title: globular-seed-input replicate 2

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

description: Whole seeds 1.0 - 1.5 mm in length were collected

data_processing:
Basecalls performed using RTA3 version 3.4.4
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2

organism: Glycine max

source_name: Soybean seeds containing globular stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10ug of polyclonal antibody raised against GmWOX9-like peptide NHHTPTSLPQTATTA in rabbit. Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Whole seeds were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

tag: developmental stage

value: globular stage

value: whole seeds

tag: antibody


status: Public on Jul 02 2020

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description:
genomic DNA methylation from mouse3586-bloodQ175
3586-blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: cy3, cy5

molecule: genomic DNA

organism: Mus musculus

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from mouse tissue

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: strain background

tag: age

tag: Sex

value: F

tag: genotype

tag: tissue

value: Blood


description:
genomic DNA methylation from mouse3695-bloodWT
3695-blood

value: M

value: WT


title: RNA-seq on GSKLSD1 treated murine leukemia cells-1

type: SRA

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description:
GSK1
processed data file: GSKRUX_normcounts.txt

library_source: transcriptomic

data_processing:
Raw reads were trimmed with BBDuk and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GSKRUX_normcounts.txt: Tab-delimited text file includes gene names and normalized counts.

molecule: total RNA

source_name: Bone marrow

growth_protocol: CEBPA/CSF3R murine leukemia cells were cultured in IMDM +20% FBS.

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen).
Libraries were constructed by BGI.

treatment_protocol: Cells were treated with DMSO, 50 nM Ruxolitinib, 2 nM GSK-LSD1 or the combination for 24 hours.

tag: strain/background

value: BALB/c

tag: cell type

value: CEBPA/CSF3R leukemia cells

tag: treatment


title: globular-seed-WOX9-like-ChIP replicate 2

library_source: genomic

value: anti-peptide GmWOX9-like


title: VN21

city: Ann Arbor

first: Jeffrey

last: Kidd

state: Michigan

address: 1241 Catherine St

institute: University of Michigan

hyb_protocol: Hybridization buffer and components recommended by Agilent were mixed with samples and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridization oven according to manufacturer’s instructions. After hybridization, slides were washed sequentially according to manufaturer’s instructions.

scan_protocol: Scanned on an NimbleGen MS 200 Microarray Scanner with multi TIFF option and 2um resolution Images were quantified using Agilent Feature Extraction Software 12.0.2.2.

data_processing: Agilent Feature Extraction Software 12.0.2.2 was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

label_protocol: 1ug of gDNA was labeled using the direct method without restriction digest according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: gDNA was extracted with phenol chloroform methods or DNeasy Blood & Tissue Kits (Qiagen, Germantown, MD)

treatment_protocol: not applicable

value: lymphocytes

tag: breed

value: Great Dane Zoey


title: VN59


title: RNA-seq on ruxolitinib treated murine leukemia cells-2

description:
RUX2
processed data file: GSKRUX_normcounts.txt

value: Ruxolitinib


description:
genomic DNA methylation from mouse3714-bloodWT
3714-blood


title: pmrA HH800

city: New Haven

first: Alexandre

last: Duprey

state: CT

address: 295 congress avenue

department: Microbial pathogenesis

institute: Yale university

description:
HH800 medium
16

data_processing:
Alignment to reference genome using bowtie 2.2.9
Differential expression analysis using cuffdiff (from cufflinks 2.2.1)
Filtering of irrelevant columns (R 3.5.2)
Genome_build: CP001363.1
Supplementary_files_format_and_content: Tab-delimited file including FPKM values for all genes

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Pure culture

growth_protocol: Cells were grown in HH (N-minimal medium supplemented with 10 mM MgCl2, 0.1% casamino acids, 0.27% glycerol, and adjusted to pH 7.7), HH800 (same as HH but with 800 μM MgCl2), or LB at 37°C.

extract_protocol:
RNA was extracted using a QIAGen RNeasy Mini kit. In addition to the included DNase treatment in the kit, DNA was further eliminated by treatment by turbo DNase (Ambion). RNA was finally re-purified using a QIAGen RNeasy Mini kit. rRNA was depleted using a RiboZero kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown until OD600= 0.8 ± 0.1. Some samples were subjected to additional treatment as described in the sample table.

tag: strain

value: 14028s pmrA


title: IN29


title: RNA-seq on ruxolitinib treated murine leukemia cells-1

description:
RUX1
processed data file: GSKRUX_normcounts.txt


description:
genomic DNA methylation from mouse3523-bloodWT
3523-blood


title: speE-oat HH800

description:
HH800 medium
15

value: 14028s speE oat


description:
genomic DNA methylation from mouse3538-bloodQ175
3538-blood


title: WT LB

description:
LB medium
13


title: NGSD3


description:
genomic DNA methylation from mouse3527-bloodQ175
3527-blood


title: WT HH800 NaCl

description:
HH800 medium with 300 μM NaCl
12


title: RNA-seq on DMSO treated murine leukemia cells-1

description:
DMSO1
processed data file: GSKRUX_normcounts.txt

value: DMSO


title: VN4


title: RNA-seq on GSKLSD1 treated murine leukemia cells 3

description:
GSK3
processed data file: LSD1i_normed_counts.txt

data_processing:
Raw reads were trimmed with BBDuk and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: LSD1i_normed_counts.txt: Tab-delimited text file includes gene names and normalized counts.

treatment_protocol: Cells were treated with DMSO or 4 nM GSK-LSD1 for 48 hours.


description:
genomic DNA methylation from mouse3640-bloodQ175
3640-blood


description:
genomic DNA methylation from mouse3510-bloodWT
3510-blood


title: WT HH + Fe

description:
HH medium with 100 μM FeSO4
11


title: ID137


title: WT HH800

description:
HH800 medium
10


title: RNA-seq on GSKLSD1 treated murine leukemia cells 2

description:
GSK2
processed data file: LSD1i_normed_counts.txt


title: RNA-seq on DMSO treated murine leukemia cells-3

description:
DMSO3
processed data file: GSKRUX_normcounts.txt


title: QA27


description:
genomic DNA methylation from mouse3531-bloodQ175
3531-blood


title: RNA-seq on DMSO treated murine leukemia cells-2

description:
DMSO2
processed data file: GSKRUX_normcounts.txt


title: PG115


title: fis HH

description:
HH medium
7


title: RNA-seq on ruxolitinib treated murine leukemia cells-3

description:
RUX3
processed data file: GSKRUX_normcounts.txt


title: IN23


title: RNA-seq on GSKLSD1 treated murine leukemia cells 1

description:
GSK1
processed data file: LSD1i_normed_counts.txt


title: ID125


title: WT HH

description:
HH medium
5


title: RNA-seq on DMSO treated murine leukemia cells 3

description:
DMSO3
processed data file: LSD1i_normed_counts.txt


title: IN18


title: RNA-seq on DMSO treated murine leukemia cells 2

description:
DMSO2
processed data file: LSD1i_normed_counts.txt


title: WT HH + novo continuous

description:
HH medium with 25 μg/mL novobiocin
3


title: RNA-seq on DMSO treated murine leukemia cells 1

description:
DMSO1
processed data file: LSD1i_normed_counts.txt


title: WT HH + H2O2 spiked

description:
HH medium, 2 mM H2O2 added 10 minutes before RNA extraction
1


title: PT49


title: WT HH + novo spiked

description:
HH medium, 150 μg/mL novobiocin added 10 minutes before extraction
2


title: CLA-57

status: Public on Jul 01 2020

city: Dallas

first: Kyung-min

last: Lee

state: TX

address: 6001 Harry Hines Blvd, NB5. 112

department: Simmons Comprehensive Cancer Center

institute: UT SOUTHWESTERN MEDICAL CENTER

data_processing:
fastq reads trimmed with bbduk  (v.35.85)
align TopHat (v.2.0.9)
count table htSeq (v.0.6.1)
Genome_build: hg19

organism: Homo sapiens

source_name: Primary breast tumor

extract_protocol:
H&E-stained FFPE sections were reviewed for assessment of ≥20% tumor cellularity with macrodissection if required. RNA was extracted using the Promega Maxwell® 16 LEV RNA FFPE Purification Kit and instrument, according to the manufacturer’s instructions.
Total RNA was quantified using a Qubit (Life Technologies) and quality was assessed using an Agilent Bioanalyzer. For samples meeting quality requirements, 100 ng of RNA was used for library preparation. First and second strand cDNA synthesis was performed, universal adapters were ligated, and coding regions were selected by two consecutive hybrid captures followed by PCR enrichment. After enrichment, the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing platforms and then pooled equimolarly.

treatment_protocol: Letrozole was supplied in tablets of 2.5 mg. The physician instructed patients to take the drug after breakfast or lunch and every day at the same time throughout the study. No dose adjustments were permitted. The maximum duration of the neoadjuvant treatment with letrozole defi ned for this study was 12 months. The patients were evaluated every 4 weeks with a clinical examination and every eight weeks with mammograms or breast ultrasounds for the fi rst four months. In the event of absence of clinical improvement after 4 months (tumour reduction below 3 mm in longest diameter), the patient was not evaluable for the primary objective. In the event of clinical or imaging improvement at Month 4, the patients continued treatment with clinical and imaging monitoring every two months. In each control, if response improvement was seen (size reduction over 2 mm), the patients continued treatment for up to 12 months. When complete or no change responses were observed (maximum clinical diameter change.

value: Primary breast tumor

tag: group

value: responder


title: CLA-55


title: CLA-54


title: CLA-58


title: CLA-56


title: CLA-53

value: nonresponder


title: CLA-52


title: CLA-51


title: CLA-50


title: CLA-49


title: CLA-46


title: CLA-47


title: CLA-48


title: ID60


title: BA19


title: P35S::PLGT_Stem5_rep1

type: RNA

city: Houghton

first: Victor

last: Busov

state: MI

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

description: Gene expression data from stems of P35S::PLGT

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the  Affymetrix GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The data were processed with RMAExpress (http://rmaexpress.bmbolstad.com/) using default analysis settings, quantile normalization and median polish.

label: biotin

organism: Populus tremula x Populus alba

source_name: 5th inernode stem segments from PLGT overexpressing plant

label_protocol: Biotinylated cRNA were prepared according to the standard one_cycle Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Greenhouse conditions

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: Stem internodal segments from the PLGT overexpressing, downregulated and control/wild type plants, were flash frozen in liquid Nitrogen and stored  at -80oC until RNA extraction.

value: 5th inernode stem segments


title: ID4669


title: RNAi_PLGT_Stem5_rep2

description: Gene expression data from stems of RNAi_PLGT

source_name: 5th inernode stem segments from WT plants


title: CLA-45


title: P35S::PLGT_Stem5_rep2


title: ID165


title: ID91


title: Wild type_Stem5_rep2

description: Gene expression data from stems of wild type

value: wild type


title: Wild type_Stem5_rep1


title: PG122


title: VN37


title: CLA-32


title: CLA-26


title: CLA-39


title: CLA-38


title: CLA-34


title: CLA-30


title: CLA-42


title: CLA-27


title: CLA-25


title: CLA-28


title: CLA-24


title: CLA-23


title: CLA-33


title: CLA-37


title: CLA-43


title: CLA-22


title: CLA-36


title: CLA-29


title: CLA-31


title: CLA-41


title: CLA-44


title: CLA-40


title: CLA-35


title: CLA-21


title: CLA-20

description: A second run was sequenced on NextSeq500 instrument


title: CLA-19


title: CLA-18


title: CLA-13


title: CLA-16


title: CLA-9


title: CLA-14


title: CLA-2


title: CLA-17


title: WT_13D_RNA_seq_rep2

city: Beijing

first: Wei

last: Xie

address: Haidian District

country: China

institute: Tsinghua University

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data

growth_protocol: ES cells were cultured in non-adhesive bacterial dishes using ES culture medium minus LIF for 4 days. Then retinoic acid (RA) (Sigma Cat. R2625) was added in to medium to the final concentration of 2ug/ml. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA (Gibco Cat. 25200-056) and plated to poly-L-ornithine (Sigma Cat. P3655) and Laminin (Invitrogen Cat. 23017-015) pre-coated dish. Cells were cultured in DMEM/F-12 (Gibco Cat. 11330-032) with B27 (Life tech. Cat. 17504-044) and were incubated for two days. The medium was switched to BME (Gibco, Cat. 21010-046) with B27 for another two days. Differentiated neurons were then harvested for subsequent analyses.

extract_protocol:
Cells were lysed using TRIzol reagent (Ambion, Cat. 15596026). RNA was extracted by isopropanol precipitation and diluted in DEPC-treated water.
10ug RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 1 hour. RNA was purified using AMPure beads. Then ribosomal RNA was removed using Ribo-Zero Magnetic Gold Kit (Epicentre). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat. E6186A) at 95°C for 5 min. Reaction was stopped and RNA was purified. First stand cDNA was synthesized with commercial kit using both oligo dT and random primers (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014), MgCl2, DTT, dUNTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2 hour incubation on thermomixer at 16°C. Then, synthesized cDNA was end-repaired, adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat. N808-0096) at 37°C for 1 hour and purified before PCR amplification. 200-500bp fragments were selected for subsequent sequencing.

tag: genotype/variation

value: mESC-derived cell


title: PKO_Uhrf1_KO_BS_seq

data_processing:
Library strategy: MethylC-seq
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Hairpin BS-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -n 2 –l 40 –k 1. Methylation levels and fidelities for all CpGs were calculated based on the mapping results and used for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 6ug genomic DNA was mixed with 25ng lambda DNA and sonicated to 200-500bp.DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Bisulfite treatment is performed using commercial kit (Zymo research, Cat. D5005). DNA was amplified and 200-500bp fragments were gel selected.

value: mESC


title: CLA-8


title: WT_mES_RNA_seq_rep1

value: WT


title: PKO_Uhrf1_KO_Dnmt3c_KO_BS_seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Uhrf1-/- Dnmt3c-/-


title: CLA-12


title: WT_13D_RNA_seq_rep1


title: CLA-5


title: TKO_mES_RNA_seq_rep1


title: CLA-10


title: CLA-1


title: TKO_mES_RNA_seq_rep2


title: CLA-11


title: CLA-6


title: TKO_13D_RNA_seq_rep1


title: WT_mES_RNA_seq_rep2


title: CLA-3


title: RNA-seq on GSKLSD1 treated murine leukemia cells-3

description:
GSK3
processed data file: GSKRUX_normcounts.txt

value: BALB/c

value: CEBPA/CSF3R leukemia cells


title: CLA-15


title: CLA-7


title: CLA-4


title: PKO_13D_RNA_seq_rep1


title: TKO_13D_RNA_seq_rep2


title: WT_mES_H3K27ac_rep2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

tag: chip-antibody

value: Active Motif, Cat # 39133


title: WT_mES_H3K4me3_rep1

value: Homemade


title: WT_mES_H3K27ac_rep1


title: WT_mES_H3K27me3_rep1


title: PKO_mES_RNA_seq_rep1


title: TKO_mES_H3K27me3_rep1


title: RNAi_PLGT_Stem5_rep1


title: PKO_mES_H3K37ac_rep1


title: TKO_mES_H3K27ac_rep1


title: PKO_mES_H3K4me3_rep1


title: TKO_mES_H3K4me3_rep1


title: WT_13D_H3K27ac_rep1


title: WT_13D_H3K4me3_rep1


title: TKO_13D_H3K27ac_rep1


title: TKO_13D_H3K4me3_rep1


title: PKO_mES_H3K27ac_rep2


title: PKO_mES_H3K27me3_rep1


title: TKO_13D_H3K27me3_rep2


title: PKO_13D_H3K4me3_rep1


title: PKO_13D_H3K27ac_rep1


title: PKO_13D_H3K27me3_rep1


title: PKO_mES_H3K27me3_rep2


title: LB74

value: lymphocytes

value: Great Dane Zoey


title: KDM3B_shYTHDC1_Input1

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

data_processing:
Quality control of MeRIP-Seq data was performed using FastQC. Low quality bases and adaptor contamination were deleted by Trimmomatic (v. 0.33.0) 8 . Raw Sequencing reads were aligned using Hisat2 (v. 2.1.0) 9 with default parameters to the hg38 or mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools (v. 1.7) 10 to remove the reads with mapping quality below 30. MACS2 (v. 2.1.1) 11 was used to identify peaks (p-value of 1e-4).
For ChIP-seq, raw sequencing reads were aligned using Bowtie (v. 2.3.4.1) 15 with default parameters to the mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools10 to remove the reads with mapping quality below 30. MACS2 11 was used to identify peaks (p-value of 1e-4).
For RNA-seq, reads mapping and processing were performed as described for MeRIP-seq data above. FeatureCounts (v. 1.6.3) 5 was used to calculate the number of reads mapped to each gene. EdgeR (v.3.22.5) 19 was used for differential expression analysis.
Genome_build: hg38/mm10

growth_protocol: HEK293T cells were grown in DMEM medium (Invitrogen) containing 10% FBS, and 1% penicillin-streptomycin. Mouse embryonic stem cell (mESC) E14TG2a was cultured with N2B27 base medium supplemented with 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.15 mM 1-thioglycerol (Sigma), 100 U/mL penicillin-streptomycin (Invitrogen), 25 μg/ml BSA (Sigma), 1μM MEK inhibitor PD0325901 (Selleck Chemicals), 3μM GSK3β inhibitor CHIR99021 (Selleck Chemicals), 2% KOSR (Thermofisher) and 1000 U/ml ESGRO leukemia inhibitory factor LIF (Millipore) on plates coated with 0.2% gelatin.

extract_protocol:
For RNA-seq, RNA was isolated using TRNzol reagent. After DNase I treatment, rRNA was removed using QIAseq FastSelect RNA Removal Kit (QIAGEN). For RIP-seq, chromatin RNA was extracted, then fragmented to about 100-300 nt-long, and incubated with anti-m6A antibody (Millipore). Then the mixture was subjected to Dynabeads protein G binding. After washing, the bound RNA was eluted by RLT and retrieved by RNeasy Plus Micro Kit (Qiagen). H3K9me2 ChIP-seq was performed using the iDeal ChIP-seq Kit for Histones (Diagenode). For KDM3B, METTL3 and Pol II ChIP-seq, cells were crosslinked, sonicated, and subjected to ChIP.
RNA-seq libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). RIP-seq libraries were generated using  SMARTer Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (Takara) following the manual. ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina.
RNA-seq, RIP-seq and ChIP-seq

treatment_protocol: GFP/FTO/ALKBH5/YTHDC1 shRNA knockdown cells were generated by lentiviral infection and puromycin selection.

tag: cell line

tag: protocol

value: ChIP


title: KDM3B_shYTHDC1_Input2


title: KDM3B_shYTHDC1_IP2


title: KDM3B_shYTHDC1_IP1


title: WT_13D_H3K27me3_rep1


title: KDM3B_D395A_IP2

value: untreated


title: KDM3B_shGFP_Input

value: shGFP


title: m6A_D395A_Input

value: RIP


title: m6A_D395A_IP


title: KDM3B_shGFP_IP


title: KDM3B_WT_IP2


title: METTL3_IP_3


title: KDM3B_D395A_Input


title: Pol2_IP


title: KDM3B_WT_Input


title: KDM3B_D395A_IP


title: METTL3_Input


title: H3K9me2_D395A_IP_2


title: METTL3_IP_1


title: KDM3B_WT_IP


title: H3K9me2_WT_IP_1


title: m6A_Input_2


title: METTL3_IP_2


title: H3K9me2_WT_Input


title: m6A_IP_2


title: m6A_Input_1


title: H3K9me2_D395A_IP_1


title: Sample_30

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

data_processing:
Base-calling: Sample mRNA libraries were prepared using Illumina mRNA True Strand kit (Covance Genomics Lab, Redmond, WA; Seattle Genomics Core, Seattle, WA) and sequenced on either an Illumina HiSeq 2500 system to generate 100 bp paired end libraries with 20-30 million reads (Covance Genomics Lab, Redmond, WA) or Illumina NovaSeq 6000 system on an S1 flow cell yielding approximately 35 million (2 x 50 bp) paired end reads.
Alignment: The RNA-seq sequences were aligned using the STAR aligner.
Normalization: The counts data were quantile normalized using the DESeq2 R package.
Differential Expression: The DESeq2 R package was used for differential expression analysis between treatment groups.
Genome_build: Mus musculus reference genome build Grch38 (release 77)
Supplementary_files_format_and_content: bulk_raw_counts.csv.gz: comma-separated text file with gzip compression containing processed counts. bulk_meta_counts.csv.gz: comma-separated text file with gzip compression with colum names sample,prep,group,treat,day

source_name: Hypothalamus samples from FGF1 and FGF19 ICV ob/ob mice

growth_protocol: Individually housed under specific-pathogen free conditions in a temperature-controlled room with a 12:12h light:dark cycle and provided with ad libitum (ad-lib) access to water and Altromin 1310 chow (Brogaarden, Denmark)

extract_protocol:
Following euthanasia, brains (Day 1, n=4 vehicle; n=10 FGF1; Day 5, n=7 vehicle; n=9 FGF1; Day 42, n=42/group) were dissected as for snRNA-seq and immediately frozen on dry ice and stored at -80°C until further processing. RNA was isolated using Qiagen RNeasy mini kit (cat# 74104), followed by High capacity cDNA Reverse transcription (from Applied Biosystems, cat# 4368813), and finally analysis using Agilent RNA 6000 Nano kit. The RNA sample concentration was between 200-350ng/μl, with 10-15ug purified RNA from each individual sample. Sample mRNA libraries were prepared using Illumina mRNA True Strand kit (Covance Genomics Lab, Redmond, WA; Seattle Genomics Core, Seattle, WA)
RNA was isolated using Qiagen RNeasy mini kit (cat# 74104), followed by High capacity cDNA Reverse transcription (from Applied Biosystems, cat# 4368813), and finally analysis using Agilent RNA 6000 Nano kit. The RNA sample concentration was between 200-350ng/l, with 10-15ug purified RNA from each individual sample. All RNA samples showed a good purity (A260/280 rations are between 2.0-2.1) and Bioanalyzer results demonstrated a good quality of RNA for all samples (RIN numbers >9.2).

value: ob/ob

value: hypothalamus

value: male

value: 11 weeks

value: intracerebral ventricular injection vehicle. Non-Diabetic pair fed to FGF1. Euthanized 1 days post injection

tag: number of mice


title: Sample_28


title: Sample_29


title: m6A_IP_1


title: Sample_27


title: Pol2_Input


title: Sample_25

value: 3 ug intracerebral ventricular injection of FGF1. Euthanized 1 days post injection


title: Sample_26


title: H3K9me2_D395A_Input


title: Sample_22


title: Sample_23


title: H3K9me2_WT_IP_2


title: Sample_19


title: Sample_18


title: Sample_16

value: intracerebral ventricular injection vehicle. Non-Diabetic pair fed to FGF1. Euthanized 42 days post injection


title: Sample_17


title: Sample_11

value: 3 ug intracerebral ventricular injection of FGF1. Euthanized 42 days post injection


title: Sample_7


title: Sample_12


title: Sample_14


title: Sample_10


title: Sample_13


title: Sample_15


title: RRB-WT2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description:
cells were isolated from small intestinal lamina propria.
ATACrawCountsBrg1

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Quality filtered reads were then mapped to mouse genome (mm10) by Bowtie2, and only uniquely mapped reads were saved.
Peak calling was done using MACS2 with an initial threshold q-value of 0.01 as cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: csv, raw counts of sequencing reads from triplicates samples with chromosome ID, chromosome start and end positions.

source_name: lamina proprial lymphocytes

extract_protocol:
Library preparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme, Nanjing, China. 1.2X Agencourt AMPure XP beads(Beckman Coulter) were used to purify libraries for sequencing.
150 paired-end sequencing was performed with Illumina NovaSeq 6000.

tag: gender

value: female

tag: mouse genotype


title: Sample_9

tag: age


title: RRB-WT3


title: RRB-KO3

value: Brg1-deficient ILC3s


title: RRB-KO1


title: RRB-WT1


title: Sample_24

tag: Sex


title: Sample_21


title: Sample_20


title: GSK3_KO_ESC_SL_GRO-seq_rep2

city: Guangzhou

first: Yiwei

last: Lai

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Library strategy: GRO-seq
Illumina bcl2fastq2.17 software was used for base-calling.
For GRO-seq,  adaptors were first trimmed with fastp (v0.20.0), only read1 were kept for further analysis. PCR duplicates were collapse using Fastx-toolkit. 20 bp PolyA sequence and 8 bp random sequence were trimmed from 3’end.
Cleandata were then aligned to  the mm10 mouse genome assembly using Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage script of deepTools with the options “ --binSize 10 --normalizeUsingRPKM”.

source_name: mouse embryonic stem cells

growth_protocol: ESCs in SL medium were cultured in DMEM/high glucose containing 15% FBS, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, and 1,000 U/ml LIF on mitomycin-C treated mouse embryonic fibroblasts (MEFs), and they were split onto 0.2% gelatin pre-coated plates prior to the experiment. ESCs in 2iL medium were cultured in a 1:1 mix of DMEM/F12  and Neurobasal medium, with N2 and B27 supplements, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, 1,000 U/ml LIF, 3 μM, and 1 μM PD0325901 on 0.2% gelatin pre-coated plates.

extract_protocol:
Nuclei from ESCs were extracted, and run-on-transcribed with BrUTP (Sigma, B7166) and other NTPs at 30 °C for 5 min. Nascent RNA was enriched by agarose coated anti-BrUTP (Sant Cruz, sc-32323). Poly(A) tail was added to the nascent RNA by Poly(A) Polymerase (NEB, M0276S) to synthese cDNA with oligo(dT) primer. GRO-seq libraries were amplified by PCR for 10 cycles and seperated by 10% TBE gel. The bands ranging from 160 bp to 300 bp were cutted and purified by isopropanol precipitation.
Libraries were sequenced on a NovaSeq 6000  sequencer according to the manufacturer’s instructions with 12Gbase PE150 reads.

value: mouse embryonic stem cells


title: ESC_SL_GRO-seq_rep1


title: ESC_SL_GRO-seq_rep2


title: ESC_2iL_GRO-seq_rep1


title: GSK3_KO_ESC_JQ1_SL_rep2

data_processing:
Illumina bcl2fastq2.17 software was used for base-calling.
For RNA-seq gene expression quantification, data were first aligned with STAR (v2.5.2) and quantified according to GENCODE vM15 in a RSEM-based pipeline.
Differentially expressed genes were determined by DESeq2 (v 1.18.1) and were defined as absolute fold change > 2, q value < 0.1. Functional annotation was further performed by ClusterProfiler (v3.6.0).
Genome_build: mm10
Supplementary_files_format_and_content: Count tables generated by RSEM are attached as supplementary files.

growth_protocol: ESCs in SL medium were cultured in DMEM/high glucose containing 15% FBS, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, and 1,000 U/ml LIF on mitomycin-C treated mouse embryonic fibroblasts (MEFs), and they were split onto 0.2% gelatin pre-coated plates prior to the experiment. ESCs in 2iL medium were cultured in a 1:1 mix of DMEM/F12  and Neurobasal medium, with N2 and B27 supplements, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, 1,000 U/ml LIF, 3 μM, and 1 μM PD0325901 on 0.2% gelatin pre-coated plates

extract_protocol:
Samples were isolated using the TRIzol™ Reagent (ThermoFisher Scientific, 15596026).
A total amount of 1 μg RNA per sample was used as input material for the library preparation. The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® following the manufacturer's recommendations.
Libraries were sequenced on a NovaSeq 6000  sequencer according to the manufacturer’s instructions with 6 Gbase PE150 reads.

treatment_protocol: ESCs cultured in SL or 2iL were treated with 100 nM JQ1 or DMSO, Cells were harvested 60 hours post treatment.


title: ESC_2iL_GRO-seq_rep2


title: Sample_8


title: GSK3_KO_ESC_JQ1_SL_rep1


title: GSK3_KO_ESC_DMSO_SL_rep2


title: GSK3_KO_ESC_DMSO_SL_rep1


title: ESC_JQ1_2iL_rep1


title: ESC_DMSO_SL_rep2


title: ESC_JQ1_SL_rep1


title: ESC_JQ1_SL_rep2


title: ESC_DMSO_2iL_rep1


title: m1_AY_Y3_D1

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

source_name: three-mo mouse BEC

growth_protocol: Mice 3 (young)

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary murine brain endothelial cells


title: m1_Young2_C6


title: m1_AY_Y3_P9


title: ESC_DMSO_SL_rep1


title: m1_Young2_H17


title: m1_AY_Y3_E17


title: m1_Young1_F17


title: m1_Young2_L15


title: m1_AY_Y3_J17


title: m1_Young2_P14


title: m1_Young1_C4


title: m1_AY_Y3_G16


title: m1_Young1_D17


title: ESC_JQ1_2iL_rep2


title: m1_Young2_B2


title: m1_Young2_H11


title: m1_Young1_K8


title: m1_Young1_I18


title: ESC_DMSO_2iL_rep2


title: m1_Young2_P6


title: m1_AY_Y3_M13


title: m1_Young1_B9


title: m1_AY_Y3_J9


title: m1_Young1_I14


title: m1_Young1_K10


title: m1_Young2_M10


title: m1_Young2_J9


title: m1_Young2_H4


title: m1_Young2_J17


title: m1_AY_Y3_A3


title: m1_AY_Y3_F12


title: m1_AY_Y3_L14


title: m1_Young2_I3


title: m1_Young1_G17


title: m1_AY_Y3_F3


title: m1_AY_Y3_O18


title: m1_Young2_P9


title: m1_Young2_K2


title: m1_Young2_H18


title: m1_AY_Y3_J3


title: m1_Young2_I14


title: m1_Young1_H3


title: m1_Young2_H16


title: m1_Young1_M18


title: m1_AY_Y3_E10


title: m1_Young1_G4


title: m1_AY_Y3_F11


title: m1_AY_Y3_O10


title: RRB-KO2


title: m1_AY_Y3_C11


title: m1_AY_Y3_O9


title: m1_Young2_F6


title: m1_Young1_B11


title: m1_Young2_F13


title: m1_Young1_H9


title: m1_AY_Y3_F7


title: m1_Young2_B6


title: m1_AY_Y3_G7


title: m1_Young1_M17


title: m1_Young1_N3


title: m1_Young2_G14


title: m1_AY_Y3_A5


title: m1_AY_Y3_J5


title: m1_Young2_A15


title: m1_Young1_C15


title: m1_Young1_L4


title: m1_AY_Y3_E16


title: m1_Young2_K4


title: m1_Young1_N15


title: m1_Young2_A3


title: m1_Young2_M15


title: m1_Young2_O16


title: m1_AY_Y3_P21


title: m1_Young2_O12


title: m1_AY_Y3_M12


title: m1_AY_Y3_A8


title: m1_Young1_E5


title: m1_AY_Y3_F15


title: m1_AY_Y3_A18


title: m1_Young2_M6


title: m1_AY_Y3_M11


title: m1_AY_Y3_N12


title: m1_Young2_I5


title: m1_AY_Y3_B8


title: m1_AY_Y3_P3


title: m1_Young2_D8


title: m1_AY_Y3_H17


title: m1_Young2_G10


title: m1_Young2_A6


title: m1_AY_Y3_E18


title: m1_Young1_N10


title: m1_Young1_H16


title: m1_Young1_M3


title: m1_Young1_J17


title: m1_AY_Y3_H6


title: m1_AY_Y3_A14


title: m1_Young2_P15


title: m1_Young2_D12


title: m1_AY_Y3_H16


title: m1_Young1_N7


title: m1_AY_Y3_G6


title: m1_Young2_C2


title: m1_AY_Y3_A6


title: m1_Young1_O10


title: m1_Young1_G15


title: m1_Young2_G8


title: m1_Young1_F6


title: m1_AY_Y3_P8


title: m1_AY_Y3_I14


title: m1_AY_Y3_K3


title: m1_AY_Y3_C8


title: m1_Young2_E12


title: m1_Young2_A18


title: m1_Young1_K11


title: m1_AY_Y3_A12


title: m1_Young1_H12


title: m1_Young1_N5


title: m1_AY_Y3_M5


title: m1_AY_Y3_A17


title: m1_Young2_C3


title: m1_Young2_B17


title: m1_Young1_K6


title: m1_Young1_O3


title: m1_Young1_G3


title: m1_AY_Y3_I8


title: m1_AY_Y3_G13


title: m1_Young2_M18


title: m1_Young1_B13


title: m1_Young2_C12


title: m1_Young1_O9


title: m1_Young2_C7


title: m1_Young1_C3


title: m1_AY_Y3_D14


title: m1_Young1_K5


title: m1_AY_Y3_G14


title: m1_Young1_I9


title: m1_Young2_G1


title: m1_Young1_L9


title: m1_Young1_J15


title: m1_Young2_K7


title: m1_Young1_J6


title: m1_Young2_J16


title: m1_Young2_C1


title: m1_Young2_M9


title: m1_Young2_C8


title: m1_Young2_A11


title: m1_AY_Y3_N5


title: m1_Young2_A10


title: m1_Young1_M13


title: m1_Young2_F10


title: m1_Young2_H12


title: GSK3_KO_ESC_SL_GRO-seq_rep1


title: m1_AY_Y3_L7


title: m1_Young1_O5


title: m1_Young2_E14


title: m1_AY_Y3_C10


title: m1_Young2_J14


title: m1_AY_Y3_A16


title: m1_Young2_H13


title: m1_Young1_C2


title: m1_Young1_H11


title: m1_Young2_N15


title: m1_Young2_P7


title: m1_Young2_B14


title: m1_AY_Y3_L15


title: m1_Young2_F16


title: m1_AY_Y3_O12


title: m1_Young1_N4


title: m1_Young2_D16


title: m1_AY_Y3_J4


title: m1_AY_Y3_H4


title: m1_AY_Y3_B9


title: m1_AY_Y3_I6


title: m1_Young2_F8


title: m1_Young1_B16


title: m1_Young2_L6


title: m1_Young2_O2


title: m1_Young1_F7


title: m1_AY_Y3_C4


title: m1_Young1_C14


title: m1_AY_Y3_J16


title: m1_AY_Y3_P15


title: m1_Young2_L8


title: m1_Young2_L13


title: m1_Young1_F8


title: m1_AY_Y3_K13


title: m1_AY_Y3_B2


title: m1_Young1_N2


title: m1_Young2_P3


title: m1_Young1_C12


title: m1_AY_Y3_D3


title: m1_Young1_E15


title: m1_AY_Y3_G5


title: m1_Young1_H17


title: m1_Young2_N14


title: m1_Young1_E18


title: m1_Young2_G11


title: m1_AY_Y3_I16


title: m1_Young1_O2


title: m1_Young1_M15


title: m1_Young2_G4


title: m1_Young1_C11


title: At.TraPR.R3

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description: processed data file: At_miRNA_counts.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with Trimmomatic 0.36
Mapping to the Arabidopsis thaliana genome (TAIR10) with Bowtie 1.2.1.1
Mapping to the Drosophila melanogaster genome (BDGP6) with Bowtie 1.2.1.1
Mapping to the Mus musculus genome (GRCm38) with Bowtie 1.2.1.1
Read counting to miRBase annotation with Rsubread 1.26.1
Read normalization with DEseq2.
Genome_build: TAIR10
Genome_build: BDGP6
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text files of library and log2 normalized miRNA read counts

organism: Arabidopsis thaliana

extract_protocol:
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with from TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.

value: inflorescence

tag: library preparation

value: TruSeq

tag: rna isolation

value: TraPR

tag: molecule subtype

value: small RNA


title: m1_AY_Y3_D11

tag: cell type


title: m1_AY_Y3_B16


title: At.TraPR.R2

tag: tissue


title: m1_AY_Y3_N13


title: At.TraPR.R1


title: m1_Young2_A13


title: m1_AY_Y3_K1


title: At.TRIzol.gel.R3

value: TRIzol & size selection


title: At.TRIzol.gel.R2


title: At.TRIzol.gel.R1


title: m1_Young2_J11


title: At.TRIzol.total.R3

value: TRIzol


title: m1_AY_Y3_L13


title: At.TRIzol.total.R2


title: m1_Young2_A5


title: m1_Young2_I8


title: At.TRIzol.total.R1


title: m1_Young2_J12


title: m1_AY_Y3_F16


title: Shahdara.ozone_III

city: Örebro

first: Luis

last: Morales

address: Fakultetsgatan 1

department: School of Science and Technology

country: Sweden

institute: Örebro University

data_processing:
The quality of raw reads was first inspected in Chipster using FastQC.
Removal of adapter sequences and trimming and cropping of the reads was done using Trimmomatic-0.33 (Bolgert et al., 2014) in single-end mode. The bases with a quality score less than 20 were trimmed from the beginning and the end of the sequences, and the reads shorter than 30 bases were removed from the analysis (-phred33, LEADING:20, TRAILING:20 and MINLEN:30).
Filtered reads were mapped to the Arabidopsis transcript reference database AtRTD2 (Zhang et al., 2017) using Kallisto V-0.43.0 (CMD:quant) (Bary et al., 2016) with 4000 bootstrap sets. The final count table for each biological replicate was obtained as the mean of the bootstrap runs.
Genome_build: Arabidopsis transcript reference database AtRTD2
Supplementary_files_format_and_content: Matrix-table including gene counts for each sample

source_name: Shahdara.ozone_whole rosette

growth_protocol: Seeds were sown on 1:1 peat: vermiculite, stratified at 4°Cfor three days in the dark, and then grown at 22°C/19°C for a week. Subsequently four geminated seedlings were transplanted into 8 × 8 cm pots containing new 1:1 peat: vermiculite mixture. The pots were randomly placed into a controlled chamber (Weiss Bio1300; Weiss Gallenkamp), where plants were grown at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.

extract_protocol:
Four rosettes per genotype from control and ozone treatment were pooled, frozen into liquid nitrogen and stored at -80°C. Three biological replicates of RNA were isolated with with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). RNA quality and concentration were measured using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared using 1µg total RNA following instructions from Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Three weeks old plants were exposed with 350 nL L-1 ozone and control clean air for two hours.

value: Shahdara

tag: developmental stage

value: 3 weeks old plants

tag: treatment

value: 350 nL L-1 ozone for 2hrs

value: whole rosette


title: Shahdara.ozone_II


title: m1_Young2_E17


title: m1_Young2_O8


title: Shahdara.ozone_I


title: Shahdara.control_II

source_name: Shahdara.control_whole rosette

value: control


title: m1_Young2_E2


title: m1_AY_Y3_H12


title: Shahdara.control_III


title: Shahdara.control_I


title: m1_Young2_G6


title: B2

city: Chang Chun

first: Zhiqiang

last: Yang

state: Jilin

address: No. 5333 Xian Road

department: College of Veterinary Medicine

institute: Jilin University

description:
B4_reads
biological replicate of biofilm

data_processing:
Illumina Casava1.7 software was used for basecalling.
fastx(version:0.0.13) processed clean reads, and removed Q20<50% and length<20nt
Genome mapping performed with bowtie2(version:2-2.0.5)
BEDTool(version:2.16.1) counted RPKM for all genes expression
Differential gene analysis under fold-change>2 and Fisher-test<0.05
Genome_build: ASM19595v2, ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Mycobacterium_tuberculosis_H37Rv_uid57777/
Supplementary_files_format_and_content: txt file include RPKM values for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: biofilm

growth_protocol: M. tuberculosis H37Rv was maintained in 7H9ADC Tween liquid medium at 37°C in an erlenmeyer to an optical density at 600 nm (OD600) of 0.7-1.0. The culture was used as inoculum at a 1:100 dilution.Dispense 15mL of Modified  Sauton Medium to a 50mL Serum bottle (TAIDA). Add 500μl of the inoculum to the medium, cap the bottle very tightly and place it undisturbed in a humidified 37°C incubator for 25 days. For planktonic growth, culture was inoculated at the same dilution in Modified Sauton Medium and incubated at 37ºC on a shaker platform maintained at 200 rpm for 25 days similarly.

extract_protocol:
Biofilms were broken into pieces by Pipette tip and harvested by centrifugation.The pellets of biofilms and planktonic cells were resuspended in Buffer RLT (1%β-mercaptoethanol) in a proportion of 6 ml of Buffer RLT per 100 ml of bacterium solution respectively. Cells were ground into powder in a mortar in liquid nitrogen and total RNA was extracted using RNeasy® Mini Kit, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

tag: incubation time

value: 25 days


title: m1_Young1_J13


title: P2

description:
6_reads
biological replicate of planktonic cells

source_name: planktonic cells


title: B1

description:
B1_reads
biological replicate of biofilm


title: m1_AY_Y3_J18


title: m1_Young1_D2


title: m1_Young2_M14


title: P1

description:
3_reads
biological replicate of planktonic cells


title: m1_Young1_M14


title: m1_Young2_E9


title: m1_AY_Y3_I7


title: m1_Young2_D13


title: m1_AY_Y3_H8


title: m1_Young1_G9


title: m1_Young2_I6


title: m1_AY_Y3_D13


title: m1_AY_Y3_J11


title: m1_AY_Y3_N10


title: m1_AY_Y3_I15


title: m1_Young2_L3


title: Monosensitized Placebo Patient 5 [P30 T0]

city: Madrid

first: Leticia

last: Mera

state: Madrid

address: Carretera Boadilla km 5300

country: Spain

institute: CEU San Pablo University

description: Gene expression data from Monosensitized Placebo Patients

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 20 hr at 48ºC on GeneChip™ Human Gene 2.1 ST Array Strip. GeneChips were washed and stained in the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™)

scan_protocol: GeneChips were scanned using the GeneAtlas™ System for Academic Customers, 230V (Applied Biosystems™).

data_processing: Data was RMA-normalized and differential expression analysis was performed using TAC 4.0 software. Pathway analysis was carried out with IPA and GSEA.

source_name: Ficoll isolated PBMCs from Monosensitized Placebo Patients

label_protocol: Biotinylated cRNA was prepared according to the GeneChip ™ WT PLUS Reagent Kit manual from 100 ng total RNA (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Not applicable

extract_protocol: PBMCs from allergic patients were isolated using Ficoll gradient protocol. Total RNA was extracted using Rneasy Mini Kit (QIAGEN). RNA was stored at -80ºC until microarray hybridization

treatment_protocol: Not applicable

tag: sensitization

value: Monosensitized

value: Placebo

tag: time point

value: T0-before SLIT

value: Ficoll isolated PBMCs


title: m1_Young2_I7

value: primary murine brain endothelial cells


title: Monosensitized Placebo Patient 5 [P30 T2]

value: T2-two years of treatment


title: m1_Young1_E3


title: Monosensitized Active Patient 3 [P27 T2]

description: Gene expression data from Monosensitized Active Patients

source_name: Ficoll isolated PBMCs from Monosensitized Active Patients

value: Active


title: Monosensitized Active Patient 3 [P27 T0]


title: Monosensitized Active Patient 4 [P28 T0]


title: m1_AY_Y3_E9


title: Monosensitized Placebo Patient 3 [P25 T2]


title: m1_Young2_C14


title: Monosensitized Placebo Patient 3 [P25 T0]


title: Monosensitized Placebo Patient 3 [P22 T0]


title: Monosensitized Placebo Patient 4 [P26 T2]


title: Polisensitized Placebo Patient 5 [P24 T2]

description: Gene expression data from Polisensitized Placebo Patients

source_name: Ficoll isolated PBMCs from Polisensitized Placebo Patients

value: Polisensitized


title: Monosensitized Placebo Patient 2 [P21 T0]


title: m1_Young2_H3


title: m1_Young1_I6


title: m1_Young2_L2


title: m1_Young1_B12


title: Monosensitized Placebo Patient 4 [P26 T0]


title: m1_Young2_O7


title: m1_Young2_O13


title: m1_Young1_D6


title: Polisensitized Placebo Patient 4 [P20 T2]


title: Monosensitized Active Patient 4 [P28 T2]


title: Monosensitized Placebo Patient 3 [P22 T2]


title: Monosensitized Placebo Patient 2 [P21 T2]


title: Polisensitized Placebo Patient 5 [P24 T0]


title: Polisensitized Placebo Patient 4 [P20 T0]


title: m1_Young2_F12


title: m1_Young1_K16


title: m1_AY_Y3_K8


title: m1_Young2_L4


title: m1_Young2_F5


title: Monosensitized Placebo Patient 1 [P16 T2]


title: m1_Young1_O1


title: m1_Young1_G10


title: Monosensitized Active Patient 2 [P17 T0]


title: Polisensitized Active Patient 4 [P15 T0]

description: Gene expression data from Polisensitized Active Patients

source_name: Ficoll isolated PBMCs from Polisensitized Active Patients


title: Monosensitized Active Patient 2 [P17 T2]


title: Polisensitized Active Patient 4 [P15 T2]


title: m1_Young2_K6


title: m1_AY_Y3_E15


title: m1_Young1_H6


title: m1_Young2_B10


title: m1_AY_Y3_B11


title: m1_Young2_M12


title: Monosensitized Placebo Patient 1 [P16 T0]


title: m1_AY_Y3_A2


title: m1_AY_Y3_M2


title: Polisensitized Active Patient 3 [P13 T2]


title: Polisensitized Placebo Patient 3 [P14 T0]


title: Polisensitized Active Patient 3 [P13 T0]


title: Polisensitized Active Patient 2 [P12 T0]


title: Polisensitized Active Patient 1 [P11 T2]


title: Polisensitized Placebo Patient 2 [P9 T2]


title: Polisensitized Active Patient 2 [P12 T2]


title: Polisensitized Active Patient 1 [P11 T0]


title: Polisensitized Placebo Patient 2 [P9 T0]


title: Polisensitized Placebo Patient 3 [P14 T2]


title: m1_Young1_H5


title: m1_Young2_A16


title: m1_AY_Y3_K11


title: m1_Young1_G7


title: m1_Young1_L8


title: m1_AY_Y3_I13


title: m1_Young1_I3


title: Polisensitized Placebo Patient 1 [P8 T2]


title: m1_AY_Y3_D12


title: Monosensitized Active Patient 1 [P1 T0]


title: Polisensitized Placebo Patient 1 [P8 T0]


title: LANS-Set2_lightToDark_set2d-rph1d_0min_ChIP_Input

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
For ChIP: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Sequencing adapters on reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of 5 copies and discarding the copies beyond that limit. Since the previous filtering steps may remove one end of a read pair but not the other, both read-pair fastq files were synced using in-house scripts to ensure proper order for alignment. As the ChIP experiments contained S. pombe spike-in, a chimeric S. cerevisae-S. pombe genome (sacCer3-ASM294v2) was generated using the genomeGenerate tool in STAR (v2.5.2b). This chimeric genome contains the full sequence of both species, allowing reads to align to their best overall fit between the two species. Once generated, read alignment was done using STAR (v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, Samtools (v1.31) and bedtools (2.26) were used to generate bigWig files for downstream analyses. To account for S. pombe spike-in, the bigwig signal was normalized by the total number of S. pombe reads per million, using the -scale option within the bedtools genomecov tool. Normalized H3K36me3 signal was obtained by dividing H3K36me3 spike-in normalized signal by H3 spike-in normalized signal for each base pair for each replicate. Some regions were devoid of any H3 signal, and these regions were flagged and excluded from further analyses regardless of H3K36me3 signal.  Deeptools (v2.5.4) was used to generate metagene plots using the normalized H3K36me3 signal. Deeptools was also used to obtain base pair by base pair signal over regions of interest such as genes, introns, and exons. This data was used to calculate the average signal per gene, excluding those regions flagged for lacking H3 signal. We set out to understand H3K36me3 signals over time, however differing levels of normalized H3K36me3 signal within genes made analysis difficult. To account for these differences, we scaled the average signal per gene throughout the time course between 0 (no signal) and 1 (the maximum signal of a gene over the time course). This yielded a relative (proportional) scale for each gene as a fraction of its maximum signal and allowed for easier comparisons of patterns within and across treatments. To yield a comprehensive gene value for plotting, H3K36me3 signal (for both mean or proportional) was the mean of all the replicates for the gene.
For RNA: Reads from the sequencer were demultiplexed using bcl2fastq (v2.20.0). Reads were trimmed using cutadapt (v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 to remove any sequencing adapters. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit (v0.0.12), with options -Q 33, -p 90, and -q 20. Reads were aligned to the sacCer3 genome using STAR (v2.5.4b) with options --quantMode TranscriptomeSAM, --outFilterMismatchNmax 2, --alignIntronMax 1000000, --alignIntronMin 20, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, and --outFilterMultimapNmax 1. To calculate the RNA abundance values, Salmon (v0.8.1) tool quant was used with options -l SR, --incompatPrior 0.0 to account for read strandedness. Samtools (v1.3.1), bedtools (v2.26), and R (v3.3.1) were used to interconvert files for downstream analyses. DESeq2 (v1.14.1) was used to determine which genes had differential expression. Venn diagrams were made using R package Vennerable (v3.0).
Genome_build: sacCer3-ASM294v2
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files for ChIP contain spike-in (S. pombe) scaled ChIP-seq signal for H3 or H3K36me3. Those ending with "normalizedByH3" contain H3K36me3 ChIP-seq signal that is normalized by matched H3 signal (spike-in scaled H3K36me3 / spike-in scaled H3). Bigwigs for RNA contain read depth normalized, non-stranded RNA-seq signal.
Supplementary_files_format_and_content: sf files contain the gene expression data (TPM) as determined by sailfish for all replicates in either Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Differential abundance files contain the DESeq2 differential genes between 0min and all other timepoints across Light to Dark (LtD) or Dark to Light (DtL) treatments.
Supplementary_files_format_and_content: Model value matrices contain the GLMM model prediction values, errors, and credible intervals for each gene across the time course. High confidence genes are those where credible interval does not cross zero, and are labeled as having a non-zero trend in the table.
Supplementary_files_format_and_content: Histone value matrices contain the average, spike-in scaled, H3 normalized H3K36me3 ChIP-seq signal for each gene and replicate.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: For ChIP-seq: Cells (either WT, set2∆, set2∆ expressing LANS-Set2, rph1∆, or rph1∆ expressing LANS-Set2) were resuspended in YPD (WT, set2∆, and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2 and rph1∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.35. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.  For RNA-seq: Cells (either WT, rph1∆, or set2∆ expressing LANS-Set2) were resuspended in YPD (WT and rph1∆) or SC−LEU (set2∆ expressing LANS-Set2) and grown overnight at 30 °C. In the morning cell density was measured at OD600 and cultures were diluted in appropriate media to a final volume of 70 mL and final OD600 of 0.3. Cultures were maintained at 30 °C until the OD600 reached 0.8−1.0.

extract_protocol:
For ChIP-seq: Cells were fixed with a 1% final concentration of formaldehyde, the fixation was quenched, cells were washed, and pellets were frozen at −80 °C. After the completion of each time course, cells were lysed using 140 mM FA lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail). Lysed cells were sonicated (Diagenode Bioruptor UCD-200) on high intensity 5 times for 5 minutes each (cycles of 30 seconds “ON” and 30 seconds “OFF”) and clarified by centrifuging at full speed for 15 minutes. Overnight immunoprecipitations of S. cerevisiae chromatin with appropriate antibodies were prepared with S. pombe chromatin spike-in control corresponding to 15% of S. cerevisiae chromatin as estimated by Bradford assay (Bio-Rad). 50 μL of Protein G Dynabeads were added to each 500 μL immunoprecipitation reaction and reactions were incubated for 2 hours. Washes were performed with 1 mL of 140 mM FA-lysis buffer, 500 mM FA-lysis buffer (50 mM HEPES, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, pH 7.5, containing protease inhibitor cocktail), LiCl solution (250 mM LiCl, 10 mM Tris, 0.5% each of NP-40 and sodium doxycholate and 1 mM EDTA) and TE pH 8.0. Elution buffer (1% SDS, 0.1 M NaHCO3) was used to elute the DNA (15 minutes shaking at 65 °C followed by centrifugation at 2,000 RPM for 2 minutes). 10 μL of 5 M NaCl was added to the eluates and 10% inputs and samples were incubated at 65 °C overnight to carry out de-crosslinking. Samples were treated with RNase for 1 hour and proteinase K for 1hour before ChIP DNA Clean & Concentrator (Zymo Research) to extract the DNA.  For RNA-seq: Cells (10 mL of log-phase cultures) were collected by centrifugation and frozen at −80 °C. , RNA was isolated by acid phenol extraction. RNA (10 μg) was treated with DNase (Promega) and purified (RNeasy column, QIAGEN).
For ChIP-seq: Bar-coded sequencing libraries were prepared as recommended by the manufacturer (KAPA Hyper Prep Kit), pooled and sequenced (Hi-Seq 2500, Illumina). Briefly, extracted DNA was end-repaired and A-tailed and adapters were ligated. Bead-based size selection was performed, libraries were amplified, and bead-based size selection was repeated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.  For RNA-seq: RNA (2.5 μg) was processed using rRNA depletion beads specific to yeast (Illumina). Bar-coded sequencing libraries were prepared as recommended by the manufacturer (TruSeq Stranded Total RNA Library Preparation Kit, Illumina), pooled and sequenced (Hi-Seq 4000, Illumina). Briefly, libraries were constructed by bead-based rRNA depletion, cDNA synthesis, and PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq 4000 following the manufacturer's protocols.

treatment_protocol: For ChIP-seq: WT, set2∆, and rph1∆ cells were collected when the OD600 reached 0.8−1.0. Cells expressing LANS-Set2 (set2∆ and rph1∆) were maintained throughout culturing in 500 μW/cm2 blue light (set2∆ and rph1∆) or in the dark (set2∆) until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.  For RNA-seq: WT and rph1∆ cells were collected when the OD600 reached 0.8−1.0. set2∆ cells expressing LANS-Set2 were maintained throughout culturing in 500 μW/cm2 blue light or in the dark until the OD600 reached 0.8−1.0 when an initial time point was collected then samples were shifted from the dark to light or the light to dark.

tag: strain

tag: genotype

tag: lans-set2 status

value: Light to Dark

tag: time after light change

value: 0 min

tag: chip antibody

tag: genome build


title: LANS-Set2_lightToDark_set2d-rph1d_60min_ChIP_Input

value: 60 min


title: LANS-Set2_lightToDark_set2d-rph1d_90min_ChIP_Input

value: 90 min


title: LANS-Set2_lightToDark_set2d-rph1d_30min_ChIP_Input

value: 30 min


title: LANS-Set2_darkToLight_40min_ChIP_input

value: Dark to Light

value: 40 min


title: Monosensitized Active Patient 1 [P1 T2]


title: m1_Young2_M11


title: WT zebrafish heart rep3

city: Potsdam

first: Salim

last: Seyfired

address: Karl-Liebknecht-Str. 24-25

country: Germany

institute: University of Potsdam

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version (Illumina).
The FASTQ files were adapter and quality trimmed using Trim Galore! (version 0.4.1) with default settings as described in the User Guide except for the setting of the quality cutoff (-q/--quality) which was set to a Phred score of 15. Trim Galore! used Cutadapt (version 1.9.1) as subroutine.
Quality control of FASTQ files was performed by FastQC (version 0.11.4) before and after trimming.
After trimming, FASTQ files were mapped against a reference genome with the splice-aware aligner STAR (version 2.5.0c) to generate BAM files.
The BAM files were built in a 2-pass Mapping (--twopassMode Basic) and were finally sorted (--outSAMtype BAM SortedByCoordinate). All other settings have been left as default as described in the manual.
Genome_build: The genome index files were created by STAR with default settings using Danio rerio sequence and annotation data (Ensembl, build GRCz10) available on Illumina’s iGenome site (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Supplementary_files_format_and_content: The mapped data was assembled and quantified per sample with the Cufflinks suite (version 2.2.1). The Cufflinks assemblies were merged with Cuffmerge and differential expression analysis was performed with Cuffdiff, setting up (--labels 'control','sih') for the two conditions and the bam files of samples S1, S2, S3 (condition 1) and S4, S5, S6 (condition 2), respectively
Supplementary_files_format_and_content: Excel file generated as output indicates the mean value for each gene of 'control' and 'sih'; P value and Q value.

organism: Danio rerio

source_name: Hearts

growth_protocol: Zebrafish embryos were kept under standard conditions (28°C temperature, in E3 medium) until 54 hpf

extract_protocol:
∼100 hearts/replicate were extracted from 54 hpf WT and tnnt2a morphant embryos, as previously described (Lombardo et al., 2015). Hearts were pooled for each condition (three biological replicates) and total RNA was extracted with Trizol (Sigma-Aldrich) using Phase Lock Gel Heavy tubes (1.5 mL, Prime 5).
cDNA libraries were prepared starting from 100 ng of RNA/replicate, using “TruSeq Stranded Total RNA Sample Preparation Kit” (Low Sample Protocol) (Ilumina). The fragment length distribution of generated libraries was monitored and the quantification was performed using the D1000 ScreenTape System (Agilent Technologies). Equal molar amounts of individual libraries were pooled, denatured with NaOH and diluted to 1.5pM.

treatment_protocol: tnnt2a morphant hearts were obtained by injecting tnnt2a morpholino (5’-CATGTTTGCTCTGATCTGACACGCA-3’), 1 ng/1-cell stage embryo

tag: genotype/variation

value: wild-type

value: Cardiac tissue

value: 54 hpf


title: tnnt2aMO zebrafish heart rep1

value: tnnt2a morpholino injection


title: LANS-Set2_darkToLight_60min_ChIP_input


title: m1_Young2_M2


title: tnnt2aMO zebrafish heart rep2


title: WT zebrafish heart rep1


title: m1_Young2_L9


title: m1_Young2_K3


title: WT zebrafish heart rep2


title: LANS-Set2_lightToDark_90min_ChIP_Input


title: LANS-Set2_darkToLight_0min_ChIP_input


title: LANS-Set2_darkToLight_20min_ChIP_input

value: 20 min


title: LANS-Set2_lightToDark_60min_ChIP_Input


title: CUTRUN2_Mut32_H2AZ

city: Hong Kong

first: Ming

middle: Kui

last: Chan

address: Tat Chee Avenue

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
For ATAC-seq data, reads were aligned to the human reference genome hg19 by BWA with default parameters. Reads from mitochondrial were removed and de-duplicated. Only paired reads were used for further analysis. MACS2 was used to call peaks with paired-end mode (q < 0.05). Coverage files for IGV visualization were generated from bam files using deepTools
For CUT&RUN seq data, reads were aligned to human reference genome hg19 and yeast reference genome sacCer3 by Bowtie 2 separately. Human reads were normalized by spike-in yeast reads using deepTools. MACS2 was used to call peaks using parental as control under p < 0.001 with paired-end mode. Mutant enriched peaks were identified by ‘DESeq2’ taking yeast spike-in reads as scale factor after counting reads within peaks using BEDTools (p  < 0.05 and log2 fold change > 0.5). Peak annotation was performed by R package ‘ChIPseeker’. For each gene, occupancy of FLAG was quantified by the number of reads located in gene body and 1 kb upstream of TSS counted by BEDTools, and subsequently normalized by the yeast spike-in factor. To identify the genes showing differential occupancy of FLAG between mutants and WT, differential occupancy analysis was further performed by ‘DESeq2’ (p < 0.01 and log2 fold change > 0.5).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deepTools; NARROWPEAK files contain peaks using parental as control called by MACS2.

growth_protocol: S2VP10 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cut & Run was performed according to the protocol described in Meers et al.(2019) with slight modifications. All reactions were performed at 4ºC unless stated otherwise. Each centrifugation step was performed at 600 g for 3 min. 4 x 106 cells was used for each reaction. Cells were washed twice with PBS and resuspended in Buffer NE1 (20 mM HEPES-KOH pH7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol, Proteinase Inhibitor). After 10 min, cells were collected and incubated in Buffer 1 (20 mM HEPES-KOH pH7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM Spermidine, 0.1% BSA, Proteinase Inhibitor) for 5 min. Cells were collected, washed once with Buffer 2 (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, Proteinase Inhibitor) and resuspended in CUT&RUN Buffer 2. Samples were incubated with antibodies for 2 hours or overnight. Samples containing primary mouse antibodies were washed twice with Buffer 2 before incubation with anti-mouse rb IgG (Jackson ImmunoResearch, 315-005-003) for one hour. Nuclei was then collected, washed twice with Buffer 2 and incubated with pA-MNase fusion protein (150 ng) for one hour. Nuclei was washed once with Buffer 2 and once with low salt buffer (3.5 mM HEPES, Proteinase Inhibitor). Upon resuspension in low salt buffer, 10 mM CaCl2 was added to each reaction. MNase digestion was stopped after 30 min with the addition of Buffer 2 (supplemented with 10 mM EDTA, 20 mM EGTA and 28.8 pg yeast spike in). Samples were incubated for 15 min at 37 ºC. DNA was purified using NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL).
CUT&RUN libraries were prepared using Ovation Ultralow System V2 (NuGEN, 0344NB).
CUT&RUN libraries were sequenced on a HiSeq X platform (Illumina) using paired end sequencing.
ATAC-seq was performed according to the protocol in Buenrostro et al. (2015). 50,000 cells were suspended in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40). Crude nuclei were isolated by centrifugation at 500 g for 10 min and resuspended in 25 ml of TD Buffer (2x reaction buffer, Illumina). Nuclei pellet was collected (500 g, 5 min) and suspended in transposition reaction mix (25 ml, 2.5 ml TDE1, 22.5 ml l H2O). The reactions were incubated at 37ºC for 30 min with gentle mixing. DNA was immediately purified using Qiagen MinElute PCR Purification kit.
ATAC-seq libraries were PCR amplified according to protocol and purified using Qiagen MinElute PCR Purification kit. Double sided bead purification (0.5x beads volume, followed by 1.3x beads volume) was performed using AMPure XP beads to enrich for fragments between 150 bp to 1000 bp. Library quality and fragment sizes were accessed using Bioanalyzer (Agilent).
ATAC-seq libraries were sequenced with 150 bp paired end sequencing on HiSeq X (Illumina).

tag: cell line

value: pancreatic cancer cell line; adenocarcinoma derived

tag: technology

value: CUT&RUN

tag: batch


title: m1_Young1_F3

tag: cell type

value: primary murine brain endothelial cells


title: tnnt2aMO zebrafish heart rep3

tag: tissue

tag: developmental stage


title: CUTRUN2_Mut3_H2AZ


title: CUTRUN2_Parental_H2AZ


title: CUTRUN2_WT7_H2AZ

value: WT


title: m1_Young2_F18


title: LANS-Set2_lightToDark_30min_ChIP_Input


title: CUTRUN2_Mut32_flag


title: LANS-Set2_lightToDark_0min_ChIP_Input


title: CUTRUN2_Mut3_flag


title: m1_Young1_H18


title: rph1d_ChIP_Input


title: CUTRUN2_Parental_flag


title: CUTRUN2_WT7_flag


title: m1_Young2_E4


title: m1_Young2_N17


title: CUTRUN1_Mut32_H2A


title: set2d_ChIP_Input


title: WT_ChIP_Input


title: CUTRUN1_Mut3_H2A


title: CUTRUN1_Parental_H2A


title: CUTRUN1_WT16_H2A


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3K36me3_ChIP_Rep3

value: H3K36me3 (raised in lab)


title: m1_Young1_J4


title: m1_AY_Y3_D5


title: CUTRUN1_Mut3_flag


title: CUTRUN1_Mut32_flag


title: CUTRUN1_WT7_H2A


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3K36me3_ChIP_Rep3

value: Light to Dark


title: CUTRUN1_Parental_flag


title: m1_AY_Y3_M17


title: m1_Young1_F5


title: CUTRUN1_WT7_flag


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3K36me3_ChIP_Rep3


title: CUTRUN1_WT16_flag


title: ATACseq2_Mut32

value: ATAC-seq


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3K36me3_ChIP_Rep3

value: 0 min


title: m1_AY_Y3_D15


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3K36me3_ChIP_Rep2

value: 90 min


title: ATACseq2_Mut3


title: ATACseq2_WT7


title: m1_Young1_M2


title: ATACseq1_Mut32


title: ATACseq1_Mut3


title: ATACseq1_WT16


title: ATACseq1_WT7


title: m1_AY_Y3_F6


title: m1_AY_Y3_A11


title: RNAseq2_WT16

data_processing:
For RNAseq data, reads were mapped to the human genome hg19 and counted by STAR 2.6.1a with default parameters. R package DESeq2 was used to perform differential expression analysis (P value <0.05 and |log2 fold change| > 0.25). bamCoverage in deepTools was used to generate bigwig files for IGV visualization using the traditional normalization method: Reads Per Kilobase per Million mapped reads (RPKM)
For PROseq data, adapter cutting, reads aligning and coverage files generating follows the pipeline illustrated by Dig et. al. Counts data was gotten from the bigwig files using R package bigwig. R package DESeq2 was used to perform differential expression analysis (P value < 0.05 and |log2 fold change| > 0.25).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: pancreatic cancer cell line; adenocarcinoma derived

extract_protocol:
Total RNA was extracted from KI cell lines (WT7, WT16, G53D3, G53D32) using the MiniBEST Universal RNA extraction kit (Takara). Ribosomal RNA was depleted removed using the NEBNext® rRNA Depletion Kit (NEB).
RNA-seq libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s protocol, followed by quality control using Bioanalyzer 2100.
RNA-seq libraries were sequenced on a HiSeq X platform (Illumina) using 150 bp paired-end sequencing.

value: pancreatic cancer cell line


title: RNAseq2_WT7


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3K36me3_ChIP_Rep2


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3K36me3_ChIP_Rep2

value: 30 min


title: RNAseq1_WT7


title: RNAseq2_Mut3


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3K36me3_ChIP_Rep1


title: RNAseq1_Mut3


title: RNAseq1_WT16


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3K36me3_ChIP_Rep1

value: 60 min


title: m1_Young2_G5


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3K36me3_ChIP_Rep1


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3K36me3_ChIP_Rep2


title: m1_Young1_E13


title: m1_AY_Y3_B1


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3K36me3_ChIP_Rep1


title: US-1642303

value: ob/ob

value: hypothalamus

tag: Sex

value: male

tag: age

value: 11 weeks

tag: treatment

value: intracerebral ventricular injection vehicle. Diabetic pair fed to FGF1. Euthanized 5 days post injection

tag: number of mice


title: rph1d_H3K36me3_ChIP_Rep3

tag: strain


title: US-1642314


title: US-1642302


title: RNAseq2_Mut32

tag: genotype


title: m1_AY_Y3_I3


title: m1_Young2_K5


title: US-1642306


title: m1_Young2_I16


title: rph1d_H3K36me3_ChIP_Rep2

tag: lans-set2 status


title: m1_AY_Y3_I2


title: m1_AY_Y3_P14


title: US-1642305


title: hepg2_16µg/ml_H3

city: hangzhou

first: jingjing

last: wang

address: WENYI  WEST road

description: After 7 days of treatment with polaprezinc at 0 or 16 µg/ml, total RNA from hepG2 cells was extracted using theTRIzol(Invitrogen; Thermo Fisher Scientific, Inc.)method.A NanoDrop ND-1000 spectrophotometer (NanoDropTechnologies; Thermo Fisher Scientific, Inc.) was used to determine RNA concentration. The criteria for absorbance ratios was established as A260/A280Z1.8 and A260/A230Z1.5. The criteria for the RNA integrity numbervalue was set at 46. Genomic DNA contamination was evaluated by gel electrophoresis. Microarray analysis was performed using Human OneArray(®) Annotation HOA v7 release 1.0（Phalanx Biotech Group, Inc. ） , which contains 31,741 mRNA probes, detecting 20,672 genes in the human genome.

hyb_protocol: HOA 7.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: HOA 7.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing:
Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.
Rosetta Resolvers computed normalized intensities, average of technical replicates.

source_name: liver cancer cells

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Human hepatic cancer cell lines cultured in RPMI 1640 medium (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco;Thermo Fisher Scientific, Inc.). The cells were maintained at 37˚C in 5% CO2.

extract_protocol: RNA extraction by Trizol Reagent ( Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Two samples were treated with polaprezinc at 0 or 16 µg/ml

value: liver cancer cells

value: hepatocellular carcinoma


title: rph1d_H3K36me3_ChIP_Rep1

tag: time after light change


title: hepg2_0µg/ml_H1


title: RNAseq1_Mut32


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3_ChIP_Rep3

tag: chip antibody

value: H3 (EMD Millipore 05-928)


title: m1_Young1_C13

value: primary murine brain endothelial cells


title: US-1642319

value: intracerebral ventricular injection vehicle. Non-Diabetic pair fed to FGF1. Euthanized 5 days post injection


title: US-1642318


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3_ChIP_Rep3

value: Light to Dark

tag: genome build


title: US-1642317


title: m1_Young2_E10


title: US-1642312


title: US-1642307


title: m1_Young2_C10


title: US-1642300


title: US-1642298


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3_ChIP_Rep3


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3_ChIP_Rep3


title: US-1642297


title: m1_Young2_G3


title: US-1642329

value: 3 ug intracerebral ventricular injection of FGF1. Euthanized 5 days post injection


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3_ChIP_Rep2


title: m1_AY_Y3_D6


title: US-1642328


title: US-1642304


title: US-1642330


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3_ChIP_Rep2


title: US-1642325


title: US-1642322


title: US-1642324


title: m1_Young2_D18


title: US-1642321


title: m1_Young1_E11


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3_ChIP_Rep2


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3_ChIP_Rep2

value: 0 min


title: LANS-Set2_lightToDark_set2d-rph1d_90min_H3_ChIP_Rep1

value: 90 min


title: m1_Young2_B7


title: SmoM2_lower_10wk_rep3

city: New York

first: Vincent

last: Fiore

state: NY

address: 1230 York St.

institute: Rockefeller University

data_processing:
Alignment: 50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: Gene_ID, Counts

molecule: polyA RNA

source_name: Mouse backskin

extract_protocol:
Adult epidermal basal cells. Each sample was pooled from 2 mice. "SmoM2_upper" denotes Sca1+ oncogenic basal cells that remain in the superficial region of BCC tumors. "SmoM2_lower" denotes Sca1- oncogenic basal cells that have invaded distally into the stroma.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research). Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >9.
TruSeq Stranded mRNA Library Preparation (Poly-A selection and Stranded RNA-Seq)

value: Mixed

value: Skin

tag: sorting markers


title: SmoM2_lower_10wk_rep2


title: SmoM2_lower_10wk_rep1


title: US-1642331

source_name: Hypothalamus samples from FGF1 and FGF19 ICV ob/ob mice


title: m1_Young1_B10


title: LANS-Set2_lightToDark_set2d-rph1d_60min_H3_ChIP_Rep1

value: 60 min


title: LANS-Set2_lightToDark_set2d-rph1d_30min_H3_ChIP_Rep1

value: 30 min


title: SmoM2_upper_10wk_rep2


title: SmoM2_upper_10wk_rep1


title: SmoM2_upper_10wk_rep3


title: m1_Young1_C6


title: m1_AY_Y3_L1


title: m1_AY_Y3_H7


title: WT_IFE_10wk_rep1

value: WT


title: m1_Young1_N8


title: WT_IFE_10wk_rep3


title: rph1d_H3_ChIP_Rep3


title: WT_IFE_10wk_rep2


title: SMAC+ICB_S15

city: Boston

first: Shengqing

last: Gu

state: MA

address: 3 Blackfan circle

institute: Dana-Farber Cancer Institute

description: SMAC+ICB treated r3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR using the default parameters.
Read count and TPM were calculated using RSEM.
Statistics for differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count and DESeq2-vst normalized values for each Sample.

source_name: established B16F10 melanoma tumors

extract_protocol:
We extracted total RNA using the miRNeasy Plus Mini Kit (Qiagen, #17004) following the manufacturer’s protocol
Total RNA samples in each experiment were submitted to Novogene Inc. for sequencing. Standard mRNA library preparation kit was used for library preparation. Paired-end 150bp sequencing was performed on Illumina HiSeq 2500.

treatment_protocol: We treated established B16F10 melanoma tumors with birinapant and/or combination anti-PD-1/CTLA-4

tag: cancer type

value: melanoma

value: skin

value: birinapant + ICB


title: SMAC+ICB_S7

description: SMAC+ICB treated r1


title: US-1642326

value: ob/ob

value: hypothalamus

value: male

value: 11 weeks


title: SMAC+ICB_S8

description: SMAC+ICB treated r2


title: LANS-Set2_lightToDark_set2d-rph1d_0min_H3_ChIP_Rep1

value: H3 (EMD Millipore 05-928)


title: ICB_S13

description: ICB treated r2

value: ICB


title: SMAC_S12

description: SMAC treated r3

value: birinapant


title: SMAC_S11

description: SMAC treated r2


title: rph1d_H3_ChIP_Rep1


title: LANS-Set2_darkToLight_60min_H3K36me3_ChIP_Rep3

value: Dark to Light

value: H3K36me3 (raised in lab)


title: m1_Young2_N10

value: primary murine brain endothelial cells


title: m1_Young1_I4


title: ICB_S5

description: ICB treated r1


title: m1_Young2_M16


title: LANS-Set2_darkToLight_40min_H3K36me3_ChIP_Rep3

value: 40 min


title: m1_AY_Y3_G9


title: LANS-Set2_darkToLight_20min_H3K36me3_ChIP_Rep3

value: 20 min


title: Vehicle_S9

description: Vehicle treated r3

value: Vehicle


title: Vehicle_S1

description: Vehicle treated r1


title: Vehicle_S2

description: Vehicle treated r2


title: rph1d_H3_ChIP_Rep2


title: LANS-Set2_darkToLight_0min_H3K36me3_ChIP_Rep3

value: 0 min


title: sgTraf3_2_IFNg_r2

description: sgTraf3-2 IFNg rep2

treatment_protocol: we treated sgControl or sgTraf3-transduced B16F10 cells with vehicle control or 1ng/ml IFNγ for 2 days

value: melanoma

tag: sgrna

value: IFNg


title: m1_Young2_D3


title: ICB_S14

description: ICB treated r3

value: skin


title: m1_AY_Y3_P7


title: LANS-Set2_darkToLight_60min_H3K36me3_ChIP_Rep2

value: 60 min


title: sgTraf3_1_IFNg_r2

description: sgTraf3-1 IFNg rep2


title: sgTraf3_1_IFNg_r1

description: sgTraf3-1 IFNg rep1


title: sgTraf3_2_IFNg_r1

description: sgTraf3-2 IFNg rep1


title: sgCtrl_IFNg_r2

description: sgRosa26 IFNg rep2


title: m1_Young1_K4


title: m1_Young1_C16


title: sgCtrl_IFNg_r1

description: sgRosa26 IFNg rep1


title: LANS-Set2_darkToLight_40min_H3K36me3_ChIP_Rep2


title: sgTraf3_2_veh_r2

description: sgTraf3-2 Vehicle rep2


title: LANS-Set2_darkToLight_20min_H3K36me3_ChIP_Rep2


title: SMAC_S3

description: SMAC treated r1


title: sgTraf3_1_veh_r2

description: sgTraf3-1 Vehicle rep2


title: LANS-Set2_darkToLight_0min_H3K36me3_ChIP_Rep2


title: sgTraf3_1_veh_r1

description: sgTraf3-1 Vehicle rep1


title: m1_Young2_D4


title: m1_AY_Y3_A13


title: sgCtrl_veh_r1

description: sgRosa26 Vehicle rep1


title: LANS-Set2_darkToLight_60min_H3K36me3_ChIP_Rep1


title: LANS-Set2_darkToLight_40min_H3K36me3_ChIP_Rep1


title: C_M2_DN

description: MHC-I/PD-L1 negative regulator screen (M2 library) - MHC-I low & PD-L1 low

data_processing:
Library strategy: CRISPR screening
The sequence reads were trimmed to remove a constant portion of the sgRNA sequences and mapped to the M1/M2 mouse genome-wide CRISPR library with MAGeCK “count” module, which computes read counts for each sgRNA. We used MAGeCK “test” module to identify MHC-I/PD-L1 regulators, for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Genome_build: mm10
Supplementary_files_format_and_content: The read count files returned from the MAGeCK

growth_protocol: We performed CRISPR screens to identify regulators of MHC-I induced by IFNγ. We first transduced 1x108 B16F10 cells with our M1/M2 mouse genome-wide CRISPR library at MOI of 0.3 to ensure that most transduced cells received only 1 virion. We cultured the transduced cells for 2 days in DMEM full media, selected with 2µg/ml puromycin for 2 days, and cultured for an additional 2 days to allow depletion of residual protein of the targeted genes. We then treated the cells with high or low dosage IFNγ to identify MHC-I regulators.

extract_protocol: We extracted genomic DNA from each sorted population or from the unsorted population by phenol-chloroform extraction, and then performed two rounds of PCR to construct the barcode-indexed sequencing library for each sample.

treatment_protocol: For identification of positive regulators, we treated the transduced cells with 10ng/ml IFNγ for 2 days, and flow-sorted 2x107 cells for the following populations: MHC-Ihi PD-L1hi, MHC-Ihi PD-L1lo, MHC-Ilo PD-L1hi, MHC-Ilo PD-L1lo.

value: 0.1ng/ml IFNg


title: sgCtrl_veh_r2

description: sgRosa26 Vehicle rep2


title: C_M2_MN

description: MHC-I/PD-L1 negative regulator screen (M2 library) - MHC-I low & PD-L1 high


title: m1_AY_Y3_E4


title: C_M2_MP

description: MHC-I/PD-L1 negative regulator screen (M2 library) - MHC-I high & PD-L1 high


title: m1_Young2_A12


title: C_M2_PN

description: MHC-I/PD-L1 negative regulator screen (M2 library) - MHC-I high & PD-L1 low


title: C_M2_Unsorted

description: MHC-I/PD-L1 negative regulator screen (M2 library) - Unsorted


title: C_M1_DN

description: MHC-I/PD-L1 negative regulator screen (M1 library) - MHC-I low & PD-L1 low


title: C_M1_PN

description: MHC-I/PD-L1 negative regulator screen (M1 library) - MHC-I high & PD-L1 low


title: LANS-Set2_darkToLight_20min_H3K36me3_ChIP_Rep1


title: m1_Young1_B15


title: LANS-Set2_darkToLight_0min_H3K36me3_ChIP_Rep1


title: m1_AY_Y3_O16


title: m1_AY_Y3_G11


title: LANS-Set2_lightToDark_90min_H3K36me3_ChIP_Rep3

value: Light to Dark

value: 90 min


title: sgTraf3_2_veh_r1

description: sgTraf3-2 Vehicle rep1


title: C_M1_MP

description: MHC-I/PD-L1 negative regulator screen (M1 library) - MHC-I high & PD-L1 high


title: C_M1_Unsorted

description: MHC-I/PD-L1 negative regulator screen (M1 library) - Unsorted


title: m1_Young2_I12


title: LANS-Set2_lightToDark_30min_H3K36me3_ChIP_Rep3

value: 30 min


title: LANS-Set2_lightToDark_60min_H3K36me3_ChIP_Rep3


title: A_M2_DN

description: MHC-I/PD-L1 positive regulator screen (M2 library) - MHC-I low & PD-L1 low

value: 10ng/ml IFNγ


title: m1_Young2_C17


title: m1_Young2_L1


title: LANS-Set2_lightToDark_0min_H3K36me3_ChIP_Rep3


title: A_M2_PN

description: MHC-I/PD-L1 positive regulator screen (M2 library) - MHC-I high & PD-L1 low


title: LANS-Set2_lightToDark_90min_H3K36me3_ChIP_Rep2


title: A_M2_MP

description: MHC-I/PD-L1 positive regulator screen (M2 library) - MHC-I high & PD-L1 high


title: A_M2_Unsorted

description: MHC-I/PD-L1 positive regulator screen (M2 library) - Unsorted


title: m1_AY_Y3_B5


title: A_M1_DN

description: MHC-I/PD-L1 positive regulator screen (M1 library) - MHC-I low & PD-L1 low


title: A_M1_PN

description: MHC-I/PD-L1 positive regulator screen (M1 library) - MHC-I high & PD-L1 low


title: LANS-Set2_lightToDark_60min_H3K36me3_ChIP_Rep2


title: C_M1_MN

description: MHC-I/PD-L1 negative regulator screen (M1 library) - MHC-I low & PD-L1 high


title: A_M1_MN

description: MHC-I/PD-L1 positive regulator screen (M1 library) - MHC-I low & PD-L1 high


title: A_M1_MP

description: MHC-I/PD-L1 positive regulator screen (M1 library) - MHC-I high & PD-L1 high


title: A_M1_Unsorted

description: MHC-I/PD-L1 positive regulator screen (M1 library) - Unsorted


title: LANS-Set2_lightToDark_0min_H3K36me3_ChIP_Rep2


title: m1_Young2_B4


title: LANS-Set2_lightToDark_30min_H3K36me3_ChIP_Rep2


title: sgTraf3_2_IFNg_r1

description: sgTraf3-2 IFNg rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using BWA using the default parameters.
We used MACS2 for peak calling.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 was applied to identify the differentially accessible regions.

extract_protocol:
ATAC-seq was performed on triplicates (200,000 cells) by the Center for Functional Cancer Epigenetics at DFCI as previously described.
Genome-wide mapping of insertion ends by high-throughput sequencing allows for multidimensional assays of the regulatory landscape of chromatin with a relatively simple protocol.

treatment_protocol:
The assay of transposase accessible chromatin (ATAC-seq) uses hyperactive Tn5 transposase to simultaneously cut and ligate adapters for high-throughput sequencing at regions of increased accessibility.
we treated sgControl or sgTraf3-transduced B16F10 cells with vehicle control or 1ng/ml IFNγ for 2 days


title: sgTraf3_2_IFNg_r2

description: sgTraf3-2 IFNg rep2


title: LANS-Set2_lightToDark_90min_H3K36me3_ChIP_Rep1


title: m1_Young1_D10


title: A_M2_MN

description: MHC-I/PD-L1 positive regulator screen (M2 library) - MHC-I low & PD-L1 high


title: sgTraf3_1_IFNg_r2

description: sgTraf3-1 IFNg rep2


title: sgCtrl_IFNg_r2

description: sgRosa26 IFNg rep2


title: m1_AY_Y3_E13


title: sgTraf3_1_IFNg_r1

description: sgTraf3-1 IFNg rep1


title: m1_Young2_K18


title: LANS-Set2_lightToDark_60min_H3K36me3_ChIP_Rep1


title: sgTraf3_2_veh_r2

description: sgTraf3-2 Vehicle rep2


title: sgTraf3_2_veh_r1

description: sgTraf3-2 Vehicle rep1


title: LANS-Set2_lightToDark_0min_H3K36me3_ChIP_Rep1


title: m1_Young1_L14


title: sgTraf3_1_veh_r2

description: sgTraf3-1 Vehicle rep2


title: sgTraf3_1_veh_r1

description: sgTraf3-1 Vehicle rep1


title: m1_Young2_M8


title: sgCtrl_veh_r2

description: sgRosa26 Vehicle rep2


title: set2d_H3K36me3_ChIP_Rep3


title: set2d_H3K36me3_ChIP_Rep2


title: m1_Young1_N11


title: 11.Th17 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 2.5

city: wuerzburg

first: Yin

last: Xiao

address: Josef schneider strasse 2

department: institute of pathology

institute: university of wuerzburg

description: C57BL/6 NFATc1/ΔS

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM and RPKM values.

growth_protocol: Mouse CD4 T cell isolation kit (Biolegend) was used to isolate CD4+ T cells from LN and spleen. The isolated CD4+ T cells were stimulated for 3 d with plate-bound anti-hamster IgG (12.5 ug/ml) and soluble anti-CD3ɛ (145-2C11, BD Pharmingen) and anti-CD28 (37.51, BD Pharmingen). The culture conditions for Th1 and Th2 were 0.5 μg/ml anti-CD3 and 1 μg/ml anti-CD28, whereas for Th17 0.25 μg/ml anti-CD3 and 1 μg/ml anti-CD28. The following cytokines for skewing Th differentiation were added to the culture: Th1: 10 ng/ml mIL-12, 2.5 μg/ml anti-mIL-4; Th2: 50 ng/ml mIL-4, 2.5 μg /ml anti-mIFN-γ; Th17: 0.5 ng/ml mTGFβ, 20 ng/ml mIL-6 (both PeproTech), 2.5 μg/ml anti-mIFN-γ, and 2.5 μg/ml anti-mIL-4. The cell culture medium (supplemented with 5 % FCS, β-Mercaptoethanol, PenStrep; Invitrogen) was RPMI for Th1 and Th2 or IMDM for Th17 cell differentiation. RNA for sequencing was extracted from cells collected on day 2.5 and day 3.5.

extract_protocol:
Cells were directly collected in RLT-Lysis buffer (Qiagen) supplemented with beta-Mercaptoethanol according to the manual. Isolation of RNA was done using Qiagen's RNeasy plus mini kit.
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 nano chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 700 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay.

value: C57BL/6 NFATc1/<delta>S

tag: time point

value: Day 2.5


title: m1_Young1_N9

tag: cell type


title: 12.Th17 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 3.5

description: C57BL/6 NFATc1/ΔS

value: Day 3.5


title: set2d_H3K36me3_ChIP_Rep1

value: H3K36me3 (raised in lab)


title: sgCtrl_veh_r1

description: sgRosa26 Vehicle rep1

tag: tissue


title: m1_Young1_L7

value: primary murine brain endothelial cells


title: WT_H3K36me3_ChIP_Rep3

value: WT


title: m1_Young1_J18


title: WT_H3K36me3_ChIP_Rep2


title: LANS-Set2_lightToDark_30min_H3K36me3_ChIP_Rep1


title: 8.Th2 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 3.5

description: C57BL/6 NFATc1/ΔS


title: m1_AY_Y3_C1


title: sgCtrl_IFNg_r1

description: sgRosa26 IFNg rep1


title: WT_H3K36me3_ChIP_Rep1


title: 5.Th2 cells differentiated from CD4+ T cells of WT mice for day 2.5

value: C57BL/6 wild type


title: 7.Th2 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 2.5

description: C57BL/6 NFATc1/ΔS


title: 6.Th2 cells differentiated from CD4+ T cells of WT mice for day 3.5


title: m1_Young2_H2


title: m1_Young1_I5


title: 3.Th1 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 2.5

description: C57BL/6 NFATc1/ΔS


title: 2.Th1 cells differentiated from CD4+ T cells of WT mice for day 3.5


title: LANS-Set2_darkToLight_60min_H3_ChIP_Rep3

value: Dark to Light

value: H3 (EMD Millipore 05-928)


title: 1.Th1 cells differentiated from CD4+ T cells of WT mice for day 2.5


title: 10.Th17 cells differentiated from CD4+ T cells of WT mice for day 3.5


title: LANS-Set2_darkToLight_40min_H3_ChIP_Rep3

value: 40 min


title: m1_Young1_N17


title: m1_AY_Y3_O6


title: m1_Young2_N6


title: LANS-Set2_darkToLight_20min_H3_ChIP_Rep3

value: 20 min


title: m1_Young1_I8


title: m1_AY_Y3_F2


title: 4.Th1 cells differentiated from CD4+ T cells of NFATc1/ΔS mice for day 3.5

description: C57BL/6 NFATc1/ΔS


title: m1_AY_Y3_P13


title: 9.Th17 cells differentiated from CD4+ T cells of WT mice for day 2.5


title: m1_Young2_M17


title: LANS-Set2_darkToLight_40min_H3_ChIP_Rep2


title: m1_Young2_P11


title: LANS-Set2_darkToLight_0min_H3_ChIP_Rep2

value: 0 min


title: LANS-Set2_darkToLight_0min_H3_ChIP_Rep3


title: LANS-Set2_darkToLight_60min_H3_ChIP_Rep1

value: 60 min


title: LANS-Set2_darkToLight_20min_H3_ChIP_Rep2


title: LANS-Set2_darkToLight_40min_H3_ChIP_Rep1


title: m1_AY_Y3_E8