title: Mouse1_GFPPeritoneumMet_S33_clean

data_processing:
library strategy: GTO sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Map reads to mm9 genome using STAR aligner
Separate aligned reads into exonic and allnonexonic
Realign exonic reads to reference genome mm9 using Kallisto and obtain read count tables
Realign allnonexonic reads to refenrence genome mm9 using Bowtie 1.0, remove PCR duplicate reads and process for CNV analysis
Genome_build: mm9
Supplementary_files_format_and_content: read count tables for RNAseq section of data, Varbin files with bincounts for DNAseq section

source_name: Mouse1_Peritoneum Metastasis

extract_protocol:
Primary tumors were dissociated using collagenase D and trypsin. They were treated with ACK lysis buffer to remove contaminating red blood cells. These dissociated cells were stained with EpCam, CD45 antibodies. Single cells were isolated by flow cytometry for GFP+, EpCAM+, GFP+EpCAM+ and CD45+ from primary tumors. GFP+ cells were isolated from various metastases
Single cells isolated into 10x Lysis Buffer with Rnase inhibitor. Next they were processed for mRNA transcription for first strand synthesis using Oligo-dT primer and cDNA generated is amplified for 15 cycles following SMART-Seq2 PCR primers. Samples were then treated ionically to fragment gDNA and cDNA to 400-700bp fragments. Later gDNA was amplified using SeqXE kit from Sigma Aldirch using manufacturer instructions. resulting cDNA and gDNA fragments are quantified.  Following this, libraries for sequencing were prepared by subjecting the 1ug of gDNA and cDNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

tag: Sex

value: male

value: Metastasis

value: Peritoneum

value: Tumor

value: GFP, Calcien Violet for Live/Dead

tag: molecule type

value: genomic DNA and mRNA


title: Mouse1_GFPPeritoneumMet_S31_clean

status: Public on Mar 30 2020

type: SRA

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: KPC1199-EGFP cells were thawed and passaged in DMEM supplemented with 10% Fetal Bovine Serum, 1% Pencillin/streptomycin

treatment_protocol: 50000 KPC1199-EGFP cells in matrigel were injected orthotopically into the pancreas of 6-8 week old C57BL/6 male mice. Tumors were allowed to grow for 6-8 weeks before tumors were extracted.

tag: strain

tag: tumor type

tag: tissue

tag: cell type

tag: marker


title: LSC-Intermediate CD34_P22

status: Public on Apr 04 2019

type: RNA

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

country: Switzerland

institute: Bern University Hospital

description:
Gene expression data
Well-defined cell populations were FACS-purified from BM of newly diagnosed AML patients and also control subjects.

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label: biotin

organism: Homo sapiens

source_name: LSC-Intermediate

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol: Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

tag: gender

value: M


title: LSC-Intermediate CD34_P23

value: F


title: LSC-Intermediate CD34_P18


title: LSC-Adverse CD34_P19

source_name: LSC-Adverse


title: LSC-Adverse CD34_P2


title: LSC-Intermediate CD34_P20


title: LSC-Intermediate CD34_P21


title: LSC-Favorable CD34_P16

source_name: LSC-Favorable


title: LSC-Favorable CD34_P17


title: LSC-Adverse CD34_P1


title: LSC-Favorable CD34_P14


title: LSC-Favorable CD34_P12


title: HSC-Ctrl CD34_C9

source_name: HSC-Ctrl


title: HSC-Ctrl CD34_C8


title: LSC-Favorable CD34_P15


title: LSC-Adverse CD34_P10


title: LSC-Favorable CD34_P13


title: HSC-Ctrl CD34_C7


title: ctrl-3

status: Public on Mar 27 2019

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

molecule: polyA RNA

source_name: In-vitro

growth_protocol: Male or female, 8-12 week old NOD.Cg-PrkdcscidIl2rgtmWjl/SzJ (NSG) mice were injected intravenously with 0.5e6 FFLuc-GFP NALM6 NALM6 leukaemia cell line. Four days later, 0.2e6, CAR T cells were administered i.v. by tail vein injection. NALM6 cells were stored in Trizol (LS) before RNA extraction. For in vitro and ex-vivo experiments, cells were cultured in RMPI/10%FBS.

extract_protocol:
RNA were extracted using Trizol standard protocol
After ribogreen quantification and quality control on bioAnalyser, 500ng of total RNA underwent library preparation using the Truseq Stranded Total RNA library preparation chemistry (Illumina), with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 51 million paired reads were generated per sample and the percent of mRNA bases was 58% on average.

treatment_protocol: Mice bearing NALM6 leukaemia cell line line were treated with 2e5 19BBζ CAR T cells

tag: cell line


title: ctrl-2


title: M6-D6

source_name: ex-vivo

tag: mice strain

value: NOD.Cg-PrkdcscidIl2rgtmWjl/SzJ (NSG)


title: M7-D6


title: ctrl-1


title: M5-D6


title: M3-D6


title: M4-D6


title: M7-D0

source_name: Relapse

tag: treatment

value: 19-BB[zeta] CAR T cells


title: M6-D0


title: M1-D6


title: M2-D6


title: M5-D0


title: HSC-Ctrl CD34_C11


title: M4-D0


title: BT549-DNA-3

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-3_S9

library_source: genomic

data_processing:
library strategy: bulk DNA sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: hg19
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

molecule: genomic DNA

source_name: BT549 Triple negative breast cancer cell line

growth_protocol: Cells were cultured in respective media at 37C, 5% CO2

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen DNeasy blood and tissue kit.
2ug of DNA was fragmented to 400bp using Covaris sonicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

treatment_protocol: No treatment

tag: cell line source

value: Breast

value: Adherent cell line

tag: labelling for flow

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: HSC-Ctrl CD34_C6


title: HSC-Ctrl CD34_C4


title: HSC-Ctrl CD34_C10


title: M3-D0


title: M2-D0


title: Mouse1_GFPPeritoneumMet_S27_clean


title: M1-D0


title: 48H pSRSF1 C

status: Public on Mar 20 2019

city: Boca Raton

first: Massimo

last: Caputi

state: Florida

address: 777 Glades Road

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
Reads quality control was carried out utilizing FastQC
Reads were aligned to the GRCh38 assembly of the human genome utilizing the HiSat2 tool running in a Galaxy environment
Aligned reads were assembled into transcripts utilizing the ENSMBL reference human transcript assembly and counted utilizing the CuffDiff2 tool running in a Galaxy environment
The following comparisons were carried out: 15H pSP6 vs 15H pSRSF1, 15H pSP6 vs 15H pRRM12, 48H pSP6 vs 48H pSRSF1, 48H pSP6 vs 48H pRRM12. Gene differentially expressed were prioritized on the base of their Log2 change in expression and the p value associated with the expression fold change.
Splicing analysis was carried out utilizing the Callisto pseudo-aligner and the IsoformSwitchAnalyzeR tool.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample and log2 value for each comparison. R data frame files contain quantification of alternative isoform switching events.

source_name: HEK293_48H pSRSF1

extract_protocol:
Total RNA was extracted either 15 hrs or 48 hrs post-transfection for each of the three biological replica. The total RNA was DNased and depleted of ribosomal RNA.
cDNA libraries were generated utilizing the TrueSeq RNA library prep kit (Illumina).
Libraries were sequenced utilizing a Illumina Illumina HiSeq 2500 sequencer at a depth of  40 million paired ends reads with 80 nt read length.

treatment_protocol: Transfection protocol: HEK293 cells were transfected utilizing Lipofectamine2000 (Invitrogene) following standard protocols and one of three expression vectors. The SRSF1 expression vector (p-CMV-SRSF1-Sport6), Sthe RSF1 RRM1 and 2 expression vector (p-CMV-RRM12-Sport6) or the control vector (p-CMV-Sport6)

tag: genotype/variation

value: Transient transfection p-CMV-SRSF1-Sport6 48Hrs


title: 48H pRRM12 C

source_name: HEK293_48H pRRM12

value: Transient transfection p-CMV-RRM12-Sport6 48Hrs


title: 48H pSP6 C

source_name: HEK293_48H pSP6

value: Transient transfection p-CMV-Sport6 48Hrs


title: 48H pRRM12 B


title: 48H pSRSF1 B


title: 48H pSP6 B


title: 48H pRRM12 A


title: 48H pSRSF1 A


title: 48H pSP6 A


title: 15H pSRSF1 C

source_name: HEK293_15H pSRSF1

value: Transient transfection p-CMV-SRSF1-Sport6 15 Hrs


title: 15H pRRM12 C

source_name: HEK293_15H pRRM12

value: Transient transfection p-CMV-RRM12-Sport6 15 Hrs


title: 15H pSRSF1 B


title: 15H pSP6 B

source_name: HEK293_15H pSP6

value: Transient transfection p-CMV-Sport6 15 Hrs


title: 15H pRRM12 B


title: 15H pSRSF1 A


title: 15H pSP6 C


title: 15H pSP6 A


title: BIV15_S3

status: Public on Feb 25 2019

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore=0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore=0.4.5
Post-trimming QC with FastQC
Splice-aware alignment with star=2.6.0c. The genome utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Merging of BAM files and index generation with samtools=1.6
Count generation with bioconductor-rsubread=1.26.1 (R version: r-base=3.4.1). The GTF file utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/rn6-GTF/Rattus_norvegicus.Rnor_6.0.90.gtf
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with differentially expressed genes in Lacz vs Bdnf-I and Lacz vs Bdnf-IV sgRNA comparisons (in separate spreadsheets). Genes are in rows, and columns contain the Ensembl ID, basemean, log2foldchange value, and other gene information (chromosome, location, etc).

organism: Rattus norvegicus

source_name: Hippocampal neuron culture

growth_protocol: Neurons were removed from hippocampal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at the UAB Helfin Genomics Core. RNA libraries were quantified and underwent sequencing (~25M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Neurons were treated as described with CRISPR sgRNAs and dCas9-VPR fusion lentiviruses on DIV 4. Media was removed and RNA was extracted on DIV 11.

value: Sprague-Dawley

value: Hippocampal neuron culture

tag: age

value: Embryonic day 18, 11 DIV

value: Bdnf-IV sgRNA


title: 15H pRRM12 A


title: BIV14_S2


title: BIV11_S1


title: B18_S14

value: Bdnf-I sgRNA


title: B17_S13


title: B16_S12


title: LZ5_S11

value: Lacz sgRNA


title: LZ2_S9


title: LZ4_S10


title: TEFF-VI

status: Public on Dec 17 2018

source_name: TEFF

growth_protocol: T cell purification and genomic editing: TN (TCR+CD62L+CCR7+CD45RA+CD95-), TSCM (TCR+CD62L+CCR7+CD45RA+CD95+) and TEFF (TCR+CD62L-CCR7-CD45RA+CD95+) were sorted by flow cytometry. The CAR cDNA was targeted to the TRAC locus of sorted naïve T cells, followed by in vitro culture and TCR-negative purification.

extract_protocol:
T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to instructions provided by the manufacturer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 30.6 million paired reads was generated per sample. At the most, ribosomal reads represented 4.69% of the total reads generated. The percent of mRNA bases averaged 69.3%.

treatment_protocol: 7 days after CAR cDNA targeting was performed, CAR T cells were stimulated with 3T3-CD19 for 24 hours, followed by magnetic selection of CD8+ T cells (Miltenyi).

value: CD8 T cells

tag: cell subset

value: CD8 T cell subset TEFF


title: TEFF-V


title: TEFF-IV


title: TEFF-III


title: TSCM-III

source_name: TSCM

value: CD8 T cell subset TSCM


title: TSCM-VI


title: TSCM-IV


title: TSCM-II


title: TSCM-V


title: TEFF-II


title: TN-V

source_name: TN

value: CD8 T cell subset TN


title: TN-IV


title: TN-III


title: TEFF-I


title: TN-VI


title: TN-II


title: TN-I


title: TSCM-I


title: TRAC-1XX-III

tag: genotype

value: CD8 T cells expressing TRAC-1XX


title: TRAC-XX3-III

value: CD8 T cells expressing TRAC-XX3


title: TRAC-1XX-II


title: TRAC-XX3-II


title: TRAC-XX3-I


title: TRAC-1928z-III

value: CD8 T cells expressing TRAC-1928z


title: TRAC-1928z-II


title: NK Combo 4

status: Public on Dec 01 2018

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (29), aligned to the human genome using STAR (30), and quantified transcript counts using HTSeq (31). Raw read counts were normalized to FPKM value for analysis.
Genome_build: Reads were aligned to the transcriptome (hg19, GRCh37.75)
Supplementary_files_format_and_content: Tab-delimited text file includes normalized FPKM value for each sample

source_name: NK cells from lung tumors

growth_protocol: For in vitro studies, cells were maintained in DMEM or RPMI supplemented with 10%  FBS and 100 IU/ml penicillin/streptomycin. For in vivo studies, female C57BL/6 mice were transplanted with KP lung tumor cells by tail vein injection. Treatment began one week post-transplantation following confirmation of lung tumor engraftment by bioluminescent imaging.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: For in vitro studies, cells were treated for 8 days with vehicle (DMSO), trametinib (25 nM), palbociclib (500nM), or both in combination. Drug media was changed every 3 days. For in vivo studies, mice were treated for 1 week with vehicle or combined trametinib (1 mg/kg body weight) or palbociclib (100 mg/kg body weight).

value: CD45+CD3-NK1.1+ NK cell

value: Combination


title: TRAC-1928z-I


title: NK Combo 3


title: NK Combo 2


title: NK Combo 1


title: NK Vehicle 5

value: Vehicle


title: NK Vehicle 3


title: NK Vehicle 4


title: NK Vehicle 2


title: NK Vehicle 1


title: Mia Palbo 1

description:
PDAC_FPKM.txt
S71_S71_L001_R1_001

source_name: Pancreatic cancer cell line

growth_protocol: Cells were maintained in DMEM or RPMI supplemented with 10%  FBS and 100 IU/ml penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a fpkm matrix of transcript counts.

treatment_protocol: Cells were treated for 8 days with vehicle (DMSO), trametinib (25 nM), palbociclib (500nM), or both in combination. Drug media was changed every 3 days.

value: Palbociclib


title: Mia Combo 1

description:
PDAC_FPKM.txt
S69_S69_L001_R1_001


title: Mia Tramet 2

description:
PDAC_FPKM.txt
S68_S68_L001_R1_001

value: Trametinib


title: Mia Tramet 1

description:
PDAC_FPKM.txt
S67_S67_L001_R1_001


title: Mia Palbo 2

description:
PDAC_FPKM.txt
S72_S72_L001_R1_001


title: Mia Combo 2

description:
PDAC_FPKM.txt
S70_S70_L001_R1_001


title: Mia Vehicle 2

description:
PDAC_FPKM.txt
S66_S66_L001_R1_001


title: Mia Vehicle 1

description:
PDAC_FPKM.txt
S65_S65_L001_R1_001


title: PANC-1 Combo 2

description:
PDAC_FPKM.txt
S64_S64_L001_R1_001


title: PANC-1 Combo 1

description:
PDAC_FPKM.txt
S63_S63_L001_R1_001


title: PANC-1 Palbo 1

description:
PDAC_FPKM.txt
S61_S61_L001_R1_001


title: PANC-1 Palbo 2

description:
PDAC_FPKM.txt
S62_S62_L001_R1_001


title: TRAC-1XX-I


title: PANC-1 Vehicle 2

description:
PDAC_FPKM.txt
S58_S58_L001_R1_001


title: PANC-1 Tramet 1

description:
PDAC_FPKM.txt
S59_S59_L001_R1_001


title: PANC-1 Tramet 2

description:
PDAC_FPKM.txt
S60_S60_L001_R1_001


title: PANC-1 Vehicle 1

description:
PDAC_FPKM.txt
S57_S57_L001_R1_001


title: 8988T Combo 2

description:
PDAC_FPKM.txt
S56_S56_L001_R1_001


title: 8988T Palbo 2

description:
PDAC_FPKM.txt
S54_S54_L001_R1_001


title: 8988T Palbo 1

description:
PDAC_FPKM.txt
S53_S53_L001_R1_001


title: 8998T Tramet 1

description:
PDAC_FPKM.txt
S51_S51_L001_R1_001


title: 8988T Vehicle 1

description:
PDAC_FPKM.txt
S49_S49_L001_R1_001


title: H460 Combo 2

description:
NSCLC_FPKM.txt
A24_S120_L002_R1_001

source_name: Lung cell line


title: H460 Palbo 2

description:
NSCLC_FPKM.txt
A23_S119_L002_R1_001


title: H460 Combo 1

description:
NSCLC_FPKM.txt
A20_S116_L002_R1_001


title: H460 Vehicle 2

description:
NSCLC_FPKM.txt
A21_S117_L002_R1_001


title: MP2

status: Public on Dec 31 2021

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: Myc;p53-/- ovarian EPO-GEMM tumor

growth_protocol: 8-12 week old WT C57BL/6 female mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left ovary and oviduct were exteriorized. 25 μl of a plasmid mix (see table below) was injected into the ovary using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two poring pulses of electrical current (50V) given for 30 ms lengths at 450 ms intervals and five transfer pulses (60V, 50 ms length, 450 ms intervals) were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole tumor tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: ovarian tumor

value: Myc;p53-/- EPO-GEMM

value: non-treated


title: H460 Palbo 1

description:
NSCLC_FPKM.txt
A19_S115_L002_R1_001


title: H460 Tramet 1

description:
NSCLC_FPKM.txt
A18_S114_L002_R1_001


title: H2030 Palbo 2

description:
NSCLC_FPKM.txt
A15_S111_L002_R1_001


title: H2030 Tramet 2

description:
NSCLC_FPKM.txt
A14_S110_L002_R1_001


title: H460 Vehicle 1

description:
NSCLC_FPKM.txt
A17_S113_L002_R1_001


title: H2030 Combo 1

description:
NSCLC_FPKM.txt
A12_S108_L002_R1_001


title: H2030 Palbo 1

description:
NSCLC_FPKM.txt
A11_S107_L002_R1_001


title: H2030 Tramet 1

description:
NSCLC_FPKM.txt
A10_S106_L002_R1_001


title: A549 Combo 2

description:
NSCLC_FPKM.txt
A08_S104_L002_R1_001


title: H2030 Vehicle 1

description:
NSCLC_FPKM.txt
A09_S105_L002_R1_001


title: A549 Tramet 2

description:
NSCLC_FPKM.txt
A06_S102_L002_R1_001


title: A549 Combo 1

description:
NSCLC_FPKM.txt
A04_S100_L002_R1_001


title: A549 Vehicle 1

description:
NSCLC_FPKM.txt
A01_S97_L002_R1_001


title: Myc_WT_#4

status: Public on Oct 23 2018

description: A09_S105 Myc_WT_#4

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.0a)
Genome wide transcript counting was performed by featureCounts (v1.6.0) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.22.1) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: p53 WT hepatocytes transduced with MYC transposons

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

treatment_protocol: Hepatocytes transduced with MYC transposons delivered by hydrodynamic tail vein injection and isolated 6 days after injection via liver perfusion.

tag: strain background

value: primary mouse hepatocytes

tag: p53 status

value: p53 wt

value: transduced with MYC transposons in vivo


title: Myc_WT_#2

description: A07_S103 Myc_WT_#2


title: Myc_WT_#3

description: A08_S104 Myc_WT_#3


title: Myc_p53null_#4

description: A06_S102 Myc_p53null_#4

source_name: p53 null hepatocytes transduced with MYC transposons

value: p53 null


title: Myc_p53null_#3

description: A05_S101 Myc_p53null_#3


title: Myc_p53null_#1

description: A04_S100 Myc_p53null_#1


title: Pvir#7_abdM [RNA-seq]

status: Public on Oct 11 2018

city: Heidelberg

first: Fanny

last: Gatzmann

address: Im Neuenheimer Feld 580

department: A130 Epigenetics

country: Germany

institute: DKFZ

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
RNA mapping: hisat2 2.0.4
calculating expression levels: RSEM-1.2.30
Genome_build: Pvir0.4
Supplementary_files_format_and_content: rsem genes.results files

organism: Procambarus virginalis

extract_protocol:
Total RNA was isolated from 20-60 mg frozen tissues. Thawed tissues were homogenized in 1 ml Trizol (Ambion), precipitated with isopropanol and resuspended in 20-100 µl RNase-free water (Gibco Life Technologies). Total RNA was treated with DNase using the RNeasy Mini Kit (Qiagen) following the manufacturer's RNeasy Mini Protocol for RNA Cleanup in combination with the On-Column DNase Digestion Protocol.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

tag: strain

value: Heidelberg laboratory strain

value: abdominal musculature


title: Pvir#7_hep [RNA-seq]

tag: tissue

value: hepatopancreas


title: HEPG2-SH3-c

status: Public on Sep 20 2018

first: Coen

last: van Solingen

state: NY

address: 435 E30th street SB 704

department: Medicine/Cardiology

institute: NYU Grossman School of Medicine

data_processing:
RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: base mean data was calculated from reads of three replicate samples. Fold change was calculated as EV over shRNA. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections (CDF analysis, IPA)

growth_protocol: HepG2 were cultivated in EMEM (Corning) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. HiSeq Paired-End 50 Cycle Lane (v4)

treatment_protocol: Short hairpin RNAs (shRNA) targeting all of the CHROME variants or a non-targeting control shRNA (EV) were cloned into the pLKO vector (Addgene, #8453) and transfected into HEK293T cells with packaging vectors psPAX2 (Addgene, #12260) and pMD2.G (Addgene, #12259). After 48 h, the culture media was isolated and used to transduce HepG2 cells.

tag: shRNA

value: stable overexpression of shRNA against CHROME

tag: cell type

value: human liver cancer cell


title: HEPG2-SH3-b


title: HEPG2-SH3-a


title: WT 1

source_name: WT ovary

value: ovary

value: WT


title: Naive2: BM Tregs isolated from naïve mice_rep2

status: Public on Nov 03 2021

description: BM Tregs isolated from naïve mice_rep2

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.15 and analyzed using ArrayStar software v.15 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: BM Tregs

extract_protocol:
Total RNA was extracted from FACS-purified BM Tregs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic Foxp3-DTR-GFP recipients. BM Tregs from CML or naive mice were then isolated for RNA extraction.

value: Bone marrow derived Tregs

value: post natal week 8


title: HEPG2-EV-c

value: stable overexpression of EV


title: HEPG2-EV-b


title: HEPG2-EV-a


title: A10_18DAS_rep4

status: Public on Aug 17 2018

city: Saint Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 North Warson Road, Donald Danforth Plant Science Center/ Eveland lab

institute: Donald Danforth Plant Science Center

data_processing:
Data were quality cheked with FASTQC.
Reads were mapped and the transcripts were quantified by Salmon (v0.8.1) (Patro et al., 2017) in a quasi mapping mode with the option –numBootstraps 30.
Salmon outputs were imported into R and TPMs, counts and transcript lengths were summarized into matrices by using the Bioconductor package tximport (v1.0.3).
Genome_build: Sviridis_311_v1
Supplementary_files_format_and_content: The biocondutor package tximport was used to import and summarize gene-level abundances.

organism: Setaria viridis

source_name: inflorescence primordia

growth_protocol: The reference S. viridis genotype A10.1 was used for this study. A10.1 seeds from two-year old stocks were used to ensure full loss of dormancy and promote synchronized germination. Seeds were planted in MetroMix 360 soil (Sun Gro Horticulture company) and grown in a controlled growth chamber with the following conditions: temperature of 31°C/23°C (day/night), light intensity of 200 µmol/sq.meter/sec for 12 hours (6am-6pm) and 50% relative humidity, at the Donald Danforth Plant Science Center’s Integrated Plant Growth Facility. Plants were fertilized with Jack’s 15-16-17 (Hummert International) twice a week.

extract_protocol:
Inflorescences were hand-dissected into fresh 100% acetone on dry ice from S. viridis seedlings at 10, 12, 14, 15, 16 and 18 DAS. Depending on the representative size at a given stage, 10-30 individual inflorescence primordia were pooled per biological replicate; three to four biological replicates were collected for each stage. All sampling was performed within a two-hour window in the morning to control for circadian effects. Acetone was removed and samples were flash-frozen in liquid nitrogen and ground into a fine powder using 3mm tungsten-carbide beads (Qiagen) in a Tissue Lyser-II. Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) with in-column DNase I treatment following manufacturer's protocols.
RNA-seq libraries were generated from 1µg total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) and size-selected for 200 bp inserts. Libraries were quantified on a bioanalyzer (Agilent 2100) using a DNA 1000 chip to confirm the insert size and quantified again on a Qubit 3.0 Fluorometer (Life Technologies) to ensure different libraries were equally loaded
Libraries were sequenced using standard Illumina protocols (Illumina, Inc.) for either paired-end (PE) or single-end (SE) sequencing at 100bp on the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.

value: accession A10.1

tag: developmental stage

value: 18 Days after sowing

value: pool of inflorescence primordia


title: A10_18DAS_rep1


title: A10_18DAS_rep2


title: MP3

value: ovarian tumor

value: Myc;p53-/- EPO-GEMM

value: non-treated


title: A10_16DAS_rep4

value: 16 Days after sowing


title: A10_16DAS_rep2


title: A10_16DAS_rep3


title: A10_16DAS_rep1


title: A10_15DAS_rep4

value: 15 Days after sowing


title: A10_15DAS_rep3


title: Naive3: BM Tregs isolated from naïve mice_rep3

description: BM Tregs isolated from naïve mice_rep3


title: A10_15DAS_rep2


title: A10_15DAS_rep1


title: A10_14DAS_rep4

value: 14 Days after sowing


title: A10_12DAS_rep4

value: 12 Days after sowing


title: A10_12DAS_rep2


title: A10_14DAS_rep1


title: A10_10DAS_rep2

value: 10 Days after sowing


title: Naive1: BM Tregs isolated from naïve mice_rep1

description: BM Tregs isolated from naïve mice_rep1


title: A10_10DAS_rep3


title: A10_10DAS_rep1


title: KC-GEMM-ESC-shArid1a.6421 #3

status: Public on Jul 03 2018

data_processing:
Illumina  read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were aligned to GRCm37-mm9 using STAR (STAR_2.5.0a), Algined reads were quantified using HTSeq (HTSeq-0.5.3). Raw read counts were normalized to FPKM value.
Differential expression analysis was performed with DESeq package in R (R-3.2.0)
Genome_build: GRCm37 - mm9
Supplementary_files_format_and_content: text file includes raw count value for each sample

growth_protocol: KC-GEMM-ESC mice (males, chimerism >90%) were put on Doxycycline diet for 5 days

extract_protocol:
Trizol RNA extraction protocol
Ribosomal RNA was depleted using RiboZero (Illumina) and stranded KAPA RNA libraries were prepared from 1ug RNA. Paired-end 50.

treatment_protocol: Pancretata were harvested at day 5 post-doxycycline diet and processed for FACS sorting as described in Methods section. mKate+ cells were sorted using Aria3 sorter, and collected directly into Trizol-LS.

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Arid1a (sh6421)

value: 5 weeks old

value: Doxycycline (5 days)

value: pancreas

value: sorted pancreaatic epithelial cells


title: KC-GEMM-ESC-shRen.713 #3

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)


title: KC-GEMM-ESC-shArid1a.1803 #3

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Arid1a (sh1803)


title: KC-GEMM-ESC-shArid1a.6421 #2


title: KC-GEMM-ESC-shArid1a.1803 #2


title: KC-GEMM-ESC-shArid1a.1803 #1


title: KC-GEMM-ESC-shRen.713 #2


title: KC-GEMM-ESC-shArid1a.6421 #1


title: KC-GEMM-ESC-shRen.713 #1


title: wt_rep2

status: Public on Dec 23 2017

data_processing:
Total RNA (1µg) was extracted (PicoPure RNA Isolation Kit; Thermo Fisher Scientific) and libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, size-selected for 200 bp inserts and quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip.
We generated an average of 40M 100bp, single-end reads using the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.
Read mapping and differential expression analysis were performed using the Tuxedo suite of open-source tools (Trapnell et al., 2013). Reads were mapped to the Setaria viridis A10.1 reference genome (http://phytozome.jgi.doe.gov; v1.1) using TopHat2 (v2.1.0) and an a priori set of 35,214 gene models. Gene-level expression values were represented by fragments per kilobase exon per million reads mapped (FPKM) and a consensus FPKM was determined for each gene based on its representation across biological replicates. Differential expression was determined using Cuffdiff (v 2.2.1)
Genome_build: Setaria viridis A10.1 reference genome v1.1
Supplementary_files_format_and_content: Single processed data file for RNAseq analysis includes expression information for all annotated S. viridis genes based on analysis with Cuffdiff v.2.2.1. Raw read counts for each sample and normalized fragments per kilobase per million reads (FPKM) are listed

growth_protocol: The bristleless1 (bsl1) mutant was identified by screening an N-Nitroso-N-methylurea (NMU) mutagenized M2 population of S. viridis. This mutant was selfed (M3) and then backcrossed to the reference line A10.1 and then the F1 selfed.  Homozygous mutants from this segregating F2 population were selfed and then used for the RNA-seq experiment.

extract_protocol:
Total RNA was extracted from pools of inflorescence tissue using the PicoPure RNA Isolation kit (Life Technologies), according to manufacturer instructions.  Messenger RNA was enriched by two successive purifications with oligo-dT coupled dynabeads (Invitrogen).
libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, size-selected for 200 bp inserts and quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip.

treatment_protocol: Mutant and wild-type A10.1 seedlings were grown in a controlled environment to ~15 DAS (Days after sowing). Inflorescence primordia were hand-dissected and flash frozen in liquid N. ~10 representative inflorescence primordia were pooled into a single biological replicate.

value: 15 Days After Sowing

value: wild-type


title: wt_rep3


title: wt_rep1


title: MBD-IN

status: Public on May 31 2016

description: Input

data_processing:
Raw single-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low-quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimum percentage of 90.
High-quality reads were aligned to the rat genome (rn5) in Galaxy using Bowtie.
Genome-aligned sequenced reads for each sample were examined using SeqMonk (Babraham institute), using Ensembl v. 70 gene and feature annotations. Due to library size, reads were extended by 250 bp to recapitulate the ~300bp fragment size average. For each sample, gene and promoter (+/-2.5kb from TSS) methylation were determined by computing the reads per million mapped reads (RPM) from MBD-IP samples.
Genome_build: Rnor_5.0 (rn5)
Supplementary_files_format_and_content: Matrix with RPM values for each sample (columns) and each gene (rows). The first row contains column identifiers. The first column contains RefSeq gene names. Promoter and gene body RPM estimates are provided in separate files.

source_name: Cortical neuronal culture, input

growth_protocol: Neurons were removed from cortical tissue at embryonic day 18, and maintained in vitro for 11 days prior to experimental treatment. Each culture well contained ~250,000 cells.

extract_protocol:
Genomic DNA was extracted, RNase-treated, and purified (DNeasy Blood and Tissue Kit, Qiagen). 2µg of total DNA was sonicated to 200-400bp and prepared for MBD-based methylated DNA capture (MethylMiner Kit, Life Technologies). MBD-IP and Input samples underwent library construction and whole-genome sequencing.
DNA sequencing was performed at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). DNA libraries were quantified with the Kapa Library Quant Kit (Kapa Biosystems), and underwent sequencing (25M total 50 bp single-end reads) on an Illumina sequencing platform (HiSeq 2000). We sequenced two biological replicates, as well as an input (non-IP) control for normalization.

treatment_protocol: Neurons were not treated prior to DNA extraction.

tag: strain/background

value: Sprague-Dawley

value: cortical neuronal culture

value: embryonic day 18, 11 DIV

value: untreated (media alone)

tag: mbd-capture

value: no


title: MBD-1

source_name: Cortical neuronal culture, MBD precipitated

value: yes


title: H2030 Combo 2

description:
NSCLC_FPKM.txt
A16_S112_L002_R1_001

tag: cell line

value: Combination


title: ecT2

description: non-polyA RNA

data_processing:
Raw paired-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimun percentage of 90.
High-quality reads were aligned to the rat genome (rn5) in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175).
Genome-aligned sequenced reads for each sample were examined using SeqMonk (Babraham institute), using Ensemble v. 70 gene and feature annotations. For each sample, gene/transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM). For PolyA- RNA-seq, estimates of pre-TSS (1kb upstream of TSS), intronic, and post-TES (2kb downstream of TES) were also quantified for comparison.
Gene expression differences between groups (i.e., untreated versus KCl) were calculated in SeqMonk using all replicates for each group. Statistical significance was assessed using Student's t-tests and an false-discovery rate of 0.05.
Genome_build: rn5
Supplementary_files_format_and_content: Matrix with FPKM values for each sample (Columns) and each gene (rows). The first row contains column identifiers. The first column contains Refseq gene names or Region IDs.

source_name: Cortical neuronal culture

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 2µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 9.5) and library construction for polyA+ or polyA- RNA sequencing. For PolyA- RNA, an additional step (removal of ribosomal RNA with NEBNext rRNA depletion kit) occured prior to adapter ligation.
Directional polyA+ and polyA- RNA llibraries were constructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq2000).

treatment_protocol: Neurons were treated as described with 25mM KCl or 1uM TTX for 1hr. Media was removed and RNA was extracted immediately following treatment.

value: Embryonic day 18, 11 DIV

tag: treatment

value: 1hr 1uM TTX inactivation


title: A549 Palbo 2

description:
NSCLC_FPKM.txt
A07_S103_L002_R1_001

value: Palbociclib


title: T2

description: polyA RNA


title: T1

description: polyA RNA


title: ecT1

description: non-polyA RNA


title: K2

description: polyA RNA

value: 1hr 25mM KCl stimulation


title: K1

description: polyA RNA


title: A549 Tramet 1

description:
NSCLC_FPKM.txt
A02_S98_L002_R1_001

value: Trametinib


title: V2

description: polyA RNA

value: Untreated (media alone)


title: V1

description: polyA RNA


title: rep2_FEA4_ChIP

status: Public on Jan 21 2015

description:
rep2_FEA4_MACS_peaks.bed
rep2_FEA4_MACS_summits.bed

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina MiSeq platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
ChIP-seq reads were aligned to the maize reference genome (AGPv2) using Bowtie (v.0.12.7;(Langmead et al., 2009)) and peak calling was performed with MACS version 1.4.0rc2 using only uniquely mapped reads (Zhang et al., 2008). Peaks were identified as significantly enriched (p<1e-05) in each of the ChIP-seq libraries compared to input DNA.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files are output of MACS.1.4.0rc2.  The peaks.bed file includes (from left to right columns) chromosome, peak start, peak stop, -10*log10(pval).  The summits.bed file includes (from left to right columns) chromosome, summit start, summit stop, tag pileup at summit.

organism: Zea mays

source_name: 2-5mm tassel primordia

growth_protocol: Developing tassel primordia, approximately 2-5mm in size, were harvested from FEA4-YFP plants grown in the field at CSHL uplands farm facility.

extract_protocol:
Following dissection, inflorescences were immediately cross-linked in buffer containing 1% formaldehyde for 15 minutes under vacuum, followed by addition of glycine to a concentration of 0.1 M, which was infiltrated for 5 minutes.  Following three washes with distilled water, the cross-linked tissues were dried with paper towels and flash frozen in liquid nitrogen.
Chromatin extracts from YFP-FEA4 plants were immunoprecipitated with anti-GFP (ab290, Abcam) antibody.  Protein A dynabeads (Invitrogen) blocked with yeast tRNA and BSA were used to capture antibody-chromatin complexes (Morohashi et al., 2012).  Following purification of immunoprecipitated DNA, libraries were constructed using the Ovation Low Input DR kit (Nugen) and barcoded to allow multiplexed sequencing.  Two input and two IP libraries were sequenced on one run of an Illumina MiSeq machine.

treatment_protocol: These experiments used families containing a transgene integration event that complemented the mutant (A399S1-7), and expression of the transgene was verified by fluorescence microscopy.

tag: chip antibody

value: anti-GFP

value: 2-5mm tassel primordia

tag: experiment

value: ChIPseq

value: normal B73


title: rep2_input

value: input


title: rep1_input

description:
rep1_FEA4_MACS_peaks.bed
rep1_FEA4_MACS_summits.bed


title: rep1_FEA4_ChIP


title: fea4_mut_rep3_ear

description: all_genes_expression_values_supp_table.txt

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina HiSeq2000 platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software on the HiSeq as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
Tophat (version 2.0.9) was used to align reads to the maize reference genome (AGPv2) based on an a priori set of 110,028 predicted maize gene models (Working Gene Set v5b.60; maizesequence.org).  We then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks (version 2.0.2) and a high-confidence subset of 39,656 maize gene models, the Filtered Gene Set (FGS v5b.60; maizeseqeunce.org).  Differential expression analysis was carried out using the R package DESeq (v.1.14.0;(Anders and Huber, 2010). An adjusted p-value of < 0.05 was used to call differentially expressed genes after multiple testing correction.  Further details are provided in Supplemental Methods in associated Pautler et al. paper.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Single processed data file for RNAseq analysis includes expression information for all Filtered Gene Set (FGS) genes based on analysis with Cufflinks v.2.0.2 and differential expression analysis with DESeq.  Gene is called significant for differential expression if adjusted p-value < 0.05.  Normalized read count averages among all samples (baseMean.Avg), wild-type biological replicates (baseMean.wt) and fea4 mutant biological replicates (baseMean.fea4) based on DESeq analysis.  These values were used in determine fold changes.  Raw read counts for each sample and normalized fragments per kilobase per million reads (FPKM) based on Cufflinks analysis.

source_name: 1mm ear primordia

growth_protocol: fea4-ref was isolated from an M2 screen of EMS-mutagenized A619 inbred maize, and was deposited in the Maize Genetics Co-Op Stock Center as fea179.  The mutation was introgressed 4-5 times into various inbred lines for phenotypic analysis in segregating families.  fea4-rel*09-5171 and fea4-rel*07-167 were found in a screen for enhancers of ramosa2 in the A619 inbred background.  Ear primordia from segregating populations were collected from field grown plants at the CSHL uplands farm facility.

extract_protocol:
Total RNA was extracted from pools of ear tissue using the PicoPure RNA Isolation kit (Life Technologies), according to manufacturer instructions.  Messenger RNA was enriched by two successive purifications with oligo-dT coupled dynabeads (Invitrogen).
Approximately 50ng of mRNA was used as input for the ScriptSeq v2 RNAseq system (Epicentre).  This kit allowed the addition of barcoded adapters (Index #4,5,6,7) to enable multiplexed sequencing in a single lane of an Illumina HiSeq2000.  Prior to sequencing, the average size distribution of the libraries was verified on a high sensitivity bioanalyzer chip.  The libraries were diluted to 10nM and concentration was verified by qPCR using standards (KAPA Biosystems).

treatment_protocol: Triplicate pools of more than ten 1mm ears were harvested from homozygous fea4 mutants and heterozygous wild-type sibling plants. Freshly dissected ear tissue was fixed in ice-cold acetone, followed by vacuum infiltration for 20 minutes, and three acetone changes of one hour each.

value: 1mm ear primordia

value: RNAseq

value: fea4/fea4 homozygous mutant


title: fea4_mut_rep1_ear


title: wt_rep3_ear

value: fea4/+ heterozygous


title: wt_rep2_ear


title: wt_rep1_ear


title: A106

status: Public on Sep 09 2014

data_processing:
Raw paired-end sequenced reads (as fastq format) underwent quality control (FASTQC) in Galaxy.
Low quality reads were filtered with the FASTX toolkit in Galaxy ("filter by quality"), with a quality cutoff of 20 and a minimun percentage of 90.
High-quality reads were aligned to the mouse genome (mm10) in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175).
Genome-aligned sequenced reads for each sample were examined using Cufflinks in Galaxy, using RefSeq gene identification from the UCSC table browser. For each sample, gene/transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM). All values were quartile-normalized to improve expression estimates of low-abundance transcripts.
Gene expression differences between groups (i.e., scrambled vs H2a.Z knockdown) were calculated in CuffDiff using all replicates for each group and per-condition dispersion modeling. Significance testing was conducted on genes with a minimum of 100 aligned reads in a locus, and statistical significance was assessed using Student's t-tests and an false-discovery rate of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with FPKM values for each sample (Columns) and each gene (rows). The first row contains column identifiers. The first column contains Refseq gene names.

source_name: H2A.Z shRNA_contextual fear conditioning

extract_protocol:
Total RNA from area CA1 of the hippocampus was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.9) and library construction for polyA+ RNA sequencing.
Directional poly-A+ RNA llibraries were contructed at HudsonAlpha Genomic Services Lab using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes). RNA libraries were quantified (Kapa Library Quant Kit, Kapa Biosystems), and underwent sequencing (25M total 50bp paired-end reads) on an Illumina sequencing platform (HiSeq2000).

value: 9-12 weeks

tag: animal condition

value: trained in contextual fear conditioning

tag: infected with

value: AAV expressing an shRNA against H2A.Z

value: CA1 of hippocampus


title: A107

tag: age


title: A104


title: A102

source_name: H2A.Z shRNA_naive

value: naïve


title: A100


title: S110

source_name: scrambled shRNA control

value: AAV expressing a scrambled shRNA control


title: S108


title: RA1_input_ear_YFP

status: Public on Nov 27 2013

data_processing:
Illumina GAII and HiSeq 2000 sequencing with SR50 were performed by the OSUCCC Nucleic Acid Shared Resource (The Ohio State University)
All image processing and base calling was done with the Illumina Real Time Analysis software as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
ChIP-seq reads were aligned to the maize reference genome (AGPv2) and peak calling was performed with MACS version 1.4.0rc2 using only uniquely mapped reads.  Peaks were identified as significantly enriched (p<1e-05) in each of the ChIP-seq libraries compared to input DNA.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files are output of MACS.1.4.0.  The peaks.bed file includes (from left to right columns) chromosome, peak start, peak stop, -10*log10(pval).  The summits.bed file includes (from left to right columns) chromosome, summit start, summit stop, tag pileup at summit.

source_name: ear primordia

growth_protocol: Tassel primordia were harvested ~4 weeks after planting, and immature ears were harvested after 6 weeks.  Analysis of plant phenotypes in F1BC2 families segregating for the transgene and ra1 mutants, showed transgenic constructs were capable of complementing the mutant.

extract_protocol:
ChIP preparation were performed as previously described (Bolduc et al. 2012; Morohashi et al. 2012).  Anti-GFP (ab290, Abcam) and anti-HA (H3663, Sigma) antibodies were used for immunoprecipitation of RA1-YFP and RA1-HA, respectively, and protein A agarose/salmon sperm DNA beads (16-157, Millipore) were used to precipitate antibody complexes.
ChIP-seq library preparation were performed as previously described (Bolduc et al. 2012; Morohashi et al. 2012).  ChIP DNA was subjected to end repair and A-base addition, followed by ligation with Illumina adapters made by annealing Mltplx_short and Mltplx_long oligos.  Library amplification was performed by PCR using Phusion Hot Start II High-Fidelity DNA Polymerase (F549L, Thermo Scientific) with MltplxPCR1.0 and PCR2.0_indx1 to 7, followed by gel-size fractionation to obtain 200-500bp fragments.

treatment_protocol: We created two native translational fusion constructs to drive the expression of tagged RA1 proteins in the endogenous expression domain.  We fused the YFP and HA-FLAG tags in frame with the RA1 coding sequence at the N-terminus.  Constructs were transformed into the HiII genetic background at the Iowa State University Plant Transformation Facility (Ames, IA).  T0 generation transformed plants were crossed to the ra1-R mutant.  T1 plants were then backcrossed to create a T2 generation segregating 1:1 for the transgene and for ra1.

tag: transgene

value: ear primordia (pool)

tag: genotype

value: ra1/ra1 B73


title: S109


title: RA1_input_ear_HA


title: RA1_ChIPseq_ear_YFP

value: YFP


title: RA1_ChIPseq_ear_HA

value: HA


title: RA1_input_tassel_YFP

source_name: tassel primordia

value: tassel primordia (pool)


title: RA1_input_tassel_HA


title: ra3_2mm_ear.2

data_processing:
Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina GAII platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software on the HiSeq as the run progressed.  Binary basecall files were then transferred to a shared Linux server for further processing and archival.  The latest version of the Illumina processing software CASAVA was used to generate fastq files.
The Tuxedo suite (Trapnell et al. 2010) was used for mapping and analysis of RNA-seq data.  Tophat (version 1.2.0) was used to align reads to the maize reference genome (AGPv2) based on an a priori set of 110,028 predicted maize gene models (Working Gene Set v5b.60; maizesequence.org).  Cuffdiff (version 1.0.2) was used to analyze differential expression using a high-confidence subset of 39,656 maize gene models, the Filtered Gene Set (FGS v5b.60; maizeseqeunce.org).  Gene-level expression values are represented by Fragments Per Kilobase exon per Million reads mapped (FPKM) and a consensus FPKM was determined for each gene based on its representation across biological replicates (Trapnell et al. 2010).  Further details are provided in Supplemental Methods in associated Eveland et al. paper.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files from Cufflinks output can be found for each sample - FPKM values at both gene level and transcript isoform level are provided.  Consolidated (combined) files from Cuffdiff output are also provided and give the FPKM values and 95% confidence intervals for expression of each gene across replicates and between developmental stages or genotypes.  All are tab-delimited txt files.

growth_protocol: For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used.  For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm.  Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage).

extract_protocol:
Total RNA was extracted using the Qiagen RNAeasy kit
RNA-seq libraries were constructed based on methods used in Li et al., Nature Genetics (2008)
RNA-seq libraries are paired end and are not strand-specific

treatment_protocol: Ear and tassel tissues were dissected as described above in "overall design".

value: pool of ra3 mutant ear primordia

tag: Stage

value: ra3/ra3 (in B73)


title: ra2_2mm_ear.3

value: pool of ra2 mutant ear primordia

value: ra2/ra2 (in B73)


title: ra3_2mm_ear.1


title: ra2_2mm_ear.2


title: ra2_2mm_ear.1


title: ra1_2mm_ear.3

value: pool of ra1 mutant ear primordia

value: ra1/ra1 (in B73)


title: ra1_2mm_ear.1


title: wt_2mm_ear.3

value: pool of B73 ear primordia


title: wt_2mm_ear.2


title: ra3_1mm_ear.2


title: ra3_1mm_ear.1


title: ra2_1mm_ear.2


title: ra2_1mm_ear.1


title: ra1_1mm_ear.2


title: RA1_ChIPseq_tassel_YFP


title: RA1_ChIPseq_tassel_HA


title: ra1_1mm_ear.1


title: ra3_2mm_ear.3


title: wt_1mm_ear.2


title: wt_1mm_ear.1


title: tassel_stg3.2

value: pool of whole B73 tassels (5-7mm)

value: wild-type B73


title: tassel_stg2.2

value: pool of whole B73 tassels (3-4mm)


title: tassel_stg3.1


title: tassel_stg2.1


title: tassel_stg1.2

value: pool of whole B73 tassels (1-2mm)


title: ra1_2mm_ear.2


title: ear_base_FM.2

value: 2mm base of 10mm B73 ear (pool)

value: FM


title: tassel_stg1.1


title: ear_base_FM.1


title: ear_mid_SM.1

value: 1mm middle of 10mm B73 ear (pool)

value: SM


title: ear_mid_SM.2


title: ear_tip_IM.SPM.2

value: 1mm tip of 10mm B73 ear (pool)

value: IM/SPM


title: ear_tip_IM.SPM.1


title: wt_2mm_ear.1


title: SKBR3-P10, biological rep2

status: Public on Jan 24 2012

description: Gene expression data at passage 10 follow-up at “drug holiday” condition

hyb_protocol: The labelled products were hybridized for 18 hr at 45C on Affymetrix Genome 133 Plus 2.0 GeneChips. GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.)

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.

source_name: SKBR3 Passage 10

label_protocol: Biotinylated mRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng total RNA.

growth_protocol: HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231 cell line was cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS.

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded (2 X l0^5 cells / T75 flasks) for 24h then media were removed and cells were freshly exposed to the 5-aza-2’-deoxycytidine (DAC) (Sigma Chemical Co.) at concentrations of l00nM in suspension culture every 24h until cultured cells reached 80-85 % confluence (~5 days). The cells were split for 10 follow-up passages at “drug holiday” condition.


title: SKBR3-P10, biological rep1

value: passage 10 follow-up at “drug holiday” condition


title: SKBR3-P7, biological rep2

description: Gene expression data at passage 7 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 7


title: SKBR3-P7, biological rep1

value: passage 7 follow-up at “drug holiday” condition


title: SKBR3-P5, biological rep2

description: Gene expression data at passage 5 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 5


title: SKBR3-P5, biological rep1

value: passage 5 follow-up at “drug holiday” condition


title: SKBR3-P3, biological rep1

description: Gene expression data at passage 3 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 3


title: SKBR3-P3, biological rep2

value: passage 3 follow-up at “drug holiday” condition


title: SKBR3-P1, biological rep2

description: Gene expression data at passage 1 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 1


title: SKBR3-P1, biological rep1

value: passage 1 follow-up at “drug holiday” condition


title: SKBR3-T, biological rep2

description: Gene expression data directly after treatment with DAC

source_name: SKBR3 Treated

value: treatment with DAC


title: SKBR3-T, biological rep1


title: MDA-P10, biological rep2

source_name: MDA-MB231 Passage 10


title: SKBR3-UT, biological rep1

description: Gene expression data before treatment with DAC

source_name: SKBR3 Un-treated


title: SKBR3-UT, biological rep2


title: MDA-P7, biological rep2

source_name: MDA-MB231 Passage 7


title: MDA-P10, biological rep1


title: MDA-P7, biological rep1


title: MDA-P3, biological rep2

source_name: MDA-MB231 Passage 3


title: MDA-P3, biological rep1


title: MDA-P5, biological rep1

source_name: MDA-MB231 Passage 5


title: MDA-P5, biological rep2


title: MDA-P1, biological rep2

source_name: MDA-MB231 Passage 1


title: BT549-DNA-2

status: Public on Mar 30 2020

description:
single cell whole genome sequencing of BT549 DNA
BT549-DNA-2_S8

data_processing:
library strategy: bulk DNA sequencing
Adapter removal and removing reads shorter than 36bp using Bbduk
Reads aligned to refenrence genome hg19 using Bowtie 1.0, remove PCR duplicate reads
The duplicate removed aligned reads were then assigned to variable length bins across the genome based on where they align in the genome
The average bin counts were calculated and used as the diploid 2N average. Bins with higher number are considered as amplified and those with lower are considered deleted. CNV profiles were generated using R.
Genome_build: hg19
Supplementary_files_format_and_content: Varbin files with bincounts for CNV analysis

source_name: BT549 Triple negative breast cancer cell line

extract_protocol:
Cells were trypsinized and spun down to get a pellet. The cells were processed using Qiagen DNeasy blood and tissue kit.
2ug of DNA was fragmented to 400bp using Covaris sonicator. Following this, libraries for sequencing were prepared by subjecting the resulting DNA fragments to end-repair, 3′ adenylation and ligation of TruSeq barcoded adapters. After ligation, DNA fragments were size selected using Ampure XP beads. A 0.75 ratio of beads to sample was used to select fragments larger than 200bp and avoid adapter dimers. These fragments were further amplified by PCR, cleaned using Qiaquick PCR Purification Kit and then once again size selected using Ampure XP beads with a 0.75 ratio of beads to sample. The final libraries were then quantified on Nanodrop and Bioanalyzer using Agilent's High Sensitivity DNA Analysis Kit. 10nM of each sample was then pooled together and the resulting pool was then sequenced single read 76bp length on the Illumina NextSeq

treatment_protocol: No treatment

tag: cell line source

value: Breast

value: Adherent cell line

tag: labelling for flow

value: RPMI with 10% FBS and 1% Pencillin/Streptomycin


title: SKBR3-DNA-3

description:
single cell whole genome sequencing of SKBR3 DNA
SKBR3-DNA-3_S12

source_name: SKBR3 Her2 overexpresson breast cancer cell line

value: DMEM with 10% FBS and 1% Pencillin/Streptomycin


title: MDA-T, biological rep2

source_name: MDA-MB231 Treated


title: MDA-T, biological rep1


title: MDA-UT, biological rep2

source_name: MDA-MB231 Un-treated


title: MDA-P1, biological rep1


title: MDA-UT, biological rep1


title: HB2-P10, biological rep2

source_name: HB2 Passage 10


title: HB2-P10, biological rep1


title: HB2-P7, biological rep2

source_name: HB2 Passage 7


title: MCF7-T

description: MicroRNA expression data directly after treatment with DAC

hyb_protocol: The labelled products were hybridized for 18 hr at 45C on Affymetrix GeneChip miRNA array (v1.0). GeneChips were washed and stained on GeneChip Fluidics 450 Workstations (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed miRNAs were defined using Partek Genomics Suite software v6.5 (Partek Incorporated, Missouri, USA) and and RMA normalization.

source_name: MCF7 Treated

label_protocol: Biotinylated microRNAs were prepared according to the FlashTag Biotin HSR RNA Labeling protocol (Genisphere) using 100ng RNA.

growth_protocol: HB2 cell line was cultured in DMEM, 10% FBS, Insulin (0.01 mg/ml, hydrocortisone (500 ng/ml). MDA-MB231, HS578T and MCF7 cell linee were cultured in DMEM, 10% FBS. SKBR3 cell line was cultured in McCoys 5A, 10% FBS. BT549 cell line was cultured in RPMI medium 1640, 10% FBS.

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN AG) according to the manufacturer's instructions. The RNeasy MinElute Cleanup Kit (QIAGEN AG) was used for isolation and purification of enriched miRNAs.


title: HB2-P7, biological rep1


title: HB2-P5, biological rep2

source_name: HB2 Passage 5


title: MCF7-UT

description: MicroRNA expression data before treatment with DAC

source_name: MCF7 Un-treated


title: HB2-P5, biological rep1


title: HB2-P3, biological rep2

source_name: HB2 Passage 3


title: HS578T-T

source_name: HS578T Treated


title: HB2-P3, biological rep1


title: A10_14DAS_rep3

source_name: inflorescence primordia

value: accession A10.1

value: 14 Days after sowing

tag: tissue

value: pool of inflorescence primordia


title: HB2-P1, biological rep2

source_name: HB2 Passage 1


title: HS578T-UT

source_name: HS578T Un-treated


title: BT549-T

source_name: BT549 Treated


title: BT549-UT

source_name: BT549 Un-treated


title: HB2-P1, biological rep1


title: A10_10DAS_rep4

value: 10 Days after sowing


title: HB2-T, biological rep2

source_name: HB2 Treated


title: SKBR3-P10

description: MicroRNA expression data at passage 10 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 10


title: SKBR3-P7

description: MicroRNA expression data at passage 7 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 7


title: HB2-T, biological rep1


title: SKBR3-P1

description: MicroRNA expression data at passage 1 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 1


title: SKBR3-P3

description: MicroRNA expression data at passage 3 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 3


title: SKBR3-P5

description: MicroRNA expression data at passage 5 follow-up at “drug holiday” condition

source_name: SKBR3 Passage 5


title: SKBR3-T

source_name: SKBR3 Treated


title: HB2-UT, biological rep1

source_name: HB2 Un-treated


title: HB2-UT, biological rep2


title: SKBR3-UT

source_name: SKBR3 Un-treated


title: MDA-P10

source_name: MDA Passage 10


title: MDA-P7

source_name: MDA Passage 7


title: MDA-P5

source_name: MDA Passage 5


title: ecK1

description: non-polyA RNA

source_name: Cortical neuronal culture

tag: strain

value: Sprague-Dawley

value: Embryonic day 18, 11 DIV

value: 1hr 25mM KCl stimulation


title: ecV2

description: non-polyA RNA

value: Untreated (media alone)


title: MDA-P1

source_name: MDA Passage 1


title: MDA-P3

source_name: MDA Passage 3


title: MDA-T

source_name: MDA Treated


title: MDA-UT

source_name: MDA Un-treated


title: HB2-P10

source_name: HB2 Passage 10

value: passage 10 follow-up at “drug holiday” condition


title: HB2-P7

source_name: HB2 Passage 7

value: passage 7 follow-up at “drug holiday” condition


title: HB2-P3

source_name: HB2 Passage 3

value: passage 3 follow-up at “drug holiday” condition


title: HB2-P5

source_name: HB2 Passage 5

value: passage 5 follow-up at “drug holiday” condition


title: HB2-P1

source_name: HB2 Passage 1

value: passage 1 follow-up at “drug holiday” condition


title: HB2-T

source_name: HB2 Treated

value: treatment with DAC


title: ramosa3_2mm_ear_rep3b

status: Public on Oct 20 2010

description: 3' tag DGE libraries with DpnII and NlaIII from ra3 mutant 2mm maize ears

data_processing:
Unique tag consolidation:  Raw sequences were extracted from the resulting image files using the open source Firecrest and Bustard applications (Illumina). Data were consolidated by read counts for unique sequences.  The consolidated, unfiltered sequence tags and raw read counts are provided as processed data files for each sample (lane of sequence).  All downstream analyses are detailed in Eveland et al., Digital gene expression signatures for Maize Development, Plant Physiol. 2010 Sep 10. [Epub ahead of print], PMID: 20833728
Alignment:  Vmatch (www.vmatch.de) sequence analysis software to map the collapsed reads to the maize reference genome.  The Vmktree feature was used to construct persistent indices for each of the 10 unmasked, assembled maize chromosomes and for an additional chromosome 0, which includes non-assembled sequence (B73 RefGen_v1).  For each of the 11 indices, the unique DpnII and NlaIII tags were queried for complete matches to all possible 20- and 21-mer sequences, respectively, using the Vmatch algorithm.  This included both sense and antisense matches and strand information for each tag was retained.  Processed data files include Vmatch alignments for sequence tags represented by at least 2 reads that align completely to the maize genome (B73 RefGen_v1) 1-3 times (alignments_complete_vmatch_DGE_comsensus_tags.txt) and the associated .gff3 file for viewing on a genome browser (DGE_complete_genomic_alignment.gff3).

source_name: 2mm maize ear (female inflorescence)

extract_protocol: Typically 500–2000 ng of DNase I-treated total RNA was used in library construction. Briefly, after double-stranded cDNA synthesis using oligo(dT) beads (Invitrogen) the cDNA was digested with an anchoring restriction enzyme (NlaIII or DpnII) and ligated to Illumina specific adapter, Adapter A, containing a recognition site for the TypeIIS restriction enzyme MmeI (New England Biolabs).  Following MmeI digestion, dephosphorylation with shrimp alkaline phosphatase (USB Corp), and purification, a second Illumina adapter, Adapter B, containing a 2-bp degenerate 3’ overhang was ligated. Tags flanked by both adapters were enriched by PCR using Phusion DNA polymerase (Finnzymes) and Gex PCR primers 1 and 2 (Illumina) following the manufacturer’s instructions. The PCR products were run on a 12% PAGE gel and the 85-bp DNA band was excised and purified using Spin-X filter column (Costar) followed by ethanol precipitation. The DNA quality was assessed and quantified using an Agilent DNA 1000 series II assay (Agilent) and the DNA sample was diluted to 10 nM.  Each sample (multiplexed DpnII and NlaIII libraries) was sequenced in a single lane of an Illumina GA flow cell.

value: ramosa3_mutant (B73 background)

tag: replication

value: Technical rep of ra3 biol rep 3


title: ramosa3_2mm_ear_rep3

value: Biological rep 3:pool of 4-5 ears


title: ramosa3_2mm_ear_rep2

value: Biological rep 2:pool of 4-5 ears


title: HB2-UT

source_name: HB2 Un-treated


title: ramosa3_2mm_ear_rep1

value: Biological rep 1:pool of 4-5 ears


title: B73_wild-type_2mm_ear_rep3

description: 3' tag DGE libraries with DpnII and NlaIII from wild-type B73 2mm maize ears

value: wild-type (B73)


title: B73_wild-type_2mm_ear_rep1


title: B73_wild-type_2mm_ear_rep2


title: H460 Trametb 2

description:
NSCLC_FPKM.txt
A22_S118_L002_R1_001

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (29), aligned to the human genome using STAR (30), and quantified transcript counts using HTSeq (31). Raw read counts were normalized to FPKM value for analysis.
Genome_build: Reads were aligned to the transcriptome (hg19, GRCh37.75)
Supplementary_files_format_and_content: Tab-delimited text file includes normalized FPKM value for each sample

source_name: Lung cell line

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a fpkm matrix of transcript counts.

value: Trametinib


title: 8998T Tramet 2

description:
PDAC_FPKM.txt
S52_S52_L001_R1_001

source_name: Pancreatic cancer cell line


title: Myc_WT_#5

description: A10_S106 Myc_WT_#5

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.0a)
Genome wide transcript counting was performed by featureCounts (v1.6.0) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.22.1) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: p53 WT hepatocytes transduced with MYC transposons

extract_protocol:
RNA was extracted using the RNAeasy mini kit (Qiagen) per manufacturer's instructions.
RNA integrity and concentration were assessed using a BioAnalyzer (Agilent).  RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: strain background

tag: cell type

value: primary mouse hepatocytes

tag: p53 status

value: p53 wt

value: transduced with MYC transposons in vivo


title: H2030 Vehicle 2

description:
NSCLC_FPKM.txt
A13_S109_L002_R1_001

tag: cell line

tag: treatment

value: Vehicle


title: 8988T Combo 1

description:
PDAC_FPKM.txt
S55_S55_L001_R1_001

value: Combination


title: 8988T Vehicle 2

description:
PDAC_FPKM.txt
S50_S50_L001_R1_001


title: A549 Palbo 1

description:
NSCLC_FPKM.txt
A03_S99_L002_R1_001

value: Palbociclib


title: A549 Vehicle 2

description:
NSCLC_FPKM.txt
A05_S101_L002_R1_001


title: A10_18DAS_rep3

source_name: inflorescence primordia

value: accession A10.1

tag: developmental stage

value: 18 Days after sowing

value: pool of inflorescence primordia


title: A10_14DAS_rep2

value: 14 Days after sowing


title: A10_12DAS_rep1

value: 12 Days after sowing


title: ecK2

description: non-polyA RNA

source_name: Cortical neuronal culture

value: Sprague-Dawley

value: Embryonic day 18, 11 DIV

value: 1hr 25mM KCl stimulation


title: MBD-2

source_name: Cortical neuronal culture, MBD precipitated

tag: strain/background

value: cortical neuronal culture

value: embryonic day 18, 11 DIV

value: untreated (media alone)

tag: mbd-capture

value: yes


title: bsl1_mutant_rep1

value: 15 Days After Sowing

tag: genotype/variation

value: bsl1 mutant


title: bsl1_mutant_rep2


title: fea4_mut_rep2_ear

description: all_genes_expression_values_supp_table.txt

source_name: 1mm ear primordia

value: 1mm ear primordia

tag: experiment

value: RNAseq

value: fea4/fea4 homozygous mutant


title: ecV1

description: non-polyA RNA

tag: age

value: Untreated (media alone)


title: A101

source_name: H2A.Z shRNA_naive

value: 9-12 weeks

tag: animal condition

value: naïve

tag: infected with

value: AAV expressing an shRNA against H2A.Z

value: CA1 of hippocampus