-C8


title: PW4-C6


title: B cell miR155 KO PolyA-seq rep2


title: PW4-C9


title: B cell miR155 KO PolyA-seq rep1


title: B cell miR155 KO PolyA-seq rep3


title: PW4-C10


title: PW4-C11


title: CD4 T cell wildtype replicate 3

data_processing:
iCLIP sequencing libraries were first de-multiplexed and then preprocessed using the cutadapt software to remove the adaptor and low-quality bases.
The processed reads were then aligned to the mouse genome (mm9) using the STAR aligner.
Multiple reads aligned to identical coordinates with the same random 7-mer in the barcode were considered PCR duplicates and were merged into a single read.
We then ran our peak-calling algorithm CLIPanalyaze on the combined read coverage from all samples to call peaks.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format, containing the read coverage profiles on all chromosomes

extract_protocol:
Cell lysate was incubated at 37°C for 5 minutes in the presence of 10 U RNase I (Ambion), and immunoprecipitated at 4°C for 2 hours using Argonaute 2 antibody.
Immuoprecipitated RNAs were first dephosphorylated at 3’ ends by PNK and then ligated to 3’ adapters (L32) using T4 RNA ligase 2, truncated KQ (NEB). The Argonaute-RNA complexes were resolved on SDS-PAGE gels, and complexes with a molecular weight corresponding to ~110-160 kDa were purified. Isolated RNAs (ranging from 40 to 200 nucleotides) were reverse-transcribed using barcoded primers. Purified cDNA libraries were circularized and re-linearized, and PCR amplified iCLIP libraries were submitted for high throughput sequencing.

treatment_protocol: Primary cells activated for 48 hours were irradiated with UV with 400 mJ, followed by 200 mJ, and then an additional 200 mJ.


title: CD4 T cell wildtype replicate 2


title: CD4 T cell wildtype replicate 1


title: CD4 T cell wildtype replicate 4


title: PW3-H9

value: female


title: PW3-H8


title: PW3-H7


title: CD4 T cell miR155 KO replicate 2


title: CD4 T cell miR155 KO replicate 4


title: CD4 T cell miR155 KO replicate 3


title: Macrophage wildtype replicate 3


title: Macrophage wildtype replicate 4


title: PW3-H4


title: PW3-H6


title: PW3-H5


title: Macrophage wildtype replicate 2


title: CD4 T cell miR155 KO replicate 1


title: PW4-C4


title: PW3-H3


title: Macrophage wildtype replicate 1


title: PW3-H10


title: Macrophage miR155 KO replicate 2


title: Macrophage miR155 KO replicate 4


title: Macrophage miR155 KO replicate 1


title: PW3-H1


title: PW3-G9


title: PW3-G8


title: PW3-G7


title: Dendritic cell wildtype replicate 2


title: PW3-G6


title: Dendritic cell wildtype replicate 1


title: PW3-G5


title: Dendritic cell miR155 KO replicate 4


title: PW3-G4


title: Dendritic cell miR155 KO replicate 3


title: Dendritic cell miR155 KO replicate 2


title: PW3-H12


title: PW3-G12


title: Macrophage miR155 KO replicate 3


title: PW3-G3


title: B cell wildtype replicate 3


title: PW3-G2


title: PW3-H11


title: Dendritic cell miR155 KO replicate 1


title: PW3-G10


title: B cell wildtype replicate 4


title: Dendritic cell wildtype replicate 3


title: Dendritic cell wildtype replicate 4


title: PW3-F9


title: PW3-G1


title: B cell wildtype replicate 1


title: PW3-F8


title: PW3-F7


title: B cell miR155 KO replicate 4


title: PW3-F6


title: PW3-F4


title: B cell miR155 KO replicate 2


title: B cell wildtype replicate 2


title: B cell miR155 KO replicate 1


title: B cell miR155 KO replicate 3


title: PW3-F2


title: PW3-F12


title: PW3-F10


title: HM #8

first: Patricia

middle: K

last: Martin

department: Pathology

institute: NYU School of Medicine

description: HM 4

data_processing:
Sequencing data was processed using Tuxedo suite;
reads were aligned with TopHat v2.1.1 against UCSC mm10 genome assembly resulting in an average of 20 million aligned pairs per sample,
normalized read counts were calculated using Cufflinks v2.2.1 against the same reference genome.
Differential gene expression was determined with Cuffdiff
gene ontology analysis performed using QIAGENʼs Ingenuity Pathway Analysis
Genome_build: mm19
Supplementary_files_format_and_content: Excel files contains FPKM values for genes with pval < 0.1 and FC > 1.25

source_name: CD11b+Ly6C+ inflammatory monocytes from the colon

growth_protocol: mice were 12 wks old, housed in BSL2 animal facility

extract_protocol:
Cd11b+Ly6C+ monocytes were sorted into trizol-LP. RNA was extracted by RNeasy Micro Kit
Nugen’s Ovation Ultralow RNA-seq system V2

treatment_protocol: mice were infected with 2x10^9 CFU of C. rodentium at 9 days prior to sacrifice

tag: tissue

value: colon

tag: background strain

value: CD11b+Ly6C+ inflammatory monocytes

tag: day post c. rodentium infection

value: 12 weeks


title: WT #7

description: B6 4

value: WT


title: WT #5

description: B6 3


title: HM #6

description: HM 3


title: HM #4

description: HM 2


title: PW3-E7

value: IgG


title: PW3-E9


title: PW3-F11


title: PW3-E4


title: WT #1

description: B6 1


title: PW3-E3


title: WT #3

description: B6 2


title: PW3-E1


title: PW3-D9


title: PW3-D6


title: PW3-F3


title: HM #2

description: HM 1


title: 10 Control3_E12.5

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Strand NGS software version 2.1 with default parpemters.
Duplicated reads were filted and normalized reads Per Kilobase of exon per Megabase of library size (NRPKM) were calculated using StransNGS software (version2.1) pipeline
Genome_build: mm10

source_name: embryonic mouse limb buds

extract_protocol:
Mouse embryonic limb buds RNA was harvest RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic mouse limb buds


title: 13 Sox9cKO3_E12.5


title: 12 Sox9cKO2_E12.5


title: 11 Sox9cKO1_E12.5


title: PW3-D5


title: 08 Control1_E12.5


title: PW3-D2


title: 07 Sox9null_4_E11.5


title: PW3-D12


title: 06 Sox9null_3_E11.5


title: PW3-D11


title: PW3-C9


title: PW3-D1


title: PW3-D10


title: 03 Control_3_E11.5


title: 02 Control_2_E11.5


title: 04 Sox9null_1_E11.5


title: PW3-C6


title: PW3-C3


title: Sox9null E11.5_Input

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Strand NGS (software version 2.0)  with default parpemters.
Duplicated reads were filted. H3K27ac peaks were identified using MACS software (version 1.4.5) with default settings. Bigwig f
BigWig files were generated using DeepTools-bamCoverage program in Galaxy server
Genome_build: mm10

molecule: genomic DNA

extract_protocol:
Mouse embryonic limb buds lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies
ChIP-seq DNA libraries wereprepared for sequencing using standard Illumina protocols

tag: tissues

tag: chip-seq antibody


title: Control_E11.5_Input


title: 01 Control_1_E11.5


title: PW3-C2


title: PW3-C5


title: PW3-C12


title: Sox9null_E11.5_H3K27ac

value: H3K27ac (ab4729, Abcam)


title: PW3-D4


title: Sox9cKO_E12.5_Input


title: Control_E11.5_H3K27ac


title: 09 Control2_E12.5


title: Sox9cKO_E12.5_H3K27ac.


title: Control_E12.5_H3K27ac


title: PW3-C10


title: PW3-B8


title: PW3-B6


title: Sox9cKO_E12.5_H3K36me3

value: H3K36me3 (ab9050, Abcam)


title: 05 Sox9null_2_E11.5


title: PW3-B5


title: Sox9cKO_E12.5_H3K4me3

value: H3K4me3 (ab8580,Abcam)


title: Control_E12.5_H3K36me3


title: PW3-B4


title: Sox9null_E11.5_H3K36me3


title: PW3-B12


title: Control_E12.5_H3K4me3


title: PW3-B11


title: PW3-B10


title: PW3-B9


title: Control_E11.5_H3K36me3


title: Control_E11.5_H3K4me3


title: Sox9null_E11.5_H3K4me3


title: Control_E12.5_Input


title: PW3-B1


title: PW3-A9


title: PW3-A5


title: PW3-A6


title: PW3-A7


title: PW3-A8


title: PW3-B7


title: PW3-A3


title: Control_E12.5_H3K27me3

value: H3K27me3 (ab6002, Abcam)


title: Sox9cKO_E12.5_H3K27me3


title: Control_E11.5_H3K4me1

value: H3K4me1 (ab8895, Abcam)


title: Control_E12.5_H3K4me1


title: Sox9cKO_E12.5_H3K4me1


title: Sox9null E11.5_H3K27me3


title: Sox9null_E11.5_H3K4me1


title: PW3-A2

value: IgA

value: vaccine


title: Control E11.5 H3K27me3


title: PW3-B3


title: PW3-A11


title: KK-ISO-D14-Rep2

city: Los Angeles

first: Fides

middle: D

last: Lay

state: CA

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

description: stranded RNA-seq

data_processing:
FastQC was used to determine library quality, and reads were trimmed using Fastx Toolkit
Raw reads were aligned to mm10 genome using STAR v2.5.3a  and gene counts were generated
Raw gene counts were transformed to counts per million (CPM) and log2-counts per million (log2-CPM) data matrix and further normalized by trimmed mean of M-values (TMM) method in the edgeR
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Thy1+ HE cells

extract_protocol:
Thy1+HE- cells were isolated from saline and ISO-treated hearts 14 or 21 days after pump implantation (n=2 per strain/condition), and then sorted directly into TRIzol® LS Reagent (Ambion).
Total RNA was extracted using the RNeasy miniElute Cleanup Kit (Qiagen), according to manufacturer’s instructions. The complementary DNA (cDNA) library was generated using reagents provided in the KAPA mRNA Hyperprep kit. The amplified cDNA library was sequenced on an Illumina HiSeq 3000 according to manufacturer’s instructions. Libraries were sequenced using 50 single-end read protocol

value: KK/HlJ

tag: treatment

value: ISO

tag: time

value: Heart

value: Thy1+ HE cells


title: KK-ISO-D21-Rep1

description: stranded RNA-seq


title: KK-ISO-D21-Rep2

description: stranded RNA-seq


title: KK-ISO-D14-Rep1

description: stranded RNA-seq


title: KK-Sham-Rep2

description: stranded RNA-seq

value: SHAM


title: PW3-A4

value: female


title: PW3-A1

value: negative


title: C3H-ISO-D21-Rep2

description: stranded RNA-seq


title: PW2-H5

value: male


title: PW2-H4


title: PW3-A12


title: PW2-H3


title: C3H-ISO-D14-Rep2

description: stranded RNA-seq


title: B6-ISO-D21-Rep2

description: stranded RNA-seq


title: C3H-ISO-D21-Rep1

description: stranded RNA-seq


title: LNCaP HIST1H1A over-expressing clone #9

city: Bethesda

first: Kendra

last: Williams

state: MD

address: 50 South Dr, Bldg 50

department: NHGRI

institute: NIH

description: HIST1H1A 9

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hypridized to the Affymetrix Human GeneChip® 2.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using standard format and protocols as described by Affymetrix.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data was processed via partek.

source_name: human prostate tumor cell line

label_protocol: Labeling was performed using GeneChip® WT Terminal Labeling and Control Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were incubated in 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from LNCaP cells using QIAGEN miRNeasy Mini Kit.

treatment_protocol: Not Applicable

tag: cell line

value: LNCaP

tag: genotype/variation

value: HIST1H1A over-expression


title: LNCaP HIST1H1A over-expressing clone #10

description: HIST1H1A 10


title: LNCaP HIST1H1A over-expressing clone #8

description: HIST1H1A 8


title: B6-ISO-D21-Rep1

description: stranded RNA-seq


title: C3H-Sham-Rep1

description: stranded RNA-seq


title: KK-Sham-Rep1

description: stranded RNA-seq


title: B6-ISO-D14-Rep2

description: stranded RNA-seq


title: PW2-H2

tag: donor id


title: PW3-A10

tag: donor gender


title: B6-Sham-Rep2

description: stranded RNA-seq


title: PW2-H1

tag: isotype


title: PW2-G9

tag: specificity


title: B6-Sham-Rep1

description: stranded RNA-seq


title: C3H-ISO-D14-Rep1

description: stranded RNA-seq


title: B6-ISO-D14-Rep1

description: stranded RNA-seq


title: C3H-Sham-Rep2

description: stranded RNA-seq


title: PW2-G8

tag: experimental batch


title: PW2-G7


title: PW2-G6


title: PW2-G4

value: IgG


title: LNCaP HIST1H1A over-expressing clone #2

description: HIST1H1A 2


title: LNCaP control clone #9

description: Ctrl 9

value: control


title: LNCaP control clone #4

description: Ctrl 4


title: LNCaP control clone #8

description: Ctrl 8


title: LNCaP control clone #3

description: Ctrl 3


title: PW2-G3


title: PW2-G2


title: JS11_2Tel+GW+LPS-1h

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 2.0 ST microarrays. After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories). The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). CEL files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the CHP files. The CHP files were normalized, log2 transformed, and summarized.

source_name: BV2 cells, Telmisartan+GW9662+LPS

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 300 ng of total RNA was used for labeling with the Ambion WT Expression Kit (cat#4411974) and Affymetrix kit (Cat # 900652).

growth_protocol: BV2 cells were cultured in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% heat inactivated FBS, 100 U/ml penicillin and 100 µg/ml streptomycin (Thermo Fisher, Grand Island, NY) at 37ºC in an atmosphere of 5% CO2. When reached 80% conﬂuence, 400 000 cells per well were seeded in 6-well plates for further experiments.

extract_protocol: Total RNA was extracted from cells.

treatment_protocol: All treatments consisted of three to five individual independent samples per group, each sample analyzed in triplicates, Groups treated only with drugs (Telmisartan, GW9662 and LPS) received the drugs for 3 hrs. Groups treated with drugs + LPS received drugs for two hours followed by LPS for 1 hr. All experiments were conducted for 3 hrs.

value: microglia cell line

value: WT


title: JS12_3Tel+GW+LPS-1h


title: C14_R_D2vsBL

city: Houston

first: Xiao

last: Ni

state: TX

address: 1515 Holcombe Blvd.

department: Dermatology

institute: MD Anderson Cancer Center

description:
251485070792_1_1
Day 2 (D2)
Biological replicate 4 of 5 Day 2 post-ECP vs Baseline, responsive

hyb_protocol: Co-hybridized at 65 °C for 18 hours to a Agilent Whole Human genome Oligo Microarray (4 × 44 K)

scan_protocol: Scanned on an Agilent G2505B scanner; Images then quantified.

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

source_name: Day 2 post-ECP responsive

label_protocol: For each hybridization, 500 ng of Cyanine 5 labeled cRNA (post-ECP sample) and 500 ng of Cyanine 3 labeled cRNA (the corresponding baseline sample) were mixed.

growth_protocol: PBMCs isolated from fresh blood of patients

extract_protocol: Total RNA extracted from PBMCs using RNeasy Mini Kit (Qiagen, USA).

value: PBMC

tag: diagnosis

value: cutaneous T-cell lymphoma (CTCL)

tag: clinical response

value: responsive

tag: timepoint

value: Day 2 (D2)

source_name: Baseline (BL)

tag: disease


title: JS09_3Tel+LPS-1h

source_name: BV2 cells, Telmisartan+LPS

tag: cell type

value: Telmisartan+LPS


title: PW2-G12

value: IgA


title: C1_R_D2vsBL.1

description:
251485014981_1_2
Day 2 (D2)
Technical replicate 1 of 2 Biological replicate 1 of 5 Day 2 post-ECP vs Baseline, responsive (replicate sample of C1_R_M1vsBL)

source_name: Day 2 post-ECP responsive replicate sample of C1_R_D2vsBL

tag: tissue


title: C16_R_M1vsBL

description:
251485070792_1_4
1 month (M1)
Biological replicate 5 of 5 1 month post-ECP vs baseline, responsive

source_name: 1 month post-ECP responsive

value: 1 month (M1)


title: C16_R_D2vsBL

description:
251485070792_1_3
Day 2 (D2)
Biological replicate 5 of 5 Day 2 post-ECP vs Baseline, responsive


title: JS07_1Tel+LPS-1h


title: C2_R_D2vsBL

description:
251485021280_1_1
Day 2 (D2)
Biological replicate 2 of 5 Day 2 post-ECP vs Baseline, responsive


title: PW2-G11

source_name: peripheral blood plasmablast


title: C1_R_M1vsBL.1

description:
251485014981_1_4
1 month (M1)
Technical replicate 2 of 2 Biological replicate 1 of 5 1 month post-ECP vs Baseline, responsive (replicate sample of C1_R_M1vsBL)

source_name: 1 month post-ECP responsive replicate sample of C1_R_M1vsBL


title: JS10_1Tel+GW+LPS-1h


title: C2_R_M1vsBL

description:
251485021280_1_2
1 month (M1)
Biological replicate 2 of 5 1 month post-ECP vs baseline, responsive


title: C14_R_M1vsBL

description:
251485070792_1_2
1 month (M1)
Biological replicate 4 of 5 1 month post-ECP vs baseline, responsive


title: JS08_2Tel+LPS-1h


title: C5_R_D2vsBL

description:
251485021336_1_1
Day 2 (D2)
Biological replicate 3 of 5 Day 2 post-ECP vs Baseline, responsive


title: C1_R_D2vsBL

description:
251485014981_1_1
Day 2 (D2)
Biological replicate 1 of 5 Day 2 post-ECP vs Baseline, responsive


title: JS12_Telmisartan+LPS-1h

treatment_protocol: All treatments consisted of three to five individual independent samples per group, each sample analyzed in triplicates, and included 1.5% DMSO (Sigma-Aldrich, St. Louis, MO). Vehicle-treated groups received 1.5% DMSO for 3 hrs. Groups treated only with drugs (Telmisartan and LPS) received the drugs for 3 hrs. Groups treated only with LPS, received vehicle for two hours, followed by LPS for 1 hr. Groups treated with drugs + LPS received drugs for two hours followed by LPS for 1 hr. All experiments were conducted for 3 hrs.


title: C13_N_M1vsBL

description:
251485070793_1_4
1 month (M1)
Biological replicate 5 of 5 1 month post-ECP vs baseline,  non-responsive

source_name: 1 month post-ECP  non-responsive

value: non-responsive


title: C1_R_M1vsBL

description:
251485014981_1_3
1 month (M1)
Biological replicate 1 of 5 1 month post-ECP vs baseline, responsive


title: C5_R_M1vsBL

description:
251485021336_1_2
1 month (M1)
Biological replicate 3 of 5 1 month post-ECP vs baseline, responsive


title: PW2-G1

value: vaccine


title: C9_N_M1vsBL

description:
251485070793_1_2
1 month (M1)
Biological replicate 4 of 5 1 month post-ECP vs baseline,  non-responsive


title: KG1a8Gy_48hr_Li8Gy_rep2

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

country: India

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

description: Gene expression after 48hr in LiCl pre-treated, 8Gy irradiated KG1a cells

hyb_protocol: Hybridized to Human Whole Genome Arrary Chip (Human 8x60K Array AMAID: 039494/ GPL17077).

scan_protocol: Images were scanned and signaled data was acquired using feature extraction software (V/0.5 Agilent Tech). The images were manually verified and found to be devoid of uneven hybridization, strikes, blobs, and other artifacts.

data_processing: Inta-Array normalization was done using GeneSpring GX 12.1 software. The gProcessed signal (dye normalized background subtracted signal intensity) was log transformed and then for each of the array the 75th percentile value was calculated. In each sample the log transformed intensity values for each probe was subtracted by the calculated 75th percentile value of the respective array and expression values were obtained.

source_name: KG1a, 48hr, Li8Gy, replicate 2

label_protocol: Following reverse transcription of RNA into cDNA, Cy3 labelled cRNA was produced by in vitro transcription.

growth_protocol: KG1a cells were grown in IMDM medium containing 20% fetal bovine serum and antibiotic and antimycotic solution, in 5% CO2 atmosphere at 37°C.

extract_protocol: RNA isolated using RNeasy Minikit (Qiagn, #74104) and quantified in Nanodrop spectrophotometer. RNA sample purity ratio was more than 1.9 for 260/280 nm, and RIN values were greater than 9.0 as evaluated on Bioanalyzer (Agilent Tech).

treatment_protocol: For irradiation of cells, Bhabhatron Teletherapy unit (Co60 as radiation source) was used.

value: bone marrow

value: acute myleogenous leukemia

value: promyeloblast, Macrophage


title: PW2-F9

value: male

value: negative


title: JS11_Telmisartan

source_name: BV2 cells, Telmisartan

value: Telmisartan


title: JS09_DMSO

source_name: BV2 cells, DMSO

value: microglia cell line

value: DMSO


title: JS10_LPS-1h

source_name: BV2 cells, LPS

value: WT

value: LPS


title: KG1a8Gy_48hr_Li8Gy_rep3

source_name: KG1a, 48hr, Li8Gy, replicate 3

value: 48hr in LiCl pre-treated, 8Gy irradiated


title: C13_N_D2vsBL

description:
251485070793_1_3
Day 2 (D2)
Biological replicate 5 of 5 Day 2 post-ECP vs Baseline, non-responsive

source_name: Day 2 post-ECP non-responsive

value: PBMC

value: cutaneous T-cell lymphoma (CTCL)

value: Day 2 (D2)


title: PW2-F8

value: IgA


title: PW2-F7


title: PW2-G10


title: C4_N_M1vsBL

description:
251485021335_1_4
1 month (M1)
Biological replicate 3 of 5 1 month post-ECP vs baseline,  non-responsive

value: non-responsive

value: 1 month (M1)


title: C9_N_D2vsBL

description:
251485070793_1_1
Day 2 (D2)
Biological replicate 4 of 5 Day 2 post-ECP vs Baseline, non-responsive


title: PW2-F6


title: KG1a8Gy_48hr_Li8Gy_rep1

source_name: KG1a, 48hr, Li8Gy, replicate 1

value: bone marrow


title: C3_N_M1vsBL

description:
251485021335_1_2
1 month (M1)
Biological replicate 2 of 5 1 month post-ECP vs baseline,  non-responsive


title: JS06_LPS-1h


title: KG1a8Gy_48hr_Li4Gy_rep2

description: Gene expression after 48hr in LiCl pre-treated, 4Gy irradiated KG1a cells

source_name: KG1a, 48hr, Li4Gy, replicate 2

value: acute myleogenous leukemia


title: JS05_DMSO


title: PW2-F5


title: C4_N_D2vsBL

description:
251485021335_1_3
Day 2 (D2)
Biological replicate 3 of 5 Day 2 post-ECP vs Baseline, non-responsive


title: KG1a8Gy_48hr_Li4Gy_rep1

source_name: KG1a, 48hr, Li4Gy, replicate 1

value: promyeloblast, Macrophage

value: 48hr in LiCl pre-treated, 4Gy irradiated


title: JS07_Telmisartan


title: PW2-F4

value: male

value: vaccine


title: PW2-F3


title: JS08_Telmisartan+LPS-1h

value: microglia cell line

value: Telmisartan+LPS


title: O5

city: Dresden

first: Konstantinos

last: Anastassiadis

address: Tatzberg 47

department: Biotechnology Center

country: Germany

institute: Technische Universitaet Dresden

data_processing:
Basecalls were performed using Illumina CASAVA version 1.8.0.
Reads were mapped to the mouse genome (version mm9) with pBWA (Peters et al., 2012).
Readcounts per gene were created based on the overlap of the uniquely mapped reads with the Ensembl Genes annotation v. 61 for mm9, using BEDtools, v. 2.11 (Quinlan and Hall, 2010).
Genome_build: NCBI m37/mm9
Supplementary_files_format_and_content: bfx245.mm9.e61.txt: Tab-separated table with the following columns: Ensembl gene id, Ensembl gene name, number of exons, total exonic length as well as counts for each sample.

source_name: Bone marrow stromal cells

growth_protocol: BMSCs were isolated by flushing the femora and tibiae of irtTA-GBD*-TAg transgenic mice and cultured cultured in Dulbecco’s Modified Eagle’s Medium, DMEM, with 1g/L D-glucose (Gibco Life Technologies), supplemented with 10% Fetal Calf Serum (FSC, PAA) and 1x Penicillin/Streptomycin. At the first passage 10-7M Dexamethasone (Dex) and 1μg/ml Doxycycline (Dox, both from Sigma) were added to BMSC growth medium to induce expression of Large T-antigen. Conditionally immortalized BMSCs grew rapidly in the presence of Dex/Dox and were routinely passaged every 3-5 days at a dilution 1:5-1:10. Cellular cloning was done by limiting dilutions or by single-cell deposition into 96-well plates using FACSAriaII cell sorter (BD Biosciences). For RNA sequencing the cells were cultured without Dex/Dox for 3 days.

extract_protocol:
Total RNA was isolated by chloroform extraction from cell lysates prepared with Trizol (Invitrogen) followed by isopropanol precipitation.
mRNA was enriched from total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturers instructions. Eluted mRNA (18µl) was directly subjected to the workflow of the NEBNext Ultra Directional RNA Library Prep Kit for Illumina. For ligation custom adaptors were used  (Adaptor-Oligo 1: 5'-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3'). Indexing was done during the PCR enrichment step using custom amplification primers carrying the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo_Seq AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, primer2: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, primer3: CAAGCAGAAGACGGCATACGAGAT NNNNNN GTGACTGGAGTT). After XP beads purification libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). For Illumina flowcell production, samples were equimolarly pooled and distributed on all lanes used for 75bp single read sequencing on Illumina HiSeq 2000.

treatment_protocol: Adipogenic progenitors were treated with 10ng/ml IFNγ for 3 days

tag: strain

value: Bone marrow

tag: Stage

value: adult


title: O6


title: PW2-F2


title: D1_N_M1vsBL

description:
251485021280_1_4
1 month (M1)
Biological replicate 1 of 5 1 month post-ECP vs baseline,  non-responsive

source_name: Baseline (BL)


title: KG1a8Gy_48hr_4Gy_rep2

description: Gene expression after 48hr in 4Gy irradiated KG1a cells

source_name: KG1a, 48hr, 4Gy, replicate 2

tag: treatment

value: 48hr in 4Gy irradiated


title: C3_N_D2vsBL

description:
251485021335_1_1
Day 2 (D2)
Biological replicate 2 of 5 Day 2 post-ECP vs Baseline, non-responsive

value: PBMC


title: KG1a8Gy_48hr_Li4Gy_rep3

source_name: KG1a, 48hr, Li4Gy, replicate 3


title: JS03_Telmisartan

value: WT

value: Telmisartan


title: KG1a8Gy_48hr_4Gy_rep1

source_name: KG1a, 48hr, 4Gy, replicate 1


title: KG1a8Gy_48hr_4Gy_rep3

source_name: KG1a, 48hr, 4Gy, replicate 3


title: JS04_Telmisartan+LPS-1h

source_name: BV2 cells, Telmisartan+LPS


title: JS02_LP-1h

value: LPS


title: D1_N_D2vsBL

description:
251485021280_1_3
Day 2 (D2)
Biological replicate 1 of 5 Day 2 post-ECP vs Baseline, non-responsive

value: cutaneous T-cell lymphoma (CTCL)

value: non-responsive

value: Day 2 (D2)


title: O4


title: KG1a_48hr_LiCl_rep2

description: Gene expression after 48hr in LiCl treated KG1a cells

source_name: KG1a, 48hr, LiCl, replicate 2

value: bone marrow

value: acute myleogenous leukemia

value: 48hr in LiCl


title: KG1a_48hr_LiCl_rep3

source_name: KG1a, 48hr, LiCl, replicate 3

value: promyeloblast, Macrophage


title: A6G


title: PW2-F12

source_name: peripheral blood plasmablast

value: male

value: IgG

value: vaccine


title: PW2-F11


title: PW2-F1

value: IgA


title: PW2-E9


title: A6

value: Bone marrow

value: adult


title: KG1a_48hr_LiCl_rep1

source_name: KG1a, 48hr, LiCl, replicate 1


title: A4G


title: PW2-E8


title: A5


title: A4


title: JS01_DMSO

source_name: BV2 cells, DMSO

value: microglia cell line

value: DMSO


title: PW2-E7


title: eWAT _Western diet_curcumin _rep3

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

country: Japan

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from the epididymal adipose tissue after 16 week feeding of Western diet containing 0.1% curcumin

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: eWAT, fed a Western diet containing 0.1% curcumin for 16 weeks

label_protocol: The fragmented biotin-labeled aRNA was synthesized from the total RNA of each mouse using the GeneChip® 3′ IVT Express Kit (Affymetrix Japan KK, Tokyo, Japan).

growth_protocol: Five-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed at 24 ± 1°C, 55 ± 5% humidity, and 12 h light/dark photocycles (dark period from 8:00 to 20:00), with free access to water and a standard nonpurified diet for 1 week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and apididymal adopose tissue were immediately collected. Total RNA was extracted from adipose tissues using TRIzol reagent and an RNeasy Mini Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were divided into three groups, housed in groups of three per cage, and fed one of the following diets: AIN93G (control); a high-fat, high-cholesterol, and high-sucrose Western-style diet [39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose] (Oriental Yeast Co., Tokyo, Japan); or the same Western diet supplemented with 0.1% curcumin for 16 weeks.

tag: Sex

value: epididymal white adipose tissue


title: A5G


title: eWAT _Western diet_curcumin _rep4


title: eWAT _Western diet_curcumin _rep5


title: WT-3m-NL-Input

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Rm 405A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
FastQC version 0.10.1  for quality analysis for FASTQ files
Bowtie2 version 2.3.4.1 for alignment
MACS v2.1.0 for peak calling
Homer v4.8 for enrichment
UCSC tools  bedClip, bed-Graph-ToBigWig for generating the bw files
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS2 and UCSC tools

source_name: Liver cells

growth_protocol: The strain of HBx-TG mice was fixed to C57BL/6 by backcrossing with the C57BL/6 strain for more than 20 generations

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with different antibodies.
NEBNext® Ultra™ DNA Library Prep Kit (NEB, UK)

tag: chip antibody

tag: age

value: 3 month

value: wild type

value: normal liver


title: PW2-E6

tag: donor id


title: A3

description: unipotent: adipogenic

data_processing:
Basecalls were performed using Illumina CASAVA version 1.8.0.
Reads were mapped to the mouse genome (NCBI m37/mm9) with pBWA (Peters et al., 2012).
Readcounts per gene were created based on the overlap of the uniquely mapped reads with the Ensembl Genes annotation v. 61 for mm9, using BEDtools, v. 2.11 (Quinlan and Hall, 2010).
Genome_build: NCBI m37/mm9
Supplementary_files_format_and_content: bfx242.mm9.e61.txt: Tab-separated table with the following columns: Ensembl gene id, Ensembl gene name, number of exons, total exonic length as well as counts for each sample.

growth_protocol: BMSCs were isolated by flushing the femora and tibiae of irtTA-GBD*-TAg transgenic mice and cultured  cultured in Dulbecco’s Modified Eagle’s Medium, DMEM, with 1g/L D-glucose (Gibco Life Technologies), supplemented with 10% Fetal Calf Serum (FSC, PAA) and 1x Penicillin/Streptomycin. At the first passage 10-7M Dexamethasone (Dex) and 1μg/ml Doxycycline (Dox, both from Sigma) were added to BMSC growth medium to induce expression of Large T-antigen. Conditionally immortalized BMSCs grew rapidly in the presence of Dex/Dox and were routinely passaged every 3-5 days at a dilution 1:5-1:10. Cellular cloning was done by limiting dilutions or by single-cell deposition into 96-well plates using FACSAriaII cell sorter (BD Biosciences). The clones were passaged and assayed for differentiation (Osteogenic, Adipogenic, Chondrogenic) after removing Dex/Dox in a 96-well plate format. For RNA sequencing the cells were cultured without Dex/Dox for 3 days.

extract_protocol:
Total RNA was isolated by chloroform extraction from cell lysates prepared with Trizol (Invitrogen) followed by isopropanol precipitation.
For strand specific RNA sequencing, mRNA was enriched from total RNA using Sera-Mag Oligo(dT) beads (Thermo Scientific) followed by library preparation with the  NEBNext mRNA Sample Prep Master Mix Set 1  (NEB).


title: WT-3m-NL-H3K27me3

tag: genotype/variation


title: OC3

description: bipotent: osteogenic, chondrogenic


title: eWAT _Western diet_curcumin _rep2


title: PW2-E5

data_processing:
Kallisto was used for alignment against the human transcriptome
Log2(TPM+1)
Applied threshold of detection, set all Log2(TPM+1) values below threshold to 0.
Applied cell filter, removed all cells with less than 40% of transcripts mapping to the human transcriptome.
Applied gene expression filter, removed all genes expressed in less than 5% of the cells
Performed Quantile normalization with the Preprocesscore package within each experimental plate
Performed Limma batch correction to remove variability associated with experimental plate and donor ID, while protecting BCR isotype and specificity.
Genome_build: HG19
Supplementary_files_format_and_content: normalized abundance measurement

extract_protocol:
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.
The Smart-seq2 protocol published in Nature Protocols by Picelli et al., 2014, was used to isolate cellular mRNA and generate single-cell libraries for RNA-sequencing.

tag: donor gender

tag: isotype


title: TG-18m-T-Input2

value: 18 month

value: HBx-TG

value: tumor


title: eWAT _Western diet_rep5

description: Gene expression data from the epididymal adipose tissue after 16 week feeding of Western diet

source_name: eWAT, fed a high fat, high colesterol and high sucrose Western diet for 16 weeks


title: AC3

description: bipotent: adipogenic, chondrogenic


title: eWAT _Western diet_rep4


title: PW2-E4

tag: specificity

tag: experimental batch


title: eWAT _Western diet_curcumin _rep1


title: eWAT _Western diet_rep3


title: TG-18m-NT-Input2

value: non-tumor


title: TG-18m-T-H3K27me3


title: A2

description: unipotent: adipogenic


title: A1

description: unipotent: adipogenic


title: eWAT _Western diet_rep2


title: PW2-E2

value: negative


title: TG-18m-NT-H3K27me3


title: O3

description: unipotent: osteogenic


title: O2

description: unipotent: osteogenic


title: O1

description: unipotent: osteogenic


title: TG-18m-T-EZH2


title: TG-18m-NT-Input1


title: PW2-E10

value: male


title: PW2-E1


title: eWAT_control_rep5

description: Gene expression data from the epididymal adipose tissue after 16 week feeding of AIN93G diet

source_name: eWAT, fed control AIN93G diet for 16 weeks


title: eWAT _Western diet_rep1


title: TG-18m-NT-EZH2


title: eWAT_control_rep3


title: OA2

description: bipotent: osteogenic, adipogenic


title: OA3

description: bipotent: osteogenic, adipogenic


title: PW2-E11


title: eWAT_control_rep2


title: eWAT_control_rep4


title: PW2-D9


title: PW2-E3

value: IgG


title: OA1

description: bipotent: osteogenic, adipogenic


title: PW2-D8

value: vaccine


title: TG-18m-T-Input1


title: Cugbp1 Liver 2

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Liver harvested from Cugbp1 KO mouse at day 3 of life

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1) was used to read out and process the microarray image files.

source_name: Liver

label_protocol: RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Male Cugbp1 KO mice were sacrificed at day 3 of life, and livers were harvested for analysis.

extract_protocol: Total RNA was isolated using RNEasy Plus mini kit according to the manufacturer's instructions.

tag: genotype

value: Cugbp1 KO

tag: age at sac

value: 3 days


title: PW2-D7

value: IgA


title: Top2-1_rpb3_S_37_IP

type: genomic

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: RNA-pol2 mapping of across the genome

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R array for 16 hours at 42 C in a hybridization oven at 60 rpm

scan_protocol: Arrays were scanned on Affymetrix geneChip Scanner 3000 7G

data_processing:
The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE)
Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

organism: Saccharomyces cerevisiae

source_name: IP fraction of Rpb3-PK Top2-1 ts at 37 degree S Phase

label_protocol: Both IP and Input samples are amplified by using Whole genome amplificatio ki protocol ( Sigma-Aldrich WGA1-50RXN) pripor to labelling with Biotin-N11-ddATP (1nMole/ul).

growth_protocol: 1X10e7 cells were synchronized at G1 phase using Alpha-factor and cells were harvested for "G1" samples. For "S" phase samples cells were released into fresh medium after washing cells with 2X YP-medium. After 15 mins of the realese from alpha factor arrest cells were harvested for Chip protocols

extract_protocol: Cells were crosslinked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction was incuabted with magnetic beads coated with anti-Flag antibody (M2-antiflag, Sigma) overnight at 4C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 50 mM Tris pH8.0, 10mM EDTA) at 65C for 20 min followed by the addition of proteinaseK to 500 µg/ml and overnight incubation at 65C. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP).

tag: strain background

value: Rpb3-PK Top2-1 ts

value: Glucose

tag: temperature

tag: category

value: Protein

tag: cellcycle

value: S Phase

tag: antibody

value: AntiFlag M2 - (Sigma)


title: Top2-1_rpb3_S_37_INPUT

description: RNA-pol2 mapping of across the genome

source_name: INPUT fraction of Rpb3-PK Top2-1 ts at 37 degree S Phase

tag: treatment


title: OAC3

description: tripotent: osteogenic, adipogenic, chondrogenic

source_name: Bone marrow stromal cells

tag: strain

tag: tissue

value: Bone marrow

tag: Stage

value: adult


title: WT_rpb3_S_37_INPUT

description: RNA-pol2 mapping of across the genome

source_name: INPUT fraction of Rpb3-PK wt at 37 degree S Phase

value: Rpb3-PK wt


title: WT_rpb3_S_37_IP

description: RNA-pol2 mapping of across the genome

source_name: IP fraction of Rpb3-PK wt at 37 degree S Phase


title: PW2-D6

tag: donor id


title: OAC1


title: PW2-D5


title: Hmo1_Hybrid_S_37_INPUT

description: RNA-DNA hybrid mapping of across the genome

source_name: INPUT fraction of RNA-DNA Hybrid in Hmo1 at 37 degree S Phase

extract_protocol: Cells were crosslinked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction was incuabted with magnetic beads coated with anti-DNA:RNA hybrid monoclonal mouse antibody S9.6 overnight at 4C. The immune complexes were washed with the following buffers 2X; Chip-lysis buffer, high-salt lysis buffer (Chip-lysis buffer + 360mM NaCl), Chip-wash buffer (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 50 mM Tris pH8.0, 10mM EDTA) at 65C for 20 min followed by the addition of proteinaseK to 500 µg/ml and overnight incubation at 65C. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP).

tag: genotype/variation

value: Hmo1 deletion

value: RNA-DNA Hybrid


title: Hmo1_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in Hmo1 at 37 degree S Phase

value: S9.6 Monoclonal Antibody


title: PW2-D4

tag: donor gender

value: male

value: negative


title: PW2-D3

tag: isotype


title: Cugbp1 Liver 3


title: Top2-1_Top1_Hybrid_S_37_INPUT

source_name: INPUT fraction of RNA-DNA Hybrid in Top2-1 ts and Top1 deletion at 28 degree S Phase

value: Top2-1 ts and Top1 deletion


title: WT Liver 3

description: Liver harvested from wildtype mouse at day 3 of life

value: Wildtype


title: Cugbp1 Liver 1

value: Cugbp1 KO

value: 3 days


title: Top2-1_Top1_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in Top2-1 ts and Top1 deletion at 28 degree S Phase


title: Top1_Hybrid_S_28_IP

source_name: IP fraction of RNA-DNA Hybrid in Top1 deletion at 28 degree S Phase

value: Top1 deletion


title: WT Liver 2


title: eWAT_control_rep1

tag: Sex

value: epididymal white adipose tissue


title: Top1_Hybrid_S_28_INPUT

source_name: INPUT fraction of RNA-DNA Hybrid in Top1 deletion at 28 degree S Phase

value: Glucose


title: PW2-D11

source_name: peripheral blood plasmablast

value: IgA

tag: specificity

value: vaccine

tag: experimental batch


title: PW2-D1


title: PW2-C9

value: IgG


title: OAC2

value: Bone marrow

value: adult


title: PW2-C7


title: WT_Hybrid_S_37_INPUT

source_name: INPUT fraction of RNA-DNA Hybrid in wt at 37 degree S Phase

value: wild type

value: S Phase


title: PW2-C6


title: Top2-1_Hybrid_S_37_INPUT

source_name: INPUT fraction of RNA-DNA Hybrid in Top2-1 ts at 37 degree S Phase

value: Top2-1 ts

value: RNA-DNA Hybrid


title: Top2-1_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in Top2-1 ts at 37 degree S Phase

value: S9.6 Monoclonal Antibody


title: PW2-E12

value: male


title: WT_Hybrid_S_37_IP

source_name: IP fraction of RNA-DNA Hybrid in wt at 37 degree S Phase


title: WT_Hybrid_S_28_INPUT

source_name: INPUT fraction of RNA-DNA Hybrid in wt at 28 degree S Phase


title: PW2-D12


title: PW2-D2

value: negative


title: WT_Hybrid_S_28_IP

source_name: IP fraction of RNA-DNA Hybrid in wt at 28 degree S Phase


title: Top1tag_Top2-1_Hmo1_Protein_S_37_INPUT

description: Protein profile across the genome

source_name: INPUT fraction of Top2-1 ts and Hmo1 deletion in Top1-Flag GLU at 37 degree S Phase

value: Top2-1 ts and Hmo1 deletion

value: Protein


title: PW2-C4


title: PW2-C5


title: PW2-C2


title: PW2-C12


title: WT Liver 1

source_name: Liver

tag: genotype

value: Wildtype

tag: age at sac

value: 3 days


title: PW2-C11


title: PW2-C8


title: PW2-C1


title: Top1tag_Top2-1_Protein_S_37_INPUT

description: Protein profile across the genome

source_name: INPUT fraction of Top2-1 ts in Top1-Flag GLU at 37 degree S Phase

tag: strain background

value: Glucose

tag: temperature


title: Top1tag_Hmo1_Protein_S_37_IP

description: Protein profile across the genome

source_name: IP fraction of Hmo1 deletion in Top1-Flag GLU at 37 degree S Phase

value: Hmo1 deletion

tag: category

tag: cellcycle

value: AntiFlag M2 - (Sigma)


title: PW2-B9

value: IgG

value: vaccine


title: Top1tag_Hmo1_Protein_S_37_INPUT

description: Protein profile across the genome

source_name: INPUT fraction of Hmo1 deletion in Top1-Flag GLU at 37 degree S Phase

tag: treatment

tag: antibody


title: Top1tag_Top2-1_Protein_S_37_IP

description: Protein profile across the genome

source_name: IP fraction of Top2-1 ts in Top1-Flag GLU at 37 degree S Phase


title: Top1tag_Protein_S_37_IP

description: Protein profile across the genome

source_name: IP fraction of Top1-Flag wt GLU at 37 degree S Phase

value: Top1-Flag wt


title: Top1tag_Protein_S_37_INPUT

description: Protein profile across the genome

source_name: INPUT fraction of Top1-Flag wt GLU at 37 degree S Phase


title: PW2-B8


title: PW2-B6


title: PW2-B7


title: PW2-B3


title: Hmo1_Supercoil_S_28_INPUT

description: Negative supercoiling mapping across the genome

source_name: INPUT fraction of Biotin tagged psoralean of Hmo1 deletion in GLU at 28 degree S Phase

extract_protocol: Cells were collected blocked using Sodium Azide (0.1%). bTMP is added and cells were incubated in dark for 90 mins and crosslinked with UV at 365nm (800 mJ/cm2). The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) using Zirconia beads. The crosslinked chromatin was sheared to an average size of 500 bp by 6X 15-second pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris. The chromatin fraction is incuabted with Dynabeads MyOne streptavidin (Invitrogen cat no. 65001) overnight at 4C.  The beads were washed 2X with each of the following buffers; wash Buffer I (20mM tris-HCL pH 8, 2mM EDTA, 150mM NaCl, 1% triton X, 0.1% SDS), wash buffer II (20mM tris-HCL pH 8, 2mM EDTA, 500mM NaCl, 1% triton X, 0.1% SDS) wash buffer III (250 mM LiCl, 10 mM Tris pH8.0, 0.5% Na deoxycholate, 0.5% NP40, 1mM EDTA) and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The bTMP-DNA complexes were eluted from the beads in 250 µl elution buffer (95% Formamide, 10mM EDTA ) at 90C for 20 min and eluted samples were cleaned with Qiagen PCR clean up kit. For Input, DNA was isolated with sheared chromatin input (1/100 of the material used for ChIP).

value: BTMP DNA-Supercoil


title: Top1_Supercoil_S_28_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of Top1 deletion in GLU at 28 degree S Phase

value: Top1 deletion

value: S Phase


title: Top2-1_Top1_Supercoil_S_37_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of Top2-1 ts and Top1 deletion in GLU at 37 degree S Phase

value: Top2-1 ts and Top1 deletion


title: PW2-C3

source_name: peripheral blood plasmablast


title: Hmo1_Supercoil_S_28_IP

source_name: IP fraction of Biotin tagged psoralean of Hmo1 deletion in GLU at 28 degree S Phase

value: Dynabeads My One Streptavidin-(Invitrogen)


title: Top1_Supercoil_S_28_IP

source_name: IP fraction of Biotin tagged psoralean of Top1 deletion in GLU at 28 degree S Phase


title: Top1tag_Top2-1_Hmo1_Protein_S_37_IP

description: Protein profile across the genome

source_name: IP fraction of Top2-1 ts and Hmo1 deletion in Top1-Flag GLU at 37 degree S Phase


title: Top2-1_Top1_Supercoil_S_37_IP

source_name: IP fraction of Biotin tagged psoralean of Top2-1 ts and Top1 deletion in GLU at 37 degree S Phase


title: PW2-B11

value: male


title: PW2-B12


title: PW2-B10


title: PW2-B2


title: PW2-B1


title: PW2-A8


title: Top2-1_Hmo1_Supercoil_S_37_IP

source_name: IP fraction of Biotin tagged psoralean of Top2-1 ts and Hmo1 deletion in GLU at 37 degree S Phase


title: Top2-1_Supercoil_S_37_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of Top2-1 ts in GLU at 37 degree S Phase

value: Top2-1 ts


title: PW2-A7


title: Hmo1_Supercoil_S_37_IP

source_name: IP fraction of Biotin tagged psoralean of Hmo1 deletion in GLU at 37 degree S Phase


title: Hmo1_Supercoil_S_37_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of Hmo1 deletion in GLU at 37 degree S Phase


title: PW2-A6


title: Top2-1_Supercoil_S_37_IP

source_name: IP fraction of Biotin tagged psoralean of Top2-1 ts in GLU at 37 degree S Phase


title: PW2-A5


title: PW2-B4


title: PW2-A4


title: WT_Supercoil_S_37_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt in GLU at 37 degree S Phase

value: wild type


title: WT_Supercoil_S_37_IP

source_name: IP fraction of Biotin tagged psoralean of wt in GLU at 37 degree S Phase


title: Top2-1_Hmo1_Supercoil_S_37_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of Top2-1 ts and Hmo1 deletion in GLU at 37 degree S Phase

value: Top2-1 ts and Hmo1 deletion


title: WT_Supercoil_G1_28_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt in GLU at 28 degree G1 Phase

value: G1 Phase


title: WT_Supercoil_S_28_IP

source_name: IP fraction of Biotin tagged psoralean of wt in GLU at 28 degree S Phase


title: WT_Supercoil_G1_28_IP

source_name: IP fraction of Biotin tagged psoralean of wt in GLU at 28 degree G1 Phase


title: PW2-A12


title: PW2-A11


title: PW2-A2


title: PW2-A10


title: WT_Supercoil_G1_GAL_28_INPUT

source_name: INPUT fraction of Biotin tagged psoralean of wt in GAL

value: Galactose


title: WT_Supercoil_G1_GAL_28_IP

source_name: IP fraction of Biotin tagged psoralean of wt in GAL