title: TIC5

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

data_processing:
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts for samples

source_name: small intestinal organoid (enteroid)

growth_protocol: 1. Sampling   To establish human small intestinal organoids (enteroids), human small intestinal samples were obtained from controls (n = 8) and patients with Crohn’s disease (n = 8) using biopsy forceps during single-balloon enteroscopy at the Samsung Medical Center, Seoul, Korea, between November 2016 and December 2018. At least four biopsy specimens were collected from the normal mucosa of the small intestine. The patients with CD were diagnosed according to the practice guidelines. In patients with CD, biopsies were performed at least 5 cm away from the ulcers.     2. Crypt Isolation From Biopsies  Endoscopic biopsy specimens were incubated in PBS with 10 mM ethylenediaminetetraacetic acid (EDTA, Thermo Fischer Scientific, San Jose, CA, USA) and 1 mM dithiothreitol (DTT, Thermo Fischer Scientific) at 4 °C on a rocker at 50 rpm for 30 min. The supernatant, containing villi and debris, was decanted and discarded. Intestinal crypts were obtained from the addition of fresh PBS and vortexing for 30 s. The supernatant containing crypts was collected and filtered through a 70-μm cell strainer (Corning, Bedford, MA, USA). This procedure was repeated three times. The fractions were combined and centrifuged at 200 × g at 4 °C for 2 min, and the pellet was suspended in a basal medium (advanced Dulbecco’s modified Eagle’s medium (DMEM)/F12 (Thermo Fischer Scientific) supplemented with antibiotic–antimycotic solution (Thermo Fischer Scientific), 10 mmol/L HEPES (Thermo Fischer Scientific), GlutaMAX (Thermo Fischer Scientific), 1× N2 (Thermo Fischer Scientific), 1× B27 (Thermo Fischer Scientific), and 1 mmol/L N-acetylcysteine (Sigma-Aldrich, St. Louis, MO, USA). The suspension was centrifuged at 200 × g at 4 °C for 2 min, and the pellet was suspended in the basal medium.    3. Three-dimensional (3D) Intestinal Crypt Culture   The isolated crypts were pelleted with three quick spins, resuspended into Matrigel (Corning), and plated in 48-well culture plates (Corning). After incubation at 37 °C for 15 min, 250 μL of maintenance medium (50% Wnt3a-conditioned medium (ATCC#CRL-2647, Manassas, VA, USA) + 50% 2× basal medium supplemented with 50 ng/mL recombinant human epidermal growth factor (Sigma-Aldrich), 100 ng/mL recombinant human noggin (R&D Systems, Minneapolis, MN, USA), 500 ng/mL recombinant human R-spondin 1 (PeproTech, Cranbury, NJ, USA), 10 mM nicotinamide (Sigma-Aldrich), 10 μM p160ROCK inhibitor (Y27632, Selleckchem, Houston, TX, USA), 10 μM p38 MAP kinase inhibitor (SB202190, Sigma-Aldrich), and 10 nM Prostaglandin E2 (PGE2, Cayman Chemical, Ann Arbor, MI, USA)) was added. A GSK3 inhibitor (CHIR99021, Stemgent, Cambridge, MA, USA) was added to the medium during the first 2 days.     4. Organoid Subculture and Maintenance   After culturing the cells for 7 days, the organoids in Matrigel were mechanically disrupted via pipetting. The dissociated organoids were washed with 10 mL of basal medium and centrifuged at 200 × g at 4 °C for 30 s. The pellet was resuspended in 2 mL of cell dissociation buffer (Thermo Fischer Scientific) and incubated in a water bath at 37 °C for 5 min. The cell pellet was resuspended in Matrigel and plated in 48-well culture plates (Corning). After incubation at 37 °C for 15 min, 250 μL of maintenance medium was added. The medium was changed every 2 days and organoids were passaged at a ratio of 1:2–1:4 on day 7 after crypt plating.    5. Construction of Enteroids Derived From Controls and CD Patients   After 4–6 passages, most of the organoids derived from controls and patients with CD in the maintenance medium formed uniform spheroids and could be passaged stably for a long time. To recapitulate the structure and function of the intestinal epithelium, the spheroids were cultured in a differentiation medium (maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2). The intestinal organoids cultured in differentiation medium (enteroids) have the presence of visually sharp borders (buddings) along their basolateral (anti-luminal) side and irregular, thickened walls composed of all the components of the epithelial cells. The differentiation medium was changed every 2 days and enteroids were cultured for 7–12 days after passage.

extract_protocol:
For library construction, RNA is extracted from a sample. After performing quality control (QC), qualified samples
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: Organoids were cultured in the maintenance medium for 2 days to obtain a stable number of organoids before inducing organoid differentiation. On day 2, the maintenance medium for organoids was replaced with the TNFɑ(30 ng/ml)-containing enteroid medium. Control and Crohn’s organoids—cultured for the long-term (passage ≥ 6)—were treated with 30 ng/ml TNFɑ every 24 hours until harvest.

value: small intestine (ileum)

tag: disease

value: Crohn's disease

tag: status

value: add 30 ng/ml of TNF-alpha in conventional organoid culture condition with differentiation medium


title: BoC60_C5_2_cetux-secondary resistant

status: Public on May 21 2021

type: RNA

city: Bochum

first: Stephan

middle: A

last: Hahn

address: Universitaetsstrasse 150

department: MGO

country: Germany

institute: Ruhr-University Bochum

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B ) using standard settings

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: cetux-secondary resistant

label_protocol: 100 ng of total RNA were labeled using the QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with  cyanine-5-CTP (Cy5)

growth_protocol: Three 1-3 mm tumor pieces of early passage xenograft tumor Bo63 soaked in matrigel were implanted via standard technology subcutaneously on the dorsal flanks of nude mice (two implantation sites per mouse; nu/nu NMRI) to establish treatment and control tumor cohorts.

extract_protocol: Total RNA isolation from 25-30 (20mm) frozen xenograft tumor sections were isolates using the mirVana™ PARIS™ Kit (Applied Biosystems) according to the manufacture`s protocol. RNA integrity was analysed using standard RNA-gel electrophoresis. Total-RNA concentration and purity of total-RNA samples was measured with the NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific).

treatment_protocol: Nude mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg, treatment was imitated when tumor size reached approc. 100-200 mm³

tag: tissue

value: patient derived colon cancer xenograft tissue

tag: response

value: partial response


title: TIC2

type: SRA

library_source: transcriptomic


title: TIC4


title: TIC1


title: TIC3


title: BoC35_K7_untreated control

source_name: untreated control


title: BoC71_C1_2_cetux-secondary resistant

value: complete response


title: BoC60_K6_untreated control


title: BoC71_C4_2_cetux-secondary resistant


title: BoC60_C5_1_cetux-secondary resistant


title: BoC69_5dC2_5_days_cetux_treatment

source_name: cetux treatment

value: stable disease


title: TIN5

value: small intestine (jejunum)


title: BoC69_K2_untreated control


title: TJC2

value: control


title: TIN1


title: TJC1


title: TJN3


title: TJN5


title: TJN4


title: TJN2


title: TIN4


title: TJC3


title: TJN1


title: IC5

value: conventional organoid culture condition with differentiation medium


title: IC4


title: IC3


title: JC5


title: JC4


title: IC1


title: IN3


title: JC1


title: IN2


title: JN5


title: JN2


title: JN1


title: JN3


title: Control MSN01-03R Rep 12

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The data processing pipeline consists of the following three steps:
First of all, use the script Build-Genome-Index.GEO.sh to generate a set of index files with a read length of 100 bp for the UCSC human genome reference library (version hg38) used by the STAR alignment program.
Secondly, launch the script Align-RNAseq-Reads.GEO.sh that uses the STAR aligner to align the 100-bp sequence reads contained in the FASTQ-format sequence data files (obtained from high-throughput random-primed mRNA-sequencing assays) to the reference library and generate the BAM-format alignment result files that contain the sequence reads tagged with alignment information, one alignment file for each sample.
Lastly, run the script Count-RNAseq-Reads.GEO.sh that uses the featureCounts program from the Subread software to assign the tagged sequence reads contained in the alignment files to corresponding genes annotated in the reference library and then create a read counts table that contains the number of sequence reads uniquely mapped to each reference gene in rows and for every sequenced sample in columns.
Genome_build: Reference-Library.tar.gz: a compressed file containing the UCSC human genome referece library (version hg38)
Supplementary_files_format_and_content: Gene-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence reads for 63 iPSC samples
Supplementary_files_format_and_content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment and feature counts

molecule: polyA RNA

source_name: primary dermal fibroblasts

growth_protocol: Cultured under growth conditions with mTeSR1 Basal Medium  (see the Section 8. Splitting/expansion of induced pluripotent stem cells (MEF/feeder-free) of the SOP document DToxS SOP CE-7.0 Reprogramming Human Fibroblasts to Human Induced Pluripotent Stem.pdf)

extract_protocol:
Total RNA was isolated using Trizol (see the SOP document DToxS SOP A-1.0 Total RNA Isolation.pdf)
Library was prepared using 500 ng of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions

treatment_protocol: Fully confluent and differentiated cells were treated with  vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

tag: source organ

value: skin

tag: cell type

value: cardiomyocytes differentiated from induced pluripotent stem cell

tag: passage number

tag: sample id

tag: rna amount (ng)

tag: nanodrop 260/280

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: Control MSN01-03R Rep 4


title: Control MSN01-03R Rep 8


title: Control MSN01-03R Rep 10


title: Control MSN01-03R Rep 9


title: Control MSN01-03R Rep 1


title: Control MSN01-03R Rep 3


title: Control MSN01-03R Rep 2


title: Control MSN01-03R Rep 11


title: Control MSN01-03R Rep 5


title: Control MSN01-03R Rep 6


title: BoC60_K8_untreated control


title: Control MSN08-13R Rep 12


title: IC2


title: Control MSN08-13R Rep 11


title: IN1


title: JN4


title: Control MSN08-13R Rep 10


title: Control MSN08-13R Rep 9


title: Control MSN08-13R Rep 8


title: Control MSN08-13R Rep 7


title: Control MSN08-13R Rep 6


title: Control MSN01-03R Rep 7


title: Control MSN08-13R Rep 3


title: Control MSN08-13R Rep 4


title: Control MSN06-07R Rep 11


title: Control MSN06-07R Rep 10


title: Control MSN06-07R Rep 9


title: Control MSN06-07R Rep 7


title: Control MSN06-07R Rep 6


title: Control MSN06-07R Rep 5


title: Control MSN06-07R Rep 4


title: Control MSN06-07R Rep 2


title: Control MSN09-04R Rep 5


title: Control MSN09-04R Rep 11


title: Control MSN06-07R Rep 1


title: Control MSN09-04R Rep 10


title: Control MSN09-04R Rep 4


title: Control MSN09-04R Rep 6


title: Control MSN09-04R Rep 9


title: Control MSN09-04R Rep 3


title: Control MSN08-13R Rep 2


title: Control MSN08-13R Rep 5


title: Control MSN09-04R Rep 1


title: Control MSN05-01R Rep 11


title: Control MSN05-01R Rep 8


title: Control MSN08-13R Rep 1


title: Control MSN09-04R Rep 7


title: Control MSN09-04R Rep 8


title: Control MSN05-01R Rep 9


title: Control MSN05-01R Rep 12


title: Control MSN05-01R Rep 7


title: Control MSN09-04R Rep 2


title: Control MSN05-01R Rep 6


title: Control MSN06-07R Rep 8


title: Control MSN05-01R Rep 5


title: Control MSN05-01R Rep 3


title: Control MSN05-01R Rep 4


title: Control MSN05-01R Rep 2


title: Control MSN05-01R Rep 1


title: Control MSN02-04R Rep 5


title: Control MSN02-04R Rep 4


title: Control MSN02-04R Rep 3


title: Control MSN02-04R Rep 2


title: NSC-EO-46

city: Tokyo

first: Yosuke

last: Tanaka

address: 5-1-1, tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh37 whole genome using TopHat2 v2.0.9 with --library-type=fr-firststrand.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.1.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Human gastric cancer cells

extract_protocol:
RNA with a high RNA integrity number underwent RNA-seq using a NEBNext Ultra Directional RNA Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human gastric cancer cells


title: NSC-EO-41


title: NSC-EO-42


title: Control MSN02-04R Rep 1


title: NSC-EO-40


title: NSC-EO-44


title: NSC-EO-37


title: NSC-EO-35


title: NSC-EO-34


title: NSC-EO-31


title: NSC-EO-30


title: NSC-EO-29


title: NSC-EO-39


title: NSC-EO-27


title: NSC-EO-33


title: NSC-EO-28


title: NSC-EO-24


title: NSC-EO-26


title: NSC-EO-22


title: NSC-EO-21


title: NSC-EO-19


title: NSC-EO-18


title: NSC-EO-17


title: NSC-EO-15


title: NSC-EO-16


title: NSC-EO-36


title: Control MSN06-07R Rep 3


title: NSC-EO-14


title: NSC-EO-32


title: NSC-EO-12


title: NSC-EO-13


title: NSC-EO-9


title: Control MSN05-01R Rep 10


title: NSC-EO-5


title: NSC-EO-3


title: NSC-EO-1


title: NSC-86E


title: NSC-EO-20


title: PEC control, biological rep2

city: Meguro-ku, Tokyo

first: Sho

last: Hangai

institute: The University of Tokyo

description: Gene expression data from macrophages simulated with necrotic cell-derived molecules

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on Clariom S Array, Mouse. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

organism: Mus musculus

source_name: Wild-type mouse peritoneal macrophage

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: Peritoneal macrophages were cultured in RPMI containing 10% fetal bovine serum, at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted with NucleoSpin RNA II (MACHREY NAGEL) according to manufacturer's instructions.

treatment_protocol: Peritoneal macrophages (2 x 105) were treated by necrotic cell-derived supernatant (2 x 106) for 2 hours.

value: Mouse peritoneal macrophage


title: NSC-85E


title: NSC-86


title: PEC supernatant, biological rep1

source_name: Wild-type mouse peritoneal macrophage, treated by necrotic cell derived supernatant

value: Mouse peritoneal macrophage, treated by necrotic cell derived supernatant


title: PEC supernatant, biological rep2


title: CD630_microaerobic_3

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

description:
630_ microaerobic_vs_aerobic
2691-AW-38-GGTGTACA-AGACGCTA_S01_L001_R1_001

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 20.0.1) platform for analysis. The Illumina paired reads option was chosen for import.
Imported reads were trimmed to remove adapters using CLC Genomics Workbench
To remove rRNA reads, all paired reads were aligned to a sequence list containing all rRNA sequences for each corresponding bacterial strain. Unmapped (non-rRNA) reads were collected and used for subsequent analysis. Steps were performed using CLC Genomics Workbench. Reference genomes NC_009089 and  NC_013315 were used for CD630 and CD196, respectively.
Expression values (as RPKM) for Gene Tracks were calculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench. For cross-comparison between strain a 'consensus genome' was generated by BLASTing every CD630 gene against each CD196 gene and generating a gene track of the resulting consensus sequences.
Comparison of samples was performed using the "Differential Expression in Two Groups" function in CLC Genomics Workbench
Output was exported to MS Excel and manually curated if neccesary
Genome_build: A CD630 - CD196 consensus genome was generated by BLAST of each CD630 gene against each CD196 gene using the "MultiBLAST" function in CLC Genomics Workbench (standard settings). For each individual BLAST event, the top hit was chosen and the consensus sequence extracted (80% identity cutoff with manual curation in the 80-90% range; 1E-70 p-value cutoff; insertion of 'N' ambiguity symbols for conflicts)
Supplementary_files_format_and_content: microaerobic vs. aerobic.xlsx

organism: Clostridioides difficile

source_name: Bacterial cells, pelleted

growth_protocol: Bacteria were grown in BHIS medium at 37°C anaerobically or with 1.5% oxygen

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit. DNA was removed by treatment with Invitrogen  TURBO Dna-free kit and rRNA was depleted using the Invitrogen RiboMinus Transcriptome Isolation kit (bacteria) and the RiboMinus Concentration Module
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

tag: strain

tag: genotype

value: Wild-type

tag: growth media

value: BHIS

tag: atmosphere

value: 1.5% oxygen

tag: temperature/final od600


title: CD630_anaerobic_3

description:
630_ microaerobic_vs_aerobic
2691-AW-35-GGCAAGTT-CTCAGAAG_S01_L001_R1_001

value: anaerobic


title: 196_microaerobic_2

description:
196_ microaerobic_vs_aerobic
2691-AW-31-GACGAACT-CAATGCGA_S01_L001_R1_001


title: CD630_anaerobic_2

description:
630_ microaerobic_vs_aerobic
2691-AW-34-GAATCACC-GAACGAAG_S01_L001_R1_001


title: CD630_microaerobic_2

description:
630_ microaerobic_vs_aerobic
2691-AW-37-CAATGCGA-GACGAACT_S01_L001_R1_001


title: CD630_microaerobic_1

description:
630_ microaerobic_vs_aerobic
2691-AW-36-GATCTTGC-CATGAGCA_S01_L001_R1_001


title: CD630_anaerobic_1

description:
630_ microaerobic_vs_aerobic
2691-AW-33-ATAACGCC-CAGGTTCA_S01_L001_R1_001


title: 196_microaerobic_1

description:
196_ microaerobic_vs_aerobic
2691-AW-30-CATGAGCA-GATCTTGC_S01_L001_R1_001


title: PEC control, biological rep1


title: 196_anaerobic_3

description:
196_ microaerobic_vs_aerobic
2691-AW-29-CTCAGAAG-GGCAAGTT_S01_L001_R1_001


title: NSC-84


title: NSC-83E


title: 196_anaerobic_2

description:
196_ microaerobic_vs_aerobic
2691-AW-28-GAACGAAG-GAATCACC_S01_L001_R1_001


title: 196_anaerobic_1

description:
196_ microaerobic_vs_aerobic
2691-AW-27-CAGGTTCA-ATAACGCC_S01_L001_R1_001


title: NSC-83


title: NSC-85


title: NSC-82E


title: NSC-EO-8


title: NSC-82


title: ATAC-Seq 48hr rep3 + dnAP-1

city: Stanford

first: Helen

middle: M

last: Blau

state: CA

address: 269 Campus Dr

department: Baxter Laboratories

institute: Stanford University

description: 48hr rep3 + dnAP-1

library_source: genomic

data_processing:
Default Illumina base calling implementation
Reads were trimmed, and then mapped to concatenated human and mouse genome using Bowtie 2
reads mapping to chrM and those with MAPQ <10 were removed
peaks were called with MACS 2
Genome_build: hg38/mm10
Supplementary_files_format_and_content: bigwig read pileup centered at Tn5 29bp footprint

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: human fibroblast + mouse ESC fusion

growth_protocol: Fibroblasts are grown in 10% FBS + DMEM. ESCs are grown with 10% FBS, 10% KSR, LIF, beta-mercaptoethanol in KO DMEM

extract_protocol:
Cells were pelleted and permeabilized in hypotonic buffer with 0.1% IGEPAL CA-630. Nuclei were treated with transposase from Illumina (Cat FC-121-1030)
Fragments were amplified with NEBNext PCR master mix and Nextera indices for 8-12 cycles

treatment_protocol: To induce dnAP-1 in fibroblasts, doxycycline was added at the beginning of the co-culture step at 1000 ng/ml

value: heterokaryon

tag: treatment

value: dnAP-1 (Tet-On)


title: ATAC-Seq 48hr rep2 + dnAP-1

description: 48hr rep2 + dnAP-1


title: 196_microaerobic_3

description:
196_ microaerobic_vs_aerobic
2691-AW-32-AGACGCTA-GGTGTACA_S01_L001_R1_001


title: ATAC-Seq 48hr rep1 + dnAP-1

description: 48hr rep1 + dnAP-1


title: ATAC-Seq 16hr rep3 + dnAP-1

description: 16hr rep3 + dnAP-1


title: NSC-81E


title: NSC-81


title: NSC-80E


title: ATAC-Seq 16hr rep2 + dnAP-1

description: 16hr rep2 + dnAP-1


title: NSC-78E


title: NSC-79E


title: NSC-78


title: NSC-79


title: NSC-76


title: NSC-77


title: NSC-75E


title: NSC-76E


title: ATAC-Seq 16hr rep2

description: 16hr rep2

value: no dnAP-1 (control)


title: ATAC-Seq 48hr rep2

description: 48hr rep2


title: ATAC-Seq 16hr rep4

description: 16hr rep4


title: ATAC-Seq 48hr rep1

description: 48hr rep1


title: ATAC-Seq 3hr rep1 + dnAP-1

description: 3hr rep1 + dnAP-1


title: ATAC-Seq 16hr rep3

description: 16hr rep3


title: NSC-75


title: ATAC-Seq 3hr rep2 + dnAP-1

description: 3hr rep2 + dnAP-1


title: ATAC-Seq 16hr rep1

description: 16hr rep1


title: NSC-73E


title: ATAC-Seq 3hr rep3

description: 3hr rep3


title: ATAC-Seq 3hr rep2

description: 3hr rep2


title: ATAC-Seq 3hr rep1

description: 3hr rep1


title: NSC-80


title: ATAC-Seq 16hr rep1 + dnAP-1

description: 16hr rep1 + dnAP-1


title: NSC-73


title: NSC-72


title: OB7d

city: Jiujiang

first: Jianjun

last: Xiong

address: 17 Lufeng Road

country: China

institute: Jiujiang University

data_processing:
The whole transcriptome sequencing data sequenced by HiseqTM Sequencer was filtered (removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of < 20) and mapped to human genome utilizing HISAT2 (PMID: 25751142).
HTSeq was used to calculate the gene count of mRNA (PMID: 25260700).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, including 3 days, 5 days, and 7 days during adipogenesis and osteoblastogenesis, respectively.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human mesenchymal stem cells

growth_protocol: The human mesenchymal stem cells (hMSCs) were expanded to passage 6 with 80-90% confluence for adipogenesis and 70% confluence for osteoblastogenesis. Adipogenic differentiation was inspired with adipogenic cocktails with 0.01 mg/mL insulin, 0.5 mM 3-isobutyl-1-methyl-xanthine, and 1.0 μM dexamethasone (Sigma, St. Louis, Mo, USA) in Gibco MEMα (Minimum Essential Medium Alpha) every three days, and osteoblastogenic differentiation was induced with the medium supplemented with FBS, ascorbic acid, β-glycerophosphate, dexamethasone, L-glutamine, penicillin and streptomycin (St. Louis, MO, USA).

extract_protocol:
We used TRIzol reagent (Invitrogen, Carlsbad, CA, USA) to isolate the total RNA from the freshly harvested adipo-osteobalstogenic samples.
The rRNA depletion library was constructed using NEBNext® UltraTM Directional RNA Library Prep kit according to the manufacturer’s instructions.

treatment_protocol: Three replicates were induced at 0, 3, 5, and 7 d separately for adipogenesis and osteoblastogenesis.

tag: stem cells

value: human marrow mesenchymal stem cells (hMSCs)

value: osteoblastogenesis at 7 day


title: ATAC-Seq 3hr rep3 + dnAP-1

description: 3hr rep3 + dnAP-1


title: NSC-71E


title: OB5d

value: osteoblastogenesis at 5 day


title: OB3d

value: osteoblastogenesis at 3 day


title: AD7d

value: adipogenesis at 7 day


title: AD5d

value: adipogenesis at 5 day


title: NSC-70


title: NSC-71


title: NSC-69


title: NSC-68


title: NSC-65E


title: NSC-65


title: 0d

value: adipogenesis at 0 day


title: NSC-67

value: Human gastric cancer cells


title: NSC-74


title: PS- CD8 T cells patient4

city: Planegg-Martinsried

first: Jan

last: Kranich

address: Grosshadernerstr. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität München

data_processing:
Sequencing reads were aligned to the human reference genome (version GRCH38.100) with STAR (version 2.7.3).
Expression values (TPM) were calculated with RSEM (version 1.3.3).
Post-processing was performed in R/bioconductor (version 4.0.3) using default parameters
Genome_build: GRCH38.100
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: CD8 T cells

extract_protocol:
Peripheral blood was collected into lithium heparin tubes (Sarstedt). PBMCs were isolated by Biocoll density gradient (Merck) centrifugation and then directly stained for FACS sorting. Live, Dump-, C8+,CCR7+CD45RA-, CCR7-CD45RA-, CCR7-CD45RA+, PS+ and PS- were directly sorted into TRIZOL on a FACSAriaFusion (BD) using a 100 μm nozzle. Total RNA was isolated and purified using Monarch columns (NEB). Poly(A)+ RNA was isolated from the total RNA sample.
First-strand cDNA synthesis was primed with a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. In this way, a strand specific PCR amplification of the cDNA was achieved using a proof-reading enzyme. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 250-700 bp was eluted from a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA size range was 250-700 bp. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 1x75 bp read length.

tag: patient diagnosis

value: CD8 T cells

tag: age

tag: patient number

tag: whomax level

value: WHOmax 4

tag: time since first diagnosis

tag: ps status

value: negative


title: PS- CD8 T cells patient3

tag: cell type


title: PS- CD8 T cells patient1

value: WHOmax 3


title: PS- CD8 T cells patient2

value: WHOmax 1


title: NSC-64E


title: PS+ CD8 T cells patient4

value: positive


title: PS+ CD8 T cells patient3


title: NSC-64


title: NSC-63


title: PS+ CD8 T cells patient2


title: NSC-61


title: PS+ CD8 T cells patient1


title: NSC-58


title: NSC-60


title: AD3d

value: adipogenesis at 3 day


title: 287_Tvm_pan-KIR_positive

city: Bilthovem

first: Rob

last: Mariman

address: Antonioe van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

data_processing:
We used an in- house pipeline to analyze the RNA sequencing data. First, reads were mapped to the human reference genome (GRCh38, release 12) using STAR (version 2.6.0) (Dobin et al., 2013). The num-ber of mapped reads were counted for each gene and compiled into an expression matrix using featureCounts (version 1.6.1) (Liao et al., 2014). The count table was used for statistical analysis and identification of DEG using DESeq2 (v1.1) (Love et al., 2014).
Genome_build: GRCh38, release 12
Supplementary_files_format_and_content: .xlsx files with normalized counts

source_name: PBMC

extract_protocol:
FACS- sorted TNAIVE, TEMRA, KIR+RA+, and NKG2A+RA+ T- cell sub-sets of six healthy donors (ages: 30, 57, 61, 63, 65, 66 years) were centrifuged at 485 g for 15 min and lysed in buffer RLT (Qiagen)   containing 1% β- mercaptoethanol. Total RNA was extracted from the cell lysates by using the RNeasy kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed by using the RNA 6000 Pico kit (Agilent Technologies) on a 2100 BioAnalyzer (Agilent Technologies). All RNA Integrity Number (RIN) scores were >7
DNA synthesis and amplification were performed by using the SMART- Seq® v4 Ultra® Low Input RNA kit for sequencing (Takara) and AMPure XP beads (Beckman Coulter) were used to purify the samples. Proper size distribution of the fragments acquired was veri-fied using the High Sensitivity DNA kit (Agilent Technologies). Next, 1 ng of cDNA was used to prepare a Nextera XT DNA library accord-ing to the manufacturer’s instruction (Illumina). Libraries were sub-sequently validated for fragment size using QIAxcel DNA Screening Kit (Qiagen) and quantified using RT- qPCR with a KAPA Library Quantification kit (KK4824, Roche/KAPA Biosystems). 23 librar-ies were pooled at equimolar concentrations and sequenced using the Illumina NextSeq 500/550 High Output Kit v2.5 (single- end, 75 cycles)

value: CD8+ T cell

tag: cell subtype


title: NSC-57E


title: 287_Tvm_NKG2A_positive


title: 287_Temra

value: Temra


title: NSC-66


title: NSC-56


title: 286_Tvm_pan-KIR_positive


title: 286_Tvm_NKG2A_positive


title: NSC-51


title: NSC-50


title: 287_T_naive


title: NSC-49E


title: 286_Temra


title: 284_Tvm_pan-KIR_positive


title: NSC-48E


title: 286_T_naive


title: NSC-49


title: NSC-48


title: 284_Tvm_NKG2A_positive


title: 284_Temra


title: NSC-47E


title: 284_T_naive


title: 281_Tvm_pan-KIR_positive


title: NSC-47


title: 281_Temra


title: NSC-46E


title: 281_Tvm_NKG2A_positive


title: NSC-46


title: NSC-57


title: NSC-44


title: 281_T_naive


title: 279_Tvm_pan-KIR_positive


title: 279_Tvm_NKG2A_positive


title: NSC-39


title: NSC-38


title: 279_Temra


title: NSC-40


title: NSC-37E


title: NSC-37


title: 279_T_naive


title: 278_Tvm_pan-KIR_positive


title: Serum_Zap70Mb1-Cre_Z50 IgM

type: protein

city: POITIERS

first: Mickaël

last: MARTIN

address: 2 rue de la Milétrie

department: Internal Medicine

country: France

institute: Poitiers University Hospital

description: raw data file: Slide2_635.gpr

hyb_protocol: Autoantigen array  protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX

scan_protocol: Genepix Pro 6.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: The net fluorescence intensity for each antigen was calculated by subtracting a PBS control that was included for each experiment as the negative control. The signal-to-noise ratio was used as a quantitative measurement of the ability to resolve the true signal from background noise.

label: 635nm cy5 labeled anti-mouse IgM

molecule: protein

label_protocol: Autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-mouse IgG) and 635 nm (cy5-labeled anti-mouse IgM)

extract_protocol: Sera diluted to 1/10e was used on the autoantigen array

value: 10 months

tag: gender

value: Female

tag: zap70 expression

tag: tissue/sample type

value: serum


title: 278_Temra


title: NSC-35E


title: Serum_Zap70Mb1-Cre_Z49 IgM

description: raw data file: Slide2_635.gpr

tag: strain


title: 278_Tvm_NKG2A_positive


title: NSC-36


title: Serum_Zap70Mb1-Cre_Z40 IgM

description: raw data file: Slide1_635.gpr

value: Male


title: 278_T_naive


title: RNA-Seq Co-culture rep3 + dnAP-1

description:
Co-culture rep3 + dnAP-1
sorted fibroblasts after culture with mouse ESCs overnight with 1mg/ml doxycycline to induce dnAP-1

data_processing:
Default Illumina base calling implementation
RNA-seq reads were mapped to a concatenated genome sequence of human GRCh38/hg38 and mouse GRCm38/mm10 annotations using STAR
transcript abundance was quantified using rsem, reported as transcripts per million (TPM)
Genome_build: hg38/mm10
Supplementary_files_format_and_content: tab-delimited text file, genes in rows, samples in columns. Header at the top delineating samples.

source_name: human fibroblast + mouse ESC co-culture

extract_protocol:
RNEasy purification kit from Qiagen for RNA extraction
Tru-Seq V2 kit according to manufacturer's protocol

value: human lung fibroblast

value: dnAP-1 (Tet-On)


title: Serum_Zap70Mb1-Cre_Z45 IgM

description: raw data file: Slide2_635.gpr


title: NSC-35


title: RNA-Seq Co-culture rep2 + dnAP-1

description:
Co-culture rep2 + dnAP-1
sorted fibroblasts after culture with mouse ESCs overnight with 1mg/ml doxycycline to induce dnAP-1


title: Serum_Zap70Mb1-Cre_Z28 IgM

description: raw data file: Slide1_635.gpr


title: NSC-34


title: RNA-Seq Co-culture rep1 + dnAP-1

description:
Co-culture rep1 + dnAP-1
sorted fibroblasts after culture with mouse ESCs overnight with 1mg/ml doxycycline to induce dnAP-1


title: NSC-32E


title: Serum_Zap70Mb1-Cre_Z24 IgM

description: raw data file: Slide1_635.gpr


title: NSC-32


title: Serum_Zap70Mb1-Cre_Z38 IgM

description: raw data file: Slide1_635.gpr


title: RNA-Seq Co-culture rep2

description:
Co-culture rep2
sorted fibroblasts after culture with mouse ESCs overnight

value: no dnAP-1 (control)


title: NSC-36E

value: Human gastric cancer cells


title: Serum_Zap70+/LSL_C69 IgM

description: raw data file: Slide2_635.gpr

value: Negative


title: Serum_Zap70+/LSL_C61 IgM

description: raw data file: Slide2_635.gpr


title: Serum_Zap70Mb1-Cre_Z62 IgM

description: raw data file: Slide2_635.gpr


title: Serum_Zap70+/LSL_C70 IgM

description: raw data file: Slide2_635.gpr


title: NSC-29


title: Serum_Zap70+/LSL_C30 IgM

description: raw data file: Slide1_635.gpr


title: Serum_Zap70+/LSL_C29 IgM

description: raw data file: Slide1_635.gpr


title: Serum_Zap70Mb1-Cre_Z11 IgM

description: raw data file: Slide1_635.gpr


title: Serum_Zap70+/LSL_C46 IgM

description: raw data file: Slide2_635.gpr


title: Serum_Zap70+/LSL_C37 IgM

description: raw data file: Slide1_635.gpr


title: RNA-Seq Co-culture rep1

description:
Co-culture rep1
sorted fibroblasts after culture with mouse ESCs overnight


title: NSC-28E


title: RNA-Seq Homokaryon

description:
Homokaryon
fibroblast fused to fibroblasts, isolated 3hrs post-fusion

source_name: human fibroblast fusion

value: homokaryon


title: Serum_Zap70+/LSL_C27 IgM

description: raw data file: Slide1_635.gpr


title: Serum_Zap70+/LSL_C23 IgM

description: raw data file: Slide1_635.gpr


title: Serum_Zap70+/LSL_C21 IgM

description: raw data file: Slide1_635.gpr


title: NSC-28


title: Serum_Zap70+/LSL_C12 IgM

description: raw data file: Slide1_635.gpr


title: RNA-Seq Fibroblast rep4

description: Fibroblast rep4

source_name: human fibroblast


title: NSC-26E


title: Serum_Zap70+/LSL_C10 IgM

description: raw data file: Slide1_635.gpr


title: RNA-Seq Fibroblast rep3

description: Fibroblast rep3


title: Serum_Zap70Mb1-Cre_Z50 IgG

description: raw data file: Slide2_532.gpr

label: 532nm cy3 labeled anti-mouse IgG


title: NSC-24E


title: Serum_Zap70Mb1-Cre_Z40 IgG

description: raw data file: Slide1_532.gpr


title: RNA-Seq Fibroblast rep1

description: Fibroblast rep1


title: Serum_Zap70Mb1-Cre_Z38 IgG

description: raw data file: Slide1_532.gpr


title: Serum_Zap70Mb1-Cre_Z49 IgG

description: raw data file: Slide2_532.gpr


title: NSC-24


title: Serum_Zap70Mb1-Cre_Z28 IgG

description: raw data file: Slide1_532.gpr


title: Serum_Zap70Mb1-Cre_Z45 IgG

description: raw data file: Slide2_532.gpr


title: NSC-23E


title: ChIP-Seq input rep1

data_processing:
Default Illumina base calling implementation
Reads were trimmed with cudadapt v 2.8 and processed with ENCODE ChIP-seq pipeline2 v1.3.6
Genome_build: hg38
Supplementary_files_format_and_content: c-Jun ChIP peaks in bed format

growth_protocol: Fibroblasts were grown in 10% FBS + DMEM.

extract_protocol:
Cells were fixed in suspension with 1% formaldehyde. Pellet was hypotonically lysted and chromatin was sheared by sonication. Antibody was added overnight. DNA was isolated with magnetic beads.
Tn5 tranposase was added to tagment the DNA on the beads. PCR was performed on the tagmented DNA to generate ChIP-seq libraries.


title: Serum_Zap70Mb1-Cre_Z11 IgG

description: raw data file: Slide1_532.gpr


title: Serum_Zap70Mb1-Cre_Z24 IgG

description: raw data file: Slide1_532.gpr


title: Serum_Zap70+/LSL_C70 IgG

description: raw data file: Slide2_532.gpr


title: ChiP-Seq c-Jun rep2


title: NSC-23


title: NSC-22


title: Serum_Zap70+/LSL_C69 IgG

description: raw data file: Slide2_532.gpr


title: Serum_Zap70+/LSL_C46 IgG

description: raw data file: Slide2_532.gpr


title: RNA-Seq Fibroblast rep2

description: Fibroblast rep2


title: Serum_Zap70+/LSL_C61 IgG

description: raw data file: Slide2_532.gpr


title: Serum_Zap70Mb1-Cre_Z62 IgG

description: raw data file: Slide2_532.gpr


title: ChiP-Seq c-Jun rep1


title: NSC-26


title: NSC-20E


title: Serum_Zap70+/LSL_C29 IgG

description: raw data file: Slide1_532.gpr


title: NSC-20


title: Serum_Zap70+/LSL_C30 IgG

description: raw data file: Slide1_532.gpr


title: ChIP-Seq input rep2


title: Serum_Zap70+/LSL_C27 IgG

description: raw data file: Slide1_532.gpr


title: Serum_Zap70+/LSL_C23 IgG

description: raw data file: Slide1_532.gpr


title: P24 knockout islets rep1

city: Vancouver

first: Brad

last: Hoffman

state: BC

country: Canada

institute: University of British Columbia

data_processing:
Raw FastQ sequencing files were combined, filtered (phred33) and trimmed to remove adapters with Trimmomatic
Salmon was used to quasi-map, assemble and quantify transcripts using the mouse GRCm38/mm10/VM24 transcriptome
Differential gene expression analysis was performed using DEseq2 in R, with the apeglm algorithm used to shrink log fold changes
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include transcript quantification and differential gene expression changes between control and knockout samples

source_name: Pancreatic islets

extract_protocol:
Islets from 3 control and 3 Dpy30 knockout male mice were isolated at P24 and 100-200 islets per mouse were handpicked into 1 mL of TRIzol reagent (Thermo Fisher Scientific). Extracted RNA was treated with TURBO DNase I (Thermo Fisher Scientific) for 20 minutes at 37°C to remove genomic DNA.
For each sample at P24, mRNA was enriched from 1000 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and 6 cDNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with 9 amplification cycles.

value: Postnatal day 24

tag: genotype

value: Dpy30 knockout


title: P24 knockout islets rep3


title: P24 knockout islets rep2


title: Serum_Zap70+/LSL_C21 IgG

description: raw data file: Slide1_532.gpr


title: NSC-18


title: Serum_Zap70+/LSL_C12 IgG

description: raw data file: Slide1_532.gpr


title: Ycg1Degron2 Heat shock TT-seq replicate 3

city: London

first: Lucy

last: Lancaster

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin, 2011) with parameters “--minimum-length=20 --quality-cutoff=20 -a AGATCGGAAGAGC”.
BWA (version 0.5.9-r16) (Li & Durbin, 2009) using default parameters was used to perform the read mapping independently to both the S. cerevisiae (assembly R64-1-1, release 90) and S. pombe (assembly ASM294v2, release 44) genomes.
Genomic alignments were filtered to only include those that were primary, uniquely mapped, and had fewer than 3 mismatches using BamTools (version 2.4.0; (Barnett et al, 2011)).
Alignments corresponding to the sense and antisense strands were obtained using SAMtools view (version 1.3.1) (Li et al, 2009) by using the flags “-f 16” and “-F 20”, respectively.
Read counts relative to protein coding genes were obtained using the featureCounts tool from the Subread package (version 1.5.1) (Liao et al, 2014). The parameters used were “-O -s 2”.
BedGraph tracks were created using the BEDTools genomeCoverageBed (version 2.26.0) (Quinlan & Hall, 2010) by normalising the genome-wide coverage relative to DESeq2 size factors generated with respect to the S. pombe transcriptome. The parameters used were “-bg -pc -strand <STRAND> -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al, 2010).
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts generated by featureCounts where gene names are rows and columns represent all samples generated in the study.
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown overnight in YNB supplemented with CSM -methionine. Cells were grown at 25°C, shaking at 200 RPM in incubators.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
Total RNA from yeast was cleaned up through column purification through the RNA Cleanup protocol within the RNeasy Mini Kit including DNase digestion (Qiagen). To measure global transcription levels a 4-TU pulsed S. pombe Total RNA was used as a spike-in for all samples, 90μg of sample Total RNA was combined with 10μg of S. pombe Total RNA. Nascent RNA from the samples containing also S. pombe spike-in RNA was isolated using TTchem-seq, this involved biotinylation of chemically fragmented Total RNA, the biotiylated nascent RNA was isolated from the fragmented Total RNA using a bead-based streptavidin pull down. 20 ng of nascent RNA was used to make libraries with the KAPA RNA HyperPrep Kit (Roche). The library was made following the manufacturer’s instructions, with adjustments to ensure small transcripts from the fragmentation were not lost. The ratio of KAPA pure beads to adapter-ligated cDNA was 0.95x in the 1st post-ligation clean up, and 1x in the 2nd post-ligation clean up. Libary quailty was assessed using a Biolanalyzer 2100 (Agilent) and nascent RNA sequencing was carried out on the Illumina HiSeq 4000 platform and typically generated approximately 19 million 76 bp strand- specific single-end reads.
library strategy: TT-seq

treatment_protocol: The control and Ycg1Degron2 were treated identically. To deplete condensin, cells were grown overnight in YNB + CSM -methioninie medium, synchronised from an OD600 of 0.2 in G1 for 2 hours then released into fresh YNB + CSM -methionine medium containing nocodozole for 1.5 hours to achieve a metaphase arrest. Methionine was added at a final concentration of 133μg/ml to shut off the MET3 promoter and indole-acetic acid (IAA, auxin) at a final concentration of 88μg/ml to degrade Ycg1 for 30 minutes. 4-TU was added to the samples at a final concentration of 5mM for 5 minutes before collection from the control and degron strains with and without methionine and auxin treatment. A sample from each strain which had undergone auxin and methionine treatment  was then heat shocked for 15minutes at 37°C for 15 minutes, followed by a 5 minute 4-TU pulse before collection

tag: strain/background

value: W303-1A, Mat a, (K.lactis URA3)pMET3-YCG1-3PK-miniAID::KANMX6, ADE2::pADH1-OsTIR1-9Myc

value: Heat shock + Met + Auxin


title: P24 control islets rep3

value: Control


title: NSC-17


title: Ycg1Degron2 Heat shock TT-seq replicate 2


title: P24 control islets rep2


title: P24 control islets rep1


title: Ycg1Degron2 Met + Auxin TT-seq replicate 2

value: Met + Auxin


title: NSC-16E


title: Ycg1Degron2 Met + Auxin TT-seq replicate 3


title: Serum_Zap70+/LSL_C37 IgG

description: raw data file: Slide1_532.gpr


title: Ycg1Degron2 Untreated TT-seq replicate 3

value: Untreated


title: Ycg1Degron2 Met + Auxin TT-seq replicate 1


title: NSC-16


title: TE #2

city: La Jolla

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

institute: UCSD

description:
2_07H4_00ZRUCSD_TE-2_BRD4_mm_i81
Processed_Chip_seq_D7.bed

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied.
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS2 algorithm (v2.1.0) with a cutoff of pvalue = 1e-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_Chip_seq_D7.bed

source_name: D7 Spleen P14 KLRG1hiCD127lo

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

value: 6-16 Weeks

tag: tissue

value: Spleen

tag: chip antibody

value: BRD4 (Bethyl cat# A301-985A)


title: Ycg1Degron2 Untreated TT-seq replicate 2

tag: treatment


title: TE #1

description:
1_07H3_00ZRUCSD_TE-1_BRD4_mm_i77
Processed_Chip_seq_D7.bed


title: NSC-18E


title: NSC-15E


title: NSC-15


title: Control Heat shock TT-seq replicate 3

value: W303-1A, Mat a, YCG1-3PK::K.lactis TRP1


title: Ycg1Degron2 Untreated TT-seq replicate 1


title: NSC-11E


title: Input

description:
3_07HT_00ZRUCSD_Pooled_Input_mm_i82
Processed_Chip_seq_D7.bed


title: Control Heat shock TT-seq replicate 2


title: Control Met + Auxin TT-seq replicate 3


title: Control Heat shock TT-seq replicate 1


title: Serum_Zap70+/LSL_C10 IgG

description: raw data file: Slide1_532.gpr

value: 10 months

value: Female

value: serum


title: Control Met + Auxin TT-seq replicate 2


title: NSC-11

value: Human gastric cancer cells


title: Ycg1Degron2 Heat shock TT-seq replicate 1


title: NSC-10E


title: NSC-10


title: Sample 120_AB804

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used. (read2 used to read cell and molecule barcodes only)
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: *_metadata_s.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

extract_protocol:
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

value: Bone marrow

value: preDC

tag: selection marker

value: CD45+ Lin−CD172α−CD11c+CD135+

tag: infection

tag: time point

value: 2 weeks

value: MCDD


title: NSC-6E


title: Control Untreated TT-seq replicate 2


title: Ycg1Degron1 M total RNA-Seq biological replicate 3

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li & Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al, 2013) was used for mapping and subsequent gene-level counting of the sequenced reads with respect to all S. cerevisiae genes downloaded from the Ensembl genome browser (assembly R64-1-1, release 90). ERCC spike-in sequences were appended to the genome fasta and GTF annotation for quantification. The parameters used were “--star-output-genome-bam --star-gzipped-read-file --forward-prob 0”, and all other parameters were kept as default.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al, 2014) within the R programming environment. A false discovery rate of 0.05 or less was used as the significance threshold for the identification of differentially expressed genes. The counts corresponding to total and polyA were normalised individually and together, omitting genes with names ending in ‘rRNA’ or ‘RDN’ as were ERCC spike-ins.
Genome_build: Ensembl R64-1-1 release 90
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
Total RNA from yeast was cleaned up through column purification through the RNA Cleanup protocol within the RNeasy Mini Kit including DNase digestion (Qiagen) prior to sequencing library preparation. For total RNA-Seq libraries, the library was contructed with KAPA RNA HyperPrep kit without the riboerase treatment. The polyA RNA-seq libraries were contructed using the KAPA mRNA HyperPrep kit according to the manufacturer's instructions. Library quality control was performed using the Agilent 2200 TapeStation with D1000 screentape (Agilent Technologies). RNA sequencing was carried out on the Illumina HiSeq 4000 platform and typically generated approximately 18 million 76 bp strand-specific single-end reads per sample.

treatment_protocol: The control and Ycg1Degron1 were treated identically. To deplete condensin log phase cells at OD600 0.2 were arrested in G1 for 1.5 hours, the cells were transitioned into YPD + IAA to deplete condensin for 2 hours and samples taken. The cells were released into fresh YPD with IAA and nocodozole for a metaphse arrest, where a second sample was taken after 2 hours.

value: W303-1A, Mat a, (K.lactis URA3)pMET3-YCG1-3PK-3miniAID::KANMX6, ADE2::pADH1-OsTIR1-9Myc

value: Release into nocodozole for a metaphase arrest for 2 hours, maintained in YPD + IAA


title: Sample 117_AB801

value: ND


title: Sample 118_AB802


title: Ycg1Degron1 M total RNA-Seq biological replicate 1


title: Ycg1Degron1 M total RNA-Seq biological replicate 2


title: Sample 119_AB803


title: NSC-6


title: Control Met + Auxin TT-seq replicate 1

value: Met + Auxin


title: Ycg1Degron1 G1 total RNA-Seq biological replicate 2

value: Alpha factor treatment for G1 arrest, transition fom YNB + CSM to YPD + IAA for 2 hours


title: Sample 115_AB799

value: liver


title: Sample 116_AB800


title: Ycg1Degron1 G1 total RNA-Seq biological replicate 1


title: Ycg1Degron1 G1 total RNA-Seq biological replicate 3


title: NSC-4E


title: Control (Ycg1-3PK)  M total RNA-Seq biological replicate 3


title: Control (Ycg1-3PK)  M total RNA-Seq biological replicate 1


title: Sample 114_AB798


title: Control Untreated TT-seq replicate 3

value: Untreated


title: NSC-4


title: Control (Ycg1-3PK)  M total RNA-Seq biological replicate 2

value: W303-1A, Mat a, YCG1-3PK::K.lactis TRP1


title: Control (Ycg1-3PK)  G1 total RNA-Seq biological replicate 3


title: Control (Ycg1-3PK)  G1 total RNA-Seq biological replicate 2


title: Sample 113_AB797


title: NSC-71-2-H3K27ac

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to GRCh37 whole genome using Burrows - Wheeler Aligner  v0.7.17.
Duplicates were removed using the samtools rmdup, and replicate experiments were merged using samtools merge.
Peaks were called using MACS2 (version 2.0).
Genome_build: GRCh37
Supplementary_files_format_and_content: peak bed files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

tag: cell types

value: H3K27ac (D5E4, Cell Signaling Technology)


title: Control Untreated TT-seq replicate 1


title: Sample 112_AB796

value: cDC


title: Control (Ycg1-3PK)  G1 total RNA-Seq biological replicate 1


title: Sample 111_AB795


title: NSC-71-1-H3K27ac


title: Ycg1Degron1 M polyA RNA-Seq biological replicate 2


title: NSC-70-2-H3K27ac


title: Ycg1Degron1 M polyA RNA-Seq biological replicate 3


title: NSC-70-1-H3K27ac


title: Sample 110_AB794


title: Ycg1Degron1 G1 polyA RNA-Seq biological replicate 3


title: NSC-69-2-H3K27ac


title: Ycg1Degron1 G1 polyA RNA-Seq biological replicate 1


title: Ycg1Degron1 G1 polyA RNA-Seq biological replicate 2


title: Sample 108_AB2642

source_name: mDC  stain + index _MCDD1.2


title: Control (Ycg1-3PK)  M polyA RNA-Seq biological replicate 2


title: Control (Ycg1-3PK)  M polyA RNA-Seq biological replicate 1


title: NSC-69-1-H3K27ac


title: Control (Ycg1-3PK)  G1 polyA RNA-Seq biological replicate 2


title: Control (Ycg1-3PK)  G1 polyA RNA-Seq biological replicate 3


title: NSC-68-2-H3K27ac


title: Control (Ycg1-3PK)  M polyA RNA-Seq biological replicate 3


title: Control (Ycg1-3PK)  G1 polyA RNA-Seq biological replicate 1


title: NSC-68-1-H3K27ac


title: Sample 105_AB2639

source_name: mDC  stain + index _ND1.1


title: NSC-67-2-H3K27ac


title: Ycg1Degron1 M polyA RNA-Seq biological replicate 1


title: RiSQ056_rnh201_YPD_2_mock_Bg

city: Bunkyo-ku

first: Tetsushi

last: Iida

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: rnh201_YPD_control_replicate2_Fw.bedgraph
processed data file: rnh201_YPD_control_replicate2_Rv.bedgraph

data_processing:
library strategy: RiSQ-seq
Basecalls performed using Real Time Analysis (RTA) 1.18.42
Background reads and rNMP reads were mapped to EF4.68 assembly using bowtie 1.0.0 with paired-end mapping.
Mapped pair reads (SAM) were converted to fragments and rNMP position (BED) by AWK scripts.
PCR-amplified reads were also converted to rNMP position (BED) by AWK scripts, and adjusted to PCR-free library scale.
Compute read coverage to single-base bin files using bedtools 2.24.0.
rNMP detection efficiency of each sample preparation was estimated from spiked-in standards by linear regression model using R 3.2.1 (lm).
rNMP accumulation level at each  42 base bin was estimated by normalization of total rNMP counts by total background counts with spiked-in standard adjustment.
For nuclear genome, rNMP reads were from PCR-amplified reads adjusted to PCR-free scale.
Genome_build: S. cerevisiae, S288C genome, EF4.68
Supplementary_files_format_and_content: Bedgraph files include rNMP accumlation level, damage per million (dpm); BED file includes biased mapping region with abberant score of rNMP level by mapping bias.

organism: Saccharomyces cerevisiae BY4741

source_name: MAT a G1 arrested yeast cells

growth_protocol: Yeast strains were exponentially grown in two flasks of 500ml 1% Bacto Yeast Extract (BD), 2% Bacto Peptone and 2% Glucose (Wako) (YPD) or low glucose media with 0.05% Glucose (CR) around 1x10^7 cells/ml and arrested cell-cycle by addition of alpha-factor at final concentration 5 ug/ml for 2.5 hour at 30C with shaking (222 rpm) in INNOVA43 shaker.

extract_protocol:
Yeast spheloplasts were lysed in pre-warmed lysis buffer (50 mM Tris-Cl pH7.5, 0.2 M NaCl, 0.1 M EDTA, 5% SDS) at 65°C by gentle pipetting and inversions. After phenol-chloroform extraction twice, nucleic acids were precipitated with twice volume of 99% ethanol, and the precipitates were rinsed with 70% ethanol. Dried nucleic acids were treated by RNase A (Wako) in 500 µl of RNase buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 0.5 mg/ml RNase A) at 37°C for 2 h. After phenol-chloroform extraction twice, genomic DNAs were purified by ethanol precipitation.
RiSQ-seq was performed with sheared genomic DNAs. Ten µg of total DNA was sheared in microTUBE (Covaris) by Covaris M220 (peak power 140W, duty factor 10%, cycle/burst 200 and duration 1 minute). Agarose-gel purified DNA (400-450 bp range) was end-repaired by KAPA library preparation kit for Illumina (Kapa Biosystems) supplement with 2 mM ATP and 2.5 mM dNTP. One µg of the size-selected DNA and  25ng of spike-in standard cocktail were used for a primary library. Pre-primary library was prepared by KAPA library preparation kit and Illumina TruSeqHT-compatible adaptors (IDT). Free 3'-OH ends of the pre-primary library were masked by terminal deoxynucleotidyl transferase (Takara) with 0.25 mM ddNTP (Roche) for 1 hour at 37°C. The fully ligated library was purified by size-selection with agarose-gel electrophoresis (primary library). For RNaseH-digested samples, 100 ng of the primary library was digested using 1xThermoPol reaction buffer, 3.75 units of RNase H and RNase HII (New England Biolabs) overnight (18 hours) at 37°C. Thirty ng of the primary library with or without RNaseH digestion was heat denatured at 100°C for 3 minutes and chilled at 0°C for 5 minutes. The denatured library was incubated with 10 µM of 701ss adaptor and 750 units of T4 DNA ligase (Kapa Biosystems) overnight (12 hours) at 20°C for secondary-adaptor ligation. After three times of library purification with AMPureXP beads (Beckman Coulter), complementary strand of the libraries were synthesized in 25 µl reaction mixture with 16 units of BstPolymerase LF, 1xThermoPol reaction buffer (New England Biolabs), 0.25 mM dNTP and 4µM of TruHTAmp7Rv primer at 65°C for 10 minutes. The size-selected libraries were directly used for paired-end sequencing by MiSeq sequencer (Illumina) to identify location of fragments and 3'-end of nicks generated with or without RNaseH treatment. For PCR-amplified sample, 5 ng of the double-stranded libraries were amplified using 5 µM of primers TruHTAmp5Fw and TruHTAmp701allSRv, using KAPA real time library amplification kit (Kapa Biosystems). Libraries were then purified with AMPureXP beads (target range over 300 bp) and sequenced as PCR-amplified samples.

tag: mating type

value: MATa

tag: genotype/variation

value: Rnh201Delta yeast strain

tag: cell cycle

value: G1-arrested by alpha factor

tag: treatment group

value: mock treatment without RNaseH


title: RiSQ055_WT_YPD_2_mock_Nick_PCR

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: WT_YPD_control_replicate2_Fw.bedgraph
processed data file: WT_YPD_control_replicate2_Rv.bedgraph

value: Parental WT yeast strain


title: RiSQ057_rnh201_YPD_2_mock_Nick


title: Sample 104_AB2638

source_name: cDC1/2 stain + index _MCDD1.2

tag: cell type

value: 2 weeks


title: RiSQ058_rnh201_YPD_2_mock_Nick_PCR


title: Sample 109_AB793


title: RiSQ054_WT_YPD_2_mock_Nick


title: NSC-67-1-H3K27ac

source_name: Human gastric cancer cells

value: Human gastric cancer cells


title: RiSQ053_WT_YPD_2_mock_Bg


title: Sample 103_AB2637

source_name: cDC1/2 stain + index _MCDD1.1

value: MCDD


title: NSC-66-2-H3K27ac


title: Sample 102_AB2636

source_name: cDC1/2 stain + index _ND1.2


title: NSC-66-1-H3K27ac


title: Sample 107_AB2641

source_name: mDC  stain + index _MCDD1.1


title: Sample 106_AB2640

source_name: mDC  stain + index _ND1.2


title: RiSQ033_rnh201_CR_1_RH_rNMP_PCR

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 13 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_CR_replicate1_Fw.bedgraph
processed data file: rnh201_CR_replicate1_Rv.bedgraph

value: RNaseH digestion


title: RiSQ034_rnh201_CR_2_RH_Bg

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_CR_replicate2_Fw.bedgraph
processed data file: rnh201_CR_replicate2_Rv.bedgraph


title: RiSQ036_rnh201_CR_2_RH_rNMP_PCR

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 13 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_CR_replicate2_Fw.bedgraph
processed data file: rnh201_CR_replicate2_Rv.bedgraph


title: NSC-65-2-H3K27ac


title: Sample 100_AB261

source_name: 4 weeks MCDD2.5

value: CD45+ Immune cells

value: 4 weeks


title: RiSQ031_rnh201_CR_1_RH_Bg

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_CR_replicate1_Fw.bedgraph
processed data file: rnh201_CR_replicate1_Rv.bedgraph


title: RiSQ032_rnh201_CR_1_RH_rNMP

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_CR_replicate1_Fw.bedgraph
processed data file: rnh201_CR_replicate1_Rv.bedgraph


title: NSC-65-1-H3K27ac


title: Sample 99_AB260

source_name: 4 weeks MCDD2.4


title: RiSQ030_rnh201_CR_1_mock_Nick_PCR

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: rnh201_CR_control_replicate1_Fw.bedgraph
processed data file: rnh201_CR_control_replicate1_Rv.bedgraph


title: RiSQ029_rnh201_CR_1_mock_Nick

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, nick-detection sample
processed data file: rnh201_CR_control_replicate1_Fw.bedgraph
processed data file: rnh201_CR_control_replicate1_Rv.bedgraph


title: NSC-64-2-H3K27ac


title: RiSQ027_rnh201_YPD_2_RH_rNMP_PCR

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 14 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_YPD_replicate2_Fw.bedgraph
processed data file: rnh201_YPD_replicate2_Rv.bedgraph


title: RiSQ028_rnh201_CR_1_mock_Bg

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_CR_control_replicate1_Fw.bedgraph
processed data file: rnh201_CR_control_replicate1_Rv.bedgraph


title: Sample 97_AB258

source_name: 4 weeks MCDD2.2


title: RiSQ035_rnh201_CR_2_RH_rNMP

description:
Rnh201Delta yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_CR_replicate2_Fw.bedgraph
processed data file: rnh201_CR_replicate2_Rv.bedgraph


title: NSC-63-2-H3K27ac


title: RiSQ025_rnh201_YPD_2_RH_Bg

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_YPD_replicate2_Fw.bedgraph
processed data file: rnh201_YPD_replicate2_Rv.bedgraph


title: RiSQ026_rnh201_YPD_2_RH_rNMP

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_YPD_replicate2_Fw.bedgraph
processed data file: rnh201_YPD_replicate2_Rv.bedgraph


title: Sample 101_AB2635

source_name: cDC1/2 stain + index _ND1.1

value: ND


title: NSC-64-1-H3K27ac


title: NSC-63-1-H3K27ac


title: RiSQ023_rnh201_YPD_1_RH_rNMP

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_YPD_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_replicate1_Rv.bedgraph


title: RiSQ024_rnh201_YPD_1_RH_rNMP_PCR

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 14 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: rnh201_YPD_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_replicate1_Rv.bedgraph


title: Sample 96_AB257

source_name: 4 weeks MCDD1.5

value: liver


title: Sample 95_AB256

source_name: 4 weeks MCDD1.4


title: NSC-61-2-H3K27ac


title: RiSQ021_rnh201_YPD_1_mock_Nick_PCR

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: rnh201_YPD_control_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_control_replicate1_Rv.bedgraph


title: RiSQ022_rnh201_YPD_1_RH_Bg

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_YPD_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_replicate1_Rv.bedgraph


title: NSC-61-1-H3K27ac


title: RiSQ018_WT_CR_2_RH_rNMP_PCR

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 10 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_CR_replicate2_Fw.bedgraph
processed data file: WT_CR_replicate2_Rv.bedgraph


title: RiSQ020_rnh201_YPD_1_mock_Nick

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, nick-detection sample
processed data file: rnh201_YPD_control_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_control_replicate1_Rv.bedgraph


title: NSC-60-2-H3K27ac


title: RiSQ017_WT_CR_2_RH_rNMP

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_CR_replicate2_Fw.bedgraph
processed data file: WT_CR_replicate2_Rv.bedgraph


title: RiSQ016_WT_CR_2_RH_Bg

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_CR_replicate2_Fw.bedgraph
processed data file: WT_CR_replicate2_Rv.bedgraph


title: Sample 94_AB255

source_name: 4 weeks MCDD1.3


title: Sample 92_AB253

source_name: 4 weeks ND2.5


title: Sample 93_AB254

source_name: 4 weeks MCDD1.2


title: RiSQ015_WT_CR_1_RH_rNMP_PCR

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 10 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_CR_replicate1_Fw.bedgraph
processed data file: WT_CR_replicate1_Rv.bedgraph


title: Sample 98_AB259

source_name: 4 weeks MCDD2.3


title: NSC-60-1-H3K27ac


title: RiSQ014_WT_CR_1_RH_rNMP

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_CR_replicate1_Fw.bedgraph
processed data file: WT_CR_replicate1_Rv.bedgraph

source_name: MAT a G1 arrested yeast cells


title: Sample 91_AB252

source_name: 4 weeks ND2.4


title: RiSQ011_WT_CR_1_mock_Nick

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, nick-detection sample
processed data file: WT_CR_control_replicate1_Fw.bedgraph
processed data file: WT_CR_control_replicate1_Rv.bedgraph


title: Sample 90_AB251

source_name: 4 weeks ND2.3


title: NSC-58-1-H3K27ac

source_name: Human gastric cancer cells


title: NSC-58-2-H3K27ac


title: Sample 89_AB250

source_name: 4 weeks ND2.2


title: NSC-57-2-H3K27ac


title: RiSQ013_WT_CR_1_RH_Bg

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_CR_replicate1_Fw.bedgraph
processed data file: WT_CR_replicate1_Rv.bedgraph


title: RiSQ008_WT_YPD_2_RH_rNMP

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_YPD_replicate2_Fw.bedgraph
processed data file: WT_YPD_replicate2_Rv.bedgraph


title: RiSQ010_WT_CR_1_mock_Bg

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_CR_control_replicate1_Fw.bedgraph
processed data file: WT_CR_control_replicate1_Rv.bedgraph


title: RiSQ007_WT_YPD_2_RH_Bg

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_YPD_replicate2_Fw.bedgraph
processed data file: WT_YPD_replicate2_Rv.bedgraph


title: RiSQ009_WT_YPD_2_RH_rNMP_PCR

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 2, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 12 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_YPD_replicate2_Fw.bedgraph
processed data file: WT_YPD_replicate2_Rv.bedgraph


title: Sample 88_AB249

source_name: 4 weeks ND1.4


title: RiSQ006_WT_YPD_1_RH_rNMP_PCR

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second-index adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 12 cycles, sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph


title: NSC-57-1-H3K27ac


title: Sample 87_AB248

source_name: 4 weeks ND1.2


title: RiSQ005_WT_YPD_1_RH_rNMP

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, rNMP-detection sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph


title: NSC-56-2-H3K27ac


title: NSC-56-1-H3K27ac


title: Sample 85_AB246

source_name: 2 weeks MCDD1.3


title: RiSQ003_WT_YPD_1_mock_Nick_PCR

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph


title: RiSQ002_WT_YPD_1_mock_Nick

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index adaptor ligation, complementary-strand synthesis, PCR-free sequencing, secondary index fraction, nick-detection sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph


title: RiSQ001_WT_YPD_1_mock_Bg

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph


title: RiSQ012_WT_CR_1_mock_Nick_PCR

description:
Parental yeast strain, YP-0.05% Dextrose culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, secondary-indexed library amplification by PCR reaction 16 cycles, sequencing, secondary index fraction, nick-detection sample
processed data file: WT_CR_control_replicate1_Fw.bedgraph
processed data file: WT_CR_control_replicate1_Rv.bedgraph


title: Sample 84_AB245

source_name: 2 weeks ND2.3


title: NSC-51-1-H3K27ac


title: RiSQ019_rnh201_YPD_1_mock_Bg

description:
Rnh201Delta yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, mock treatment without RNaseH, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: rnh201_YPD_control_replicate1_Fw.bedgraph
processed data file: rnh201_YPD_control_replicate1_Rv.bedgraph


title: NSC-50-2-H3K27ac


title: Sample 83_AB244

source_name: 2 weeks ND1.3


title: 73_K30_V1

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38 Ensemble release 86)  genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: GRCh38 Ensemble release 86: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ectocervical tissue biopsies

extract_protocol:
Total RNA was purified using the Qiagen RNeasy Micro Kit
cDNA was generated using the Clontech SMARTseq v4 Ultra Low Input kit and libraries were prepared for sequencing using the Illumina NexteraXT DNA kit

tag: subjectid

tag: locationcode

value: K

tag: visit

tag: bv

value: T


title: NSC-50-1-H3K27ac

value: H3K27ac (D5E4, Cell Signaling Technology)


title: 70_K27_V3

value: F


title: 72_K28_V3


title: Sample 82_AB243

source_name: 8 weeks ND2.5

tag: strain

value: 8 weeks


title: 71_K28_V1


title: RiSQ004_WT_YPD_1_RH_Bg

description:
Parental yeast strain, YPD culture G1-arrested by alpha factor replicate 1, extract DNA, Covaris shearing, spike-in standard fragments addition, TruSeqHT-compatible adaptor ligation, 3'OH masking by TdT and ddNTP, RNaseH digestion, heat denatured library, second index-adaptor ligation, complementary-strand synthesis, PCR-free sequencing, primary index fraction, background sample
processed data file: WT_YPD_control_replicate1_Fw.bedgraph
processed data file: WT_YPD_control_replicate1_Rv.bedgraph

value: MATa


title: 68_K26_V3


title: 69_K27_V1


title: 66_K25_V3


title: 65_K25_V1


title: Sample 81_AB242

source_name: 8 weeks ND1.5

tag: tissue


title: Sample 86_AB247

source_name: 2 weeks MCDD2.3


title: 74_K30_V3


title: 64_K24_V3


title: 63_K24_V1


title: Sample 79_AB240

source_name: 8 weeks MCDD1.3


title: 67_K26_V1


title: 62_K23_V3


title: NSC-48-2-H3K27ac

tag: chip antibody


title: Sample 80_AB241

source_name: 8 weeks MCDD2.3


title: 61_K23_V1


title: Sample 78_AB239

source_name: 8 weeks ND2.3


title: NSC-48-1-H3K27ac


title: 60_K22_V3


title: 59_K22_V1


title: Sample 77_AB238

source_name: 8 weeks ND1.3


title: 58_K16_V3


title: NSC-47-2-H3K27ac


title: NSC-47-1-H3K27ac


title: 57_K16_V1


title: 56_K14_V3


title: Sample 76_AB214

source_name: 8 weeks MCDD2.5


title: Sample 75_AB213

source_name: 8 weeks MCDD1.5


title: NSC-46-2-H3K27ac

source_name: Human gastric cancer cells


title: NSC-49-2-H3K27ac


title: NSC-49-1-H3K27ac


title: 55_K14_V1


title: 54_K13_V3


title: NSC-46-1-H3K27ac


title: 53_K13_V1


title: 52_K09_V3


title: Sample 74_AB195

source_name: 8 weeks MCDD2.2


title: 51_K09_V1


title: Sample 73_AB194

source_name: 8 weeks MCDD1.2


title: 50_K08_V3


title: NSC-44-2-H3K27ac


title: Sample 72_AB193

source_name: 8 weeks ND2.2


title: 48_K07_V3


title: NSC-44-1-H3K27ac


title: Sample 71_AB192

source_name: 8 weeks ND1.2


title: 47_K07_V1


title: NSC-40-2-H3K27ac


title: 46_K05_V3


title: 45_K05_V1


title: NSC-40-1-H3K27ac


title: Sample 70_AB191

source_name: 8 weeks MCDD2.1


title: 41_K01_V1


title: 42_K01_V3


title: 44_K03_V3


title: NSC-51-2-H3K27ac


title: NSC-39-2-H3K27ac


title: Sample 69_AB190

source_name: 8 weeks MCDD1.1


title: 40_P34_V3

source_name: Ectocervical tissue biopsies

value: P


title: NSC-38-2-H3K27ac


title: Sample 68_AB189

source_name: 8 weeks ND2.1


title: 38_P31_V3


title: 39_P34_V1


title: NSC-39-1-H3K27ac


title: 37_P31_V1


title: NSC-38-1-H3K27ac


title: 35_P30_V1


title: 36_P30_V3


title: 49_K08_V1


title: 32_P27_V3


title: NSC-37-1-H3K27ac


title: 30_P24_V3


title: 31_P27_V1


title: 28_P23_V3


title: NSC-37-2-H3K27ac


title: NSC-36-2-H3K27ac


title: NSC-35-2-H3K27ac


title: 29_P24_V1


title: 26_P22_V3


title: NSC-36-1-H3K27ac


title: 27_P23_V1


title: NSC-35-1-H3K27ac


title: 34_P29_V3


title: 33_P29_V1


title: 23_P21_V1


title: 22_P20_V3


title: Sample 65_AB186

source_name: 2 weeks  MCDD2.1


title: Sample 62_AB183


title: Sample 63_AB184

source_name: 2 weeks  ND1.2


title: Sample 64_AB185

source_name: 2 weeks  ND2.2


title: Sample 67_AB188

source_name: 8 weeks ND1.1


title: 24_P21_V3


title: Sample 60_AB181

source_name: 2 weeks  ND2.1


title: NSC-34-2-H3K27ac


title: 21_P20_V1


title: Sample 59_AB180

source_name: 2 weeks  ND1.1


title: Sample 66_AB187

source_name: 2 weeks  MCDD2.2


title: Sample 61_AB182

source_name: 2 weeks  MCDD1.1


title: 20_P18_V3


title: 25_P22_V1


title: NSC-34-1-H3K27ac

source_name: Human gastric cancer cells


title: 19_P18_V1


title: 18_P12_V3


title: 16_P11_V3


title: NSC-32-1-H3K27ac


title: 15_P11_V1


title: 14_P09_V3


title: NSC-29-2-H3K27ac


title: Sample 56_AB177

source_name: 2 weeks ND2.5


title: 13_P09_V1


title: Sample 55_AB176

source_name: 2 weeks ND1.5


title: 10_P07_V3


title: Sample 58_AB179

source_name: 2 weeks MCDD2.5


title: NSC-29-1-H3K27ac


title: 9_P07_V1


title: 8_P06_V3


title: 12_P08_V3


title: NSC-28-2-H3K27ac


title: Sample 57_AB178

source_name: 2 weeks MCDD1.5


title: 7_P06_V1


title: 11_P08_V1


title: 6_P04_V3


title: NSC-26-2-H3K27ac


title: 5_P04_V1


title: NSC-32-2-H3K27ac


title: Sample 53_AB174

source_name: 4 weeks MCDD 1.1


title: Sample 51_AB172

source_name: 4 weeks ND 1.1


title: Sample 50_AB144

source_name: 8 weeks MCDD2.6


title: Sample 54_AB175

source_name: 4 weeks MCDD 1.2


title: Sample 52_AB173

source_name: 4 weeks ND 1.2


title: 4_P02_V3

source_name: Ectocervical tissue biopsies


title: NSC-26-1-H3K27ac


title: NSC-24-2-H3K27ac


title: NSC-28-1-H3K27ac


title: 3_P02_V1


title: 1_P01_V1


title: 17_P12_V1


title: 2_P01_V3


title: NSC-24-1-H3K27ac


title: NSC-23-2-H3K27ac


title: Sample 48_AB142

source_name: 8 weeks ND2.6


title: Sample 47_AB141

source_name: 8 weeks ND1.6


title: Abdominal aorta DKO2

city: Shanghai

first: hengyuan

last: zhang

address: 160 Pu Jian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Libraries were sequenced on the Illumina sequencing platform (Illumina HiSeq X Ten) and 125 bp/150 bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic, then mapped with the designated reference genome GRCm38.p6 using hisat2
The number of reads mapped to the protein-coding gene in each sample was obtained Using htseq-count software, and the FPKM value of protein-coding gene expression was calculated using cufflinks software.
Differentially expressed genes (DEGs) were identified using the DESeq R package functions to estimate Size Factors and nbinomTest.
Genome_build: GRCm38.p6

source_name: Abdominal aorta

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.RNA quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: 8 weeks ApoE-/- and ApoE-/-Nur77-/- male mice were exposed to Ang II for up to 28 days

value: Abdominal aorta

tag: age

tag: genotype

tag: treatment

value: exposed to Ang II for up to 28 days

tag: gender

value: male


title: Abdominal aorta DKO4


title: Abdominal aorta DKO3


title: Sample 45_AB139

source_name: 2 weeks MCDD1.6

tag: selection marker

tag: infection

tag: time point

value: 2 weeks


title: Sample 46_AB140

source_name: 2 weeksMCDD2.6

value: MCDD


title: Abdominal aorta DKO1


title: NSC-23-1-H3K27ac

tag: cell types

value: Human gastric cancer cells


title: Sample 44_AB138

source_name: 2 weeks ND2.6

value: CD45+ Immune cells


title: NSC-22-2-H3K27ac

source_name: Human gastric cancer cells


title: Abdominal aorta ApoE2

value: ApoE-/-


title: Abdominal aorta ApoE3


title: Abdominal aorta ApoE1


title: WT3

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

institute: Universitätsklinikum Erlangen

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the GRCM38 mouse genome with STAR 2.5.4b
Gene-wise counts were generated with featureCounts 1.6.4
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Combined table with summarized gene-wise counts for each sample generated with featureCounts

source_name: Bone Marrow Plasma Cell

extract_protocol:
Plasma cells were FACS-purified from bone marrow (CD138+ TACI+) and sorted directly into Trizol (Qiagen) Lysis reagent. Total RNA was isolated with the miRNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Low input kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

value: wild type

value: bone marrow plasma cells (TACI+ CD138+)


title: WT2


title: NSC-22-1-H3K27ac


title: NSC-20-2-H3K27ac


title: Sample 49_AB143

source_name: 8 weeks MCDD1.6

value: liver


title: miR148a-gKO1


title: miR148a-gKO2


title: Sample 42_AB1095

source_name: MCDD2 blood cDC

value: Blood

value: cDC


title: NSC-20-1-H3K27ac

value: H3K27ac (D5E4, Cell Signaling Technology)


title: WT1


title: Sample 41_AB1094

source_name: MCDD1 blood cDC


title: NSC-18-2-H3K27ac


title: NSC-18-1-H3K27ac