title: single cells 48h rep2

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
expression_mat.csv.gz
kept_barcode.csv.gz
tsne_3d_coordinate.csv.gz

data_processing:
bulk RNA-seq: trimmed with Trim Galore v0.4.5, mapped with hisat2 v2.1.0 onto TAIR10, counts obtained with FeatureCounts and Araport11 annotation
scRNA-seq: raw fastqs processed with CellRanger v1.3.0 with modified STAR parameters to improve mapping of SNP-containing reads to the TAIR10 genome N-masked for Cvi-0 SNPs. When applicable, cells were then genotyped and empty cells removed with emptyDrops. Further quality control was performed using {\it scater} (v1.14.6) to remove cells with 1) more than three median absolute deviations (MADs) of the log 10 read counts below the median values; 2) more than three MADs of the log10 genes detected below the median. Then, {\it calculateAverage} was used to remove low-abundance genes with average count not above 0. Genes induced during protoplasting as above-mentioned were removed before applying normalization method {\it calculateSumFactors} with pool-based size factors used from {\it scran}. Highly variable genes (HVGs) were selected by {\it modelGeneVar} and {\it getTopHVGs} with biological variance threshold set as 0. FastMNN was then performed using HVGs to integrate data sets from each sample. MNN dimension reductions were applied to construct a SNN graph with function provided in {\it scran}, and Louvain algorithm from {\it igraph} was followed to group cells into clusters. MNN dimension reductions were also applied to generate t-SNE at 2 dimensions for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bulk_controls_counts.txt.gz:raw count matrix in tsv format for the bulk RNA-seq. kept_barcode.csv.gz: Col-0 single cell barcodes passing quality filters in each sample, in csv format. expression_mat.csv.gz: raw count matrix for the selected single cells, in csv format. tsne_3d_coordinate.csv.gz: cell coordinates and cluster identity on the 3D t-SNE plot.

organism: Arabidopsis thaliana

source_name: germinating seed

growth_protocol: Col-0 and Cvi-0  seeds were sown on MS media plates (containing 3\% sucrose). Seeds were sterilised and stratified for 48 h of cold (4\degree) dark stratification (S) before being transferred to continuous light (SL) (at 22\degree) and collected after 12 h SL, 24 h SL and 48 h SL. Three biological replicates were collected.

extract_protocol: single cells: 10X Chromium 3’end v2; bulk: TruSeq Stranded Total RNA with Ribo-Zero Plant kit

value: embryo

tag: dissociation

value: single cells

tag: time in light


title: RNAseq_U266_MAF-OE_rep1

status: Public on Aug 01 2023

type: SRA

city: London

first: Nikolaos

last: Trasanidis

address: Hammersmith Campus, Commonwealth Building, 4th Floor,, Du Cane Road, Imperial College London

department: Department of Immunology and Inflammation,

country: United Kingdom

institute: Imperial College London

library_source: transcriptomic

data_processing:
Bcl2Fastq (v2.20) software used for basecalling.
ChIP-seq analysis: Alignment was performed with bowtie2 against the hg38/GRCh38 genome. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling (ChIP versus Input)  was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. Bedtools was used to operate on genomic regions (union, intersections, etc.).
RNA-seq analysis: Alignment was performed using STAR (2.5.3a) against hg38/GRCh3 genome. The “Rsubread” Bioconductor package was used to obtain gene-level read counts. The “DESeq2” Bioconductor package was used for data normalization and differential expression analysis across different conditions of knock-down experiments in each cell line.
ATAC-seq analysis:  Alignment was performed with bowtie2 against the hg38/GRCh38 genome. Trimming was performed using TrimGalore. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. DESeq2 and ODIN were used for differential ATAC-seq analysis across conditions and treatments. Bedtools was used to operate on genomic regions (union, intersections, etc.).
Assembly: GRCh38
Supplementary files format and content: bedfile
Supplementary files format and content: BigWig
Supplementary files format and content: raw counts

molecule: total RNA

organism: Homo sapiens

extract_protocol: NEBNext Ultra II RNA Library Prep kit for Illumina (NEB)

tag: cell type

value: Multiple myeloma cell line

tag: cell line

tag: treatment

tag: antibody


title: RNAseq_U266_MAF-OE_rep2


title: single cells 48h rep1

tag: tissue


title: GEX patient5_scACTP_1

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

library_source: transcriptomic single cell

data_processing:
The scRNA-Seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count (10X Genomics, version 4.0.0). Filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used and processed using the Seurat R package version 4.0.1.
For live-sorted cells from ACT product data (5`GEX), we defined and removed low-quality cells containing more than 10% of mitochondrial reads.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in tab-separted format

source_name: melanoma

extract_protocol:
TILs were generated in the GMP manufacturing facilities of the Centre of Thérapies Expérimentales (CTE) of the Centre Hospitalier Universitaire Vaudois (CHUV) under specific conditions previously described (Gannon et al., Cytotherapy, 2020). Some TILs of the infusion product were cryopreserved in 90% human serum + 10% DMSO for translational studies. The day of the assay, the samples of the infused T cell product were thawed and TILs undergone overnight recovery in R8 medium supplemented with 3000 IU/mL IL-2 (Proleukin) or fresh TILs were directly used. TILs were resuspended in PBS + 0.04% BSA and DAPI (Invitrogen) staining was performed.
Live cells were sorted with a BD FACS Melody sorter and manually counted to assess viability with Trypan blue. Live TILs were resuspended at a density of 600-1200 cells µL-1 with a viability of >90% and subjected to a 10X Chromium instrument for single-cell analysis. The standard protocol of 10X Genomics was followed and the reagents for the Chromium Single Cell 5’ Library and V(D)J library (v1.0 or v1.1 Chemistry) were used. 15’000 cells were loaded per sample. Using a microfluidic technology, single-cell were captured and lysed, mRNA was reverse transcribed to barcoded cDNA using the provided reagents (10X Genomics). 14 PCR cycles were used to amplify cDNA and the final material was divided into two fractions: first fraction was target-enriched for TCRs and V(D)J library was obtained according to manufacturer protocol (10X Genomics). The second fraction was processed for 5’ gene expression library following the manufacturer’s instruction (10X Genomics). Barcoded V(D)J libraries and GEX libraries were pooled and sequenced by an Illumina HiSeq 4000 sequencer.

value: melanoma

tag: patient

tag: time

value: ACT product

value: expanded TILs


title: single cells 12h rep2


title: raw_C57_20141433_E15.5 (Run 2)

city: Leiden

first: Jan

last: Wijnholds

address: Albinusdreef 2

department: Ophthalmology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
•Performed sequencing using Life Technologies SOLiD5500, single end, 50 bp. Reads aligned against mm10, bamgen.mqv.threshold set to 20 (Lifescope v2.5)
•Genes with no counts in any of the samples were removed. Filtering: Genes with more than 1 count-per-million reads (CPM) in 5 or more of the samples were kept. Normalization: TMM (edgeR), weighted trimmed mean of M-values (to the reference) is used (Robinson & Oshlack, 2010).
•Original gene symbols mapped to other gene identifiers using biomaRt, using Ensembl (v90). The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship.
•Benjamini-Hochberg false discovery rate to correct for multiple testing of the resulting p-values. Analysis was performed using R v3.4.1 and Bioconductor v3.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and CPMs for each sample

organism: Mus musculus

source_name: neuro retina

growth_protocol: All mice used were maintained on a 99.9% C57BL/6JOlaHsd genetic background with a 12 h day-night cycle and supplied with food and water ad libitum. Crb1KO (Crb1-/-) mice (van de Pavert et al., 2004) were crossed with a retinal Crb2ΔRPC (Crb2F/FChx10CreTg/+ clone P1E9) mouse strain (Alves et al., 2013b; Rowan and Cepko, 2004) to ablate both Crb1 and Crb2 during retinal development from retinal progenitor cells. Cre starts to be expressed around E9.5 in the retina (Rowan and Cepko, 2004). The previously made Chx10Cre mice were generated by knocking in GFP-Cre-IRES-AP cDNA in exon-1 of the Chx10 gene on a Bacterial Artificial Chromosomes (BAC; -55 kb Chx10 of ATG to +22 kb off of the polyadenylation sequence) (Rowan and Cepko, 2004). Interestingly, the last exon of the Abcd4 gene is only ~7000 bp from the last exon of the Chx10 gene thus was on the BAC. Others have shown that large BACS containing several genes can lead to overexpression of flanking genes (Kolisnyk et al., 2013; Ting and Feng, 2014). We believe the integration of the cDNA in close proximity to the Abcd4 gene and being both on the BAC may have led to the overexpression of the Abcd4 gene in Crb1KOCrb2ΔRPC mice. Crb1KOCrb2ΔRPC mice were compared to littermate Crb1KOCrb2F/F mice not expressing Cre. C57BL/6JOlaHsd mice have a 365 kb deletion ablating the Mmrn1 and Snca and express low levels of Abcd4 (Gajović et al., 2006; Specht and Schoepfer, 2004). The C57BL/6J substrain (from the Jackson Laboratory) carries a 5-exon-spanning deletion in the Nnt gene but C57BL/6JOlaHsd have a wildtype Nnt gene (Huang et al., 2006).

extract_protocol: Ovation RNA-Seq System V2 (NuGEN) for cDNA amplificationV2.

treatment_protocol: Total of 50 Samples over two separate Runs (Run1/Run2). Two outliers were removed. Input RNA had RIN>8.

value: neuro retina

tag: genetic background

value: retinal cells

tag: genotype

value: wild type

tag: developmental stage


title: ATACseq_U266_MAF-OE_rep2

library_source: genomic

molecule: genomic DNA

extract_protocol: custom method (see paper Methods)


title: single cells 24h rep1


title: RNAseq_U266_EV_rep1


title: RNAseq_U266_EV_rep2


title: bulk control 48h dissociated rep2

description:
col_48_p3
bulk_controls_counts.txt.gz

value: dissociated


title: ATACseq_U266_MAF-OE_rep1


title: GEX patient2_scACTP_1


title: bulk control 48h dissociated rep1

description:
col_48_p1
bulk_controls_counts.txt.gz


title: bulk control 48h non-dissociated rep3

description:
col_48_np4
bulk_controls_counts.txt.gz

value: intact


title: ATACseq_U266_EV_rep2


title: raw_C57_20141435_E15.5 (Run 2)


title: ATACseq_U266_EV_rep1


title: bulk control 48h non-dissociated rep2

description:
col_48_np3
bulk_controls_counts.txt.gz


title: RNAseq_MAF_sh4_JJN3_rep2

value: anti-MAF shRNA (sh4)


title: raw_C57_20141434_E15.5 (Run 2)


title: GEX patient11_scACTP_1


title: bulk control 48h non-dissociated rep1

description:
col_48_np1
bulk_controls_counts.txt.gz


title: RNAseq_MAF_sh1_JJN3_rep2

value: anti-MAF shRNA (sh1)


title: single cells 24h rep2


title: bulk control 24h dissociated rep3

description:
col_24_p4
bulk_controls_counts.txt.gz


title: bulk control 24h dissociated rep2

description:
col_24_p3
bulk_controls_counts.txt.gz


title: RNAseq_scrbl_JJN3_rep2

value: scrbl


title: single cells 12h rep1


title: RNAseq_MAF_sh1_JJN3_rep1


title: bulk control 24h dissociated rep1

description:
col_24_p1
bulk_controls_counts.txt.gz


title: RNAseq_scrbl_JJN3_rep1


title: bulk control 24h non-dissociated rep2

description:
col_24_np3
bulk_controls_counts.txt.gz


title: bulk control 24h non-dissociated rep1

description:
col_24_np1
bulk_controls_counts.txt.gz


title: bulk control 12h dissociated rep3

description:
col_12_p4
bulk_controls_counts.txt.gz


title: RNAseq_MAF_sh1_MM1S_rep2


title: RNAseq_MAF_sh4_MM1S_rep2


title: bulk control 12h dissociated rep2

description:
col_12_p3
bulk_controls_counts.txt.gz


title: RNAseq_scrbl_MM1S_rep2


title: bulk control 12h dissociated rep1

description:
col_12_p1
bulk_controls_counts.txt.gz


title: RNAseq_scrbl_MM1S_rep1


title: RNAseq_MAF_sh4_MM1S_rep1


title: RNAseq_MAF_sh1_MM1S_rep1


title: bulk control 12h non-dissociated rep3

description:
col_12_np4
bulk_controls_counts.txt.gz


title: bulk control 12h non-dissociated rep2

description:
col_12_np3
bulk_controls_counts.txt.gz


title: DFO

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

country: USA

institute: University of Michigan

description: Gene expression data from colons.

data_processing:
Data quality were checked via fastQC
Raw reads were aligned using STAR
Aligned reads were assigned to genes using Cuffdiff
Genome_build: GRCh37
Supplementary_files_format_and_content: Cuffdiff counts output

source_name: treated tumor colonoids

growth_protocol: The tumor colonoids culture plates were placed in a 37°C incubator for 30 min to solidify the Matrigel, followed by the addition of 1mL serum-free Keratinocyte Growth Media Gold (KGMG, Catalogue: 00195769, Lonza, Basel, Switzerland).

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

treatment_protocol: After 24 hours of plating, colonoids were treated with DFO (0 or 100 μM) in KGMG for 4 days with fresh media change every other day.

value: colon


title: Con

description: Gene expression data from colons.

source_name: control tumor colonoids


title: RNAseq_MAF_sh4_JJN3_rep1


title: 60H64N-1

city: Miami

first: Dmitry

last: Velmeshev

state: FL

address: 1501 NW 10th ave, BRB 629

department: Psychiatry

institute: Universtiy of Miami

data_processing:
Read mapping to USCS GRCh38 transcript set with Bowtie2 version 2.1.0
Gene expression level estimation using RSEM v1.2.15.
TMM (trimmed mean of M-values) was gene expression normalization
Genome_build: GRCh38

growth_protocol: The tissue model is an organotypic culture of normal human oral keratinocytes grown on the top of fibroblasts, and cultured in serum-free medium to form a 3D differentiated tissue histologically similar to buccal mucosa. The 3D tissue EpiOral was purchased from MatTek Corporation (Ashland, MA).  The tissues were treated with different concentrations of everolimus for 60h (0, 32, 64 ng/ml).

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen,  Germantown, MD)
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq  poly(A) selected kit with 201-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.

treatment_protocol: Everolimus, 0, 32, 64 ng/mL

tag: hours in vitro

tag: everolimus concentration (ng/ml)

value: 32 ng/mL of Everolimus


title: bulk control 24h non-dissociated rep3

description:
col_24_np4
bulk_controls_counts.txt.gz


title: 60H64N-3


title: 60H32N-3


title: Rat CD4+ T-MBP cells, spleen Grk2 KO, rep R1

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

country: Germany

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

description: Column names: R1NT, R2NT, R3NT, R1Grk2, R2Grk2, R3Grk2

data_processing:
Fastq files were aligned with RNA STAR (version 2.7.2b) to the reference genome Rnor_6.0.102 with default parameters and without trimming
HTSeq-count (version 1.0.0) was then used
Differential expression determined with DESeq2 (version 2.11.40.7+galaxy1), with estimateSizeFactors = poscounts and otherwise default parameters. Batch correction per animal was performed when applicable
All further analysis was run with R (version 4.0.0+)
Rnor_6.0
Tab-delimited txt file of DESeq2 results
Tab-delimited txt file of normalized counts output from the DESeq2 software

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Sorted CD4+ T-MBP cells from spleen

growth_protocol: Cells were transferred to Lewis rats three days before isolation. Prior to transfer, cells were kept in TCGF (complete DMEM supplemented with 10 % Horse serum and 2 % of PMA-stimulated EL4IL2 cell culture supernatant and 1 % Pen/Strep) for four days to expand the number of T cells. Then, the T cells were restimulated for two days with 50 Gy irradiated thymocytes in complete DMEM supplemented with 1 % rat serum and 10 µg/ml MBP, and transferred.

extract_protocol:
The spleen was dissected and homogenized by passing through a metal strainer. Erythrocytes were removed by treating with ACK buffer for 3 min on ice and CD4+ T cells were enriched using the EasySep™ Rat CD4+ T Cell Isolation Kit (StemCell technologies), before purification by sorting based on their fluorescent markers, BFP for control and GFP for KO
The library was prepared from total RNA using the Collibri 3' mRNA Library Prep Kits for Illumina Systems (Thermo Fisher). Amplification of transcripts was confirmed with Agilent Bioanalyzer on DNA 1000 Chips

value: Sorted CD4+ T-MBP cells from spleen

value: Grk2 KO

tag: strain

value: Lewis rat

value: day 3 post transfer


title: Rat CD4+ T-MBP cells, spleen Grk2 KO, rep R3

description: Column names: R1NT, R2NT, R3NT, R1Grk2, R2Grk2, R3Grk4


title: Rat CD4+ T-MBP cells, spleen NT control to Grk2 KO, rep R3

value: WT


title: Rat CD4+ T-MBP cells, spleen NT control to Grk2 KO, rep R2

description: Column names: R1NT, R2NT, R3NT, R1Grk2, R2Grk2, R3Grk3


title: 60H32N-1


title: 60H0N-3


title: 60H0N-2


title: Ascitic chickens, Male, rep 2

city: Tabriz

first: Karim

last: Hasanpur

state: Azarbaijan

address: Jam-e-jam

country: Iran

institute: university of Tabriz

description: matrix column name:AscitesMale2

data_processing:
Raw sequence data (FASTQ format) were pre-processed using FastQC (version 0.10.1) and Trimmomatic (version 0.10.1) software and poor quality reads were eliminated from the data to ensure the success of analyses. Indexing of the reference genome was performed using Bowtie2 v2.0.6, and paired-end clean reads were aligned to the ensembl Gallus gallus Build 5.0 reference genome (asia.ensembl.org/Gallus_gallus/info/index) using TopHat v2.0.9 with the mismatch being set to 3. RseQC software (version 0.10.1) was used for quality control of the mapped reads.
Assembly of the transcripts was performed using cufflinks (version 0.10.1) followed by merging of all assemblies using cuffmerge (version 0.10.1). Cuffdiff (version 0.10.1) was utilized to obtain a list of significantly differentially expressed novel genes.
The total number of reads mapped to each gene was counted using HTSeq v0.6.1. Differential expression analysis of known genes was performed using the DEseq2 package (1.22.1) in R software (version 3.5.1) based on the variance-stabilized normalized read counts (Love et al. 2014). Genes with adjusted-pvalues < 0.05 (using Benjamini and Hochberg’s approach) were classified as significantly differentially expressed.
Supplementary files format and content: Gallus gallus Build 5.0
Supplementary files format and content: tab-delimited text file include count matrix for all samples

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was extracted from the 32 liver tissue samples using RNSol reagent (ROJE Technologies, Iran), according to the manufacturer’s protocol. The high-quality RNA of four samples were pooled and finally 8 pooled-samples were obtained (2 ascitic-males, 2 ascitic-females, 2 healthy-males and 2 healthy-females). To eliminate any contaminating DNA, DNase I (Ambion, Austin, TX) digestion step was performed after RNA extraction. The quality and quantity of the pooled-RNAs were determined by measuring the absorbance at 260 nm, 280 nm and 230 nm and calculating the A260/A280 and A260/A230 ratio using a NanoDrop ND-2000 spectrophotometer (Nano-drop Technologies, Wilmington, DE). In addition, DNA and protein contaminations or RNA degradation were monitored on 1% agarose gel.
To guarantee the reliability of the data, quality control (QC) was performed at each step of the procedure including sample test, library preparation, and sequencing. After the quality control of the samples (using Nanodrop, Agarose Gel Electrophoresis and Agilent 2100), those samples with RNA integrity number above 7.5 were used for library preparation. Then, mRNA was enriched using oligo(dT) beads. The mRNA was fragmented randomly by adding fragmentation buffer and cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. The qualified libraries were fed into the Illumina sequencers after pooling according to its effective concentration and expected data volume.

treatment_protocol: The chickens were raised on floor pens under normal condition until day 21. The house temperature was kept 32-34°C during the first and second days of age and then was gradually lowered by 1°C every other day until 24°C was reached on day 21 at which the cold temperature challenge was started. The temperature of house maintained 18°C from day 22 onward until the end of experiment (day 48). In order to enhance the probability of incidence of pulmonary hypertension in almost all of the susceptible chickens, the cold temperatures was combined with high-energy diets.

value: Liver

tag: Sex

value: Male

tag: health-status

value: Water belly

value: Day 42

value: ascitic


title: Ascitic chickens, Male, rep 1

description: matrix column name:AscitesMale1


title: Ascitic chickens, Female, rep 2

description: matrix column name:AscitesFemale2

value: Female


title: Healthy chickens, Male, rep 2

description: matrix column name:HealthyMale2

value: Healthy


title: CH1359_2_17

city: Shenzhen

first: Siyu

last: Yang

address: No.628, Zhenyuan Rd, Guangming (New) Dist., Shenzhen

country: China

institute: The Seventh Affiliated Hospital of Sun Yat-Sen University

data_processing:
Illumina Casava2.19 software used for for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ftp://ftp.ensembl.org/pub/release-92/fasta/danio_rerio/dna/
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Danio rerio

source_name: retina

extract_protocol:
Retinas were removed, flash frozen on dry ice and RNA was harvested usingTrizol reagent Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: retina

value: flrt2 mutant


title: CH13591_19


title: 60H32N-2


title: CH13591_8_ysy


title: Healthy chickens, Female, rep 2

description: matrix column name:HealthyFemale2


title: bulk control 12h non-dissociated rep1

description:
col_12_np1
bulk_controls_counts.txt.gz

value: embryo

tag: dissociation

value: intact


title: CH135912_16


title: Rat CD4+ T-MBP cells, spleen Grk2 KO, rep R2


title: Ascitic chickens, Female, rep 1

description: matrix column name:AscitesFemale1


title: 60H64N-2

value: 32 ng/mL of Everolimus


title: Healthy chickens, Female, rep 1

description: matrix column name:HealthyFemale1


title: AB1_8_ysy

value: wildtype


title: AB1_19


title: AB1_8


title: Rat CD4+ T-MBP cells, spleen NT control to Grk2 KO, rep R1

value: Sorted CD4+ T-MBP cells from spleen


title: AB12_16


title: PMVEC_PFKB3_KO_HYP_FRUCTOSE_REP_3

city: Mobile

last: Roberts

state: AL

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

data_processing:
Analysis was conducted by Novogene.
Reads with adapter contamination, uncertain nucleotides constituting more than 10 per cent of either read (N > 10%), and low-quality nucleotides (Base Quality less than 5) constituting more than 50 per cent of the read were removed.
Gnee counts were generating by aligning the filtered reads to the rat reference genome (Rnor_6.0) using HISAT2.
Differential gene expression analysis was performed using DESeq2.
Assembly: Rnor_6.0
Supplementary files format and content: Excel (.xlsx) file containing raw gene counts for each sample. First column is Ensembl gene identifier, subsequent columns are raw read counts for each sample (column name same as sample name), and remaining columns are gene annotation info (name, position, length, biotype, description, transcription factor family).

source_name: PMVEC

growth_protocol: Wild-type and PFKFB3 knockout PMVECs were incubated in media containing glucose (25 mM) or fructose (25 mM) under normoxia or hypoxia for 24 hours.

extract_protocol:
Total RNA samples were processed by Novogene.
Library preparation was performed by Novogene.

value: PMVEC

value: pulmonary microvascular endothelial cells

value: PFKFB3 KO

value: hypoxia, fructose


title: 60H0N-1


title: PMVEC_PFKB3_KO_HYP_FRUCTOSE_REP_2


title: CAT8_DMSO_B_S26_RNA-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CAT8-3xV5 IAA7::URA3

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CAT8-3xV5 IAA7::URA3


title: PMVEC_PFKB3_KO_HYP_GLUCOSE_REP_3

value: hypoxia, glucose


title: CAT8_DMSO_C_S27_RNA-seq


title: CAT8_3IAA_C_S30_RNA-seq


title: CAT8_DMSO_A_S25_RNA-seq


title: CAD1_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 CAD1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 CAD1-3xV5 IAA7::URA3


title: Healthy chickens, Male, rep 1

description: matrix column name:HealthyMale1

value: Liver

value: Male

value: Day 42


title: CAT8_3IAA_B_S29_RNA-seq


title: PMVEC_PFKB3_KO_HYP_FRUCTOSE_REP_1


title: CAT8_3IAA_A_S28_RNA-seq


title: PMVEC_PFKB3_KO_NORM_FRUCTOSE_REP_3

value: normoxia, fructose


title: CAD1_DMSO_A_S19_RNA-seq


title: PMVEC_PFKB3_KO_HYP_GLUCOSE_REP_1


title: CAD1_3IAA_B_S23_RNA-seq


title: CAD1_3IAA_C_S24_RNA-seq


title: PMVEC_PFKB3_KO_NORM_FRUCTOSE_REP_2


title: CAD1_3IAA_A_S22_RNA-seq


title: CAD1_DMSO_B_S20_RNA-seq


title: BAS1_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 BAS1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 BAS1-3xV5 IAA7::URA3


title: PMVEC_PFKB3_KO_NORM_FRUCTOSE_REP_1


title: BAS1_DMSO_B_S44_RNA-seq


title: PMVEC_PFKB3_KO_NORM_GLUCOSE_REP_3

value: normoxia, glucose


title: PMVEC_PFKB3_WT_HYP_FRUCTOSE_REP_3

value: WT


title: BAS1_DMSO_A_S43_RNA-seq


title: PMVEC_PFKB3_KO_NORM_GLUCOSE_REP_1


title: PMVEC_PFKB3_KO_NORM_GLUCOSE_REP_2


title: BAS1_3IAA_C_S48_RNA-seq


title: BAS1_3IAA_B_S47_RNA-seq


title: PMVEC_PFKB3_WT_HYP_FRUCTOSE_REP_2


title: BAS1_3IAA_A_S46_RNA-seq


title: PMVEC_PFKB3_KO_HYP_GLUCOSE_REP_2


title: AZF1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 AZF1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 AZF1-3xV5 IAA7::URA3


title: PMVEC_PFKB3_WT_HYP_FRUCTOSE_REP_1


title: AZF1_DMSO_B_S38_RNA-seq


title: AZF1_DMSO_A_S37_RNA-seq


title: AZF1_3IAA_C_S42_RNA-seq


title: PMVEC_PFKB3_WT_NORM_FRUCTOSE_REP_3


title: PMVEC_PFKB3_WT_HYP_GLUCOSE_REP_1


title: PMVEC_PFKB3_WT_HYP_GLUCOSE_REP_3


title: PMVEC_PFKB3_WT_NORM_FRUCTOSE_REP_2


title: AZF1_3IAA_A_S40_RNA-seq


title: PMVEC_PFKB3_WT_NORM_FRUCTOSE_REP_1


title: PMVEC_PFKB3_WT_NORM_GLUCOSE_REP_3


title: LCS7744_KA_M_Clean_Data1.fq.gz

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include expression analysis between Samples

source_name: Breast

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol, frozen, and shipped on dry ice.
Library construction was performed by LCSciences (Houston, TX).
RNA sequencing was performed by LCSciences (Houston, TX) for total RNA sequencing (150 bp PE, 40 million reads per sample).

value: Breast

value: Breast cancer Cell Line

value: M(mock)


title: PMVEC_PFKB3_WT_NORM_GLUCOSE_REP_2

value: PMVEC

value: pulmonary microvascular endothelial cells


title: ASG1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ASG1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ASG1-3xV5 IAA7::URA3


title: ASG1_DMSO_B_S32_RNA-seq


title: ASG1_3IAA_B_S35_RNA-seq


title: ASG1_DMSO_A_S31_RNA-seq


title: PMVEC_PFKB3_WT_NORM_GLUCOSE_REP_1


title: PMVEC_PFKB3_WT_HYP_GLUCOSE_REP_2


title: ASG1_3IAA_C_S36_RNA-seq


title: ARO80_3IAA_B_S29_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ARO80-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ARO80-3xV5 IAA7::URA3


title: LCS7744_KA_L_Clean_Data1.fq.gz

value: L(LU-102, our inhibitor)


title: ARO80_3IAA_A_S28_RNA-seq


title: ASG1_3IAA_A_S34_RNA-seq


title: LCS7744_KA_CL_Clean_Data1.fq.gz

value: CL (CGI and LU)


title: ARG80_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ARG80-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ARG80-3xV5 IAA7::URA3


title: ARO80_DMSO_B_S26_RNA-seq


title: ARO80_DMSO_A_S25_RNA-seq


title: ARO80_3IAA_C_S30_RNA-seq


title: ARG80_3IAA_B_S17_RNA-seq


title: AFT2_DMSO_A_S7_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 AFT2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 AFT2-3xV5 IAA7::URA3


title: AFT2_3IAA_C_S12_RNA-seq


title: ARO80_DMSO_C_S27_RNA-seq


title: ARG80_3IAA_A_S16_RNA-seq


title: ARG80_DMSO_B_S14_RNA-seq


title: LCS7744_KA_C_Clean_Data1.fq.gz

value: C(CGI-1746, BTK inhibitor)


title: ARG80_3IAA_C_S18_RNA-seq


title: LCS7744_KA_B_Clean_Data1.fq.gz

value: B(bortezomib)


title: AFT2_3IAA_B_S11_RNA-seq


title: ADR1_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ADR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ADR1-3xV5 IAA7::URA3


title: ADR1_DMSO_B_S20_RNA-seq


title: AFT2_3IAA_A_S10_RNA-seq


title: AFT2_DMSO_B_S8_RNA-seq


title: AZF1_3IAA_B_S41_RNA-seq


title: ARG80_DMSO_A_S13_RNA-seq


title: ADR1_DMSO_A_S19_RNA-seq


title: ADR1_3IAA_B_S23_RNA-seq


title: ADR1_3IAA_C_S24_RNA-seq


title: AFT2_DMSO_C_S9_RNA-seq


title: ACA1_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 ACA1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 ACA1-3xV5 IAA7::URA3


title: ACA1_DMSO_A_S13_RNA-seq


title: ACA1_DMSO_C_S15_RNA-seq


title: ACA1_3IAA_C_S18_RNA-seq


title: ACA1_3IAA_A_S16_RNA-seq


title: ACA1_3IAA_B_S17_RNA-seq


title: ADR1_3IAA_A_S22_RNA-seq


title: GCN4_SM_input_B_ChIP-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GCN4-3x Flag::KanMx

extract_protocol:
ChIP-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or SM, Raffinose or Galactose.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GCN4-3x Flag::KanMx

value: SM starvation


title: GCN4_SM_input_A_ChIP-seq


title: GCN4_SM_C_ChIP-seq


title: GCN4_SM_input_C_ChIP-seq


title: GCN4_input_B_ChIP-seq


title: GCN4_input_A_ChIP-seq


title: GCN4_C_ChIP-seq


title: GCN4_A_ChIP-seq


title: GAL4_input_C_ChIP-seq

source_name: MAT{alpha} ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAL4-13x Myc::HPH

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAL4-13x Myc::HPH


title: GCN4_SM_B_ChIP-seq


title: GAL4_galactose_input_A_ChIP-seq

value: Galactose induction


title: GAL4_galactose_input_B_ChIP-seq


title: GAL4_input_B_ChIP-seq


title: GCN4_B_ChIP-seq


title: GAL4_galactose_input_C_ChIP-seq


title: GCN4_input_C_ChIP-seq


title: GAL4_galactose_C_ChIP-seq


title: GAL4_input_A_ChIP-seq


title: GAL4_galactose_A_ChIP-seq


title: GAL4_C_ChIP-seq


title: GAL4_B_ChIP-seq


title: GCN4_SM_A_ChIP-seq


title: GAL4_galactose_B_ChIP-seq


title: GAL4_A_ChIP-seq


title: ZAP1_B_ChEC-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Assembly: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary files format and content: Processed data is provided in a bigwig format and contains spike-in normalized signal per base pair.
Library strategy: ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ZAP1-MNase::TRP1

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ZAP1-MNase::TRP1


title: YRR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YRR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YRR1-MNase::TRP1


title: YRR1_B_ChEC-seq


title: ZAP1_A_ChEC-seq


title: ZAP1_C_ChEC-seq


title: YRM1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YRM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YRM1-MNase::TRP1


title: YRM1_C_ChEC-seq


title: YRR1_A_ChEC-seq


title: YOX1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YOX1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YOX1-MNase::TRP1


title: YRM1_A_ChEC-seq


title: YPR015C_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YPR015C-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YPR015C-MNase::TRP1


title: YOX1_B_ChEC-seq


title: YOX1_A_ChEC-seq


title: YNR063W_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YNR063W-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YNR063W-MNase::TRP1


title: YPR015C_B_ChEC-seq


title: YNR063W_B_ChEC-seq


title: YNR063W_A_ChEC-seq


title: YLL054C_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YLL054C-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YLL054C-MNase::TRP1


title: YKL222C_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YKL222C-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YKL222C-MNase::TRP1


title: YKL222C_B_ChEC-seq


title: YLL054C_A_ChEC-seq


title: YKL222C_A_ChEC-seq


title: YLL054C_C_ChEC-seq


title: YJL206C_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YJL206C-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YJL206C-MNase::TRP1


title: YJL206C_A_ChEC-seq


title: YJL206C_B_ChEC-seq


title: YPR015C_C_ChEC-seq


title: YHP1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YHP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YHP1-MNase::TRP1


title: YHP1_B_ChEC-seq


title: YHP1_C_ChEC-seq


title: YAP7_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YAP7-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YAP7-MNase::TRP1


title: YAP7_A_ChEC-seq


title: YAP6_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YAP6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YAP6-MNase::TRP1


title: YAP1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YAP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YAP1-MNase::TRP1


title: YAP6_C_ChEC-seq


title: YAP1_C_ChEC-seq


title: YAP6_A_ChEC-seq


title: YAP5_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 YAP5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 YAP5-MNase::TRP1


title: YAP1_B_ChEC-seq


title: YAP5_B_ChEC-seq


title: XBP1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 XBP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 XBP1-MNase::TRP1


title: YAP5_A_ChEC-seq


title: WTM2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 WTM2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 WTM2-MNase::TRP1


title: XBP1_C_ChEC-seq


title: WHI5_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 WHI5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 WHI5-MNase::TRP1


title: YAP7_C_ChEC-seq


title: WHI5_C_ChEC-seq


title: WTM2_A_ChEC-seq


title: WAR1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 WAR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 WAR1-MNase::TRP1


title: WTM2_B_ChEC-seq


title: WAR1_C_ChEC-seq


title: VHR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 VHR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 VHR1-MNase::TRP1


title: VHR1_B_ChEC-seq


title: WAR1_A_ChEC-seq


title: VHR1_A_ChEC-seq


title: USV1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 USV1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 USV1-MNase::TRP1


title: USV1_C_ChEC-seq


title: URC2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 URC2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 URC2-MNase::TRP1


title: XBP1_A_ChEC-seq


title: UPC2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 UPC2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 UPC2-MNase::TRP1


title: URC2_A_ChEC-seq


title: UPC2_B_ChEC-seq


title: URC2_C_ChEC-seq


title: UGA3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 UGA3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 UGA3-MNase::TRP1


title: UME6_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 UME6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 UME6-MNase::TRP1


title: USV1_A_ChEC-seq


title: UME6_B_ChEC-seq


title: UGA3_A_ChEC-seq


title: WHI5_B_ChEC-seq


title: TYE7_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TYE7-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TYE7-MNase::TRP1


title: TYE7_A_ChEC-seq


title: UME6_C_ChEC-seq


title: TUP1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TUP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TUP1-MNase::TRP1


title: TUP1_C_ChEC-seq


title: TUP1_A_ChEC-seq


title: TOS8_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TOS8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TOS8-MNase::TRP1


title: TOS8_B_ChEC-seq


title: THI3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 THI3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 THI3-MNase::TRP1


title: TOS8_A_ChEC-seq


title: THI3_B_ChEC-seq


title: THI3_A_ChEC-seq


title: TFA1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TFA1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TFA1-MNase::TRP1


title: UPC2_A_ChEC-seq


title: TFA1_A_ChEC-seq


title: UGA3_B_ChEC-seq


title: TEC1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TEC1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TEC1-MNase::TRP1


title: TFA1_B_ChEC-seq


title: TDA9_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 TDA9-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 TDA9-MNase::TRP1


title: TEC1_A_ChEC-seq


title: TDA9_C_ChEC-seq


title: TYE7_B_ChEC-seq


title: TEC1_B_ChEC-seq


title: SWR1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWR1-MNase::TRP1


title: TDA9_A_ChEC-seq


title: SWR1_C_ChEC-seq


title: SWP82_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWP82-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWP82-MNase::TRP1


title: SWI6_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWI6-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWI6-MNase::TRP1


title: SWP82_A_ChEC-seq


title: SWI6_B_ChEC-seq


title: SWI5_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWI5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWI5-MNase::TRP1


title: SWP82_B_ChEC-seq


title: SWI5_B_ChEC-seq


title: SWI5_A_ChEC-seq


title: SWI4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWI4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWI4-MNase::TRP1


title: SWI4_A_ChEC-seq


title: SWI3_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SWI3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SWI3-MNase::TRP1


title: SWI4_B_ChEC-seq


title: SWI3_C_ChEC-seq


title: SUT2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SUT2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SUT2-MNase::TRP1


title: SUT1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SUT1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SUT1-MNase::TRP1


title: SUM1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SUM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SUM1-MNase::TRP1


title: SUT1_A_ChEC-seq


title: SUB1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SUB1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SUB1-MNase::TRP1


title: SUB1_C_ChEC-seq


title: SUT2_A_ChEC-seq


title: SUT2_C_ChEC-seq


title: STP4_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STP4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STP4-MNase::TRP1


title: SWR1_B_ChEC-seq


title: STP4_C_ChEC-seq


title: STP4_B_ChEC-seq


title: SUB1_A_ChEC-seq


title: SWI6_A_ChEC-seq


title: SUM1_B_ChEC-seq


title: STP2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STP2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STP2-MNase::TRP1


title: SUM1_C_ChEC-seq


title: STP2_B_ChEC-seq


title: STP1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STP1-MNase::TRP1


title: STP1_B_ChEC-seq


title: STP1_A_ChEC-seq


title: SWI3_B_ChEC-seq


title: STE12_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STE12-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STE12-MNase::TRP1


title: STE12_A_ChEC-seq


title: SUT1_B_ChEC-seq


title: STB5_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STB5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STB5-MNase::TRP1


title: STB1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 STB1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 STB1-MNase::TRP1


title: STB5_B_ChEC-seq


title: STB1_B_ChEC-seq


title: SRL3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SRL3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SRL3-MNase::TRP1


title: SRL3_B_ChEC-seq


title: SPN1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SPN1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SPN1-MNase::TRP1


title: SOK2_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SOK2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SOK2-MNase::TRP1


title: SNT2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SNT2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SNT2-MNase::TRP1


title: SNT2_C_ChEC-seq


title: SPN1_B_ChEC-seq


title: SOK2_C_ChEC-seq


title: SRL3_A_ChEC-seq


title: SPN1_C_ChEC-seq


title: STE12_C_ChEC-seq


title: SOK2_B_ChEC-seq


title: STP2_A_ChEC-seq


title: SNF5_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SNF5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SNF5-MNase::TRP1


title: STB5_A_ChEC-seq


title: SNF5_B_ChEC-seq


title: SMP1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SMP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SMP1-MNase::TRP1


title: SMP1_A_ChEC-seq


title: SKO1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SKO1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SKO1-MNase::TRP1


title: STB1_A_ChEC-seq


title: SKO1_B_ChEC-seq


title: SKO1_A_ChEC-seq


title: SNT2_A_ChEC-seq


title: SKN7_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SKN7-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SKN7-MNase::TRP1


title: SKN7_B_ChEC-seq


title: SFP1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SFP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SFP1-MNase::TRP1


title: SKN7_A_ChEC-seq


title: SFP1_B_ChEC-seq


title: SFP1_A_ChEC-seq


title: SNF5_C_ChEC-seq


title: SFL1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SFL1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SFL1-MNase::TRP1


title: RTG3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RTG3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RTG3-MNase::TRP1


title: SFL1_C_ChEC-seq


title: SDD4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SDD4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SDD4-MNase::TRP1


title: SFG1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 SFG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SFG1-MNase::TRP1


title: SMP1_C_ChEC-seq


title: RTG3_B_ChEC-seq


title: SFG1_A_ChEC-seq


title: SDD4_B_ChEC-seq


title: SFG1_B_ChEC-seq


title: RTG1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RTG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RTG1-MNase::TRP1


title: RTG1_C_ChEC-seq


title: RSF1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RSF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RSF1-MNase::TRP1


title: RTG3_A_ChEC-seq


title: RTG1_A_ChEC-seq


title: RSF1_B_ChEC-seq


title: RPH1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RPH1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RPH1-MNase::TRP1


title: RSF1_A_ChEC-seq


title: SFL1_A_ChEC-seq


title: ROX1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 ROX1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 ROX1-MNase::TRP1


title: SDD4_A_ChEC-seq


title: RPH1_A_ChEC-seq


title: ROX1_B_ChEC-seq


title: ROX1_A_ChEC-seq


title: RME1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RME1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RME1-MNase::TRP1


title: RME1_A_ChEC-seq


title: RLM1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RLM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RLM1-MNase::TRP1


title: RLM1_B_ChEC-seq


title: RIM101_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RIM101-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RIM101-MNase::TRP1


title: RIF1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RIF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RIF1-MNase::TRP1


title: RGM1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RGM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RGM1-MNase::TRP1


title: RGM1_A_ChEC-seq


title: RFX1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RFX1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RFX1-MNase::TRP1


title: RIF1_C_ChEC-seq


title: RIM101_A_ChEC-seq


title: RIM101_C_ChEC-seq


title: REB1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 REB1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 REB1-MNase::TRP1


title: RFX1_C_ChEC-seq


title: RPH1_B_ChEC-seq


title: RDS2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RDS2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RDS2-MNase::TRP1


title: RME1_C_ChEC-seq


title: RDS2_C_ChEC-seq


title: REB1_A_ChEC-seq


title: RDR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RDR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RDR1-MNase::TRP1


title: RDR1_B_ChEC-seq


title: RLM1_C_ChEC-seq


title: RBA50_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RBA50-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RBA50-MNase::TRP1


title: RBA50_B_ChEC-seq


title: RDS2_A_ChEC-seq


title: RDR1_A_ChEC-seq


title: RAP1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RAP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RAP1-MNase::TRP1


title: RFX1_A_ChEC-seq


title: RIF1_A_ChEC-seq


title: REB1_B_ChEC-seq


title: RAP1_A_ChEC-seq


title: RAD23_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RAD23-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RAD23-MNase::TRP1


title: RAD23_C_ChEC-seq


title: RAD23_A_ChEC-seq


title: RAD4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 RAD4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 RAD4-MNase::TRP1


title: RAD4_B_ChEC-seq


title: PUT3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PUT3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PUT3-MNase::TRP1


title: RBA50_C_ChEC-seq


title: RAD4_A_ChEC-seq


title: PUT3_A_ChEC-seq


title: PUT3_B_ChEC-seq


title: PPR1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PPR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PPR1-MNase::TRP1


title: POG1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 POG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 POG1-MNase::TRP1


title: POG1_C_ChEC-seq


title: PPR1_C_ChEC-seq


title: PPR1_A_ChEC-seq


title: PIP2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PIP2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PIP2-MNase::TRP1


title: POG1_A_ChEC-seq


title: PIP2_C_ChEC-seq


title: PHO2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PHO2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PHO2-MNase::TRP1


title: PHO4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PHO4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PHO4-MNase::TRP1


title: PHO4_A_ChEC-seq


title: PIP2_A_ChEC-seq


title: RGM1_B_ChEC-seq


title: RAP1_B_ChEC-seq


title: PHO2_B_ChEC-seq


title: PHO2_A_ChEC-seq


title: PHD1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PHD1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PHD1-MNase::TRP1


title: PHD1_B_ChEC-seq


title: PHD1_A_ChEC-seq


title: PDR8_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PDR8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PDR8-MNase::TRP1


title: PDR8_B_ChEC-seq


title: PDR3_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PDR3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PDR3-MNase::TRP1


title: PDC2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PDC2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PDC2-MNase::TRP1


title: PDR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 PDR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 PDR1-MNase::TRP1


title: PDR1_B_ChEC-seq


title: PDR3_C_ChEC-seq


title: PDR8_A_ChEC-seq


title: PDC2_A_ChEC-seq


title: PDC2_B_ChEC-seq


title: PDR3_A_ChEC-seq


title: OPI1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 OPI1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 OPI1-MNase::TRP1


title: OPI1_A_ChEC-seq


title: PDR1_A_ChEC-seq


title: OPI1_C_ChEC-seq


title: OAF3_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 OAF3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 OAF3-MNase::TRP1


title: OAF3_A_ChEC-seq


title: PHO4_B_ChEC-seq


title: OAF3_C_ChEC-seq


title: NRM1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 NRM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 NRM1-MNase::TRP1


title: NRM1_A_ChEC-seq


title: NRG1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 NRG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 NRG1-MNase::TRP1


title: NRG1_B_ChEC-seq


title: NDD1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 NDD1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 NDD1-MNase::TRP1


title: NDD1_C_ChEC-seq


title: NDD1_B_ChEC-seq


title: NRG1_A_ChEC-seq


title: NCB2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 NCB2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 NCB2-MNase::TRP1


title: NCB2_B_ChEC-seq


title: MSS11_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MSS11-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSS11-MNase::TRP1


title: NCB2_A_ChEC-seq


title: MSS11_C_ChEC-seq


title: NRM1_C_ChEC-seq


title: MSN4_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MSN4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSN4-MNase::TRP1


title: MSN4_B_ChEC-seq


title: MSN4_C_ChEC-seq


title: MSN2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MSN2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSN2-MNase::TRP1


title: MSA2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MSA2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MSA2-MNase::TRP1


title: MSN2_C_ChEC-seq


title: MSS11_A_ChEC-seq


title: MSN2_A_ChEC-seq


title: MSA2_A_ChEC-seq


title: MSA2_B_ChEC-seq


title: MOT3_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MOT3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MOT3-MNase::TRP1


title: MOT1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MOT1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MOT1-MNase::TRP1


title: MOT3_A_ChEC-seq


title: MOT1_B_ChEC-seq


title: MOT3_C_ChEC-seq


title: lib64235

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: colon

extract_protocol:
Unfractionated colon biopsies taken from IBD patients before and during treatment with vedolizumab were processed for RNAsequencing. SMARTseq v4 chemistry was used to generate cDNA following the manufacturer's instructions.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with paired-end 53-base reads and a target depth of 5 million reads per sample.

tag: donorid

tag: vedolizumab treatment

value: on

tag: vedolizuman response

value: Non-Responder

tag: study group

value: CrohnsDisease


title: lib64234


title: lib64236


title: MOT1_A_ChEC-seq


title: MIG2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MIG2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MIG2-MNase::TRP1


title: lib64232

value: Responder


title: MIG2_B_ChEC-seq


title: lib64230


title: lib64229


title: lib64231

source_name: ileum


title: lib64233


title: MIG2_A_ChEC-seq


title: MIG1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MIG1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MIG1-MNase::TRP1


title: lib64228

value: pre

value: UlcerativeColitis


title: lib64227


title: MIG1_A_ChEC-seq


title: lib64226


title: lib64225


title: lib64224


title: lib64222


title: MGA1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MGA1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MGA1-MNase::TRP1


title: MGA1_A_ChEC-seq


title: MGA1_C_ChEC-seq


title: lib64221


title: MET32_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MET32-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MET32-MNase::TRP1


title: MET32_B_ChEC-seq


title: lib64219


title: MET31_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MET31-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MET31-MNase::TRP1


title: lib64223


title: MET32_A_ChEC-seq


title: lib64220


title: MET31_B_ChEC-seq


title: MET31_A_ChEC-seq


title: MET4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MET4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MET4-MNase::TRP1


title: lib64216


title: lib64215


title: lib64214


title: lib64217


title: lib64218


title: MET4_B_ChEC-seq


title: MIG1_B_ChEC-seq


title: MET4_A_ChEC-seq


title: lib64213


title: MED15_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MED15-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MED15-MNase::TRP1


title: lib64211


title: MED15_A_ChEC-seq


title: MED15_B_ChEC-seq


title: lib64212


title: MED8_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MED8-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MED8-MNase::TRP1


title: lib64209


title: MCM1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MCM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MCM1-MNase::TRP1


title: MED8_B_ChEC-seq


title: lib64208


title: lib64206


title: MCM1_B_ChEC-seq


title: lib64205


title: MED8_A_ChEC-seq


title: lib64204


title: lib64203


title: MBP1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MBP1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MBP1-MNase::TRP1


title: MBP1_C_ChEC-seq


title: lib64201


title: MAL13_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MAL13-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MAL13-MNase::TRP1


title: MBP1_B_ChEC-seq


title: lib64202


title: MAL13_B_ChEC-seq


title: lib64200


title: MCM1_A_ChEC-seq


title: lib64199


title: lib64210

value: on


title: MAC1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 MAC1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 MAC1-MNase::TRP1


title: MAC1_A_ChEC-seq


title: lib64207

value: Non-Responder

value: CrohnsDisease


title: MAC1_B_ChEC-seq


title: lib64197


title: lib64196


title: lib64195


title: lib64193

value: Responder


title: lib64192


title: lib64194


title: lib64190


title: LYS14_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 LYS14-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 LYS14-MNase::TRP1


title: LEU3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 LEU3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 LEU3-MNase::TRP1


title: LYS14_B_ChEC-seq


title: LYS14_C_ChEC-seq


title: LEU3_B_ChEC-seq


title: KAR4_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 KAR4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 KAR4-MNase::TRP1


title: KAR4_C_ChEC-seq


title: lib64189

source_name: colon

value: pre


title: LEU3_A_ChEC-seq


title: lib64188


title: lib64187


title: IXR1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 IXR1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 IXR1-MNase::TRP1


title: MAL13_A_ChEC-seq


title: lib64186

source_name: ileum


title: lib64198


title: lib64185


title: lib64184


title: IXR1_B_ChEC-seq


title: INO4_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 INO4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 INO4-MNase::TRP1


title: IXR1_A_ChEC-seq


title: lib64183


title: lib64191


title: lib64182


title: INO4_B_ChEC-seq


title: lib64181


title: lib64180


title: INO4_A_ChEC-seq


title: KAR4_A_ChEC-seq


title: INO2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 INO2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 INO2-MNase::TRP1


title: lib64179


title: INO2_B_ChEC-seq


title: IFH1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 IFH1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 IFH1-MNase::TRP1


title: INO2_A_ChEC-seq


title: lib64177

value: UlcerativeColitis


title: IFH1_B_ChEC-seq


title: lib64174


title: lib64178


title: IFH1_A_ChEC-seq


title: lib64175


title: HSF1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HSF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HSF1-MNase::TRP1


title: HSF1_B_ChEC-seq


title: HSF1_A_ChEC-seq


title: lib64176


title: lib64173


title: lib64171


title: lib64172


title: HMS2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HMS2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HMS2-MNase::TRP1


title: lib64170


title: HMS2_A_ChEC-seq


title: lib64169


title: lib64168


title: lib64167


title: HMS2_B_ChEC-seq


title: HIR3_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HIR3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HIR3-MNase::TRP1


title: lib64166

value: on


title: lib64165


title: HIR2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HIR2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HIR2-MNase::TRP1


title: HIR2_C_ChEC-seq


title: HCM1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HCM1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HCM1-MNase::TRP1


title: HCM1_C_ChEC-seq


title: lib64162


title: lib64163

value: Non-Responder


title: lib64159

value: Responder

value: CrohnsDisease


title: HAP5_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAP5-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAP5-MNase::TRP1


title: lib64161


title: lib64158


title: lib64160


title: lib64157


title: HAP5_C_ChEC-seq


title: HAP5_A_ChEC-seq


title: HCM1_A_ChEC-seq


title: lib64155


title: lib64154

value: Unk


title: HAP4_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAP4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAP4-MNase::TRP1


title: HAP4_C_ChEC-seq


title: lib64156

value: pre


title: HIR3_C_ChEC-seq


title: lib64164


title: HAP3_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAP3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAP3-MNase::TRP1


title: HIR3_A_ChEC-seq


title: HIR2_A_ChEC-seq


title: HAP4_B_ChEC-seq


title: lib64151

source_name: jejunum


title: lib64150


title: HAP2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAP2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAP2-MNase::TRP1


title: lib64149


title: lib64146


title: HAL9_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAL9-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAL9-MNase::TRP1


title: lib64147

source_name: colon

value: UlcerativeColitis


title: HAP2_A_ChEC-seq


title: HAP3_C_ChEC-seq


title: lib64152


title: lib64153


title: HAL9_A_ChEC-seq


title: lib64144


title: lib64143


title: HAC1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAC1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAC1-MNase::TRP1


title: HAC1_B_ChEC-seq


title: HAP3_A_ChEC-seq


title: lib64141


title: lib64142


title: HAA1_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 HAA1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 HAA1-MNase::TRP1


title: patient13_B30_TCRbeta

data_processing:
Deep sequencing of the TCR beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Assembly: IMGT data base was used to identifiy TCR
Supplementary files format and content: txt files containing the list of TCR and their frequencies
Library strategy: TCR-seq

source_name: blood

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction and as described in Genolet et al., Cell Report Methods, 2013.
Libraries were prepare using targeted TCR amplification

value: blood

tag: cell type

value: peripheral blood mononuclear cell (PBMC)

value: post-ACT


title: patient13_ACTP_TCRbeta

source_name: expanded TILs

tag: tissue

value: expanded TILs

value: ACT product


title: GZF3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GZF3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GZF3-MNase::TRP1


title: HAA1_A_ChEC-seq


title: patient13_T0siteA_TCRbeta

source_name: tumor

value: tumor

value: tumor-infiltrating lymphocytes (TILs)

tag: patient

value: pre-ACT


title: HAP2_B_ChEC-seq


title: GZF3_B_ChEC-seq


title: patient13_T0siteB_TCRbeta

tag: time


title: HAL9_B_ChEC-seq


title: patient12_T0_TCRbeta


title: patient12_B30_TCRbeta


title: GZF3_A_ChEC-seq


title: lib64148

value: on

value: Responder


title: lib64145

value: pre


title: GLN3_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GLN3-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GLN3-MNase::TRP1


title: GLN3_A_ChEC-seq


title: GLN3_B_ChEC-seq


title: patient11_B30_TCRbeta


title: patient11_T0_TCRbeta


title: HAC1_A_ChEC-seq


title: GCR2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GCR2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GCR2-MNase::TRP1


title: HAA1_B_ChEC-seq


title: patient11_B0_TCRbeta


title: GCR2_A_ChEC-seq


title: patient8_B30_TCRbeta


title: GCR2_B_ChEC-seq


title: patient1_B30_TCRbeta


title: GCN4_WT_SM_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 gcn4 delta::NatMX pGCN4-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pGCN4-MNase::LEU2

tag: treatment

value: SM starvation


title: GCN4_WT_SM_B_ChEC-seq

tag: genotype


title: patient13_B0_TCRbeta


title: BP+Huaier 2

city: China

first: Shengwei

last: Jiang

state: Guangdong

address: Xueyuan road 1098

department: Shenzhen University General Hospital

institute: Shenzhen University

data_processing:
Illumina Casava1.7 software used for basecalling.
fastp v0.20.0 for quality control
HISAT2 version 2.1.0 for mapping reads to the grch38 genome
featureCounts v1.6.1 was used to count reads
Assembly: grch38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreatic cancer

growth_protocol: MIA PaCa-2l cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA of cells was extracted by TRIzol (Thermo Fisher Scientific, 15596026, USA,) and sent to the company (Novogene) to perform a standard RNA-sequencing procedure.
RNA-seq libraries were constructed using a NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA). The library preparations were sequenced on an Illumina Novaseq 6000 platform, and 150 bp paired-end reads were generated.

treatment_protocol: Cell treated with 12.5 μg/ml BP or 12.5 μg/ml BP + 10 mg/ml Huaier

value: pancreatic cancer

tag: cell line

value: MIA PaCa-2

value: pancreatic cancer cells

value: WT

value: BP+Huaier


title: BP+Huaier 1


title: BP+Huaier 3


title: BP1

value: BP


title: GCN4_WT_SM_A_ChEC-seq


title: GCN4_WT_C_ChEC-seq


title: patient1_B0_TCRbeta

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: BP3


title: GCN4_dbdmut_SM_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 gcn4 delta::NatMX pGCN4-dbdmut-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pGCN4-dbdmut-MNase::LEU2


title: CM16 PDX, mouse D65, stable

city: Los Angeles

first: Bodour

last: Salhia

state: CA

address: 1450 Biggy St 2nd floor, Los Angeles, CA 90033

department: Department Of Translational Genomics

institute: University of Southern California

data_processing:
Sequences were aligned with STAR and read counting was performed with htseq
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw counts for all samples

source_name: breast cancer brain metastasis PDX

extract_protocol:
RNA was extracted using Allprep DNA/RNA kit (Qiagen)
Libraries were prepared using the KAPA mRNA HyperPrep Kit

treatment_protocol: 20 mg/kg AZD1390 oral, with 2.5 Gy radiation for 4 days

value: breast cancer brain metastasis PDX

value: AZD1390 + Radiation

value: Study endpoint


title: GCN4_WT_A_ChEC-seq


title: CM16 PDX, mouse D61, stable


title: GCN4_dbdmut_SM_A_ChEC-seq


title: GCN4_dbdmut_B_ChEC-seq


title: GCN4_SM_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GCN4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GCN4-MNase::TRP1


title: GCN4_SM_C_ChEC-seq


title: GCN4_admut_SM_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 gcn4 delta::NatMX pGCN4-admut-MNase::LEU2

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pGCN4-admut-MNase::LEU2


title: CM14 PDX, mouse D21, stable


title: CM07 PDX, mouse D63, stable


title: GCN4_SM_A_ChEC-seq


title: GCN4_admut_C_ChEC-seq


title: CM07 PDX, mouse D42, progression


title: CM07 PDX, mouse D32, progression


title: CM07 PDX, mouse D14, stable


title: CM16 PDX, mouse D54, stable


title: GCN4_dbdmut_SM_B_ChEC-seq


title: CM16 PDX, mouse D21, progression


title: ChIPseq_H3K4me2_U266_MAF-OE_rep3

description:
ChIPseq_H3K4me2_U266_MAF-OE_rep1n2_regions.bed
ChIPseq_H3K4me2_U266_MAF-OE_rep1n2_signal.bw

data_processing:
Bcl2Fastq (v2.20) software used for basecalling.
ChIP-seq analysis: Alignment was performed with bowtie2 against the hg38/GRCh38 genome. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling (ChIP versus Input)  was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. Bedtools was used to operate on genomic regions (union, intersections, etc.).
RNA-seq analysis: Alignment was performed using STAR (2.5.3a) against hg38/GRCh3 genome. The “Rsubread” Bioconductor package was used to obtain gene-level read counts. The “DESeq2” Bioconductor package was used for data normalization and differential expression analysis across different conditions of knock-down experiments in each cell line.
ATAC-seq analysis:  Alignment was performed with bowtie2 against the hg38/GRCh38 genome. Trimming was performed using TrimGalore. The samtools package was used to convert sam to bam files. Duplicate reads were removed using the Picard MarkDuplicates function. Peak calling was performed using MACS2. Genome browser tracks and heatmap enrichment plots were generated using Deeptools, with signal values  normalized as Fold  Change over Input. The MSPC package was used to obtain overlapping peaks between biological replicates. DESeq2 and ODIN were used for differential ATAC-seq analysis across conditions and treatments. Bedtools was used to operate on genomic regions (union, intersections, etc.).
Assembly: GRCh38
Supplementary files format and content: bedfile
Supplementary files format and content: BigWig
Supplementary files format and content: raw counts

extract_protocol: NEBNext Ultra II ChIP-seq Library Prep Master Mix (NEB)

value: Multiple myeloma cell line

tag: antibody


title: GCN4_dbdmut_C_ChEC-seq


title: CM14 PDX, mouse D61, stable


title: CM14 PDX, mouse D55, stable


title: CM14 PDX, mouse D34, progression


title: GCN4_WT_B_ChEC-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 gcn4 delta::NatMX pGCN4-MNase::LEU2


title: ChIPseq_Input_U266_EV_rep4

description:
ChIPseq_H3K4me2_U266_EV_rep1n2_regions.bed
ChIPseq_H3K4me2_U266_EV_rep1n2_signal.bw

value: Input


title: GCN4_A_ChEC-seq


title: GCN4_admut_SM_C_ChEC-seq

value: SM starvation


title: ChIPseq_H3K4me2_U266_MAF-OE_rep4


title: GAT1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAT1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAT1-MNase::TRP1


title: CM14 PDX, mouse D22, progression


title: CM07 PDX, mouse D53, stable


title: BP2

value: pancreatic cancer

value: MIA PaCa-2

value: pancreatic cancer cells


title: GCN4_admut_B_ChEC-seq


title: GCN4_admut_SM_A_ChEC-seq


title: GAL80_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAL80-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAL80-MNase::TRP1


title: GCN4_admut_A_ChEC-seq


title: GCN4_C_ChEC-seq


title: ChIPseq_H3K4me2_U266_EV_rep3


title: ChIPseq_Input_U266_MAF-OE_rep2

description:
ChIPseq_MAF_U266_MAF-OE_rep1n2_regions.bed
ChIPseq_MAF_U266_MAF-OE_rep1n2_signal.bw


title: CM14 PDX, mouse D53, stable


title: GCN4_dbdmut_A_ChEC-seq


title: GCN4_B_ChEC-seq


title: ChIPseq_Input_U266_MAF-OE_rep3


title: GAT2_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAT2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAT2-MNase::TRP1


title: CM07 PDX, mouse D11, stable


title: GAT2_C_ChEC-seq


title: ChIPseq_Input_U266_MAF-OE_rep4


title: GAL4_raffinose_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 GAL4-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 GAL4-MNase::TRP1

value: Grown in YP_raffinose


title: ChIPseq_H3K27Ac_U266_MAF-OE_rep1

description:
ChIPseq_H3K27ac_U266_MAF-OE_rep1n2_regions.bed
ChIPseq_H3K27ac_U266_MAF-OE_rep1n2_signal.bw


title: GAT2_A_ChEC-seq


title: GAL4_galactose_C_ChEC-seq

value: Galactose induction


title: GAT1_C_ChEC-seq


title: GAL4_galactose_B_ChEC-seq


title: ChIPseq_Input_U266_EV_rep2

description:
ChIPseq_MAF_U266_EV_rep1n2_regions.bed
ChIPseq_MAF_U266_EV_rep1n2_signal.bw


title: ChIPseq_Input_U266_EV_rep3


title: ChIPseq_Input_U266_EV_rep1


title: ChIPseq_H3K27Ac_U266_EV_rep2

description:
ChIPseq_H3K27ac_U266_EV_rep1n2_regions.bed
ChIPseq_H3K27ac_U266_EV_rep1n2_signal.bw


title: GAT1_B_ChEC-seq


title: GAL4_galactose_A_ChEC-seq


title: ChIPseq_H3K4me2_U266_EV_rep4


title: GAL4_B_ChEC-seq


title: GAL4_A_ChEC-seq


title: GAL80_B_ChEC-seq


title: GAL80_A_ChEC-seq


title: FZF1_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 FZF1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 FZF1-MNase::TRP1


title: ChIPseq_Input_U266_MAF-OE_rep1


title: ChIPseq_H3K2ac_JJN3_rep1

description:
ChIPseq_H3K27ac_JJN3_rep1_regions.broadPeak
ChIPseq_H3K27ac_JJN3_rep1_signal.bw

value: no treatment


title: ChIPseq_MAF_U266_MAF-OE_rep2

value: anti-MAF


title: ChIPseq_H3K27Ac_U266_MAF-OE_rep2


title: GAL4_raffinose_B_ChEC-seq


title: GAL4_raffinose_A_ChEC-seq


title: freeMNase_B_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pBDF2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pBDF2-MNase::TRP1


title: ChIPseq_MAF_JJN3_rep1

description:
ChIPseq_MAF_JJN3_rep1_regions.bed
ChIPseq_MAF_JJN3_rep1_signal.bw

value: Multiple myeloma cell line


title: freeMNase_A_ChEC-seq


title: GAL4_C_ChEC-seq


title: FKH2_C_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 FKH2-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 FKH2-MNase::TRP1


title: ChIPseq_MAF_U266_MAF-OE_rep1


title: ChIPseq_MAF_H929_rep1

description:
ChIPseq_MAF_H929_rep1_regions.bed
ChIPseq_MAF_H929_rep1_signal.bw


title: ChIPseq_H3K27Ac_U266_EV_rep1


title: FKH2_B_ChEC-seq


title: FKH2_A_ChEC-seq


title: ChIPseq_Input_JJN3_rep1

value: Input


title: ChIPseq_MAF_U266_EV_rep1


title: FZF1_A_ChEC-seq


title: ChIPseq_Input_MM1S_rep1

description:
ChIPseq_MAF_MM1S_rep1n2_regions.bed
ChIPseq_MAF_MM1S_rep1n2_signal.bw


title: ChIPseq_MAF_U266_EV_rep2


title: FZF1_C_ChEC-seq


title: FKH1_A_ChEC-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 FKH1-MNase::TRP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 FKH1-MNase::TRP1