title: CCl4_BXH22_KccJ

description: PolyA RNA


title: CCl4_BXH2_TyJ

status: Public on Mar 22 2021

type: SRA

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

description: PolyA RNA

library_source: transcriptomic

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) with 100 bootstrap replicates using kallisto v0.46.
Differential expression was performed using sleuth (v 0.30).
Gene counts and TPM values were tabulated with tximport.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt files are tab-delimited text containing either gene counts or gene TPMs.
Supplementary_files_format_and_content: *.h5 files are HDF5 files generated by kallisto containing pseudo alignment counts and bootstrapping estimates for analysis with sleuth R package.

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA from mouse liver samples (one mouse per strain) was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation protocol.
Paired-end mode to a length of 2x76 base pairs using the Illumina HiSeq2500 platform.

treatment_protocol: CCl4 was administered intraperitoneally at a dose of 5 microliters of 10% solution in olive oil (both CCl4 and olive oil from Sigma-Aldrich, St. Louis, MO) per gram of body weight. CCl4 injections were started at 10-12 weeks age and given twice weekly for 6 weeks. Olive oil was used for vehicle-injected mice. Mice were sacrificed 72 hours after the final injection and their livers were harvested for RNA (snap-frozen) and histology (formalin-fixed and paraffin-embedded).

tag: strain

tag: tissue

value: Liver

tag: treatment


title: Vehicle_BXH2_TyJ

description: PolyA RNA

value: Vehicle


title: CCl4_BXH19_TyJ

description: PolyA RNA


title: Vehicle_BXH19_TyJ

description: PolyA RNA


title: CCl4_BXH4_TyJ

description: PolyA RNA


title: Vehicle_C58_J

description: PolyA RNA


title: Vehicle_BXH10_TyJ

description: PolyA RNA


title: CCl4_BXH10_TyJ

description: PolyA RNA


title: Vehicle_BXD87_RwwJ

description: PolyA RNA


title: CCl4_BXD9_TyJ

description: PolyA RNA


title: CCl4_BXD87_RwwJ

description: PolyA RNA


title: Vehicle_BXD75_RwwJ

description: PolyA RNA


title: CCl4_BXD84_RwwJ

description: PolyA RNA


title: Vehicle_BXD84_RwwJ

description: PolyA RNA


title: CCl4_C57BL_6J

description: PolyA RNA


title: Vehicle_BXD56_RwwJ

description: PolyA RNA


title: CCl4_BXD6_TyJ

description: PolyA RNA


title: Vehicle_BXD6_TyJ

description: PolyA RNA


title: CCl4_BXD75_RwwJ

description: PolyA RNA


title: Vehicle_BXH4_TyJ

description: PolyA RNA


title: CCl4_BXD56_RwwJ

description: PolyA RNA


title: CCl4_BXD55_RwwJ

description: PolyA RNA


title: CCl4_BXD5_TyJ

description: PolyA RNA


title: Vehicle_BXD9_TyJ

description: PolyA RNA


title: CCl4_BXD48_RwwJ

description: PolyA RNA


title: Vehicle_BXD44_RwwJ

description: PolyA RNA


title: CCl4_BXD42_TyJ

description: PolyA RNA


title: Vehicle_BXD42_TyJ

description: PolyA RNA


title: CCl4_BXD40_TyJ

description: PolyA RNA


title: CCl4_BXD44_RwwJ

description: PolyA RNA


title: Vehicle_BXD34_TyJ

description: PolyA RNA


title: CCl4_BXD38_TyJ

description: PolyA RNA


title: Vehicle_BXD40_TyJ

description: PolyA RNA


title: Vehicle_BXD38_TyJ

description: PolyA RNA


title: Vehicle_BXD32_TyJ

description: PolyA RNA


title: CCl4_BXD34_TyJ

description: PolyA RNA


title: CCl4_BXD32_TyJ

description: PolyA RNA


title: Vehicle_BXD27_TyJ

description: PolyA RNA


title: CCl4_BXD27_TyJ

description: PolyA RNA


title: Vehicle_BXD24_TyJ-Cep290rd16_J

description: PolyA RNA


title: Vehicle_BXD22_TyJ

description: PolyA RNA


title: Vehicle_BXD55_RwwJ

description: PolyA RNA


title: CCl4_BXD24_TyJ-Cep290rd16_J

description: PolyA RNA


title: Vehicle_BXD48_RwwJ

description: PolyA RNA


title: CCl4_BXD22_TyJ

description: PolyA RNA


title: Vehicle_BXD21_TyJ

description: PolyA RNA


title: Vehicle_BXD5_TyJ

description: PolyA RNA


title: Vehicle_BXD2_TyJ

description: PolyA RNA


title: CCl4_BXD2_TyJ

description: PolyA RNA


title: CCl4_BXD21_TyJ

description: PolyA RNA


title: CCl4_BXD19_TyJ

description: PolyA RNA


title: CCl4_BXD18_TyJ

description: PolyA RNA


title: Vehicle_BXD18_TyJ

description: PolyA RNA


title: Vehicle_BXD16_TyJ

description: PolyA RNA


title: Vehicle_BXD14_TyJ

description: PolyA RNA


title: Vehicle_BXD15_TyJ

description: PolyA RNA


title: CCl4_BXD16_TyJ

description: PolyA RNA


title: Vehicle_BXD13_TyJ

description: PolyA RNA


title: CCl4_BXD12_TyJ

description: PolyA RNA


title: CCl4_BXD14_TyJ

description: PolyA RNA


title: Vehicle_BXD12_TyJ

description: PolyA RNA


title: CCl4_BXD1_TyJ

description: PolyA RNA


title: CCl4_BXD13_TyJ

description: PolyA RNA


title: Vehicle_BXD1_TyJ

description: PolyA RNA


title: Vehicle_BXA8_PgnJ

description: PolyA RNA


title: CCl4_BXA8_PgnJ

description: PolyA RNA


title: Vehicle_BXD19_TyJ

description: PolyA RNA


title: Vehicle_BXA7_PgnJ

description: PolyA RNA


title: Vehicle_BXA24_PgnJ

description: PolyA RNA


title: Vehicle_BXA4_PgnJ

description: PolyA RNA


title: Vehicle_BXA2_PgnJ

description: PolyA RNA


title: CCl4_BXA2_PgnJ

description: PolyA RNA


title: CCl4_BXA4_PgnJ

description: PolyA RNA


title: CCl4_BXA24_PgnJ

description: PolyA RNA


title: CCl4_BXA14_PgnJ

description: PolyA RNA


title: Vehicle_BXA14_PgnJ

description: PolyA RNA


title: Vehicle_BXA13_PgnJ

description: PolyA RNA


title: CCl4_BXA13_PgnJ

description: PolyA RNA


title: Vehicle_BXA12_PgnJ

description: PolyA RNA


title: CCl4_BXA12_PgnJ

description: PolyA RNA


title: CCl4_BXA11_PgnJ

description: PolyA RNA


title: Vehicle_BXA11_PgnJ

description: PolyA RNA


title: CCl4_BXD15_TyJ

description: PolyA RNA


title: CCl4_BXA1_PgnJ

description: PolyA RNA


title: CCl4_BXD11_TyJ

description: PolyA RNA


title: Vehicle_BXA1_PgnJ

description: PolyA RNA


title: CCl4_BXA7_PgnJ

description: PolyA RNA


title: CCl4_BUB_BnJ

description: PolyA RNA

value: BUB/BnJ


title: Vehicle_BTBR_T__Itpr3tf_J

description: PolyA RNA

value: BTBR T+ Itpr3tf/J


title: CCl4_BALB_cJ

description: PolyA RNA

value: BALB/cJ


title: Vehicle_BALB_cJ

description: PolyA RNA


title: Vehicle_BALB_cByJ

description: PolyA RNA

value: BALB/cByJ


title: Vehicle_AXB8_PgnJ

description: PolyA RNA


title: CCl4_AXB8_PgnJ

description: PolyA RNA


title: Vehicle_AXB6_PgnJ

description: PolyA RNA


title: CCl4_AXB6_PgnJ

description: PolyA RNA


title: Vehicle_AXB5_PgnJ

description: PolyA RNA


title: CCl4_AXB5_PgnJ

description: PolyA RNA


title: Vehicle_BUB_BnJ

description: PolyA RNA


title: CCl4_AXB4_PgnJ

description: PolyA RNA


title: Vehicle_AXB19b_PgnJ

description: PolyA RNA


title: Vehicle_AXB2_PgnJ

description: PolyA RNA


title: CCl4_AXB19b_PgnJ

description: PolyA RNA


title: CCl4_AXB2_PgnJ

description: PolyA RNA


title: Vehicle_AXB19a_PgnJ

description: PolyA RNA


title: Vehicle_AXB4_PgnJ

description: PolyA RNA


title: Vehicle_AXB19_PgnJ

description: PolyA RNA


title: Vehicle_AXB13_PgnJ

description: PolyA RNA


title: CCl4_AXB19_PgnJ

description: PolyA RNA


title: CCl4_AXB13_PgnJ

description: PolyA RNA


title: Vehicle_AXB12_PgnJ

description: PolyA RNA


title: CCl4_AXB10_PgnJ

description: PolyA RNA


title: CCl4_AXB1_PgnJ

description: PolyA RNA


title: Vehicle_AXB10_PgnJ

description: PolyA RNA


title: CCl4_BALB_cByJ

description: PolyA RNA


title: Vehicle_AKR_J

description: PolyA RNA

value: AKR/J


title: daftg_GCBcells_rep3

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: splenic germinal center B cells from mice immunized with sheep red blood cells

data_processing:
Sequencing data were acquired through the default Illumina pipeline using bcl2fastq pipeline
reads were aligned to mus musculus reference mm10 using HiSat2 with options --dta --trim5 5 --add-chrname --ignore-quals -q  -k 1
raw counts were generated using featureCounts with options -T 4 -t exon -g gene_name, using reference genes mm10 from ncbi
Genome_build: grcm38
Supplementary_files_format_and_content: Tab delimited text file of raw gene counts

growth_protocol: Murine splenic germinal center B cells (B220+, FAS+, GL7+) from immunized mice were sorted into cold sorting buffer, washed once with cold PBS, and resuspended in Trizol.

extract_protocol:
Total RNA was isolated from sorted, viable GC (B220+, GL7+, Fas+) B cells using Direct-zolTM RNA MicroPrep kit (catalog # R2061) as recommended by the manufactuer. Briefly, an equal volume of absolute ethanol was added into each sample lysated in Trizol. Samples were mixed, transferred into Zymo-Spin IC Colomns in Collection Tubes, centrifuged and washed. Samples were then treated with DNase I (included in kit) and washed again. DNase/RNase-Free Water (included in kit) was added to elute RNA.
Libraries were prepared using the Takara SMART-Seq v4 Ultra Low Input RNA kit (catalog # 634891), as recommended by the manufacturer. An oligo-dT primed capture of total message RNA was used to produce full length transcripts from very low inputs of total RNA (10 ng total RNA input per sample). Samples were indexed using unique dual indices.
All 12 libraries were sequenced on a single lane (12-plex) of a  NextSeq 550 instrument on High Output mode, generating at least 30M 100nt single-end reads per sample.

treatment_protocol: Cg1-cre(+/-); DAF-Tg(+/+) or Cg1-cre(+/-);DAF-Tg(fl/fl) mice were immunized intraperitoneally with sheep red blood cells. Splenic germinal center B cells were sorted using fluorescence activated cell sorting (FACSAriaII device) 10 days post-immunization using specific fluorochrome-labeled antibodies.

tag: cell type

value: splenic germinal center B cells

tag: genotype


title: daftg_GCBcells_rep2


title: Vehicle_AXB1_PgnJ

description: PolyA RNA


title: CCl4_AKR_J

description: PolyA RNA


title: CCl4_A_J

description: PolyA RNA

value: A/J


title: Vehicle_A_J

description: PolyA RNA


title: daftg_GCBcells_rep1


title: Vehicle_129X1_SvJ

description: PolyA RNA


title: CCl4_129X1_SvJ

description: PolyA RNA


title: cg1_cre_GCBcells_rep3


title: cg1_cre_GCBcells_rep2


title: cg1_cre_GCBcells_rep1


title: MM.1S_TAF3spikein_DMSO_ChIPseq

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using BWA.
IGVtools version 2.8.2 is utilized to generate binned coverage data from BAM file using the parameter “-w 25 -e [extension bp]”.
The raw count TDFs are then normalized by reads per million (RPM).
For Drosophila spiked-in samples, RPM values for each bin is further multiplied by the ratio of human reads (hg19) to Drosophila reads (dm6).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Peak files are TDF files for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: multiple myeloma cell line

growth_protocol: MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
MM.1S cells were crosslinked, lysed and sonicated. For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) or the Illumina TruSeq ChIP Library Preparation Kit according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were treated with DMSO for 24h.

tag: cell line

value: multiple myeloma cell line

value: DMSO for 24h

tag: chip antibody

value: TAF3 antibody (Dr. Shannon Lauberth), Spike-in antibody (Active Motif, 61686, lot00419007)


title: MM.1S_TAF3spikein_JQKD82_ChIPseq

treatment_protocol: MM.1S cells were treated with 1 µM JQKD82 for 24h.

value: 1 uM JQKD82 for 24h


title: CCl4_AXB19a_PgnJ

description: PolyA RNA


title: MM.1S_MYC_RNAPIISer5pspikein_DMSO_ChIPseq

treatment_protocol: MM.1S cells were transduced with MYC by retrovirus. The infected cells were selected with G418, and then treated with DMSO for 48h.

tag: transduction

value: MYC

value: DMSO for 48h

value: Phospho-Rpb1 CTD (Ser5) (Cell signaling technology,13523, lot1), Spike-in antibody (Active Motif, 61686, lot00419007)


title: ArabidopsisBRM-GFP-IP-bio2

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

country: China

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

organism: Arabidopsis thaliana

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction.  Libraries were constructed by the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607), VAHTSTM DNA Adapters set3 - set6 for Illumina® (N805) and VAHTS® DNA Clean Beads (N411-02, Vazyme) according to the manufacturer’s protocol. protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

value: Seedling

tag: developmental stage

tag: antibody

value: GFP (ab290, abcam)


title: ArabidopsisBRM-GFP-IP-bio1


title: MM.1S_MYC_RNAPIISer5pspikein_JQKD82_ChIPseq

treatment_protocol: MM.1S cells were transduced with MYC by retrovirus. The infected cells were selected with G418, and then treated with 1 µM JQKD82 for 48h.

value: 1 uM JQKD82 for 48h


title: MM.1S_empty_RNAPIISer5pspikein_JQKD82_ChIPseq

treatment_protocol: MM.1S cells were transduced with empty vector by retrovirus. The infected cells were selected with G418, and then treated with 1 µM JQKD82 for 48h.

value: empty vector


title: MM.1S_empty_RNAPIISer5pspikein_DMSO_ChIPseq

treatment_protocol: MM.1S cells were transduced with empty vector by retrovirus. The infected cells were selected with G418, and then treated with DMSO for 48h.


title: Arabidopsis brm-1 brd1,2,13 rep2

data_processing:
Sequencing separately at Novogene, using Illumina nova-seq (Sequencing method: Hiseq-PE150).
Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings.
To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for wt, brm-1, brd1,2,13 and brm-1 brd1,2,13.

extract_protocol:
Total RNA was isolated from 14-day-old seedling using the HiPure Plant RNA Mini Kit C (Cat#R4151-02C, Lot#RIH05-01) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: LD (long day)

tag: ecotype


title: Arabidopsis brm-1 brd1,2,13 rep3


title: Arabidopsis brm-1 brd1,2,13 rep1


title: MM.1S_MYC_JQKD82_RNAseq, replicate2

description: MM1S_MYC_JQKD82_spike_all_fpkm_exprs_norm.txt

data_processing:
Sequenced reads were aligned to the reference human genome (hg38 or hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective refseq of transcripts using the featureCounts tool or RSEM.
Differential gene expression analysis to compare JQKD82-treated samples with control DMSO-treated samples was performed using DESeq2.
For MYC overexpression experiments, RNA-seq was normalized by a per-cell spike in strategy with ERCC standards.
The data were transformed by Loess normalization with the ERCC transcripts using the R statistical package.
Genome_build: hg38, or hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were treated with 1 µM JQKD82 or DMSO for 48h.


title: MM.1S_MYC_JQKD82_RNAseq, replicate1


title: MM.1S_MYC_DMSO_RNAseq, replicate2


title: Arabidopsis brm-1 rep3


title: Arabidopsis brd1,2,13 rep3


title: MM.1S_empty_JQKD82_RNAseq, replicate2


title: Arabidopsis brm-1 rep2


title: MM.1S_empty_JQKD82_RNAseq, replicate1


title: CCl4_BTBR_T__Itpr3tf_J

description: PolyA RNA

value: BTBR T+ Itpr3tf/J

value: Liver


title: MM.1S_empty_DMSO_RNAseq, replicate1


title: Arabidopsis BRM-GFP-input

value: none (input)


title: Arabidopsis brm-1 rep1


title: Arabidopsis WT rep2


title: DIS380003-V7

city: Vancouver

first: Don

middle: D

last: Sin

state: BC

address: Room 166, 1081 Burrard Street

country: Canada

institute: Centre for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia

data_processing:
RNA-seq reads were mapped and quantified to the GENCODE genome reference (assembly GRCh37, release 31) using Salmon (0.13.1)
Number of reads mapped to each transcript were summarized to gene level using R package Tximport (1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with number of reads for every gene and every sample

source_name: Bronchial epithelial cells

extract_protocol:
RNA was extracted from cytological brush specimens stored in QIAzol RNA lysis buffer (QIAGEN, Stockach, Germany) using the RNeasy Plus kit (QIAGEN) according to the manufacturer’s instructions. Sample quality control was performed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA)
For qualifying samples, libraries were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs, Ipswich, MA, USA)

tag: subject

value: SAL/FLU

tag: timepoint

value: post-treatment


title: Arabidopsis WT rep3


title: DIS380002-V7


title: DIS380003-V3

value: pre-treatment


title: DIS380002-V3


title: Arabidopsis BRD2-dBromo-GFP-IP-bio2


title: Arabidopsis WT rep1


title: Arabidopsis BRD2-dBromo-GFP-Input


title: MM.1S_MYC_DMSO_RNAseq, replicate1

value: multiple myeloma cell line


title: DIS320085-V3

value: FOR


title: DIS320085-V7


title: Arabidopsis BRD13-GFP-IP-bio2


title: DIS380001-V3


title: Arabidopsis brd1,2,13 rep1


title: Arabidopsis brd1,2,13 rep2


title: DIS320084-V3

value: FOR/BUD


title: DIS320084-V7


title: Arabidopsis BRD13-GFP-Input


title: MM.1S_empty_DMSO_RNAseq, replicate2


title: DIS320080-V7


title: Arabidopsis BRD2-GFP-IP-bio1


title: Arabidopsis BRD13-GFP-IP-bio1


title: DIS320080-V3


title: DIS320079-V3


title: Arabidopsis BRD1-GFP-IP-bio2


title: Vehicle_BXD11_TyJ

description: PolyA RNA

value: Vehicle


title: DIS320077-V7


title: Arabidopsis BRD1-GFP-IP-bio1


title: Arabidopsis BRD2-GFP-Input


title: Arabidopsis BRD2-dBromo-GFP-IP-bio1


title: Arabidopsis BRD1-GFP-Input


title: DIS320074-V7


title: DIS320076-V3

value: Not randomized


title: CCl4_AXB12_PgnJ

description: PolyA RNA


title: Arabidopsis brd1,2,13_BRM-GFP-IP-bio1


title: Arabidopsis brd1,2,13_BRM-GFP-IP-bio2


title: DIS320074-V3


title: DIS320071-V3


title: DIS320071-V7


title: ATACseq_ZFSssI_line1

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: ATACseq for ZFSssI_line1

data_processing:
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

growth_protocol: Plant materials  All plants in this study were grown under long-day conditions (16 h light/8 h dark). The fwa-4 mutant has been described previously (Johnson et al.,2014), as have the fwa nrpd1, fwa drm1 drm2 and fwa nrpe1 lines (Gallego-Bartolome et al., 2019). The pMDC123-ZF-3xFLAG-SssI plasmid was transformed into Agrobacterium AGLO and transformed into the different backgrounds by Agrobacterium-mediated floral dipping. T1 transgenic plants were grown on 1/2 MS medium + Glufosinate 50 μg/mL (Goldbio) in growth chambers under long-day conditions and transplanted to soil. The selection of transgenic lines for experiments was based on i) early flowering T1 plants for the lines in the fwa backgrounds and  ii) protein expression by WB for the lines in the Col-0 background. Following transgenic generations were germinated directly on soil and presence of the transgene was done by genotyping. Plants were not selected for homozygocity except for the T4 populations used for the ChIP experiment. Controls in this study correspond to untransformed plants of the different backgrounds used coming from the same seed stock. Flowering time was scored by counting the total number  rosette and caulinar leaves. In the flowering time dot plots, each dot represents the flowering time of individual plants. Plants with 20 or fewer leaves were considered early flowering. The samples used for all our genomics data correspond to inflorescence tissue collected during the day.

extract_protocol:
ATAC-seq libraries were prepared as previously described (Potok et al., 2019). Briefly, inflorescence tissues were first collected for nuclei extraction as previously described (Hetzel et al.,2016, Liu et al., 2018).
Then transposition reaction was conducted in 25 µL of 2×DMF buffer (66 mM Tris-acetate (pH = 7.8), 132 K-Acetate, 20 mM Mg-Acetate, 32% DMF) mixed with 2.5 µL Tn5 and 22.5 µL nuclei suspension and incubated at 37 °C for 30 min. Transposed DNA fragments were then purified with ChIP DNA Clean & Concentrator Kit (Zymo, cat. no. D5205). Libraries were then amplified as described before (Potok et al., 2019, Buenrostro et al., 2013) .

value: inflorescence

value: Columbia 0


title: ATACseq_ZFSssI_line2

description: ATACseq for ZFSssI_line2


title: DIS320070-V7


title: Arabidopsis brd1,2,13_BRM-GFP-Input

value: Seedling


title: Arabidopsis BRD2-GFP-IP-bio2

value: GFP (ab290, abcam)


title: DIS320070-V3


title: DIS320069-V7


title: ATACseq_col

description: ATACseq for col


title: ChIP_H3K27me3_ZFSssI_line2

description: ChIPseq for H3K27me3_ZFSssI_line2

extract_protocol:
ChIPs were performed as described previously (GallegoBartolome et al.,2019). Briefly, 2 grams of inflorescences from untransformed Col-0 and T4 homozygous populations of two independent transgenic lines expressing ZF-SssI were ground in liquid nitrogen and fixed for 10 min in Nuclei Isolation buffer containing 1% formaldehyde. After stopping the reaction with glycine, nuclei were isolated, chromatin was sheared using a Bioruptor Plus (Diagenode) and immunoprecipitated overnight at 4°C with the following antibodies: Anti-FLAG M2 (F1804, Sigma), H3K4me1 (Ab8895, Abcam), H3K4me3 (04-745, Millipore), H3K36me3 (Ab9050, Abcam), H3K27me3 (07-449, Millipore), H3 (Ab1791, Abcam), H2A (Ab13923, Abcam), H2AZ (Ref Potok et al, Nat Comm, 2019), PanH3Ac (39140, Active motif). Chromatin-bound proteins were immunoprecipitated with a 1:1 mixture of magnetic Protein A and Protein G Dynabeads (Invitrogen) for 3 h at 4°C, washed with low salt, high salt, LiCl and TE buffers for 10 min each at 4°C and eluted for 2 x20 minutes at 65°C with elution buffer. Reversal crosslink was done overnight at 65°C, followed by proteinase K treatment at 45°C for 5 h. DNA was purified using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Fisher Scientific) and precipitated with NaAc/EtOH and GlycoBlue (Invitrogen) overnight at −20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions.


title: ChIP_H3K27me3_col

description: ChIPseq for H3K27me3_col


title: DIS320077-V3


title: DIS320067-V7


title: DIS320066-V7


title: ChIP_H2AZ_ZFSssI_line2_rep2

description: ChIPseq for H2AZ_ZFSssI_line2_rep2


title: DIS320067-V3


title: ChIP_H2AZ_ZFSssI_line1_rep2

description: ChIPseq for H2AZ_ZFSssI_line1_rep2


title: ChIP_H2AZ_col_rep2

description: ChIPseq for H2AZ_col_rep2


title: DIS320066-V3


title: DIS320063-V7


title: WGBS_ZFSssI_T5_line2_minus_rep2_part1

description: WGBS for ZFSssI_T5_line2_minus_rep2_part1

extract_protocol:
For T2 and T3 WGBS, DNA from inflorescences of adult plants was extracted following a CTAB-based method.  For T4 and T5 WGBS, DNA from inflorescences of adult plants was extracted using the DNeasy Plant Mini Kit (QIAGENE).
For T2 and T3 WGBS, 100 ng of DNA was sheared to 200 bp with a Covaris S2 (Covaris) and used for library preparation using the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. For T4 and T5 WGBS, 250 ng of DNA was sheared to 200 bp with a Covaris S2 (Covaris) and used for library preparation using the Epitect Bisulfite Conversion kit (QIAGEN) and the Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters following the manufacturer’s instructions.


title: DIS320062-V3


title: DIS320060-V3


title: WGBS_ZFSssI_T5_line1_minus_rep1_part1

description: WGBS for ZFSssI_T5_line1_minus_rep1_part1


title: DIS320062-V7


title: DIS320057-V7


title: WGBS_ZFSssI_T5_line1_minus_rep2_part1

description: WGBS for ZFSssI_T5_line1_minus_rep2_part1


title: DIS320057-V3


title: WGBS_ZFSssI_T4_line2_minus_rep2

description: WGBS for ZFSssI_T4_line2_minus_rep2


title: ChIP_H3K27me3_ZFSssI_line1

description: ChIPseq for H3K27me3_ZFSssI_line1


title: WGBS_col_rep2_for_T5_part1

description: WGBS for col_rep2_for_T5_part1


title: WGBS_col_rep1_for_T5_part1

description: WGBS for col_rep1_for_T5_part1


title: WGBS_ZFSssI_T4_line2_minus_rep1

description: WGBS for ZFSssI_T4_line2_minus_rep1


title: DIS320069-V3


title: WGBS_ZFSssI_T4_line1_minus_rep2

description: WGBS for ZFSssI_T4_line1_minus_rep2


title: DIS320055-V3


title: DIS320056-V7


title: WGBS_ZFSssI_T4_line1_minus_rep1

description: WGBS for ZFSssI_T4_line1_minus_rep1


title: DIS320055-V7


title: DIS320054-V7


title: DIS320063-V3


title: DIS320053-V7


title: WGBS_ZFSssI_T5_line2_minus_rep1_part1

description: WGBS for ZFSssI_T5_line2_minus_rep1_part1


title: DIS320053-V3


title: WGBS_col_rep1_for_T2_T3

description: WGBS for col_rep1_for_T2_T3


title: WGBS_col_rep1_for_T4

description: WGBS for col_rep1_for_T4


title: WGBS_col_rep2_for_T2_T3

description: WGBS for col_rep2_for_T2_T3


title: WGBS_col_rep2_for_T4

description: WGBS for col_rep2_for_T4


title: DIS320051-V7


title: DIS320051-V3


title: DIS320050-V3


title: DIS320050-V7


title: DIS320047-V7


title: BSPCR_fwa_nrpd1

description:
PCR amplified DNA
BS-PCR over FWA in fwa_nrdp1_region1to3

data_processing:
Library strategy: BSPCR-seq
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

extract_protocol:
BS-PCR-seq was performed as previously described (GallegoBartolome et al., 2019). Briefly, leaf tissues from adult plants of representative T2 lines containing the ZF-SssI transgene were collected and DNA was extracted following a CTAB-based method. Bisulfite conversion was done using the Epitect Bisulfite Conversion kit (QIAGEN). The following regions of FWA were analyzed: Region 1 (chr4: 13038143-13038272); Region 2 (chr4: 13038356-13038499); Region3 (chr4: 13038568-13038695), which cover fragments of the promoter and 5′ transcribed region of FWA. Pfu Turbo Cx (Agilent) was used to amplify bisulfite-treated DNA using primers containing Illumina adaptors. The primers used are listed in Table S1.
For each sample, individual PCR products from each of the three FWA regions were pooled and purified using AMPure beads (Beckman Coulter) before making the libraries. Libraries were made from purified PCR products using a TruSeq Nano DNA Library Prep kit for Neoprep automated library preparation machine (Illumina), a Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters or an Ovation Ultralow V2 kit (NuGEN). Libraries were sequenced on Illumina HiSeq 2000 or HiSeq 2500.


title: DIS320049-V7


title: DIS320045-V3


title: DIS320044-V7


title: BSPCR_fwa

description:
PCR amplified DNA
BS-PCR over FWA in fwa_region1to3

value: fwa


title: BSPCR_fwa_nrpe1

description:
PCR amplified DNA
BS-PCR over FWA in fwa_nrde1_region1to3


title: DIS320044-V3


title: DIS320043-V7


title: DIS320049-V3


title: DIS320045-V7


title: DIS320041-V7


title: BSPCR_fwa_drm12

description:
PCR amplified DNA
BS-PCR over FWA in fwa_drm1_drm2_region1to3


title: DIS320040-V3


title: DIS320043-V3


title: DIS320054-V3


title: DIS320039-V7


title: DIS320037-V7


title: DIS320039-V3


title: Cebpap30/p30 cells - ATAC rep3 [ATAC_p30/p30_3]

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
ChIP-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Differential ChIP-seq analysis with DiffBind (version 2.16.0)
Differential ChIP-seq analysis was performed with an in-house script applying a sliding window approach (available on request) using csaw (version 1.20.0) and edgeR
Peaks were annotated using HOMER (version 4.9.1)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
ATAC-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Alignment against the mouse reference genome (mm10) with BWA (version 0.7.15-r1140) and further processing with SAMtools (version 1.4).
Peaks were called with MACS2 (version 2.1.0)
Further characterization and visualization of called peaks was done with ChIPseeker (version 1.22.1) for the binding sites and with deepTools (version 3.0.2-1-ac19361)
RNA-seq data:
Quality check with FastQC (version 0.11.4)
Preprocessing with PRINSEQ-lite (version 0.20.4)
Splicing aware alignment against the mouse reference genome (mm10) was done with STAR (version 2.5.0b)
Counts per gene were obtained with featureCounts (version 1.6.0)
Differential expression analysis was performed with DESeq2 (version 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content:
ChIP-seq: bigWig files hold coverage information for the C/EBPa-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ChIP-seq: bigWig files hold coverage information for the H3K27ac-ChIP with sh Cebpa knock-down, control (Ren) and respective input-controls (IN)
ATAC-seq: bigWig files hold coverage information for the three p30/p30 replicates
SRNA-seq: The tab-delimited text file includes the normalized gene expression for the sh knock-down of Cebpa and control (shRen)

source_name: Cebpap30/p30 cells - ATAC

growth_protocol: Cells are grown in RPMI supplemented with 10 % FCS and 2 mM glutamine, 100 U/ml penicillin and   100 µg/ml streptomycin and IL-3 (5ng/ml).

extract_protocol:
Total RNA for RNA-seq was isolated using the RNeasy Mini Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Indicated samples were treated with Doxycyline (1µg/mL) 48 hrs prior to harvest for sequencing.

value: myeloid progenitor cell model for p30-driven AML

tag: strain background


title: DIS320040-V7


title: Cebpap30/p30 cells - ATAC rep2 [ATAC_p30/p30_2]


title: DIS320036-V7


title: Cebpap30/p30 cells - ATAC rep1 [ATAC_p30/p30_1]


title: MAIT_INF_KO_2

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

description: Bcl11b KO Infected

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts extracted from bam files using htseq

source_name: MAIT cells

extract_protocol:
WT and Bcl11b KO MAIT cells were sorted from naïve or salmonella infected mouse lungs. Cells were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared using New England Biolabs NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat# E7770S) according to the manufacturer's instructions. Library quality and concentration was checked on a bioanalyzer (Agilent High Sensitivity DNA Kit #5067-4626) and by Qubit (Qubit™ dsDNA HS Assay Kit #Q32854). Libraries were sequenced on a NextSeq500.

value: Bcl11bF/F PlzfCre+

value: Lung

value: MAIT

value: Salmonella infection

value: KO


title: MAIT_INF_KO_1

description: Bcl11b KO Infected


title: DIS320047-V3

value: pre-treatment


title: MAIT_INF_WT_2

description: Bcl11b WT Infected

value: WT


title: DIS320036-V3

value: SAL/FLU


title: MAIT_SS_WT_2

description: Bcl11b WT SS

value: Steady state


title: MAIT_SS_WT_1

description: Bcl11b WT SS


title: MAIT_SS_KO_1

description: Bcl11b KO SS


title: DIS320035-V7

value: FOR/BUD

value: post-treatment


title: MAIT_INF_WT_1

description: Bcl11b WT Infected


title: DIS320035-V3


title: DIS320034-V7


title: DIS320033-V7


title: DIS320033-V3


title: DIS320037-V3

value: FOR


title: DIS320032-V7


title: WGBS_ZFSssI_in_fwa_line2

description: WGBS for ZFSssI_in_fwa_line2

value: inflorescence

value: Columbia 0


title: WGBS_ZFSssI_in_fwa_line1

description: WGBS for ZFSssI_in_fwa_line1


title: BSPCR_col

description:
PCR amplified DNA
BS-PCR over FWA in Col-0_region1to3


title: DIS320032-V3


title: DIS320031-V7


title: PF-SE22_2

type: genomic

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

country: Germany

institute: Charite

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip and Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
using R (version 4.0.2)  minfi_1.36.0 package
arrays from different plattforms were combined using combineArrays function; beta values were normalized using minfi PreprocessFunnorm function; detection p-values was calculated using detectionP function; for methylated and unmethylated signals preprocess, Illumina function was used for normalization

label: cy3, cy5

source_name: infratentorial

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tumor samples using Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol

tag: gender

value: m

tag: age

tag: subtype

value: mixed, distinct


title: PF-SE36_2

value: f


title: DIS320031-V3


title: HDF_DA_48h

city: Grand Rapids

first: Gerd

middle: P.

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE.

department: Center for Epigenetics

institute: Van Andel Research Institute

data_processing:
Library strategy: circle-damage-seq
fastq files containing sequencing reads were hard-clipped from the 3’ end to 2x80 nucleotide length using Trim_Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned to the hg19 reference genome using BWA-MEM with default parameters.
Duplicate alignments were marked and removed with the ‘removeDups’ SAMBLASTER option.
Divergently aligned read pairs (pairs facing away from each other) with a single nucleotide gap between reads were selected by selecting SAM records with TLEN of 3. TLEN equals the distance between the mapped end of the template and the mapped start of the template. Records with TLEN=3 represent divergently aligned reads with 1 nucleotide between mates.
Sequences for the 3 nucleotides representing the last nucleotide of each read and the gapped base were identified using BEDtools
To  visualize the reads, bam files were produced by selecting SAM records with TLEN of 3 and visualized with the Integrative Genomics Viewer version 2.8.9. The tracks were displayed with a ‘view as pairs’ option to show pairs together with a line joining the ends.
Genome_build: mm10 for MEF and hg19 for HDF cells
Supplementary_files_format_and_content: Chromosome name, start position, stop position, and inferred strand (+/-) for all selected read pair loci were written to a BED file.

source_name: Human skin fibroblasts

growth_protocol: MEF cells were cultured in DMEM high glucose (Invitrogen; Carlsbad, CA) containing 15% fetal bovine serum and used at passage number <5. Human skin fibroblasts (HDF) cells were obtained from ATCC (Cat. PCS-201-012) and grown using the Fibroblast Growth Kit (ATCC, Cat. PCS-201-041) supplemented with 2% fetal bovine serum.

extract_protocol:
After the irradiation or further incubation, genomic DNA was isolated using Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, CA) according to the manufacturer’s instruction manual.
Genomic DNAs were framgmeted to an averge length of 300 bp and circuliarized with T4 DNA ligase at 16°C overnight. Non-circularized linear DNA were removed with Plasmid-Safe ATP-Dependent DNAse treatment. To generate DNA double-strand breaks at CPD lesions, the circularized DNA was treated with T4-PDG and APE1 followed by E. coli phrB photolyase, and then S1 nuclease to create double-strand breaks with ligatable ends. To generate double-strand breaks at deaminated CPD sites, the circularized DNA was initially treated with E. coli phrB photolyase and followed by UDG (NEB) and APE1 treatment, and then S1 nuclease to create double-strand breaks with ligatable ends. A-tailed with Klenow fragment exo- (NEB) and then adaptor was ligated with NEBNext Ultra II Ligation Master Mix and followed by incubation with USER enzyme (NEB). The purified DNA libraries were amplified by PCR with NEBNext Ultra II Q5 Master mix and NEBNext i5 and i7 primers and used for DNA sequencing.

treatment_protocol: To induce CPD adducts, cells were irradiated with 1000 J/m2 dose of UVB. For mapping deaminated CPDs, HDF cells were irradiated with 4000 J/m2 dose of UVB and incubated the cells for 24 or 48 hours at 37°C before harvesting and DNA isolation.

value: HDF

value: 4000 J/m2 of UVB

tag: repair time

value: 48 hrs


title: HDF_DA_24h

tag: treatment

value: 24 hrs


title: DIS320030-V7


title: HDF_DA_0h

value: 0 hr


title: HDF_DA_NT


title: HDF_CPD

value: 1000 J/m2 of UVB


title: PF-SE23_2


title: DIS320027-V7


title: DIS320028-V3

value: pre-treatment


title: HDF_CPD_NT


title: DIS320026-V7


title: DIS320026-V3


title: DIS320034-V3


title: DIS320025-V3


title: HDF_DA_48h_800M


title: DIS320024-V7


title: DIS320023-V3

value: SAL/FLU


title: DIS320018-V7


title: DIS320018-V3


title: DIS320019-V7


title: DIS320020-V3


title: DIS320017-V7


title: DIS320030-V3


title: DIS320019-V3


title: DIS320017-V3


title: DIS320016-V7


title: DIS320016-V3


title: HepG2_1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters  -p 6 -N 1 --un-gz
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and CPM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file containing CPM values

source_name: liver cancer derived cell line

growth_protocol: A549, ES2, MV3, PANC1 and HepG2 cells were cultured in DMEM supplemented with 10% FBS. BE(2)C cells  were cultured in EMEM:DMEM/F12 (1:1) medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
For A549, ES2, MV3 and PANC1 cells, 50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Small RNA-seq libraries for HepG2 and B(E)2C cells were prepared by Novogene (Hong Kong).

treatment_protocol: A549, ES2, MV3, PANC1 and HepG2 cells were harvested for RNA extraction 48 hours upon seeding. BE(2)C cells were harvested 24 hours upon seeding for RNA extraction.

tag: sirna

value: parental cell line

tag: passages

value: harvested 48h upon seeding


title: DIS320028-V7

value: post-treatment


title: HepG2_2

tag: cell line


title: DIS320027-V3

value: FOR


title: KATOIIIWT RNA-seq

city: masbashi

first: Rie

last: Sano

state: gunma

address: 3-39-22 showa-machi

department: Legal Medicine

institute: Gunma University

description: Wild-type KATOIII

data_processing:
Basecalls performed using bcl2fastq v1.84.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the Human reference genome (hg19) using Tophat 2.0.13 (bowtie2-2.2.3).
The read counts allocated for each gene and transcript (UCSC version 2013.12.31) were quantified using TMM (Trimmed Mean of M-values) method using StrandNGS 2.6 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg19
Supplementary_files_format_and_content: An excel format file (XLSX) includes TMM quantification values and UCSC gene annotations of all samples.

source_name: KATOIII JCRB0611

growth_protocol: A human gastric cancer cell line KATOIII (JCRB0611) was grown in 45% RPMI 1640 plus 45% minimum essential medium (MEM) containing 10% FBS and 0.5% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from cultured cells using the acid guanidine thiocyanate/acid phenol method
Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Inc., Ipswich, MA) according to the manufacturer’s protocols.

tag: tissue

value: stomach

value: Signet ring cell carcinoma

tag: genotype

value: Wild-type KATOIII


title: BE2C_1

source_name: neuroblastoma derived cell line


title: BE2C_2


title: DIS320014-V3


title: DIS320014-V7


title: DIS320024-V3


title: DIS320013-V7


title: DIS320013-V3


title: KATOIIIB3 RNA-seq

description: genomic deletion of the sequences +22,579/+22,740 and +22,579/+22,742 from ABO translation start site


title: sshsd8612_n_mir

city: Montreal

first: Pierre

last: Paradis

state: QC

address: 3755 ch. de la Côte-Sainte-Catherine

institute: Lady Davis Institute for medical research, Jewish General Hospital, McGill University

data_processing:
Bcl2fastq-1.8.4 (Illumina) was used for base-calling, adapter trimming, sample identification by barcode and bcl-to-fastq conversion.
FastQC was used for sequence quality control. Only samples with >25 base quality at every position were included in the data analysis.
Sequences were mapped to the Rattus norvegicus release-86 genome using STAR 2.3.1. For small RNA sequence alignment, the option --outFilterMismatchNoverLmax 0.05 was used to allow maximal mismatch ratio of 0.05 (no mismatch allowed for reads <20 nt and 1 mismatch allow per 20 nt).
miRDeep2 2.0.0.5 was used for microRNA annotation, assembly and counting. The miRBase database (http://www.mirbase.org/) was used as a source of known microRNAs and for homolog searching of novel microRNAs.
Differential expression analysis was done in R 3.2.3 (https://www.r-project.org) using package EdgeR 3.6.8. A trimmed mean of M-values (TMM) method in the EdgeR protocol was used for sequence read normalization. Only microRNAs with expression levels over 10 read per million mapped reads per sample were analyzed.
One sample from small RNA sequencing was very far from any cluster in multidimensional scaling plots of distances between gene expression profiles and was excluded from the study.
Genome_build: Rattus norvegicus release-86 genome
Supplementary_files_format_and_content: The xlsx files contain normalized expression levels

organism: Rattus norvegicus

source_name: Aorta

extract_protocol:
A small piece of frozen aorta (≤100 mg) was cut in the Petri dish on dry ice to prevent melting. The piece of aorta was homogenized in 1 mL of mirVana miRNA lysis/binding buffer (ThermoFisher Scientific, Waltham, MA, USA) in a 5 mL tube for 1 min at maximum speed with a Polytron PT 1600 E homogenizer (Brinkmann Instruments, Mississauga, ON, Canada) equipped with a dispersing aggregate PT-DA 1607/2EC. The homogenate was centrifuged at 1500 x g for 2 min at 4 °C to remove foam generated during homogenization, and processed for total RNA extraction using the mirVana miRNA isolation kit in accordance with the manufacturer’s instructions, followed by genomic DNA removal with the TURBO DNA-free kit (ThermoFisher Scientific) according to the manufacturer’s protocols. The concentration and purity of the RNA were assessed with a NanoDrop ND-100 spectrophotometer (ThermoFisher Scientific). RNA quality was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) of ≥8 were used for RNA library construction.
One microgram of total RNA (n = 6 per group) was used for small RNA library construction using the TruSeq small RNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's protocol.
Small RNAs were sequenced using the HiSeq 2500 system (Illumina, 1 x 51 bp single-end, rapid mode) with the goal to obtain 30 million reads per sample.

treatment_protocol: Four- to 6-week-old male SS and congenic rats containing the Brown Norway (BN) chromosome 2 distal portion (identified as SBA or S2Ba) and middle segment (identified as SBB or S2Bb) were fed NSD or HSD (4% NaCl) up to 12-to-13 weeks old.

tag: genotype/variation

value: Dahl SS salt-sensitive rats

tag: diet

value: High salt diet


title: DIS320011-V7


title: sshsd8613_n_mir


title: KATOIIIB4 RNA-seq

description: genomic deletion of the sequences +22,580/+22,740 and +22,580/+22,742 from ABO translation start site


title: sshsd8611_n_mir


title: sshsd7780_n_mir


title: DIS320011-V3


title: sshsd7476_n_mir


title: DIS320009-V7

value: FOR/BUD


title: DIS320009-V3


title: DIS320008-V7


title: sbbhsd9134_n_mir

value: Congenic SS rat containing the BN Chr2 middle segment


title: sbbhsd9736_n_mir


title: sbbhsd858_n_mir


title: sbbhsd9737_n_mir


title: sbbhsd7785_n_mir


title: sbbhsd857_n_mir


title: DIS320008-V3


title: Mutant 18 months old, rep 3

type: RNA

city: Sevilla

first: María Isabel

middle: Álvarez

last: Vergara

state: Sevilla

address: C/Manuel Siurot, sn

country: Spain

institute: Instituto de Biomedicina de Sevilla

description: ARN from CD31+ endothelial cells from the brain cortex

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data from the extraction software Expression Console was imported to the R statistical processing environment using the LIMMA/Bioconductor package. Quality of the data was assessed using Array Quality Metrics package. Data were normalized using Robust Multi-Array (RMA) method using LIMMA/Bioconductor package
MTA-1_0 data (probe group file)
MTA-1_0.na34.mm10.transcript.csv (meta-probeset file)
RMA signal estimates from R processing of raw CEL

label: biotin

source_name: Mutant, 18 months old, endothelial cells from the brain cortex

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Endothelial cells from brain cortex were isolated using specific marker (CD31+) by cytometry flow. Immune cell contamination was discared through CD11b. Whole transcript from each sample was extracted with Trizol.

treatment_protocol: Not applicable

value: 18 months old

value: brain cortex

tag: cell type

value: endothelial cells


title: Mutant 18 months old, rep 1


title: Mutant 18 months old, rep 2


title: DIS320007-V7


title: sbahsd9726_n_mir

value: Congenic SS rat containing the BN Chr2 distal portion


title: sshsd7779_n_mir


title: WT 18 months old, rep 1

source_name: WT, 18 months old, endothelial cells from the brain cortex

value: Wild type


title: DIS320007-V3

value: pre-treatment


title: DIS320006-V3


title: WT 18 months old, rep 2


title: sbahsd7465_n_mir


title: sbahsd9078_n_mir


title: sbahsd9557_n_mir


title: sbahsd7464_n_mir


title: WT 18 months old, rep 3


title: ss5823_n_mir

value: Normal salt diet


title: DIS320005-V7


title: ss5824_n_mir


title: DIS320005-V3


title: sbb1736_n_mir


title: ss3786_n_mir


title: ss3241_n_mir


title: ss4724_n_mir


title: sbb1735_n_mir


title: sbahsd9728_n_mir


title: DIS320006-V7


title: DIS320003-V7


title: DclrB-3

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

description:
AllSamples.GeneExpression.FPKM.txt
clrB-3_FPKM

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (fragments per kilobaseof exon per million fragments mapped) for differential expression analysis.
Genome_build: Penicillium oxalicum 114-2 sequences (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: FPKMs

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in VMM medium with 2% glucose as carbon resource for 22 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 24 h. Total RNA was extracted for DGE analysis.

extract_protocol: Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.

tag: strain

value: clrB deletion

tag: medium

value: Mandel’s medium with 1% wheat bran and 1 % cellulose as carbon resource

tag: culture time

value: 24 h after transferring washed mycelia to the new medium


title: DIS320003-V3

tag: subject

tag: timepoint


title: ss3788_n_mir


title: sbb1734_n_mir


title: DclrB-2

description:
AllSamples.GeneExpression.FPKM.txt
clrB-2_FPKM


title: sbb1704_n_mir


title: DrcoA-3

description:
AllSamples.GeneExpression.FPKM.txt
rcoA-3_FPKM

value: rcoA deletion


title: sbb1703_n_mir


title: DrcoA-1

description:
AllSamples.GeneExpression.FPKM.txt
rcoA-1_FPKM


title: DrcoA-2

description:
AllSamples.GeneExpression.FPKM.txt
rcoA-2_FPKM


title: DIS320002-V3

value: FOR


title: sbb1702_n_mir


title: DIS320001-V7

value: SAL/FLU

value: post-treatment


title: 114-2-3

description:
AllSamples.GeneExpression.FPKM.txt
114-3_FPKM

value: 114-2 (wild type)


title: DIS320004-V3

value: FOR/BUD


title: PANC1_siI1_3

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

source_name: pancreas cancer derived cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation.

treatment_protocol: 72 (A-549, ES-2, MV-3) or 96 (PANC-1) hours upon transfection cells were harvested for RNA extraction.

value: siRNA pool against IGF2BP1

value: harvested 96h upon transfection


title: 114-2-2

description:
AllSamples.GeneExpression.FPKM.txt
114-2_FPKM


title: DIS320001-V3


title: 114-2-1

description:
AllSamples.GeneExpression.FPKM.txt
114-1_FPKM


title: sba5033_n_mir


title: PANC1_siI1_2


title: sba3898_n_mir


title: sba5032_n_mir


title: DclrB-1

description:
AllSamples.GeneExpression.FPKM.txt
clrB-1_FPKM


title: sba5031_n_mir


title: PANC1_siI1_1


title: PANC1_siC_3

value: Control siRNA


title: DIS320002-V7


title: sba3888_n_mir


title: SSHSD8613 [RNA-Seq]

data_processing:
Bcl2fastq-1.8.4 (Illumina) was used for base-calling, adapter trimming, sample identification by barcode and bcl-to-fastq conversion.
FastQC was used for sequence quality control. Only samples with >25 base quality at every position were included in the data analysis.
Sequences were mapped to the Rattus norvegicus release-86 genome using STAR 2.3.1.
Differential expression analysis was done in R 3.2.3 (https://www.r-project.org) using package EdgeR 3.6.8. A trimmed mean of M-values (TMM) method in the EdgeR protocol was used for sequence read normalization. Only mRNAs and ncRNAs with expression levels over 10 read per million mapped reads per sample were analyzed.
One sample from total RNA sequencing was very far from any cluster in multidimensional scaling plots of distances between gene expression profiles and was excluded from the study.
Genome_build: Rattus norvegicus release-86 genome
Supplementary_files_format_and_content: The xlsx files contain normalized expression levels

extract_protocol:
A small piece of frozen aorta (≤100 mg) was cut in the Petri dish on dry ice to prevent melting. The piece of aorta was homogenized in 1 mL of mirVana miRNA lysis/binding buffer (ThermoFisher Scientific, Waltham, MA, USA) in a 5 mL tube for 1 min at maximum speed with a Polytron PT 1600 E homogenizer (Brinkmann Instruments, Mississauga, ON, Canada) equipped with a dispersing aggregate PT-DA 1607/2EC. The homogenate was centrifuged at 1500 x g for 2 min at 4 °C to remove foam generated during homogenization, and processed for total RNA extraction using the mirVana miRNA isolation kit in accordance with the manufacturer’s instructions, followed by genomic DNA removal with the TURBO DNA-free kit (ThermoFisher Scientific) according to the manufacturer’s protocols. The concentration and purity of the RNA were assessed with a NanoDrop ND-100 spectrophotometer (ThermoFisher Scientific). RNA quality was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) of ≥8 were used for RNA library construction.
One microgram of total RNA (n = 6 per group) was used for total RNA library construction using the TruSeq total RNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer's protocol.
Total RNA was sequenced using the HiSeq 2500 system (Illumina, 2 x 75 bp pair-end high-output mode) with the goal to obtain 30 million reads per sample.

value: Dahl SS salt-sensitive rats

value: High salt diet

tag: Sex

value: male


title: PANC1_siC_2


title: siCLAP-1 mouse DRG

city: Zhuhai

first: Bin

last: Wang

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

institute: Guangdong institute of intelligence and science technoloty

description: siCLAP-1 mouse DRG

data_processing:
Check quality of RNA-seq reads using fastqc (version 0.11.8) with default parameters.
Reads were aligned to mouse genome assembly (mm10) using HISAT2 (Kim et al., 2015) (version 2.1.0, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10) with annotations from refFlat, knownGene and ensGene.
Gene counts were calculated for each single cell/sample using featureCounts (Liao et al., 2014) (version: 1.6.2, parameter: -t exon -g gene_id -O --fraction -p -s 0).
Raw gene counts were normalized by transcripts per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: tab split text file (txt)

source_name: Mouse dorsal root ganglion

growth_protocol: 8 weeks old male mice (C57BL/6J)

extract_protocol:
Total RNA from L4/5 DRGs were extracted with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB)

treatment_protocol: The mice following intrathecal injection of siRNAs including siNC or siCLAP.

value: siCLAP


title: siNC-3 mouse DRG

description: siNC-3 mouse DRG

value: siNC


title: siCLAP-3 mouse DRG

description: siCLAP-3 mouse DRG


title: sba3890_n_mir

value: Congenic SS rat containing the BN Chr2 distal portion

value: Normal salt diet


title: siCLAP-2 mouse DRG

description: siCLAP-2 mouse DRG


title: MV3_siI1_2

source_name: melanoma derived cell line

value: harvested 72h upon transfection


title: SSHSD8611 [RNA-Seq]


title: MV3_siI1_3


title: siNC-1 mouse DRG

description: siNC-1 mouse DRG


title: siNC-2 mouse DRG

description: siNC-2 mouse DRG


title: MV3_siI1_1


title: SSHSD7476 [RNA-Seq]


title: MV3_siC_3


title: SSHSD7779 [RNA-Seq]


title: SSHSD7780 [RNA-Seq]


title: RPE NoTx_C4

city: Charlottesville

first: Akhil

last: Varshney

state: Virginia

address: 415 Lane Rd

department: Ophthalmology and Center for Advanced Vision Science

institute: University of Virginia

data_processing:
Raw fastq reads were aligned to hg19 using STAR version 2.5.3a with outFilterMismatchNMax set to 10.
Aligned reads were mapped to Alu regions using featureCounts version 1.6.1.
The featureCounts alignment SAM file was filtered to only include Alu reads (having tag ‘XS:Z:Assigned’). Alu reads from each raw fastq were combined into one SAM file.
Alu reads were mapped to protein coding genes in gencode v27 using featureCounts version 1.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is the ‘*.counts’ file produced by featureCounts and quantifies the number of raw Alu reads mapped to each protein coding gene in gencode v27.

source_name: cytoplasmic fractions of primary human RPE cells

growth_protocol: Primary human RPE cells were maintained in DMEM supplemented with 10% FBS and antibiotics. All cells were maintained at 37 °C in a 5% CO2 environment.

extract_protocol:
RPE cells were lysed with gentle extraction buffer prepared in 1X PBS containing 1% v/v Triton X-100 (Sigma-Aldrich) and 1 mM EDTA for 15 min on ice. Lysate was centrifuged at 1000Xg for 10 min at 4 °C to pellet-out nuclei. The lysate supernatant was used as the cytoplasmic fraction.
Pippin-fractionated ssDNA samples were converted to dsDNA by the Seq Plex Enhanced DNA Amplification Kit (Sigma-Aldrich, SEQXE) without additional fragmentation to enrich for DNA between 200-800 bp. Amplification was monitored by RT-PCR, and cycle number (20–25 cycles) was set as 2-3 cycles after the amplification plateau, as suggested by the manufacturer. 1 μg of dsDNA library was prepared for sequencing with the NEXTflex® Rapid DNA Sequencing Kit (Bioo Scientific).

value: primary retinal pigment epithelial cells


title: RPE NoTx_C3


title: MV3_siC_1


title: SBBHSD9737 [RNA-Seq]

value: Congenic SS rat containing the BN Chr2 middle segment


title: RPE NoTx_C2


title: RPE NoTx_C1


title: SBBHSD9736 [RNA-Seq]


title: SBBHSD9134 [RNA-Seq]


title: ES2_siI1_3

source_name: ovarian cancer derived cell line


title: ES2_siI1_2


title: SBBHSD858 [RNA-Seq]


title: ES2_siI1_1


title: SSHSD8612 [RNA-Seq]


title: ES2_siC_3


title: SBBHSD857 [RNA-Seq]


title: MV3_siC_2


title: ES2_siC_2


title: ES2_siC_1


title: SBAHSD9728 [RNA-Seq]


title: A549_siI1_3

source_name: lung cancer derived cell line


title: A549_siI1_2


title: SBAHSD9078 [RNA-Seq]


title: SBAHSD9557 [RNA-Seq]


title: SBAHSD7465 [RNA-Seq]


title: A549_siI1_1


title: SBAHSD7464 [RNA-Seq]


title: SBBHSD7785 [RNA-Seq]


title: ChIP_PanH3Ac_ZFSssI_line2

description: ChIPseq for PanH3Ac_ZFSssI_line2

value: inflorescence

tag: ecotype

value: Columbia 0


title: A549_siC_2


title: A549_siC_1


title: ChIP_PanH3Ac_ZFSssI_line1

description: ChIPseq for PanH3Ac_ZFSssI_line1


title: 5_Ctrl

city: Baltimore

first: Crystal

last: Aguh

state: Maryland

address: 1500 Orleans St, CRB II Suite 200

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Patient 5 Control

hyb_protocol: Hybridized for 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization created quantile-normalized log2 transcript-level signal values, which were used in teh subsequent ANOVA analysis.    Transcript annotation was subsequently updated.

source_name: Scalp, control

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using manufacturer's protocol.

extract_protocol: Total RNA was extracted with the QIAGEN RNeasy Fibrous Tissue Mini Kit using manufacturer's protocol.

treatment_protocol: Samples submerged in 2mL tubes containing RNAlater stabilization reagent, stored at 4°C for 24hr, then at -80◦C.

value: scalp

tag: ccca status

value: Control

tag: patient id

tag: disease state

value: Central Centrifugal Cicatricial Alopecia


title: 5_CCCA

description: Patient 5 Affected

source_name: Scalp, affected

value: Affected


title: 3_CCCA

description: Patient 3 Affected


title: 4_CCCA

description: Patient 4 Affected


title: 2_Ctrl

description: Patient 2 Control


title: SS5823 [RNA-Seq]


title: SBAHSD9726 [RNA-Seq]


title: SS5824 [RNA-Seq]


title: 4_Ctrl

description: Patient 4 Control


title: 1_CCCA

description: Patient 1 Affected


title: 2_CCCA

description: Patient 2 Affected


title: 3_Ctrl

description: Patient 3 Control


title: ChIP_PanH3Ac_col

description: ChIPseq for PanH3Ac_col

extract_protocol:
ChIPs were performed as described previously (GallegoBartolome et al.,2019). Briefly, 2 grams of inflorescences from untransformed Col-0 and T4 homozygous populations of two independent transgenic lines expressing ZF-SssI were ground in liquid nitrogen and fixed for 10 min in Nuclei Isolation buffer containing 1% formaldehyde. After stopping the reaction with glycine, nuclei were isolated, chromatin was sheared using a Bioruptor Plus (Diagenode) and immunoprecipitated overnight at 4°C with the following antibodies: Anti-FLAG M2 (F1804, Sigma), H3K4me1 (Ab8895, Abcam), H3K4me3 (04-745, Millipore), H3K36me3 (Ab9050, Abcam), H3K27me3 (07-449, Millipore), H3 (Ab1791, Abcam), H2A (Ab13923, Abcam), H2AZ (Ref Potok et al, Nat Comm, 2019), PanH3Ac (39140, Active motif). Chromatin-bound proteins were immunoprecipitated with a 1:1 mixture of magnetic Protein A and Protein G Dynabeads (Invitrogen) for 3 h at 4°C, washed with low salt, high salt, LiCl and TE buffers for 10 min each at 4°C and eluted for 2 x20 minutes at 65°C with elution buffer. Reversal crosslink was done overnight at 65°C, followed by proteinase K treatment at 45°C for 5 h. DNA was purified using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Fisher Scientific) and precipitated with NaAc/EtOH and GlycoBlue (Invitrogen) overnight at −20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions.


title: SS4724 [RNA-Seq]


title: 1_Ctrl

description: Patient 1 Control


title: MM.1S_RNAPIIspikein_shKDM5A_ChIPseq

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using BWA.
ChIP-seq peaks were called using MACS2 (Model-Based Analysis of ChIP-seq) with p=1X10-7 in "narrow" mode.
ENCODE blacklisted regions were removed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Peak files are BED files for each sample.

source_name: multiple myeloma cell line

extract_protocol:
MM.1S cells were crosslinked, lysed and sonicated. For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: MM.1S cells were transduced with shKDM5A by lentivirus. The infected cells were selected with puromycin.

value: multiple myeloma cell line

tag: chip antibody

value: RNA polymerase II (EMD Millipore, 05-623, lot3135371), Spike-in antibody (Active Motif, 61686, lot00419007)


title: SS3788 [RNA-Seq]

value: Dahl SS salt-sensitive rats


title: MM.1S_RNAPIIspikein_shLuc_ChIPseq

treatment_protocol: MM.1S cells were transduced with shLuc by lentivirus. The infected cells were selected with puromycin.

tag: cell line


title: A549_siC_3

tag: sirna

value: Control siRNA

tag: passages


title: MM.1S_H3K4me3spikein_shKDM5A_ChIPseq

value: H3K4me3 (EMD Millipore,07-473, lot2973059), Spike-in antibody (Active Motif, 61686, lot00419007)


title: ChIP_H2AZ_ZFSssI_line2

description: ChIPseq for H2AZ_ZFSssI_line2

data_processing:
BS-PCR-seq analysis was conducted as previously described (Gallego-Bartolome et al., 2019). Briefly, raw sequencing reads with designed BS-PCR primers were first filtered and trimmed based on the primer sequence with customized scripts. Trimmed reads were then mapped to the reference TAIR10 genome with BSMAP (Xi et al., 2009) (v.2.74) by allowing maximal two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described 19. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were excluded for further analysis. To visualize the BS-PCR-seq data, only cytosines within amplified regions were kept and plotted with R (ggplot2 package, https://ggplot2.tidyverse.org/).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
WGBS analysis was performed as previously described (Gallego-Bartolome et al.,2019). Raw reads were first aligned to the reference TAIR10 genome using BSMAP (Xi  et al., 2009) (v2.74) by allowing up to two mismatches (-v 2), one best hit (-w 1) and to both strands (-n 1). Methylation level at each cytosine was then calculated with BSMAP (methratio.py) script by only keeping unique mapped reads (-u). Reads with more than three consecutive methylated CHH sites were removed as previously described (Cokus  et al.,2008). Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between ZF-SssI and Col-0 were defined similar to before using the R package DMRcaller (Gallego-Bartolome et al.,2019). To increase coverage for DMR analysis, biological replicates were merged for each genotype (ZF-SssI + and ZF-SssI -), each generation (T2 to T5) and each transgenic lines (line 1 and line 2). In general, the whole TAIR10 genome was divided into 200 bp bins, and only bins with at least four cytosines, with each cytosine covered at least four times, more than 10% more methylation in ZF-SssI than Col-0, and a significance level of less than 0.05 were kept. To define hCG DMRs for T2 and T3, the intersect hCG DMRs of two transgenic lines in each generation were first calculated, then the union set of T2 and T3 in the same genotype (either ZF-SssI + or ZF-SssI -) were kept. DMRs overlapping with 200 bp bins in each cluster were considered as DMRs specific for certain clusters. Genomic location for DMRs and mCG equivalent control were annotated using the Homer (Heinz  et al.,2010) ‘annotatePeaks’ function with default parameters. For T4 and T5, two transgenic lines were separated in order to trace the heritable hCG DMRs. To define heritable hCG DMRs, T2 ZF-SssI – were compared with T2 ZF-SssI + and the shared hCG DMRs were considered as heritable hCG DMRs in T2 ZF-SssI –. For T3 ZF-SssI + and ZF-SssI -, hCG DMRs were overlapped with T2 ZF-SssI +. For T4 ZF-SssI – heritable hCG sites, DMRs were first intersected with T3 ZF-SssI + and then intersected with T2 ZF-SssI + while T5 ZF-SssI – heritable hCG sites were further intersected with T4 ZF-SssI – hCG DMRs.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al., 2019, Buenrostro et al., 2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmead et al., 2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al., 2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al., 2014) or deepTools (Ramirez et al., 2014).
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text
For ChIP-seq data, raw reads were first mapped to the reference TAIR10 genome with Bowtie (Langmead et al.,2009) (v0.12.8) by allowing uniquely mapped reads and maximal two mismatches. PCR-duplicated reads were then filtered with SAMTools (Li  et al.,2009) (v 1.19) . To call ZF-SssI FLAG peaks, the MACS2 calldiff function (Zhang et al.,2008) (v 2.1.2) was used to compare ZF-SssI FLAG ChIP-seq and Col-0 FLAG ChIP-seq data with default parameters. Genomic location and enriched motifs of ZF-SssI FLAG-specific peaks were then annotated with Homer (Heinz et al.,2010) ‘annotatePeaks’ and ‘findMotifGenome’ functions using 100 bp flanking the summit of the peaks. Promoter regions were defined as default in homer (upstream 1kb and downstream 100bp of TSS). ChIP-seq data visualizations were performed using ngs.plot (Shen  et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig
ATAC-seq analysis was performed as previously described (Potok et al.,2019, Buenrostro et al.,2013). Briefly, paired-end reads were aligned to the TAIR10 reference genome with bowtie (Langmeadet al.,2009) (v0.12.8) by allowing maximal two mismatches, uniquely mapped reads (-m 1) and the maximal 2 kb distance between pairs (-X 2000). PCR duplicated reads were removed using SAMTools (Li et al.,2009) (v1.19) ‘rmdup’ function and visualized with ngs.plot (Shen et al.,2014) or deepTools (Ramirez et al.,2014).
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

tag: tissue

tag: genotype


title: ChIP_H2AZ_ZFSssI_line1

description: ChIPseq for H2AZ_ZFSssI_line1


title: MM.1S_H3K4me3spikein_shLuc_ChIPseq

tag: cell type


title: SS3241 [RNA-Seq]

tag: genotype/variation

tag: diet

value: male


title: ChIP_H2AZ_col_rep1

description: ChIPseq for H2AZ_col_rep1


title: ChIP_H2A_ZFSssI_line2_rep1

description: ChIPseq for H2A_ZFSssI_line2_rep1


title: SBB1736 [RNA-Seq]


title: PANC1_siC_1

value: harvested 96h upon transfection


title: SBB1735 [RNA-Seq]

value: Normal salt diet


title: MM.1S_H3K4me3spikein_DMSO_ChIPseq

tag: treatment

value: DMSO for 48h


title: MM.1S_H3K4me3spikein_JQKD82_ChIPseq

value: 1 uM JQKD82 for 48h


title: ChIP_H2A_col

description: ChIPseq for H2A_col


title: ChIP_H3_ZFSssI_line1

description: ChIPseq for H3_ZFSssI_line1


title: SBB1704 [RNA-Seq]

value: Congenic SS rat containing the BN Chr2 middle segment


title: ChIP_H3_ZFSssI_line2

description: ChIPseq for H3_ZFSssI_line2

value: inflorescence


title: MM.1S_H3K4me3_DMSO_ChIPseq


title: ChIP_H3_col

description: ChIPseq for H3_col

value: Columbia 0


title: MM.1S_INPUT(forRNAPII)_JQKD82_ChIPseq


title: SBB1702 [RNA-Seq]


title: MM.1S_INPUT(forH3K4me3)_DMSO_ChIPseq


title: SS3786 [RNA-Seq]


title: SBB1734 [RNA-Seq]


title: SBA5033 [RNA-Seq]

value: Congenic SS rat containing the BN Chr2 distal portion


title: SBB1703 [RNA-Seq]


title: SBA5032 [RNA-Seq]


title: ChIP_H3K36me3_ZFSssI_line2

description: ChIPseq for H3K36me3_ZFSssI_line2


title: ChIP_H2A_ZFSssI_line1_rep1

description: ChIPseq for H2A_ZFSssI_line1_rep1


title: MM.1S_RNAPII_DMSO_ChIPseq

value: RNA polymerase II (EMD Millipore, 05-623, lot3135371)


title: MM.1S_INPUT(forRNAPII)_DMSO_ChIPseq


title: ChIP_H3K36me3_col

description: ChIPseq for H3K36me3_col


title: SBA5031 [RNA-Seq]


title: MM.1S_RNAPII_JQKD82_ChIPseq


title: MM.1S_RNAPIISer2p_JQKD82_ChIPseq

value: Phospho-Rpb1 CTD (Ser2) (Cell signaling technology,13499, lot1)


title: Langerhans cell triplicate 2

city: Singapore

first: Christiane

last: Ruedl

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

data_processing:
Illumina bcl2fastq for fastq generation
Sequenced reads were trimmed for adaptor sequence and poor quality reads with Trim_Galore v0.4.5 with parameters -q 20 --stringency 5 --paired
Map trimmed reads to GRCm38 with STAR v2.6.0a using the "multi-sample 2-pass mapping" approach
Gene's read counting with featureCount from the subread package v1.4.6-p5, with parameter -s 0 --primary, on the gene annotation GTF file from GENCODE M19
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression count matrix

source_name: Lymph node antigen presenting cell (sorted cells)

extract_protocol:
Invitrogen Picopure RNA kit
NuGen Ovation® Mouse RNA-Seq System 1-16 protocol

treatment_protocol: Tissue was collected digested by collagenase to single cells, which were sorted into different populations by FACS aria III.

value: Langerhans cell

tag: strain


title: MM.1S_INPUT(forRNAPIISer2p5p)_JQKD82_ChIPseq

city: Kumamoto

first: Hiroto

last: Ohguchi

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

value: multiple myeloma cell line


title: ChIP_H3K4me3_ZFSssI_line2

description: ChIPseq for H3K4me3_ZFSssI_line2


title: SBA3898 [RNA-Seq]


title: SBA3890 [RNA-Seq]


title: MM.1S_RNAPIISer5_DMSO_ChIPseq

value: Phospho-Rpb1 CTD (Ser5) (Cell signaling technology,13523, lot1)


title: ChIP_H3K4me3_ZFSssI_line1

description: ChIPseq for H3K4me3_ZFSssI_line1


title: Langerhans cell triplicate 1


title: cDC1 duplicate 3


title: MM.1S_RNAPIISer5p_JQKD82_ChIPseq


title: ChIP_H3K4me3_col

description: ChIPseq for H3K4me3_col


title: ChIP_H3K4me1_ZFSssI_line2

description: ChIPseq for H3K4me1_ZFSssI_line2


title: MM.1S_RNAPIISer2p_DMSO_ChIPseq


title: iP002_HNF1A

first: Adrian

middle: Kee Keong

last: Teo

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

institute: IMCB, A*STAR

description: HiPSCs and H9 cells were differentiated along the pancreatic lineage into endocrine progenitors and β-like cells as described previously (Pagliuca et al., 2014), with some modifications. Cells were dissociated into single cells using TrypLETM Express Enzyme and passed through 40µM cell strainer before being re-plated at 106cells/ml in mTESR medium supplemented with 10μM Y-27632 in suspension culture on non-treated 6 well plates (Eppendorf). Cells were cultured at 37°C with 5% CO2 on a rotating platform. Differentiation was initiated 48h after cell dissociation (designated as “D0”). In general, 2–3 independent hiPSC lines per subject were used in experiments, with biological triplicates analysed for each line.

data_processing:
The sequenced reads were filtered based on the quality score of each read and alignments. Reads with phred score < 20 were removed. Reads were mapped to the human reference genome (hg19) using Bowtie2. Aligned reads were analyzed by the MACS peak finder program with detault settings to identify enrichment peaks (FDR 10% cutoff) corresponding to putative HNF1A-bound sites. Only reads which uniquely mapped to the human genome were used.
bam file were generated using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: peaks and bedgraph

source_name: human skin fibroblast

growth_protocol: HiPSCs generated from human fibroblast cells and H9 ESCs were cultured at 37°C with 5% CO2 in DMEM/F-12 supplemented with 15 mM HEPES (STEMCELL Technologies), 20% KnockOut™ serum replacement (KOSR), L-glutamine, NEAA (Life Technologies) and 10 ng/ml FGF2 (Miltenyi Biotec). HPSCs were seeded on irradiated CF-1 mouse embryonic fibroblasts (MEFs) and hiPSC media was replaced every 24 hours. HPSCs were split when the cells reached 80% confluency.

extract_protocol:
∼200-300 hPSC-derived endocrine progenitors clumps were dissociated using TrypLE Express Enzyme cross-linked with 3.3 mg/ml of dimethyl 3,3'-dithiobispropionimidate and 1 mg/ml of 3,3’-dithiodipropionic acid di(Nhydroxysuccinimide ester) (both Sigma Aldrich) for 30 minutes at room temperature and with 1% formaldehyde (Amresco) for 15 minutes. The cross-linking reaction was quenched with 0.125 M glycine and cells were first lysed in cell lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl and 0.2% NP-40) and then in nuclear lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA and 1% SDS) on ice in the presence of protease inhibitors on ice. Nuclear lysates were diluted in IP dilution buffer (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 0.01% SDS and 1% Triton X-100) and sonicated for 30s on/45s off for 12 cycles using a Q500 sonicator (QSonica) with microtip probes at 30% power. Sonicated samples were pre-cleared using 10 μg rabbit IgG (Santa Cruz) and Protein A/G agarose beads. Agarose beads were removed by centrifugation and a portion of the supernatant was collected as the input control. Samples were divided equally and incubated with 10 μg of HNF1A antibody (Abcam ab96777) or rabbit IgG overnight at 4°C. The following day, samples were incubated with Protein A/G agarose beads and the beads were recovered and washed with IP wash buffer and Tris-EDTA buffer. The immunoprecipitated DNA was eluted from the beads using IP elution buffer (100 mM NaHCO3, 1% SDS, 100 mM DTT). Samples were successively treated with RNaseA, NaCl and Proteinase K. DNA was extracted by phenol/chloroform extraction.
For ChIP-seq, libraries were prepared using the Solexa ChIP-seq DNA Sample Prep Kit (IP102-1001). After amplification, DNA fragments between 180 and 400 bp were gel extracted and sent for sequencing. Libraries were sequenced by the Genome Institute of Singapore using the Illumina Genome Analyzer II as single-end 35 bp reads

value: hiPSC-derived pancreatic endocrine progenitor

value: Abcam ab96777


title: iP002_HNF1A INPUT


title: ChIP_H3K36me3_ZFSssI_line1

description: ChIPseq for H3K36me3_ZFSssI_line1


title: MM.1S_INPUT(forRNAPIISer2p5p)_DMSO_ChIPseq


title: H9_HNF1A INPUT

source_name: human embryonic stem cell line

value: hESC-derived pancreatic endocrine progenitor

value: Wild Type


title: Host derived LClike cell triplicate 1

value: Host derived LClike cell


title: Host derived LClike cell triplicate 3


title: H9_HNF1A


title: Donor derived LClike cell triplicate 3

value: Donor derived LClike cell


title: MM.1S_INPUT(forKDM5A)_ChIP-seq

value: Not applicable.


title: ChIP_H3K4me1_col

description: ChIPseq for H3K4me1_col


title: MM.1S_KDM5A_ChIP-seq

value: KDM5A (Bethyl Laboratories, A300-897A, lot3)


title: ChIP_H3K4me1_ZFSssI_line1

description: ChIPseq for H3K4me1_ZFSssI_line1


title: ChIP_FLAG_ZFSssI_line1

description: ChIPseq for FLAG_ZFSssI_line1


title: iAgB_HNF1A INPUT


title: ChIP_FLAG_ZFSssI_line2

description: ChIPseq for FLAG_ZFSssI_line2


title: SBA3888 [RNA-Seq]

value: Normal salt diet

value: male


title: cDC1 duplicate 1


title: Donor derived LClike cell triplicate 2


title: Donor derived LClike cell triplicate 1


title: Host derived LClike cell triplicate 2


title: RNAseq_ZFSssI_T3_line1_plus_rep4

description: RNAseq data for ZFSssI_T3_line1_plus_rep4

molecule: polyA RNA

extract_protocol:
Total RNA from inflorescences was extracted using Direct-zol kit (ZYMO research).
1 μg of total RNA was used to prepare libraries using the TruSeq Stranded mRNA kit (Illumina).

value: inflorescence

value: Columbia 0


title: RNAseq_ZFSssI_T3_line1_plus_rep3

description: RNAseq data for ZFSssI_T3_line1_plus_rep3


title: KO_S1

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 3 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with force_counts set to 2000. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: brain

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

value: brain

tag: age

value: 5 months

tag: gender


title: KO_S4


title: KO_S3


title: KO_S2


title: iPSC-ProT Cells

city: Toronto

first: Juan-Carlos

last: Zúñiga-Pflücker

address: 2075 Bayview Avenue

institute: Sunnybrook Research Institute

data_processing:
A total of 2,761 cells were sequenced and the resulting data were aligned and quantified using the CellRanger 3.1 pipeline (3’ v3 chemistry) using the GRCh38 human reference genome. Sequencing data were analyzed using R software version 4.0.0 with the package Seurat, version 3.1.
Sequencing data was normalized and scaled using the SCTransform wrapper in Seurat. To reduce the impacts of cell cycle on cell clustering and dimensionality reduction, a custom set of cell cycle genes were regressed before further analysis. Cell subsetting based on gene expression was done to identify and analyze T-lineage clusters and differential gene expression between clusters.
10x Genomics Cell Ranger 3.1.0.
Single Cell 3' v3 chemistry.
Genome_build: GRCh38 human reference genome.
Supplementary_files_format_and_content: features.tsv, barcodes.tsv, matrix.mtx

source_name: Human pluripotent stem cells

growth_protocol: iPSC CD34+ cells were cultured with DL4-mbeads for 7 days in StemSpan SFEM II supplemented with StemSpan T Cell Progenitor Expansion Supplement (StemCell Technologies) at 37°C in 5% CO2 incubator, at which time CD45+CD34+CD7+ cells were sorted.

extract_protocol:
PSC-derived CD45+CD34+CD7+ cells were sorted.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: IPS11 (Alstem Cell Advancements)

value: iPSC-derived progenitor T cells


title: WT_S4


title: Human_H3K27ac_Input_1

description: CD3+ CD161+ TCR Vα7.2+

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the hg19 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2
High confidence peaks were determined using IDR with a threshold IDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

source_name: MAIT cells

extract_protocol:
Chromatin was immunoprecipitated using the Active Motif Low Cell ChIP-seq kit (53084) using 100,000 cells. Chromatin was sheared using a Diagenode Bioruptor Pico (B01060002)
Libraries were generated using the Active Motif Low Cell ChIP-seq kit (53084).

value: peripheral blood

value: MAIT cells

tag: group

value: Input

value: none (input)


title: RNAseq_ZFSssI_T3_line1_plus_rep2

city: Haining

first: Wanlu

last: Liu

address: 718 East Haizhou Rd.,

institute: Zhejiang University

description: RNAseq data for ZFSssI_T3_line1_plus_rep2

tag: ecotype


title: Human_H3K27ac_MAIT_1

first: Dorina

last: Avram

address: 12902 Magnolia Drive, MRC4

institute: Moffitt Cancer Center

description: CD3+ CD161+ TCR Vα7.2+

value: Treatment


title: Human_H3K27ac_MAIT_2

description: CD3+ CD161+ TCR Vα7.2+


title: ChIP_FLAG_col

description: ChIPseq for FLAG_col


title: RNAseq_ZFSssI_T3_line1_plus_rep1

description: RNAseq data for ZFSssI_T3_line1_plus_rep1


title: RNAseq_ZFSssI_T2_line1_plus_rep3

description: RNAseq data for ZFSssI_T2_line1_plus_rep3


title: WT_S3


title: iAgB_HNF1A

value: hiPSC-derived pancreatic endocrine progenitor

value: Wild Type

value: Abcam ab96777


title: WT_S1