title: BACHD, SPI-24, 8 weeks, bio rep5

city: Rehovot

first: Rivka

last: Dikstein

address: 234 Herzel

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse genome using STAR
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization and differential expression was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel file includes the normalized counts and DESEq2 output

source_name: brain

extract_protocol:
Following mice sacrification, brains were removed, sliced and small punch-size pieces of tissue from the striatum were immediately placed in Bio-Tri RNA. Total RNA was further extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research).
The RNA-seq libraries were prepared with the TruSeq Stranded mRNA Library Prep (Cat #20020594; Illumina).

treatment_protocol: DMSO (control) or SPI-24 were delivered to BACHD mice for 8 weeks using osmotic pumps.

value: brain

value: BACHD

value: striatum cells

value: HD mutant


title: pig 14 skin, site 6b, no ID IL-15

status: Public on Nov 20 2023

type: SRA

city: St. Louise

first: CANXIN

last: XU

state: MO

address: 4340 Duncan Ave

department: Pharmacology

country: USA

institute: Aclaris Therapeutics, Inc.

library_source: transcriptomic

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl Sscrofa11.1.99
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

molecule: total RNA

organism: Sus scrofa

source_name: skin

extract_protocol:
Total RNA was extracted using RNeasy lipid tissue mini kit (QIAGEN).
RiboZero Gold

treatment_protocol: IL-15 (200ng in100ul saline) (Abcam) was injected intradermally in prepared grids on Yorkshire swine skin. After 3 hours, the injected site was biopsied and the entire biopsy piece was placed into 0.4ml Trizol (ThemoFisher) and immediately the tube containing the biopsy was put into dry ice/EtOH and frozen until RNA extraction.

tag: tissue

value: skin

tag: genotype

value: WT

tag: treatment

value: Control


title: wild type, H3K27me3, replicate 1

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

country: Germany

institute: Ruhr-University Bochum

library_source: genomic

data_processing:
Sequence reads were trimmed with fastp (Chen et al. 2018, Bioinformatics 34:i884-i890) and mapped with bowtie2 (Langmead and Salzberg 2012, Nat Methods 9:357-359). MACS2callpeak was used to call broad peaks (Zhang et al. 2008, Genome Biol 9:R137).
Assembly: Sordaria macrospora genome version 4, BioProject ID: PRJNA744349, acc. no. for the seven chromsomes are CP083903-CP083909
Supplementary files format and content: The .bed files were generated by broad peak calling with MACS2 and contain the following columns (tab-delimited): 1. name of chromosome, 2. start position of peak on chromosome, 3. end position of peak on chromosome, 4. name of peak, 5. score (indicates how dark a peak will be displayed in a browser), 6. strand ("." denotes not orientation was assigned), 7. signal value (measurement of overall enrichment for the region), 8. pvalue (measurement of statistical significance, given as -log10), 9. qvalue (measurement of statistical significance using false discovery rate, given as -log10)

molecule: genomic DNA

organism: Sordaria macrospora

source_name: mycelium

growth_protocol: Strains were grown in liquid complete medium at 27 °C in constant light for 2 days (wild type) or 3 days (delta-asf1, the slower-growing mutant was grown longer to reach the same developmental stage)

extract_protocol:
Mycelia were harvested by filtering, washed and ground to powder in liquid nitrogen.
Crosslinking was performed in 1% formaldehyde for 15 minutes, followed by 15 minutes of quenching by addition of glycerin. The powder was washed multiple times in isotonic buffer. Lysis was performed on ice, by addition of an NP-40 based lysis buffer with proteinase inhibitors. Clear chromatin extracts were harvested by multiple centrifugation steps. MNase based shearing was done under Ca2+ rich conditions with 230 U MNase per ml sample for 105 minutes at 37 °C. After stopping with EDTA, 10 µl Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 antibodies (Cell Signaling, Danvers, MA, USA) or Histone H3 Antibody (ChIP Formulated) #2650 (Cell Signaling) were added to 1 ml samples and incubated at 4 °C over night on a spinning wheel. Pull down was performed after incubation of the solution with 40 µl of Protein A/G PLUS-Agarose: sc-2003 (Santa Cruz Biotechnology, Dallas, TX, USA). After washing, the DNA fragments were extracted by incubation of the beads with an SDS rich buffer, overnight decrosslinking and phenol / chloroform extraction.

value: mycelium

value: wild type

tag: chip antibody


title: dHeps isolated from CCl4-injured mice, 5C-G, Day16 [7.5C-G RNA-seq]

city: Beijing

first: pengyan

last: lin

state: Beijing

address: No.5 Yiheyuan Road Haidian

department: College of Future Technology,

country: China

institute: Peking university

data_processing:
Bulk RNA-seq data were processed to obtain a gene count matrix of all samples using the featureCounts tool of the subread software. The count matrix was used for differential analysis with DESeq2 (Love et al., 2014).
Assembly: Mus musculus genome GRCm39
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was harvested using  EasyPure® RNA Kit (TransGen)
RNA libraries for RNA-seq were prepared using NEBNext@ Ultra™  RNA Library Prep Kit for Illumina@ (#E7530) following manufacturer's protocols.

value: liver

tag: cell type

value: hepatocytes

value: 5C.G in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: BACHD, SPI-24, 8 weeks, bio rep4

tag: cell line


title: delta-asf1, H3K27me3, replicate 1


title: pig 14 skin, site 7e, no ID IL-15


title: BACHD, SPI-24, 8 weeks, bio rep3


title: delta-asf1, histone H3, replicate 1


title: BACHD, SPI-24, 8 weeks, bio rep2


title: BACHD, SPI-24, 8 weeks, bio rep1


title: BACHD, DMSO, 8 weeks. bio rep5

value: DMSO (control)


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [1.DMSO_2 RNA-seq]

value: DMSO in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: pig 13 skin, site 12e , 3 hours post ID 200ng IL-15

value: ID 200ng IL-15


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [2.DMSO_3 RNA-seq]


title: pig 14 skin, site 12c, 3 hours post ID 200ng IL-15


title: dHeps isolated from CCl4-injured mice, 5C, Day16 [5CH2 RNA-seq]

value: AAV-TBG-Cre:Rosa-LSL-tdTomato mice

value: 5C in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: pig 14 skin, site 12d, 3 hours post ID 200ng IL-15


title: Skin, post-treatment, Patient3 [yysh]

city: Guangzhou

first: Juzi

last: Liu

state: --- Select One ---

address: North Guangzhou Avenue 1838, Nanfang Hospital

institute: Southern Medical University

description: yysh

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: TXT files include FPKM values for each Sample

organism: Homo sapiens

source_name: Human Facial Skin

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Human Facial Skin

tag: subject status

value: patients diagnosed with morphea

value: sequential fat grafting of autologous fat and cryopreserved stromal vascular fraction (SVF)-gel

tag: time point

value: 12 months after treatment


title: Skin, post-treatment, Patient1 [sqsh]

description: sqsh


title: Skin, pre-treatment, Patient3 [yysq]

description: yysq

value: before treatment


title: Skin, post-treatment, Patient2 [hssh]

description: hssh


title: BACHD, DMSO, 8 weeks. bio rep4

value: brain

value: BACHD

value: striatum cells

value: HD mutant


title: BACHD, DMSO, 8 weeks. bio rep3


title: dHeps isolated from CCl4-injured mice, 5C, Day16 [5CH1 RNA-seq]

value: liver


title: Skin, pre-treatment, Patient2 [hssq]

description: hssq


title: dHeps isolated from CCl4-injured mice, 3C, Day16 [3C2 RNA-seq]

value: hepatocytes

value: 3C in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: pig 13 skin, site 12c, 3 hours post ID 200ng IL-15

value: skin

value: WT


title: dHeps isolated from CCl4-injured mice, 5C, Day16 [4.5C_5 RNA-seq]


title: Skin, pre-treatment, Patient1 [sqsq]

description: sqsq


title: BACHD, DMSO, 8 weeks. bio rep1

value: DMSO (control)


title: BACHD, DMSO, 8 weeks. bio rep2


title: dHeps isolated from CCl4-injured mice, 5C, Day16 [3.5C_4 RNA-seq]


title: dHeps isolated from CCl4-injured mice, 3C, Day16 [3C1 RNA-seq]

value: AAV-TBG-Cre:Rosa-LSL-tdTomato mice


title: plasma derived from patients with pulmonary embolism 18

type: RNA

city: Hannover

first: Ke

last: Xiao

address: Carl-Neuberg-Straße 1

department: IMTTS

institute: Medizinische Hochschule Hannover (MHH)

description:
pulmonary embolism
A panel of miRNAs was analysed in plasma of 20 out of 177 randomly selected patients with acute PE and 20 sex- and age-matched healthy volunteers via human TaqMan array MicroRNA A + B Cards Set (Applied Biosystems) following the manufacturer’s recommendation. Prior to polymerase chain reactions (PCR), two steps consisting of reverse transcription (RT) and pre-amplification were conducted. The Megaplex PreAmp Primers, consisting of two pools of gene-specific forward and reverse primers (Pool A and Pool B) were used to enable the unbiased pre-amplification of the miRNA cDNA target by PCR

data_processing: CT values were normalzed and analyzed using DataAssist Software v3.01

label: FAM

source_name: plasma

growth_protocol: Venous blood samples for subsequent biomarker measurements were collected from healthy patients and patients with acute PE. Blood samples were processed using standard operating procedures, immediately stored at -80°C and analysed in batches after a single thaw. Routine laboratory parameters were measured as part of the clinical routine at the Department of Clinical Chemistry of the University Medical Centre Goettingen, Germany

extract_protocol: RNA was extracted with miRNeasy Plasma/Serum Kit; To remove heparin in RNA samples after RNA isolation, samples were treated with heparinase

treatment_protocol: no treatments

value: plasma


title: plasma derived from patients with pulmonary embolism 20


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [D2 RNA-seq]

value: DMSO in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: plasma derived from patients with pulmonary embolism 17


title: Parental monotypic LEC+WM852

city: Helsinki

first: Päivi

middle: M

last: Ojala

address: Haartmaninkatu 8

department: Department of Medicine

country: Finland

institute: University of Helsinki

description:
Sample 2
barcodes.tsv
genes.tsv
matrix.mtx

library_source: transcriptomic single cell

data_processing:
Data processing and analysis were performed using 10x Genomics Cell Ranger v2.1.1 pipelines
The “cellranger mkfastq” was used to produce FASTQ (raw data) files and “cellranger count” to perform alignment, filtering and UMI counting.
mkfastq was run using the Illumina bcl2fastq v2.2.0 and alignment was done against human genome GRCh38
Cellranger aggr pipeline was used to combine data from multiple samples into an experiment-wide gene-barcode matrix and analysis.
The filtered count matrices were pre-processed and clustered using the Seurat V4.3.0 tool in an RStudio V2023.03.0 environment (R V4.2.3)
Assembly: GRCh38
Supplementary files format and content: Aggregated matrix files (*matrix.mtx) containing cell counts
Supplementary files format and content: Tab separated metadata files (genes.tsv and barcodes.tsv).  In barcodes.tsv, -1 corresponds to Sample 1, -2 corresponds to Sample 2.

extract_protocol:
Endothelial cells were sorted with flow cytometry using BD Influx. 4% BSA in PBS was added to the cell suspension to a final concentration of 0.04% and the cell viability and concentration was measured.  Cells were kept on ice until continuation of the 10X Genomics Single Cell Protocol.
The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 2 chemistry

value: endothelial cells plus melanoma cell line

value: control


title: HaCaT_Tet-on-Luc, Dox+, Day3, rep2

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

institute: Harvard Medical School

data_processing:
Alignment to the human hg19 assembly was conducted by STAR 5.02 (Dobin et al., 2013) on the DNAnexus platform
Normalization and differential expression by  DESeq2 were performed through a HOMER v4.10.4 implementation of the package in R.
Assembly: hg19
Supplementary files format and content: Hacat_Ik_Luc_Induction.noadj.txt

molecule: polyA RNA

source_name: HaCaT

growth_protocol: The HaCaT keratinocyte cells were grown at 37 °C in DMEM medium supplemented with 10% ‘Tet System Approved FBS’ (Clontech),  penicillin (100 units/ml) and streptomycin sulfate (100 μg/ml) in humidified atmosphere of 5% CO2.

extract_protocol:
Total RNAs were prepared using the Direct-zol RNA Miniprep (Zymo Research) and 1mg of total RNA was used for the construction of sequencing libraries.
The TruSeq Stranded mRNA Library prep kit was used for construction of cDNA libraries for RNA-sequencing (Illumina). The cDNA libraries were ligated with indexed primers and amplified by PCR for 10 cycles, multiplexed and sequenced in house with an Illumina NextSeq550 system.

treatment_protocol: Doxycycline (Dox) was added into the culture medium to a final concentration of 0.1μg/ml to induce the expression of IKAROS (HaCaT_Tet-on_Ik1) or Luciferase (HaCaT_Tet-on_Luc).

value: HaCaT

value: keratinocyte

value: Treated with 0.1μg/ml Doxycycline

tag: time

value: Day 3


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [D1 RNA-seq]


title: HaCaT_Tet-on-Luc, Dox+, Day3, rep1


title: Melanoma co-cultured LEC

description:
Sample 1
barcodes.tsv
genes.tsv
matrix.mtx

source_name: LEC

value: LEC

value: endothelial cells

value: co-culture


title: dHeps isolated from CCl4-injured mice, 3C, Day16 [3CL2]

data_processing:
ATAC-seq analysis includes peak calling with MACS (version 2.1.2), differential peak detection with RPKM, and visualization with EnrichedHeatmap. Coverage tracks of the samples were generated with the alignment of reads (BAM file) with the bamCoverage function from deepTools (Ramirez et al., 2014). The number of reads per bin was calculated and normalized by reads per kilobase per million mapped reads (RPKM).
Assembly: mm10
Supplementary files format and content: bigwig files for each Sample

extract_protocol:
5× 10^4 cells were used for every single reaction. Cells were washed in cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) for 10 min, and nuclei were spun at 500 g for 10 min using a refrigerated centrifuge
ATAC-seq libraries were prepared using Trueprep DNA library Prep Kit V2 for Illumina (vazyme).

value: liver

value: hepatocytes


title: HaCaT_Tet-on-Ikzf1, Dox+, Day3, rep2


title: plasma derived from patients with pulmonary embolism 16


title: dHeps isolated from CCl4-injured mice, 3C, Day16 [3CL1]

value: 3C in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: HaCaT_Tet-on-Ikzf1, Dox+, Day2, rep2

value: Day 2


title: ATAC-Seq MDA-MB-231 shKDM2B 2

city: Columbus

first: Alessandro

last: La Ferlita

state: OH

department: The James Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed, and adapters were removed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were then aligned to the human genome using Bowtie 2 (v.2.4.5) (Langmead and Salzberg, 2012) and, following this, they were converted into BAM format, sorted for coordinates, and indexed using samtools (v.1.6) (Li et al., 2009).
Sorted BAM files were used for peak calling by MACS2 (v.2.2.7.1) (Zhang et al., 2008). Only peaks with a p-value < 0.05 were used for further analyses.
Significant peaks were annotated based on their location relative to the TSS of protein-coding genes, by CHIPpeakAnno (v.3.30.1) (Zhu et al., 2010), using the genomic coordinates retrieved from ENSEMBL (internal to CHIPpeakAnno).
Differences in chromatin accessibility were assessed by comparing the peaks in the shKDM2B and EV samples, with the DiffBind R package (https://bioconductor.org/packages/release/bioc/html/DiffBind.html). Peak differences with an adjusted p-value (Benjamini-Hochberg correction) < 0.05 were considered significant.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: triple negative breast cancer

growth_protocol: MDA-MB-231 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) (Millipore-Sigma, Cat. D5796) supplemented with penicillin/streptomycin (Corning, Cat. 30-002-CI), nonessential amino acids (Corning, Cat. 25-025-CI), l-glutamine (Corning, Cat. 25-005-CI), sodium pyruvate (Millipore-Sigma, Cat. S8636), plasmocin 2.5 ng/μL (Invivogen, Cat. ant-mpp), and 10% fetal bovine serum (Fisher Scientific, Cat. MT35010CV). Cells were cultured at 37C at 5% CO2.

extract_protocol:
Samples were prepared using the ATAC-Seq kit (Active Motif, Cat 53150).
For library preparation, tagmented DNA was amplified, using unique combinations of i7/i5 indexed primers, and on Illumina's Nextera adapters. The final step in library purification was a clean-up with SPRI beads (Beckman Coulter, Cat. B23317). The quality of the libraries was confirmed using the Bioanalyzer high sensitivity DNA assay (Agilent Technologies). Libraries were prepared from three biological replicates.

value: MDA-MB-231 cells

value: triple negative breast cancer

value: KDM2B knockdown


title: ATAC-Seq MDA-MB-231 shKDM2B 3


title: ATAC-Seq MDA-MB-231 shKDM2B 1


title: HaCaT_Tet-on-Ikzf1, Dox+, Day1, rep2

value: Day 1


title: plasma derived from patients with pulmonary embolism 19

value: plasma


title: ATAC-Seq MDA-MB-231 EMPTY VECTOR 3

value: WT


title: plasma derived from patients with pulmonary embolism 13


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [D2]

value: AAV-TBG-Cre:Rosa-LSL-tdTomato mice

value: DMSO in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: dHeps isolated from CCl4-injured mice, DMSO, Day16 [D1]


title: HaCaT_Tet-on-Luc, Dox-, rep2

value: HaCaT

value: keratinocyte

value: No Doxycycline

value: Day 0


title: HaCaT_Tet-on-Ikzf1, Dox+, Day3, rep1

value: Treated with 0.1μg/ml Doxycycline

value: Day 3


title: plasma derived from patients with pulmonary embolism 11


title: plasma derived from patients with pulmonary embolism 12


title: dHeps isolated from CCl4-injured mice, Day 0 [C4]

value: liver

value: hepatocytes


title: ATAC-Seq MDA-MB-231 EMPTY VECTOR 2


title: ATAC-Seq MDA-MB-231 EMPTY VECTOR 1


title: hepatocytes isolated from healthy mice, Day 0 [H2]


title: HaCaT_Tet-on-Ikzf1, Dox+, Day1, rep1


title: dHeps isolated from CCl4-injured mice, Day 0 [C3]


title: HaCaT_Tet-on-Ikzf1, Dox+, Day2, rep1

value: Day 2


title: plasma derived from patients with pulmonary embolism 9


title: plasma derived from patients with pulmonary embolism 10


title: plasma derived from patients with pulmonary embolism 15


title: HaCaT_Tet-on-Luc, Dox-, rep1


title: plasma derived from patients with pulmonary embolism 8


title: HaCaT_Tet-on-Ikzf1, DoxD3, Input

data_processing:
Read alignment was performed on the hg19 assembly with the STAR 5.02 genome alignment algorithm (--alignIntronMax 1 --alignEndsType EndToEnd) on the DNAnexus platform (https://www.dnanexus.com/)
Picard-tools 4.0.3 (Broad Institute) were used to remove PCR duplicates.
Peak calling was performed using MACS2 2.1.1 (Zhang et al., 2008) with input chromatin as control and with a q-value (minimum FDR) cutoff of 0.05. Model building with --mfold of 5, 50 was used for transcription factors, H3K4me3and H3K27ac. The –broad flag was used to identify enriched regions for spreading histone marks such as H3K4me1, H3K27ac, H3K9me3.
Normalized “pileup.bedgraphs” were used after indexing for browser visualization.
Bigwigs were obtained from the “pileup” files for visualization using bedGraphToBigWig v4.
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: HaCaT cell

extract_protocol:
Cells were fixed in 1% of fresh formaldehyde for 10 minutes at room temperature, quenched with glycine and washed twice with ice-cold PBS. Cells were re-suspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 minutes at 4°C, pelleted, and then re-suspended in lysis buffer 2 (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8) for 5 minutes at 4°C. Cells were finally re-suspended in RIPA buffer (50mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Nadeoxycholate, 0.2% SDS, 0.5 mM PMSF, and 1x Protease inhibitor cocktail (Roche)) to a final concentration of 5x107 cells/ml. Chromatin was sonicated to an average size of 350bp with a Branson Sonifier 450 equipped with a micro probe. Chromatin was cleared by centrifugation at 20,000xg for 10 minutes, and then incubated with 5-10μg of antibodies pre-bound to Dynabeads protein G (Life technologies) and rotated overnight at 4°C. After extensive washing on beads, bound chromatin was eluted and de-crosslinked in 300μl of elution buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, 0.3M NaCl) overnight at 65°C. Proteinases K was added to a final concentration of 200 μg/ml and incubated at 45°C for 2 hours. DNA was ethanol precipitated, re-suspended in TE and purified using the DNA Clean & Concentrator-5 kit (Zymo Research).
Purified ChIP DNA was end repaired, end adenylated, and then ligated with Illumina Truseq indexed adaptors. The ligated DNA was purified with AMPure XP beads (Beckman Coulter) and then amplified with KAPA HiFi DNA Polymerase (KAPA Biosystems) for 8 to 13 cycles. After amplification, the library DNA was size selected with AMPurex XP beads to 200-600 bp range, and the purified libraries were multiplexed for sequencing in house with an Illumina NextSeq 550 system.

value: HaCaT cell

value: Treated with 0.1mg/ml Dox for 3 days


title: MDA-MB-231 EV, 2% input rep2

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed, and adapters were removed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads in FASTQ format were then aligned to the human genome using Bowtie 2 (v.2.4.5) (Langmead and Salzberg, 2012) and, following this, they were converted to the BAM format, sorted for coordinates, and indexed using samtools (v.1.6) (Li et al., 2009).
Sorted BAM files of the replicates were merged by samtools (v.1.6) (Li et al., 2009) using the function merge. Merged BAM files were finally used as input for MACS2 (v.2.2.7.1) (Zhang  et al., 2008) in order to perform the peak calling. Only peaks with a q-value < 0.05 were used for further analyses.
Significant peaks were annotated based on their location relative to the TSS of coding-protein genes by CHIPpeakAnno (v.3.30.1) (Zhu et al., 2010) using the genomic coordinates retrieved from ENSEMBL (internal to CHIPpeakAnno)
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample) [replicates were merged prior peak calling]

source_name: MDA-MB-231 cells Empty Vector

extract_protocol:
Samples were prepared using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads), Cell Signaling Technology, #9005
ChIP-Seq libraries were prepared using the DNA Library Prep Kit for Illumina (Cell Signaling Technology, Cat 56795) and the Multiplex Oligos for Illumina (Dual Index Primers) (Cell Signaling Technology, Cat. 47538). The starting material for Library construction was: 5 ng of immunoprecipitated DNA for KDM2B, 1 ng for c-MYC and 50 ng for H3K4me3, H3K27me3, and H2AK119ub and 50 ng of the input DNA.

value: MDA-MB-231 cells Empty Vector

value: triple negative breast cancer

value: No antibody (input)


title: plasma derived from patients with pulmonary embolism 14

value: plasma


title: hepatocytes isolated from healthy mice, Day 0 [H1]

value: AAV-TBG-Cre:Rosa-LSL-tdTomato mice


title: MDA-MB-231, 2% input rep1

source_name: MDA-MB-231 cells parental

value: MDA-MB-231 cells parental


title: plasma derived from patients with pulmonary embolism 7


title: Large preB_inducible IkE5 deletion, 4OHT induction day12, CTCF HiChIP, rep1

data_processing:
instrument model: Illumina NEXTseq550 and Novaseq6000
Sequencing reads were aligned to the mouse mm10 assembly and processed into normalized contact maps with the HiC-Pro 2.8.0 pipeline (Servant et al., 2015) on the DNAnexus platform.
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v1.11.08) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: mm10
Supplementary files format and content: hic
Library strategy: HiChIP

source_name: large Pre-B cell (CD19+CD43+BP1+)

growth_protocol: Sorted wild-type IkE5fl/fl Rosa26-ERT2-Cre large pre-B cells were expanded for 6 days on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. They were then re-plated onto stromal cells with 0.2 μM of 4-OHT (Sigma H7904) or with an equal volume of DMSO as control. Cells were harvested at different time points (1-18 days) of culture in the presence of 4-OHT or DMSO.

extract_protocol:
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use.
HiChIP assays were performed according to the previously published protocol (Mumbach et al., 2016) with minor modifications. Briefly, ~10 million cells were crosslinked with 1% Formaldehyde for 10 mins at room temperature and lysed with Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40) supplemented with protease inhibitors for 30 mins at 4C. Chromatin was digested by the DpnII restriction enzyme for two hours at 37C. The 5’ overhang of the digested DNA were filled with dCTP, dGTP, dTTP and biotinl14-dATP by DNA Polymerase I, Large Klenow Fragment, and then ligated by T4 DNA ligase for 4 hours at room temperature. Chromatin was sonicated in Nuclear Lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.6% SDS), 1:2 diluted in ChIP Dilution buffer (2% Triton X-100, 300 mM NaCl, 0.2% NaDoc), and then processed with regular chromatin immunoprecipitation using antibodies against H3K27ac, SMC1a, CTCF, or IKAROS. The DNA junctions labelled by Biotin-14-dATP were then enriched by Streptavidin C1 magnetic beads and processed with Nextera DNA library preparation (Illumina). The DNA libraries were size-selected by Ampure XP beads (300-700bp) and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.

treatment_protocol: In vitro deletion of IkE5 was induced by addition of of 4-OHT (Sigma H7904, final concentration 0.2 μM ) or with an equal volume of DMSO as control.

value: large Pre-B cell (CD19+CD43+BP1+)

value: IkE5 fl/fl, Rosa26-ERT2-Cre

value: Treat with 0.2mM 4OHT for 12 days


title: HaCaT_Tet-on-Luc, DoxD3, Input

value: keratinocyte


title: MDA-MB-231, 2% input rep2


title: MDA-MB-231 EV, H3K27ac rep2


title: plasma derived from patients with pulmonary embolism 6


title: HaCaT_Tet-on-Ikzf1, DoxD3, IKAROS

value: IKAROS (EMD Millipore, MABE912 & MABE913)


title: Large preB_inducible IkE5 deletion, 4OHT induction day3, CTCF HiChIP, rep1

value: Treat with 0.2mM 4OHT for 3 days


title: Large preB_inducible IkE5 deletion, DMSO control, CTCF HiChIP, replicate 1

value: Treat with DMSO for 3-12 days


title: plasma derived from patients with pulmonary embolism 5


title: MDA-MB-231 EV, H3K27ac rep1


title: Large preB_inducible IkE5 deletion, 4OHT induction day12, H3K27ac HiChIP,  rep2


title: HaCaT_Tet-on-Ikzf1, DoxD3, SMC1A

value: SMC1A (Bethyl, A300-055A)


title: MDA-MB-231, H2AK119ub rep2


title: plasma derived from patients with pulmonary embolism 4


title: MDA-MB-231 EV, 2% input rep1


title: Large preB_inducible IkE5 deletion, 4OHT induction day3, H3K27ac HiChIP,  rep2


title: HaCaT_Tet-on-Luc, DoxD3, SMC1A


title: plasma derived from patients with pulmonary embolism 3


title: MDA-MB-231, H2AK119ub rep1


title: Large preB_inducible IkE5 deletion, DMSO control, H3K27ac HiChIP, rep2


title: HaCaT_Tet-on-Ikzf1, DoxD3, CTCF

value: CTCF (Abcam, ab188488)


title: plasma derived from patients with pulmonary embolism 2


title: Large preB_inducible IkE5 deletion, 4OHT induction day12, H3K27ac HiChIP, rep1


title: MDA-MB-231, H3K27me3 rep2


title: HaCaT_Tet-on-Luc, DoxD3, CTCF

value: HaCaT cell


title: MDA-MB-231, H3K27me3 rep1


title: Large preB_inducible IkE5 deletion, DMSO control, H3K27ac HiChIP, rep1


title: plasma derived from healthy control patients 20

description:
control
A panel of miRNAs was analysed in plasma of 20 out of 177 randomly selected patients with acute PE and 20 sex- and age-matched healthy volunteers via human TaqMan array MicroRNA A + B Cards Set (Applied Biosystems) following the manufacturer’s recommendation. Prior to polymerase chain reactions (PCR), two steps consisting of reverse transcription (RT) and pre-amplification were conducted. The Megaplex PreAmp Primers, consisting of two pools of gene-specific forward and reverse primers (Pool A and Pool B) were used to enable the unbiased pre-amplification of the miRNA cDNA target by PCR


title: plasma derived from patients with pulmonary embolism 1


title: Large preB_inducible IkE5 deletion, 4OHT induction day3, H3K27ac HiChIP, rep1


title: MDA-MB-231, H3K4me3 rep1


title: Large preB cell, WT, IKAROS HiChIP, rep1

growth_protocol: Sorted wild-type and IkE5Δ/Δ large pre-B cells were cultured on OP9 stroma in DMEM ( D-5671; Sigma) supplemented with 10% FBS (2442; Sigma), 50 μM 2-mercaptoethanol, 100 μg/ml penicillin, 100 μg/ml streptomycin, 1× Glutamax (35050-062; Gibco), 10 mM HEPES (156-30-80; Gibco) and 1× sodium pyruvate (11360-070; Gibco) in the presence of 5ng/ml of IL-7. Stroma adherent large pre-B cells from WT or IKDN cultures were detached with 0.2% trypsin (EDTA free) for 2 minutes at room temperature. Large pre-B cells were ~ 99% of the cells in suspension as determined by flow cytometry.

extract_protocol:
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use.
HiChIP assays were performed according to the previously published protocol (Mumbach et al., 2016) with minor modifications. Briefly, ~10 million cells were crosslinked with 1% Formaldehyde for 10 mins at room temperature and lysed with Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP40) supplemented with protease inhibitors for 30 mins at 4C. Chromatin was digested by the MboI restriction enzyme for two hours at 37C. The 5’ overhang of the digested DNA were filled with dCTP, dGTP, dTTP and biotinl14-dATP by DNA Polymerase I, Large Klenow Fragment, and then ligated by T4 DNA ligase for 4 hours at room temperature. Chromatin was sonicated in Nuclear Lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.6% SDS), 1:2 diluted in ChIP Dilution buffer (2% Triton X-100, 300 mM NaCl, 0.2% NaDoc), and then processed with regular chromatin immunoprecipitation using antibodies against H3K27ac, SMC1a, CTCF, or IKAROS. The DNA junctions labelled by Biotin-14-dATP were then enriched by Streptavidin C1 magnetic beads and processed with Nextera DNA library preparation (Illumina). The DNA libraries were size-selected by AMPure XP beads (300-700bp) and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.

value: Wild-type (IKE5 fl/fl, Cre-)

tag: hichip antibody

value: IKAROS (Millipore:MABE912 & MABE913, Abcam, ab191394)


title: HaCaT_Tet-on-Luc, DoxD3, H3K27ac

value: Treated with 0.1mg/ml Dox for 3 days

value: H3K27ac (Abcam, ab4729)


title: HaCaT_Tet-on-Ikzf1, DoxD3, H3K4me3

value: H3K4me3 (Active Motif AM39155)


title: HaCaT_Tet-on-Ikzf1, DoxD3, H3K27ac


title: HaCaT_Tet-on-Luc, DoxD3, H3K4me3


title: plasma derived from healthy control patients 19

value: plasma


title: MDA-MB-231, ATF4 rep2

value: MDA-MB-231 cells parental

value: triple negative breast cancer


title: plasma derived from healthy control patients 17


title: plasma derived from healthy control patients 18


title: MDA-MB-231, ATF4 rep1


title: Large preB cell, WT, SMC1a HiChIP, rep2

value: large Pre-B cell (CD19+CD43+BP1+)

value: SMC1a (Bethyl, A300-055A)


title: plasma derived from healthy control patients 16


title: HaCaT_Tet-on-Ikzf1, DoxD3, H3K4me1

value: keratinocyte

value: H3K4me1 (Active Motif AM39297)


title: HaCaT_Tet-on-Luc, DoxD3, H3K4me1


title: MDA-MB-231, MYC rep2

value: MYC


title: MDA-MB-231, MYC rep1


title: Large preB cell, WT, SMC1a HiChIP, rep1


title: MDA-MB-231, H3K4me3 rep2


title: MDA-MB-231, KDM2B rep2


title: plasma derived from healthy control patients 14


title: 4_5_no_Peptide HaCaT

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

description:
4_5_no_Peptide
Illumina stranded mRNA

data_processing:
equimolar amounts of each library were sequenced on a NextSeq 550 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using a 75 Cycles High Output Kit with a single index, and single-end (SE) run parameters
Image analysis and base calling were done by the Real Time Analysis Software (RTA, v2.4.11). The resulting “.bcl” files were converted into “.fastq” files with the bcl2fastq software (v2.20.0.422).
 low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90% of the reads needing a quality phred score > 20. Homertools 4.7 (Heinz et al., 2010) were used for PolyA-tail trimming, and reads with a length < 17 were removed.
PicardTools 1.78 (https://broadinstitute.github.io/picard/) were used to compute the quality metrics with CollectRNASeqMetrics. With STAR 2.3 (Dobin et al., 2013), the filtered reads were mapped against human genome 38 using default parameters.
Count data and RPKM tables with Ensembl identifiers and gene symbols were generated by mapping filtered reads against union transcripts using a custom pipeline.
Mapping was carried out with bowtie2 version 2.2.4 (Langmead and Salzberg, 2012) against union human genes: every gene is represented by a union of all its transcripts (exons).
The count values (RPKM and raw counts) were calculated by running CoverageBed from Bedtools v2.26.0 (Quinlan and Hall, 2010) of the mapped reads together with the human annotation file (Ensembl 90) in gtf format and parsing the output with custom perl scripts.
The input tables containing the replicates for groups to compare were created by a custom perl script.
Assembly: human genome 38

growth_protocol: TexMACS medium + 2% Pen/Strep

extract_protocol:
Qiagen RNEasy
Illumina mRNA stranded
oligo-dT capture and cDNA synthesis

treatment_protocol: Human influenza-specific T cells were thawed and rested o/n in CLM medium (RPMI supplemented with 10% AB Human Serum, 0.01% 50mM 2-MercaptoEtOH, 1% 1M HEPES and 1% Penicillin/Streptomycin). 30,000 MRC-5 cells/ well were seeded and grown to full confluency in DMEM o/n before pulsing the cells with varying concentrations of influenza peptide (GILGFVFTL; 0 ng/ml, 1 ng/ml, 10 ng/ml or 100 ng/ml) for 1hr. Cells were washed twice before adding 30,000 influenza-specific T cells in TexMACS with 2% Penicillin/Streptomycin. No T cell condition was primed with 100ng/ml peptide. SNs were harvested and used to stimulate 30,000 HaCaT cells/well. HaCaT cells were sequenced 24hrs after stimulation with SNs.

value: skin

value: HaCaT

value: epithelial cells, keratinocyte immortal

value: WT


title: Large preB cell, IKDN, CTCF HiChIP, rep2

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)

value: CTCF (Abcam, ab188488)


title: plasma derived from healthy control patients 13


title: Large preB cell, WT, CTCF HiChIP, rep2

value: Wild-type (IKE5 fl/fl, Cre-)


title: 2_5_no_Peptide HaCaT

description:
2_5_no_Peptide
Illumina stranded mRNA


title: Large preB cell, IKDN, SMC1a HiChIP, rep2


title: MDA-MB-231, KDM2B rep1


title: ITD-14_Untreated [scRNA-seq]

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Fastq files from single-cell sequencing experiments were aligned to the human genome (version hg38) using the count function in CellRanger v5.0.1 from 10x genomics (Zheng et al. 2017; PMID:28091601) using gene models from ensembl as the reference transcriptome.
Assembly: hg38
Supplementary files format and content: Read counts and cell barcodes in hdf5 format produced by CellRanger count
Supplementary files format and content: Tab-Delimited file with cell barcodes and inferred cell cycle phase and cell type

source_name: CD34 positive AML primary cells

growth_protocol: Primary AML cells for scRNA-seq were cultured on hMSC feeders as described above in the following media: SFEMII (StemCell Technologies), 1 μM UM729 (StemCell Technologies), 750 nM StemReginin 1 (StemCell Technologies) supplemented with 150 ng/ml SCF, 100 ng/ml TPO, 10 ng/ml IL-3, 10 ng/ml G-CSF (Perpro tech).

extract_protocol:
Cells were loaded on a Chromium Single Cell Instrument (10X Genomics), to recover 5000 single cells.
Library generation was performed using the Chromium single cell 3’ library and gel bead kit v3.1. Illumina sequencing was performed on a NovaSeq 6000 S1 run in paired-end mode for 150 cycles at a depth of 20000 reads per cell

treatment_protocol: After 1 passage (1 week) in culture cells were treated for 24 h with 10 μM CBFβi or 0.1 % DMSO in the absence of UM729 and StemReginin 1. After treatment cells were sorted for CD45 using magnetic beads (Miltenyi Biotec).

value: CD34 positive AML primary cells

tag: patient

value: Untreated


title: CHH treated with 3C for 3 days after 5 days of treatment of 50ng/mL TGFβ1 [X8_FRAS220051276.1r RNA-seq]

data_processing:
Bulk RNA-seq data were processed to obtain a gene count matrix of all samples using the featureCounts tool of the subread software. The count matrix was used for differential analysis with DESeq2 (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM and count values for each Sample

value: liver

value: cryopreserved human hepatocytes (CHH)

value: hepatocytes

value: 3C in serum-free Hepatocyte Maintenance Medium (Lonza) for 16 days


title: 1_5_no_Peptide HaCaT

description:
1_5_no_Peptide
Illumina stranded mRNA


title: 4_4_1ng_Peptide HaCaT

description:
4_4_1ng_Peptide
Illumina stranded mRNA


title: Large preB cell, IKDN, CTCF HiChIP, rep1

value: large Pre-B cell (CD19+CD43+BP1+)


title: plasma derived from healthy control patients 10

value: plasma


title: plasma derived from healthy control patients 12


title: Large preB cell, WT, CTCF HiChIP, rep1


title: Large preB cell, IKDN, SMC1a HiChIP, rep1

value: SMC1a (Bethyl, A300-055A)


title: Large preB cell, IKDN, H3K27ac HiChIP, rep2

value: H3K27ac (Abcam, ab4729)


title: plasma derived from healthy control patients 11


title: plasma derived from healthy control patients 9


title: 3_4_1ng_Peptide HaCaT

description:
3_4_1ng_Peptide
Illumina stranded mRNA

value: skin


title: CHH treated with 3C for 3 days after 5 days of treatment of 50ng/mL TGFβ1 [X7_FRAS220051275-1r RNA-seq]


title: plasma derived from healthy control patients 15


title: Large preB cell, WT, H3K27ac HiChIP, rep2


title: 2_4_1ng_Peptide HaCaT

description:
2_4_1ng_Peptide
Illumina stranded mRNA

value: HaCaT


title: CHH treated with DMSO for 3 days after 5 days of treatment of 50ng/mL TGFβ1 [X6_FRAS220051274-1r RNA-seq]


title: Large preB cell, IKDN, H3K27ac HiChIP, rep1


title: 3_5_no_Peptide HaCaT

description:
3_5_no_Peptide
Illumina stranded mRNA

value: epithelial cells, keratinocyte immortal


title: ITD-14_CBFBi [scRNA-seq]

value: CBFBi


title: CHH treated with DMSO for 3 days after 5 days of treatment of 50ng/mL TGFβ1 [X5_FRAS220051273.1r RNA-seq]

value: WT


title: 1_4_1ng_Peptide HaCaT

description:
1_4_1ng_Peptide
Illumina stranded mRNA


title: plasma derived from healthy control patients 7


title: Large preB cell, WT, H3K27ac HiChIP, rep1


title: 4_3_10ng_Peptide HaCaT

description:
4_3_10ng_Peptide
Illumina stranded mRNA


title: CHH, 5 days of treatment of 50ng/ml TGFβ1 [X14_FRAS220051280.1r RNA-seq]

value: 5 days of treatment of 50ng/ml TGFβ1


title: plasma derived from healthy control patients 6


title: 2_3_10ng_Peptide HaCaT

description:
2_3_10ng_Peptide
Illumina stranded mRNA


title: 3_3_10ng_Peptide HaCaT

description:
3_3_10ng_Peptide
Illumina stranded mRNA


title: HaCaT_Tet-on-Ikzf1, DoxD3, IKAROS HiChIP, rep1

data_processing:
instrument model: Illumina NEXTseq550 and Novaseq6000
Sequencing reads were aligned to the human hg19 assembly and processed into normalized contact maps with the HiC-Pro 2.8.0 pipeline (Servant et al., 2015) on the DNAnexus platform.
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v1.11.08) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: hg19
Supplementary files format and content: hic
Library strategy: HiChIP

treatment_protocol: Doxycycline (Dox) was added into the culture medium to a final concentration of 0.1μg/ml to induce the expression of IKAROS (HaCaT_Tet-on-Ikzf1) or Luciferase (HaCaT_Tet-on-Luc).

value: Keratinocyte

value: Treated with 0.1μg/ml Dox for 3 days


title: plasma derived from healthy control patients 5


title: HaCaT_Tet-on-Ikzf1, DoxD3, IKAROS HiChIP, rep2


title: plasma derived from healthy control patients 4


title: plasma derived from healthy control patients 3


title: HaCaT_Tet-on-kzf1, DoxD3, CTCF HiChIP


title: 4_2_100ng_Peptide HaCaT

description:
4_2_100ng_Peptide
Illumina stranded mRNA


title: 1_3_10ng_Peptide HaCaT

description:
1_3_10ng_Peptide
Illumina stranded mRNA


title: Large preB_inducible IkE5 deletion, 4OHT induction D4

data_processing:
instrument model: Illumina NEXTseq550 and Novaseq6000
Sequencing reads were aligned to the mouse mm10 assembly and processed into normalized contact maps with the HiC-Pro 2.8.0 pipeline (Servant et al., 2015) on the DNAnexus platform.
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v1.11.08) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: mm10
Supplementary files format and content: hic

extract_protocol:
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use.
In situ Hi-C was performed following the established protocol (Rao et al., 2014) with minor modifications. Briefly, nuclei were permeabilized, and DNA was digested overnight with 100 U MboI. The ends of the restriction fragments were labeled using biotin-14-dATP and then ligated in a 1.2 mL final volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp with a Covaris E220 evolution instrument (Covaris, Woburn, MA). Ligation junctions were then pulled down with streptavidin beads, and DNA fragments were end-repaired, dA-tailed and Illumina adapters ligated. Libraries were produced by 8 cycles of PCR amplification with KAPA Hifi DNA polymerase (Roche). The Hi-C libraries were size selected with AMPure XP beads and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.

value: IkE5 fl/fl, Rosa26-ERT2-Cre

value: Treated with 0.2mM 4OHT for 4 days


title: HaCaT_Tet-on-Luc, DoxD3, CTCF HiChIP


title: plasma derived from healthy control patients 8


title: Large preB, IKDN, rep 2

value: IkE5D/D (IKE5 fl/fl, Cd2-cre)


title: atdamt1_h3

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: 10-day-old atdamt1 seedlings were heat treated for 2.5 hours and used for RNA extraction. mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapter
Trimmed sequence reads were mapped to TAIR10 using STAR
Differential expression analysis was performed by DESeq2
Assembly: TAIR10
Supplementary files format and content: Excel files include RPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
Total RNA was harvested using Trizol. mRNA was purified by oligo-dT beads
RNA libraries for mRNA-seq were prepared using NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols

treatment_protocol: Wild type and atdamt1 seedlings were heat treated for 2.5 hours

tag: ecotype

value: Seedlings

value: heat treatment

value: 2.5 hours


title: 3_2_100ng_Peptide HaCaT

description:
3_2_100ng_Peptide
Illumina stranded mRNA


title: Large preB_inducible IkE5 deletion, 4OHT induction D18

value: large Pre-B cell (CD19+CD43+BP1+)

value: Treated with 0.2mM 4OHT for 18 days


title: atdamt1_h2


title: plasma derived from healthy control patients 2

value: plasma


title: Large preB_inducible IkE5 deletion, 4OHT induction D12

value: Treated with 0.2mM 4OHT for 12 days


title: HaCaT_Tet-on-Ikzf1, DoxD3, H3K27ac HiChIP

value: HaCaT


title: Large preB, WT, rep 2

value: Wild-type (IKE5 fl/fl, Cre-)


title: 2_2_100ng_Peptide HaCaT

description:
2_2_100ng_Peptide
Illumina stranded mRNA

value: skin

value: epithelial cells, keratinocyte immortal


title: Large preB_inducible IkE5 deletion, DMSO Ctl/D0

value: Treated with DMSO for 4-18 days


title: Large preB, IKDN, rep 1


title: atdamt1_h1


title: plasma derived from healthy control patients 1


title: 4_1_noTcells_100ng_ml_Peptide HaCaT

description:
4_1_noTcells_100ng_ml_Peptide
Illumina stranded mRNA

value: WT


title: 1_2_100ng_Peptide HaCaT

description:
1_2_100ng_Peptide
Illumina stranded mRNA


title: HaCaT_Tet-on-Ikzf1, Dox Day2

data_processing:
instrument model: Illumina NEXTseq550 and Novaseq6000
Sequencing reads were aligned to the human hg19 assembly and processed into normalized contact maps with the HiC-Pro 2.8.0 pipeline (Servant et al., 2015) on the DNAnexus platform.
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v1.11.08) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: hg19
Supplementary files format and content: hic

extract_protocol:
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use.
In situ Hi-C was performed following the established protocol (Rao et al., 2014) with minor modifications. Briefly, nuclei were permeabilized, and DNA was digested overnight with 100 U DpnII. The ends of the restriction fragments were labeled using biotin-14-dATP and then ligated in a 1.2 mL final volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp with a Covaris E220 evolution instrument (Covaris, Woburn, MA). Ligation junctions were then pulled down with streptavidin beads, and DNA fragments were end-repaired, dA-tailed and Illumina adapters ligated. Libraries were produced by 8 cycles of PCR amplification with KAPA Hifi DNA polymerase (Roche). The Hi-C libraries were size selected with AMPure XP beads and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.

value: Keratinocyte

value: Treated with 0.1μg/ml Dox for 2 days


title: HaCaT_Tet-on-Ikzf1, Dox Day3

value: Treated with 0.1μg/ml Dox for 3 days


title: 3_1_noTcells_100ng_ml_Peptide HaCaT

description:
3_1_noTcells_100ng_ml_Peptide
Illumina stranded mRNA


title: 2_1_noTcells_100ng_ml_Peptide HaCaT

description:
2_1_noTcells_100ng_ml_Peptide
Illumina stranded mRNA


title: atdamt1_C2

description: 10-day-old atdamt1 seedling mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: control

value: 0 hour


title: HaCaT_Tet-on-Luc, Dox Day2


title: HaCaT_Tet-on-Luc, Dox Day3


title: lung, 21 days after infection, replicate 2

city: Giessen

first: Rolf

middle: David

last: Glaser

address: Aulweg 128

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-Universität Giessen

description: 10x Genomics

data_processing:
Library demulitplexing and FASTQ file generation was performed using Illuminas bcl2fastq (2.19.0.316).
Sequencing reads were aligned using STAR solo (2.7.9a) in the Velocyto mode to the mm10 reference genome. During the alignment UMI deduplication was performed by STAR, as well.
The resulting UMI count matrix was processed further using Scanpy (1.7.2).
The raw UMI count matrix was filtered, normalized and log transformed. PCAs were calculated and used to integrate the various datasets with Harmony. Leiden clustering was performed on the knn embedded matrix. For further investigations leiden clusters calculated with a resolution of 1.4 were used.
A two-dimensional visualization of the cells was achieved by calculating UMAPs. Clusters were annotated using the scMCA (0.2.0) R (4.0.3) package.
Differentially expressed genes were calculated using the rank_genes_groups Scanpy function. RNA velocity analysis was performed using the scVelo package (0.2.4).
Gene set enrichment analysis was done using clusterProfiler (3.18.1) and fgsea (1.16.0) packages in R using GO and KEGG annotations.
Assembly: mm10
Supplementary files format and content: H5AD file exported from Scanpy (suitable for visualization in scRNA-seq browsers like cellxgene).

source_name: CD11c+ bronchoalveolar lavage fluid (BALF)

growth_protocol: All mice together with their respective littermate controls were bred under specific pathogen-free conditions and were used between 10 and 14 weeks of age.

extract_protocol:
FACS sorted cells were stained with SytoxTM (Thermofisher Scientific) for dead cell exclusion. 10 000 sorted viable cells per time point were loaded into 10x Genomics Chromium.
Library preparation was conducted according to the manufacturer indications (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121).

treatment_protocol: Mice were anaesthetized and oro-tracheally inoculated with 2.5-5x102 plaque-forming units (pfu) of influenza A virus PR8 (A/PR/8/1934(H1N1)) diluted in 70μl sterile PBS-/-.

value: C57BL/6 mice

value: IAV (PR/8, H1N1) infection

value: 21 days after infection


title: lung, 21 days after infection, replicate 1

description: 10x Genomics

value: CD11c+ bronchoalveolar lavage fluid (BALF)


title: lung, 21 days after infection, replicate 3

description: 10x Genomics


title: atdamt1_C1

value: Seedlings


title: HaCaT_Tet-on-Luc, DoxD3, H3K27ac HiChIP


title: 1_1_noTcells_100ng_ml_Peptide HaCaT

description:
1_1_noTcells_100ng_ml_Peptide
Illumina stranded mRNA


title: lung, 35 days after infection, replicate 3

description: 10x Genomics

value: 35 days after infection


title: ATAC_HPB-ALL_Baseline

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
ATAC-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ATAC-seq reads were remove duplicate with Picard MarkDuplicates package. Multiple mapping reads were removed using samtools view -q 10
ATAC-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-5, keep-dup=all, --SPMR were used to normalized the bedGraph output.The signal has been floored to 0.1 after bdgcmp subtract function.
Assembly: hg19
Supplementary files format and content: narrowPeak files of ATAC-seq
Supplementary files format and content: bigWig files of ATAC-seq

source_name: HPB-ALL cells

growth_protocol: HPB-ALL overexpressing TAL1 and LMO1 were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the ATAC-seq samples and sequencing of paired-end 150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end ATAC-Seq sequencing

treatment_protocol: The cells are incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

value: HPB-ALL cells


title: WT_h3

description: 10-day-old wild type seedlings were heat treated for 2.5 hours and used for RNA extraction. mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: wild type

value: heat treatment

value: 2.5 hours


title: 6_3_Tcellsonly MRC5

description:
6_3_Tcellsonly
Illumina stranded mRNA

source_name: lung

extract_protocol:
Qiagen Rneasy
oligo-dT capture and cDNA synthesis

treatment_protocol: Human influenza-specific T cells were thawed and rested o/n in CLM medium (RPMI supplemented with 10% AB Human Serum, 0.01% 50mM 2-MercaptoEtOH, 1% 1M HEPES and 1% Penicillin/Streptomycin). 30,000 MRC-5 cells/ well were seeded and grown to full confluency in DMEM o/n before pulsing the cells with varying concentrations of influenza peptide (GILGFVFTL; 0 ng/ml, 1 ng/ml, 10 ng/ml or 100 ng/ml) for 1hr. Cells were washed twice before adding 30,000 influenza-specific T cells in TexMACS with 2% Penicillin/Streptomycin. No T cell condition was primed with 100ng/ml peptide. SNs were harvested and used to stimulate 30,000 MRC-5 cells/well. MRC-5 cells were sequenced 24hrs after stimulation with SNs.

value: lung

value: fibroblast

value: Tcellsonly


title: WT_h2


title: ATAC_C21_TAL1/LMO1 overexpression

value: ATAC_C21_TAL1/LMO1 overexpression


title: lung, 35 days after infection, replicate 1

description: 10x Genomics


title: ATAC_C25_TAL1/LMO1 overexpression

value: ATAC_C25_TAL1/LMO1 overexpression


title: WT_h1


title: Large preB, WT, rep 1

value: large Pre-B cell (CD19+CD43+BP1+)

value: Wild-type (IKE5 fl/fl, Cre-)


title: 6_1_Tcellsonly MRC5

description:
6_1_Tcellsonly
Illumina stranded mRNA

value: WT


title: atdamt1_C3

value: control

value: 0 hour


title: 6_2_Tcellsonly MRC5

description:
6_2_Tcellsonly
Illumina stranded mRNA


title: 5_3_noTcells MRC5

description:
5_3_noTcells
Illumina stranded mRNA

value: noTcells


title: WT_C3

description: 10-day-old wild type seedling mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: Seedlings


title: lung, 0 days after infection, replicate 5

description: 10x Genomics

value: CD11c+ bronchoalveolar lavage fluid (BALF)

value: C57BL/6 mice

value: IAV (PR/8, H1N1) infection

value: 0 days after infection


title: Jurkat_dTAG_RUNX1

data_processing:
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files of GATA3 and RUNX1
Supplementary files format and content: bigWig files of GATA3 and RUNX1
Library strategy: CUT&RUN

source_name: Jurkat cells

growth_protocol: TAL1-FKBP12 Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end Cut&Run-Seq sequencing

treatment_protocol: The cells were incubated with CUTANA pA/G-Mnase. Chromtin fragments were purified utilizing a Cutana DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and analyzed on Illumina Novaseq at GENEWIZ Azenta Life Sciences Co. Ltd.

value: T-ALL

value: dTAG

tag: antibody


title: Jurkat_dTAG_GATA3


title: lung, 0 days after infection, replicate 4

description: 10x Genomics


title: WT_C2

value: wild type


title: WT_C1


title: lung, 35 days after infection, replicate 2

description: 10x Genomics

value: 35 days after infection


title: lung, 0 days after infection, replicate 3

description: 10x Genomics


title: 5_1_noTcells MRC5

description:
5_1_noTcells
Illumina stranded mRNA

value: lung

value: fibroblast


title: lung, 0 days after infection, replicate 2

description: 10x Genomics


title: 4_3_noPeptide MRC5

description:
4_3_noPeptide
Illumina stranded mRNA

value: noPeptide


title: lung, 0 days after infection, replicate 1

description: 10x Genomics


title: Jurkat_dTAG_IgG

value: Control


title: Jurkat_DMSO_GATA3

value: DMSO


title: Jurkat_DMSO_IgG


title: Brg1 YF-to-S biol rep 2

city: Providence

first: Collin

last: Ganser

state: Rhode Island

address: 171 Meeting St. Room 571

department: Molecular Microbiology and Immunology

institute: Brown University

data_processing:
Sequence reads were trimmed to remove adapter-dimers and low-quality reads using Trimmomatic (v0.39); parameters = leading:3, trailing:3, minLength:20
Timmed sequence reads were aligned to C. albicans A21 reference genome using STAR (v2.7.11a); parameters = intronMin;20, intronMax;1000
Aligned sequence reads were counted using HTSeq (v2.0.4)
Raw counts were normalized using DESeq2 (Bioconductor v3.17), log2 fold change > 2, padj < 0.05
Assembly: C. albicans A21 reference genome
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: comma-delimited value file includes normalized counts for each sample
Supplementary files format and content: comma-delimited value file includes differentially expressed genes between WT and YF-to-S mutants for Brg1 strains
Supplementary files format and content: comma-delimited value file includes differentially expressed genes between WT and YF-to-S mutants for Efg1 strains

organism: Candida albicans

source_name: Yeast

growth_protocol: C. albicans strains were grown overnight in YPD at 30°C. Overnight cultures were diluted 1:30 into Spider medium and grown at 37°C for 6 h.

extract_protocol:
RNA was purified from cells with the MasterPure Yeast RNA Purification Kit (LGC Biosearch Technologies) with DNAse I treatment.
PolyA RNA was isolated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and use to create multiplexed libraries with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB).

value: Yeast

value: brg1/BRG1 YF-to-S PrLD

value: Spider medium 37C 6 h


title: Brg1 YF-to-S biol rep 3


title: Brg1 YF-to-S biol rep 1


title: lung, 14 days after infection, replicate 3

description: 10x Genomics

value: 14 days after infection


title: dTAG_SIX6_4C

data_processing:
4C-seq reads were mapped to human hg19 reference genome using bwa-mem program with default parameters.
The aligned reads were processed using r3CSeq R package.
Primer sequence were utilized (GIMAP FWD Primer: "GGCACTCAGCCCCCCTTTCTT" REV Primer: "GGTCCTCAGAACCAGCCCT" and SIX6 FWD Primer: "TGCCCCTAAGAAGGCCCT" and REV Primer: "CTTTAGAACCGGAGAGTGGAGA") to get the viewpoint-of-interest and with the getReadCountPerRestrictionFragment and getInteractions functions in r3Cseq package.
The interactions from viewpoint were quantified and a heatmap were plot using plotDomainogramNearViewpoint function where the interactions intensity were visualized.
Assembly: hg19
Supplementary files format and content: bedGraph RPM for GIMAP and SIX6
Library strategy: 4C-Seq

extract_protocol:
Library construction from the 4C-seq samples and sequencing of paired-end 100-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end 4C-Seq sequencing

treatment_protocol: A total of 10 million cells were harvested, rinsed with warm FBS-free medium twice, and crosslinked in a 1% formaldehyde solution for 10 minutes at room temperature. Crosslinked cells were resuspended in cell lysis buffer and subjected to two rounds of enzymatic digestion, ligation and purification.

tag: 4c target

value: SIX6 gene region


title: lung, 14 days after infection, replicate 2

description: 10x Genomics

value: CD11c+ bronchoalveolar lavage fluid (BALF)

value: C57BL/6 mice


title: Brg1 WT biol rep 3


title: 4_1_noPeptide MRC5

description:
4_1_noPeptide
Illumina stranded mRNA

value: WT


title: 5_2_noTcells MRC5

description:
5_2_noTcells
Illumina stranded mRNA

value: noTcells


title: 3_3_1ngPeptide MRC5

description:
3_3_1ngPeptide
Illumina stranded mRNA


title: dTAG_GIMAP4_4C

value: T-ALL

value: GIMAP4 gene region


title: Brg1 WT biol rep 2


title: lung, 14 days after infection, replicate 1

description: 10x Genomics

value: IAV (PR/8, H1N1) infection


title: 3_2_1ngPeptide MRC5

description:
3_2_1ngPeptide
Illumina stranded mRNA

value: lung


title: DMSO_SIX6_4C


title: Brg1 WT biol rep 1


title: lung, 7 days after infection, replicate 3

description: 10x Genomics

value: 7 days after infection


title: Jurkat_DMSO_RUNX1


title: Efg1 YF-to-S biol rep 3

value: efg1/EFG1 YF-to-S PrLD


title: 2_3_10ngPeptide MRC5

description:
2_3_10ngPeptide
Illumina stranded mRNA

value: fibroblast


title: 4_2_noPeptide MRC5

description:
4_2_noPeptide
Illumina stranded mRNA

value: noPeptide


title: DMSO_GIMAP4_4C


title: SC_ML2

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome (GRh38-1.2.0) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).Then, gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Assembly: GRh38-1.2.0
Supplementary files format and content: matrix file

source_name: Sertoli cell

extract_protocol:
Total RNA was extracted from 10^6 cells using TRIzol Reagent (Thermo Fisher Scientific). 3 mg per sample were constructed into  libraries through NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer’s manuals.
Sequencing data were generated on Illumina NovaSeq 6000 platform with 150-bp paired-end read length by Novogene.

value: Sertoli cell

value: debris and ML-SA1


title: Efg1 YF-to-S biol rep 2

value: Yeast

value: Spider medium 37C 6 h


title: SC_ML1


title: lung, 7 days after infection, replicate 1

description: 10x Genomics


title: T3

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Assembly: Zm-TPD-CSHL-1.0
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Zea mays

source_name: four leaf stage leaves after three days of Spodoptera frugiperda feeding

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

value: four leaf stage leaves


title: Efg1 YF-to-S biol rep 1


title: 2_2_10ngPeptide MRC5

description:
2_2_10ngPeptide
Illumina stranded mRNA


title: 2_1_10ngPeptide MRC5

description:
2_1_10ngPeptide
Illumina stranded mRNA


title: Efg1 WT biol rep 3


title: SC_G1

value: debris


title: CK3

source_name: four leaf stage leaves


title: 1_3_100ngPeptide MRC5

description:
1_3_100ngPeptide
Illumina stranded mRNA


title: SCNC2


title: Efg1 WT biol rep 2


title: 3_1_1ngPeptide MRC5

description:
3_1_1ngPeptide
Illumina stranded mRNA


title: 1_2_100ngPeptide MRC5

description:
1_2_100ngPeptide
Illumina stranded mRNA


title: T1

source_name: four leaf stage leaves after one day of Spodoptera frugiperda feeding


title: lung, 7 days after infection, replicate 2

description: 10x Genomics

value: CD11c+ bronchoalveolar lavage fluid (BALF)

value: C57BL/6 mice


title: 1_1_100ngPeptide MRC5

description:
1_1_100ngPeptide
Illumina stranded mRNA

value: WT


title: SCNC1


title: CK1


title: Lungs of RSKI pig-2

status: Public on Nov 19 2023

city: Chang Chun

first: Feng

last: Li

address: xi an street

institute: Jilin University

data_processing:
CLC genomics Workbench V 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quelity sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GCF_000003025.6_Sscrofa11.1 using CLC genomic benchwork (parameters - mismath cost: 2 insertion cost:3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Lungs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 μg of total RNA was used for the construction of sequence libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufacture's protocols.

value: Lungs

value: RSAD2 Knock-in


title: Lungs of RSKI pig-1


title: Lungs of RSKI pig-3


title: SC_G2


title: Lungs of Control pig-3


title: Lungs of Control pig-2


title: Lungs of Control pig-1


title: Efg1 WT biol rep 1


title: WT, cold stress, rep2

city: Wuhan

first: Dan

last: Hu

address: Shizishanjie NO.1

institute: Huazhong Agricultural University

data_processing:
Raw data were trimmed for adaptor sequence/low-quality sequence using fastp/0.23.4
Clean data were mapped to MSU 7.0 using hisat2/2.2.1
Gene count was performed using StringTie/2.1.4 and DEGs was analysed by R package DESeq2.
Assembly: MSU ver7.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Oryza sativa

source_name: shoots of four-leaf seedling stage

extract_protocol:
Total RNA was harvested using TRIzol reagent (invitrogen), 2 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocol.

value: shoots of four-leaf seedling stage

value: ZH11 background


title: osdreb2b, cold stress, rep3

value: osdreb2b knockout


title: ossro1c, cold stress, rep2

value: ossro1c knockout


title: WT, cold stress, rep3


title: WT, cold stress, rep1


title: osdreb2b, cold stress, rep2


title: ossro1c, cold stress, rep3


title: 90_chargedaa_to_random_3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

institute: Weizmann Institute of Science

description: RNA-seq

data_processing:
demultiplexing with AdapterRemoval, --trim3p 0 21
identification of UMI with umi_tools extract, --bc-pattern=NNNNNNNNN
mapping the reads with bowtie2, -p8 --local --very-sensitive --trim-to 30 -x
sorting and indexing with samtools
deduplication of UMI with umi_tools dedup
calculation of coverage with bedtools coverage -counts -s -a
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: proceesed data files contain counts mapped with bedttols coverage in format of  (chromosome, chromosome location (start), chromosome location (stop), systemic name, number, strand, counts)

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose

extract_protocol:
RNA-seq: modified protocol of the nucleospin 96 RNA kit (Macherey-Nagel, Duren, Germany). Specifically, cell lysis was done in a 96 deep-well plate by adding 450 μl of lysis buffer containing 1 M sorbitol (Sigma-Aldrich), 100 mM EDTA, and 0.45 μl lyticase (10 IU/μl). The plate was incubated at 30°C for 30 minutes in order to break the cell wall and then centrifuged for 10 minutes at 2,500 rpm, and the supernatant was removed. From this point, extraction proceeded as in the protocol of nucleospin 96 RNA kit, only substituting β-mercaptoethanol with DTT 1M.
RNA libraries were created as described before (Chapal et al., 2019)

treatment_protocol: The cells were treated with H2O2 in final concentration of 0.3mM for 20 minutes in 30 degrees with constant shaking

tag: strain

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_chargedaa_to_random_3)-Mnase (kanMX)


title: 90_chargedaa_to_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_chargedaa_to_N)-Mnase (kanMX)


title: 90_D_charged_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_D_charged)-Mnase (kanMX)


title: ossro1c, cold stress, rep1


title: 90_D_charged_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 90_E_charged_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_E_charged)-Mnase (kanMX)


title: 90_chargedaa_to_random_3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 90_chargedaa_to_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 90_chargedaa_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_chargedaa_to_A)-Mnase (kanMX)


title: 90_chargedaa_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 70p_30n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(70p_30n_chargeratio)-Mnase (kanMX)


title: 80p_20n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(80p_20n_chargeratio)-Mnase (kanMX)


title: 80p_20n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 90p_10n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90p_10n_chargeratio)-Mnase (kanMX)


title: 90_chargedaa_to_random_2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_chargedaa_to_random_2)-Mnase (kanMX)


title: 90_E_charged_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 60p_40n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(60p_40n_chargeratio)-Mnase (kanMX)


title: 70p_30n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 90_chargedaa_to_F_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90_chargedaa_to_F)-Mnase (kanMX)


title: osdreb2b, cold stress, rep1


title: 90_chargedaa_to_random_2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 60p_40n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 50p_50n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(50p_50n_chargeratio)-Mnase (kanMX)


title: 30p_70n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(30p_70n_chargeratio)-Mnase (kanMX)


title: 30p_70n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 50p_50n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 40p_60n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(40p_60n_chargeratio)-Mnase (kanMX)


title: 90_chargedaa_to_F_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 20p_80n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(20p_80n_chargeratio)-Mnase (kanMX)


title: 10p_90n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(10p_90n_chargeratio)-Mnase (kanMX)


title: 10p_90n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Y_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(Y_nextto_N)-Mnase (kanMX)


title: T_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(T_nextto_N)-Mnase (kanMX)


title: Y_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: T_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: S_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(S_to_A)-Mnase (kanMX)


title: S_to_A_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: 20p_80n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: S_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: S_shift_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(S_shift)-Mnase (kanMX)


title: S_shift_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: S_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(S_nextto_N)-Mnase (kanMX)


title: S_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep8x4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep8x4)-Mnase (kanMX)


title: rep8x3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep8x3)-Mnase (kanMX)


title: rep8x4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: S_to_A_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ST_deletion_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ST_deletion)-Mnase (kanMX)


title: 40p_60n_chargeratio_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep8x2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep8x2)-Mnase (kanMX)


title: ST_deletion_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep8x3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep8_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep8)-Mnase (kanMX)


title: rep8x2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5x3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep5x3)-Mnase (kanMX)


title: rep5x4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep5x4)-Mnase (kanMX)


title: rep5x2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep5x2)-Mnase (kanMX)


title: rep8_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep5)-Mnase (kanMX)


title: rep4x2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep4x2)-Mnase (kanMX)


title: rep5x2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5x3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep3x4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep3x4)-Mnase (kanMX)


title: rep4x3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep4x3)-Mnase (kanMX)


title: rep1x4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep1x4)-Mnase (kanMX)


title: rep4x3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep4x2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep4)-Mnase (kanMX)


title: rep1x2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep1x2)-Mnase (kanMX)


title: rep1x3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep1x3)-Mnase (kanMX)


title: rep4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep3x4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5x4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep1x4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep1x3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep1x2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep0x2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep0x2)-Mnase (kanMX)


title: rep0x2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep1_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep1)-Mnase (kanMX)


title: rep1_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep0x4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep0x4)-Mnase (kanMX)


title: rep0_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep0)-Mnase (kanMX)


title: rep0_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: raax4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(raax4)-Mnase (kanMX)


title: rep0x4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: randomaa_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(randomaa)-Mnase (kanMX)


title: randomaa_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: raax2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(raax2)-Mnase (kanMX)


title: raax2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Q_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(Q_nextto_N)-Mnase (kanMX)


title: PG_shift_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(PG_shift)-Mnase (kanMX)


title: R_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(R_nextto_N)-Mnase (kanMX)


title: Q_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: PG_shift_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: PG_shift_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: P_is_placed_next_to_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(P_is_placed_next_to_N)-Mnase (kanMX)


title: R_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: P_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(P_to_A)-Mnase (kanMX)


title: PG_shift_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: raax4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: P_is_placed_next_to_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NQ_to_A_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(NQ_to_A)-Mnase (kanMX)


title: NQ_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: P_is_placed_next_to_N_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NS_swapped_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(NS_swapped)-Mnase (kanMX)


title: P_is_placed_next_to_N_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NQ_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NS_swapped_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NQ_shift_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(NQ_shift)-Mnase (kanMX)


title: N_to_Y_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_Y)-Mnase (kanMX)


title: P_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NQ_shift_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_Y_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: NQ_deletion_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(NQ_deletion)-Mnase (kanMX)


title: NQ_deletion_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_T_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_T)-Mnase (kanMX)


title: N_to_S_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_S)-Mnase (kanMX)


title: N_to_T_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_S_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_R_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_R)-Mnase (kanMX)


title: N_to_Q_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_Q)-Mnase (kanMX)


title: N_to_R_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_Q_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_E_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_E)-Mnase (kanMX)


title: N_to_E_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_Q_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_D_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(N_to_D)-Mnase (kanMX)


title: Msn2_Zfonly_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(-delta-131aas from C terminus)-Mnase (kanMX)


title: N_to_D_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_E_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: MSN2_start_nls_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(-delta-573aas from N terminus)-Mnase (kanMX)


title: MSN2_start_nls_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Zfonly_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sMik_m2_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 S.mikatae Msn2 non-DBD Mnase::kanMX


title: Msn2_sMik_m2_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKud_m4_Tail_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 S.kudriazevii Msn4 non-DBD Mnase::kanMX


title: Msn2_sKud_m4_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKud_m4_Tail_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKud_m2_Tail_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 S.kudriazevii Msn2 non-DBD Mnase::kanMX


title: Msn2_sKlu_m_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 L.kluyveri Msn non-DBD Mnase::kanMX


title: Msn2_sKud_m2_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKud_m4_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Scramble3 Mnase::kanMX


title: Msn2_sKud_m2_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKud_m2_Tail_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: N_to_E_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Scramble2 Mnase::kanMX


title: Msn2_Scramble10_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Scramble10 Mnase::kanMX


title: Msn2_Scramble10_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble1_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Scramble1 Mnase::kanMX


title: Msn2_Scramble1_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble1_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble1_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sCerm4T_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2  S.cerevisiae Msn4 non-DBD Mnase::kanMX


title: Msn2_sCerm4T_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sBay_m4_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 S.bayanus Msn4 non-DBD Mnase::kanMX


title: Msn2_sCas_m4_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 N.castellii Msn4 non-DBD Mnase::kanMX


title: Msn2_sBay_m4_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sCas_m2_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 N.castellii Msn2 non-DBD Mnase::kanMX


title: Msn2_sCas_m2_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sBay_m2_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 S.bayanus Msn2 non-DBD Mnase::kanMX


title: Msn2_sCas_m4_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sKlu_m_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_lWal_m_Tail_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 L.walti Msn non-DBD Mnase::kanMX


title: Msn2_lWal_m_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_lWal_m_Tail_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sBay_m2_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_kLac_m_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 K.lactis Msn non-DBD Mnase::kanMX


title: Msn2_lWal_m_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_sBay_m2_Tail_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dTAD_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-267aaNterm Mnase::kanMX


title: Msn2_dTAD_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-267aaNterm Mnase::kanMX


title: Msn2_dTAD_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dTAD_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotB_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2  -delta-MotifB Mnase::kanMX


title: Msn2_dMotB_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotB_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotB_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotA_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-Motif A Mnase::kanMX


title: Msn2_dMotA_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotA_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_cGla_m4_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 C.glabrata Msn4 non-DBD Mnase::kanMX


title: Msn2_dGal11_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Mnase::kanMX -delta-Gal11::NatMX6


title: Msn2_cGla_m4_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_cGla_m4_Tail_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_kLac_m_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dGal11_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dMotA_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_cGla_m2_Tail_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 C.glabrata Msn2 non-DBD Mnase::kanMX


title: Msn2_cGla_m2_Tail_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_604_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-604aaNterm Mnase::kanMX