title: Mouse4_blood_CD8Tcells_CITE

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 4 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins
M4_Blood.rds

source_name: Mouse 4


title: Mouse4_blood_CD8Tcells_VDJ

status: Public on Jan 13 2021

type: SRA

city: Boston

first: Osmaan

last: Shahid

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Immunology

country: USA

institute: Harvard Medical School

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 4 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the TCR sequencing data.
M4_Blood.rds

library_source: transcriptomic

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline (v3.0.2)
Data normalization, dimension reduction, and differential expression analysis were performed using R version 3.6.1 and the Seurat R package (version 3)
When applicable, samples were integrated using the SCTransform Method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Genome_build: mm10
Supplementary_files_format_and_content: .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR data, matching status, and other data in the @meta.data field.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: C57BL/6 mice received 100,000 MC38 tumor cells subcutaneously in the flank on day 0. Peripheral blood was isolated using retroorbital collection prior to euthanasia, and then tumors were collected from the same mice after euthanasia. Leukocytes were enriched from peripheral blood using histopaque gradients. Tumor-infiltrating lymphocytes were enriched from tumor samples by performing digestion with collagenase I followed by discontinous percoll gradient. CD8+ CD44+ T cells from blood and CD8+ T cells from tumors were sorted using a BD Aria sorter prior to performing 10X.

extract_protocol:
Sorted CD8+ CD44+ T cells from peripheral blood and sorted CD8+ T cells from tumors were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
For samples with gene expression and T cell receptor sequencing only, protocol number CG000086 Rev G from 10X Genomics (User Guide, Chromium Single Cell V(D)J Reagent Kits) was used. For samples with had gene expression, T cell receptor sequencing, and CITE seq to detect Feature Barcodes, protocol number CG000208 RevD from 10X Genomics (User Guide, Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 with Feature Barcoding technology for Cell Surface Protein) was used
10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing, and for some samples Feature Barcode detection)

treatment_protocol: Mice did not receive any treatments.

tag: tissue

value: peripheral blood

tag: cell type

value: CD8+ CD44+ T cells

tag: mouse strain


title: Mouse5_MC38_tumor_CD8Tcells_CITE

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 5. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins.  These files contain the CITE seq data to detect protein expression using Feature Barcodes.
M5_Tumor.rds

source_name: Mouse 5

value: MC38 tumor

value: CD8+ T cells


title: Mouse4_blood_CD8Tcells_GEX

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 4 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the gene expression data.
M4_Blood.rds


title: Mouse4_MC38_tumor_CD8Tcells_GEX

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 4. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the gene expression data.
M4_Tumor.rds


title: PAE 2wk Female 2

status: Public on Jan 14 2021

type: RNA

city: Bryan

first: Amanda

last: Mahnke

state: TX

address: 8447 Riverside Parkway

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University Health Science Center

description: PAE

data_processing: miRNAs expressed in >80% of samples (either PAE or cont) were normalized to average miRNA expression for each sample, with undetermined values replaced with 1+highest CT for each miRNA

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

label_protocol: Exiqon miRCURY LNA Universal RT cDNA synthesis kit, ExiLENT SYBR green master mix

extract_protocol: Qiagen miRNeasy Mini Kit with 1.2ug MS2 carrier RNA per sample

tag: gender

value: Female

tag: age

tag: participant number

tag: analysis inclusion

value: Included


title: Mouse4_MC38_tumor_CD8Tcells_VDJ

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 4. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the TCR sequencing data.
M4_Tumor.rds


title: Mouse3_MC38_tumor_CD8Tcells_GEX

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 3. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M3_Tumor.rds

source_name: Mouse 3


title: Mouse3_blood_CD8Tcells_GEX

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 3 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M3_Blood.rds


title: GFPPC3_Exo1

city: Herston

first: Harley

middle: Rose

last: Robinson

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMRBerghofer

description:
miRNA
GFP-PC3 extracellular vesicles

data_processing:
Base calls were generated using the Illumina NextSeq500 software, RTA (v2.1.3).
Trimming of adaptor sequences was completed using cutadapt (v1.9) for the following adaptors: >TruSeq1  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  >TruSight1  GCGAATTTCGACGATCGTTGCATTAACTCGCGA  Trimmed reads shorter than 1 base were discarded if any.
Alignment to the whole known human miRNAome (miRbase v21) using STAR (v2.5.2a) and the following non-default parameters: --outFilterMismatchNoverLmax 0.05  --outFilterMatchNmin 16  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --alignIntronMax 1
Using samtools (v1.3), we merged and coordinate sorted the alignments
Data was filtered using the following cut off: rowSums(row>20) >=2, where rowSums is the sum of all counts for miRNA across all replicates and test conditions.
miRNAs were normalised using empirical normalization method from the RUVseq package and DESeq2 (default parameters)
Genome_build: human mature sequences miRBase v21
Supplementary_files_format_and_content: tab-delimited text file contains raw counts for identified miRNAs, pre- and post- filter, and normalised counts.

source_name: Advanced prostate cancer

growth_protocol: Cells maintained in 37°C, 5% CO2, in 5%FBS/RPMI-1640. Stable cell lines were maintained in 0.1 mg/ml G418 (Gibco).

extract_protocol:
Extracellular vesicles were extracted using ultracentrifugation. Subsequent total RNA extraction from both EVs and cells completed using Trizol reagent. Small RNA were selected for sequencing using the NEBNext Small RNA library Prep Kit.
Small RNA were selected for sequencing using the NEBNext Small RNA library Prep Kit. Libraries were size selected using a Perkin Elmer Labchip XT

value: Epithelial cell line

tag: ectopic expression

value: GFP

tag: cell line


title: Mouse3_MC38_tumor_CD8Tcells_VDJ

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 3. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M3_Tumor.rds


title: Mouse2_blood_CD8Tcells_VDJ

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 2 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M2_Blood.rds

source_name: Mouse 2


title: Mouse3_blood_CD8Tcells_VDJ

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 3 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M3_Blood.rds


title: Mouse4_MC38_tumor_CD8Tcells_CITE

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 4. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins
M4_Tumor.rds


title: PAE 2wk Male 1

description: PAE

value: Male


title: Epithelial cells WT infected 1

first: Matthew

middle: K

last: Waldor

address: 181 Longwood Avenue

department: Microbiology

data_processing:
Reads were trimmed using TrimGalore! (Galaxy tool version 0.4.3.1) using automatic adapter sequence detection
Reads were mapped to rabbit genome OryCun2.0 GCA_000003625.1 using RNA STAR (Galaxy tool version 2.6.0b-1)
Read count matrix was created from mapped reads using featureCounts (Galaxy tool 1.6.4+galaxy1) using OryCun2.0 Ensembl Annotation from May 2019
Genome_build: OryCun2.0 GCA_000003625.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

source_name: Infant rabbit colonic epithelial cells

extract_protocol:
Colonic epithelial and lamina propria cells were harvested and preserved using Trizol reagent. Total RNA was extracted using the Direct-Zol RNA MiniPrep Plus (Zymo)
mRNA libraries were prepared using KAPA mRNA HyperPrep kit (Roche)

tag: agent

value: WT EHEC

value: Epithelial cells


title: Mouse2_blood_CD8Tcells_GEX

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 2 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M2_Blood.rds


title: Mouse1_blood_CD8Tcells_VDJ

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 1 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M1_Blood.rds

source_name: Mouse 1


title: Mouse2_MC38_tumor_CD8Tcells_VDJ

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 2. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M2_Tumor.rds


title: Mouse1_blood_CD8Tcells_GEX

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 1 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M1_Blood.rds


title: Mouse1_MC38_tumor_CD8Tcells_VDJ

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 1. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the TCR sequencing data.
M1_Tumor.rds


title: Mouse2_MC38_tumor_CD8Tcells_GEX

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 2. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M2_Tumor.rds


title: Mouse1_MC38_tumor_CD8Tcells_GEX

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 1. 10X 5' gene expression and paired T cell receptor sequencing were performed. These files contain the gene expression data.
M1_Tumor.rds


title: Kiernan_2Inputs_F0-F00

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

library_source: genomic

data_processing:
Raw reads filtering perfomed with fastq_illumina_filter (version 0.1)
Raw reads quality control perfomed with Fastqc (version 0.11.2)
Reads alignment with BWA (0.7.10) on HG38 human genome version
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized either by corresponding input or by the average of four inputs (subtraction) using RPGC normalization
Genome_build: HG38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

molecule: genomic DNA

source_name: HeLa cell

growth_protocol: HeLa cells were grown in Dulbecco modified Eagle's minimal essential medium (DMEM) (sigma-Aldrich D6429), supplemented with 10% FCS, and containing 1% Penicillin streptomycin (Sigma P4333). All cells were grown in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
ChIP experiments were performed in HeLa cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit

treatment_protocol:
MRN complex was depleted by transducing HeLa cells with shRNA expressing lentiviral particles for 4 days.
Heat shock was performed on HeLa cells by incubating the celss for one hour at 42°C
RNAPII build up was performed by treating HeLa cells with 150µM DRB for 0, 1 or 3h as indicated. "Release" samples were treated for 3h with DRB then washed and harvested after 1h of incubation at 37°C

tag: treatment

tag: passages

tag: chip antibody


title: SD3A-WT2

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality of sequencing reads was assessed using fastQC (Andrews, 2010).
Reads were mapped against the human genome (hg19) and human rRNA sequences using ContextMap version 2.7.9 (Bonfert et al., 2015) (using BWA (Li and Durbin, 2009) as short read aligner and default parameters).
Number of read fragments per gene were determined from the mapped RNA-Seq reads using featureCounts (strand-specific for stranded libraries, non-strand-specific otherwise) (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Counts in tab delimited text file

source_name: GBM Glioma Stem Cells

growth_protocol: Glioblastoma stem cell (GSC) lines were propagated in neural stem cell media (Neurocult NS-A proliferation kit (human), Stemcell Technologies), supplemented with bFGF (10 ng/ml; Peprotech), EGF  (20 ng/ml; Peprotech) and Heparin (0.0002%; Stemcell Technologies) as adherent cultures on cell culture dishes that were coated with laminin (10 µg/ml in PBS; 1 hr in cell culture incubator; Invitrogen). For passaging, cells were dissociated with Accutase (Gibco).

extract_protocol:
RNA was collected from GBM cells cultured on laminin-coated dishes with RNeasy (QIAGEN).
Libraries for Illumina Next Generation sequencing were prepared with NEBNext Ultra Directional RNA Library Prep Kit (NEB E7420).

tag: disease state

value: glioblastoma

value: GBM Glioma Stem Cells

tag: genotype

value: WT


title: SD3A-WT1


title: Kiernan_2Inputs_H0-H00


title: SD3A-WT3


title: SD3A-KO1

value: KO


title: SD3A-AKO1


title: SD3A-1-AWT1


title: SD3-AKO4


title: SD3-AWT2


title: SD3A-AWT1


title: SD3-AKO3


title: SD3-AKO2


title: SD3-AWT3


title: SD3-AKO1


title: SD2-AWT3


title: SD2-AWT2


title: SD2-AWT1


title: SD2-AKO3


title: SD2-AKO2


title: SD1-WT2


title: SD3A-KO2


title: SD2-AKO1


title: SD1-WT3


title: SD3A-KO3


title: SD1-KO2


title: SD1-WT1


title: SD1-KO1


title: SD3A-1-AKO1


title: SD1-KO3


title: PDX samples number 58

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
RNA was isolated and 65bp single-end sequencing was performed on an Illumina HiSeq2500. Sequence samples from PDX were mapped to the mouse reference genome (Mus musculus mm10) and the human genome (Homo sapiens hg38) using TopHat (2.0.12) with default settings (Trapnell et al., 2009). XenofilteR was applied to filter sequence reads from mouse origin (Kluin et al., 2018). Filtered sequence reads were counted using HTSeq-count (Anders et al., 2015).
Genome_build: hg38
Raw read count data from bam files filtered for mouse reads with XenofilteR (PMID:30286710)
Supplementary_files_format_and_content: counts

source_name: Human mesothelioma cells grown in immune deficiemt mouse

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: mesothelioma cells


title: SD3-AWT1


title: PDX samples number 54


title: PDX samples number 56


title: PDX samples number 55


title: PDX samples number 53


title: PDX samples number 50


title: Wild type, administered 7.5 ug Alt Ext 1

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing: cellranger (v3.0.2)

source_name: CD45+ cells from lung

growth_protocol: standard mouse facility

extract_protocol:
Lung were harvested on day 7 and digested using DNAse (0.1%) and collagenase (2mg/ml) for 30 minutes at 37C.
10Xgenomics Single Cell 3' v2

treatment_protocol: PBS or Alt Ext on day0, 3, 6

tag: Sex

value: female

value: wild type

value: Alt Ext Ext (7.5ug)


title: PDX samples number 51


title: Wild type, administered 7.5 ug Alt Ext 2

value: male


title: gut microbiome

city: Little Rock

first: Umesh

middle: D

last: Wankhade

state: Arkansas

department: Pediatrics

institute: University of Arkansas Medical Sciences

description: Microbial DNA

data_processing:
The processing and quality-filtering of reads were performed by using scripts in QIIME (v1.9.1) and other in-house scripts. Paired reads were stitched with PEAR, an over-lapping paired-end reads merger algorithm, which evaluated all possible paired-end read overlaps, minimizing false-positive hits . The reads were further filtered based on Phred quality scores and, for chimeric reads, using USEARCH61 . The filtered reads (mean counts per sample = 37,971) were de-multiplexed within QIIME and samples with less than 5000 reads were excluded from further analysis. UCLUST was used to cluster sequences into operational taxonomical units (OTUs based on >97% identity) . Operational taxonomical unit (OTU)-picking was performed using an open-reference method which encompassed the clustering of reads against a reference sequence collection, as well as picking out the reads which failed to align with any known reference sequence in the database . To eliminate erroneous mislabeling, the resulting OTU tables were checked for mislabeling sequences . Representative sequences were further aligned using PyNAST with the Greengenes core-set alignment template . Construction of a phylogenetic tree was performed using the default (FASTTREE) method in QIIME [35]. OTUs were normalized by the predicted 16S copy number and functions were predicted with the use of GreenGenes 13_5 databases for KEGG Orthologs.
Supplementary_files_format_and_content: .Biom (Otu based)

organism: mouse gut metagenome

source_name: mouse fecal DNA

growth_protocol: The mice were group-housed (4–5 mice per cage) in an Association for the Assessment and Accreditation of Laboratory Animal Care-approved animal facility at the Arkansas Children’s Research Institute, with a constant temperature of 22 °C and the lights on from 6:00 a.m. to 6:00 p.m daily. The Institutional Animal Care and Use Committee at the University of Arkansas for Medical Sciences approved all of the animal procedures. Four-week-old male and female C57BL/6J mice were produced from several breeding pairs using multiple dams. The male and female mice were randomly divided into four different groups. The number of mice per group was dictated by power analysis. Using the effect sizes.

extract_protocol:
The extracted DNA was quantitated spectrophotometrically and stored at −20 °C. Fifty nanograms of genomic DNA were utilized for the amplification of the V4 variable region of the 16S rRNA gene using 515F/806R primers. Forward and reverse primers were dual-indexed, as described by Kozich et al., to accommodate the multiplexing of up to 384 samples per run. Paired-end sequencing (2 × 250 bp) of pooled amplicons was carried out on an Illumina MiSeq with ~30% of PhiX DNA.
Paired-end sequencing (2 × 250 bp) of pooled amplicons was carried out on an Illumina MiSeq with ~30% of PhiX DNA

treatment_protocol: The mice were randomized to either a control diet (TD.95092, Harlan Teklad, MA, USA) or a blueberry-supplemented diet (containing 5% (by wt) freeze-dried blueberry powder (TD.10679, Harlan Teklad, MA, USA)) provided ad libitum.

tag: mouse diet

value: Control and blueberry

tag: mouse gender

value: Male and female mice

tag: mouse genotype

value: WT and GPR109 knockout


title: Wild type, administered vehicle (PBS)

value: vehicle control (PBS)


title: CMS_H1_RNA

city: Zhengzhou

first: Shuaifei

last: Lu

state: Henan

address: Jinshui East Road 156

country: China

institute: Henan University of Chinese Medicine

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: hippocampus

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: The control group was placed in a separate room without stress, while the CUMS group were subjected to a chronic unpredictable mild stress included water deprivation, continuous lighting, cage tilt (45°), soiled cage, intermittent white noise (85 dB), stroboscopic lighting (300 flashes/min), paired housing, novel object in the home cage , restraint (2 h), empty bottle, inversion of day/night light cycle.

tag: strain

tag: tissue

value: hippocampus

value: 8 weeks old

tag: group

value: saline


title: CMS_H2_RNA

tag: age


title: CMS_H3_RNA


title: Bai_H2_RNA

value: baicalin


title: Bai_H1_RNA


title: 17586_Spo7_rep1_ChIP-exo

city: Ithaca

first: B. Franklin

last: Pugh

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.3 with the following setting: q-value (0.01) and the rest of the options as recommended defaults.
Genome_build: sacCer3
Supplementary_files_format_and_content: bw, bed format, ChExMix peak calls

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: antibody

value: TAP-tag:Sigma i5006

tag: growthmedia

value: YPD

tag: assaytype

value: ChIP-exo


title: 14410_Rpb10_rep1_ChIP-exo


title: 14380_Trm5_rep1_ChIP-exo


title: PDX samples number 57

tag: cell type


title: 12031_Rtf1_rep1_ChIP-exo


title: 14412_Rei1_rep1_ChIP-exo


title: 17807_Zms1_rep1_ChIP-exo


title: 14413_Pta1_rep1_ChIP-exo


title: 14846_Mks1_rep1_ChIP-exo

value: HA-tag:Santa Cruz sc-7392


title: PDX samples number 52

value: mesothelioma cells


title: 11933_Ysh1_rep1_ChIP-exo


title: 17015_Yta7_rep2_ChIP-exo


title: 11983_Zap1_rep2_ChIP-exo


title: 13785_Ysh1_rep2_ChIP-exo


title: 11817_Zap1_rep1_ChIP-exo


title: 11893_Yta7_rep1_ChIP-exo


title: 17054_Yrr1_rep2_ChIP-exo


title: 14400_Ysa1_rep1_ChIP-exo


title: 14857_Yra1_rep1_ChIP-exo


title: 28271_Yrm1_rep1_ChIP-exo


title: Bai_H3_RNA


title: 28357_Yox1_rep3_ChIP-exo


title: 20464_Yox1_rep1_ChIP-exo


title: 13454_Ypr1_rep1_ChIP-exo


title: 21012_Yox1_rep2_ChIP-exo


title: 15801_Yng2_rep2_ChIP-exo


title: 12446_Yng2_rep1_ChIP-exo


title: 11831_Yng1_rep1_ChIP-exo


title: 17793_YLL032C_rep1_ChIP-exo


title: 17952_Yku80_rep1_ChIP-exo


title: 18478_Yku70_rep1_ChIP-exo


title: 14189_Yhm2_rep1_ChIP-exo


title: 20463_Yku80_rep2_ChIP-exo


title: 17138_Yen1_rep1_ChIP-exo


title: 28327_YLR278C_rep1_ChIP-exo


title: 20024_Ydr1_rep1_ChIP-exo

value: Weil Lab


title: 14852_Yrr1_rep1_ChIP-exo


title: 11887_Ycs4_rep1_ChIP-exo


title: 17024_Ycs4_rep2_ChIP-exo


title: 17878_Yap1_rep1_ChIP-exo


title: 18492_Yap5_rep2_ChIP-exo


title: 12002_Yap7_rep1_ChIP-exo


title: 17973_Yap3_rep1_ChIP-exo


title: 17774_Xbp1_rep1_ChIP-exo


title: 20460_Yap1_rep2_ChIP-exo


title: 11832_Yaf9_rep1_ChIP-exo


title: 11980_Wtm2_rep1_ChIP-exo


title: 14807_Whi5_rep2_ChIP-exo


title: 14406_Whi5_rep1_ChIP-exo


title: 11917_War1_rep1_ChIP-exo


title: 11829_Vps75_rep1_ChIP-exo


title: 16019_Yhp1_rep1_ChIP-exo


title: 18490_Vps72_rep2_ChIP-exo


title: 17974_Wtm1_rep1_ChIP-exo


title: 11888_Ycg1_rep1_ChIP-exo


title: 14198_Yap7_rep2_ChIP-exo


title: 11982_Yap5_rep1_ChIP-exo


title: 15777_Vps71_rep2_ChIP-exo


title: 11902_Vps36_rep1_ChIP-exo


title: 11840_Vps71_rep1_ChIP-exo


title: 13463_Vid22_rep1_ChIP-exo


title: 18500_Vid27_rep1_ChIP-exo


title: 14438_Utp9_rep1_ChIP-exo


title: 16224_Vid22_rep2_ChIP-exo


title: 17049_Vid21_rep2_ChIP-exo


title: 14181_War1_rep2_ChIP-exo


title: 14829_Vid21_rep1_ChIP-exo


title: 13468_Utp8_rep1_ChIP-exo


title: 12847_Utp15_rep1_ChIP-exo


title: 14524_Utp5_rep1_ChIP-exo


title: 17943_Utp4_rep1_ChIP-exo


title: 11901_Uth1_rep1_ChIP-exo


title: 18458_Urc2_rep2_ChIP-exo


title: 14528_Utp10_rep1_ChIP-exo


title: 14361_Ura6_rep1_ChIP-exo


title: 17122_Urc2_rep1_ChIP-exo


title: 13153_Vps72_rep1_ChIP-exo


title: 14358_Ung1_rep1_ChIP-exo


title: 13775_Ume6_rep2_ChIP-exo


title: 20456_Upc2_rep1_ChIP-exo


title: 14755_Ura4_rep1_ChIP-exo


title: 12027_Ume1_rep1_ChIP-exo


title: 11017_Ume6_rep1_ChIP-exo


title: 20128_Ubp8_rep5_ChIP-exo

tag: treatment

value: 6 min heat shock


title: 17214_Uga3_rep1_ChIP-exo


title: 13472_Ubc13_rep1_ChIP-exo


title: 14981_Ubp8_rep3_ChIP-exo


title: 11963_Ubp8_rep2_ChIP-exo


title: 11962_Ubp8_rep1_ChIP-exo


title: 12447_Ubp12_rep1_ChIP-exo


title: 15672_Ubp8_rep4_ChIP-exo


title: 12465_Uaf30_rep1_ChIP-exo


title: 12850_Uba2_rep1_ChIP-exo


title: 17561_Uaf30_rep2_ChIP-exo


title: 13777_Ure2_rep1_ChIP-exo


title: 15773_Tup1_rep2_ChIP-exo


title: 12851_Trp5_rep1_ChIP-exo


title: 11919_Tpk1_rep1_ChIP-exo


title: 17191_Tpk2_rep2_ChIP-exo


title: 17579_Tpk1_rep2_ChIP-exo


title: 17009_Ume1_rep2_ChIP-exo


title: 14192_Tpk3_rep1_ChIP-exo


title: 14826_Tra1_rep1_ChIP-exo


title: 17121_Tos4_rep1_ChIP-exo


title: 11906_Tor1_rep1_ChIP-exo


title: 17140_Top2_rep1_ChIP-exo


title: 14976_Tpd3_rep1_ChIP-exo


title: 16031_Top3_rep1_ChIP-exo


title: 17771_TOP1_rep2_ChIP-exo


title: 11821_TOP1_rep1_ChIP-exo


title: 17123_Tod6_rep1_ChIP-exo


title: 17144_Tom1_rep1_ChIP-exo


title: 15245_Tpk2_rep1_ChIP-exo


title: 13782_Tup1_rep1_ChIP-exo


title: 20021_TOA1_rep3_ChIP-exo


title: 14466_Tip41_rep1_ChIP-exo


title: 17806_Tho1_rep2_ChIP-exo


title: 14838_TOA1_rep1_ChIP-exo


title: 14647_Thp2_rep1_ChIP-exo


title: 14447_Trm1_rep1_ChIP-exo


title: 12463_Tma46_rep1_ChIP-exo


title: 17872_Thp2_rep2_ChIP-exo


title: 14353_Tho1_rep1_ChIP-exo


title: 14364_Tif1_rep1_ChIP-exo


title: 11984_Thp1_rep1_ChIP-exo


title: 17563_Tfg2_rep1_ChIP-exo


title: 14275_Tfg1_rep2_ChIP-exo


title: 12069_Thi3_rep1_ChIP-exo


title: 14158_Tfc8_rep2_ChIP-exo


title: 17981_TFC6_rep2_ChIP-exo


title: 17966_Tfc4_rep2_ChIP-exo


title: 14159_Tfc7_rep2_ChIP-exo


title: 11838_Tfc7_rep1_ChIP-exo


title: 14821_Tfc4_rep1_ChIP-exo


title: 11986_TFC6_rep1_ChIP-exo


title: 13779_Tfc3_rep2_ChIP-exo


title: 11835_Tfc3_rep1_ChIP-exo


title: 14166_TFC1_rep2_ChIP-exo


title: 17053_TOA1_rep2_ChIP-exo


title: 17137_Tfb6_rep1_ChIP-exo


title: 11867_TFC1_rep1_ChIP-exo


title: 14258_Tfb4_rep2_ChIP-exo


title: 11871_Tfb4_rep1_ChIP-exo


title: 14472_Tfb1_rep1_ChIP-exo


title: 14257_Tfb3_rep2_ChIP-exo


title: 12100_Tfa2_rep1_ChIP-exo


title: 20023_TFA1_rep3_ChIP-exo


title: 17795_Tfb2_rep2_ChIP-exo


title: 11836_Tfc8_rep1_ChIP-exo


title: 14971_Tfb1_rep2_ChIP-exo


title: 14276_TFA1_rep2_ChIP-exo


title: 12099_Tfg1_rep1_ChIP-exo


title: 14600_Tfa2_rep2_ChIP-exo


title: 11870_Tfb3_rep1_ChIP-exo


title: 12101_TFA1_rep1_ChIP-exo


title: 17134_Tel2_rep1_ChIP-exo


title: 14657_Tea1_rep2_ChIP-exo


title: 14369_Tea1_rep1_ChIP-exo


title: 20453_Tda9_rep2_ChIP-exo


title: 17223_Tec1_rep1_ChIP-exo


title: 11845_Tbs1_rep1_ChIP-exo


title: 11825_Tbf1_rep1_ChIP-exo


title: 11865_Taf9_rep1_ChIP-exo


title: 15205_Taf9_rep2_ChIP-exo


title: 14155_Tbf1_rep2_ChIP-exo


title: 14868_Tap42_rep1_ChIP-exo


title: 15186_Taf8_rep2_ChIP-exo


title: 14651_Tfb2_rep1_ChIP-exo


title: 20018_TAF7_rep3_ChIP-exo


title: 11740_Taf8_rep1_ChIP-exo


title: 15208_TAF7_rep2_ChIP-exo


title: 20017_Taf6_rep3_ChIP-exo


title: 15206_Taf6_rep2_ChIP-exo


title: 20016_Taf5_rep3_ChIP-exo


title: 17874_Taf4_rep2_ChIP-exo


title: 11768_Taf5_rep1_ChIP-exo


title: 11864_Taf6_rep1_ChIP-exo


title: 15190_Taf5_rep2_ChIP-exo


title: 15183_Taf4_rep1_ChIP-exo


title: 20013_Taf2_rep3_ChIP-exo


title: 14162_Tbs1_rep2_ChIP-exo


title: 17880_Tda9_rep1_ChIP-exo


title: 15198_Taf2_rep2_ChIP-exo


title: 17873_Taf3_rep2_ChIP-exo


title: 11846_Taf2_rep1_ChIP-exo


title: 11861_Taf3_rep1_ChIP-exo


title: 17961_Taf14_rep2_ChIP-exo


title: 20012_Taf14_rep3_ChIP-exo


title: 17574_Taf14_rep1_ChIP-exo


title: 11863_Taf12_rep1_ChIP-exo


title: 15209_Taf13_rep2_ChIP-exo


title: 17944_Taf11_rep2_ChIP-exo


title: 15775_Taf12_rep2_ChIP-exo


title: 12856_Taf11_rep1_ChIP-exo


title: 11860_Taf13_rep1_ChIP-exo


title: 20008_Taf10_rep3_ChIP-exo


title: 15185_Taf10_rep2_ChIP-exo


title: 11741_Taf10_rep1_ChIP-exo


title: 20007_Taf1_rep3_ChIP-exo


title: 20015_Taf4_rep3_ChIP-exo


title: 11988_TAF7_rep1_ChIP-exo


title: 15184_Taf1_rep2_ChIP-exo


title: 11744_Taf1_rep1_ChIP-exo


title: 12015_Swi6_rep1_ChIP-exo


title: 11751_Swr1_rep1_ChIP-exo


title: 18001_Swi6_rep2_ChIP-exo


title: 18016_Swi5_rep2_ChIP-exo


title: 12059_Swi5_rep1_ChIP-exo


title: 15779_Swr1_rep2_ChIP-exo


title: 12000_Swi4_rep1_ChIP-exo


title: 14277_Swi3_rep2_ChIP-exo


title: 12102_Swi3_rep1_ChIP-exo


title: 17972_Swd3_rep2_ChIP-exo


title: 14814_Swd3_rep1_ChIP-exo


title: 17859_Swi1_rep2_ChIP-exo


title: 11995_Swi1_rep1_ChIP-exo


title: 17977_Swd2_rep2_ChIP-exo


title: 15785_Swc7_rep2_ChIP-exo


title: 19312_Swd1_rep2_ChIP-exo


title: 12433_Suv3_rep1_ChIP-exo


title: 14176_Sut1_rep2_ChIP-exo


title: 11839_Swc7_rep1_ChIP-exo


title: 17801_Swd1_rep1_ChIP-exo


title: 11809_Sum1_rep1_ChIP-exo


title: 20006_Sub1_rep3_ChIP-exo


title: 18459_Sub1_rep2_ChIP-exo


title: 17124_Sub1_rep1_ChIP-exo


title: 11997_Sut1_rep1_ChIP-exo


title: 13776_Sum1_rep2_ChIP-exo


title: 13786_Swi4_rep2_ChIP-exo


title: 20022_Sua7_rep3_ChIP-exo


title: 12275_Sua7_rep2_ChIP-exo


title: 17035_Stp2_rep2_ChIP-exo


title: 11743_Sua7_rep1_ChIP-exo


title: 11929_Stp4_rep1_ChIP-exo


title: 11987_Swd2_rep1_ChIP-exo


title: 13139_Stp2_rep1_ChIP-exo


title: 15812_Sth1_rep3_ChIP-exo


title: 20452_Stp4_rep2_ChIP-exo


title: 11808_Stp1_rep1_ChIP-exo


title: 17947_Stm1_rep1_ChIP-exo


title: 14293_Stp1_rep2_ChIP-exo


title: 15805_Sth1_rep2_ChIP-exo


title: 12862_Ste12_rep1_ChIP-exo


title: 14531_Sth1_rep1_ChIP-exo


title: 14394_Std1_rep1_ChIP-exo


title: 11918_Stb5_rep1_ChIP-exo


title: 11910_Stb4_rep1_ChIP-exo


title: 15802_Ste12_rep2_ChIP-exo


title: 18503_Stb4_rep2_ChIP-exo


title: 17149_Stb2_rep1_ChIP-exo


title: 12431_Stb3_rep1_ChIP-exo


title: 17787_Ssn8_rep2_ChIP-exo


title: 14783_Stb1_rep1_ChIP-exo


title: 17886_Stb3_rep2_ChIP-exo


title: 11881_Ssn8_rep1_ChIP-exo


title: 11880_Ssn2_rep1_ChIP-exo


title: 14835_Ssn3_rep1_ChIP-exo


title: 15253_Ssl2_rep2_ChIP-exo


title: 11747_Ssl2_rep1_ChIP-exo


title: 15477_Ssl1_rep2_ChIP-exo


title: 15215_Ssl1_rep1_ChIP-exo


title: 13481_Ssa1_rep1_ChIP-exo


title: 16036_Srb6_rep1_ChIP-exo


title: 13156_Srb5_rep1_ChIP-exo


title: 11879_Srb8_rep1_ChIP-exo


title: 12050_Srb4_rep1_ChIP-exo


title: 17120_Stb6_rep1_ChIP-exo


title: 18470_Srb6_rep2_ChIP-exo


title: 17948_Srd1_rep1_ChIP-exo


title: 14182_Stb5_rep2_ChIP-exo


title: 13800_Spt8_rep2_ChIP-exo


title: 13816_Srb4_rep2_ChIP-exo


title: 11866_Spt8_rep1_ChIP-exo


title: 20004_Spt7_rep5_ChIP-exo


title: 20115_Spt7_rep6_ChIP-exo


title: 14262_Ssn2_rep2_ChIP-exo


title: 18475_Spt7_rep4_ChIP-exo


title: 17879_Srb5_rep2_ChIP-exo


title: 14638_Spt7_rep3_ChIP-exo


title: 11961_Spt7_rep2_ChIP-exo


title: 11960_Spt7_rep1_ChIP-exo


title: 15664_Spt6_rep2_ChIP-exo


title: 11894_Srm1_rep1_ChIP-exo


title: 15219_Spt6_rep1_ChIP-exo


title: 14416_Srb2_rep1_ChIP-exo


title: 12835_Spt5_rep1_ChIP-exo


title: 11748_Spt4_rep1_ChIP-exo


title: 15181_Spt4_rep2_ChIP-exo


title: 15774_Spt3_rep2_ChIP-exo


title: 15220_Spt3_rep1_ChIP-exo


title: 11834_Spt21_rep1_ChIP-exo


title: 13209_Spt23_rep1_ChIP-exo


title: 13795_Spt21_rep2_ChIP-exo


title: 15911_Spt20_rep1_ChIP-exo


title: 15493_Spt2_rep2_ChIP-exo


title: 12931_Spt2_rep1_ChIP-exo


title: 14259_Spt16_rep3_ChIP-exo


title: 8600_Spt15_rep2_ChIP-exo

value: Abcam ab61411

value: 3 min heat shock


title: 20001_Spt15_rep4_ChIP-exo


title: 8633_Spt16_rep1_ChIP-exo


title: 8602_Spt15_rep3_ChIP-exo


title: 8599_Spt15_rep1_ChIP-exo


title: 14759_Spt10_rep1_ChIP-exo


title: 17133_Spp1_rep1_ChIP-exo


title: 13469_Spe2_rep1_ChIP-exo


title: 18463_Spp1_rep2_ChIP-exo


title: 12009_Sok2_rep1_ChIP-exo


title: 20984_Soh1_rep2_ChIP-exo


title: 13809_Sok2_rep2_ChIP-exo


title: 17848_Soh1_rep1_ChIP-exo


title: 20003_Spt3_rep3_ChIP-exo


title: 14193_Snt2_rep2_ChIP-exo


title: 15787_Spt5_rep2_ChIP-exo


title: 11939_Snt2_rep1_ChIP-exo


title: 17798_Spt20_rep2_ChIP-exo


title: 14483_Sod1_rep1_ChIP-exo


title: 17587_Snt1_rep1_ChIP-exo


title: 11872_Spt16_rep2_ChIP-exo


title: 11859_Snf8_rep1_ChIP-exo


title: 12071_Snf4_rep1_ChIP-exo


title: 17857_Snf5_rep1_ChIP-exo


title: 13799_Snf6_rep2_ChIP-exo


title: 17999_Snf2_rep2_ChIP-exo


title: 14760_Snf7_rep1_ChIP-exo


title: 17939_Spt10_rep2_ChIP-exo


title: 14978_Snf11_rep2_ChIP-exo


title: 12080_Snf2_rep1_ChIP-exo


title: 17938_Snf1_rep1_ChIP-exo


title: 14458_Snf11_rep1_ChIP-exo


title: 14844_Smp1_rep1_ChIP-exo


title: 17154_Smt3_rep1_ChIP-exo


title: 17132_Smd1_rep1_ChIP-exo


title: 18462_Smd1_rep2_ChIP-exo


title: 17934_Smc4_rep2_ChIP-exo


title: 11886_Smc3_rep1_ChIP-exo


title: 14376_Smc1_rep1_ChIP-exo


title: 17988_Smc3_rep2_ChIP-exo


title: 11889_Smc4_rep1_ChIP-exo


title: 14996_Smc1_rep2_ChIP-exo


title: 14594_Sko1_rep1_ChIP-exo


title: 15654_Sko1_rep2_ChIP-exo


title: 14389_Slt2_rep1_ChIP-exo


title: 14471_Sks1_rep1_ChIP-exo


title: 14969_Skn7_rep2_ChIP-exo


title: 14464_Skn7_rep1_ChIP-exo


title: 11858_Snf6_rep1_ChIP-exo


title: 13451_Ski6_rep1_ChIP-exo


title: 17882_Sir3_rep2_ChIP-exo


title: 14784_Sir4_rep1_ChIP-exo


title: 12952_Sir3_rep1_ChIP-exo


title: 16039_Sir2_rep2_ChIP-exo


title: 18491_Sir4_rep2_ChIP-exo


title: 14758_Sir2_rep1_ChIP-exo


title: 13475_Sml1_rep1_ChIP-exo


title: 14845_Sip4_rep1_ChIP-exo


title: 17856_Sin3_rep2_ChIP-exo


title: 13792_Sin3_rep1_ChIP-exo


title: 18489_Sif2_rep2_ChIP-exo


title: 13146_Sif2_rep1_ChIP-exo


title: 14863_Skp1_rep1_ChIP-exo


title: 15778_Sgv1_rep2_ChIP-exo


title: 11827_Sgv1_rep1_ChIP-exo


title: 14491_Sgi1_rep1_ChIP-exo


title: 20000_Sgf73_rep3_ChIP-exo


title: 15793_Sgf73_rep2_ChIP-exo


title: 12459_Sgf73_rep1_ChIP-exo


title: 19999_Sgf29_rep3_ChIP-exo


title: 17217_Sgf29_rep2_ChIP-exo


title: 12466_Sgf29_rep1_ChIP-exo


title: 13366_Sgf11_rep3_ChIP-exo


title: 13365_Sgf11_rep2_ChIP-exo


title: 20607_Sgf11_rep4_ChIP-exo


title: 14619_Sfp1_rep2_ChIP-exo


title: 11852_Sgf11_rep1_ChIP-exo


title: 17861_Sin4_rep2_ChIP-exo


title: 20451_Sfh1_rep2_ChIP-exo


title: 17573_Sin4_rep1_ChIP-exo


title: 14459_Sfl1_rep1_ChIP-exo


title: 19313_Shg1_rep2_ChIP-exo


title: 14977_Sfl1_rep2_ChIP-exo


title: 12450_Sfp1_rep1_ChIP-exo


title: 12458_Set5_rep1_ChIP-exo


title: 17803_Shg1_rep1_ChIP-exo


title: 11755_Set2_rep1_ChIP-exo


title: 17852_Sfh1_rep1_ChIP-exo


title: 16049_Set3_rep2_ChIP-exo


title: 16042_Set1_rep2_ChIP-exo


title: 13791_Set2_rep2_ChIP-exo


title: 14475_Ser2_rep1_ChIP-exo


title: 12443_Set1_rep1_ChIP-exo


title: 11843_Sds3_rep1_ChIP-exo


title: 17925_Sda1_rep1_ChIP-exo


title: 15650_Sdc1_rep2_ChIP-exo


title: 13479_Sch9_rep1_ChIP-exo


title: 12086_Sdc1_rep1_ChIP-exo


title: 12064_Scc4_rep1_ChIP-exo


title: 17930_Scc2_rep2_ChIP-exo


title: 11909_Scc2_rep1_ChIP-exo


title: 17560_Sas5_rep1_ChIP-exo


title: 18017_Sas3_rep1_ChIP-exo


title: 17156_Sap30_rep2_ChIP-exo


title: 16030_Sas2_rep1_ChIP-exo


title: 15771_Sap30_rep1_ChIP-exo


title: 13806_Sip3_rep1_ChIP-exo


title: 17937_Sas4_rep1_ChIP-exo


title: 18015_Rxt3_rep2_ChIP-exo


title: 16037_Rxt2_rep1_ChIP-exo


title: 12855_Sam4_rep1_ChIP-exo


title: 12933_Rxt1_rep1_ChIP-exo


title: 22433_Rvb1_rep2_ChIP-exo


title: 18018_Rxt1_rep2_ChIP-exo


title: 14267_Sen1_rep2_ChIP-exo


title: 17014_Rvb1_rep1_ChIP-exo


title: 11907_Sen1_rep1_ChIP-exo


title: 14538_Rvb2_rep1_ChIP-exo


title: 11915_Rtt106_rep1_ChIP-exo


title: 17933_Rtt109_rep1_ChIP-exo


title: 12944_Rtt103_rep1_ChIP-exo


title: 17585_Rts2_rep2_ChIP-exo


title: 16032_Rtt102_rep2_ChIP-exo


title: 12106_Rts2_rep1_ChIP-exo


title: 11976_Rtg3_rep1_ChIP-exo


title: 15189_Rtg3_rep2_ChIP-exo


title: 14463_Rtg2_rep1_ChIP-exo


title: 18499_Rtr1_rep1_ChIP-exo


title: 12942_Rxt3_rep1_ChIP-exo


title: 11742_Rtg1_rep1_ChIP-exo


title: 14623_Rtf1_rep2_ChIP-exo


title: 19834_Rsc9_rep3_ChIP-exo


title: 14862_Rsp5_rep1_ChIP-exo


title: 17853_Rxt2_rep2_ChIP-exo


title: 15804_Rsc8_rep2_ChIP-exo


title: 12276_Rsc9_rep1_ChIP-exo


title: 19898_Rsc9_rep4_ChIP-exo


title: 12079_Rsc8_rep1_ChIP-exo


title: 15806_Rsc9_rep2_ChIP-exo


title: 15807_Rsc6_rep2_ChIP-exo


title: 15810_Rsc58_rep3_ChIP-exo


title: 12454_Set3_rep1_ChIP-exo


title: 11856_Rsc6_rep1_ChIP-exo


title: 15814_Rsc6_rep3_ChIP-exo


title: 16576_Rtt103_rep2_ChIP-exo


title: 15803_Rsc58_rep2_ChIP-exo


title: 11855_Rsc58_rep1_ChIP-exo


title: 11890_Rtt102_rep1_ChIP-exo


title: 17885_RSC4_rep1_ChIP-exo


title: 17048_Rsc30_rep1_ChIP-exo


title: 19678_Rsc3_rep4_ChIP-exo


title: 15808_Rsc3_rep2_ChIP-exo


title: 15809_Rsc1_rep3_ChIP-exo


title: 11848_Rsc3_rep1_ChIP-exo


title: 15816_Rsc1_rep4_ChIP-exo


title: 17957_Rsc2_rep1_ChIP-exo


title: 15165_Rsc1_rep2_ChIP-exo


title: 14477_Rrp42_rep1_ChIP-exo


title: 12065_Rsc1_rep1_ChIP-exo


title: 14427_Rrp4_rep1_ChIP-exo


title: 12837_Rrn7_rep1_ChIP-exo


title: 17207_Rrn9_rep2_ChIP-exo


title: 16516_Rrn9_rep1_ChIP-exo


title: 17130_Rpo31_rep1_ChIP-exo


title: 14424_Rrn6_rep1_ChIP-exo


title: 12038_Rrd1_rep1_ChIP-exo


title: 18461_Rpo31_rep2_ChIP-exo


title: 16531_Rrn5_rep1_ChIP-exo


title: 17782_Rpo21_rep1_ChIP-exo


title: 15815_Rsc3_rep3_ChIP-exo


title: 20990_Rrn10_rep2_ChIP-exo


title: 17212_Rrn5_rep2_ChIP-exo


title: 19307_Rpo21_rep2_ChIP-exo


title: 15005_Rrn6_rep2_ChIP-exo


title: 13807_Rpn4_rep2_ChIP-exo


title: 11941_Rpn4_rep1_ChIP-exo


title: 20448_Rrn10_rep1_ChIP-exo


title: 14371_Rpn14_rep1_ChIP-exo


title: 17854_Rph1_rep2_ChIP-exo


title: 16038_Rph1_rep1_ChIP-exo


title: 17858_Rpd3_rep2_ChIP-exo


title: 14654_RPC40_rep2_ChIP-exo


title: 11754_Rpd3_rep1_ChIP-exo


title: 19326_Rpc82_rep1_ChIP-exo


title: 14652_Rpc53_rep2_ChIP-exo


title: 12846_Rrn11_rep1_ChIP-exo


title: 14356_RPC40_rep1_ChIP-exo


title: 18484_Rpc37_rep2_ChIP-exo


title: 17964_Rpc37_rep1_ChIP-exo


title: 14298_Rpc17_rep2_ChIP-exo


title: 14351_Rpc53_rep1_ChIP-exo


title: 11869_Rpb9_rep1_ChIP-exo


title: 14280_Rpb7_rep2_ChIP-exo


title: 11884_Rpc19_rep1_ChIP-exo


title: 14780_Rpn11_rep1_ChIP-exo


title: 14834_Rpb4_rep1_ChIP-exo


title: 14614_Rpc25_rep2_ChIP-exo


title: 11823_Rpc17_rep1_ChIP-exo


title: 12115_Rpb7_rep1_ChIP-exo


title: 17052_Rpb4_rep2_ChIP-exo


title: 11746_Rpb3_rep2_ChIP-exo


title: 8929_Rpb3_rep1_ChIP-exo


title: 12123_Rpb2_rep1_ChIP-exo


title: 17572_Rpa49_rep1_ChIP-exo


title: 16026_Rpa43_rep2_ChIP-exo


title: 11868_RPB11_rep1_ChIP-exo


title: 13801_RPB11_rep2_ChIP-exo


title: 12097_Rpa34_rep1_ChIP-exo


title: 17562_Rpa34_rep2_ChIP-exo


title: 14260_Rpa43_rep1_ChIP-exo


title: 17596_Rpa190_rep2_ChIP-exo


title: 19335_Rpc34_rep2_ChIP-exo


title: 12421_Rpc25_rep1_ChIP-exo


title: 19398_Rpb3_rep3_ChIP-exo


title: 14256_Rpb9_rep2_ChIP-exo


title: 11876_Rpa190_rep1_ChIP-exo


title: 12104_Rpa14_rep1_ChIP-exo


title: 14776_Rpa135_rep1_ChIP-exo


title: 17578_Rpa14_rep2_ChIP-exo


title: 18502_Rox1_rep2_ChIP-exo


title: 11822_Rpa12_rep1_ChIP-exo


title: 17804_Rox3_rep1_ChIP-exo


title: 12871_Rox1_rep1_ChIP-exo


title: 17888_Rpa135_rep2_ChIP-exo


title: 19404_Rox3_rep2_ChIP-exo


title: 14633_Rna14_rep2_ChIP-exo


title: 12935_Rna14_rep1_ChIP-exo


title: 17997_Rlr1_rep2_ChIP-exo


title: 14454_Rms1_rep1_ChIP-exo


title: 14816_Rlr1_rep1_ChIP-exo


title: 17871_Rlm1_rep2_ChIP-exo


title: 17996_Rlf2_rep1_ChIP-exo


title: 13150_Rlm1_rep1_ChIP-exo


title: 14789_Rio2_rep1_ChIP-exo


title: 16010_Rim101_rep1_ChIP-exo


title: 19331_Rif2_rep2_ChIP-exo


title: 17883_Rif2_rep1_ChIP-exo


title: 17117_Rif1_rep2_ChIP-exo


title: 12428_Rif1_rep1_ChIP-exo


title: 14794_Rib1_rep1_ChIP-exo


title: 16011_Rgt1_rep1_ChIP-exo


title: 13812_Rgr1_rep2_ChIP-exo


title: 20446_Rgt1_rep2_ChIP-exo


title: 12047_Rgm1_rep1_ChIP-exo


title: 17780_Rgm1_rep2_ChIP-exo


title: 16548_Rfx1_rep2_ChIP-exo


title: 12938_Rfx1_rep1_ChIP-exo


title: 15012_Rfa1_rep1_ChIP-exo


title: 17776_Rfc1_rep1_ChIP-exo


title: 17777_Rfc5_rep1_ChIP-exo


title: 14281_Ret1_rep2_ChIP-exo


title: 12119_Ret1_rep1_ChIP-exo


title: 20445_Ref2_rep2_ChIP-exo


title: 14869_Reg2_rep1_ChIP-exo


title: 18479_Ref2_rep1_ChIP-exo


title: 12467_Reb1_rep2_ChIP-exo


title: 14425_Rhr2_rep1_ChIP-exo


title: 12124_Rgr1_rep1_ChIP-exo


title: 14197_Rcs1_rep2_ChIP-exo


title: 14968_Rds2_rep2_ChIP-exo


title: 14461_Rds2_rep1_ChIP-exo


title: 14539_Rfm1_rep1_ChIP-exo


title: 14853_Rdr1_rep1_ChIP-exo


title: 14819_Rco1_rep1_ChIP-exo


title: 19998_Rap1_rep3_ChIP-exo


title: 17962_Rai1_rep1_ChIP-exo


title: 11765_Rap1_rep1_ChIP-exo


title: 15258_Rap1_rep2_ChIP-exo


title: 16230_Rat1_rep1_ChIP-exo


title: 15260_Rad6_rep2_ChIP-exo


title: 11753_Rad6_rep1_ChIP-exo


title: 20974_Rad9_rep2_ChIP-exo


title: 14787_Rad57_rep1_ChIP-exo


title: 14433_Rad54_rep1_ChIP-exo


title: 13461_Rad52_rep1_ChIP-exo


title: 13447_Rad50_rep1_ChIP-exo


title: 14663_Rad51_rep1_ChIP-exo


title: 14502_Rad30_rep1_ChIP-exo


title: 17791_Rad3_rep2_ChIP-exo


title: 14388_Rad2_rep1_ChIP-exo


title: 13155_Rad3_rep1_ChIP-exo


title: 13476_Pwp1_rep1_ChIP-exo


title: 14372_Pzf1_rep1_ChIP-exo


title: 14282_Rpb2_rep2_ChIP-exo


title: 12872_Put3_rep1_ChIP-exo


title: 18482_Pub1_rep2_ChIP-exo


title: 14373_Pus4_rep1_ChIP-exo


title: 12074_Pup1_rep1_ChIP-exo


title: 14381_Rmt2_rep1_ChIP-exo


title: 13455_Ptc3_rep1_ChIP-exo


title: 14375_Rib4_rep1_ChIP-exo


title: 14999_Pub1_rep1_ChIP-exo


title: 14795_Rad55_rep1_ChIP-exo


title: 15003_Pta1_rep2_ChIP-exo


title: 14832_Rpc34_rep1_ChIP-exo


title: 12424_Qri8_rep1_ChIP-exo


title: 14533_Psy2_rep1_ChIP-exo


title: 14790_Qri1_rep1_ChIP-exo


title: 17970_Psh1_rep1_ChIP-exo


title: 14864_Prr2_rep1_ChIP-exo


title: 26016_Put3_rep2_ChIP-exo


title: 18469_Prp46_rep2_ChIP-exo


title: 17155_Prp46_rep1_ChIP-exo


title: 17965_Prp45_rep2_ChIP-exo


title: 18465_Prp4_rep2_ChIP-exo


title: 17141_Prp4_rep1_ChIP-exo


title: 13459_Pre4_rep1_ChIP-exo


title: 14501_Pre8_rep1_ChIP-exo


title: 13473_Pre2_rep1_ChIP-exo


title: 17153_Pog1_rep1_ChIP-exo


title: 17150_Pol2_rep1_ChIP-exo


title: 14285_Pob3_rep2_ChIP-exo


title: 12117_Png1_rep1_ChIP-exo


title: 14393_Pnc1_rep1_ChIP-exo


title: 12932_Pop2_rep1_ChIP-exo


title: 12141_Reb1_rep1_ChIP-exo


title: 17135_Pol1_rep1_ChIP-exo


title: 17772_Plo2_rep1_ChIP-exo


title: 12840_Plp1_rep1_ChIP-exo


title: 16013_RIM20_rep1_ChIP-exo


title: 17143_Plo1_rep1_ChIP-exo


title: 18476_Pip2_rep2_ChIP-exo


title: 12849_Pho85_rep1_ChIP-exo


title: 17892_Prp45_rep1_ChIP-exo


title: 16604_Pip2_rep1_ChIP-exo


title: 14833_Rpc31_rep1_ChIP-exo


title: 14840_Pho4_rep1_ChIP-exo


title: 15191_Pho23_rep2_ChIP-exo


title: 11761_Pho23_rep1_ChIP-exo


title: 12137_Pho2_rep1_ChIP-exo


title: 12060_Pob3_rep1_ChIP-exo


title: 17018_Phd1_rep2_ChIP-exo


title: 20443_Pdr3_rep2_ChIP-exo


title: 18497_Pdr1_rep2_ChIP-exo


title: 16586_Pdr1_rep1_ChIP-exo


title: 17769_Pdr3_rep1_ChIP-exo


title: 14395_Pct1_rep1_ChIP-exo


title: 12055_Pgd1_rep1_ChIP-exo


title: 13802_Rpc19_rep2_ChIP-exo


title: 14596_Phd1_rep1_ChIP-exo


title: 13819_Pgd1_rep2_ChIP-exo


title: 13442_Pdc1_rep1_ChIP-exo


title: 13148_Pcf11_rep1_ChIP-exo


title: 12085_Pat1_rep1_ChIP-exo


title: 14530_Pap1_rep1_ChIP-exo


title: 17875_Pap1_rep2_ChIP-exo


title: 15772_Paf1_rep2_ChIP-exo


title: 14870_Pcl9_rep1_ChIP-exo


title: 16546_Rpa12_rep2_ChIP-exo


title: 14186_Plp2_rep1_ChIP-exo


title: 15486_Pcf11_rep2_ChIP-exo


title: 11750_Paf1_rep1_ChIP-exo


title: 12037_Pho80_rep1_ChIP-exo


title: 17928_Pab1_rep1_ChIP-exo


title: 12001_Rcs1_rep1_ChIP-exo


title: 14470_Otu1_rep1_ChIP-exo


title: 16527_Orc6_rep2_ChIP-exo


title: 14534_Orc6_rep1_ChIP-exo


title: 18467_Orc5_rep2_ChIP-exo


title: 17147_Orc4_rep1_ChIP-exo


title: 16352_Orc1_rep2_ChIP-exo


title: 17148_Orc5_rep1_ChIP-exo


title: 19306_Orc2_rep2_ChIP-exo


title: 14474_Orc1_rep1_ChIP-exo


title: 14995_Oaf3_rep2_ChIP-exo


title: 17775_Orc2_rep1_ChIP-exo


title: 12054_Nut2_rep1_ChIP-exo


title: 14404_Oaf1_rep1_ChIP-exo


title: 14858_Nup42_rep1_ChIP-exo


title: 12007_Nsp1_rep1_ChIP-exo


title: 17779_Nto1_rep1_ChIP-exo


title: 18007_Nut1_rep1_ChIP-exo


title: 18485_Nut1_rep2_ChIP-exo


title: 15792_Nrm1_rep2_ChIP-exo


title: 14779_Nsr1_rep1_ChIP-exo


title: 12878_Nrm1_rep1_ChIP-exo


title: 14812_Nrg1_rep2_ChIP-exo


title: 14265_Nrd1_rep2_ChIP-exo


title: 14355_Oaf3_rep1_ChIP-exo


title: 16023_Nrg2_rep2_ChIP-exo


title: 11900_Nrd1_rep1_ChIP-exo


title: 14419_Nrg1_rep1_ChIP-exo


title: 17926_Npl6_rep1_ChIP-exo


title: 17863_Nut2_rep2_ChIP-exo


title: 18460_Npl3_rep2_ChIP-exo


title: 12110_Nsa2_rep1_ChIP-exo


title: donor_37_Ftot

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
Quality control of all samples was performed using the FastQC software v0.11.5.
Samples were aligned to the UCSC hg38 version of the human using STAR-2.5.3a aligner,  and a count table was directly obtained with STAR. Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package.
Normalization was performed using edgeR algorithm. Raw counts were normalized to obtain Counts Per Million mapped reads (CPM) and Reads Per Kilobase per Million mapped reads (RPKM). Only genes with a CPM greater than 1 in at least 1 sample were retained for downstream analyses.
The heterogeneity of the data was evaluated with a Principal Component Analysis (PCA)-plot of the log-transformed normalized CPM, evaluating whether they clustered with similar samples in the same dataset. Sample number 36 was excluded from downstream analyses due to possible experimental contaminations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Amniotic Fluid Stem cells

growth_protocol: hAFSCs were grown in culture medium (αMEM) supplemented with 20% foetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin (all from EuroClone Spa, Milano, Italy).

extract_protocol:
100 ng of total RNA were used to isolate mRNA using NEXTflex™ Poly(A) Beads (Bioo Scientific, Burleson Rd, Austin, TX, USA), as reported in the producer protocol.
The obtained mRNA was used to prepare the RNA library using NEXTflex™ Rapid Directional qRNA-Seq™ Kit (Bioo Scientific, Burleson Rd, Austin, TX, USA), following the instructions. This kit contains a set of 96 distinct molecular labels on the sequencing adapters. Each label consists of an 8 nucleotide barcode tag. During the ligation reaction, each cDNA fragment end independently and randomly ligates to a single label from this pool of 96 adapters to result in a total of 96 x 96 = 9,216 possible combinations across both ends. For every clone sequenced, paired-end reads reveal the chosen label on each end along with adjoining cDNA sequence.

treatment_protocol: hAFSCs sub-populations were sorted using a label-free, flow-assisted fractionation protocol through Celector® technology (Stem Sel Ltd., Bologna, Italy).

tag: donor

tag: fraction

value: Ftot


title: donor_37_F3


title: donor_37_F1


title: donor_37_F4


title: donor_36_F3


title: donor_36_F2


title: donor_36_Ftot


title: donor_34_F2


title: donor_36_F4


title: donor_34_Ftot


title: donor_34_F1


title: 11998_Nrg2_rep1_ChIP-exo


title: donor_17_F3


title: 16555_Rad9_rep1_ChIP-exo


title: donor_24_Ftot


title: 18466_Orc4_rep2_ChIP-exo


title: donor_24_F4


title: 13154_Not5_rep1_ChIP-exo


title: donor_24_F3


title: donor_17_F2


title: donor_24_F2


title: donor_18_F3


title: donor_15_F4


title: donor_17_Ftot


title: donor_18_F2


title: donor_15_F3


title: donor_01_F4


title: donor_15_F2


title: donor_01_Ftot


title: 14429_Reg1_rep1_ChIP-exo


title: donor_01_F2


title: donor_36_F1


title: donor_01_F1


title: donor_15_Ftot


title: RNA1 - Puro3

city: Phoenix

last: Huentelman

state: AZ

address: 445 N Fifth Street

department: Neurogenomics

institute: Translational Genomics Research Institute

data_processing:
fastqs generated with bcl2fastq v2.18
reads  aligned with STAR v2.7.3a
abundance measurements obtained with featureCounts from Subread package v2.0.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes sequenced exon counts

source_name: neuroblastoma cells

growth_protocol: 1.4E07 cells plated in an uncoated well of a 6-well plate in 3.0mL equal parts EMEM (ATCC, Manassas, VA, USA) and Ham's F-12 Nutrient Mix (Gibco, Thermo Fisher Scientific, Waltham,  MA) supplemented with 10% FBS (Gibco). Media changed daily until the fourth day when RNA was extracted.

extract_protocol:
Zymo Quick-RNA miniprep kit
SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio Inc., Kusatsu, Shiga, Japan)

tag: cell line

tag: exogenous vectors

value: pSBbi-Hyg-APP, pSBbi-Pur

tag: library prep kit

value: Illumina TruSeq RNA Library Prep Kit v2


title: RNA1 - ABCC1(WT)1

value: pSBbi-Hyg-APP, pSBbi-Pur-ABCC1(WT)


title: RNA1 - Puro2


title: RNA1 - Puro1


title: RNA1 - ABCC1(WT)2


title: IC99 (T8) T36_A

city: Toronto

first: Aaron

last: Schimmer

state: ON

address: 101 College Street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description:
TAK243 (30 nM), day 36, replicate#1
IC99 (T8) T36_A

data_processing:
Basecalls performed using Illumina RTA version 2.4.11
Reads in fastq files are trimmed then mapped to the sgRNA library using bowtie
A python script uses samtools to count the mapped reads in the bam files and report the raw counts
Raw mapped counts were used as input to MaGECK algorithm to rank top hits
To normalize the raw counts, read counts for each sgRNA was divided by the total sum of read counts for that sample, and multiplied by 1,000,000 to give a count per million mapped reads for each sgRNA. To convert to log 2, 1 was added to each sample, followed by taking log2
Supplementary_files_format_and_content: Text file with genes and their targeting sgRNAs including the sequences and counts (raw, normalized and log2 normalized) of these sgRNAs across all sample replicates

source_name: OCI-AML2 cells

growth_protocol: OCI-AML2 were cultured in Iscove’s modified Dulbecco’s medium (IMDM). The genome-wide CRISPR/Cas9 knockout screen was performed in OCI-AML2 cells stably expressing Cas9 (OCI-AML2-Cas9). To generate these cells, OCI-AML2 cells were transduced with a Cas9 in a lentiviral vector, Lenti-Cas9-2A-Blast (Addgene plasmid#73310). The cells were selected with blasticidin (10 μg/mL) for 6 days. Single-cell clones were obtained by plating in a 96-well plate at a density of 0.4 cell/well, and a clonal population with high Cas9 expression was selected.  OCI-AML2-Cas9 cells were transduced with a pooled library (TKO-90k library) of 91,320 guide RNAs (gRNAs) in lentiviral vectors targeting 17,232 genes at a ratio of 6 gRNAs per gene. These cells were transduced at a multiplicity of infection (MOI) of approximately 0.3-0.4 to obtain coverage of at least 200-fold per gRNA. One day post-transduction, cells were treated with puromycin (2μg/mL) for 48h to select transduced cells.

extract_protocol:
Genomic DNA was extracted from pellets of 20-50x10^6 cells using the QIAamp Blood Maxi kit (Cat#51194)
The Toronto KnockOut (TKO) CRISPR Library - Version 1 (90K sub-library) was used (addgene catalog# 1000000069). Protocol of library construction is detailed in Hart et al. High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell. 2015;163(6):1515-26.
Pooled genome-wide CRISPR/Ca9 knockout screen

treatment_protocol: Cells were treated with DMSO or TAK-243 at its IC90 (25 nM) or IC99 (30 nM) for 32 days or 36 days

tag: tumor

value: Acute myeloid leukemia

tag: agent

tag: time point

value: day 36

value: Myeloid blood cells


title: IC99 (T4) T32_B

description:
TAK243 (30 nM), day 32, replicate#2
IC99 (T4) T32_B

value: day 32


title: IC99 (T8) T36_B

description:
TAK243 (30 nM), day 36, replicate#2
IC99 (T8) T36_B


title: 17126_Npl3_rep1_ChIP-exo

value: TAP-tag:Sigma i5006


title: IC99 (T4) T32_C

description:
TAK243 (30 nM), day 32, replicate#3
IC99 (T4) T32_C


title: IC99 (T4) T32_A

description:
TAK243 (30 nM), day 32, replicate#1
IC99 (T4) T32_A


title: IC90 T32_C

description:
TAK243 (25 nM), day 32, replicate#3
IC90 T32_C


title: RNA1 - ABCC1(WT)3


title: donor_01_F3


title: TSS-seq (+TEX) rep2

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description:
Sample 2
Processed data file(s):
TSS_TEX_Profile.gff.gz

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
To capture transcriptional start site (TSS), corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts.
gff file is generated by in-house script
Genome_build: ASM584v1
Supplementary_files_format_and_content: .gff file. We followed that gff format definition of "http://www.sanger.ac.uk/resources/software/gff/spec.html" but some columns are ignored because they do not affect the visualization. In detail, fields are: <contig id> <source but ignored> <feature> <start> <end> <MRSP height> <strand> <frame ignored> [attributes] [comments].  In this, we defined MRSP (Mapped Reads Start Position) as a number of reads that are started at the genomic position. For the reads that are mapped to reverse strand, we assigned minus value for the visualization convenience. To reduces inter-library variance, we converted the value as of 1 million reads similar to RPKM. In biological meaning, MRSP indicates cross-linked sites for the ChIP-exo and putative TSS site TSS-seq and so on.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: TSS-seq (+TEX)

growth_protocol: Glycerol stocks of E. coli K12 strain MG1655 were inoculated into M9 minimal media supplemented 0.2% glucose and grown at 30 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 30 ℃ to mid-exponential phase (OD600 nm ~ 0.6).

extract_protocol:
rRNA-depeleted total RNA extracted from the cells cultured in M9 minimal media at 30 ℃ was used to perform dRNA-seq6,7. To remove RNA with a 5’-monophosphate end, the residual mRNA was treated by 1 U terminator exonuclease (Epicentre) and 10U SUPERase-In (Invitrogen) at 30°C for 60 min. The reaction was terminated by adding 1 μL of 100 mM EDTA (pH 8.0), followed by phenol-chloroform extraction and ethanol precipitation.
The 5’-triphosphate end of primary RNA was then converted to a 5’-monophosphate end with 20 U RNA 5’ polyphosphatase (Epicentre) and 10 U SUPERase-In at 37°C for 60 min, followed by phenol-chloroform extraction and ethanol precipitation. The RNA sample was incubated with 100 pmol of 5’-RNA adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC), 20 nmol ATP, 10 U SUPERase-In, and 20 U T4 RNA Ligase at 37 °C for 3 hr. The adapter-ligated mRNA was hybridized with 100 pmol of random 3’ overhanging primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNN) and then converted to cDNA by 600 U SuperScript II (Invitrogen), 30 U SUPERase-In, 30 nmol dNTPs, 1 µg actinomycin D, and 100 nmol DTT at 25 °C for 10 min and 42 °C for 60 min in order. The enzymatic reaction was inactivated by incubation at 70 °C for 15 min. The residual RNAs were removed by incubation with 1 N NaOH at 65 °C for 30 min and then neutralization with 1 N HCl. A fraction of the cDNA between 100 bp and 350 bp was extracted using Pippin PrepTM (Sage science, Beverly, MA) and dissolved in 20 µL ddH2O. The cDNA was amplified using a mixture of 1 µL cDNA, 0.5 µL Phusion Polymerase (NEB), 1 µL dNTPs (10 mM each), 1 µL SYBR green (Bio-Rad), and 1 µL of P1 and P2 primer mix (25 µM each). The samples were cycled to 94 ℃ for 10 s, 57 ℃ for 20 s, and 72 ℃ for 20 s (total 13-17 cycles). The amplification was monitored and stopped at the beginning of the saturation point. A fraction of the amplified DNA between 150 bp and 400 bp was then extracted using Pippin PrepTM. A second PCR amplification was performed with 1 µL of the cDNA to a total mass up to 1 µg with 6-8 cycles. The amplified DNA libraries were then purified and subject to next-generation sequencing.

treatment_protocol: For rifampicin-treated cells, rifampicin dissolved in methanol was added to a final concentration of 150 μg/mL with subsequent stirring for 30 min. Cell growth was monitored at OD600 nm to verify the inhibitory effects of rifampicin.

tag: terminator exonuclease (tex) treatment

value: yes


title: TSS-seq (-TEX) rep1

description:
Sample 3
Processed data file(s):
TSS_TAP_Profile.gff.gz

source_name: TSS-seq (-TEX)

value: no


title: TSS-seq (+TEX) rep1

description:
Sample 1
Processed data file(s):
TSS_TEX_Profile.gff.gz


title: mock by IgG

description: Sample 4

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
To capture target protein binding sites, corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts.
gff file is generated by in-house script
Genome_build: ASM584v1
Supplementary_files_format_and_content: .gff files. We followed that gff format definition of "http://www.sanger.ac.uk/resources/software/gff/spec.html" but some columns are ignored because they do not affect the visualization. In detail, fields are: <contig id> <source but ignored> <feature> <start> <end> <MRSP height> <strand> <frame ignored> [attributes] [comments].  In this, we defined MRSP (Mapped Reads Start Position) as a number of reads that are started at the genomic position. For the reads that are mapped to reverse strand, we assigned minus value for the visualization convenience. To reduces inter-library variance, we converted the value as of 1 million reads similar to RPKM. In biological meaning, MRSP indicates cross-linked sites for the ChIP-exo and putative TSS site TSS-seq and so on.

source_name: mock by IgG

extract_protocol:
Cultured cells (50 mL) were cross-linked by 1% formaldehyde at room temperature for 30 min, followed by adding 2 mL of 2.5 M glycine for the quenching of the unused formaldehyde. After washing three times with 50 mL of ice-cold Tris-buffered saline (TBS), the washed cells were resuspended in 0.5 mL of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg/mL RNaseA, protease inhibitor cocktail and 1 kU Ready-Lyse lysozyme (Epicentre, Madison, WI) and incubated at 37 oC for 30 min. The cells were then treated with 0.5 mL of 2×IP buffer (100 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 2%(v/v) Triton X-100, and protease inhibitor cocktail), followed by incubation on ice for 30 min. The lysate was then sonicated in an ice bath to fragment the chromatin complexes using Sonic Dismembrator Model 500 (four times for 20 s each, output level, 2.5). After removing cell debris by centrifugation, the size distribution of fragmented DNA in the resulting supernatant was confirmed using agarose gel electrophoresis (200-400 bp).
After stringent sequential washings, the IP-DNAs were reverse-crosslinked from DNA-protein complexes at 65 oC overnight. The RNAs and proteins in the supernatant were degraded with 1 µg RNase A and 8 µg protease K, respectively. The IP-DNAs were further purified using Qiagen PCR purification kit. The purified IP-DNAs were then modified and amplified by TruSeq DNA Sample Prep Kit v2 for the Illumina next-generation sequencing according to the manufacturer’s instruction (Illumina). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns.

tag: chip antibody

value: Normal IgG [Millipore, catalog# 12-371, lot# DAM1774722] and Dynabeads Pan mouse IgG [Invitrogen, catalog# 11041, lot# 131306200]


title: IC99 (T8) T36_C

description:
TAK243 (30 nM), day 36, replicate#3
IC99 (T8) T36_C

tag: tissue


title: RNA-seq rep2

description:
Sample 2
Processed data file(s):
RNAseq_RPKM.txt.gz, Eco30M9_Profile.gff.gz

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
The expression levels were based upon the RPKM metric obtained from strand-specific manner.
gff file is generated by in-house script
Genome_build: ASM584v1
Supplementary_files_format_and_content: The .txt file reports RPKM values.
Supplementary_files_format_and_content: .gff file. We followed that gff format definition of "http://www.sanger.ac.uk/resources/software/gff/spec.html" but some columns are ignored because they do not affect the visualization. In detail, fields are: <contig id> <source but ignored> <feature> <start> <end> <MRSP height> <strand> <frame ignored> [attributes] [comments].  In this, we defined MRSP (Mapped Reads Start Position) as a number of reads that are started at the genomic position. For the reads that are mapped to reverse strand, we assigned minus value for the visualization convenience. To reduces inter-library variance, we converted the value as of 1 million reads similar to RPKM. In biological meaning, MRSP indicates cross-linked sites for the ChIP-exo and putative TSS site TSS-seq and so on.

source_name: RNA-seq

extract_protocol:
From the cells cultured in M9 minimal media at 30 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY).
50 ng of the fragmented RNA was converted to sequencing library using TruSeq® Stranded mRNA Sample Prep Kit in accordance with manufacturer’s instruction (Illumina).

tag: seq method

value: Directional RNA-seq


title: Sigma 70 ChIP-seq

description: Sample 1

source_name: Sigma 70 ChIP-seq

value: anti-σ70 subunit (clone:2G10) antibodies [Neoclone, catalog# WP004]


title: RNAP (+Rif) ChIP-seq

description: Sample 2

source_name: RNAP (+Rif) ChIP-seq

value: anti-RNAP β subunit (clone:NT63) [Neoclone, catalog# WP002, lot# 2011 E 19-002]


title: mock by IgG for RNAP-Rif rep2

description:
Sample 12
Processed data file(s):
RNAP_NoRif_ChIPexo.gff.gz

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
To capture target protein binding sites, corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts.
gff file is generated by in-house script
Genome_build: ASM584v1
Supplementary_files_format_and_content: .gff files.  We followed that gff format definition of "http://www.sanger.ac.uk/resources/software/gff/spec.html" but some columns are ignored because they do not affect the visualization. In detail, fields are: <contig id> <source but ignored> <feature> <start> <end> <MRSP height> <strand> <frame ignored> [attributes] [comments].  In this, we defined MRSP (Mapped Reads Start Position) as a number of reads that are started at the genomic position. For the reads that are mapped to reverse strand, we assigned minus value for the visualization convenience. To reduces inter-library variance, we converted the value as of 1 million reads similar to RPKM. In biological meaning, MRSP indicates cross-linked sites for the ChIP-exo and putative TSS site TSS-seq and so on.

source_name: mock by IgG for RNAP-Rif

growth_protocol: Glycerol stocks of E. coli K12 strain MG1655 were inoculated into M9 minimal media supplemented 0.2% glucose and grown at 30 oC with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 30 ℃ to mid-exponential phase (OD600 nm ~ 0.6).

extract_protocol:
Cultured cells (50 mL) were cross-linked by 1% formaldehyde at room temperature for 30 min, followed by adding 2 mL of 2.5 M glycine for the quenching of the unused formaldehyde. After washing three times with 50 mL of ice-cold Tris-buffered saline (TBS), the washed cells were resuspended in 0.5 mL of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg/mL RNaseA, protease inhibitor cocktail and 1 kU Ready-Lyse lysozyme (Epicentre, Madison, WI) and incubated at 37 oC for 30 min. The cells were then treated with 0.5 mL of 2×IP buffer (100 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 2%(v/v) Triton X-100, and protease inhibitor cocktail), followed by incubation on ice for 30 min. The lysate was then sonicated in an ice bath to fragment the chromatin complexes using Sonic Dismembrator Model 500 (four times for 20 s each, output level, 2.5). After removing cell debris by centrifugation, the size distribution of fragmented DNA in the resulting supernatant was confirmed using agarose gel electrophoresis (200-400 bp).
Prior to the reverse-crosslinking in the ChIP precedure, the IP-DNA in the crosslinked DNA-protein complexes attached on the magnetic beads were end-polished using T4 DNA polymerase (NEB, Ipswich, MA), ligated with the annealed adaptor 1 (5’- Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT and 5’- OH-AGATCGGAAGAGC-OH), nick-repaired using phi29 polymerase (NEB), and disgested with λ exonuclease (NEB) as reported previously. Between the enzymatic treatments, the crosslinked DNA-protein complexes were sequentially washed with 10 mM TE (pH 8.0) and 10 mM Tris-HCl (pH 7.5-8.0). The magnetic beads were then resuspended in 50 µL of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS, and 1 mM EDTA). The exonuclease-treated IP-DNA (IP-exo-DNA) was then reverse-crosslinked from DNA-protein complexes at 65 ℃ overnight. The RNAs and proteins in the supernatant were degraded with 1 µg of RNase A (Invitrogen) and 8 µg of protease K (Invitrogen), respectively. The IP-exo-DNAs were further purified using Qiagen PCR purification kit according to the manufacturer’s instruction (QIAGEN, Hilden, Germany). The purified IP-exo-DNAs were denatured at 95 oC and extended by P1 primer (5’-OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). Subsequently, the extended ends of the IP-exo-DNAs were ligated with the annealed adaptor 2 (5’-OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT and 5’-OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG). The ligated DNA products were purified using Qiagen PCR purification kit and were PCR-amplified by P2 primer (5’-OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and P3 primer (5’-OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT). The degenerative sequence (the underlined 6Ns) in the P3 primer indicates the index sequence for the Illumina next-generation sequencing (Illumina, San Diego, CA). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns.


title: RNAP (-Rif) ChIP-exo rep2

description:
Sample 10
Processed data file(s):
RNAP_NoRif_ChIPexo.gff.gz

source_name: RNAP (-Rif) ChIP-exo


title: RNAP (-Rif) ChIP-seq

description: Sample 3

source_name: RNAP (-Rif) ChIP-seq


title: RNAP (-Rif) ChIP-exo rep1

description:
Sample 9
Processed data file(s):
RNAP_NoRif_ChIPexo.gff.gz


title: mock by IgG for RNAP-Rif rep1

description:
Sample 11
Processed data file(s):
RNAP_NoRif_ChIPexo.gff.gz


title: TSS-seq (-TEX) rep2

description:
Sample 4
Processed data file(s):
TSS_TAP_Profile.gff.gz


title: RNAP (+Rif) ChIP-exo rep2

description:
Sample 6
Processed data file(s):
RNAP_Rif_ChIPexo.gff.gz

source_name: RNAP (+Rif) ChIP-exo


title: RNAP (+Rif) ChIP-exo rep1

description:
Sample 5
Processed data file(s):
RNAP_Rif_ChIPexo.gff.gz


title: mock by IgG for RNAP+Rif rep1

description:
Sample 7
Processed data file(s):
RNAP_Rif_ChIPexo.gff.gz

source_name: mock by IgG for RNAP+Rif


title: mock by IgG for Sigma 70 rep1

description:
Sample 3
Processed data file(s):
RpoD30_ChIPexo.gff.gz, RpoD30_ChIPexo_smoothed.gff.gz

source_name: mock by IgG for Sigma 70


title: mock by IgG for RNAP+Rif rep2

description:
Sample 8
Processed data file(s):
RNAP_Rif_ChIPexo.gff.gz


title: IC90 T32_B

description:
TAK243 (25 nM), day 32, replicate#2
IC90 T32_B


title: Sigma 70 ChIP-exo rep1

description:
Sample 1
Processed data file(s):
RpoD30_ChIPexo.gff.gz, RpoD30_ChIPexo_smoothed.gff.gz

source_name: Sigma 70 ChIP-exo


title: mock by IgG for Sigma 70 rep2

description:
Sample 4
Processed data file(s):
RpoD30_ChIPexo.gff.gz, RpoD30_ChIPexo_smoothed.gff.gz


title: Sigma 70 ChIP-exo rep2

description:
Sample 2
Processed data file(s):
RpoD30_ChIPexo.gff.gz, RpoD30_ChIPexo_smoothed.gff.gz


title: IC0 T36_A

description:
DMSO, day 36, replicate#1
IC0 T36_A

value: DMSO


title: IC0 T32_C

description:
DMSO, day 32, replicate#3
IC0 T32_C


title: IC0 T36_B

description:
DMSO, day 36, replicate#2
IC0 T36_B


title: IC90 T32_A

description:
TAK243 (25 nM), day 32, replicate#1
IC90 T32_A


title: RNA-seq rep1

description:
Sample 1
Processed data file(s):
RNAseq_RPKM.txt.gz, Eco30M9_Profile.gff.gz


title: IC0 T32_A

description:
DMSO, day 32, replicate#1
IC0 T32_A


title: donor_18_F1


title: T0_1

description:
untreated, day 0, replicate#1
T0_1

value: untreated

value: day 0


title: IC0 T32_B

description:
DMSO, day 32, replicate#2
IC0 T32_B


title: T0_2

description:
untreated, day 0, replicate#2
T0_2


title: OCI-AML3 5 nM AC220 24 hr Replicate 1

first: Stefan

last: Bjelosevic

address: 450 Brookline Ave

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Sequencing reads were trimmed using cutadapt (v1.9.1) and aligned to the Hg19 reference genome using HISAT 2 (v2.0.4)
Read counting across genomic regions was performed using the Subread (v2.0.0) featureCounts function and differential gene expression analysis was performed in Rstudio (R v3.6.1) using Voom-Limma (v3.42.2)
Genome_build: Hg19
Supplementary_files_format_and_content: Comma separated values file of featureCounts counts; Comma separated values file of normalized (voom-limma) counts

source_name: OCI-AML3 Cell Line

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10-20 percent heat-inactivated fetal bovine serum, 100U/mL penicillin, 100µg/mL streptomycin and 2mM GlutaMAX at 37 degrees celcius and 5 percent carbon dioxide

extract_protocol:
Cells were lysed in TriZol reagent and total DNAse-treated RNA isolated using the Zymogen RNA mini-prep kit.
RNA libraries were prepared using the Lexogen QuantSeq 3'-mRNA Seq Library Prep kit

treatment_protocol: MV4-11 and OCI-AML3 cells were treated with DMSO (untreated control) or 5 nM of the FLT3 inhibitor Quizartinib (AC220) for 24 hours

value: Acute myeloid leukaemia cell line

value: AC220 5 nM, 24 hours


title: OCI-AML3 5 nM AC220 24 hr Replicate 3


title: OCI-AML3 5 nM AC220 24 hr Replicate 2


title: OCI-AML3 DMSO 24 hr Replicate 2

value: DMSO-treated control


title: OCI-AML3 DMSO 24 hr Replicate 3


title: MV4-11 5 nM AC220 24 hr Replicate 1

source_name: MV4-11 Cell Line


title: MV4-11 5 nM AC220 24 hr Replicate 3


title: MV4-11 5 nM AC220 24 hr Replicate 2


title: OCI-AML3 DMSO 24 hr Replicate 1


title: IC0 T36_C

description:
DMSO, day 36, replicate#3
IC0 T36_C

value: Acute myeloid leukemia


title: OCI-AML3 DMSO RNA Pol II

data_processing:
Sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14)
Basic QC performed on fastq files using FASTQC (v0.11.6)
Fastq files were aligned to a Hg19 reference genome performed with Bowtie2 (v2.3.5) to generate SAM files
SAM files converted to BAM files using Samtools (v1.4.1). BAM files were sorted, indexed and potential PCR duplicates removed
Peak calling was performed with MACS2 (v2.2.5) and bigWig files were generated from sorted, indexed BAM files using Deeptools (v3.3.1)
Average read density across defined genomic regions were defined using the Deeptools computeMatrix function and plotHeatmap, plotProfiles functions were used to generate chromatin occupancy heatmaps and profiles
HOMER (v4.10) was used for quantification and annotation of the ChIP-Seq datasets, for determining peak scores of ATF4 target genes, and for de novo motif discovery on ATF4 bound sites
Genome_build: Hg19
Supplementary_files_format_and_content: bigWig files of ATF4 and RNAPII occupancy across the genome in CPM; narrowPeak file of peak calling locations via MACS2

extract_protocol:
Cells were cross-linked with formaldehyde solution, nuclei were extracted and sonicated using a Covaris ultrasonicator. Protein-bound chromatin was isolated using indicated antibody and decrosslinked DNA was isolated using the Zymogen ChIP DNA Clean and Concentrator Kit
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) and 200 - 500 base pair fragments were selected using a Pippin Prep (1.5% agarose, Sage Science)

value: RNA polymerase II, clone CTD4H8 (Millipore 05-623)

value: DMSO (untreated control), 24 hours


title: OCI-AML3 AC220 ATF4

value: ATF4, clone D4B8 (Cell Signaling 11815S)

value: Quizartinib (AC220; 5nM) 24 hours


title: MV4-11 DMSO 24 hr Replicate 1


title: MV4-11 AC220 RNA Pol II


title: MV4-11 DMSO 24 hr Replicate 2


title: MV4-11 DMSO 24 hr Replicate 3


title: MV4-11 AC220 ATF4


title: OCI-AML3 AC220 RNA Pol II


title: MV4-11 DMSO ATF4


title: MV4-11 DMSO RNA Pol II


title: OCI-AML3 DMSO ATF4


title: Zb0_shNBS1_Input

source_name: HeLa cell

value: anti-NBS1 shRNA

tag: passages


title: Zb0_shC_Input

value: control shRNA


title: Zb0_shMRE11_Input

value: anti-MRE11 shRNA


title: Zh8_DRB_Block_NBS1

value: DRB treatment 3h

value: Bethyl A300-289A


title: OCI-AML3 Input DNA


title: T0_3

description:
untreated, day 0, replicate#3
T0_3

source_name: OCI-AML2 cells

value: Myeloid blood cells


title: Zh3_DRB_1h_NBS1

value: DRB treatment 1h

value: Santa Cruz 55492


title: Zh16_DRB_Release_NBS1

value: 1h post-DRB treatment


title: Zh15_DRB_Release_PolII


title: N0_N00-Input_L001_R1_001


title: Zh11_DRB_NT_PolII


title: Zd6_Heatshock_Pol2

value: heat shock


title: Zh12_DRB_NT_NBS1


title: Zh4_DRB_1h_PolII


title: MV4-11 Input DNA

value: Acute myeloid leukaemia cell line


title: Zd5_Heatshock_MRE11

value: Bethyl A303-998A


title: Zd4_Heatshock_NBS1


title: Zd3_Untreated_Pol2


title: Zb13-bis_ShMRE11_PolII


title: Zh7_DRB_Block_PolII


title: Zb15-bis_ShMRE11_NBS1


title: Zb12-bis_ShNBS1_NBS1


title: Zb14-bis_ShMRE11_MRE11


title: Zb10-bis_ShNBS1_PolII


title: Zb11-bis_ShNBS1_MRE11


title: Zb9-bis_ShC_NBS1


title: Zb7-bis_ShC_PolII


title: Zb8-bis_ShC_MRE11


title: Zd1_Untreated_NBS1


title: Zb6_shMRE11_Ser2PolII

value: Abcam 5055


title: rna_seq_scramble_repl2

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: processed data file: rnaseq_featureCounts_exp_matrix.txt, 3scr_3shSALL4_gene_exp.txt

data_processing:
Cut&Run - Cut and Run Analysis Pipeline (CnRAP) scripts can be found on github (https://github.com/mbassalbioinformatics/CnRAP).  Raw fastq files were trimmed with Trimmomatic (REF, v0.36 tested) in paired end mode with the flags “ILLUMINACLIP: <adapter_path> Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25”. Next, the kseq trimmer developed by the Orkin lab was run on each fastq file, there were no flags to modify.  For alignment, BWA (v0.7.17-r1188 tested) was first run in “aln” mode on a masked hg38 genome downloaded from UCSC to create *.sai files.  Next, BWA was run in “sampe” mode with the flag “-n 20” on the *.sai files.  Afterwards, stampy (v1.0.32 tested) was run in “--sensitive" mode.  For mapping statistics, bamtools (v2.5.1 tested) “stat” was used.  Post alignment, unmapped reads were removed from bam files using bamtools with the flags “filter -isMapped true.”  Next, using samtools (v1.5 tested), bam files were sorted (“sort -l 9 -O bam”), had read pair mates fixed (“fixmate”) and indexed (“index”).  Bam coverage maps were generated using bamCoverage from the deeptools suite (v2.5.7 tested).  The same procedure was run to align fastq files to a masked genome Saccharomyces Cerevisiae v3 (sacCer3), also downloaded from UCSC.    In preparation for peak calling, a normalization factor was determined for each hg38 aligned replicate based on the corresponding number of proper-pairs aligned to the sacCer3 genome, as recommended in the Henikoff pipeline.  This was calculated as follows  normalization_factor=10,000,000\(#proper_pairs/2).  The number of ‘proper-pairs’ was extracted from the bamtools mapping statistics calculated previously. Next, from the hg38 aligned bams, ‘proper-paired’ reads were extracted using samtools with the flags “view -b -f 2 -F 524” with the output piped into bedtools with the flags “genomecov -bg -scale <normalization_factor> -ibam stdin.”  This produced bed files of ‘proper-paired’ reads that have been normalized to the number of reads aligned back to the sacCer3 genome.  Bedgraphs of these normalized bed files were generated as intermediary files to facilitate generation of bigwig coverage maps using the bedGraphToBigWig from UCSC (v4).  For peak calling, the recently developed SEACR (v1.1 tested) was utilized and run in both “stringent” and “relaxed” mode to produce peak files with the flag “non” as the bed files were already normalized to the number of yeast spike-in reads.  Subsequently peak file columns were re-arranged to facilitate motif discovery using both HOMER (v4.10 tested, flags “-size given,50,100,200 -mask -p 20 -S 50”) and MEME (v5.0.5 tested, “-dreme-m 50 -meme-nmotifs 50”).  Peaks were annotated using the R package ChIPSeeker (v1.20.0 tested).  Overlapping peak subsets were generated using mergePeaks.py from the HOMER suite with the flag “-d 1000”.
NicE-seq - Raw fastq reads were trimmed and mapped in the same way as described above for CUT&RUN data. Peaks were called with Model-based Analysis of ChIP-seq (MACS) (v2.1.1.20160309) for scrambled control sample and SALL4 KD sample separately. Unique peaks to each sample was identified with HOMER mergePeaks function. bamCoverage (described above for CUT&RUN) was used to generate BigWig files for visualization.
RNA-Seq - The raw fastq reads were trimmed using TrimGalore (v.0.4.5) and mapped to hg38 genome downloaded from UCSC using STAR. The read counts table was generated with the featureCounts. Differential gene expression analysis was performed to compare scrambled control samples with SALL4 KD samples using DESeq2 and the fold change was plotted as a volcano plot using ggplot2.
Genome_build: (human) hg38, (yeast) saccer3
Supplementary_files_format_and_content: peak files; gene x features expression matrix tab delimited text

growth_protocol: SNU398 cells were grown in RPMI media with 10% FBS

extract_protocol: Pair-end (75bp) Illumina sequencing was performed on the barcoded and amplified libraries

treatment_protocol: SNU398 cells were transduced with scrambled shRNA and RNA was extracted by Trizol 72hours after transduction

value: Hepatocellular Carcinoma cell line

tag: genotype/variation

value: scrambled shRNA


title: rna_seq_scramble_repl1


title: rnaseq_SALL4KD_repl2

treatment_protocol: SNU398 cells were transduced with shRNA-2 (Supplementary Table S3) and RNA was extracted by Trizol72 hours after transduction


title: Zb4_shC_Ser2PolII

data_processing:
Raw reads filtering perfomed with fastq_illumina_filter (version 0.1)
Raw reads quality control perfomed with Fastqc (version 0.11.2)
Reads alignment with BWA (0.7.10) on HG38 human genome version
Bigwig files were generated using deeptools (3.2.0) bamCompare and normalized either by corresponding input or by the average of four inputs (subtraction) using RPGC normalization
Genome_build: HG38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

extract_protocol:
ChIP experiments were performed in HeLa cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit


title: 7-day-old wild-type rice seedlings Rep1

city: Wuhan

first: Jie

last: Zhao

address: No. 299, Bayi Road, Wuchang District,

institute: Wuhan University

data_processing:
The transcriptome sequencing experiment process includes RNA extraction, RNA sample quality detection, library construction, library purification, library detection, library quantification, sequencing cluster generation, and computer sequencing
The length we obtained was 150bp, and the numbers of reads were 49948012, 43922662, 43510058 and 52841196. Htseq software (V 0.6.1) was used for gene expression calculation, DESeq2 (V1.6.3) of Bioconductor software was used for gene difference analysis, and DEXSeq (V1.18.4) software was used for differential exon usage analysis
Genome_build: Oryza sativa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: 7-day-old wild-type rice seedlings

extract_protocol:
The samples were lysed with Trizol reagent. RNA was extracted with chloroform and precipitated with isopropanol. 75% alcohol was used to clean the impurities, and finally RNA was dissolved with RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Japonica

tag: age

value: wild type

value: seedlings


title: 7-day-old wild-type rice seedlings Rep2


title: 7-day-old mre11 rice seedlings Rep2

source_name: 7-day-old mre11 rice seedlings

value: mre11 mutant


title: Profiling of RNA from rRNA-depleted RNA library from liver metastases [C-LM_3]

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx

data_processing:
Base calling was performed using CASAVA 1.8.2 software
The data processing was divided into 2 workflows:
CircRNA analysis:
Raw reads were mapped to the human genome (hg19 assembly) using STAR version 2.5.3a with the setting --outFilterMismatchNoverLmax to 0.05. Reads were counted using htseq-count version 0.9.1 with Ensembl release 75 genome annotation reference.
For circRNA detection reads were mapped to the human genome (hg19) using bwa mem version 0.7.5a-r405 with the following options: -t 20 -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3. Bwa mem output was processed using find_circ2 (https://github.com/rajewsky-lab/find_circ2) to detect backspliced reads. circRNA candidates flagged by find_circ2 as SHORT or HUGE were discarded. The list was further filtered by keeping only circRNA candidates that were supported by 2 or more unique reads in a given sample and spliced from annotated splice sites. The number of fragments overlapping head-to-tail junctions were used as a measure of circRNA expression.
Differential expression analysis was performed within R using DESeq2 version 1.22.2. The circRNA head-to-tail junction counts were merged with htseq-count output prior to normalization by DESeq2. CircRNAs and genes that were supported by less than 10 reads in total across all samples were discarded.
Genome_build: hg19
Differential gene expression analysis:
Raw reads were mapped to the human genome (hg38 assembly) using STAR version 2.7.0a with --outFilterMultimapNmax 2000000000 and --outSAMmultNmax 1 settings. Reads were counted using Rsubread 1.34.7 with Ensembl release 98 genome annotation reference.
Differential expression analysis was performed within R using DESeq2 version 1.24.0.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including count tables and DESeq2 outputs

source_name: Control Liver metastases (C-LM)

growth_protocol: HT29 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
Tumor samples (PT and LM) were cutted into smaller pieces before putting them into the lysing matrix tubes, type "D" (MP Biomedicals). Tubes with 1 ml TRIzol (Invitrogen) were cooled on ice before samples were added. Tumors were homogenized using Fastprep-24-System with 1x 45 sec. @ full speed in TRIzol. After homogenisation, total RNA from tumor samples was isolated according to TRIzol's protocol. Total RNA from HT29 cells was isolated using TRIzol according to TRIzol's protocol without homogenisation steps.
Workflow consists of double-stranded cDNA generation using a customizable mixture of random and poly(T) priming, fragmentation of double-stranded cDNA, end repair to generate blunt ends, adaptor ligation, strand selection via nucleotide analog-targeted degradation, InDA-C-mediated adaptor cleavage and PCR amplification to produce the final library. The detailed protocol can be found at the user guide Ovation Human FFPE RNA-Seq System.

treatment_protocol: Three SCID mice were initially used for tumor development to collect RNA for RNA sequencing (RNA-seq) via intrasplenic implantation. HT29 cells were dissociated with trypsin, washed once with DMEM supplemented with 10% FCS, 1% PS and then resuspended to the desired concentration in Hank's Balanced Salt Solution (HBSS, Sigma). All animals receiving tumor cell injections were injected with the same quantity of cells (500 000 cells per animal). Abdominal access was obtained via a left subcostal skin and peritoneal wall incision. The spleen was gently exteriorized. 5 µl of 500 000 tumor cells were injected with a 10 µl Hamilton syringe (BD Biosciences). The needle was slowly retracted and the injection site pressed with a moist cotton swab to prevent leakage. The spleen was returned to the peritoneal cavity; peritoneum and skin were closed by running sutures and wound clips. Bioluminescence measurement was performed weekly or every 3 days. For this purpose, mice were anaesthetized, injected with 100 µl of 30 mg/ml D-luciferin (Biosynth, Staad, Switzerland) for 3 min, and emitted photons were registered for 3 min using Xenogen IVIS Lumina Imaging System (Caliper Life Sciences). Primary tumor (either subcutaneous tumor or in spleen) and metastases in the liver resections were performed when the tumor size was big enough or when the bioluminescence measurement was significant. All tumors were collected in RNAlater (Thermo Scientific).

tag: cell type

value: Liver metastases from control mice


title: Zd2_Untreated_MRE11

tag: treatment


title: rnaseq_SALL4KD_repl1

treatment_protocol: SNU398 cells were transduced with shRNA-2 (Supplementary Table S3) and RNA was extracted by Trizol 72 hours after transduction


title: Profiling of RNA from rRNA-depleted RNA library from primary tumors [C-PT_2]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx

source_name: Control Primary tumor (C-PT)

value: Primary tumor from control mice


title: Profiling of RNA from rRNA-depleted RNA library from primary tumors [C-PT_1]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx


title: Profiling of RNA from rRNA-depleted RNA library from HT29 cells [HT29_3]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx

source_name: HT29 cells

value: HT29.hCG.Luc colorectal cancer cell line


title: Profiling of RNA from rRNA-depleted RNA library from liver metastases [C-LM_2]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx


title: Profiling of RNA from rRNA-depleted RNA library from liver metastases [C-LM_1]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx


title: Profiling of RNA from rRNA-depleted RNA library from primary tumors [C-PT_3]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx


title: Zb5_shNBS1_Ser2PolII

value: anti-NBS1 shRNA


title: Profiling of miRNA from total RNA library from liver metastases of control mice [C-LM_2]

description:
C-LM_2
total small RNA
miRNA_DE.xlsx

data_processing:
HiSeq analysis pipeline: HCS 2.2.38, Casava 1.8.2
The following analysis steps were performed with miRDeep2 version 2.0.0.8 within Galaxy server software (http://galaxyproject.org/):
Clipping of Illumina TruSeq 3'-adapters (recognition sequence: TGGAATTCTCGGGTGCCAAGG). Discarding all resulting sequences shorter than 18 bp. Collapsing the list of all remaining reads to unique insert sequences with corresponding number of appearance. Software: miRDeep2 mapper.
Mapping and counting against human miRNAs from www.mirbase.org (Version 22.1; Oct. 2018) with standard parameters. Software: miRDeep2 Quantifier.
Differential expression analysis was performed within R using DESeq2 version 1.24.0.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: miRNA_DE.xlsx: Excel file including count tables and DESeq2 outputs.

extract_protocol:
Tumor samples (PT and LM) were cut into smaller pieces before putting them into the lysing matrix tubes, type "D" (MP Biomedicals). Tubes with 1 ml TRIzol (Invitrogen) were cooled on ice before samples were added. Tumors were homogenized using Fastprep-24-System with 1x 45 sec. @ full speed in TRIzol. After homogenisation, total RNA from tumor samples was isolated according to TRIzol's protocol. Total RNA from HT29 cells was isolated using TRIzol according to TRIzol's protocol without homogenisation steps.
In short, an adenylated adapter was ligated to the 3’ end of the total RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA inserts were cut out. PCR products from these gel slices were eluted, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements.

treatment_protocol: Five SCID mice were initially used for tumor development to collect RNA for RNA sequencing (RNA-seq) via intrasplenic implantation. HT29 cells were dissociated with trypsin, washed once with DMEM supplemented with 10% FCS, 1% PS and then resuspended to the desired concentration in Hank's Balanced Salt Solution (HBSS, Sigma). All animals receiving tumor cell injections were injected with the same quantity of cells (500 000 cells per animal). Abdominal access was obtained via a left subcostal skin and peritoneal wall incision. The spleen was gently exteriorized. 5 µl of 500 000 tumor cells were injected with a 10 µl Hamilton syringe (BD Biosciences). The needle was slowly retracted and the injection site pressed with a moist cotton swab to prevent leakage. The spleen was returned to the peritoneal cavity; peritoneum and skin were closed by running sutures and wound clips. Bioluminescence measurement was performed weekly or every 3 days. For this purpose, mice were anaesthetized, injected with 100 µl of 30 mg/ml D-luciferin (Biosynth, Staad, Switzerland) for 3 min, and emitted photons were registered for 3 min using Xenogen IVIS Lumina Imaging System (Caliper Life Sciences). Treated mice (Two mice #4 and # 5) with topotecan received 1mg topotecan per 1 kg of bodyweight. Control mice (Three mice #1, #2, #3) served as control mice. Primary tumor (from spleen) and metastases in the liver resections were collected in RNAlater (Thermo Scientific) when the tumor size was big enough or when the bioluminescence measurement was significant.


title: Profiling of miRNA from total RNA library from liver metastases of LDM topotecan treated mice [T-LM_4]

description:
T-LM_4
total small RNA
miRNA_DE.xlsx

source_name: Treated Liver metastases (T-LM)

value: Liver metastases from LDM topotecan treated mice


title: Profiling of miRNA from total RNA library from primary tumors [C-PT_3]

description:
C-PT_3
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from liver metastases of control mice [C-LM_1]

description:
C-LM_1
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from liver metastases of LDM topotecan treated mice [T-LM_5]

description:
T-LM_5
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from liver metastases of control mice [C-LM_3]

description:
C-LM_3
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from HT29 cells [HT29_1]

description:
HT29_1
total small RNA
miRNA_DE.xlsx


title: Profiling of RNA from rRNA-depleted RNA library from HT29 cells [HT29_1]

description:
RNASeq_DE.xlsx
circRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from primary tumors [C-PT_1]

description:
C-PT_1
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from primary tumors [C-PT_2]

description:
C-PT_2
total small RNA
miRNA_DE.xlsx


title: Profiling of miRNA from total RNA library from HT29 cells [HT29_2]

description:
HT29_2
total small RNA
miRNA_DE.xlsx