title: R-VEC Tubes 1 week 2

value: d7 tube formation, Stem Span tube media


title: 10x_158

status: Public on May 01 2020

type: SRA

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

library_source: transcriptomic

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted. For the subset of cells processed with 10X, we used CellRanger with the default parameters.
We examined as quality control the number of genes detected in each cell and conservatively excluded cells with fewer than 2,000 detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited files containing log2(TPM/10+1) values (TPM=transcript-per-million reads) of 9609 cells profiled by 10x droplet scRNA-seq (10x file) and of 1297 cell profiled by SmartSeq2 (SS2 file). All quantified 23,686 genes are included in the SS2 file and 11,548 genes detected in at least 10 cells are included in the 10x file. Header lines include Cell ID, patient ID, time point of sample acquisition, and the cells assignment into clusters and coordinates in a tSNE analysis (as shown in an associated manuscript).

molecule: polyA RNA

organism: Homo sapiens

source_name: Malignant ascites  single cell

extract_protocol:
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina). For a subset of samples, single cells were processed through the 10X Chromium 3 Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

treatment_protocol: Ascites fluid was drained by an interventional radiologist and transferred for further processing in closed vacuum bottles. De-identified patient information, including their ovarian cancer histology, stage, treatment history, and BRCA mutation status were collected. Immediately following drainage, malignant ascites was transported on ice, aliquoted into 50 mL conical tubes (BD Falcon) and spun for 5 min at 580 × g at 4°C. The supernatant was aspirated and the remaining pellet was resuspended with 5 mL of hypotonic lysis buffer ACK (Life technologies) and incubated on ice for 5 min. 20 ml of PBS was used to quench the lysis buffer. Cell suspensions were pooled and pipetted into a new 50 mL conical tube through a 100 µm mesh and spun for 5 min at 580 × g at 4°C. Hypotonic lysis was repeated until no visible red blood cell component was present, usually for a total of 2-3 times (for the plate-based approach). Following red blood cell lysis, the cell pellet was resuspended in PBS with 2% (v/v) FBS. These cells were then used for both plate-based and droplet-based scRNA-seq. For plate-based scRNA-seq, cells were labeled with the following fluorophore-conjugated flow-cytometry antibodies: live/dead stain with Calcein-AM (LifeTechnologies), 7-AAD (7-Aminoactinomycin D) (LifeTechnologies), CD45-FITC (LifeTechnologies), EpCAM-PE (Miltenyi Biotec) and CD24-PE/Cy7 (BioLegend). Cells were incubated for 30 min on ice in the dark. Cells were washed twice by resuspending with PBS with 2% (v/v) FBS and spun 5 min at 580 × g at 4°C. Flow-cytometry and sorting was performed on a BD Biosciences cell sorter (IIu or UV). Following doublet exclusion, Calceinhigh7AAD-CD45-EPCAM+CD24+ single cells were sorted into 96-well microtiter plates (on a plate chiller) that were prepared with 10uL cell lysis buffer (TCL + 1% β-mercaptoethanol). Following completion of cell sorting, plates were covered with aluminum lids, vortexed for 10 seconds, centrifuged for 2 min at 580 × g at 4°C and immediately placed on dry ice prior to storage at -80°C.

tag: cell type

value: Malignant ascites  single cell

tag: patient id

tag: time point


title: R-VEC Flat 2

city: New York

first: Brisa

last: Palikuqi

state: NY

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

data_processing:
RNA-seq reads were aligned using STAR version 2.6.0c.  The STAR index was made with the GENCODE GRCh38.p12 or GENCODE GRCm38.p6 primary assembly and corresponding GENCODE annotation file --sjdbGTFfile gencode.v28.annotation.gtf or  --sjdbGTFfile gencode.vM17.annotation.gtf, respectively.
Fragments mapping uniquely to genes in the GENCODE v28 (for human samples) or GENCODE vM17 (for mouse samples) main GTF were counted using featureCounts version v1.6.2.
Genome_build: GRCh38.p12 (human), GRCm38.p6 (mouse)
Supplementary_files_format_and_content: featureCount output files

molecule: total RNA

source_name: HUVEC

extract_protocol: RNA libraries were prepared for sequencing using Illumina's TruSeq RNA Library Preparation Kit v2

tag: growth protocol

value: R-VEC induction

tag: treatment protocol

value: d0 tube formation, Stem Span tube media

tag: extraction protocol

value: picopure


title: R-VEC Tubes 4 weeks 1

value: R-VEC stabilization

value: 4 weeks tube formation, Stem Span tube media


title: 10x_156


title: Liver metasis Replicate 2

type: RNA

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Liver biopsy of metasis from subject 2

hyb_protocol: 825ng of sample and 825ng of Cy5 labelled reference RNA were added to a nuclease free microcentrifuge tube. Subsequently, 11 µl of 10x blocking agent and 2.2 µl of fragmentation buffer (Agilent, catalogue number 5188-5281) were added. Nuclease free water was added to each sample to bring the total volume to 55 µl. Each sample was then incubated to 60 degrees centigrade for 30 minutes in the dark.    55µl of 2xGExhybridisation buffer (HI-RPM, Agilent, catalogue number 5188-5281) was then added to each sample and gently mixed using the pipette.     Hybridization Chamber Gaskett slides (Agilent, catalogue number G2534-60011) were loaded into the Agilent SureHyb chamber base (Agilent, catalogue number G2534A) with the label facing up and sitting flush. Each sample was then loaded onto the gasket slides, ensuring not to introduce air bubbles. The whole Human Genome microarray slides (4x44k, Agilent, catalogue number G4112F) were then placed flush on top of the gasket slides with the samples ‘sandwiched’ in between. The SureHyb chamber cover was added and the clamp ‘hand-tightened’. Care was taken to ensure any air-bubbles were moving freely with rotation, as bubbles that were stuck would have created artefacts. SureHyb chambers were then placed into a rotisserie inside a hybridisation oven rotator (Agilent, catalogue number G2530-60029), and incubated at 65 degrees centigrade for 17 hours, rotating at 10rpm.    The microarray slides were then washed in pre-warmed gene expression wash buffer solutions I, II and III (Agilent, catalogue number 5188-5327). The solutions were pre-warmed and used if there was no precipitate. Slides were removed from the oven, and carefully separated from the gasket slide submerged in buffer I. Each slide was then placed into a universal tube filled with buffer I using servile forceps, and rotated on a spiramix (Spiramix 5, Denley, Serial Number: 2672) for 1 minute in the dark. Each slide was then carefully placed into a tube with buffer II, and rotated as before for 1 minute. Each slide was then carefully submerged in buffer III for 3 seconds, and slowly removed. Each slide was then inserted into a Hybridization Chamber (Agilent, catalogue number G2534A), placed into the Agilent Microarray Scanner (Agilent, catalogue number G2565BA), and scanned immediately.    Feature extraction was then undertaken. Feature extraction was a process by which information from the probe features was extracted from the microarray scan data. The raw images were evaluated using Agilent Feature Extraction software (version X). The Feature Extraction files were then imported into GeneSpring X and normalised.

scan_protocol: Each slide was inserted into a Hybridization Chamber (Agilent, catalogue number G2534A), placed into the Agilent Microarray Scanner (Agilent, catalogue number G2565BA).

data_processing: Agilent Feature Extraction v9.1.3.1 standard Common reference image analysis protocol was used. Following feature extraction Data was imported into GeneSpring 10 (Agilent Technologies) using the standard two colour experiment protocol. Note that as the universal Human Reference was labelled with Cy5 all arrays were dye swapped such that the ratio of interest (Cy3/Cy5) could be obtained

source_name: Liver Biopsy of metasis

label_protocol: 500 ng of RNA was added to a sterile microcentrifuge tube and the volume was increased to 8.3 µl using nuclease free water. Spike-mix A (Agilent, catalogue number 5188-5279) was then diluted with dilution buffer 3 times; 1:20, then 1:40 then 1:16 dilutions. Two microlitres of diluted Spike-mix A and 1.2 µl of T7 promoter primer (Agilent, catalogue number 5190-2306) were added, to total the volume at 11.5 µl.    T7 promoter primer was denatured in a water bath at 65 degrees centigrade for 10 minutes and then placed on ice. 5x First Strand buffer (Agilent, catalogue number 5190-2306) was heated in a water bath at 800C for 4 minutes. The cDNA master mix was then produced.    The cDNA master mix was mixed in a separate sterile microcentrifuge tube. The following volumes were added per sample being labelled. The cDNA master mix per sample included; 4 µl 5x First Strand buffer, 2 µl 0.1 M DTT (Agilent, catalogue number 5190-2306), 1 µl 10mM dNTP mix (Agilent, catalogue number 5190-2306), 1 µl MMLV-RT (Agilent, catalogue number 5190-2306)) and 0.5 µl RNaseOut (Agilent, catalogue number 5190-2306). The total volume, per sample being labelled, was 8.5µl. Subsequently, 8.5µl of the cDNA master mix solution was then added to each sample. Samples were then incubated in a water bath for 2 hours at 40 degrees centigrade.    Each sample was then incubated at 650C for 15 minutes, in a water bath, briefly spun in the variable speed microcentrifuge for a few seconds and then placed on ice.     50% polyethylene glycol (PEG, Agilent, catalogue number 5190-2306) solution was then warmed to 40 degrees centigrade for 1 minute and the transcription master mix was then constructed in a separate nuclease free microcentrifuge tube. Transcription master mix consisted of 15.3 µl nuclease free water, 20 µl 4x transcription buffer, 6µl 0.1 M DTT, 8µl NTP mix (Agilent, catalogue number 5190-2306), 6.4µl 50% PEG, 0.5µl RNaseOut, 0.6µl inorganic pyrophosphatase (Agilent, catalogue number 5190-2306), 0.8µl T7 RNA polymerase (Agilent, catalogue number 5190-2306) and 2.4µl of Cyanine 3-CTP (Cy3, Agilent, catalogue number 5190-2306). The total volume per sample being labelled was 60µl.    Sixty microlitre of the transcription master mix was then added to each sample and mixed using gentle pipetting. Samples were then incubated in a water bath at 40 degrees centigrade for 4 hours. Samples were then stored at -80 degrees centigrade in the dark.

growth_protocol: Following liver resection, the specimen was removed from the abdominal cavity under sterile conditions. Sterile techniques were employed to minimise exposure of the tissue samples to ribonucleases. Also, samples were taken from the liver within 10 minutes of removing of the liver from the abdominal cavity. Three tissue samples of approximately 30-50 mg were taken from the liver specimen of each patient; the metastasis, the ‘halo’ and the liver parenchyma respectively, using a size 22 sterile blade scalpel, sterile forceps and 3 sterile tru-cut biopsy needles.

extract_protocol: 15 to 30 mg of stored tissue was placed into RNase-free microcentrifuge eppendorfs (Eppendorf, catalogue 5417R), each containing a 5 mm stainless steel bead.  600 µl of prepared Buffer RPE was then added. Each column was then placed into a rotor-stator homogeniser (manufactured by Retsch) which simultaneously disrupted and homogenise the tissue for 2 minutes. The plate containing the columns was then rotated by 1800C and the process was repeated for a further 2 minutes. The columns were inspected and the process repeated as necessary until the samples were uniformly homogeneous.     The lysate was transferred into a QIAshredder spin column (Qiagen, Inc., catalogue number 74134) placed in a 2 ml collection tube.    Seventy percent ethanol was then added to the flow-through solution at a ratio of 1:1, and mixed well by pipetting. 700 µl of the sample was then added to an RNeasy spin column and placed in a 2 ml collection tube. This was then spun in the variable speed microcentrifuge for 30s at 10,000 rpm at 210C. The remainder of the solution for each sample was then pipetted into the appropriate RNeasy spin column and this process was repeated until all the sample volume, including any precipitant, was used.    700 µl of Buffer RW1 (Qiagen, Inc., catalogue number 74134) was added to the RNeasy spin column and spun in the variable speed microcentrifuge for 30s at 10,000 rpm at 210C. The flow-through was discarded and the RNeasy spin column was retained.    500 µl of Buffer RPE was then added to the RNeasy spin column and spun in the variable speed microcentrifuge for 30 s at 10,000 rpm at 210C. The flow-through was discarded and the RNeasy spin column was retained. The wash with 500 µl of Buffer RPE was repeated and spun in the variable speed microcentrifuge for 2 minutes at 10,000 rpm at 210C and the flow-through was discarded. The RNeasy spin column was then spun in the variable speed microcentrifuge for a further 1 minute at 10,000 rpm at 210C to eliminate any possible carryover of Buffer RPE or residual flow-through.    The RNA was then eluted into RNase-free water (Qiagen, Inc., catalogue number 74134). The RNeasy spin column was transferred to a new 1.5ml microcentrifuge tube. 50 µl of RNase-free water was added directly to the spin column membrane, allowed to stand for 1 minute, and then spun in the variable speed microcentrifuge for 1 minute at 10,000 rpm at 210C, to elute the RNA. The test tubes containing the RNA were placed into a bucket of ice, using sterile conditions, and stored at -80 degrees centigrade.

treatment_protocol: Having been taken from the resected liver, the biopsy samples were immediately stored in RNAlater RNA stabilisation reagent in a sterile microcentrifuge tube at room temperature for 1-2 hours and subsequently stored at -20 degrees centigrade until processed and analysed.

tag: tissue

value: Liver

tag: tumour stage

value: Metasis

source_name: Stratagene Universal Human Reference

tag: universal human reference

value: total RNA from 10 human cell lines


title: R2shp53-WNT1_SA_replicate2 [miRNA]

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

country: France

institute: IRCM

hyb_protocol: 12 mg of cRNA fragmented were  hybridized for 16 h at 45 C, washed and stained in the Affymetrix Fluidics Station 450 with Hybridization Wash & Stain kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G 2Xgain

data_processing: Robust Multi-array Average (RMA) method (R package affy), further analysis was restricted to homo sapiens mir (HSA annotation)

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Express

growth_protocol: MEBM medium supplemented with antibiotics (Gibco/Thermo-Fisher, Illkirch-Graffenstaden, France), 1M HEPES, hydrocortisone, insulin, EGF, BPE and Gentamycine (MEGM single Quots, Lonza, Levallois-Perret, France)

extract_protocol: For miR profiling total RNA were extracted uzing Trizol (Invitrogen/Thermo-Fisher, Illkirch-Graffenstaden, France ) according to manufacturer’s instructions.

treatment_protocol: Primary HMEC cultures were transduced with amphotropic retroviral supernatants produced by 293T cells transfected with one of the   following retroviral constructs: pSUPER.retro.hygro-shp53, pBABE.neo-CCNE1, pLNC-WNT1, pBABE.puro-HRASV12.   Transduction was followed by a 3 weeks period of antibiotic selection.

tag: gender

value: female

value: primary human mammary epithelial cells (HMECs)

tag: transduced with


title: R-VEC Tubes 1 week 1

value: R-VEC remodeling


title: 10x_155


title: R-VEC Flat 1

value: d0 tube fromation,  Stem Span tube media


title: R2shp53-WNT1_SA_replicate1 [miRNA]


title: R2shp53-WNT1_Late_replicate1 [miRNA]


title: 10x_154


title: R2shp53-RASV12_SA_replicate2 [miRNA]


title: R2shp53-RASV12_SA_replicate1 [miRNA]


title: Liver Halo of metasis Replicate 1

description: Liver biopsy of Halo of metasis from subject 1

source_name: Liver Biopsy of Halo of metasis

value: Halo of Metasis


title: R2shp53-WNT1_Late_replicate2 [miRNA]


title: 10x_153


title: ne8h rep 4

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

description:
D_ne8h
mRNA
processed data file: ne.matrix.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to the transcriptome (Ensembl annotation v 91) using salmon v0.11.2 with default parameters (Patro et al.)
Reads mapping to the genes and transcripts were also counted using salmon v 0.11.2.
The wild type (wt) samples were used as a reference in pam16-3, while samples with empty pESC-URA plasmid (ev samples) were control in pRip1 comparisons.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: *.matrix.tsv: Tab-delimited text files including raw gene counts for each sample.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: The BY4741 cells transformed with pESC-URA plasmid expressing pRip1-FLAG protein under the control of the Cup1 promoter were grown on minimal synthetic medium (0.67% (w/v) yeast nitrogen base, 0.079% (w/v) CSM amino acid mix, without uracil) containing 2% (w/v) sucrose as carbon source. The yeast culture was carried at 28 °C to the early logarithmic growth phase and were further induced with 100 μM CuSO4 for 8, 4 or 1h. Pam16 wild type and the mutant pam16-3 sample were grown on minimal synthetic medium (0.67% (w/v) yeast nitrogen base, 0.079% (w/v) CSM amino acid mix) containing 2% (w/v) sucrose as carbon source at permissive temperature 19oC to the early logarithmic growth phase and shifted to a restrictive temperature of 37oC for 8, 4 or 1h. The samples grown at permissive 19 oC were used as a reference. 2.5 OD600 units of cells were harvested by centrifugation (5000 g, 5 min, 4°C), re-suspended in 125 µl of RNAlater solution (Thermo Fisher Scientific, Waltham, MA USA) and incubated for 1h at 4°C.

extract_protocol:
The defrost sample were spin 5000 x g for 5 min at 4 °C to remove thoroughly the supernatants. The loosen pellet were re-suspended in 200 uL PBS. To this sample 600 uL of Buffer RLT (Qiagen) was added along with acid-washed glass beads, and cells were shaken in cell disruptor for 10 min at max speed at 4 °C. The further processing was performed with agreement of the RNA extraction from Qiagen Purification of Total RNA Kit for Yeast with Optimal On-Column DNase Digestion (RNeasy Mini Kit (50), Cat No./ID: 74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq stranded mRNA Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: The pRip1 samples were induced with 100 μM CuSO4 for 8, 4 or 1h. Pam16 wild type and the mutant pam16-3 sample after growing to the early logarithmic phase were shifted to a restrictive temperature of 37oC for 8, 4 or 1h.

tag: strain/background

tag: genotype/variation


title: R2shp53-CCNE1_SA_replicate2 [miRNA]


title: R2shp53-RASV12_Late_replicate2 [miRNA]


title: R2shp53-RASV12_Late_replicate1 [miRNA]


title: Liver metasis Replicate 1

description: Liver biopsy of metasis from subject 1


title: R2shp53-CCNE1_SA_replicate1 [miRNA]


title: 10x_157


title: 10x_152


title: ne8h rep 2

description:
B_ne8h
mRNA
processed data file: ne.matrix.tsv


title: ne8h rep 3

description:
C_ne8h
mRNA
processed data file: ne.matrix.tsv


title: R2shp53-CCNE1_Late_replicate2 [miRNA]


title: R2shp53-CCNE1_Late_replicate1 [miRNA]


title: R2shP53_Late_replicate2 [miRNA]


title: R2shP53_Early_replicate2 [miRNA]


title: R2shP53_Late_replicate1 [miRNA]


title: ne8h rep 1

description:
A_ne8h
mRNA
processed data file: ne.matrix.tsv


title: 10x_150


title: R2shP53_Early_replicate1 [miRNA]


title: 10x_149


title: 10x_147


title: R2_replicate2 [miRNA]


title: 10x_148


title: R2_replicate1 [miRNA]


title: ev8h rep 3

description:
C_ev8h
mRNA
processed data file: ev.matrix.tsv


title: 10x_151


title: ev8h rep 2

description:
B_ev8h
mRNA
processed data file: ev.matrix.tsv


title: 10x_146


title: ev8h rep 1

description:
A_ev8h
mRNA
processed data file: ev.matrix.tsv


title: Liver metasis Replicate 3

description: Liver biopsy of metasis from subject 3


title: rip8h rep 4

description:
D_rip8h
mRNA
processed data file: rip.matrix.tsv


title: 10x_145


title: Tumor macrophage, replicate 2 [KP-TUMOR-MAC2]

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Gene expression data from tumor macrophages.

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45ºC to Mouse Gene 1.0 ST Arrays using the GeneChip Hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip 3000 7G scanner.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

label: Biotin

organism: Mus musculus

label_protocol: cDNA biotinylated by terminal transferase end labeling according to the standard Affymetrix WT Pico protocol starting with 2ng of RNA (GeneChip® WT Pico Reagent Kit Manual Target Preparation for GeneChip®Whole Transcript (WT) Expression Arrays, 2015, Affymetrix)

growth_protocol: Primary macrophages isolated from tumors and immediately lysed to extract RNA.

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

treatment_protocol: Not applicable.

value: Primary macrophages


title: ev8h rep 4

description:
D_ev8h
mRNA
processed data file: ev.matrix.tsv


title: 10x_144


title: Tumor macrophage, replicate 1 [KP-TUMOR-MAC1]


title: rip8h rep 3

description:
C_rip8h
mRNA
processed data file: rip.matrix.tsv


title: SUIT-2 HLM

city: Fukuoka Shi

first: Haimin

last: Feng

address: Maidashi 3-1-1

country: Japan

institute: department of Sugery and Oncology

description: high metastasis cell lines

hyb_protocol: Standard Illumina hyridization protocol

scan_protocol: Standard Illumina scanning protocol (BeadArray Reader; Illumina)

data_processing: The data were normalized by quantile normalization using lumi and preprocess package in R. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.

source_name: SUIT-2 high liver metastatic cell lines

label_protocol: Illumina Totalprep RNA Amplification Kit (Ambion)

growth_protocol: Cells were maintained in Dulbecco's modified Eagle’s medium (DMEM)+ 10% FBS

extract_protocol: RNA extraction protocol not provided

treatment_protocol: BALB/c AJcl nu/nu female mice were purchased from CLEA (Tokyo, Japan) and transported to our institution at 4-weeks-old. After 1 week, parental PANC-1 and SUIT-2 cells (1×106 cells) were injected into the tail of the pancreas. The mice were humanely killed at 4–7 weeks after injection. Tiny hepatic metastases were harvested and minced. We performed primary culture using minced tissue with collagenase, and the cell culture was then injected into the pancreas. This process was repeated five times to establish the highly metastatic PANC-1 and SUIT-2 cell line.

tag: original cell line

value: pancreatic cancer

tag: treatment

value: implanted and harvested in mice

tag: sites

value: hepatic metastasis from mice


title: PANC-1 HLM

description: high metastasis cell lines

source_name: PANC-1 high liver metastatic cell lines


title: OBS_PRE Female obese 4 days 10001322039_J

city: Orlando

first: Rick

last: Vega

state: FL

address: 303 E. Princeton

institute: AdventHealth

description:
OBS_PRE
obese

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalization with IlluminaGUI in R

source_name: Vastus lateralis muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Muscle biopsies were obtained in the fasted state

extract_protocol: Muscle biopsies were obtained using a Berstrom needle. The biopsy was trimmed of visible adipose tissue and flash frozen in liquid nitrogen. Total RNA was isolated using the RNeasy fibrous tissue kit.

value: Vastus lateralis

tag: Sex

value: Female

tag: days

tag: time

value: PRE

tag: groups

value: OBS

tag: group

value: obese


title: SUIT-2 WT

description: wild type pancreatic cancer cells as control

source_name: SUIT-2 cell lines wild type

tag: cell type

value: control

value: hepatic metastasis from human


title: PANC-1 WT

source_name: PANC-1 cell lines wild type

value: primary sites in pancreas


title: OBS_PRE Female obese 4 days 10001322039_K

description:
OBS_PRE
obese


title: OBS_PRE Female obese 4 days 10001322039_I

description:
OBS_PRE
obese


title: 10x_142

value: Malignant ascites  single cell

tag: patient id

tag: time point


title: 10x_143


title: ne4h rep 4

description:
D_ne4h
mRNA
processed data file: ne.matrix.tsv


title: rip8h rep 1

description:
A_rip8h
mRNA
processed data file: rip.matrix.tsv


title: OBS_PRE Male obese 4 days 10001322039_G

description:
OBS_PRE
obese

tag: tissue

value: Male


title: LA_PRE Male ATHLETE 4 days 10001322039_F

description:
LA_PRE
lean active

value: LA

value: ATHLETE


title: 10x_141


title: rip8h rep 2

description:
B_rip8h
mRNA
processed data file: rip.matrix.tsv


title: 10x_140


title: OBS_PRE Female obese 4 days 10001322039_L

description:
OBS_PRE
obese


title: OBS_PRE Female obese 4 days 10001322039_H

description:
OBS_PRE
obese


title: LA_PRE Male ATHLETE 4 days 10001322039_B

description:
LA_PRE
lean active


title: ne4h rep 2

description:
B_ne4h
mRNA
processed data file: ne.matrix.tsv


title: ne4h rep 3

description:
C_ne4h
mRNA
processed data file: ne.matrix.tsv


title: 10x_138


title: 10x_139


title: LA_PRE Male ATHLETE 4 days 10001322039_C

description:
LA_PRE
lean active


title: 10x_137


title: ne4h rep 1

description:
A_ne4h
mRNA
processed data file: ne.matrix.tsv


title: LA_PRE Male ATHLETE 4 days 10001322039_E

description:
LA_PRE
lean active


title: ev4h rep 3

description:
C_ev4h
mRNA
processed data file: ev.matrix.tsv


title: 10x_136


title: LA_PRE Male ATHLETE 4 days 10001322039_A

description:
LA_PRE
lean active


title: ev4h rep 2

description:
B_ev4h
mRNA
processed data file: ev.matrix.tsv


title: LOS_POST Female LEAN 23 days 10001322038_J

description:
LOS_POST
lean/overweight sedentary

value: POST

value: LOS

value: LEAN


title: LOS_POST Male LEAN 23 days 10001322038_L

description:
LOS_POST
lean/overweight sedentary


title: LA_PRE Male ATHLETE 4 days 10001322039_D

description:
LA_PRE
lean active


title: LOS_PRE Female LEAN 4 days 10001322038_I

description:
LOS_PRE
lean/overweight sedentary


title: LOS_PRE Male LEAN 4 days 10001322038_K

description:
LOS_PRE
lean/overweight sedentary


title: LOS_POST Female LEAN 23 days 10001322038_H

description:
LOS_POST
lean/overweight sedentary


title: LOS_PRE Female LEAN 4 days 10001322038_G

description:
LOS_PRE
lean/overweight sedentary


title: LOS_PRE Female LEAN 4 days 10001322038_E

description:
LOS_PRE
lean/overweight sedentary


title: 10x_135


title: LOS_POST Female LEAN 23 days 10001322038_D

description:
LOS_POST
lean/overweight sedentary


title: LOS_POST Male LEAN 23 days 10001322038_B

description:
LOS_POST
lean/overweight sedentary


title: ev4h rep 4

description:
D_ev4h
mRNA
processed data file: ev.matrix.tsv


title: ev4h rep 1

description:
A_ev4h
mRNA
processed data file: ev.matrix.tsv


title: rip4h rep 4

description:
D_rip4h
mRNA
processed data file: rip.matrix.tsv


title: 10x_133


title: LOS_PRE Male LEAN 4 days 10001322038_A

description:
LOS_PRE
lean/overweight sedentary


title: CD31-CD45-EpCAM+CD133-  [72199]

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
OVA
SAMPLE 34

hyb_protocol: 750 ng of amplified biotin-labelled cDNA generated from these samples were randomized and hybridized onto three Illumina Human HT-12 v4 BeadChips. BeadChips were incubated at 48 °C at rotation speed 5 for 15 hours for hybridization.

scan_protocol: The BeadChips were washed and stained as per Illumina protocol and scanned on the iScan (Illumina).

data_processing: Data files were quantified in GenomeStudio Version 2011.1 (Illumina). Probe intensities were normalized between arrays using quantile normalization and transformed using the logarithm of base 2.

label_protocol: 5 ng of RNA per sample were amplified using the Ovation pica WTA V2 kit Nugen) as per the manufacturer’s instructions. Amplified cDNA from each sample was labelled following Nugen Illumina solution application Note #2

growth_protocol: Sorted populations were washed with PBS

extract_protocol: RNA was extracted using the Rneasy Plus Micro kit (Qiagen).

tag: subject id

value: high-grade serous ovarian cancer (HGSOC)

tag: cell marker

value: epithelial


title: 10x_132


title: rip4h rep 3

description:
C_rip4h
mRNA
processed data file: rip.matrix.tsv


title: LOS_POST Female LEAN 23 days 10001322038_F

description:
LOS_POST
lean/overweight sedentary

value: Vastus lateralis


title: rip4h rep 2

description:
B_rip4h
mRNA
processed data file: rip.matrix.tsv


title: 10x_134


title: LOS_PRE Female LEAN 4 days 10001322038_C

description:
LOS_PRE
lean/overweight sedentary

value: Female


title: 10x_131


title: rip4h rep 1

description:
A_rip4h
mRNA
processed data file: rip.matrix.tsv


title: ne1h rep 4

description:
D_ne1h
mRNA
processed data file: ne.matrix.tsv


title: CD31-CD45-EpCAM+CD133+  [72199]

description:
OVA
SAMPLE 33


title: CD31-CD45-EpCAM+CD133+  [72143]

description:
OVA
SAMPLE 31


title: 10x_129


title: CD31-CD45-EpCAM+CD133-  [72130]

description:
OVA
SAMPLE 29


title: CD31-CD45-EpCAM+CD133+  [72130]

description:
OVA
SAMPLE 28


title: 10x_128


title: CD31-CD45-EpCAM-CD49e+ [72143]

description:
CAF
SAMPLE 30

value: CAF


title: CD31-CD45-EpCAM-CD49e+ [72130]

description:
CAF
SAMPLE 27


title: 10x_127


title: ne1h rep 3

description:
C_ne1h
mRNA
processed data file: ne.matrix.tsv


title: CD31-CD45-EpCAM+CD133-  [72143]

description:
OVA
SAMPLE 32


title: CD31-CD45-EpCAM+CD133-  [71853]

description:
OVA
SAMPLE 26


title: ne1h rep 2

description:
B_ne1h
mRNA
processed data file: ne.matrix.tsv


title: CD31-CD45-EpCAM+CD133+  [71853]

description:
OVA
SAMPLE 25


title: CD31-CD45-EpCAM-CD49e+ [71853]

description:
CAF
SAMPLE 24


title: ne1h rep 1

description:
A_ne1h
mRNA
processed data file: ne.matrix.tsv


title: CD31-CD45-EpCAM+CD133+  [71423]

description:
OVA
SAMPLE 22


title: 10x_130


title: CD31-CD45-EpCAM-CD49e+ [71423]

description:
CAF
SAMPLE 21


title: CD31-CD45-EpCAM+CD133-  [71423]

description:
OVA
SAMPLE 23


title: 10x_126


title: CD31-CD45-EpCAM+CD133+  [71377]

description:
OVA
SAMPLE 19


title: ev1h rep 4

description:
D_ev1h
mRNA
processed data file: ev.matrix.tsv


title: 10x_123


title: 10x_122


title: CD31-CD45-EpCAM-CD49e+ [71377]

description:
CAF
SAMPLE 18


title: ev1h rep 1

description:
A_ev1h
mRNA
processed data file: ev.matrix.tsv


title: rip1h rep 4

description:
D_rip1h
mRNA
processed data file: rip.matrix.tsv


title: 10x_121


title: 10x_125


title: ev1h rep 3

description:
C_ev1h
mRNA
processed data file: ev.matrix.tsv


title: CD31-CD45-EpCAM+CD133-  [71029]

description:
OVA
SAMPLE 17


title: 10x_124


title: rip1h rep 3

description:
C_rip1h
mRNA
processed data file: rip.matrix.tsv


title: ev1h rep 2

description:
B_ev1h
mRNA
processed data file: ev.matrix.tsv


title: rip1h rep 2

description:
B_rip1h
mRNA
processed data file: rip.matrix.tsv


title: CD31-CD45-EpCAM+CD133+  [71029]

description:
OVA
SAMPLE 16


title: CD31-CD45-EpCAM+CD133-  [70924]

description:
OVA
SAMPLE 14


title: CD31-CD45-EpCAM-CD49e+ [70924]

description:
CAF
SAMPLE 12


title: 10x_119


title: CD31-CD45-EpCAM+CD133-  [71377]

description:
OVA
SAMPLE 20


title: CD31-CD45-EpCAM+CD133+  [68584]

description:
OVA
SAMPLE 7


title: CD31-CD45-EpCAM-CD49e+ [67794]

description:
CAF
SAMPLE 4


title: CD31-CD45-EpCAM-CD49e+ [70535]

description:
CAF
SAMPLE 9


title: CD31-CD45-EpCAM+CD133+  [67794]

description:
OVA
SAMPLE 5


title: CD31-CD45-EpCAM+CD133-  [68584]

description:
OVA
SAMPLE 8


title: CD31-CD45-EpCAM+CD133+  [70535]

description:
OVA
SAMPLE 10


title: CD31-CD45-EpCAM+CD133-  [67794]

description:
OVA
SAMPLE 6


title: CD31-CD45-EpCAM+CD133+  [65846]

description:
OVA
SAMPLE 2


title: CD31-CD45-EpCAM+CD133+  [70924]

description:
OVA
SAMPLE 13


title: CD31-CD45-EpCAM+CD133-  [65846]

description:
OVA
SAMPLE 3


title: 10x_120


title: CD31-CD45-EpCAM-CD49e+ [71029]

description:
CAF
SAMPLE 15


title: CD31-CD45-EpCAM+CD133-  [70535]

description:
OVA
SAMPLE 11


title: rip1h rep 1

description:
A_rip1h
mRNA
processed data file: rip.matrix.tsv


title: glp-1 no RNAi input

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
SG0219_lib54
DNA extracted from fragmented chromatin
glp-1 no RNAi input

library_source: genomic

data_processing:
Pooled libraries were sequenced on an Illumina HiSeq 2500 platform (rapid run mode, 50-nt single-end run, and index sequencing). De-multiplexed raw data in fastq format were provided by the sequencing service facility
Fastq files of each library were aligned directly to C. elegans genome (WS190 version) using the Bowtie alignment program (version 1.2.2), only perfect alignments were reported and used.
Rpkm value for each 1kb is calculated by the number of reads that perfectly aligned to both strands of 1kb-non-overlaping regions, normalized by the sequencing depth of the library in million.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: .txt file containing rpkm values of all 1kb regions for 43 ChIP-seq Libraries: H3K23me1(3), H3K23me2 (3), H3K23me3 (20), H3K9me3 (16), H3K27me3 (1) and 9 input libraries. In WT for each antibody except H3K27me3 there is at least one replicate of three different feedings: OP50, oma-1 RNAi, and GFP RNAi. For H3K9me3 and H3K23me3 there is additional heritable RNAi for omai-1. In addition in H3K23me and H3K9me3 there are two replicates for the following strains: set-32(red11), LG III: hrde-1(tm1200), glp-1(e2141), and met-2(n4256) set-25 (ok5021).

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Young adult whole animal

growth_protocol: C. elegans strain N2 was used as the standard WT strain. Alleles used in this study were LG I: set-32(red11), LG III: hrde-1(tm1200), glp-1(e2141), set-25(n5021), set-32(ok1457), met-2(n4256) set-25 (ok5021). Worms were cultured on NGM plates with E. coli OP50  as the food source in a temperature controlled incubator at 20°C.  Synchronized worms were raised at 20°C and young adult worm samples were collected.

extract_protocol:
Synchronized young adult worms were first washed off the plates with M9 buffer.  E. coli OP50 bacteria washed off together with the worms were separated and removed by loading the worms to 10% sucrose cushion and centrifuging for 1 minute at 600g in a clinical centrifuge. Worms were then pulverized by grinding in liquid nitrogen with a pre-chilled mortar and pestle and were stored at −80°C.
Worm grinds from approximately 5000 worms were used for each chromatin immunoprecipitation experiment according to the procedure described in (Ni 2014). Anti-H3K9me3 (ab8898, Abcam) and anti-H3K23me3 (61500, Active Motif) antibodies were used for the H3K9me3 and H3K23me3 ChIP, respectively. Each ChIP experiments usually yielded 5–10 ng DNA. The entire ChIP DNA or 10 ng DNA in the case of ChIP input was used to make DNA library with the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instruction. For each sample in a given assay worm grinds were thawed and subsequently crosslinked and sonicated to produce fragments between 200-500bp according to protocol described in (Ni, 2016). Samples were then used for ChIP (H3K23me1,2,3, H3K9me3, H3K27me3) or stored for library prep as input DNA. IP was performed with the following antibodies: anti-H3K9me3 (ab8898, Abcam), anti-H3K23me1 (39388, Active Motif), anti-H3K23me2 (39654, Active Motif), anti-H3K23me3 (61500, Active Motif), and anti-H3K27me3 (39535, Active Motif). For each antibody ~0.5-1.5% of input DNA was pulled down, with DNA yields between ~5-25 ng. 5 ng or less of DNA was used for library preparation using KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instruction. PCR was performed on library DNA for 12-17 cycles after which all libraries were pooled according to Illumina HiSeq specifications. Sequencing was sent to Illumina and carried out according to the following specifications: 50-nt single-end run, dedicated index sequencing. Dedicated 6-mer indexes were used to demultiplex the libraries of different samples.

treatment_protocol: Worms were grown on NGM plates at 20°C with the following food sources: OP50 E. coli  (no RNAi), oma-1 E. coli (plasmid SG42), GFP E. coli (plasmid SG221), smg-1 E. coli (plasmid SG27). Worms were synchronized by bleaching, subsequent starvation and released at the L1 stage onto described plates. Each assay in this study used grinds of ~5000 worms for each condition. For RNAi experiments, worms were grown for three to four generations on RNAi culture before grinding. For heritable RNAi experiments we used the protocol described in (Gu, 2012) Briefly, worms were raised on oma-1 RNAi plates for three generations before synchronization and release onto OP50 E. coli plates without dsRNA feed. Worms were collected at P0, F1, F2, F3, F4 generations for grinding.

tag: genotype

tag: RNAi

value: no RNAi

tag: chip antibody

value: input


title: 10x_118


title: WT8h rep 4

description:
IV_WT8h
mRNA
processed data file: WT.matrix.tsv

tag: strain/background

tag: genotype/variation

value: wild type


title: 10x_117


title: glp-1 no RNAi H3K9me3 ChIP

description:
SG0616_lib32
DNA extracted from fragmented chromatin
glp-1 no RNAi H3K9me3 ChIP

value: H3K9me3, Abcam:ab8898


title: 10x_116


title: WT8h rep 2

description:
II_WT8h
mRNA
processed data file: WT.matrix.tsv


title: WT8h rep 3

description:
III_WT8h
mRNA
processed data file: WT.matrix.tsv


title: glp-1 no RNAi H3K23me3 ChIP

description:
SG0219_lib53
DNA extracted from fragmented chromatin
glp-1 no RNAi H3K23me3 ChIP

value: H3K23me3, Active Motif:61500


title: hrde-1 oma-1 RNAi H3K9me3 ChIP rep2

description:
SG0315_lib45
DNA extracted from fragmented chromatin
hrde-1 oma-1 RNAi H3K9me3 ChIP rep2

value: oma-1 RNAi


title: 10x_115

value: Malignant ascites  single cell


title: hrde-1 no RNAi input

description:
SG0315_lib61
DNA extracted from fragmented chromatin
hrde-1 no RNAi input


title: hrde-1 no RNAi H3K9me3 ChIP

description:
SG0315_lib53
DNA extracted from fragmented chromatin
hrde-1 no RNAi H3K9me3 ChIP


title: hrde-1 no RNAi H3K23me3 ChIP rep2

description:
SG1218_lib18
DNA extracted from fragmented chromatin
hrde-1 no RNAi H3K23me3 ChIP rep2


title: WT8h rep 1

description:
I_WT8h
mRNA
processed data file: WT.matrix.tsv


title: 10x_113


title: hrde-1 no RNAi H3K23me3 ChIP rep1

description:
SG0219_lib8
DNA extracted from fragmented chromatin
hrde-1 no RNAi H3K23me3 ChIP rep1


title: CD31-CD45-EpCAM-CD49e+ [65846]

description:
CAF
SAMPLE 1


description:
SG0219_lib22
DNA extracted from fragmented chromatin
met-2 set-25 oma-1 RNAi H3K23me3 ChIP rep1


title: 10x_112


title: met-2 set-25 no RNAi input

description:
SG0315_lib62
DNA extracted from fragmented chromatin
met-2 set-25 no RNAi input


description:
SG1218_lib4
DNA extracted from fragmented chromatin
met-2 set-25 oma-1 RNAi H3K23me3 ChIP rep2


title: met-2 set-25 no RNAi H3K9me3 ChIP rep2

description:
SG0315_lib54
DNA extracted from fragmented chromatin
met-2 set-25 no RNAi H3K9me3 ChIP rep2


title: 10x_111


title: pam8h rep 3

description:
III_pam8h
mRNA
processed data file: pam.matrix.tsv


title: pam8h rep 2

description:
II_pam8h
mRNA
processed data file: pam.matrix.tsv


title: met-2 set-25 no RNAi H3K23me3 ChIP

description:
SG0219_lib10
DNA extracted from fragmented chromatin
met-2 set-25 no RNAi H3K23me3 ChIP


title: pam8h rep 1

description:
I_pam8h
mRNA
processed data file: pam.matrix.tsv


title: met-2 set-25 no RNAi H3K9me3 ChIP rep1

description:
SG0315_lib44
DNA extracted from fragmented chromatin
met-2 set-25 no RNAi H3K9me3 ChIP rep1


title: set-32 oma-1 RNAi H3K9me3 ChIP

description:
SG0615_lib32
DNA extracted from fragmented chromatin
set-32 oma-1 RNAi H3K9me3 ChIP


title: WT4h rep 4

description:
IV_WT4h
mRNA
processed data file: WT.matrix.tsv


title: 10x_109


title: 10x_110


title: set-32 mutant no RNAi H3K9me3 ChIP

description:
SG0615_lib5
DNA extracted from fragmented chromatin
set-32 mutant no RNAi H3K9me3 ChIP


title: set-32 oma-1 RNAi H3K23me3 ChIP rep1

description:
SG0219_lib21
DNA extracted from fragmented chromatin
set-32 oma-1 RNAi H3K23me3 ChIP rep1


title: WT4h rep 3

description:
III_WT4h
mRNA
processed data file: WT.matrix.tsv


title: set-32 mutant no RNAi input

description:
SG0615_lib16
DNA extracted from fragmented chromatin
set-32 mutant no RNAi input


title: set-32 mutant no RNAi H3K23me3 ChIP

description:
SG0219_lib9
DNA extracted from fragmented chromatin
set-32 mutant no RNAi H3K23me3 ChIP


title: set-32 oma-1 RNAi H3K23me3 ChIP rep2

description:
SG1218_lib3
DNA extracted from fragmented chromatin
set-32 oma-1 RNAi H3K23me3 ChIP rep2


title: 10x_108


title: 10x_114


title: WT4h rep 2

description:
II_WT4h
mRNA
processed data file: WT.matrix.tsv


title: WT smg-1 RNAi H3K9me3 ChIP

description:
SG0219_lib24
DNA extracted from fragmented chromatin
WT smg-1 RNAi H3K9me3 ChIP

value: WT (N2)

value: smg-1 RNAi


title: WT smg-1 RNAi H3K23me3 ChIP

description:
SG0219_lib12
DNA extracted from fragmented chromatin
WT smg-1 RNAi H3K23me3 ChIP


title: WT oma-1 RNAi H3K9me3 ChIP-seq

description:
SG0315_lib43
DNA extracted from fragmented chromatin
WT oma-1 RNAi H3K9me3 ChIP-seq


title: WT4h rep 1

description:
I_WT4h
mRNA
processed data file: WT.matrix.tsv


title: 10x_106


title: WT oma-1 RNAi input

description:
SG0918_lib46
DNA extracted from fragmented chromatin
WT oma-1 RNAi input


title: hrde-1 oma-1 RNAi H3K9me3 ChIP rep1

description:
SG1218_lib2
DNA extracted from fragmented chromatin
hrde-1 oma-1 RNAi H3K9me3 ChIP rep1


title: WT oma-1 RNAi H3K23me3 ChIP-seq rep2

description:
SG1218_lib1
DNA extracted from fragmented chromatin
WT oma-1 RNAi H3K23me3 ChIP-seq rep2


title: pam4h rep 4

description:
IV_pam4h
mRNA
processed data file: pam.matrix.tsv


title: 10x_105


title: WT oma-1 RNAi H3K23me3 ChIP-seq rep1

description:
SG0918_lib43
DNA extracted from fragmented chromatin
WT oma-1 RNAi H3K23me3 ChIP-seq rep1


title: 10x_104


title: pam4h rep 3

description:
III_pam4h
mRNA
processed data file: pam.matrix.tsv


description:
SG1218_lib26
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F4 H3K9me3 ChIP, WT

value: oma-1 Heritable RNAi


title: 10x_103


title: WT oma-1 RNAi H3K23me1 ChIP-seq

description:
SG0918_lib37
DNA extracted from fragmented chromatin
WT oma-1 RNAi H3K23me1 ChIP-seq

value: H3K23me1,  Active Motif:39388


title: 10x_102


description:
SG1218_lib25
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F3 H3K9me3 ChIP, WT


title: 10x_101


description:
SG1218_lib24
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F2 H3K9me3 ChIP, WT


title: WT1h rep 4

description:
IV_WT1h
mRNA
processed data file: WT.matrix.tsv


description:
SG0219_lib5
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F4 H3K23me3 ChIP, WT


title: oma-1 feeding, F0, H3K9me3 ChIP, WT

description:
SG0219_lib6
DNA extracted from fragmented chromatin
oma-1 feeding, F0, H3K9me3 ChIP, WT


description:
SG0219_lib4
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F3 H3K23me3 ChIP, WT


title: WT1h rep 3

description:
III_WT1h
mRNA
processed data file: WT.matrix.tsv


description:
SG0219_lib3
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F2 H3K23me3 ChIP, WT


description:
SG0219_lib2
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F1 H3K23me3 ChIP, WT


title: WT1h rep 2

description:
II_WT1h
mRNA
processed data file: WT.matrix.tsv


title: 10x_100


title: 10x_99


title: WT oma-1 RNAi H3K23me2 ChIP-seq

description:
SG0918_lib40
DNA extracted from fragmented chromatin
WT oma-1 RNAi H3K23me2 ChIP-seq

value: H3K23me2,  Active Motif:39654


title: pam4h rep 2

description:
II_pam4h
mRNA
processed data file: pam.matrix.tsv


title: 10x_107


title: 10x_98


title: WT input rep3

description:
SG0918_lib45
DNA extracted from fragmented chromatin
WT input rep3


title: WT input rep2

description:
SG0315_lib60
DNA extracted from fragmented chromatin
WT input rep2


description:
SG1218_lib23
DNA extracted from fragmented chromatin
post oma-1 feeding, OP50 feeding, F1 H3K9me3 ChIP, WT


title: WT input rep1

description:
SG0219_lib13
DNA extracted from fragmented chromatin
WT input rep1


title: oma-1 feeding, F0, H3K23me3 ChIP, WT

description:
SG0219_lib1
DNA extracted from fragmented chromatin
oma-1 feeding, F0, H3K23me3 ChIP, WT


title: WT H3K9me3 ChIP-seq

description:
SG0315_lib52
DNA extracted from fragmented chromatin
WT H3K9me3 ChIP-seq


title: 10x_97


title: WT1h rep 1

description:
I_WT1h
mRNA
processed data file: WT.matrix.tsv


title: pam1h rep 3

description:
III_pam1h
mRNA
processed data file: pam.matrix.tsv


title: pam1h rep 4

description:
IV_pam1h
mRNA
processed data file: pam.matrix.tsv


title: pam4h rep 1

description:
I_pam4h
mRNA
processed data file: pam.matrix.tsv


title: WT H3K23me3 ChIP-seq

description:
SG0918_lib42
DNA extracted from fragmented chromatin
WT H3K23me3 ChIP-seq


title: WT H3K27me3 ChIP-seq

description:
SG0315_lib56
DNA extracted from fragmented chromatin
WT H3K27me3 ChIP-seq

value: H3K27me3,  Active Motif:39535


title: 10x_96


title: pam1h rep 2

description:
II_pam1h
mRNA
processed data file: pam.matrix.tsv


title: WT H3K23me2 ChIP-seq

description:
SG0918_lib39
DNA extracted from fragmented chromatin
WT H3K23me2 ChIP-seq


title: WT H3K23me1 ChIP-seq

description:
SG0918_lib36
DNA extracted from fragmented chromatin
WT H3K23me1 ChIP-seq


title: 10x_95


title: WT GFP RNAi input

description:
SG0918_lib47
DNA extracted from fragmented chromatin
WT GFP RNAi input

value: GFP RNAi


title: pam1h rep 1

description:
I_pam1h
mRNA
processed data file: pam.matrix.tsv


title: WT GFP RNAi H3K23me3 ChIP-seq

description:
SG0918_lib44
DNA extracted from fragmented chromatin
WT GFP RNAi H3K23me3 ChIP-seq


title: 10x_93


title: WT GFP RNAi H3K23me1 ChIP-seq

description:
SG0918_lib38
DNA extracted from fragmented chromatin
WT GFP RNAi H3K23me1 ChIP-seq


title: WT GFP RNAi H3K23me2 ChIP-seq

description:
SG0918_lib41
DNA extracted from fragmented chromatin
WT GFP RNAi H3K23me2 ChIP-seq


title: WT0h rep 4

description:
IV_WT0h
mRNA
processed data file: WT.matrix.tsv


title: 10x_92


title: WT0h rep 3

description:
III_WT0h
mRNA
processed data file: WT.matrix.tsv


title: 10x_91


title: WT0h rep 2

description:
II_WT0h
mRNA
processed data file: WT.matrix.tsv


title: WT0h rep 1

description:
I_WT0h
mRNA
processed data file: WT.matrix.tsv


title: pam0h rep 4

description:
IV_pam0h
mRNA
processed data file: pam.matrix.tsv


title: ApoE-KO_Scl-Ab_day113, rep9

city: South San Francisco

first: Yudong

last: He

state: CA

address: 1120 Veteran Blvd

institute: Amgen

data_processing:
RNA-seq data were aligned and summarized using OmicSoft’s Array Studio software (www.omicsoft.com/array-studio.php; Oshell.exe v10.0). Genes with critical issues on gene models were removed from statistical analysis. These issues included duplicated regions, high GC content, and overlapping transcripts. The RNA-seq dataset from each time point was analyzed separately. For each time point, genes with FPKQ ≥1 in ≥5 samples in the pairwise group comparison were selected for further statistical testing. Differential expression analysis was performed using DESeq2 v1.10.1 for group comparison. For a given comparison, raw read counts for genes were compared between the 2 conditions using DESeq2 following a negative binomial distribution, and gene expression fold changes were calculated using normalized counts. Genes with a Benjamini-Hochberg corrected P value <0.05 and fold change between the 2 conditions ≥2 or ≤0.5 were selected as significantly differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: The gene- and transcript-level expression of each RNA-Seq sample was reported by Oshell as an FPKM (Fragments per Kilobase per Million sequenced) value. FPKM is an expression measurement based on the count of library fragments that map to a given feature (gene or transcript) normalized for feature length and the number of fragments sequenced. These values were adjusted on a per-sample basis using 70th percentile normalization, yielding a final expression metric which we refer to as “FPKQ”.

growth_protocol: C57BL/6 female mice (ApoE KO and wild-type [WT]) were obtained from Jackson Laboratories (Bar Harbor, ME, USA). Animals were group-housed (up to 5 animals of the same dosing group together) in polycarbonate cages. Each animal was identified with a subcutaneous electronic identification chip implanted in the lumbar area.

extract_protocol:
RNA sequencing (RNA-seq) analyses were performed on mice tissues in the vehicle, Scl-Ab–treated WT, and ApoE KO-OVX groups. At scheduled necropsy, a region of the aortic arch matching the scan region for µCT was collected using polymerase chain reaction clean procedures. In addition, the innominate, left carotid, and left subclavian arteries were each sectioned at their junctions with the aortic arch. The lumen of the aorta was flushed with RNase-free saline and the adventitial fat gently scraped away using a sterile cotton swab. The aortic tissue was then washed briefly in RNase-free saline, placed in cryo-tubes, snap-frozen in liquid nitrogen, and stored at –80°C. Samples were subjected to dry pulverization before being homogenized in buffer (350 µL of Qiagen RLT buffer with 10% BME [Qiagen, Germantown, MD, USA]). The homogenate was transferred to an RNase-free 1.5 mL centrifuge tube, after which 95 µL RNase-free water and 5 µL of a 20 mg/mL Proteinase K solution were added. Samples were incubated at 55°C for 10 minutes, centrifuged, and the supernatant collected. RNA was then extracted using an RNeasy Micro Kit (Qiagen) with on-column DNase treatment (Qiagen) according to the manufacturer’s instructions. RNA concentration and integrity were assessed using a Bioanalyzer (Agilent, Santa Clara, CA, USA). Samples with ≥80 ng total RNA that had RNA integrity numbers ≥7 were used for sequencing.
Library preparation and RNA-seq was performed by Q2 Solutions (Morrisville, NC). Sequencing libraries were created using the IlluminaTruSeq Stranded mRNA method.

treatment_protocol: Mice were provided a high-fat diet (TD.88137 adjusted-calories diet, 42% from fat [Envigo RMS, Indianapolis, IN, USA]), starting at 5–6 weeks old. Mice were ovariectomized at 7–8 weeks old. At 9–10 weeks old, ApoE KO and WT-OVX mice weighing between 16.6 and 29.9 g were randomized into 2 treatment groups (n=144/group), and each received either vehicle (10 mM sodium acetate, 9.0% sucrose, 0.004% polysorbate 20, pH 5) or Scl-Ab (r13C7 10 mg/kg, an engineered form of romosozumab with frameworks and constant regions, including the Fc region, substituted from the rat to reduce immunogenicity in rodents [Amgen Inc., Thousand Oaks, CA, USA]), subcutaneously once weekly for 3, 8, or 16 weeks. The Scl-Ab dose of 10 mg/kg was predicted to provide a 4-fold multiple of clinical exposure to romosozumab 210 mg once monthly, based on AUC. At termination, they were anesthetized under isoflurane before undergoing a whole-body cardiac perfusion at each time point.

tag: strain

tag: age

value: 25-26 weeks

value: ApoE-KO

tag: treatment

value: Scl-Ab

value: Aortic arch


title: ApoE-KO_Scl-Ab_day113, rep8

tag: Sex

value: Female

tag: time


title: ApoE-KO_Scl-Ab_day113, rep10


title: ApoE-KO_Scl-Ab_day113, rep7


title: ApoE-KO_Scl-Ab_day113, rep4


title: ApoE-KO_Scl-Ab_day113, rep2


title: ApoE-KO_Scl-Ab_day113, rep1


title: ApoE-KO_Scl-Ab_day113, rep6


title: 10x_90


title: 10x_88


title: pam0h rep 2

description:
II_pam0h
mRNA
processed data file: pam.matrix.tsv


title: ApoE-KO_Scl-Ab_day113, rep5


title: 10x_89


title: ApoE-KO_Scl-Ab_day113, rep3


title: WT_Scl-Ab_day113, rep8

value: WT


title: WT GFP RNAi H3K9me3 ChIP-seq

description:
SG0315_lib40
DNA extracted from fragmented chromatin
WT GFP RNAi H3K9me3 ChIP-seq

value: H3K9me3, Abcam:ab8898


title: pam0h rep 1

description:
I_pam0h
mRNA
processed data file: pam.matrix.tsv


title: 10x_87


title: 10x_86


title: WT_Scl-Ab_day113, rep7


title: WT_Scl-Ab_day113, rep6


title: WT_Scl-Ab_day113, rep5


title: WT_Scl-Ab_day113, rep4


title: 10x_85


title: pam0h rep 3

description:
III_pam0h
mRNA
processed data file: pam.matrix.tsv


title: K56R_double_5

city: Worcester

first: Caitlin

middle: F

last: Connelly

state: MA

address: 364 Plantation Street, LRB

department: Biochemistry & Molecular Pharmacology

institute: University of Massachusetts Medical School

data_processing:
Reads were aligned using tophat version 2.0.12, using bowtie2 version 2-2.1.0
For 3' end RNA-seq samples, reads were counted at each transcript (using annotations from Xu Z, Steinmetz LM 2009 to count reads in the 3' UTR) using featureCounts, filtering chimeric reads, multimapping reads, and reads with read quality < Q30.
genome build: SacCer3
processed data files format and content: featureCounts output- contains the following columns: Geneid, Chr, Start, End, Strand, Length, and counts at that feature

source_name: Saccharomyces cerevisiae log phase cells

growth_protocol: Yeast were grown in YEPD to mid-log phase

extract_protocol:
RNA Extraction was done using TRIzol (Thermo Fisher Scientific), followed by ethanol precipitation.  RNA samples were Dnase I treated using the Rneasy Kit (Qiagen).
3' end RNA-seq was performed as follows. Briefly, 0.5 μg total RNA was used for each library.  Reverse transcription was performed using SmartScribe Reverse Transcriptase (Clontech).  First, RNA was incubated with 1 μl oligo dT primer (containing sequence for the PCR primer to prime off of, followed by a barcode then by poly dT sequence) for 3 minutes at 72 degrees.  Reverse transcription was done using 2 μl 5x buffer, 0.7 μl dNTP mix, 1 μl 20 mM DTT, 0.3 μl 100mM MgCl2, and 1 μl SmartScribe RT enzyme, incubating at 42 degrees for 1 hour, followed by 70 degrees for 15 minutes.  Samples were pooled and cleaned up using AmpureXP beads (Agencourt). After this step, the equivalent of 1 sample of cDNA resulting from 0.5 μg of total RNA was used for the following steps (i.e. if we pooled 10 samples together, we then used 1/10 of the resulting cDNA for the remaining steps). We then performed tagmentation using Nextera DNA kit (Illumina) at 55 degrees for 8 minutes using 0.5 μl Tagment DNA enzyme.  We then added 5 μl 0.2% SDS to stop the tagmentation reaction.  2x bead cleanup was done using AmpureXP beads (Agencourt).  PCR with one primer specific to the tagmentation- applied adapter and one primer specific to the poly-dT primer was done using HiFi KAPA polymerase for 12 cycles, followed by cleanup using 0.8X AMPure beads.

tag: sequencing batch


title: WT_Scl-Ab_day113, rep3


title: WT_Scl-Ab_day113, rep2


title: K56R_double_4


title: 10x_84

tag: cell type


title: WT_Scl-Ab_day113, rep1


title: 10x_83

tag: patient id


title: ApoE-KO_Vehicle_day113, rep10

value: Vehicle


title: K56R_double_3


title: ApoE-KO_Vehicle_day113, rep9


title: ApoE-KO_Vehicle_day113, rep8


title: ApoE-KO_Vehicle_day113, rep7


title: 10x_82

tag: time point


title: 10x_81


title: K56R_H3Y_4


title: K56R_H3Y_5


title: ApoE-KO_Vehicle_day113, rep6

tag: tissue


title: K56R_H3Y_3


title: ApoE-KO_Vehicle_day113, rep5


title: ApoE-KO_Vehicle_day113, rep3


title: ApoE-KO_Vehicle_day113, rep4


title: K56R_H3X_5


title: ApoE-KO_Vehicle_day113, rep2


title: 10x_79


title: K56R_H3X_4


title: WT_Vehicle_day113, rep10


title: WT_Vehicle_day113, rep9


title: K56R_H3X_3


title: 10x_78


title: WT_Vehicle_day113, rep8


title: 10x_77


title: 10x_94


title: 10x_76


title: WT_Vehicle_day113, rep6


title: pseudo_wt_19


title: WT_Vehicle_day113, rep7


title: WT_Vehicle_day113, rep3


title: WT_Vehicle_day113, rep5


title: 10x_74


title: K18R_double_5


title: pseudo_wt_18


title: 10x_80


title: K18R_double_4


title: WT_Vehicle_day113, rep1


title: WT_Vehicle_day113, rep2


title: ApoE-KO_Scl-Ab_day57, rep10

value: 17–18 weeks


title: 10x_73

value: Malignant ascites  single cell


title: ApoE-KO_Vehicle_day113, rep1


title: K18R_double_3


title: ApoE-KO_Scl-Ab_day57, rep8


title: 10x_72


title: ApoE-KO_Scl-Ab_day57, rep9


title: ApoE-KO_Scl-Ab_day57, rep7


title: ApoE-KO_Scl-Ab_day57, rep5


title: K18R_H3Y_4


title: ApoE-KO_Scl-Ab_day57, rep6


title: ApoE-KO_Scl-Ab_day57, rep4


title: K18R_H3Y_5


title: 10x_75


title: 10x_70


title: K18R_H3Y_3


title: 10x_71


title: 10x_69


title: WT_Vehicle_day113, rep4


title: ApoE-KO_Scl-Ab_day57, rep3


title: 10x_68


title: K18R_H3X_5


title: ApoE-KO_Scl-Ab_day57, rep2


title: K18R_H3X_4


title: 10x_67


title: WT_Scl-Ab_day57, rep8


title: K18R_H3X_3


title: WT_Scl-Ab_day57, rep6


title: 10x_66


title: WT_Scl-Ab_day57, rep5


title: WT_Scl-Ab_day57, rep7


title: pam8h rep 4

description:
IV_pam8h
mRNA
processed data file: pam.matrix.tsv


title: WT_Scl-Ab_day57, rep3


title: 10x_65


title: WT_Scl-Ab_day57, rep1


title: WT_Scl-Ab_day57, rep2


title: K14R_double_5


title: ApoE-KO_Scl-Ab_day57, rep1


title: pseudo_wt_17


title: pseudo_wt_16


title: 10x_62


title: 10x_63


title: K14R_double_4


title: ApoE-KO_Vehicle_day57, rep7


title: ApoE-KO_Vehicle_day57, rep6


title: WT_Scl-Ab_day57, rep9


title: K14R_double_3


title: ApoE-KO_Vehicle_day57, rep8


title: 10x_61


title: ApoE-KO_Vehicle_day57, rep4


title: WT_Scl-Ab_day57, rep4


title: 10x_60


title: K14R_H3Y_5


title: ApoE-KO_Vehicle_day57, rep3


title: ApoE-KO_Vehicle_day57, rep2


title: K14R_H3Y_4


title: ApoE-KO_Vehicle_day57, rep1


title: 10x_64


title: 10x_59


title: ApoE-KO_Vehicle_day57, rep10


title: ApoE-KO_Vehicle_day57, rep9


title: K14R_H3Y_3


title: WT_Vehicle_day57, rep5


title: 10x_58


title: K14R_H3X_5


title: ApoE-KO_Vehicle_day57, rep5


title: 10x_57


title: 10x_56


title: WT_Vehicle_day57, rep1


title: WT_Vehicle_day57, rep3


title: K14R_H3X_4


title: WT_Vehicle_day57, rep2


title: ApoE-KO_Scl-Ab_day22, rep9

value: 12–13 weeks


title: 10x_55


title: K14R_H3X_3


title: ApoE-KO_Scl-Ab_day22, rep7


title: ApoE-KO_Scl-Ab_day22, rep6


title: 10x_54


title: pseudo_wt_14


title: ApoE-KO_Scl-Ab_day22, rep4


title: ApoE-KO_Scl-Ab_day22, rep5


title: ApoE-KO_Scl-Ab_day22, rep3


title: 10x_53


title: ApoE-KO_Scl-Ab_day22, rep2


title: WT_Vehicle_day57, rep4


title: 10x_52


title: K37Q_double_5


title: ApoE-KO_Scl-Ab_day22, rep1


title: WT_Scl-Ab_day22, rep5


title: 10x_51


title: WT_Scl-Ab_day22, rep6


title: WT_Scl-Ab_day22, rep4


title: K37Q_double_4


title: ApoE-KO_Scl-Ab_day22, rep8


title: K37Q_double_3


title: 10x_49


title: 10x_50


title: K37Q_H3Y_4


title: K37Q_H3Y_5


title: ApoE-KO_Vehicle_day22, rep8


title: pseudo_wt_15


title: ApoE-KO_Vehicle_day22, rep7


title: 10x_47


title: ApoE-KO_Vehicle_day22, rep4


title: ApoE-KO_Vehicle_day22, rep3


title: 10x_46


title: ApoE-KO_Vehicle_day22, rep5


title: K37Q_H3X_5


title: ApoE-KO_Vehicle_day22, rep2


title: K37Q_H3X_4


title: 10x_45


title: K37Q_H3X_3


title: ApoE-KO_Vehicle_day22, rep1


title: WT_Scl-Ab_day22, rep3


title: WT_Vehicle_day22, rep7


title: WT_Scl-Ab_day22, rep1


title: WT_Vehicle_day22, rep8


title: WT_Scl-Ab_day22, rep2


title: 10x_48


title: WT_Vehicle_day22, rep6


title: 10x_44


title: pseudo_wt_13


title: 10x_43


title: 10x_42


title: pseudo_wt_12


title: ApoE-KO_Vehicle_day22, rep6


title: K37Q_H3Y_3


title: WT_Vehicle_day22, rep5


title: WT_Vehicle_day22, rep3


title: K36Q_double_5


title: WT_Vehicle_day22, rep4


title: WT_Vehicle_day22, rep2


title: 10x_41


title: Sf3b1WT-3

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
Raw data were aligned to hg19/mm10 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples, mm10 for mouse
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR
Supplementary_files_format_and_content: column 1:  chromosome
Supplementary_files_format_and_content: column 2:  first base of the intron (1-based)
Supplementary_files_format_and_content: column 3:  last base of the intron (1-based)
Supplementary_files_format_and_content: column 4:  strand (0:  undefined, 1:  +, 2:  -)
Supplementary_files_format_and_content: column 5:  intron  motif:  0:  non-canonical;  1:  GT/AG,  2:  CT/AC,  3:  GC/AG,  4:  CT/GC,  5: AT/AC, 6:  GT/AT
Supplementary_files_format_and_content: column 6:  0:  unannotated, 1:  annotated (only if splice junctions database is used)
Supplementary_files_format_and_content: column 7:  number of uniquely mapping reads crossing the junction
Supplementary_files_format_and_content: column 8:  number of multi-mapping reads crossing the junction
Supplementary_files_format_and_content: column 9:  maximum spliced alignment overhang

source_name: Splenic B-cell

extract_protocol:
Splenic B cells (B220+CD3-Gr1-Mac1-Ter119- cells) were FACS-sorted from recipient mice of bone marrow cells (that were harvested from primary mice with indicated genotypes) and RNA was extracted by using Qiagen Rneasy mini kit.
Poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300-bp DNA fragments were isolated and sequenced on an Illumina HiSeq 2000 (~100M 101 bp reads per sample).

value: wild type


title: WT_Vehicle_day22, rep1


title: K36Q_double_4


title: Sf3b1WT-2


title: Sf3b1WT-1


title: K36Q_double_3


title: 10x_39


title: Sf3b1K700E-3


title: 10x_38


title: Sf3b1K700E-2


title: K36Q_H3Y_5


title: EuMyc_Sf3b1WT-3

value: Myc transgene


title: K36Q_H3Y_4


title: EuMyc_Sf3b1WT-2


title: EuMyc_Sf3b1WT-1


title: K36Q_H3X_5


title: K36Q_H3Y_3


title: EuMyc_Sf3b1K700E-2

value: Sf3b1K700E+Myc transgene


title: EuMyc_Sf3b1K700E-1


title: EuMyc_Sf3b1K700E-3


title: Sf3b1K700E-1


title: K36Q_H3X_4


title: 10x_34


title: 10x_35


title: 10x_33


title: 10x_40


title: K36Q_H3X_3


title: pseudo_wt_11


title: 10x_37


title: 10x_32


title: 10x_36


title: pseudo_wt_10


title: 10x_31


title: 10x_30


title: R2K_double_5


title: R2K_double_4


title: 10x_29


title: R2K_double_3


title: 10x_28


title: R2K_H3Y_5


title: R2K_H3Y_4


title: R2K_H3Y_3


title: R2K_H3X_5


title: R2K_H3X_4


title: 10x_26


title: 10x_27


title: 10x_25


title: 10x_24


title: 10x_23


title: R2K_H3X_3


title: 10x_22


title: pseudo_wt_9


title: 10x_21


title: pseudo_wt_8


title: 201516250010_R05C01_Nonsmoker

type: genomic

city: Research Triangle Park

first: Dana

last: Hancock

state: NC

address: 3040 East Cornwallis Road

institute: RTI International

description: postmortem nucleus accumbens from a nonsmoker

hyb_protocol: DNA was profiled with the Infinium MethylationEPIC BeadChip array using the manufacturer's protocol.

scan_protocol: The Illumina MethylationEPIC array hybridization and scanning were performed at the Lieber Institute for Brain Development.

data_processing: Raw data resulted from GenomeStudio software (Illumina)

label: Cy5, Cy3

source_name: nucleus accumbens

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from dissected postmortem nucleus accumbens tissue using the Qiagen AllPrep DNA/RNA Mini Kit (Cat No./ID: 80204).

tag: current smoking status

value: Nonsmoker

tag: age at death

tag: sex (m, male; f, female)

value: M

tag: ancestry (cauc, caucasian; aa, african american)

value: CAUC


title: 201516250032_R08C01_Nonsmoker

value: F

value: AA


title: 201516250032_R05C01_Nonsmoker


title: 201516240019_R08C01_Nonsmoker


title: 201516250030_R02C01_Nonsmoker


title: 201516250012_R07C01_Nonsmoker


title: 201516280017_R08C01_Nonsmoker


title: K4A_H3Y_1

data_processing:
Reads were aligned using tophat version 2.0.12, using bowtie2 version 2-2.1.0
For strand-specific RNA-Seq samples, reads at each CDS were counted using featureCounts, filtering multimapping reads, duplicate reads, reads with read quality <q30, chimeric reads, and reads not mapping to the coding strand.
genome build: SacCer3
processed data files format and content: featureCounts output- contains the following columns: Geneid, Chr, Start, End, Strand, Length, and counts at that feature

extract_protocol:
RNA Extraction was done using TRIzol (Thermo Fisher Scientific), followed by ethanol precipitation.  RNA samples were Dnase I treated using the Rneasy Kit (Qiagen).
Strand-specific RNA-seq was performed as described in Levin JZ et al. (2010). Briefly, polyA RNA was isolated using Oligo(dT)25 magnetic beads (NEB). We used 200 ng of poly(A)+ RNA for each library. Zinc-ion fragmentation was done using RNA fragmentation reagent (Ambion) for 2 minutes at 70 degrees. We synthesized first-strand cDNA by adding 4 μl 5× first-strand buffer, 2 μl 100 mM DTT, 1 μl 10 mM dNTPs, 4 μg of actinomycin D, 200 U SuperScript III and 1 μl RNase-OUT (all reagents from Invitrogen), incubating at room temperature for 10 min followed by 1 h at 55 °C. We cleaned up first-strand cDNA using RNAClean XP beads (Agencourt) to remove dNTPs and resuspended in 104 μl H2O. We synthesized second-strand cDNA by adding 4 μl of 5× first-strand buffer, 2 μl of 100 mM DTT, 4 μl of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 μl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16 °C for 2 h (remaining reagents from Invitrogen). End repair, A-tailing, and adapter ligation were done using Epicentre reagents, using 50ng of ligated adapters. We then incubated 1 U USER (NEB) with adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. We performed PCR with Phusion High-Fidelity DNA polymerase. We removed PCR primers using 1.8 volumes of AMPure beads.


title: 201516250032_R02C01_Nonsmoker


title: 10x_20


title: 10x_19


title: 201516240040_R05C01_Nonsmoker


title: 201516260008_R02C01_Nonsmoker


title: 201516240031_R01C01_Nonsmoker


title: 201516280040_R02C01_Nonsmoker


title: 201516260019_R06C01_Nonsmoker


title: 201516250012_R08C01_Nonsmoker


title: 201516260028_R06C01_Nonsmoker


title: 201516260008_R08C01_Nonsmoker


title: K4A_H3X_1


title: 201516240031_R04C01_Nonsmoker


title: 201516260028_R04C01_Nonsmoker


title: 201516250042_R02C01_Nonsmoker


title: 201516240041_R01C01_Nonsmoker


title: K56Q_H3Y_1


title: 201516240018_R07C01_Nonsmoker


title: 201516280022_R08C01_Nonsmoker


title: 10x_17


title: K56Q_H3X_1


title: 201516240018_R04C01_Nonsmoker


title: 10x_16


title: 10x_15


title: 201516250012_R01C01_Nonsmoker


title: 10x_14


title: K4Q_H3Y_1


title: delta4-20_H3Y_1

value: Mata; delta(hht-hhf1); delta(hht2-hhf2); leu2-3,112; ura3-62; trp1; his3+ "127A" =  wt-1a (hht2- L127A, L131V; HHT2; TRP1, CEN)+ pPK642 = delta4-20-1B (hht2- delta4-20, L110I, A111W, L131I)-HHF2, LEU2, CEN)


title: 201516240040_R08C01_Nonsmoker


title: 201516250050_R01C01_Nonsmoker


title: 201516250030_R03C01_Nonsmoker


title: 10x_13


title: K4Q_H3X_1


title: delta4-20_H3X_1

value: Mata; delta(hht-hhf1); delta(hht2-hhf2); leu2-3,112; ura3-62; trp1; his3+ pPK638 =  delta4-20-1a (hht2- delta4-20, L127A, L131V; HHT2; TRP1, CEN)+ P44 = wt-1B (hht2- L110I, A111W, L131I)-HHF2, LEU2, CEN)


title: 10x_12


title: 10x_11


title: T45A_H3Y_1


title: 10x_10


title: 201516240009_R04C01_Nonsmoker


title: K36R_H3Y_1


title: T45A_H3X_1


title: 10x_9


title: K36R_H3X_1


title: 10x_18


title: 10x_8


title: 201516240034_R04C01_Nonsmoker


title: K4R_H3Y_1


title: 10x_7


title: K4R_H3X_1


title: 10x_6


title: 201516280005_R05C01_Nonsmoker


title: K79A_H3Y_2


title: 201516240034_R02C01_Nonsmoker


title: 201516240054_R04C01_Nonsmoker


title: 201516280017_R01C01_Nonsmoker


title: 201516240019_R03C01_Nonsmoker


title: K79A_H3X_2


title: 201516260028_R02C01_Nonsmoker


title: 201516240042_R03C01_Nonsmoker


title: 10x_5


title: 201516260008_R04C01_Nonsmoker


title: 201516280060_R04C01_Nonsmoker


title: 201516280040_R01C01_Nonsmoker


title: 201516250045_R03C01_Nonsmoker


title: K79A_H3Y_1


title: 201516240018_R06C01_Nonsmoker


title: 201516240018_R02C01_Nonsmoker


title: K79A_H3X_1


title: 10x_3


title: 201516250012_R03C01_Nonsmoker


title: 201516250032_R01C01_Nonsmoker


title: 201516250029_R07C01_Nonsmoker


title: 10x_4


title: pseudo_wt_batch_8_2


title: 201516280022_R03C01_Nonsmoker


title: 201516240034_R01C01_Nonsmoker


title: 201516250045_R07C01_Nonsmoker


title: 201516250050_R08C01_Nonsmoker


title: PD1_plus_CD28_plus_4

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Reads were aligned on a human reference sequence (hg19) using Bowtie2
Number of mapped reads on each gene was calculated using Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: csv file that includes raw count data of the eight samples

source_name: Lung tumor

extract_protocol:
Tumors were dissociated by Gentle MACS and RNA was harvested using Trizol reagent. QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)  was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung tumor

tag: histology

value: Adenocarcinoma


title: 201516280047_R07C01_Nonsmoker


title: pseudo_wt_batch_4


title: 201516250050_R06C01_Nonsmoker


title: PD1_plus_CD28_minus_4


title: 201516250010_R03C01_Nonsmoker


title: 10x_1


title: 201516240031_R08C01_Nonsmoker


title: pseudo_wt_batch_3


title: 201516240054_R08C01_Nonsmoker


title: PD1_plus_CD28_plus_3


title: 201516250029_R06C01_Nonsmoker


title: pseudo_wt_batch_8_1


title: pseudo_wt_batch_2


title: PD1_plus_CD28_minus_3


title: 201516280022_R06C01_Nonsmoker


title: K56R_double_2


title: 201516260030_R03C01_Nonsmoker


title: 10x_2


title: PD1_plus_CD28_plus_2


title: K56R_H3Y_2


title: PD1_plus_CD28_minus_2


title: 201516250032_R03C01_Nonsmoker


title: PD1_plus_CD28_plus_1


title: K56R_H3X_2


title: K56R_double_1


title: PD1_plus_CD28_minus_1


title: 201516260055_R06C01_Nonsmoker


title: K56R_H3Y_1


title: 201516260008_R03C01_Nonsmoker


title: K56R_H3X_1


title: LM sample 10

city: Heidelberg

first: Thomas

last: Schmidt

state: Baden-Württemberg

address: Im Neuenheimer Feld 110

department: Department of General, Visceral and Transplantation Surgery

country: Germany

institute: University Hospital Heidelberg

data_processing:
Transcript level quantification was performed by using the Salmon Transcription Quantification package (version 0.9.1) on Galaxy server with default parameters.
Homo sapiens geonome assembly GRCh38 (hg38) was used as the reference genome.
Gene level quantification was performed by using R/Bioconductor package "tximport" with EnsDb.Hsapiens.v86 annotation package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values at gene level (Ensembl Gene ID)

source_name: Tumor Tissue

extract_protocol:
Tumor tissues were removed, flash frozen on dry ice, and RNA was harvested using the mini RNA extraction kit (Qiagen, Germany; 74106). Sequencing was performed by the GeneCore at the EMBL (Heidelberg, Germany) on an Illumina HiSeq 2000 platform using the Truseq stranded mRNA kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver metastase


title: 201516260030_R04C01_Nonsmoker


title: LM sample 9


title: 201516260019_R07C01_Nonsmoker


title: 201516240007_R01C01_Nonsmoker


title: 201516250030_R08C01_Nonsmoker


title: 201516250032_R06C01_Nonsmoker


title: 201516260019_R03C01_Nonsmoker


title: 201516260029_R08C01_Nonsmoker


title: LM sample 8


title: K37Q_H3Y_2


title: LM sample 7


title: K37Q_double_2


title: 201516250045_R02C01_Nonsmoker


title: 201516240040_R03C01_Nonsmoker


title: LM sample 6


title: 201516280005_R08C01_Nonsmoker


title: K37Q_double_1


title: 201516250010_R01C01_Nonsmoker


title: 201516240007_R06C01_Nonsmoker


title: 201516240041_R08C01_Nonsmoker


title: 201516280017_R06C01_Nonsmoker


title: K37Q_H3X_2


title: LM sample 5


title: 201516240034_R03C01_Nonsmoker


title: 201516280060_R07C01_Nonsmoker


title: 201516280047_R01C01_Nonsmoker


title: LM sample 3


title: K37Q_H3X_1


title: 201516240042_R05C01_Nonsmoker


title: 201516240054_R03C01_Nonsmoker


title: K36Q_double_2


title: 201516260028_R03C01_Nonsmoker


title: 201516260028_R05C01_Nonsmoker


title: 201516280005_R07C01_Nonsmoker


title: LM sample 2


title: 201516260055_R03C01_Nonsmoker


title: LM sample 1


title: 201516260029_R02C01_Nonsmoker


title: LM sample 4


title: K36Q_double_1


title: 201516260030_R05C01_Nonsmoker


title: 201516260008_R05C01_Nonsmoker


title: PTU sample 12

value: colorectal primary tumor


title: PTU sample 11


title: K36Q_H3X_2


title: PTU sample 10


title: 201516250042_R08C01_Nonsmoker


title: K36Q_H3X_1


title: 201516260030_R07C01_Nonsmoker


title: PTU sample 9


title: K36Q_H3Y_1


title: K37Q_H3Y_1


title: K36Q_H3Y_2


title: K27Q_double_2


title: 201516240019_R06C01_Nonsmoker


title: 201516240042_R01C01_Nonsmoker


title: 201516250042_R06C01_Nonsmoker


title: 201516250030_R05C01_Nonsmoker


title: 201516240019_R02C01_Nonsmoker


title: PTU sample 7


title: K27Q_H3Y_2


title: 201516260030_R08C01_Nonsmoker


title: 201516250042_R03C01_Nonsmoker


title: 201516240019_R01C01_Nonsmoker


title: 201516240009_R07C01_Nonsmoker


title: 201516240034_R07C01_Nonsmoker


title: K27Q_double_1


title: PTU sample 8


title: PTU sample 6


title: K27Q_H3Y_1


title: K27Q_H3X_2


title: PTU sample 4


title: K27Q_H3X_1


title: 201516250030_R04C01_Nonsmoker


title: PTU sample 3


title: 201516260055_R04C01_Nonsmoker


title: 201516260019_R08C01_Nonsmoker


title: 201516240009_R03C01_Nonsmoker


title: K27R_double_2


title: 201516280040_R04C01_Nonsmoker


title: 201516240018_R03C01_Nonsmoker


title: PTU sample 5


title: PTU sample 2


title: 201516240042_R02C01_Nonsmoker


title: 201516240040_R07C01_Nonsmoker


title: K27R_H3Y_2


title: 201516240041_R07C01_Nonsmoker


title: PTU sample 1


title: K27R_double_1


title: 201516260028_R01C01_Nonsmoker


title: MAFs sample 6

data_processing:
Transcript level quantification was performed by using the Salmon Transcription Quantification package (version 0.9.1) on Galaxy server with default parameters.
Homo sapiens geonome assembly GRCh38 (hg38) was used as the reference genome.
Gene level quantification was performed by using R/Bioconductor package "tximport" with EnsDb.Hsapiens.v86 annotation package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count values at gene level (HGNC Symbol)

source_name: Primary Cells

value: primary fibroblasts


title: K27R_H3X_2


title: MAFs sample 5


title: K27R_H3Y_1


title: MAFs sample 4


title: 201516250050_R05C01_Nonsmoker


title: 201516250030_R01C01_Nonsmoker


title: K27R_H3X_1


title: 201516260008_R07C01_Nonsmoker


title: 201516240009_R02C01_Nonsmoker


title: 201516240009_R08C01_Nonsmoker


title: MAFs sample 3


title: K18Q_double_2


title: K18Q_H3Y_2


title: 201516260019_R04C01_Nonsmoker


title: MAFs sample 1


title: K18Q_H3X_2


title: MAFs sample 2


title: 201516280047_R04C01_Nonsmoker


title: 201516240007_R07C01_Nonsmoker


title: 201516240031_R07C01_Nonsmoker


title: CAFs sample 6


title: 201516240019_R05C01_Nonsmoker


title: K18Q_double_1


title: 201516250012_R05C01_Nonsmoker


title: CAFs sample 5


title: K18Q_H3Y_1


title: 201516250050_R02C01_Nonsmoker


title: 201516250010_R04C01_Nonsmoker


title: 201516240042_R07C01_Nonsmoker


title: 201516240018_R01C01_Nonsmoker


title: 201516280022_R07C01_Nonsmoker


title: 201516250029_R05C01_Nonsmoker


title: CAFs sample 4


title: 201516280017_R05C01_Nonsmoker


title: 201516250029_R08C01_Nonsmoker


title: K18R_double_2


title: 201516280060_R06C01_Nonsmoker


title: CAFs sample 3


title: K18Q_H3X_1


title: K18R_H3Y_2


title: CAFs sample 2


title: CAFs sample 1


title: K18R_H3X_2


title: 201516240042_R04C01_Nonsmoker


title: 201516280047_R02C01_Nonsmoker


title: 201516240054_R01C01_Nonsmoker


title: 201516250012_R02C01_Nonsmoker


title: CD34_donor39_D14_F

city: Philadelphia

first: Gerd

middle: A

last: Blobel

state: PA

address: 3615 Civic Center Blvd, ARC 316

department: Division of Hematology

institute: Children's Hospital of Philadelphia

description:
CD34 erythroid day 14, donor 39, F-cell
2038

data_processing:
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Gene set Gencode v29 was used for mapping the reads to the human genome (hg38 assembly) using STAR
RSEM was used for gene quantification
Genome_build: hg38
Supplementary_files_format_and_content: tsv file

source_name: CD34 erythroid cultures

extract_protocol:
RNA from sorted cells was purified using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher) following the supplied protocol, except crosslink reversal was done at 50oC for 45 minutes. Following RNA elution, a second DNAse treatment step was done using the DNA-free DNA Removal Kit (ThermoFisher).
Approximately 100 ng of treated RNA was then depleted for rRNA and globins using the Ribo-Zero removal reagents and protocol from the ScriptSeq Complete kit (Illumina Cat # BHMR1224), followed by purification using the RNeasy MinElute Clean Up kit (Qiagen Cat # 74202). Sequencing libraries were then constructed from depleted RNA using the TruSeq Stranded Total RNA kit (Illumina Cat # 20020598) and PCR-amplified for 13 cycles. The size and quality of each library were then evaluated by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and quantified using qPCR. Libraries were sequenced in paired-end mode on the NextSeq 500 to generate 2 x 76 bp reads using Illumina-supplied kits as appropriate.

tag: cell line

value: CD34 erythroid

tag: differentiation day

value: day 14

tag: hbf expression

value: HbF high


title: CD34_donor39_D14_A

description:
CD34 erythroid day 14, donor 39, A-cell
2037

value: HbF low


title: 201516240042_R08C01_Nonsmoker


title: K18R_double_1

tag: strain


title: 201516240040_R01C01_Nonsmoker


title: CD34_donor21_D14_F

description:
CD34 erythroid day 14, donor 21, F-cell
2036

tag: treatment


title: 201516240009_R05C01_Nonsmoker


title: 201516260030_R01C01_Nonsmoker


title: 201516250029_R04C01_Nonsmoker


title: 201516280060_R01C01_Nonsmoker


title: CD34_donor21_D14_A

description:
CD34 erythroid day 14, donor 21, A-cell
2035


title: 201516250050_R04C01_Nonsmoker


title: K18R_H3X_1


title: 201516250042_R05C01_Nonsmoker


title: 201516280022_R04C01_Nonsmoker


title: K14Q_H3Y_2


title: CD34_donor39_D11_A

description:
CD34 erythroid day 11, donor 39, A-cell
2033

value: day 11


title: K14Q_H3X_2


title: 201516240007_R03C01_Nonsmoker

value: Nonsmoker


title: CD34_donor21_D11_F

description:
CD34 erythroid day 11, donor 21, F-cell
2032


title: 201516260055_R07C01_Nonsmoker


title: K18R_H3Y_1


title: 201516240031_R05C01_Nonsmoker

value: M


title: K14Q_double_1


title: 201516280005_R01C01_Nonsmoker


title: 201516260028_R08C01_Nonsmoker


title: K14Q_H3Y_1


title: 201516260029_R04C01_Nonsmoker

value: CAUC


title: CD34_donor39_D8_F

description:
CD34 erythroid day 8, donor 39, F-cell
2030

value: day 8


title: 201516240031_R06C01_Nonsmoker


title: 201516250029_R02C01_Nonsmoker


title: 201516240031_R03C01_Nonsmoker

value: F


title: K14Q_double_2


title: CD34_donor39_D11_F

description:
CD34 erythroid day 11, donor 39, F-cell
2034


title: K14Q_H3X_1


title: CD34_donor21_D11_A

description:
CD34 erythroid day 11, donor 21, A-cell
2031


title: CD34_donor39_D8_A

description:
CD34 erythroid day 8, donor 39, A-cell
2029


title: 201516260029_R07C01_Nonsmoker


title: K14R_double_2


title: CD34_donor21_D8_F

description:
CD34 erythroid day 8, donor 21, F-cell
2028


title: K14R_H3Y_2


title: CD34_donor21_D8_A

description:
CD34 erythroid day 8, donor 21, A-cell
2027


title: K14R_H3X_2


title: CD34_donor2_d11_POM_F

description:
CD34 erythroid day 11, donor 2, pomalidomide, F-cell
2281

value: Pomalidomide


title: 201516280047_R03C01_Nonsmoker

value: AA


title: 201516280005_R06C01_Nonsmoker


title: K14R_double_1


title: 201516250010_R02C01_Nonsmoker


title: CD34_donor2_d11_POM_A

description:
CD34 erythroid day 11, donor 2, pomalidomide, A-cell
2280


title: K14R_H3Y_1


title: 201516280047_R08C01_Nonsmoker


title: 201516280017_R02C01_Nonsmoker


title: 201516260019_R01C01_Nonsmoker


title: CD34_donor2_d11_HU_F

description:
CD34 erythroid day 11, donor 2, hydroxyurea, F-cell
2279

value: Hydroxyurea


title: 201516250012_R06C01_Nonsmoker


title: 201516250012_R04C01_Nonsmoker


title: CD34_donor2_d11_HU_A

description:
CD34 erythroid day 11, donor 2, hydroxyurea, A-cell
2278


title: S10A_double_2


title: CD34_donor2_d11_CTRL_F

description:
CD34 erythroid day 11, donor 2, control, F-cell
2277

value: Control


title: S10A_H3Y_2


title: K14R_H3X_1


title: 201516250010_R08C01_Smoker

description: postmortem nucleus accumbens from a smoker

value: Smoker


title: CD34_donor2_d11_CTRL_A

description:
CD34 erythroid day 11, donor 2, control, A-cell
2276


title: 201516240040_R04C01_Nonsmoker

description: postmortem nucleus accumbens from a nonsmoker


title: 201516240019_R07C01_Smoker


title: S10A_H3X_2


title: 201516280017_R07C01_Nonsmoker


title: 201516240054_R05C01_Nonsmoker


title: CD34_donor1_d11_POM_F

description:
CD34 erythroid day 11, donor 1, pomalidomide, F-cell
2235


title: 201516240041_R06C01_Smoker


title: 201516240007_R02C01_Nonsmoker


title: 201516240034_R08C01_Smoker


title: 201516240054_R02C01_Nonsmoker


title: CD34_donor1_d11_POM_A

description:
CD34 erythroid day 11, donor 1, pomalidomide, A-cell
2234


title: 201516260029_R06C01_Smoker


title: 201516250010_R07C01_Smoker


title: S10A_double_1


title: 201516240031_R02C01_Nonsmoker


title: 201516240054_R07C01_Smoker


title: S10A_H3Y_1


title: CD34_donor1_d11_HU_F

description:
CD34 erythroid day 11, donor 1, hydroxyurea, F-cell
2233


title: S10A_H3X_1


title: K9Q_double_1


title: CD34_donor1_d11_HU_A

description:
CD34 erythroid day 11, donor 1, hydroxyurea, A-cell
2232


title: 201516280005_R02C01_Smoker


title: 201516260055_R01C01_Smoker


title: 201516240041_R04C01_Smoker


title: K9Q_H3Y_1


title: 201516250032_R04C01_Smoker


title: CD34_donor1_d11_CTRL_A

description:
CD34 erythroid day 11, donor 1, control, A-cell
2230


title: K9Q_H3X_1


title: H2C_64_F

description:
HUDEP2 cas9, clone 6-4, F-cell
1898

source_name: HUDEP2C Cells

value: day 7


title: CD34_donor1_d11_CTRL_F

description:
CD34 erythroid day 11, donor 1, control, F-cell
2231


title: 201516240040_R02C01_Smoker


title: 201516240018_R08C01_Smoker


title: 201516240018_R05C01_Smoker


title: H2C_64_A

description:
HUDEP2 cas9, clone 6-4, A-cell
1897


title: 201516250050_R03C01_Smoker


title: 201516250032_R07C01_Nonsmoker


title: 201516280060_R08C01_Nonsmoker


title: 201516250029_R01C01_Nonsmoker


title: 201516280047_R06C01_Smoker


title: K9R_H3X_2


title: H2C_63_F

description:
HUDEP2 cas9, clone 6-3, F-cell
1896


title: K9R_double_2


title: K9R_H3Y_2


title: K9R_double_1


title: H2C_63_A

description:
HUDEP2 cas9, clone 6-3, A-cell
1895


title: H2C_62_F

description:
HUDEP2 cas9, clone 6-2, F-cell
1894


title: 201516240054_R06C01_Smoker


title: 201516280040_R05C01_Smoker


title: 201516240009_R06C01_Smoker


title: H2C_62_A

description:
HUDEP2 cas9, clone 6-2, A-cell
1893


title: K9R_H3Y_1


title: K9R_H3X_1


title: NF2 (Non-painful)_set2_N3

city: Boston

first: Gary

last: Brenner

address: 15 Parkman Street

department: Anesthesia Critical Care and Pain Medicine

institute: Massachusetts General Hospital

data_processing:
Illumina Bcl2fastq v2.17 was used to demultiplex raw bcl files and generate fastq files
Transcriptome mapping was performed with SALMON (PMID:28263959) using the Ensembl annotation of hg19 reference genome
Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: hg19
Supplementary_files_format_and_content: TPM, NumReads

source_name: Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue block from human NF2 patient

extract_protocol:
Prior to the RNA extraction from Formalin-fixed, Paraffin-embedded (FFPE) tumor tissue slides (5-10µm sections), pathology revision was performed on a H&E stained tumor sections to confirm the tumor presence, histology, and grade of differentiation. Next, FFPE sections were de-paraffinized and re-hydrated in sequential steps and subjected to Cresyl violet (0.5% w/v) guided macro-dissection using RNAase free scalpel. This method was utilized to ensure at least 80% tumor cell content within the samples subjected to nucleic acid extraction. During RNA extraction, Cresyl violet stain was utilized as it minimizes the chemical modification of nucleic acids compared to H&E staining. FFPE RNA extraction was performed was using miRNeasy FFPE kit (Cat No. 217504, QIAGEN, USA) and DNase digestion was performed using RNase-Free DNase Set (Cat No. 79254 QIAGEN, USA) following manufacturer’s instructions.
Libraries were prepared using Roche Kapa Biosystems RiboErase and RNA HyperPrep sample preparation kits from 300ng of RNA. Prior to library prep, purified total RNA samples were evaluated for quality by Agilent Bioanalyzer to calculate RIN score and DV200. RNA samples with a RIN score >7 as well as RNA samples with a RIN <7 but DV200 >50% were fragmented at 94°C for 8min per manufacturer’s instructions. RNA samples with RIN <7 and DV200 < 50% were not fragmented and RT primers were annealed at 65°C for 1min. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Roche Kapa Biosystems library quantification kit following manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: Neurofibromatosis II (NF2) tumor sample

tag: site of tumor extracted (location)

value: Extra cranial

tag: sample id in rnaseq analysis

tag: patient tumor related pain status

value: Non-Painful


title: R2K_double_2

tag: sequencing batch


title: 201516240007_R08C01_Smoker


title: 201516280047_R05C01_Smoker


title: 201516250042_R01C01_Smoker


title: 201516240040_R06C01_Smoker


title: 201516260008_R06C01_Smoker


title: 201516280022_R05C01_Smoker


title: 201516280060_R05C01_Smoker


title: 201516260030_R06C01_Smoker


title: NF2 (Non-painful)_set2_N1

value: Paraspinal


title: 201516250030_R07C01_Smoker


title: R2K_H3X_2


title: 201516240041_R05C01_Smoker


title: R2K_double_1


title: NF2  (painful)_set2_Y4

value: Spinal

value: Painful


title: 201516240042_R06C01_Smoker


title: NF2 (Non-painful)_set2_N2

value: Brachial Plexus


title: R2K_H3Y_2


title: 201516240009_R01C01_Smoker

value: M


title: R6_HEK293_151_input_control

city: New York

first: James

last: Gregory

address: 101 Ave of the Americas

institute: New York Genome Center

description: HEK293 monoculture

data_processing:
basecalls were performed using bcl2fastq
fastqs were trimeed with trimGalore
fastqs were aligned to an hg38/mm20/GFP/mCherry combined reference using STAR (v2.5.2)
reads were counted with Samtools or FeatureCounts
Genome_build: mm20/hg38
Supplementary_files_format_and_content: Gene count files were generated using featureCounts

growth_protocol: standard cell culture

extract_protocol:
RNA from standard extracts or immunoprecipitation with the indicated antibody
SMART-seq cDNA prep followed by Nextera DNA Flex

tag: target ip cell type

tag: ip antibody

tag: ip order


title: 201516280060_R03C01_Smoker

tag: current smoking status

value: CAUC


title: NF2  (painful)_set2_Y3

tag: tissue

value: Groin


title: 201516240019_R04C01_Smoker

tag: age at death

tag: sex (m, male; f, female)

value: F


title: 201516250042_R07C01_Smoker

tag: ancestry (cauc, caucasian; aa, african american)


title: DOS-8

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
DNA methylation
canine_MethValues_allSamples_crossSpecies.txt

data_processing:
Illumina specific adapter sequences and low quality sequences were removed from raw sequencing data using Trimmomatic50. Reads were aligned to a bisulfite converted human (hg19) or canine (canfam3.1) genome using WALT51. Duplicate sequences were removed from alignment data using MethPipe52 duplicate-remover and bisulfite conversion rates were estimated for each sample using bsrate. All samples had conversion efficiencies > 99%. Sequencing depths for each sample were such that an average of 88.3% and 81.3% of targeted CpGs were sequenced at a 10X depth or higher. MethPipe methcounts was used to calculate methylation levels and read coverage at individual CpGs in each sample. A custom perl script was used to isolate CpGs with a read depth of 10 or greater and MethPipe roimethstats was used to summarize methylation levels in 500 bp windows, generated by BEDtools53 windowBed, along the capture targets in each genome.  CpG methylation levels were expressed as a value between 0 and 1.
USCS utility liftOver with the appropriate genome wide alignment file was used to convert the canine genomic coordinates for each 500bp window from CanFam3.1 to hg19. and the human genomic coordinates for each 500bp window to GRCh38. Converting both sets of coordinates to GRCh38 resulted in the highest number of 500bp windows being conserved between the two species. Genomic regions were considered homologs if the converted GRCh38 coordinates were within 1,000bp of each other as calculated by BEDtools closest.
Genome_build: hg19, canfam3.1

organism: Canis lupus familiaris

source_name: primary osteosarcoma

extract_protocol: Tumor tissues were removed from -86℃ and sectioned to avoid areas of necrosis. Thirty mg of tissue were placed in 80 µL of phosphate buffered saline (PBS) solution and pulverized in a tissue homogenizer. Isolation of genomic DNA was done according to the manufacturer’s protocol using the QIAamp DNA Mini Kit from Qiagen.Illumina library preparation, bisulfited converted and bead capture was performed as specified in the Roch SeqCap Epi protocol outlined in Li et al (doi: 10.1093/nar/gkv244)

value: osteosarcoma


title: 201516280017_R04C01_Smoker

value: AA


title: NF2  (painful)_set2_Y2


title: DOS-75


title: DOS-85


title: R2K_H3X_1


title: DOS-71


title: NF2  (painful)_set2_Y1

value: Skin-left thigh


title: R2K_H3Y_1


title: DOS-68


title: Mtx_Input_H3K27me3_rep2

city: Beijing

first: Qiu

last: Xie

state: Beijing

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

country: China

institute: Peking Union Medical College Hospital

data_processing:
Raw data were trimmed using TrimGalore version 0.6.0.
RNA-seq reads were aligned to the mm10 genome assembly using Tophat2 version 2.1.1. ChIP-seq for histone modifications and ATAC-seq reads were aligned to the mm10 genome assembly using STAR version 2.7.0d. ChIP-seq for CTCF were aligned to the mm10 genome assembly using Bowtie2
Gene expression was calculated using Cufflinks version 2.2.1 and differentially expressed genes were called using Cuffdiff version 2.2.1.
Peaks were called using MACS version 1.4.2 with the following setting: -p 1-6, --keep-dup auto, -w -S, --space 50, --nolambda, --nomodel.
Genome_build: mm10
Supplementary_files_format_and_content: peaks.bed were generated using MACS version 1.4.2 with the following setting: -p 1-6, --keep-dup auto, -w -S, --space 50, --nolambda, --nomodel.

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells Sv/129 (mESCs) were kindly provided by Xuanwu Hospital (Beijing, China). The cells were cultured as previously described 15. Briefly, mESCs were maintained on mitotically inactivated primary mouse embryonic fibroblasts prior to cultivation under feeder-free conditions. The cells were kept at 37°C in a humidified atmosphere with 5% CO2, and passaged every 2–3 days. A split ratio of 1:4 to 1:7 was performed.

extract_protocol:
For RNA isolation, total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s recommendations. reverse transcription was carried out using the TransScript First-Strand cDNA Synthesis SuperMix (TransGen Biotech, Beijing, China). For ChIP, In accordance with the manufacturer’s protocol, a SimpleChIP™ Enzymatic Chromatin IP Kit (CST) was used for the ChIP assays. Briefly, formaldehyde cross-linked chromatin was obtained from about 2×107 mESCs. Cross-linked chromatin was immunoprecipitated with antibodies to H3K4me1, H3K4me3, H3K27me3, H3K27ac, H3K9me3, gamma-phosphorylated H2AX and CTCF. Non-specific mouse IgG and H3 were used for negative and positive controls, respectively.
For RNA-seq, briefly, total RNA was treated with the Epicentre Ribo-Zero kit to remove the all the rRNAs. The remaining RNAs were processed using the TruSeq RNA Sample Prep Kit according to the Illumina protocol. Then, RT-PCR was performed with Phusion High-Fidelity DNA polymerase, Index (X) Primer, and Universal PCR primers. Finally, the products were purified using the AMPure XP system, and library quality was evaluated on an Agilent Bioanalyzer 2100 system. The RNA library was sequenced on an Illumina Hiseq 4000 platform, and 150 bp paired-end reads were generated. For ChIP-seq, DNA libraries of H3K4me1,H3K27ac, H3K4me3, H3K27me3, H3K9me3, phospho S139 gamma H2A.X and CTCF were prepared for HiSeq 4000 sequencing as previously before.

treatment_protocol: 0.12 μM Methotrexate (MTX, Sigma) were treated at 24 h against mESCs as MTX treatment. Other drugs refer to Etoposide (Sigma) was at 5 μM, NU7026 (Calbiochem) was at 5mM.

tag: cell type

value: MTX-treated mESC

tag: chip antibody


title: DOS-67