title: RNAseq_GC_br2_tr2

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

description: biological replicate2, technical replicate2

data_processing:
base calling: solexa pipeline
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)

source_name: Gerninal center B cell

growth_protocol: Mouse B cells were isolated following standard procedures from 4-6 week old male C57BL/6J mice. In vitro activated mouse B cells were prepared from single cell suspensions  isolated from 4-6 week old male C57BL/6J mice. Cells were incubated with erythrocyte  lysis buffer, and depleted from CD43 positive cells by MACS selection (Miltenyi).  CD43-cells (>95% purity) were seeded in 6-well plates at an initial density of 0.1 x 106  cells per ml and cultured for 72 hours in advanced RPMI 1640 containing 10% FBS, LGlutamin  (200 mcM), HEPES (10 mM), β-Mercaptoethanol (55 nM), Penicillin  (10.000U/ml), and Streptomycin (10 mcg/ml) supplemented either with LPS (50 ng/ml)  and Dextran-coupled anti-IgD (2.5 ng/ml) or LPS (50 ng/ml) and IL-4 (2.5 ng/ml).

extract_protocol:
mRNA isolation: Extract total RNA using Trizol. Using at least 10μg of total  RNA and extract mRNA with Invitrogen Dynabeads mRNA Purification kit  [cat610.06].  Run the mRNA sample through the beads twice to eliminate rRNA  Contamination (this is critical). Elute mRNA in 15ul of TE and take an OD.  mRNA Fragmentation: Fragment 100ng mRNA with 1μl of 10X Fragmentation  Solution [Ambion cat#AM8740].  Incubate at 70C for 5 minutes using a PCR  thermocycler.  Quench with 1μl of Stop Solution [Ambion cat9264G] and incubate  on ice. Purifiy fragmentation reaction using G‐50 Sephadex Quick Spin Columns  (Roche, cat#11 274 015 001). Speed‐Vac concentrate to approximately 10μl  1st Strand synthesis: Follow SuperScript III First Strand Kit [Invitrogen  cat#18080‐051] protocol for 1st Strand Synthesis but using 3μg/μl of Random  Primers.   2nd Strand Synthesis: Add 61µL of H2O to the first strand cDNA synthesis mix.  Add 10µl of 10× second strand buffer (500 mM Tris‐HCl pH7.8, 50 mM MgCl2, 10  mM DTT) and 3µl of dNTP mix (10 mM). Mix well and incubate on ice for 5 minutes.  Add 1µl of RNaseH (2U/µL, Invitrogen, #18021‐014) and 5µl of DNA Pol I (10U/µL,  Invitrogen, #18010‐025). Mix well and incubate at 16°C in a thermocycler for 2.5  hours. Cleanup the reaction using a Qiagen’s MiniElute column.  Wash with 5  volumes of PBI buffer and elute with 30µl of warm (50°C) elution buffer (provided  with the kit).  Blunt Ends: Follow Epicentre End‐It end repair kit (ER0720) to generate blunt  ends  o 1‐34 µl DNA (100 ng or less) + H2O  o 5 µl 10x End repair buffer  o 5 µl 2.5 mM each dNTP  o 5 µl 10 mM ATP  o 1 µl Enzyme mix  Incubate at RT for 45 minutes and cleanup the reaction with a MiniElute  column.  Wash with 5 volumes of PBI buffer and elute with 30ul of warm  (50°C) elution buffer.  PolyA synthesis:  o 30 µl of DNA  o 9.5 µl of H2O o 5 µl of Taq buffer   o 1.5 µl of 50 mM MgCl2   o 1 µl of 10 mM ATP   o 3 µl of Taq DNA polymerase (5u/µl, Invitrogen, cat10342‐020)   Incubate at 70°C for 40 minutes in thermocycler. Cleanup the reaction using a   Qiagen’s MiniElute column.  Wash with 5 volumes of PBI buffer and elute   with 15µl of warm (50°C) elution buffer.   Oligo Adapter Ligation:  o 15 µl DNA   o 2 µl H2O   o 2.5 µl 10x T4 DNA ligase buffer   o 3 µl Adapter Oligo Mix (Solexa)   o 2.5 µl T4 DNA ligase (400000 u/ml, NEB)   Incubate at RT O/N   cDNA Purification:  Cleanup the reaction with a MiniElute column.  Wash with 5 volumes of PBI buffer   and elute with 20µl of warm (50°C) elution buffer. Add 5µl of 5X loading dye, and   loaded on a 2% agarose long gel.  Run at 120V for 7 hours. Under the blue light, cut   the invisible 200bp band. Isolate using Qiagen’s gel extraction kit.  Elude the DNA   with 11.5ul of warm elution buffer.    PCR Amplification  o 10.5 µl of DNA    o 12.5 µl of master mix (Phusion polymerase from Solexa kit)   o 1 µl of PCR primer 1(2x diluted)   o 1 µl of PCR primer 2(2x diluted)   o 15 cycles of 98˚C for 30 s and 98˚C 10 s, 65˚C 30 s and 72˚C 30 s   o 5 minutes at 72˚C   Cleanup reaction with PCR purification kit (minielute).  Use 5 volumes of PBI buffer   and eluded with 15µl of warm (50˚C) elution buffer. PCR products can be stored at   4C   Pico‐Green Quantification  Use Picogreen to quantify the amount of DNA and validate the purity of the library   using Agilent DNA 1000 [Cat#5067‐1504]. Dilute DNA to a concentration of 10nM   using 0.1%Tween in Qiagen’s elution buffer. Store DNA at ‐20C until Solexa analysis.
mRNA-seq: 50 cycles of single-end and paired end sequencing data were acquired on Genome Analyzer II (Illumina)

tag: organ

value: lymph nodes

tag: experimental type

value: mRNAseq


title: EzrinT567D positive hepatocytes

status: Public on Mar 27 2020

type: RNA

city: Pittsburgh

first: George

middle: K.

last: Michalopoulos

state: Pennsylvania

address: 200 Lothrop Street

country: USA

institute: University of Pittsburgh

description:
Gene expression data at 2 months in fast food diet-fed mice
EzrinT567D positive hepatocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: GFP+ (i.e. EzrinT567D positive) hepatocytes isolated from liver one week after plasmid injection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 6-8 weeks old male FVB mice were fed with chow diet with drinking water

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

treatment_protocol: For hydrodynamic tail vein injection, PT3EF5α EzrinT567D (10μg) and pCMV/SB (0.8μg) were diluted into 2ml 0.9% NaCl solution, sterile filtered with 0.2μm filters, and then injected into mouse lateral tail vein within 5–7 seconds.

tag: strain

value: FVB

tag: Sex

value: male

tag: tissue

value: liver

tag: cell type

value: hepatocytes

tag: group

value: EzrinT567D positive


title: Healthy Control without CA C027

city: Rotterdam

first: Hemmo

last: Drexhage

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description:
Healthy Control without CA
Control 1

data_processing:
Matrix normalized worksheet report normalized signal against housekeeping gene ABL1:(Ct_Target − Ct_ABL1)
Fold Change worksheet report relative signal to the average healthy control value: (dCT- AVG dCT Healthy Controls)
ddCT (relative values)

label: FAM

organism: Homo sapiens

source_name: Monocytes

label_protocol: 1 ug RNA was converted into cDNA using the High Capacity cDNA synthesis kit (Applied Biosystems)

extract_protocol: Total RNA was extracted using QIAgen Rneasy Mini kit

tag: sex (0=m)

tag: group (0=control)

tag: age

tag: bmi

tag: episodes

tag: ctanysubscale (0=no)

tag: ctqemoabuse

tag: ctqphyabuse

tag: ctqsexabuse

tag: ctqemoneglect

tag: ctqphyneglect


title: WHEL ID 5250

city: La Jolla

first: Loki

last: Natarajan

address: 3855 Health Sciences DR

institute: University of California, San Diego

description:
NanoString reporter probe
X2895382958_8

hyb_protocol: Transcript expression was quantified with 250 ng of total RNA using the NanoString nCounter analysis system with a custom miRGE CodeSet. Assay reactions were assembled per manufacturer’s specifications (NanoString Technologies, INC Seattle, WA).

scan_protocol: See manufacturer's website http://www.nanostring.com for procedures.  Digital Analyzer was set to scan at 1155 FOV (fields of view).

data_processing: R-NanoStringNorm package was used to normalize data. Code count normalization used 6 positive controls and background subtraction used 8 negative controls. All expression values were first log2 transformed.  For mRNAs, five (ACTB, PSMC4, MRPL19, RPLPO, SF3A1) genes were used as housekeepers; the data matrix elements are relative gene expression values (log2 transformed) compared to log2 value of the geometric mean of the five house-keepers within each sample. For miRNAs, log2 expression values are presented.  For miRNAs, quantile normalization was performed. Normalized datasets for both mRNA and miRNA are available on the series record. Sample data tables include data only for mRNAs.

source_name: primary breast cancer

extract_protocol: Unstained slides from archival specimens with ≥ 40% tumor cellularity were incubated at 65 °C for 30 minutes and deparaffinized using Citrisolv  (Fisher Scientific, Pittsburgh, PA) followed by ethanol wash. Tumor tissues were macrodissected into RNAse-free microfuge tubes, and nucleic acids isolated using the Qiagen AllPrep FFPE kit (#80234).  Manufacturer’s instructions were followed with the exception that the proteinase K digestion step was extended to an overnight incubation for the DNA isolation.

value: primary breast cancer


title: RNAseq_aB72h_br2

type: SRA

state: MD

description: 72h activation, biological replicate2

library_source: transcriptomic

source_name: activated B cell

tag: genotype

value: WT

tag: organ

value: spleen

tag: experimental type


title: WHEL ID 3313

description:
NanoString reporter probe
X2895383084_8

label_protocol: See manufacturer's website http://www.nanostring.com for procedures

tag: tissue


title: WHEL ID 5306

description:
NanoString reporter probe
X2895382957_7


title: WHEL ID 5312

description:
NanoString reporter probe
X2895382961_1


title: RNAseq_MZ

source_name: Marginal zone B cell


title: WHEL ID 7027

description:
NanoString reporter probe
X2895382952_4


title: Healthy Control without CA C026

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C025

description:
Healthy Control without CA
Control 1


title: RNAseq_GC_br1

description: biological replicate1


title: RNAseq_B1

source_name: B1 B cell

value: peritoneal cavity


title: WHEL ID 9215

description:
NanoString reporter probe
X2895382960_11


title: EzrinT567D negative hepatocytes

description:
Gene expression data at 2 months in Chow-fed mice
EzrinT567D negative hepatocytes

source_name: GFP- (i.e. EzrinT567D negative) hepatocytes isolated from liver one week after plasmid injection

tag: strain

tag: Sex

tag: cell type

value: EzrinT567D negative


title: WHEL ID 1216

description:
NanoString reporter probe
X2895382955_5


title: WHEL ID 1272

description:
NanoString reporter probe
X2895382956_6


title: WHEL ID 1258

description:
NanoString reporter probe
X2895382947_3


title: WHEL ID 1277

description:
NanoString reporter probe
X2895382945_1


title: Healthy Control without CA C024

description:
Healthy Control without CA
Control 1

tag: sex (0=m)

tag: group (0=control)


title: RNAseq_hsc

source_name: HSC/HPC cell

value: bone marrow


title: WHEL ID 1264

description:
NanoString reporter probe
X2895382944_12


title: WHEL ID 5212

description:
NanoString reporter probe
X2895382943_10


title: Healthy Control without CA C023

description:
Healthy Control without CA
Control 1

tag: age

tag: bmi


title: RNAseq_preB

source_name: preB cell


title: RNAseq_GC_br2_tr1

description: biological replicate2 technical replicate1


title: WHEL ID 1207

description:
NanoString reporter probe
X2895382942_9


title: WHEL ID 5277

description:
NanoString reporter probe
X2895382941_8


title: RNAseq_aB72h_br1_tr2

description: 72h activation, biological replicate1, technical replicate2


title: Healthy Control without CA C021

description:
Healthy Control without CA
Control 1

tag: episodes

tag: ctanysubscale (0=no)


title: Healthy Control without CA C022

description:
Healthy Control without CA
Control 1

tag: ctqemoabuse

tag: ctqphyabuse


title: WHEL ID 1193

description:
NanoString reporter probe
X2895382946_2


title: Healthy Control without CA C020

description:
Healthy Control without CA
Control 1

tag: ctqsexabuse

tag: ctqemoneglect


title: WHEL ID 1226

description:
NanoString reporter probe
X2895382937_5


title: WHEL ID 1275

description:
NanoString reporter probe
X2895382940_7


title: RNAseq_aB72h_br1_tr1

description: 72h activation, biological replicate1, technical replicate1

tag: genotype


title: WHEL ID 1270

description:
NanoString reporter probe
X2895382939_6


title: ctrl

city: hefei

first: sun

last: xuedan

address: daoxiangcun

country: China

institute: ustc

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adenocarcinoma human alveolar basal epithelial cells


title: OISD5_siNT_Rep3

city: Philadelphia

first: Satish

last: Sati

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw reads were trimmed using trim galore. The reads that passed trim galore were analysed using methpipe package (version 3.4.3). Briefly the reads were mapped to hg19 genome reference using “walt”, and PCR duplicates were removed with “duplicate-remover” in methpipe package. The output files were then analyzed using “methcounts” to obtain methylation levels at each cytosine site for both strands. Then “merge-methcounts” was used to merge all replicates.
Genome_build: hg19
Supplementary_files_format_and_content: CpG sites which were covered with at least 10 reads were taken for downstream analysis.  The resulting files were converted into bigwig format.

molecule: genomic DNA

source_name: Human fetal lung fibroblats (Oncogene induced, treated with siRNA against NT)

growth_protocol: Modified Eagle’s Medium + 10% fetal bovine serum + 1 mM sodium pyruvate+ 2 mM L-glutamine + 0.1 mM MEM nonessential amino acids

extract_protocol:
The genomic DNA was isolated by using DNeasy Blood & Tissue Kit.
Two micrograms of genomic DNA were spiked with unmethylated bacteriophage λ DNA (5 ng of λ DNA per microgram of genomic DNA; Promega) and with methylated T7 phage DNA (5 ng of T7 DNA per microgram of genomic DNA). The DNA was sheared to 50–500 bp in size using Covaris LE220 ultrasonicator, and fragments of 150–300 bp were size-selected using AMPure XP beads (Agencourt Bioscience). The libraries were constructed using the KAPA Library Preparation Kit with no PCR Library Amplification/Illumina series (Roche-Kapa Biosystems). After adaptor ligation, NEXTFLEX® Bisulfite-Seq Barcodes (Perkin Elmer), the DNA was treated with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's instructions. Enrichment for adaptor-ligated DNA was carried out through seven PCR cycles using KAPA HiFi HotStart Uracil+ReadyMix PCR 2x Kit (Roche-Kapa Biosystems). Library quality was monitored using the Agilent 2100 Bioanalyzer DNA 7500 assay, and the library concentration was estimated using quantitative PCR using the KAPA Library Quantification Kit for Illumina® Platforms, v1.14 (Roche-Kapa Biosystems).  Paired-end DNA sequencing (2×101 bp) of the oxBS and BS libraries was performed using the HiSeq2000 (Illumina) with TruSeq SBS Kit v3-HS following the manufacturer’s protocol with HiSeq Control Software (HCS) 1.5.15.1 or using TruSeq SBS and flow cell kit v4. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48 for v3 and RTA 1.18.66.3 for v4) and followed by generation of FASTQ sequence files.

tag: treatment

value: siRNA against NT


title: WHEL ID 5251

description:
NanoString reporter probe
X2895382933_1


title: WHEL ID 1206

description:
NanoString reporter probe
X2895382936_4


title: shGUARDIN


title: WHEL ID 5271

description:
NanoString reporter probe
X2895382935_3


title: Healthy Control without CA C019

description:
Healthy Control without CA
Control 1

tag: ctqphyneglect


title: WHEL ID 5286

description:
NanoString reporter probe
X2895382932_12

tag: tissue


title: WHEL ID 1269

description:
NanoString reporter probe
X2895382934_2


title: Healthy Control without CA C018

description:
Healthy Control without CA
Control 1


title: WHEL ID 1188

description:
NanoString reporter probe
X2895382931_11


title: Healthy Control without CA C017

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C016

description:
Healthy Control without CA
Control 1


title: WHEL ID 5257

description:
NanoString reporter probe
X2895382930_10


title: OISD5_siNT_Rep2


title: WHEL ID 5253

description:
NanoString reporter probe
X2895382929_9


title: WHEL ID 1252

description:
NanoString reporter probe
X2895382927_6


title: WHEL ID 5278

description:
NanoString reporter probe
X2895382928_7


title: Healthy Control without CA C015

description:
Healthy Control without CA
Control 1


title: OISD5_siDNMT1

source_name: Human fetal lung fibroblats (Oncogene induced, treated with siRNA against DNMT1)

value: siRNA against DNMT1


title: WHEL ID 1211

description:
NanoString reporter probe
X2895382923_4


title: WHEL ID 7165

description:
NanoString reporter probe
X2895382925_5


title: Healthy Control without CA C014

description:
Healthy Control without CA
Control 1


title: RNAseq_OISD5_siNT4_Rep2

data_processing:
STAR version 2.5.0b was used to aligne the fastq files to the hg19 reference genome. Following alignment PCR duplicates were removed and STAR  “inputAlignmentsFromBAM” runMode was employed to generate RPM normalized strand-specific coverage tracks. Reads overlapping with annotated genes (Ensembl build GRCh37) were counted using the summarizeOverlaps function from the R package “GenomicAlignments” in strand-specific, paired –end mode. FPKM (Fragments per kilobase per million mapped fragments) counts and differential expression was estimated using DeSeq2 (Love et. al., 2014).
Text file with 2 columns - Official Gene Symbol, fpkm counts per gene,
Genome_build: hg19

source_name: Human fetal lung fibroblats (Oncogene induces senescent)

growth_protocol: Modified Eagle’s Medium + 10% fetal bovine serum + 1 mM sodium pyruvate+ 2 mM L-glutamine + 0.1 mM MEM nonessential amino acids + 20nM 4-hydroxy-tamoxifen

extract_protocol:
Cells were rinsed with PBS once and then lysed immediately on plate by adding TRIzol (ThermoFisher, Cat.N: 15596026) and scraped with cell scraper. The lysate was transferred to the DNAse-RNAse free tubes and incubated at room temperature for 5 min. Thereafter samples were vortexed for 20 seconds, 0.2x volumes of chloroform was added, tubes were mixed by inverting and samples were centrifuged at 13,000 rpm at 4°C for 15 min. The aqueous phase was then processed using the RNeasy Mini Kit (QIAGEN, Cat.N: 74104) with DNase treatment, according to the manufacturer’s instructions.
Purified RNA (maximum of 1ug) was used for library generation using the TruSeq Stranded Total RNA Library Kit (Illumina, RS-122-2301). In brief, rRNA was depleted using RiboZero Gold, RNA was fragmented and first strand cDNA was synthesized in the presence of actinoMycin D. Second strand cDNA was then synthesised in the presence of dUTP and dsDNA was selected using AMPure XP beads. DNA was then 3'-adenylated, ligated to Illumina adapters and PCR-amplified for 10-12 cycles.

tag: sorting


title: WHEL ID 1135

description:
NanoString reporter probe
X2895382920_3


title: WHEL ID 7043

description:
NanoString reporter probe
X2895382918_1


title: WHEL ID 7159

description:
NanoString reporter probe
X2895382919_2


title: Healthy Control without CA C013

description:
Healthy Control without CA
Control 1


title: OISD5_siNT_Rep1


title: Healthy Control without CA C012

description:
Healthy Control without CA
Control 1


title: RNAseq_OISD5_siNT4_Rep1


title: RNAseq_OISD5_siDNMT1_Rep2


title: RNAseq_OISD5_siDNMT1_Rep1


title: WHEL ID 3193

description:
NanoString reporter probe
X2895382915_11


title: WHEL ID 1246

description:
NanoString reporter probe
X2895382914_10


title: RNAseq_RS_Senescent_Rep3

source_name: Human fetal lung fibroblats (Replicative senescent)

value: WI-38 Primary cells


title: WHEL ID 9134

description:
NanoString reporter probe
X2895382910_7


title: WHEL ID 7126

description:
NanoString reporter probe
X2895382913_9


title: Healthy Control without CA C011

description:
Healthy Control without CA
Control 1


title: WHEL ID 1214

description:
NanoString reporter probe
X2895382908_4


title: WHEL ID 1222

description:
NanoString reporter probe
X2895382912_8


title: Healthy Control without CA C010

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C009

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C008

description:
Healthy Control without CA
Control 1


title: RNAseq_RS_Senescent_Rep2


title: WHEL ID 9194

description:
NanoString reporter probe
X2895382907_3


title: WHEL ID 1177

description:
NanoString reporter probe
X2895382906_2


title: RNAseq_RS_Senescent_Rep1


title: WHEL ID 7154

description:
NanoString reporter probe
X2895382905_1


title: WHEL ID 5134

description:
NanoString reporter probe
X2895382902_10


title: WHEL ID 9104

description:
NanoString reporter probe
X2895382903_11


title: RNAseq_RS_Proliferative_Rep3

source_name: Human fetal lung fibroblats (Proliferative)


title: RNAseq_RS_Proliferative_Rep2


title: WHEL ID 7112

description:
NanoString reporter probe
X2895382909_6


title: RNAseq_RS_Proliferative_Rep1


title: WHEL ID 7111

description:
NanoString reporter probe
X2895382901_9


title: WHEL ID 1186

description:
NanoString reporter probe
X2895382900_8


title: Healthy Control without CA C006

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C004

description:
Healthy Control without CA
Control 1


title: WHEL ID 7011

description:
NanoString reporter probe
X2895382897_5


title: Healthy Control without CA C005

description:
Healthy Control without CA
Control 1


title: RNAseq_OISD10_Rep2


title: Healthy Control without CA C007

description:
Healthy Control without CA
Control 1


title: WHEL ID 7078

description:
NanoString reporter probe
X2895382898_6


title: RNAseq_OISD10_Rep1


title: WHEL ID 5201

description:
NanoString reporter probe
X2895382895_2


title: WHEL ID 7014

description:
NanoString reporter probe
X2895382893_12


title: WHEL ID 7065

description:
NanoString reporter probe
X2895382894_1


title: Healthy Control without CA C003

description:
Healthy Control without CA
Control 1


title: WHEL ID 7121

description:
NanoString reporter probe
X2895382896_3


title: Healthy Control without CA C002

description:
Healthy Control without CA
Control 1


title: Healthy Control without CA C001

description:
Healthy Control without CA
Control 1


title: WHEL ID 7049

description:
NanoString reporter probe
X2895382892_11


title: RNAseq_OISD6_Rep2


title: RNAseq_OISD6_Rep1


title: WHEL ID 5069

description:
NanoString reporter probe
X2895382890_9


title: WHEL ID 7067

description:
NanoString reporter probe
X2895382899_7


title: WHEL ID 7050

description:
NanoString reporter probe
X2895382904_12


title: WHEL ID 1150

description:
NanoString reporter probe
X2895382891_10


title: RNAseq_OISD4_Rep3


title: WHEL ID 1151

description:
NanoString reporter probe
X2895382886_5


title: WHEL ID 1170

description:
NanoString reporter probe
X2895382887_6


title: WHEL ID 7031

description:
NanoString reporter probe
X2895382889_8


title: WHEL ID 7116

description:
NanoString reporter probe
X2895382888_7


title: RNAseq_OISD2_Rep3


title: RNAseq_OISD4_Rep1


title: WHEL ID 7051

description:
NanoString reporter probe
X2895382884_3


title: WHEL ID 1129

description:
NanoString reporter probe
X2895382882_11


title: RNAseq_OISD4_Rep2


title: WHEL ID 3081

description:
NanoString reporter probe
X2895382885_4


title: WHEL ID 5145

description:
NanoString reporter probe
X2895382881_10


title: WHEL ID 1121

description:
NanoString reporter probe
X2895382883_1


title: RNAseq_OISD2_Rep2


title: RNAseq_OISD0_Rep3

source_name: Human fetal lung fibroblats (Uninduced Proliferative)


title: WHEL ID 9073

description:
NanoString reporter probe
X2895382878_7


title: WHEL ID 5094

description:
NanoString reporter probe
X2895382880_9


title: RNAseq_OISD0_Rep2


title: WHEL ID 9088

description:
NanoString reporter probe
X2895382879_8


title: WHEL ID 9081

description:
NanoString reporter probe
X2895382877_6


title: RNAseq_OISD0_Rep1


title: WHEL ID 5100

description:
NanoString reporter probe
X2895382873_2


title: WHEL ID 9093

description:
NanoString reporter probe
X2895382874_3


title: WHEL ID 3038

description:
NanoString reporter probe
X2895382870_10


title: WHEL ID 3060

description:
NanoString reporter probe
X2895382871_12


title: WHEL ID 3039

description:
NanoString reporter probe
X2895382869_9


title: ChIP_RS_Senescent_H3K27me3_Rep2

description:
ChIP_RS_Senescent_H3K27me3_rpm.bw
ChIP_RS_Senescent_H3K27me3_peaks.bed

data_processing:
Raw sequencing reads were mapped to  hg19 reference genome using Bowtie2. PCR duplicates were removed using Samtools and normalized genome coverage tracks were generated from uniquely mapping reads (mapq>30) using deepTools2.  In order to avoid double counting for paired-end data, reads with mates were extended to match the fragment size defined by the two read mates, and the second read mate was discarded. Single-end reads, unmated reads, mate reads that map too far apart (>4x fragment length) were extended by 200bp. Biological replicates were pooled and coverage was then calculated as reads per million of mapped reads (RPM) in 10bp bins.To determine the peaks for ChIPs with narrow binding profiles (CTCF,  H3K4me3), datasets were processed using MACS2 pipeline  with default parameters. For broad marks (H3K9me3 and H3K27me3) SICER2 was used with default parameters.
bigWig file represents the average (from two replicates) genome coverage in Reads per Million in 10bp bins. Peak files are in compressed narrowPeak/Broad peak format
Genome_build: hg19

extract_protocol: Cells were fixed on plate with 1% formaldehyde solution  (Pierce; 28908) in complete MEM fro 10 minutes. 125mM glycine (Final) was then added and insubated for 5 minutes to quench formaldehyde. The cells were then scraped and the cells were immediately pelleted, frozen in liquid nitrogen and stored at -80C until further use. 1x10^6 cells per IP for chromatin marks, or 2.5x10^6 cells for CTCF were then thawed on ice, resuspended in cold cell lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40) + 1xEDTA-free Protease Inhibitors. Cells were lysed for 30min, and resuspended in 50ul per IP cold nuclei lysis buffer (50mM Tris pH8, 10mM EDTA, 1% SDS) + 1xProtease Inhibitors. Nuclei were lysed for 60min at 4C with rotation and then sonicated for 16-18 cycles using Bioruptor (Diagenode). After sonication, 10x volumes of IP dilution buffer (20mM Tris pH8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS + protease inhibitors) was added, chromatin was precleared using 25ul Protein A dynabeads (ThermoFisher, Cat.N: 10002D) / 1mL for 1hrs at 4C with rotation.  Meanwhile, 25ul beads / IP were washed once with cold 0.5% BSA in PBS, and incubated with the antibody for 4-5hrs at 4C in 0.5ml 0.5% BSA in PBS). Beads were then washed once with 0.5% BSA in PBS, added to the precleared chromatin and incubated overnight at 4C with rotation. Beads were then washed once with cold IP wash buffer 1 (20mM Tris pH8, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt wash buffer (20mM Tris pH8, 2mM EDTA, 500mM NaCl, 1% Triton X-100,0.1% SDS), once with cold IP wash buffer 2 (10mM Tris pH8,1mM EDTA,250mM LiCl,1% NP-40,1% sodium deoxycholate) and twice with cold TE buffer (1mM Tris pH8, 1mM EDTA). DNA:protein complexes were then eluted twice for 15min at 65C in 100ul elution buffer (100mM NaHCO3, 1%SDS) each time. 16ul 5M NaCl was then added and samples + inputs were reverse cross-linked at 65C, RNase A and proteinase K treated and purified using ultrapure phenol/chloroform (ThermoFisher, Cat.N: 15593-049).

tag: antibody


title: WHEL ID 9068

description:
NanoString reporter probe
X2895382867_7


title: ChIP_RS_Senescent_H3K27me3_Rep1

tag: cell type


title: RNAseq_OISD2_Rep1


title: WHEL ID 9082

description:
NanoString reporter probe
X2895382868_8


title: WHEL ID 9079

description:
NanoString reporter probe
X2895382875_4


title: WHEL ID 9074

description:
NanoString reporter probe
X2895382876_5


title: WHEL ID 3017

description:
NanoString reporter probe
X2895382863_3


title: WHEL ID 3063

description:
NanoString reporter probe
X2895382862_2


title: WHEL ID 9090

description:
NanoString reporter probe
X2895382864_4


title: WHEL ID 5096

description:
NanoString reporter probe
X2895382865_5


title: WHEL ID 3056

description:
NanoString reporter probe
X2895382872_1


title: ChIP_RS_Senescent_H3K9me3_Rep1

description:
ChIP_RS_Senescent_H3K9me3_rpm.bw
ChIP_RS_Senescent_H3K9me3_peaks.bed


title: WHEL ID 3037

description:
NanoString reporter probe
X2895382858_10


title: WHEL ID 3027

description:
NanoString reporter probe
X2895382861_1


title: ChIP_RS_Senescent_H3K4me3_Rep1

description:
ChIP_RS_Senescent_H3K4me3_rpm.bw
ChIP_RS_Senescent__H3K4me3_peaks.bed


title: ChIP_RS_Senescent_IN_Rep2

value: input


title: WHEL ID 5080

description:
NanoString reporter probe
X2895382856_7


title: ChIP_RS_Senescent_H3K9me3_Rep2


title: WHEL ID 9080

description:
NanoString reporter probe
X2895382866_6


title: WHEL ID 1092

description:
NanoString reporter probe
X2895382855_6


title: WHEL ID 3013

description:
NanoString reporter probe
X2895382860_12


title: WHEL ID 5083

description:
NanoString reporter probe
X2895382854_5


title: ChIP_RS_Senescent_H3K4me3_Rep2


title: WHEL ID 3006

description:
NanoString reporter probe
X2895382853_4


title: ChIP_RS_Proliferative_H3K9me3_Rep2

description:
ChIP_RS_Proliferative_H3K9me3_rpm.bw
ChIP_RS_Proliferative_H3K9me3_peaks.bed


title: ChIP_RS_Proliferative_H3K27me3_Rep2

description:
ChIP_RS_Proliferative_H3K27me3.bw
ChIP_RS_Proliferative_H3K27me3_peaks.bed


title: ChIP_RS_Proliferative_H3K27me3_Rep1


title: WHEL ID 9066

description:
NanoString reporter probe
X2895382851_2


title: WHEL ID 5087

description:
NanoString reporter probe
X2895382852_3


title: WHEL ID 5066

description:
NanoString reporter probe
X2895382850_12


title: WHEL ID 3044

description:
NanoString reporter probe
X2895382849_11


title: WHEL ID 3035

description:
NanoString reporter probe
X2895382859_11


title: WHEL ID 5075

description:
NanoString reporter probe
X2895382857_9


title: WHEL ID 3050

description:
NanoString reporter probe
X2895382848_10


title: ChIP_RS_Proliferative_H3K4me3_Rep2

description:
ChIP_RS_Proliferative_H3K4me3_rpm.bw
ChIP_RS_Proliferative_H3K4me3_peaks.bed


title: ChIP_RS_Senescent_IN_Rep1


title: ChIP_RS_Proliferative_H3K9me3_Rep1


title: ChIP_RS_Proliferative_H3K4me3_Rep1


title: WHEL ID 5064

description:
NanoString reporter probe
X2895382845_7


title: WHEL ID 1058

description:
NanoString reporter probe
X2895382844_6


title: WHEL ID 3003

description:
NanoString reporter probe
X2895382846_8


title: WHEL ID 3045

description:
NanoString reporter probe
X2895382847_9


title: ChIP_RS_Proliferative_IN_Rep1


title: ChIP_RS_Proliferative_IN_Rep2


title: WHEL ID 5073

description:
NanoString reporter probe
X2895382842_3


title: ChIP_OISD10_H3K27me3_Rep2

description:
ChIP_OISD10_H3K27me3_rpm.bw
ChIP_OISD10_H3K27me3_peaks.bed


title: WHEL ID 5079

description:
NanoString reporter probe
X2895382843_4


title: WHEL ID 9058

description:
NanoString reporter probe
X2895382841_2


title: WHEL ID 9040

description:
NanoString reporter probe
X2895382838_11


title: ChIP_OISD10_H3K27me3_Rep1


title: ChIP_OISD10_H3K9me3_Rep2

description:
ChIP_OISD10_H3K9me3_rpm.bw
ChIP_OISD10_H3K9me3_peaks.bed


title: WHEL ID 3053

description:
NanoString reporter probe
X2895382839_12


title: ChIP_OISD10_H3K9me3_Rep1


title: WHEL ID 9026

description:
NanoString reporter probe
X2895382836_8


title: WHEL ID 9045

description:
NanoString reporter probe
X2895381985_7


title: WHEL ID 9057

description:
NanoString reporter probe
X2895381984_6


title: WHEL ID 9007

description:
NanoString reporter probe
X2895381983_5


title: WHEL ID 1019

description:
NanoString reporter probe
X2895381982_4


title: WHEL ID 9036

description:
NanoString reporter probe
X2895381981_3


title: ChIP_OISD10_H3K4me3_Rep2

description:
ChIP_OISD10_H3K4me3_rpm.bw
ChIP_OISD10_H3K4me3_peaks.bed


title: ChIP_OISD10_H3K4me3_Rep1


title: WHEL ID 5090

description:
NanoString reporter probe
X2895382840_1


title: G4_d3_Cy5-PDS_1uM_plus_1uM_PDS_comp_rep1

type: other

city: Bethesda

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

description: 1uM Cy5-PDS + 1nM PDS G4 array experiment, ssDNA + 100mM KCl

hyb_protocol: Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with proteins or small molecules. The binding reactions were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS. Protein-bound arrays were incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20. Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: Protein or molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation. Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units. Microarrays with the fewest number of saturated spots were used for further analysis.

data_processing: An intensity value was calculated for each target sequence by computing the median signal intensity across probes containing an identical probe identifier (ProbeID)

molecule: other

organism: synthetic construct

source_name: 1uM Cy5-PDS + 1uM PDS, G4 design 3

label_protocol: All chimeric proteins were expressed via in vitro translation (IVT) reactions using the PURExpress In Vitro Protein Synthesis Kit (NEB). For all IVT reactions, 288ng of plasmid was added to 80uL of IVT mixture and reactions were carried out at 37°C for 2 hours. Expression of all protein constructs was confirmed via Western Blot.

extract_protocol: We synthesized Cy5-labeled pyridostatin (Cy5-PDS). We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1). N-terminal Glutathione S-transferase (GST) tagged human nucleolin IGF2, CNBP, and helicase (FANCJ, PIF1, BLM, WRN, DHX36) plasmids were synthesized by GenScript. TMPyP4 was obtained from Sigma Aldrich (Catalog number 613560). GST-tagged purified recombinant bovine DHX36 was provided by the Ferre D’Amare lab (National Institutes of Health, Bethesda).

treatment_protocol: Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation. Binding experiments were then performed as previously described (Badis et al., Science 2009). For validation experiments, microarrays were also treated with 100mM lithium chloride (LiCl) to inhibit G4 formation.   For experiments examining dsDNA, single-stranded DNA probes were made double-stranded using a primer complementary to a 24-mer constant sequence on the array probes following the method described previously (Badis et al., Science 2009). Double-stranding efficiency was monitored using 4% Cy3-dCTP.

tag: molecule name

value: 1uM Cy5-PDS + 1uM PDS

tag: dna type

value: ssDNA

tag: array treatment

value: 100mM KCl


title: G4_d3_Cy5-PDS_1uM_plus_0uM_PDS_ctrl_rep2

description: 1uM Cy5-PDS + 0uM PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 0uM PDS, G4 design 3

value: 1uM Cy5-PDS + 0uM PDS


title: G4_d3_Cy5-PDS_1uM_plus_0uM_PDS_ctrl_rep1


title: ChIP_OISD6_H3K9me3_Rep1

description:
ChIP_OISD6_H3K9me3_rpm.bw
ChIP_OISD6_H3K9me3_peaks.bed


title: G4_d3_Cy5-PDS_1uM_plus_60nM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 60nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

hyb_protocol: Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with proteins or small molecules.   The binding reactions were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  Protein-bound arrays were incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: Protein or molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation.  Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units.  Microarrays with the fewest number of saturated spots were used for further analysis.

source_name: 1uM Cy5-PDS + 60nM TMPyP4, G4 design 3

label_protocol: All chimeric proteins were expressed via in vitro translation (IVT) reactions using the PURExpress In Vitro Protein Synthesis Kit (NEB).  For all IVT reactions, 288ng of plasmid was added to 80uL of IVT mixture and reactions were carried out at 37°C for 2 hours.  Expression of all protein constructs was confirmed via Western Blot.

extract_protocol: We synthesized Cy5-labeled pyridostatin (Cy5-PDS).  We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1).   N-terminal Glutathione S-transferase (GST) tagged human nucleolin IGF2, CNBP, and helicase (FANCJ, PIF1, BLM, WRN, DHX36) plasmids were synthesized by GenScript.   TMPyP4 was obtained from Sigma Aldrich (Catalog number 613560). GST-tagged purified recombinant bovine DHX36 was provided by the Ferre D’Amare lab (National Institutes of Health, Bethesda).

treatment_protocol: Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation.  Binding experiments were then performed as previously described (Badis et al., Science 2009). For validation experiments, microarrays were also treated with 100mM lithium chloride (LiCl) to inhibit G4 formation.     For experiments examining dsDNA, single-stranded DNA probes were made double-stranded using a primer complementary to a 24-mer constant sequence on the array probes following the method described previously (Badis et al., Science 2009).  Double-stranding efficiency was monitored using 4% Cy3-dCTP.

value: 1uM Cy5-PDS + 60nM TMPyP4


title: WHEL ID 9065

description:
NanoString reporter probe
X2895382837_10


title: ChIP_OISD6_H3K4me3_Rep1

description:
ChIP_OISD6_H3K4me3_rpm.bw
ChIP_OISD6_H3K4me3_peaks.bed


title: G4_d3_Cy5-PDS_1uM_plus_1uM_PDS_comp_rep2


title: ChIP_OISD6_H3K27me3_Rep1

description:
ChIP_OISD6_H3K27me3_rpm.bw
ChIP_OISD6_H3K27me3_peaks.bed


title: ChIP_OISD6_H3K9me3_Rep2


title: ChIP_OISD10_IN_Rep2


title: ChIP_OISD6_H3K4me3_Rep2


title: G4_d3_Cy5-PDS_1uM_plus_60nM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_100uM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 100uM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 100uM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 100uM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_200uM_DC34_comp_rep2

description: 1uM Cy5-PDS + 200uM DC-34 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 200uM DC-34, G4 design 3

value: 1uM Cy5-PDS + 200uM DC-34


title: G4_d3_Cy5-PDS_1uM_plus_20uM_DC34_comp_rep1

description: 1uM Cy5-PDS + 20uM DC-34 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 20uM DC-34, G4 design 3

value: 1uM Cy5-PDS + 20uM DC-34


title: G4_d3_Cy5-PDS_1uM_plus_200uM_DC34_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_1000X_DMSO_ctrl_rep2

description: 1uM Cy5-PDS + 1000X DMSO G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 1000X DMSO, G4 design 3

value: 1uM Cy5-PDS + 1000X DMSO


title: ChIP_OISD10_IN_Rep1


title: G4_d3_Cy5-PDS_1uM_plus_100uM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_10uM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 10uM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 10uM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 10uM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_20uM_DC34_comp_rep2


title: G4_d3_Cy5-PDS_1uM_plus_10uM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_1uM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 1uM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 1uM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 1uM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_500nM_TMPyP4_comp_rep1

description: 1uM Cy5-PDS + 500nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 500nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 500nM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_300nM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 300nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 300nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 300nM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_500nM_TMPyP4_comp_rep2


title: G4_d3_Cy5-PDS_1uM_plus_1uM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_1000X_DMSO_ctrl_rep1


title: ChIP_OISD6_IN_Rep2


title: ChIP_OISD6_H3K27me3_Rep2


title: ChIP_OISD6_IN_Rep1


title: ChIP_OISD2_H3K27me3_Rep1

description:
ChIP_OISD2_H3K27me3.bw
ChIP_OISD2_H3K27me3_peaks.bed


title: ChIP_OISD2_H3K27me3_Rep2


title: ChIP_OISD2_H3K9me3_Rep2

description:
ChIP_OISD2_H3K9me3.bw
ChIP_OISD2_H3K9me3_peaks.bed


title: G4_d3_Cy5-PDS_1uM_plus_300nM_TMPyP4_comp_rep1


title: ChIP_OISD2_H3K4me3_Rep2

description:
ChIP_OISD2_H3K4me3.bw
ChIP_OISD2_H3K4me3_peaks.bed


title: G4_d3_Cy5-PDS_1uM_plus_100nM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 100nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 100nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 100nM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_100nM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_30nM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 30nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 30nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 30nM TMPyP4


title: G4_d3_Cy5-PDS_1uM_plus_30nM_TMPyP4_comp_rep1


title: G4_d3_Cy5-PDS_1uM_plus_10nM_TMPyP4_comp_rep1

description: 1uM Cy5-PDS + 10nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 10nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 10nM TMPyP4


title: G4_d3_DHX36-G4BD_Li_rep2

type: protein

description: DHX36 (residues 1-157) G4 array experiment, ssDNA + 100mM LiCl

molecule: protein

source_name: DHX36 (residues 1-157), G4 design 3

value: DHX36 (residues 1-157)

value: 100mM LiCl


title: G4_d3_Cy5-PDS_1uM_plus_1nM_TMPyP4_comp_rep2

description: 1uM Cy5-PDS + 1nM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 1nM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 1nM TMPyP4

value: ssDNA


title: G4_d3_Cy5-PDS_1uM_plus_0uM_TMPyP4_ctrl_rep1

description: 1uM Cy5-PDS + 0uM TMPyP4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS + 0uM TMPyP4, G4 design 3

value: 1uM Cy5-PDS + 0uM TMPyP4

value: 100mM KCl


title: G4_d3_Cy5-PDS_1uM_plus_0uM_TMPyP4_ctrl_rep2


title: G4_d3_Cy5-PDS_1uM_plus_1nM_TMPyP4_comp_rep1


title: ChIP_OISD2_H3K4me3_Rep1

source_name: Human fetal lung fibroblats (Oncogene induces senescent)


title: G4_d3_DHX36-G4BD_Li_rep1


title: G4_d3_DHX36_Li_rep2

description: DHX36 G4 array experiment, ssDNA + 100mM LiCl

source_name: DHX36, G4 design 3


title: ChIP_OISD2_IN_Rep2

value: input


title: G4_d3_WRN_Li_rep1

description: WRN G4 array experiment, ssDNA + 100mM LiCl

source_name: WRN, G4 design 3

value: WRN


title: ChIP_OISD2_IN_Rep1


title: G4_d3_WRN_Li_rep2


title: G4_d3_DHX36_Li_rep1


title: ChIP_OISD2_H3K9me3_Rep1


title: ChIP_OISD0_H3K27me3_Rep2

description:
ChIP_OISD0_H3K27me3.bw
ChIP_OISD0_H3K27me3_peaks.bed

source_name: Human fetal lung fibroblats (Uninduced Proliferative)


title: G4_d3_BLM_Li_rep2

description: BLM G4 array experiment, ssDNA + 100mM LiCl

source_name: BLM, G4 design 3

value: BLM


title: G4_d3_PIF1_Li_rep2

description: PIF1 G4 array experiment, ssDNA + 100mM LiCl

source_name: PIF1, G4 design 3


title: G4_d3_Cy5-PDS_1uM_plus_10nM_TMPyP4_comp_rep2


title: ChIP_OISD0_H3K27me3_Rep1


title: G4_d3_BLM_Li_rep1


title: G4_d3_PIF1_Li_rep1


title: G4_d3_FANCJ-DBD_Li_rep2

description: FANCJ (residues 11-442) G4 array experiment, ssDNA + 100mM LiCl

source_name: FANCJ (residues 11-442), G4 design 3

value: FANCJ (residues 11-442)


title: ChIP_OISD0_H3K9me3_Rep1

description:
ChIP_OISD0_H3K9me3.bw
ChIP_OISD0_H3K9me3_peaks.bed


title: G4_d3_FANCJ_Li_rep2

description: FANCJ G4 array experiment, ssDNA + 100mM LiCl

source_name: FANCJ, G4 design 3

value: FANCJ


title: ChIP_OISD0_H3K4me3_Rep2

description:
ChIP_OISD0_H3K4me3.bw
ChIP_OISD0_H3K4me3_peaks.bed


title: ChIP_OISD0_IN_Rep2


title: ChIP_OISD0_H3K4me3_Rep1


title: G4_d3_FANCJ-DBD_Li_rep1


title: ChIP_OISD0_IN_Rep1


title: G4_d3_CNBP_Li_rep2

description: CNBP G4 array experiment, ssDNA + 100mM LiCl

source_name: CNBP, G4 design 3

value: CNBP


title: G4_d3_FANCJ_Li_rep1


title: G4_d3_IGF2_Li_rep2

description: IGF2 G4 array experiment, ssDNA + 100mM LiCl

source_name: IGF2, G4 design 3


title: G4_d3_IGF2_Li_rep1


title: G4_d3_NCL3_Li_rep2

description: NCL (residues 272-647) G4 array experiment, ssDNA + 100mM LiCl

source_name: Nucleolin (residues 272-647), G4 design 3

value: NCL (residues 272-647)


title: G4_d3_NCL3_Li_rep1


title: HiC_OISD5_siNT4_1

data_processing:
Library strategy: HiC-Seq
Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690) wa sused to process Hi-C data. Raw sequencing reads were mapped to  hg19 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 33) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman).
Genome_build: hg19

extract_protocol:
HiC sample preperation was performed using the in-situ method (Rao et. al., 2014) with minor modifications. Briefly, the cells were digested overnight at 37 degree C with 500U of DpnII. Following digestion,  biotin filling and proximity ligation was carried out for 4 hours at 18 degree C with 2000U T4 DNA Ligase. After reverse-crosslinking,the  DNA was purified employing ethanol precipitation method and sheared to 350-450bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described (Rao et al., 2014). NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.


title: HiC_OISD5_siDNMT1_1


title: HiC_OISD5_siDNMT1_2


title: G4_d3_CNBP_Li_rep1


title: G4_d3_NCL2_Li_rep2

description: NCL (residues 272-710) G4 array experiment, ssDNA + 100mM LiCl

source_name: Nucleolin (residues 272-710), G4 design 3

value: NCL (residues 272-710)


title: G4_d3_Cy5-PDS_0.3uM_Li_rep1

description: 0.3uM Cy5-PDS G4 array experiment, ssDNA + 100mM LiCl

source_name: 0.3uM Cy5-PDS, G4 design 3

value: 0.3uM Cy5-PDS


title: G4_d3_Cy5-PDS_0.3uM_Li_rep2


title: G4_d3_NCL2_Li_rep1


title: G4_d3_Cy5-BG4_0.03_Li_rep1

description: 1/30 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM LiCl

source_name: 1/30 dilution Cy5-BG4, G4 design 3

value: 1/30 dilution Cy5-BG4


title: G4_d3_Cy5-BG4_0.03_Li_rep2


title: G4_d3_PureDHX36_plusATP_rep1

description: Purified DHX36 + 500mM ATP G4 array experiment, ssDNA + 100mM KCl

organism: Bos taurus

source_name: Purified DHX36 + 500mM ATP, G4 design 3

value: Purified DHX36 + 500mM ATP


title: G4_d3_PureDHX36_minusATP_rep2

description: Purified DHX36 + 0mM ATP G4 array experiment, ssDNA + 100mM KCl

source_name: Purified DHX36 + 0mM ATP, G4 design 3

value: Purified DHX36 + 0mM ATP


title: G4_d3_PureDHX36_minusATP_rep1


title: HiC_RS_Senescent_2

source_name: Human fetal lung fibroblats (Replicative senescent)

value: WI-38 Primary cells


title: HiC_RS_Senescent_1


title: HiC_RS_Proliferative_2

source_name: Human fetal lung fibroblats (Proliferative)


title: HiC_RS_Proliferative_1


title: G4_d3_DHX36-G4BD_rep2

description: DHX36 (residues 1-157) G4 array experiment, ssDNA + 100mM KCl

source_name: DHX36 (residues 1-157), G4 design 3

value: DHX36 (residues 1-157)


title: HiC_OISD10_2

source_name: Human fetal lung fibroblats (Oncogene induces senescent)


title: 160181

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

description: non-polyploid chromophobe rcc, classic histological type, pT1bNxMx

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: chromophobe rcc

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

tag: sample type

value: chromophobe rcc


title: HiC_OISD10_1


title: HiC_OISD6_2


title: 194882

description: polyploid chromophobe rcc, classic histological type, pT3aNxMx


title: G4_d3_WRN-DBD_rep1

description: WRN (residues 558-993) G4 array experiment, ssDNA + 100mM KCl

source_name: WRN (residues 558-993), G4 design 3

value: WRN (residues 558-993)

value: ssDNA


title: 193815

description: non-polyploid chromophobe rcc, Eosinophilic variant, pT1bNxMx


title: G4_d3_DHX36_rep1

description: DHX36 G4 array experiment, ssDNA + 100mM KCl

source_name: DHX36, G4 design 3

value: 100mM KCl


title: G4_d3_DHX36-G4BD_rep1


title: HiC_OISD4_2


title: G4_d3_PureDHX36_plusATP_rep2


title: G4_d3_PIF1_rep2

description: PIF1 G4 array experiment, ssDNA + 100mM KCl

source_name: PIF1, G4 design 3


title: G4_d3_DHX36_rep2


title: G4_d3_PIF1_rep1


title: 184573

description: non-polyploid chromophobe rcc, Eosinophilic variant, pT3aNxMx


title: ChIP_OISD0_H3K9me3_Rep2

description:
ChIP_OISD0_H3K9me3.bw
ChIP_OISD0_H3K9me3_peaks.bed

source_name: Human fetal lung fibroblats (Uninduced Proliferative)


title: G4_d3_BLM-DBD_rep1

description: BLM (residues 676-1024) G4 array experiment, ssDNA + 100mM KCl

source_name: BLM (residues 676-1024), G4 design 3

value: BLM (residues 676-1024)


title: 173446


title: G4_d3_WRN-DBD_rep2


title: G4_d3_BLM-DBD_rep2


title: G4_d3_WRN_rep2

description: WRN G4 array experiment, ssDNA + 100mM KCl

source_name: WRN, G4 design 3

value: WRN


title: G4_d3_BLM_rep1

description: BLM G4 array experiment, ssDNA + 100mM KCl

source_name: BLM, G4 design 3

value: BLM


title: HiC_OISD2_2


title: G4_d3_FANCJ-DBD_rep2

description: FANCJ (residues 11-442) G4 array experiment, ssDNA + 100mM KCl

source_name: FANCJ-DBD, G4 design 3

value: FANCJ (residues 11-442)


title: 173140

description: non-polyploid chromophobe rcc, Eosinophilic variant, pT1bN0Mx


title: HiC_OISD2_1


title: HiC_OISD6_1


title: G4_d3_FANCJ-DBD_rep1


title: 181984

description: non-polyploid chromophobe rcc, classic histological type, pT1aNxMx


title: 152493

description: non-polyploid chromophobe rcc, Eosinophilic variant, pT4N1M1


title: HiC_OISD0_1


title: HiC_OISD4_1


title: G4_d3_BLM_rep2


title: 164423

description: non-polyploid chromophobe rcc, Eosinophilic variant, pT2bN0Mx


title: G4_d3_FANCJ_rep2

description: FANCJ G4 array experiment, ssDNA + 100mM KCl

source_name: FANCJ, G4 design 3

value: FANCJ


title: G4_d3_WRN_rep1


title: HiC_OISD0_2


title: 13T532


title: 142020

description: non-polyploid chromophobe rcc, classic histological type, pT3aNxMx


title: G4_d3_FANCJ_rep1


title: WT Replicate 1

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

description: Replicate used

data_processing:
Illumina Casava1.7 software used for base-calling
Genome index for single cell analysis was built using the Drosophila melanogaster Release 6 (dm6) reference genome assembly using 10X genomics cellranger (version 3.0.0) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for each replicate.
The Cell Ranger output was used for clustering and dimension reduction and primary analysis using the R package Seurat (v2.3.4). A filtration criteria of minimum 775 genes and a maximum of 2200 genes and 18000 UMIs was set. Cells with greater than 1% mitochondrial expression were removed.
Pseudo-temporal inference analysis was done on subsets of cell clusters that were processed in Seurat, using Monocle (v2).
Genome_build: dm6
Supplementary_files_format_and_content: WTDmelOvary3days_14825cells_genes.tsv is a cellranger processed file; together with barcodes,tsv and matrix.mtx, this is input for Seurat pipeline
Supplementary_files_format_and_content: WTDmelOvary3days_14825cells_barcodes.tsv is a cellranger processed file; together with genes.tsv and matrix.mtx, this is input for Seurat pipeline
Supplementary_files_format_and_content: WTDmelOvary3days_14825cells_matrix.mtx is a cellranger processed file; together with genes.tsv and barcodes,tsv, this is input for Seurat pipeline.
Supplementary_files_format_and_content: 12671cells_primary_ovary.loom was produced by converting the Seurat object to loom. The Seurat object was produced by using standard Seurat (v2.3.1) pipeline for dimension reduction and clustering, following which it was updated to the new Seurat 3.1.0 format. This dataset represents pre-filtered cells.
Supplementary_files_format_and_content: 7053cells_highquality_ovary.loom was produced by converting the Seurat object to loom. The Seurat object was produced by using a sample-specific Seurat (v2.3.1) pipeline for dimension reduction and clustering, following which it was updated to the new Seurat 3.1.0 format. This dataset represents high quality cells, as produced post-filtering as described in the paper.
Supplementary_files_format_and_content: 1,837cells_early_somatic_trajectory.rds is the Monocle2 CellDataSet object for early somatic trajectory.
Supplementary_files_format_and_content: 479cells_polarstalk_trajectory.rds is the Monocle2 CellDataSet object for the polar-stalk cell fate trajectory.
Supplementary_files_format_and_content: 798cells_anteriorfollicle_trajectory.rds is the Monocle2 CellDataSet object for anterior egg chamber follicle cell fate trajectory.
Supplementary_files_format_and_content: 1666cells_symmetrybreaking_trajectory.rds is the Monocle2 CellDataSet object for follicle cell trajectory during symmetry-breaking.
Supplementary_files_format_and_content: 2691cells_MEswitch_trajectory.rds is the Monocle2 CellDataSet object for follicle cell trajectory during the mitotic-endocycle switch.

organism: Drosophila melanogaster

source_name: Total RNA from fruit fly ovary

growth_protocol: 100 adult ovaries from 50 female Drosophila melanogaster flies maintained at 25°C, with access to males and yeast supplements for 3 days

extract_protocol:
Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument flow cell for a 100-cycle sequencing run.

value: w-

value: ovary

tag: age

value: 3 days

tag: Sex

value: female

tag: protocol

value: access to yeast supplements and males at 25 degree C


title: G4_d3_CNBP_rep2

description: CNBP G4 array experiment, ssDNA + 100mM KCl

source_name: CNBP, G4 design 3

value: CNBP


title: G4_d1_BLM_rep2

description: human BLM G4 array experiment, ssDNA + 100mM KCl

source_name: BLM, G4 design 1

extract_protocol: We synthesized Cy5-labeled pyridostatin (Cy5-PDS). We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1). N-terminal Glutathione S-transferase (GST) tagged human nucleolin, IGF2, CNBP, BLM, and FANCJ plasmids were synthesized by GenScript.

treatment_protocol: Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation. Protein binding microarray experiments were then performed as previously described (Badis et al., Science 2009).  For experiments examining dsDNA, single-stranded DNA probes were made double-stranded using a primer complementary to a 24-mer constant sequence on the array probes following the method described previously (Badis et al., Science 2009). Double-stranding efficiency was monitored using 4% Cy3-dCTP.

value: human BLM


title: 12T1723

description: non-polyploid chromophobe rcc, classic histological type, pT2bNxMx


title: 12T546


title: late_cyt_RNA_B

city: Seville

first: Juan

middle: Pablo

last: Couso

address: Carretera de Utrera, Km 1

country: Spain

institute: Centro Andaluz de Biologia del Desarrollo

description: cytoplasmic poly-A RNA

data_processing:
Library strategy: Ribo-Seq
Sequencing reads were clipped, trimmed and aligned to an rRNA, snoRNA, snRNA & tRNA reference using Bowtie, discarding the alignments and collecting unaligned reads (Ingolia et al 2012).
Unaligned reads were mapped to the whole genome of Drosophila melanogaster FlyBase (Release 6.13) using HISAT2, default setiings.
Profiles of ribosome footprints  were constructed by quantifying the number of footprint reads aligned at each position within the feature (ORF) of interest. Ribosome density was computed by scaling read counts for each feature-by-feature length and by the total number of genome-aligned reads, using Rsamtool package (http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html).
For framing analyses, all ribosome footprints were aligned to a custom transcriptome assembly consisting of every ORF studied in its -18 and +15 mRNA context.
For each ORF, the number of reads per frame was counted using the R package "riboSeqR", and the probability of randomly obtaining framing as good or better that the observed was calculated using the R expression "pbinom([framed_reads]-1, [all_reads], 1/3, lower.tail=FALSE)"
Genome_build: FB2016_05 Dmel (Release r6.13)
Supplementary_files_format_and_content: Summary of ribosome density (expressed as RPKM) , framing (expressed as a p-value derived from a binomial test), transcription, ribosome-binding and translation calls, as well as Z-score analysis of translational regulation for annotated canonical protein-coding genes, short coding-sequences (shortCDSs) and upstream ORFs.

source_name: Embryo

growth_protocol: Wild-type Drosophila melanogaster flies (Oregon-R) were grown in standard cages with molasses egg-laying plates containing yeast paste.

extract_protocol:
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
28-34 nt ribosome footprints and 50-80 nt mRNA fragments were gel purified and prepared as previously described (Ingolia et al, 2012; Ingolia et al, 2009; Ingolia et al, 2011) for Next Generation Sequencing.
Libraries were sequenced on Illumina NextSeq and MiSeq machines with 50, 75 and 150bp SingleEnd read protocol.

treatment_protocol: After removing pre-laying plates, embryos were flash frozen, turned into powder using a pre-chilled pestle and mortar and homogenized in Lysis Buffer at 4°C for 20 min.

tag: developmental window

value: 16-24 hours

tag: developmental stage

value: late

tag: replicate

value: replicate B


title: G4_d1_BLM_rep1

value: ssDNA


title: mid_cyt_RNA_B

description: cytoplasmic poly-A RNA

value: 8-16 hours

value: mid


title: early_cyt_RNA_B

description: cytoplasmic poly-A RNA

value: 0-8 hours

value: early


title: G4_d1_FANCJ_rep2

description: human FANCJ G4 array experiment, ssDNA + 100mM KCl

source_name: FANCJ, G4 design 1

value: human FANCJ

value: 100mM KCl


title: G4_d1_FANCJ_rep1


title: late_polysome_B

description: ribosome footprint


title: G4_d3_CNBP_rep1


title: G4_d3_NCL3_rep1

description: NCL (residues 272-647) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-647), G4 design 3

value: NCL (residues 272-647)


title: G4_d3_IGF2_rep1

description: IGF2 G4 array experiment, ssDNA + 100mM KCl

source_name: IGF2, G4 design 3


title: G4_d3_NCL2_rep1

description: NCL (residues 272-710) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-710), G4 design 3

value: NCL (residues 272-710)


title: G4_d3_NCL2_rep2


title: mid_polysome_B

description: ribosome footprint


title: G4_d1_CNBP_rep2

description: human CNBP G4 array experiment, ssDNA + 100mM KCl

source_name: CNBP, G4 design 1

extract_protocol: We synthesized Cy5-labeled pyridostatin (Cy5-PDS).  We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1).   N-terminal Glutathione S-transferase (GST) tagged human nucleolin, IGF2, CNBP, BLM, and FANCJ plasmids were synthesized by GenScript.

treatment_protocol: Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation.  Protein binding microarray experiments were then performed as previously described (Badis et al., Science 2009).  For experiments examining dsDNA, single-stranded DNA probes were made double-stranded using a primer complementary to a 24-mer constant sequence on the array probes following the method described previously (Badis et al., Science 2009).  Double-stranding efficiency was monitored using 4% Cy3-dCTP.

value: human CNBP


title: G4_d1_CNBP_rep1


title: G4_d1_IGF2_rep4

description: human IGF2 G4 array experiment, ssDNA + 100mM KCl

source_name: IGF2, G4 design 1

value: human IGF2


title: early_polysome_B

description: ribosome footprint


title: G4_d1_IGF2_rep3


title: late_polysome_T

description: ribosome footprint

value: replicate T


title: G4_d1_IGF2_rep2


title: mid_polysome_T

description: ribosome footprint


title: RIPK1E-KO_P3_5

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

country: Germany

institute: University of Cologne

data_processing:
Base calling:Illumina RTA v3.4.4
Adaptor trimming:Illumina bcl2fastq2 v2.20.0
RNA-Seq data alignment to Mouse Genome GRCm38.78
Genome_build: GRCm38.78
Supplementary_files_format_and_content: log2normalisedcounts.csv

source_name: Epidermis

extract_protocol:
Qiagen RNA Isolation kit
Illumina TruSeq totalRNA pus ribo-zero gold

value: Epidermis

tag: genotype


title: RIPK1E-KO_P3_4


title: G4_d1_IGF2_rep1


title: G4_d3_NCL3_rep2


title: G4_d1_NCL3_rep2

description: human NCL(residues 272-647) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-647), G4 design 1

value: human NCL(residues 272-647)


title: G4_d3_Cy5-BG4_0.03_rep5

description: 1/30 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1/30 dilution Cy5-BG4, G4 design 3

value: 1/30 dilution Cy5-BG4


title: G4_d3_Cy5-BG4_0.03_rep6


title: G4_d3_NCL1_rep1

description: NCL G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin, G4 design 3

value: NCL


title: G4_d3_NCL1_rep2


title: G4_d1_NCL2_rep2

description: human NCL(residues 272-710) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-710), G4 design 1

value: human NCL(residues 272-710)


title: G4_d3_Cy5-BG4_0.03_rep4

value: ssDNA


title: G4_d3_IGF2_rep2


title: G4_d1_NCL3_rep1


title: Wild type_P3_5

value: Wild type


title: Wild type_P3_4


title: G4_d3_Cy5-BG4_0.03_rep3


title: Wild type_P3_3


title: G4_d3_Cy5-BG4_0.03_rep2


title: G4_d3_Cy5-BG4_0.03_rep1


title: RIPK1E-KO_P3_3


title: G4_d1_NCL2_rep1


title: G4_d1_NCL1_rep2

description: human NCL G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (full-length), G4 design 1

value: human NCL


title: G4_d1_NCL1_rep1


title: RIPK1E-KO_P3_2


title: G4_d1_Cy5-BG4_0.1_rep2

description: 1/10 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1/10 Cy5-BG4, G4 design 1

value: 1/10 dilution Cy5-BG4


title: G4_d3_Cy5-BG4_0.01_rep3

description: 1/100 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1/100 dilution Cy5-BG4, G4 design 3

value: 1/100 dilution Cy5-BG4


title: G4_d3_Cy5-BG4_0.01_rep4


title: G4_d3_Cy5-BG4_0.01_rep2


title: G4_d3_Cy5-BG4_0.01_rep1


title: Wild type_P3_2


title: NOD.Rag

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

description: NOD.Rag

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Pancreatic islets

extract_protocol:
Pancreatic islets were isolated and dispersed into single-cell suspension using non-enzymatic Cell Dissociation Solution (Sigma-Aldrich) for 5 min at 37°C. Then to block Fc-receptors engaging, the cell suspensions were incubated at 4°C for 15 min in PBS (pH 7.4) supplemented with 1% BSA and 50% of FC-block (made in-house). For surface staining, cells were incubated with fluorescently labeled antibodies (1:200 v/v) supplemented with Fixable viability Dye eFuor780 (1:1000 v/v) at 4°C for 20 minutes. Cells were then washed and analyzed by flow cytometry or subjected to FACS. Live CD45+, CD31+, and CD45-CD90+ cells were sorted using islet cells from 4-12 mice per one sample. After sorting, cells were pelleted and resuspended in 10% FBS (HyClone) in PBS (pH 7.4) 1x10^3 cells/μl and loaded onto the Chromium Controller (10X Genomics).
Samples were processed using the Chromium Single Cell 3’ Library & Gel Bead Kit following the manufacturer’s protocol. 10X Single Cell 3' v2.

tag: strain/background

value: 8-16 weeks

value: female

value: Pancreatic islet-infiltrating cells


title: RIPK1E-KO_P3_1


title: G4_d1_Cy5-BG4_0.01_rep1

source_name: 1/100 Cy5-BG4, G4 design 1

value: 100mM KCl


title: G4_d1_Cy3-dCTP_dsDNA_rep2

description: Cy3-dCTP dsDNA spike-in + 100mM KCl

source_name: Cy3-dCTP, G4 design 1

value: 4percent Cy3-dCTP

value: dsDNA


title: G4_d1_Cy3-dCTP_dsDNA_rep1

description: Cy3-dCTP dsDNA spike-in + 100mM KCl


title: NOD.Ifngr1

value: 8 weeks


title: G4_d1_Cy5-BG4_0.01_rep2


title: NOD_4_wks_2

value: NOD/ShiLtJ (NOD)

value: 4 weeks


title: G4_d1_Cy5-BG4_0.1_rep1


title: G4_d3_Cy5-BG4_0.003_rep2

description: 1/300 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1/300 dilution Cy5-BG4, G4 design 3

value: 1/300 dilution Cy5-BG4


title: Wild type_P3_1

value: Epidermis


title: G4_d2_CNBP_rep1

description: CNBP G4 array experiment, ssDNA + 100mM KCl

source_name: CNBP, G4 design 2

extract_protocol: We synthesized Cy5-labeled pyridostatin (Cy5-PDS).  We obtained BG4 conjugated with FluoProbes®647H (Cy5-BG4) from Absolute Antibody (product number Ab00174-1.1).   N-terminal Glutathione S-transferase (GST) tagged human nucleolin, IGF2, and CNBP  were synthesized by GenScript.

value: human CNBP


title: G4_d3_Cy5-BG4_0.001_rep2

description: 1/1000 dilution Cy5-BG4 G4 array experiment, ssDNA + 100mM KCl

source_name: 1/1000 dilution Cy5-BG4, G4 design 3

value: 1/1000 dilution Cy5-BG4

value: ssDNA


title: G4_d2_CNBP_rep2


title: G4_d1_Cy5-PDS_1uM_rep3

description: 1uM Cy5-PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 1uM Cy5-PDS, G4 design 1

value: 1uM Cy5-PDS


title: G4_d2_IGF2_rep2

source_name: IGF2, G4 design 2

value: human IGF2


title: G4_d2_NCL3_rep2

description: NCL(residues 272-647) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-647), G4 design 2

value: human NCL(residues 272-647)


title: G4_d3_Cy5-BG4_0.003_rep1


title: G4_d3_Cy5-BG4_0.001_rep1


title: G4_d2_NCL3_rep1


title: G4_d3_Cy5-PDS_0.3uM_rep4

description: 0.3uM Cy5-PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 0.3uM Cy5-PDS, G4 design 3

value: 0.3uM Cy5-PDS


title: G4_d3_Cy5-PDS_1uM_rep1

source_name: 1uM Cy5-PDS, G4 design 3


title: G4_d2_IGF2_rep1

description: IGF2 G4 array experiment, ssDNA + 100mM KCl


title: G4_d2_NCL2_rep2

description: NCL(residues 272-710) G4 array experiment, ssDNA + 100mM KCl

source_name: Nucleolin (residues 272-710), G4 design 2

value: human NCL(residues 272-710)


title: G4_d1_Cy5-PDS_1uM_rep2


title: G4_d2_NCL2_rep1


title: G4_d3_Cy5-PDS_1uM_rep2


title: G4_d1_Cy5-PDS_1uM_dsDNA_rep2

description: 1uM Cy5-PDS G4 array experiment, dsDNA + 100mM KCl


title: G4_d1_Cy5-PDS_1uM_rep1


title: G4_d1_Cy5-PDS_1uM_dsDNA_rep1


title: G4_d2_Cy5-PDS_1uM

source_name: 1uM Cy5-PDS, G4 design 2


title: NOD_4_wks_1

value: female

value: Pancreatic islet-infiltrating cells


title: G4_d3_Cy5-PDS_0.3uM_rep3

value: 100mM KCl


title: G4_d3_Cy5-PDS_0.3uM_rep2


title: NOD_15_wks

value: 15 weeks


title: G4_d1_Cy5-PDS_0.3uM_rep3

source_name: 0.3uM Cy5-PDS, G4 design 1


title: G4_d2_Cy5-PDS_0.3uM

source_name: 0.3uM Cy5-PDS, G4 design 2


title: G4_d1_Cy5-PDS_0.3uM_rep2


title: G4_d1_Cy5-PDS_0.3uM_rep1


title: Sample30: Rifapentine Treated 3_TechReplicate2

status: Public on Mar 26 2020

city: Omaha

first: SHETTY RAVI

last: DYAVAR

state: NE

address: 4040 EMILE ST

department: Pharmacy Practice and Science

institute: University of Nebraska Medical Center

data_processing:
RNA sequence raw data files generated from sequencing on Illumina HiSeq 2500 instrument were assembled and aligned to hg19 human genome reference using STRAND NGS software
Gene expression levels were calculated using fragments per kilobase of transcript per million mapped reads (FPKM).
Differential gene expression between rifampin or rifabutin or rifapentine treated samples versus vehicle (methanol at 0.0025%) treated RNA samples was then performed with STRAND NGS software.
Rifampin treated versus vehicle (methanol, 0.0025%); Rifabutin treated versus vehicle (methanol, 0.0025%) and Rifapentine treated versus vehicle (methanol, 0.0025%) analyses were performed to identify the genes that are regulated in response to individual drugs. We kept filters, 1.5 minimum fold change and p value <0.05 to identify significantly regulated transcripts.

source_name: Hepatocytes (Primary)

growth_protocol: Induction qualified human primary hepatocytes derived from three healthy (drug/tobacco/alcohol free) volunteers were purchased from Invitrogen and Lonza Biosciences. Cells were seeded at 0.5 Million per well in a six well plate and were cultured in Williams E medium without phenol red (CAT#A1217601) supplemented with Hepatocyte thawing and plating supplements (CAT#CM3000) and incubated at 37 °C. Medium was replaced with Williams E medium without phenol red supplemented with Hepatocyte maintenance cocktail (CAT#CM4000) and were incubated for 48 hrs with daily changes of culture medium before drug treatments.

extract_protocol:
Lysates were prepared in RLT buffer supplied along with Rneasy fibrous tissue extraction kit (Qiagen, USA) and the total RNA was extracted from rifampin, rifabutin and rifapentine treated hepatocytes.
Complimentary DNA (cDNA) libraries for RIFA treated PHH samples were constructed using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA). All samples were subjected to 50-cycle, single-read sequencing in the HiSeq2500 (Illumina, USA) and were demultiplexed using Bcl2Fastq v2.17.1.14 (Illumina). Short cDNA fragment data were compiled in FASTQ format.

treatment_protocol: Induction qualified human primary hepatocytes were treated with RIF, RFB and RPT at 10µM concentration for 72 hrs. with the corresponding untreated (negative) and 0.0025% methanol (vehicle) treated controls.

value: primary hepatocytes

tag: donor

tag: no treatment

value: NO

tag: vehicle (methanol at 0.0025%) treated

tag: rifampin (10mm) treated

tag: rifabutin (10mm) treated

tag: rifapentine (10mm) treated

value: YES


title: G4_d3_Cy5-PDS_0.1uM_rep2

description: 0.1uM Cy5-PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 0.1uM Cy5-PDS, G4 design 3

tag: molecule name

value: 0.1uM Cy5-PDS

tag: dna type


title: Control 2

city: Bengaluru

first: Sona

last: Rajakumari

state: Karnataka

address: CV Raman Road

country: India

institute: Indian Institute of Science

description: processed data file: Expression_Counts.xlsx

data_processing:
Sequence data quality was checked for base call quality distribution and sequencing adapter contamination using FastQC and MultiQC software.
Then, raw sequence reads were processed to remove adapter sequences and low quality bases using fastp.
The QC passed reads were mapped onto indexed Mouse reference genome (GRCm 38.90) using STAR2 aligner.
Further, the PCR and optical duplicates were marked and removed using Picard tools.
Using featureCounts software, gene level expression values were obtained.
Expression similarity between biological replicates were checked by Spearman correlation and Principal Components Analysis.
Differential expression analysis was carried out using edgeR package after normalizing the data based on trimmed mean of M (TMM) values.
Genes with absolute log2 fold change ≥ 2 and adjusted p-value (FDR) ≤ 0.05 were considered significant.
The expression profile of the differentially expressed genes across the samples is presented in volcano plots and heatmap.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_Counts.xlsx: Excel file contains the raw read counts of reads mapped to each gene as estimated by featureCounts program.

source_name: Myoblast

extract_protocol:
Total RNA was isolated from control and treated cells using Trizol.
1ug of total RNA was used to enrich mRNA with NEBNext Poly(A) mRNA magnetic isolation Module (E7490, New England Biolabs, USA) as per the manufacturer's instructions.
The enriched mRNA was used for library preparation. NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770, New England Biolabs, USA) was used to prepare the library by following the manufacturer's instructions.
The NEBNext Multiplex Oligos for Illumina (E7335S, New England Biolabs, USA) was used to perform polymerase chain reaction (PCR) to generate indexed sequencing libraries.
The library quality and quantity were checked using Agilent Bioanalyzer 2100 with DNA 1000 kits and Qubit dsDNA HS Assay Kit.

treatment_protocol: C2C12 cells were differentiated up to 8 days with or without 50 µM SML in adipogenic medium.

tag: cell line

tag: cell type

value: Myoblast cell line

tag: treatment

value: Control


title: SML Treated 1

value: Sesaminol (SML)


title: G4_d1_Cy5-PDS_0.1uM

source_name: 0.1uM Cy5-PDS, G4 design 1

value: ssDNA

tag: array treatment


title: SML Treated 2


title: Control 1


title: Sample29: Rifapentine Treated 3_TechReplicate1

tag: tissue


title: G4_d3_Cy5-PDS_0.03uM_rep2

description: 0.03uM Cy5-PDS G4 array experiment, ssDNA + 100mM KCl

source_name: 0.03uM Cy5-PDS, G4 design 3

value: 0.03uM Cy5-PDS


title: G4_d3_Cy5-PDS_0.3uM_rep1


title: G4_d2_Cy5-PDS_0.1uM

source_name: 0.1uM Cy5-PDS, G4 design 2


title: G4_d1_Cy5-PDS_0.03uM

source_name: 0.03uM Cy5-PDS, G4 design 1


title: Sample28: Rifapentine Treated 2_TechReplicate2


title: Sample25: Rifapentine Treated 1_TechReplicate1


title: Sample26: Rifapentine Treated 1_TechReplicate2


title: G4_d3_Cy5-PDS_0.1uM_rep1


title: G4_d2_Cy5-PDS_0.03uM

source_name: 0.03uM Cy5-PDS, G4 design 2


title: Sample23: Rifabutin Treated 3_TechReplicate1


title: Sample19: Rifabutin Treated 1_TechReplicate1


title: Sample18: Rifampin Treated 3_TechReplicate2


title: Sample17: Rifampin Treated 3_TechReplicate1


title: Sample27: Rifapentine Treated 2_TechReplicate1


title: Sample15: Rifampin Treated 2_TechReplicate1


title: Sample24: Rifabutin Treated 3_TechReplicate2


title: Sample14: Rifampin Treated 1_TechReplicate2


title: Sample11: Vehicle Treated Control 3_TechReplicate1


title: G4_d3_Cy5-PDS_0.03uM_rep1


title: Sample12: Vehicle Treated Control 3_TechReplicate2


title: Sample10: Vehicle Treated Control 2_TechReplicate2


title: Sample9: Vehicle Treated Control 2_TechReplicate1


title: Sample2: Untreated Control 1_TechReplicate2


title: Sample8: Vehicle Treated Control 1_TechReplicate2


title: Sample3: Untreated Control 2_TechReplicate1


title: Sample20: Rifabutin Treated 1_TechReplicate2


title: Sample22: Rifabutin Treated 2_TechReplicate2


title: Sample7: Vehicle Treated Control 1_TechReplicate1


title: Sample13: Rifampin Treated 1_TechReplicate1


title: Sample21: Rifabutin Treated 2_TechReplicate1


title: Sample1: Untreated Control 1_TechReplicate1

description: Sample 1_4079UNTR


title: Sample4: Untreated Control 2_TechReplicate2


title: Sample6: Untreated Control 3_TechReplicate2


title: Sample16: Rifampin Treated 2_TechReplicate2


title: pool.9_tumor.1423R

city: Dallas

first: Ping

last: Mu

state: TX

address: 6000 Harry Hines Blvd., NA6.308A

department: Human Oncology and Pathogenesis

institute: UT Southwestern Medical Center

description: pool-9-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)

data_processing:
Transform files from Fastq to Fasta (galaxy)
Clip sequences at TACATC (galaxy)
Filter sequences by length (22bp, galaxy)
Reverse-complement (galaxy)
Collapse sequences to number of reads (galaxy)
Align with shRNA guide sequences (use join from Galaxy)
Genome_build: shRNA sequences
Supplementary_files_format_and_content:
Fasta to tabular (galaxy).  For each shRNA and condition, the number of matching reads was normalized to the total number of library-specific reads per lane (10 million total reads per pool) and used for further analysis, which were reported in the processed data column as normalized count.
prostate_cancer_human_deletome.txt: A tab-delimted file containing a pooled shRNA library targeting genes most frequently deleted in primary or metastatic prostate cancer, annotated from a survey of six prostate cancer genomic datasets. (Barbieri et al., 2012; Grasso et al., 2013; Holcomb et al., 2009; Kim et al., 2007; Network, 2015; Taylor et al., 2010).
RIGER data matrix of tumor sequencing results: As requested by reviewers, a probabilistic ranking algorithm (used for in vitro screens (RIGER) to our in vivo screen) was adapted to identify true hits. However, because in vivo library screening is noisier than in vitro library screening and there are clearly stochastic effects, tumors were collected on week 16 before control tumors arise, resulting in the collection of very different numbers of resistant tumors from each pool. Thus, this data was not directly used as a probabilistic matrix, which would require the same number of repeats an in vitro library. To use a probabilistic ranking algorithm such as RIGER, the hairpin reads (in the tumors which did not score by week 16) was records as "0" because they failed to enriched quicker than the stochastic enriched hairpins, in order to have a working matrix for a probabilistic statistic model. This file is the data matrix of tumor reads ready to use by RIGER-E, which has 14 data columns including 13 (reads in tumors, maxi tumor number is 13) + 1 (reads in plasmid).

growth_protocol: LNCaP/AR cell line was generated and maintained as previously described (Chen et al 2003). Cells were cultured at 37° C (5% CO2) in high-glucose RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% HEPES, 1% Sodium Pyruvate, 1% penicillin-streptomycin and 1% L-Glutamine. In vivo xenograft experiments were done by subcutaneous injection of 2 × 106 LNCaP/AR cells (100 μl in 50% Matrigel [BD Biosciences, San Jose, CA] and 50% growth media) into the flanks of castrated male SCID mice.

extract_protocol:
Resistant LNCaP/AR xenograft tumors were harvested and the genomic DNA was isolated by two rounds of phenol extraction using PhaseLock tubes (5prime) followed by isopropanol precipitation.
All genomic DNAs from tumors, plasmid or pregraft cells were PCR amplified using a protocol previously described (Zuber NBT 2011). Libraries were analyzed on an Illumina HiSeq 2500 and 18 nucleotides of the guide strand were sequenced using a custom primer as previously described (Zuber Nature 2011).

treatment_protocol: Daily gavage treatment with 10mg/kg enzalutamide was initiated on the day of injection. Once tumors were palpable, tumor size was measured weekly by tumor measuring system Peira TM900 (Peira bvba, Belgium).

tag: sample type

value: tumor extracted from right side

value: LNCaP/AR cells

value: enzalutamide


title: pool.9_tumor.1424R


title: pool.9_tumor.1426R


title: pool.9_tumor.1425R


title: pool.9_tumor.1425L

value: tumor extracted from left side


title: pool.9_tumor.1424L


title: pool.9_tumor.1426L


title: pool.9_tumor.1422R


title: pool.9_tumor.1423L


title: pool.9_tumor.1422L


title: pool.8_tumor.1421R

description: pool-8-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: Sample5: Untreated Control 3_TechReplicate1


title: pool.8_tumor.1421L


title: pool.8_tumor.1419L


title: pool.8_tumor.1419R


title: pool.8_tumor.1420L


title: pool.8_tumor.1420R


title: pool.7_tumor.7843L

description: pool-7-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.7_tumor.7845L


title: pool.7_tumor.7843R


title: pool.7_tumor.7844

value: only one tumor extracted from this animal


title: pool.8_tumor.1417L


title: pool.8_tumor.1418R


title: pool.7_tumor.7845R


title: pool.8_tumor.1418L


title: pool.8_tumor.1417R


title: pool.7_tumor.7842R


title: pool.6_tumor.1416L

description: pool-6-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.6_tumor.1415R


title: pool.6_tumor.1414R


title: pool.6_tumor.1415L


title: pool.6_tumor.1413L


title: pool.6_tumor.1414L


title: pool.6_tumor.1413R


title: pool.7_tumor.7841L


title: pool.6_tumor.1412R


title: pool.6_tumor.1412L


title: pool.5_tumor.1411R

description: pool-5-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.5_tumor.1411L


title: pool.5_tumor.1410L


title: pool.5_tumor.1409R


title: pool.7_tumor.7842L


title: pool.5_tumor.1409L


title: pool.7_tumor.7841R


title: pool.5_tumor.1410R


title: pool.5_tumor.1408R


title: pool.43_tumor.608L

description: pool-43-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.43_tumor.608R


title: pool.43_tumor.609L


title: pool.43_tumor.609R


title: pool.43_tumor.607R


title: pool.43_tumor.607L


title: pool.5_tumor.1407L


title: pool.5_tumor.1407R


title: pool.43_tumor.606R


title: pool.43_tumor.605R


title: pool.43_tumor.605L


title: pool.42_tumor.1912L

description: pool-42-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.42_tumor.1915L


title: pool.41_tumor.7880R

description: pool-41-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.42_tumor.1916L


title: pool.41_tumor.7879R


title: pool.42_tumor.1915R


title: pool.5_tumor.1408L


title: pool.41_tumor.7880L


title: pool.41_tumor.7877R


title: pool.41_tumor.7877L


title: pool.41_tumor.7879L


title: pool.41_tumor.7878R


title: pool.43_tumor.606L


title: pool.41_tumor.7876R


title: pool.41_tumor.7876L


title: pool.40_tumor.1909L

description: pool-40-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.4_tumor.7847R

description: pool-4-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.4_tumor.7848R


title: pool.4_tumor.7850L


title: pool.40_tumor.1909R


title: pool.4_tumor.7847L


title: pool.4_tumor.7849R


title: pool.37_tumor.604L

description: pool-37-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.4_tumor.7846R


title: pool.37_tumor.603R


title: pool.4_tumor.7846L


title: pool.42_tumor.1912R


title: pool.37_tumor.1369R


title: pool.37_tumor.1371L


title: pool.37_tumor.603L


title: pool.4_tumor.7850R


title: pool.4_tumor.7849L


title: pool.37_tumor.1371R


title: pool.37_tumor.1369L


title: pool.37_tumor.1368R


title: pool.41_tumor.7878L


title: pool.37_tumor.604R


title: pool.37_tumor.1368L


title: pool.36_tumor.1896L

description: pool-36-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.36_tumor.1894R


title: pool.36_tumor.1893R


title: pool.36_tumor.1894L


title: pool.36_tumor.1892R


title: pool.35_tumor.599L

description: pool-35-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.36_tumor.1892L


title: pool.35_tumor.597R


title: pool.35_tumor.597L


title: pool.34_tumor.7875R

description: pool-34-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.34_tumor.7873R


title: pool.34_tumor.7872R


title: pool.34_tumor.7872L


title: pool.35_tumor.595L


title: pool.33_tumor.593R

description: pool-33-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.33_tumor.593L


title: pool.35_tumor.596L


title: pool.35_tumor.596R


title: pool.34_tumor.7875L


title: pool.34_tumor.7874L


title: pool.33_tumor.591L


title: pool.34_tumor.7874R


title: pool.33_tumor.595R


title: pool.33_tumor.591R


title: pool.34_tumor.7873L


title: pool.36_tumor.1896R


title: pool.36_tumor.1893L


title: pool.32_tumor.1891R

description: pool-32-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.33_tumor.594R


title: pool.32_tumor.1891L


title: pool.33_tumor.594L


title: pool.32_tumor.1890R


title: pool.33_tumor.590R


title: pool.32_tumor.1890L


title: pool.33_tumor.590L


title: pool.34_tumor.7871R


title: pool.34_tumor.7871L


title: pool.32_tumor.1889L


title: pool.31_2_tumor.7870Rr

description: pool-31.2-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.32_tumor.1887R


title: pool.31_2_tumor.7869Rr


title: pool.32_tumor.1888L


title: pool.31_2_tumor.7869Lr


title: pool.31_2_tumor.7867Rr


title: pool.32_tumor.1889R


title: pool.31_2_tumor.7868Lr


title: pool.31_2_tumor.7866Rr


title: pool.31_2_tumor.7867Lr


title: pool.31_1_tumor.7869R

description: pool-31.1-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.31_1_tumor.7867L


title: pool.31_2_tumor.7868Rr


title: pool.31_1_tumor.7868R


title: pool.31_1_tumor.7868L


title: pool.31_2_tumor.7870Lr


title: pool.31_1_tumor.7866L


title: pool.31_1_tumor.7866R


title: pool.30_tumor.1884L

description: pool-30-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.30_tumor.1885R


title: pool.31_1_tumor.7870L


title: pool.31_1_tumor.7867R


title: pool.31_2_tumor.7866Lr


title: pool.30_tumor.1882R


title: pool.31_1_tumor.7870R


title: pool.3_tumor.7855L

description: pool-3-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.3_tumor.7855R


title: pool.31_1_tumor.7869L


title: pool.30_tumor.1886L


title: pool.3_tumor.7854R


title: pool.3_tumor.7854L


title: pool.3_tumor.7853R


title: pool.3_tumor.7851R


title: pool.3_tumor.7852


title: pool.29_tumor.1878R

description: pool-29-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.29_tumor.1881R


title: pool.29_tumor.1879L


title: pool.29_tumor.1877R


title: pool.28_tumor.1876R

description: pool-28-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.28_tumor.1875L


title: pool.27_tumor.629R

description: pool-27-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.3_tumor.7851L


title: pool.28_tumor.1872L


title: pool.27_tumor.629L


title: pool.27_tumor.626R


title: pool.28_tumor.1873L


title: pool.27_tumor.625R


title: pool.27_tumor.625L


title: pool.27_tumor.626L


title: pool.28_tumor.1872R


title: pool.27_tumor.1363L


title: pool.26_tumor.7834R

description: pool-26-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.3_tumor.7853L


title: pool.28_tumor.1875R


title: pool.28_tumor.1874L


title: pool.26_tumor.589L


title: pool.26_tumor.588L


title: pool.26_tumor.586R


title: pool.26_tumor.589R


title: pool.26_tumor.586L


title: pool.25_tumor.7836L

description: pool-25-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.25_tumor.7836R


title: pool.25_tumor.7835L


title: pool.26_tumor.585R


title: pool.25_tumor.7835R


title: pool.25_tumor.7834R


title: pool.25_tumor.7833L


title: pool.25_tumor.7832


title: pool.23_tumor.580R

description: pool-23-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.23_tumor.583R


title: pool.23_tumor.581R


title: pool.25_tumor.7834L


title: pool.23_tumor.1352L


title: pool.23_tumor.583L


title: pool.26_tumor.585L


title: pool.27_tumor.1363R


title: pool.26_tumor.588R


title: pool.23_tumor.580L


title: pool.23_tumor.1351R


title: pool.23_tumor.1350L


title: pool.23_tumor.1351L


title: pool.22_tumor.624R

description: pool-22-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.22_tumor.621R


title: pool.22_tumor.622L


title: pool.22_tumor.624L


title: pool.22_tumor.621L


title: pool.21_tumor.579R

description: pool-21-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.21_tumor.578R


title: pool.21_tumor.579L


title: pool.21_tumor.577R


title: pool.21_tumor.578L


title: pool.21_tumor.577L


title: pool.21_tumor.576R


title: pool.21_tumor.575R


title: pool.20_tumor.7840L

description: pool-20-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.20_tumor.7840R


title: pool.21_tumor.575L


title: pool.20_tumor.7838R


title: pool.20_tumor.7839R


title: pool.20_tumor.7839L


title: pool.20_tumor.7838L


title: pool.20_tumor.7837L


title: pool.2_tumor.7860L

description: pool-2-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.2_tumor.7860R


title: pool.2_tumor.7857R


title: pool.2_tumor.7857L


title: pool.2_tumor.7856L


title: pool.19_tumor.1871L

description: pool-19-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.19_tumor.1870R


title: pool.2_tumor.7858L


title: pool.19_tumor.1870L


title: pool.19_tumor.1868R


title: pool.19_tumor.1867L


title: pool.19_tumor.1869L


title: pool.21_tumor.576L


title: pool.18_tumor.1866R

description: pool-18-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.20_tumor.7837R


title: pool.18_tumor.1865L


title: pool.17_tumor.1460L

description: pool-17-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.17_tumor.1461R


title: pool.17_tumor.1460R


title: pool.17_tumor.1459L


title: pool.17_tumor.1461L


title: pool.18_tumor.1862L


title: pool.17_tumor.1459R


title: pool.2_tumor.7858R


title: pool.17_tumor.1458R


title: pool.2_tumor.7856R


title: pool.16_tumor.1456R

description: pool-16-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.17_tumor.1458L


title: pool.17_tumor.1457L


title: pool.17_tumor.1457R


title: pool.19_tumor.1869R


title: pool.16_tumor.1456L


title: pool.16_tumor.1454R


title: pool.16_tumor.1455R


title: pool.18_tumor.1865R


title: pool.16_tumor.1455L


title: pool.16_tumor.1452R


title: pool.16_tumor.1453R


title: pool.16_tumor.1452L


title: pool.16_tumor.1454L


title: pool.15_tumor.1451L

description: pool-15-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.15_tumor.1449L


title: pool.15_tumor.1449R


title: pool.16_tumor.1453L


title: pool.14_tumor.1445R

description: pool-14-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.14_tumor.1446R


title: pool.14_tumor.1446L


title: pool.14_tumor.1444L


title: pool.14_tumor.1443L


title: pool.14_tumor.1442L


title: pool.14_tumor.1443R


title: pool.14_tumor.1442R


title: pool.14_tumor.1444R


title: pool.13_tumor.574R

description: pool-13-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.13_tumor.572R


title: pool.13_tumor.571R


title: pool.13_tumor.572L


title: pool.13_tumor.570L


title: pool.13_tumor.571L


title: pool.15_tumor.1451R


title: pool.13_tumor.1359R


title: pool.15_tumor.1450R


title: pool.13_tumor.1358R


title: pool.13_tumor.1357R


title: pool.13_tumor.1358L


title: pool.13_tumor.1354R


title: pool.13_tumor.1354L


title: pool.14_tumor.1445L


title: pool.12_tumor.1436R

description: pool-12-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.30_tumor.1882L

description: pool-30-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.12_tumor.1436L


title: pool.12_tumor.1434R


title: pool.12_tumor.1434L


title: pool.12_tumor.1433R


title: pool.12_tumor.1432R


title: pool.11_tumor.1441R

description: pool-11-normalizedcount.txt (see tumor_TXT_files.tar archive linked at foot of Series record)


title: pool.12_tumor.1433L


title: pool.12_tumor.1432L


title: pool.30_tumor.1883R


title: pool.11_tumor.1439R


title: pool.11_tumor.1440R


title: pool.11_tumor.1440L


title: pool.11_tumor.1439L


title: pool.11_tumor.1438R


title: pool.13_tumor.1359L


title: pool.11_tumor.1438L


title: pool.11_tumor.1437R