title: SCAR_439_H3K27me3_T3_r1

description: EdU-labelled genomic DNA


title: 5_hd_p190A_1

status: Public on Jun 15 2023

type: SRA

city: Boston

first: Steen

last: Hansen

state: MA

address: Enders Building, Room 1016

department: GI Division

country: USA

institute: Boston Children's Hospital

description:
all_counts_LATSkd.csv
p190A_2.expected_count

library_source: transcriptomic

data_processing:
Sequence reads were filtered with SOAPnuke software to remove read with adapters, unknown bases, and low-quality reads.
Genome mapping of filtered reads to reference genome GRCh38 was performed using HISAT2 and Bowtie2 software.
Raw data of RNA-seq were normalized and processed using R package DEseq2
Assembly: GRCh38
Supplementary files format and content: all_counts_LATSkd.csv include raw count values for all the samples

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: H661 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen) (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was subjected to Oligo dT selection for enrichment of mRNA followed by reverse transcription and second strand synthesis.

treatment_protocol: 1x10^6 cells were plated in a 6-well plate and cultured for 1 week to reach saturation density

tag: tissue

value: cell line

tag: cell line

tag: genotype

value: wild-type p190A expression

tag: treatment

value: culture to saturation density


title: 4_hd_p190A_1

description:
all_counts_LATSkd.csv
p190A_1.expected_count


title: SCAR_439_H3K27me3_T0_r1

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description: EdU-labelled genomic DNA

library_source: genomic

data_processing:
Library strategy: SCAR-seq
adapters and low quality reads were filtered with cutadapt version 2.5
reads were mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Genome_build: mm10
Supplementary_files_format_and_content: SCAR-seq Partition scores in bigwig format

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA.

extract_protocol:
After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase under native conditions. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
OTHER

treatment_protocol: Cells were incubated in EdU media (f.c. 10 um)  for 15 min and then either collected (T0) or cultured for indicated maturation intervals (T3; T8) in media without EdU before collection.

tag: strain


title: SCAR_438_H3K27me3_T8_r1

description: EdU-labelled genomic DNA


title: luminal A cancer 1

type: RNA

city: Seoul

first: Yesol

last: Kim

address: Cheongpa-ro 47-gil 100, Yongsan-gu

country: South Korea

institute: Sookmyung Women's University

hyb_protocol: The labeled RNA samples were dried in a Vacuum Concentrator for one hour. Once samples are completely dried, they were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. Arrays were hybridized in 45 µl of the mixture, and then rotated at 20 rpm for 20 h at 55°C. Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System

scan_protocol: Agilent Gene expression were scanned on a Agilent Technologies G4900DA SureScanner using 3 µm resolution

data_processing: Data were acquired using Agilent Feature Extraction software version 11.0.1.1

source_name: luminal A cancer tissue 1

label_protocol: 100 ng total RNA was dephosphorylated(PO4) at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour

extract_protocol: Total RNA from human tissue was isolated using TRIzol (Life Technologies) following the manufacturer's protocol.

tag: gender

value: female

tag: disease subtype

value: Luminal A

value: luminal A cancer tissue


title: luminal A cancer 2

source_name: luminal A cancer tissue 2


title: K562, Control, Input, r2, b2, ChIP-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were mapped to human genome using bowtie2 (version 2.4.1) in default mode: search for the multiple alignments, report the best one.
Peaks were called using HOMER mode in histone (for histone modification ChIP-seq) or factor (for hranscriptional factor ChIP-seq) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: K562 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 2nM L-glutamine and antibiotics in cellular incubator with 5% CO2 at 37C.

extract_protocol:
Cells were fixed with 1% formaldehyde. ChIP was preformed with the iDeal ChIP-seq kit for Histone marks (Diagenode) or the the iDeal ChIP-seq kit for Transcription Factors (Diagenode)
Library preparation was performed with KAPA HyperPrep Kit for NGS DNA Library Prep (Roche) according to the manufacturer’s protocols.

tag: cell type

value: Human immortalized myelogenous leukemia cell line

value: Control

tag: chip antibody


title: 3_hd_ctrl_1

description:
all_counts_LATSkd.csv
control_3.expected_count

value: wild type


title: K562, RBFOX2 KD, Input, r1, b2, ChIP-seq

value: RBFOX2 knockdown


title: K562, RBFOX2 KD, Input, r2, b2, ChIP-seq


title: SCAR_438_H3K27me3_T3_r1

description: EdU-labelled genomic DNA


title: K562, Control, Input, r1, b2, ChIP-seq


title: luminal A adjacent normal 2

source_name: luminal A adjacent normal tissue 2

value: normal

value: luminal A adjacent normal tissue


title: K562, RBFOX2 KD, SUZ12, r2, b2, ChIP-seq

value: Rabbit monoclonal anti-SUZ12 (Cat#3737, Cell Signaling Technology)


title: SCAR_438_H3K27me3_T0_r1

description: EdU-labelled genomic DNA


title: luminal A adjacent normal 1

source_name: luminal A adjacent normal tissue 1


title: 1_hd_ctrl_1

description:
all_counts_LATSkd.csv
control_1.expected_count


title: HER2 cancer 3

source_name: HER2 cancer tissue 3

value: HER2 cancer tissue


title: SCAR_410_H3K27me3_T8_r1

description: EdU-labelled genomic DNA

value: wildtype


title: 2_hd_ctrl_1

description:
all_counts_LATSkd.csv
control_2.expected_count


title: K562, RBFOX2 KD, SUZ12, r1, b2, ChIP-seq


title: HER2 cancer 2

source_name: HER2 cancer tissue 2


title: K562, Control, SUZ12, r2, b2, ChIP-seq


title: Carbon_2

city: Beijing

first: Shuyu

last: Liu

address: Shuang Qing Road 18

institute: Research Center for Eco-Environmental Sciences

data_processing:
Base-calling was performed with the BGISEQ-500 software, version 0.3.8.1111
Reads were filtered by Trimmomatic (v0.360), summarized with SOAPnuke (v1.4.0).
The clean data were alignment to the reference genome, GRCh3.p11(hg38), and the expected counts were calculated by using Bowtie2 (v2.2.5).
Differentially expressed genes (DEGs) analyzed with the DEGseq software
Genome_build: Genome_build: GCF_000001405.37_GRCh38.p11
Supplementary_files_format_and_content: csv file include FPKM values for each sample and each gene

source_name: monolayer-derived alveolar cells

growth_protocol: hESC–derived alveolar cell-like cells were generated in monolayer fashion with or without nano carbon black treatment or in organoid system.

extract_protocol:
Total cell lysates were collected and RNA were extracted and purified with enrichment columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100 ng/mL nano carbon black were applied for the treated samples.

value: hESC-derived alveolar cells

tag: phenotype

value: alveolar cell-like cells

value: 100 ng/mL nano carbon black


title: Carbon_1


title: HER2 cancer 1

source_name: HER2 cancer tissue 1


title: SCAR_410_H3K27me3_T3_r1

description: EdU-labelled genomic DNA


title: K562, Control, SUZ12, r1, b2, ChIP-seq


title: SCAR_410_H3K27me3_T0_r1

description: EdU-labelled genomic DNA


title: ChIP_442_K9me3_input_r2

data_processing:
Files were processed using the ENCODE ChIP-seq pipeline version 1.3.6: adapters and low quality reads were filtered with cutadapt version 2.5 and mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7) and bam files converted to tagAlign files
peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 (narrow peaks, H3K4me3) or --nomodel --broad -p 0.01 –-broad-cutoff 0.1 (broad peaks, H3K27me3 and H3K9me3)
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq peak bed files called with macs2, narrow peaks (H3K4me3) and broad peaks (H3K27me3,H3K9me3)

extract_protocol:
Cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase under native conditions. Native Drosophila chromatin was spiked in and mononucleosomal fragments were immunoprecipitated, followed by library preparation and sequencing.
Libraries were prepared using standard Illumina protocols (KAPA Hyper Prep kit).

treatment_protocol: Samples were untreated.


title: HER2 adjacent normal 3

source_name: HER2 adjacent normal tissue 3

value: HER2 adjacent normal tissue


title: HER2 adjacent normal 2

source_name: HER2 adjacent normal tissue 2


title: v_2

value: untreated


title: 515_AMlib3_966_IP

city: Rehovot

first: Alexander

last: Maman

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: 966 m6A negative control

data_processing:
Internal barcode demultiplexing with inhouse pythong script according to Read2 position 4-10 (raw data supplied here is after this step)
alignment using STAR/2.5.3a  with added options of -(--bamRemoveDuplicatesType UniqueIdentical , --outSAMtype BAM SortedByCoordinate ,--alignIntronMax 500 , --alignEndsType Local)
reads to gene alloacation and coverage summary using txtools/0.0.7.4
m6A levels quantified using in house R-script(see paper)
Assembly: SK1, NCBI37/mm9
Supplementary files format and content: rds files of reads alloction created using txtools, contatining. Chr-chromosom, gencoor-genomic coordinates, strand - strand , gene - gene name, txcoor- transcript coordinates, refSeq - annotated nucleotide at this position, cov - total coverage at this position, start_5p-5p reads starting at this position,end_3p-reads ending at this location
Library strategy: m6A-seq2

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD (1.0% (w/v) yeast extract, 2.0% (w/v) peptone, 2.0% (w/v) glucose, and supplemented with uracil (2.5 mg/l) and adenine (1.25 mg/l)). To induce meiosis a standard protocol for sporulation was followed as described previously {Varier, 2022 #262} . In short, cells were grown until saturation for 24h in YPD, then grown in pre-sporulation medium BYTA (1.0% (w/v) yeast extract, 2.0% (w/v) bacto tryptone, 1.0% (w/v) potassium acetate, 50 mM potassium phthalate) for about 16 h, and shifted to sporulation medium (SPO) (0.3% (w/v) potassium acetate and 0.02% (w/v) raffinose)). All experiments were performed at 30°C in a shaker incubator at 300 rpm

extract_protocol:
RNA extraction was performed from yeast pellets using Acid Phenol:Chloroform pH 4.5 and Tris-EDTA-SDS (TES) buffer (0.01 M Tris-HCl pH 7.5, 0.01 M EDTA, 0.5% w/v SDS). Samples were further treated with rDNase (cat no 740.963, Macherey-Nagel) and column purified (cat no 740.948, Macherey-Nagel).
m6A levels were determined by m6A-seq2, as previously described {Dierks, 2021 #308; Schwartz, 2013 #4}.Briefly, RNA was poly-A selected twice using Dynabeads mRNA DIRECT kit, and fragmented to ~150 bp fragments. 3’ RNA barcode adaptors were then ligated (see Table S6), and all samples were pooled for m6A-IP-based enrichment. 90% of the mRNA material was subjected to two rounds of immunoprecipitation using two distinct anti-m6A antibodies, as follows: The RNA was first incubated for four hours with protein G beads (invitrogen) coupled to a Synaptic Systems poly-clonal m6A antibody (cat. 7945). Next, it was incubated overnight with protein A beads (invitrogen) coupled to a Cell Signaling poly-clonal m6A antibody (cat. D9D9W). RNA from input and IP libraries were reverse transcribed and PCR amplified as previously described  {Dierks, 2021 #308}. cDNA libraries were quantified using Qubit RNA HS kit (Life technologies) and Tapestation High Sensitivity D1000 ScreenTape (Agilent Technologies), pooled with a ratio of ⅓ Input to ⅔ IP samples, and sequenced.

treatment_protocol: For Auxin depleted experiments- To enable efficient depletion of mini-AID strains (Slz1, Vir1, Pab1 and Npl3), 1 mM of indole-3-acetic acid (IAA) and 50 µM of CuSO4 were added 2 hours after cells were shifted to SPO and samples collected at 4 hours in SPO.  As a control, the same volume of dimethyl sulphoxide (DMSO) was added to the yeast culture.

value: MATa ho::LYS2,lys2, ndt80::LEU2 ime4::HIS3, MATalpha lys2,ho::LYS2 ndt80::LEU2 ime4::HIS3

value: SPO

tag: time


title: organoid_2

source_name: organoid system-derived alveolar cells


title: K562, RBFOX2 KD, Input, r2, b1, ChIP-seq


title: v_1


title: K562, Control, Input, r2, b1, ChIP-seq


title: 515_AMlib3_966_input

description: 966 m6A negative control

value: MATa ho::LYS2,lys2, ndt80::LEU2, MATalpha lys2,ho::LYS2, ndt80::LEU2


title: K562, RBFOX2 KD, Input, r1, b1, ChIP-seq

value: Human immortalized myelogenous leukemia cell line


title: 515_AMlib3_9392C_IP

description: ygl036w (vir1) deletion

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN


title: ChIP_421_K9me3_input_r2


title: ChIP_410_K9me3_input_r2


title: ChIP_442_K9me3_input_r1


title: mono_2


title: K562, RBFOX2 KD, H3K4me3, r2, b1, ChIP-seq

value: Rabbit anti-H3K4me3 (Cat#9751, Cell Signaling Technology)


title: mono_1


title: HER2 adjacent normal 1

source_name: HER2 adjacent normal tissue 1

value: female


title: organoid_1


title: 515_AMlib3_9392C_input

description: ygl036w (vir1) deletion


title: K562, Control, Input, r1, b1, ChIP-seq

value: Control


title: ChIP_439_K9me3_input_r1


title: K562, RBFOX2 KD, H3K4me3, r1, b1, ChIP-seq

value: RBFOX2 knockdown


title: Rice ac4C IP replicate 2

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: ac4C, rep2

data_processing:
Adapters were removed from reads with the AdapterRemoval tool with adapter sequence 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'.
Reads were then mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.

organism: Oryza sativa

source_name: 15-day-old seedlings

growth_protocol: Arabidopsis seedlings were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC. Oryza sativa L. ssp. japonica cultivar Nipponbare plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 mmol m-2 s -1.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.
acRIP-seq

tag: rip antibody

value: ac4C (abcam, ab252215)

tag: variety

value: Nipponbare

tag: age

value: seedlings


title: ChIP_439_K9me3_input_r2


title: ChIP_421_K9me3_input_r1


title: 515_AMlib3_9392B_input

description: ygl036w (vir1) deletion


title: K562, Control, H3K4me3, r2, b1, ChIP-seq


title: Rice ac4C IP replicate 1

description: ac4C, rep1


title: K562, Control, H3K4me3, r1, b1, ChIP-seq


title: 515_AMlib3_9392A_IP

description: ygl036w (vir1) deletion


title: Rice Input replicate 2

description: Input, rep2


title: ChIP_442_H3K9me3_r2

tag: antibody


title: ChIP_410_K9me3_input_r1

value: wildtype


title: Rice Input replicate 1

description: Input, rep1


title: ChIP_439_H3K9me3_r2


title: CAG wildtype cells

city: Jiangsu Nanjing

first: Deng

middle: Zhen

last: Dong

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

description: C_OE_PNPO_Vs_C_WT_YYX.mRNA_diffgene.results

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple Myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CAG

value: Multiple Myeloma cells


title: CAG PNPO-OE cells

value: PNPO-OE


title: 515_AMlib3_9307C_IP

description: ygl036w (vir1) deletion


title: 515_AMlib3_9392A_input

description: ygl036w (vir1) deletion


title: Rice IgG control replicate 2

description: IgG, rep2

value: Rabbit IgG


title: Rice IgG control replicate 1

description: IgG, rep1


title: 515_AMlib3_9307C_input

description: ygl036w (vir1) deletion


title: ARP1 PNPO-OE cells

description: A_OE_PNPO_Vs_A_WT_YYX.mRNA_diffgene.results


title: ChIP_442_H3K9me3_r1


title: ChIP_410_H3K9me3_r2

description: 410_H3K9me3_ChIP_pr.original.reproducible_peaks.broadPeak.bed.gz


title: ChIP_421_H3K9me3_r2


title: ARP1 wildtype cells


title: D7.5 No-cre mouse scRNA-seq RL-30T

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

library_source: transcriptomic single cell

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: The filtered feature count matrix was generated from Cell Ranger.

source_name: Uterus

growth_protocol: The female mice were fed with normal chow, and housed with its female littermates until 8 weeks old.

extract_protocol:
The mouse uterus were incubated with Trypsin to dissociate into single cells. The single cell flows were loaded into the 10X genomics single cell chip.
RNA libraries were prepared by Chromium Single Cell 3’ Library & Gel Bead Kit v3.1

treatment_protocol: The females were mated with stud males and dissected at pregnancy day 7.5

value: Uterus

tag: Sex

tag: tissue collection

value: single cell isolation

tag: timing

value: Pregnancy day 7.5


title: 515_AMlib3_9307B_input

description: ygl036w (vir1) deletion

tag: cell line

value: SPO


title: 515_AMlib3_9392B_IP

description: ygl036w (vir1) deletion

tag: genotype

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG YGL036W::KAN


title: Input_e14_17

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

data_processing:
Basecalls were performed using IonSuite
ChIP-seq reads were aligned to USCS mm10 genome with Bowtie version 2.3.5.1 and convert to sam files.
sam files were convert to bam, remove duplicates, sort and index with samtools 1.9.
bam files were downsampled to 60 million reads per sample using sambamba 0.7.1
Peaks were called using MACS2 2.2.7.1 with the broad peak, significance broad-cut-off q-value <=0.01
BigWig were generated using bamCoverage (deepTools 3.5.1) from sorted and indexed BAM files.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: dermal fibroblasts of WT skin

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using diagenode Bioruptor 300. Chromatin was incubated with H3K27me3 antibody (Active Motif AB_2561020). Immunoprecipitation was done using Pierce ChIP-grade Protein A magnetic beads.
Library was prepared using IonTorrent Ion Plus Fragment Library Kit

value: dermal fibroblasts of WT skin

value: input

tag: developmental stage


title: ChIP_439_H3K9me3_r1

source_name: Embryonic stem cells

tag: strain


title: D7.5 Cre mouse scRNA-seq

tag: tissue

value: female

value: Prl8a2icre/+ Sun1-GFPLsL/+


title: 515_AMlib3_9307A_IP

description: ygl036w (vir1) deletion

tag: treatment


title: ChIP_421_H3K9me3_r1


title: 515_AMlib3_9307A_input

description: ygl036w (vir1) deletion

tag: cell type


title: E17_1

tag: chip antibody


title: ChIP_410_H3K9me3_r1


title: E14_2


title: Atrx+_DMSO_H4K16ac

city: Houston

first: Prit Benny

last: Malgulwar

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

institute: U.T. M.D. ANDERSON CANCER CENTER

data_processing:
Generated ChIP-seq data underwent quality-control measures using the FASTQC tool and aligned to the mm9 reference genome with Bowtie2 (version 2.4.5).
Only unique mapped reads were retained. MACS2 callpeak (version 2.2.7.1) was used for calling peaks from BAM files with default parameters.
BED files were further subjected to gene annotation using GREAT (version 4) analysis  with Basal plus extension parameters (Proximal: 5kb upstream, 1kb downstream, plus distal upto 1000kb).
For MEME analysis, ChIP-MEME was utilized using default parameters. Peak annotation and visualization were performed using the PAVIS annotation tool.
Assembly: mm9
Supplementary files format and content: BED

source_name: Primary cell line

growth_protocol: Neuroepithelial progenitor Cells (NPCs) were grown in NeuroCult Basal Medium containing NeuroCult Proliferation Supplement, 20 ng/ml EGF, 10 ng/ml basic FGF, 2 μg/ml heparin (Stemcell Technologies), 50 units/ml penicillin, and 50 μg/ml streptomycin (Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 37% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit using 20 ng of DNA was used as starting material for input and IP samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Atrx- NPCs were treated with Sirt2 inhibitors (AGK2: 1uM) or DMSO vehicle for 48 hours

value: Primary cell line

value: Neuroepithelial progenitor cell


title: Atrx+_DMSO_H3K27me3

value: H3K27me3 (Abcam, ab6002)


title: 515_AMlib3_841_IP

description: 841 m6A positive control

value: MATa ho::LYS2,lys2, ndt80::LEU2 ime4::HIS3, MATalpha lys2,ho::LYS2 ndt80::LEU2 ime4::HIS3


title: ChIP_442_K4me3_input_r2


title: 515_AMlib3_9307B_IP

description: ygl036w (vir1) deletion


title: ChIP_439_K4me3_input_r2


title: 515_AMlib3_7030C_IP

description: ime4 deletion

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3 , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG ime4:URA3


title: Atrx+_AGK2_H4K16ac


title: 515_AMlib3_841_input

description: 841 m6A positive control

value: MATa ho::LYS2,lys2, ndt80::LEU2, MATalpha lys2,ho::LYS2, ndt80::LEU2


title: 515_AMlib3_7030C_input

description: ime4 deletion


title: Atrx+_AGK2_H3K27me3


title: ChIP_410_K4me3_input_r2

value: wildtype


title: Atrx-_DMSO_H4K16ac


title: E17_2


title: ChIP_421_K4me3_input_r2


title: 515_AMlib3_7030B_input

description: ime4 deletion


title: 515_AMlib3_7030B_IP

description: ime4 deletion


title: Atrx+_DMSO_H3K4me1

value: H3K4me1 (Abcam, ab4729)


title: ChIP_442_K4me3_input_r1


title: ChIP_439_K4me3_input_r1


title: Atrx+_AGK2_H3K4me1


title: E14_1


title: 515_AMlib3_7030A_IP

description: ime4 deletion


title: Atrx-_DMSO_H3K27ac

value: H3K27ac (Abcam, ab8895)


title: Atrx-_DMSO_H3K27me3


title: 515_AMlib3_7030A_input

description: ime4 deletion


title: ChIP_421_K4me3_input_r1


title: ChIP_410_K4me3_input_r1


title: ChIP_442_H3K4me3_r2


title: Atrx-_DMSO_H3K4me1


title: miR-27b mimic-transfected Huh-7 cells rep1

city: Osaka

first: Hiroyuki

last: Mizuguchi

address: Suita Yamadaoka 1-6

country: Japan

institute: Osaka university

description: Gene expression 48hr after transfection of mimics.

hyb_protocol: 600 ng of Cy3-labelled fragmented cRNA  in hybridization buffer was hybridized overnight (17 hours, 65 C) to Ajilent Whole Human Genome Oligo Microarrays 8x60K V2.  After hybridization, microarrays were washed 1 minute at room temperature follwed by a second wash with GE Wash Buffer 2 (Agilent) for 1 minute.

scan_protocol: Fluorescence signals of the hybridized Ajilent Microarrays were detected using Agilent's Microarray Scanner System.

data_processing:
The Agilent Feature Extraction Software was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction9, rejects outliers and calculates statistical confidences.
FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system.

source_name: Huh-7 cells, miR-27b mimic, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Agilent Low Input Quick Amp Labelling Kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technology).

growth_protocol: Huh-7 cells were ciltured with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using Isogen (Nippon gene) following the manufacturer's instructions.  Quality of RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Huh-7 cells were transfected with miRNA mimics at 10nM using RNAiMAX (invitrogen) and cultured for 48hrs.

tag: transfection

value: miR-27b mimic


title: Control mmic-transfected Huh-7 cells rep2

source_name: Huh-7 cells, control mimic, replicate 2

value: control mimic


title: Control mmic-transfected Huh-7 cells rep3

source_name: Huh-7 cells, control mimic, replicate 3


title: miR-27b mimic-transfected Huh-7 cells rep2

source_name: Huh-7 cells, miR-27b mimic, replicate 2


title: w1118 rat anti-HDAC3 second replicate

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

data_processing:
usegalaxy.eu
CUT&Tag sequencing adapters were trimmed using Trim Galore. In addition to adapter removal, low-quality ends (<20) were trimmed from reads. Reads that became shorter than 20 bp were discarded.
CUT&Tag sequencing reads were mapped to dm6 using Bowtie2 (bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700).
bigwig coverage tracks were generated by normalization to the effective genome size (dm6)
Peaks were called using MACS2 (significance cut-off q-value <=0.05) and peaks with a score <= 15 were discarded. Overlapped peaks between different replicates/antibodies were identified using the Join tool. The obtained peaks were annotated with ChIPseeker.
Assembly: dm6
Supplementary files format and content: bigwig for coverage
Supplementary files format and content: bed for peaks
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: Whole embryo

growth_protocol: Embryos were grown at 25°C

extract_protocol:
Crude nuclear extract was prepared in Nuclear Extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0,1% Triton X-100, 20% glycerol) followed by binding to Concanavalin A-coated beads (Polysciences, Inc. 86057-3) and incubation with primary antibody. Tagmentation was performed using Protein A-Tn5 fusion protein.
Following tagmentation DNA was amplified using primers from Nextera Index Kit.

value: Whole embryo

value: Rat anti-HDAC3

value: 2-4h after egg laying


title: 515_AMlib3_1511C_IP

description: WT

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG

value: SPO

tag: time


title: Atrx-_AGK2_H4K16ac


title: ChIP_439_H3K4me3_r2


title: Atrx-_AGK2_H3K27ac


title: Control mmic-transfected Huh-7 cells rep1

source_name: Huh-7 cells, control mimic, replicate 1


title: shHDAC3 rat anti-HDAC3 second replicate

value: tub-GAL4/shRNA HDAC3


title: 515_AMlib3_1511A_IP

description: WT


title: Site H  individual 7

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.6.6
Mapping on the reference Transcriptom of Hyla orientalis with Bowtie2 and RSEM
RSEM results imported with tximport in R and analysed with DESeq2
Polymorphism analysis with GATK haplotypeCaller v 4.2.0.0
Assembly: Unpublished de novo transcriptom assembly of Hyla orientalis
Supplementary files format and content: vcf with variant SNP

organism: Hyla orientalis

source_name: tibia muscle

extract_protocol:
Trizol extraction followed by column purification on Quick RNA Miniprep kit (Zymoreasearch)
Stranded mRNA kit (Illumina). Paired end with dual Index UD IDT (illumina)

treatment_protocol: Sampling of wild individuals in the chernobyl exclusion zone and in Slavutych area

value: tibia muscle

value: Wild type

tag: location

value: captured in Slavutich region

tag: treatment group

value: not exposed


title: Atrx-_AGK2_H3K4me1

value: Primary cell line

value: Neuroepithelial progenitor cell


title: w1118 rabbit anti-HDAC3

value: Rabbit anti-HDAC3


title: Site H  individual 8


title: 515_AMlib3_1511C_input

description: WT


title: Atrx-_AGK2_H3K27me3

value: H3K27me3 (Abcam, ab6002)


title: w1118 rat anti-HDAC3


title: 515_AMlib3_1511B_IP

description: WT


title: e18.5 scATAC-seq

description: 10X Genomics ATAC v1.1

library_source: genomic single cell

data_processing:
Fastq files were aligned using cellranger-atac-2.1.0
Assembly: mm10 (cellranger-arc-mm10-2020-A-2.0.0)

source_name: Skin

extract_protocol:
Murine skin collected at E14.5 and E18.5. Enzymatic separation of dermis from epidermis. The dermis were then digested to single cell suspension. Nuclei isolation was performed to achieve single nuclei solution.
Library was performed according to the manufacter’s instructions for Chromium Next GEM ATAC v1.1 from single nuclei solution.

value: Mixed

value: Skin

tag: age


title: ChIP_421_H3K4me3_r2

tag: antibody


title: Site H  individual 5


title: e14.5 scATAC-seq

description: 10X Genomics ATAC v1.1


title: 515_AMlib3_1511B_input

description: WT


title: ChIP_410_H3K4me3_r2

description: 410_H3K4me3_ChIP_pr_R1.original.reproducible_peaks.narrowPeak.bed.gz

value: wildtype


title: ChIP_421_H3K4me3_r1


title: ChIP_410_H3K4me3_r1


title: ChIP_442_H3K4me3_r1


title: Site H  individual 6


title: ZNF845_ChIPexo

city: Lausanne

first: Jonas

last: de Tribolet-Hardy

address: Bâtiment SV 0405

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads).
Reads with mapping quality lower than 10,  from the UCSC blacklist, or from a greylist derived from TI using GreyListChIP Bioconductor package were removed from the analysis.
Peaks were called using MACS v2.2.4 with default parameters except “--keep-dup all” and -q 0.01
Assembly: hg19
Supplementary files format and content: bedfile obtained for MACS

source_name: transduced HEK293T cell line

growth_protocol: Human embryonic kidney-derived 293T cells  were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Chromatin was prepared by resuspending 3x107 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follow: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
Total inputs and chromatin immunoprecipitated samples were prepared for libraries using 10 ng of material. After end-repair and A-tailing, Illumina IDT indexes were ligated to the samples. Aliquots were tested in qPCR to determine the optimal number of PCR cycles needed to amplify each library without reaching saturation. Libraries were amplified with, size-selected using Ampure XP beads (Beckman Coulter), and always quality-checked on a Bioanalyzer DNA high sensitivity chip (Agilent) and quantified with a Qubit dsDNA HS assay kit (Qubit 2.0 Fluorometer, Invitrogen)

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/mL) for 7 days and induced using doxycyclin (1 ug / mL) for a few days before fixation with formaldehyde (1% for 10 min).

value: transduced HEK293T cell line

value: Human embryonic kidney

value: Anti-HA :clone 16B12, Covance


title: 515_AMlib3_1511A_input

description: WT

value: MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG , MATalpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG


title: C57, DDC, week14

city: Guangzhou

first: Hui

address: Xinzao Road No.1

institute: Guangzhou Medical University

description:
DDC
nuclear RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, genes.tsv, matrix.mtx).

source_name: Liver

extract_protocol:
After collecting 200mg of fresh liver tissue, remove the unwanted attachment tissue, properly drain the residual blood and other liquids, cut the tissue into 1~2mm3 size fragments in a Petri dish, and quickly transfer the fragments to the cryopreservation tube and snap freeze in liquid nitrogen for 5 min, after which it can be transferred to an ultra-low temperature freezer or liquid nitrogen for preservation. At 4 °C, nuclear suspension preparation is performed with sucrose density gradient centrifugation, using a 2 ml specification Dounce homogenizer for extraction, and all reagents need to be pre-cooled.
Library was performed according to the manufacturer’s instructions (single cell 3’ protocol and 10x Genomics). This technology samples a pool of ~750000 barcodes to separately index each cell’s transcriptome. It does so by partitioning thousands of cells into nanoliter-scale Gel Bead-In EMulsions (GEMs), where all generated cDNA share a common 10x Barcode. Upon dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, the GEMs are broken and the pooled fractions are recovered. Then, full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction. Finally, R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, Atailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Liver

value: cholangiocyte

value: WT

value: fed the control diet with 0.1% DDC


title: Site G  individual 8

value: tibia muscle

value: Wild type

value: captured in Slavutich region


title: Site H  individual 4

value: not exposed


title: ZNF836_ChIPexo


title: C57, Control, week14

description:
Control
nuclear RNA

value: fed the control diet


title: ChIP_442_K27me3_input_r2


title: ChIP_439_K27me3_input_r2


title: ZNF829_ChIPexo


title: WT scRNAseq

description: 10X Genomics V3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Cell Ranger output files were processed to create loom files required for RNA velocity analysis
Assembly: mm10
Supplementary files format and content: loom files

extract_protocol:
Single-cell suspension from whole skin collected at E18.5 of Kdm6bWT and Kdm6bKO mice were processed and prepared for 10X Genomics 3' Gene Expression kit (v3)
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: Site G  individual 5


title: KO scRNAseq

description: 10X Genomics V3


title: Site G  individual 7


title: VC,40Hz,1hr,11

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

description: 10x Genomics

data_processing:
Creation of count matrices was completed with 10x Genomics Cell Ranger 7.0.1 using 10x Genomics Cloud Analysis, introns included
Assembly: mm10
Supplementary files format and content: Tape archive of filtered count matrix output from 10x Genomics Cloud Analysis, unpack tar for barcodes and feature tab-separated values and matrix file

source_name: Visual Cortex, Right Hemisphere

extract_protocol:
Flash frozen right visual cortices were sent to Admera Health for tissue dissociation and extraction
10x Chromium Next GEM Single Cell 3' GEM v3.1 library preparation, 5000 cells

value: Visual Cortex, Right Hemisphere

tag: Sex

value: Male

value: 40Hz AV flicker

tag: duration


title: ChIP_442_K27me3_input_r1


title: ChIP_439_H3K4me3_r1


title: ZNF814_ChIPexo


title: ZNF780B_ChIPexo


title: ChIP_421_K27me3_input_r2


title: Site G  individual 6


title: ZNF841_ChIPexo


title: ChIP_421_K27me3_input_r1


title: VC,40Hz,1hr,12

description: 10x Genomics


title: VC,40Hz,1hr,10

description: 10x Genomics


title: ZNF773_ChIPexo


title: Site H  individual 3


title: Site G  individual 4


title: ZNF761_ChIPexo


title: ChIP_410_K27me3_input_r2

value: wildtype


title: VC,40Hz,1hr,09

description: 10x Genomics


title: ChIP_439_K27me3_input_r1


title: VC,20Hz,1hr,07

description: 10x Genomics

value: 20Hz AV flicker


title: Site G  individual 3


title: VC,20Hz,1hr,08

description: 10x Genomics


title: Site G  individual 2


title: ZNF728_ChIPexo

value: transduced HEK293T cell line

value: Human embryonic kidney


title: ChIP_410_K27me3_input_r1


title: ZNF726_ChIPexo

value: Anti-HA :clone 16B12, Covance


title: ChIP_439_H3K27me3_r2


title: VC,20Hz,1hr,06

description: 10x Genomics


title: Site F individual 9

value: captured in chernobyl exclusion zone

value: exposed to radiocontamination


title: Site G  individual 1


title: VC,20Hz,1hr,05

description: 10x Genomics

value: WT


title: ZNF75A_ChIPexo


title: VC,Light,1hr,04

description: 10x Genomics

value: ambient light


title: ZNF727_ChIPexo


title: ZNF717_ChIPexo


title: ChIP_442_H3K27me3_r2


title: ChIP_421_H3K27me3_r2


title: ChIP_410_H3K27me3_r2

description: 410_H3K27me3_ChIP_pr.original.reproducible_peaks.broadPeak.bed.gz


title: ZNF713_ChIPexo


title: Site F individual 7

value: tibia muscle


title: Site F individual 6

value: Wild type


title: VC,Light,1hr,03

description: 10x Genomics


title: Site F individual 8


title: Site F individual 5


title: VC,Light,1hr,02

description: 10x Genomics


title: ChIP_442_H3K27me3_r1


title: ZNF709_ChIPexo


title: VC,Light,1hr,01

description: 10x Genomics


title: Site F individual 4


title: ChIP_439_H3K27me3_r1


title: Site F individual 3


title: ChIP_421_H3K27me3_r1


title: ZNF721_ChIPexo


title: ZNF689_ChIPexo


title: ChIP_410_H3K27me3_r1


title: Site F individual 11


title: ZNF688_ChIPexo


title: Site F individual 10


title: 06_10dLSK

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

institute: Fukushima Medical University

data_processing:
Basecalls performed using bcl2fastq v2.20.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the mouse reference genome (mm10) using Tophat 2.1.1 (bowtie2-2.2.3).
The read counts allocated for each gene and transcript (RefSeq Genes 2013.04.01) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.2 software (Agilent Technologies, Santa Clara, CA).
Genome_build: mm10
Supplementary_files_format_and_content: An excel format file (XLSX) includes TMM quantification values and RefSeq gene annotations of all samples.

source_name: Hematopoietic stem/progenitor cells

extract_protocol:
Total RNA was purified from sorted cells using miRNeasy Micro Kit (QIAGEN, Valencia, CA, USA) with manufacturer's instructions.
Each of 5 ng of the total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) according to the manufacturer’s protocols.

value: LSK cells

value: bone marrow

tag: genotype/variation

value: Calr-frameshift KI mice (del10)


title: ZNF676_ChIPexo

tag: cell line


title: ZNF670_ChIPexo

tag: genotype


title: Site E individual 6


title: Site E individual 5


title: Kdm6bKO_4

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Alignment was done to UCSC mm10 genome using Bowtie version 2.3.5.1 and convert to sam files.
sam files were convert to bam, remove duplicates, sort and index with samtools 1.9.
bam files were downsampled to 60 million reads per sample using sambamba 0.7.1
Peaks were called using MACS2 2.2.7.1 with the broad peak, significance broad-cut-off q-value <=0.01
BigWig were generated using bamCoverage (deepTools 3.5.1) from sorted and indexed BAM files.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: Fibroblasts

growth_protocol: AmnioMAX, cell cultured at 37 degrees C, 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Cells were processed with Cell Signaling SimpleChIP Plus Enzymatic Chromatin IP Kit #9005 and H3K27me3 Antibody (Active Motif)
ChIP-seq libraries were prepared using the KAPA Hyper Library Preparation Kit.

treatment_protocol: Fibroblasts were flowsorted for GFP+ indicating conditional knock-out

value: Fibroblasts


title: Kdm6bWT_9


title: ZNF665_ChIPexo


title: Kdm6bKO_3


title: Input_Kdm6b


title: 04_WTLSK


title: VC,40Hz,1hr,Rep7

description: ID 178 Visual Cortex

data_processing:
Alignment was performed by Molecular Research Lab (https://mrdnalab.com) and data was validated for fastq integrity and quality. Each library was split between four lanes and .fastq files were merged using DNAstar ArrayStar. Next, Qseq reads were mapped using the mouse reference genome GRCm39 (GCF_000001635.27). For the read assignment, the threshold was set at 20bp and 80% of the bases matching within each read. Duplicated reads were eliminated and genes with less than 20 total raw counts were removed from analysis. Gene counts were normalized using DESeq2 in R.
Supplementary files format and content: DEseq2-normalized count values in csv format.

source_name: Brain Tissue

extract_protocol: RNA was isolated from mouse visual cortices  tissues using Qiagen RNeasy kit (217804; Qiagen; Hilden, Germany) according to the manufacturer’s protocols.

value: Brain Tissue

tag: brain region

value: visual cortex

value: Male


title: VC,40Hz,1hrRep6

description: ID 153 Visual Cortex


title: Site E individual 4


title: ZNF705B_ChIPexo


title: VC,40Hz,1hr,Rep5

description: ID 143 Visual Cortex


title: DeL9_12c

first: Irene

last: Guzmán-Benito

state: Vaud

address: Biophore, UNIL-SORGE

department: DBMV

institute: UNIL

data_processing:
Clean reads were obtained by removing adaptor tags and reads containing poly-N and low-quality reads from raw data. Paired-end clean reads were mapped to the Arabidopsis TAIR v10 reference genome using HISAT2 software. To quantify the gene expression level, HTSeq v0.6.1 was used to calculate the number of mapped reads of each gene, and then normalize the results to the expected number of Fragments Per Kilobase of transcript sequence per Millions of base-pairs sequenced (FPKM). Differential expression analysis between groups (three biological replicates per condition) was performed using DESeq2 R package (1.18.0). The resulting p values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted p value ≤0.05 found by DESeq2 were deemed as differentially expressed (DEG). A functional classification of DEGs including Gene Ontology (GO) and KEGG was done. GO enrichment analysis of DEGs was implemented by tGOseq R package, in which gene length bias was corrected. KOBAS software was used to test the statistical enrichment of DEGs in the KEGG database GO terms and KEGG pathways with corrected p value ≤0.05 were considered significantly enriched by DEGs.
Assembly: Arabidopsis TAIR v10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in controlled environmental chambers under long day conditions (16h day/8h night) at 22°C. Seeds were surface-sterilized and sown on plates contained ½ Murashige and Skoog (MS) medium supplemented with MES (0,5g/L), 1% sucrose and 0,9% Plant agar (Duchefa Biochemie, Haarlem, The Netherlands). Seedling were transferred to soil seven-to-ten days after germination.

extract_protocol:
RNeasy plant minikit (QIAGEN) followed by DNase treatment according to manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. First strand cDNA from mRNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. NEBNext Adaptor with hairpin loop structure were ligated. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: Arabidopsis seedlings were sprayed with 30 μM DEX (H2O was used as control) for 4 or 12 days at 24 h intervals.

value: seedling

value: 30 uM DEX

tag: days of_treatment

value: 12 days

value: BIR1 L9 transgenic

tag: replicate

value: Rep 3


title: Site E individual 3

tag: tissue

value: captured in chernobyl exclusion zone

value: exposed to radiocontamination


title: 05_2iLSK

tag: cell type

tag: strain

value: Calr-frameshift KI mice (ins2)


title: VC,40Hz,1hr,Rep4

description: ID 142 Visual Cortex

value: WT

tag: treatment


title: ZNF607_ChIPexo

value: transduced HEK293T cell line

value: Human embryonic kidney

tag: chip antibody

value: Anti-HA :clone 16B12, Covance


title: Site E individual 7

value: tibia muscle

value: Wild type

tag: location


title: ZNF677_ChIPexo


title: DeL9_4c

value: 4 days


title: Site E individual 2

tag: treatment group


title: Kdm6bWT_7

value: Fibroblasts


title: ZNF606_ChIPexo


title: VC,40Hz,1hr,Rep3

description: ID 121 Visual Cortex

value: Brain Tissue

value: visual cortex

tag: age

value: Male


title: ZNF589_ChIPexo


title: ZNF630_ChIPexo


title: DeL9_12b

value: seedling

value: 30 uM DEX

value: 12 days

value: Rep 2


title: VC,40Hz,1hr,Rep1

description: ID 94 Visual Cortex


title: MoL9_12c

value: MOCK

value: BIR1 L9 transgenic

value: Rep 3


title: Site D individual 9

value: captured in chernobyl exclusion zone

value: exposed to radiocontamination


title: VC,20Hz,1hr,Rep7

description: ID 180 Visual Cortex

value: WT


title: ZNF586_ChIPexo

value: transduced HEK293T cell line

value: Human embryonic kidney

value: Anti-HA :clone 16B12, Covance


title: DeL9_12a

value: Rep 1


title: Site D individual 7

value: tibia muscle

value: Wild type


title: Site D individual 8


title: VC,20Hz,1hr,Rep6

description: ID 177 Visual Cortex

value: Brain Tissue

value: visual cortex

value: Male


title: ZNF585B_ChIPexo


title: Site D individual 6


title: VC,20Hz,1hr,Rep5

description: ID 176 Visual Cortex


title: ZNF583_ChIPexo


title: Site D individual 5


title: MoL9_4b

value: seedling

value: 4 days


title: MoL9_4c

value: MOCK


title: MoL9_12a

value: 12 days

value: BIR1 L9 transgenic


title: VC,20Hz,1hr,Rep4

description: ID 155 Visual Cortex


title: ZNF568_ChIPexo_rep1


title: Site E individual 1

value: captured in chernobyl exclusion zone


title: VC,40Hz,1hr,Rep2

description: ID 119 Visual Cortex


title: DeL9_4a

value: 30 uM DEX


title: ZNF587_ChIPexo


title: DeL9_4b

value: Rep 2


title: Site D individual 4

value: exposed to radiocontamination


title: ZNF569_ChIPexo_rep2

value: transduced HEK293T cell line

value: Human embryonic kidney


title: VC,20Hz,1hr,Rep3

description: ID 149 Visual Cortex

value: WT


title: ZNF568_ChIPexo

value: Anti-HA :clone 16B12, Covance


title: MoL9_4a

value: Rep 1


title: MoL9_12b


title: Site D individual 3

value: tibia muscle

value: Wild type


title: VC,20Hz,1hr,Rep2

description: ID 144 Visual Cortex

value: Brain Tissue

value: visual cortex

value: Male


title: DeWT_12c

value: seedling

value: wildtype

value: Rep 3


title: VC,20Hz,1hr,Rep1

description: ID 141 Visual Cortex


title: Site D individual 1

value: captured in chernobyl exclusion zone


title: DeWT_12b

value: 30 uM DEX

value: 12 days


title: ZNF554_ChIPexo


title: ZNF544_ChIPexo


title: Site D individual 16

value: exposed to radiocontamination


title: ZNF519_ChIPexo

value: transduced HEK293T cell line


title: Site D individual 15


title: DeWT_12a


title: DeWT_4c

value: 4 days


title: Flox-BAT rep2

city: WuHan

first: Dong

last: Yang

address: No.5  HangKong Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 (ensembl_mus_musculus_grcm38_p6_gca_000001635_8)  whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: tab-delimited xls files include readcount values for each Sample ...

source_name: BAT

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 2°C).

extract_protocol:
Total RNA from each sample was extracted using RNAiso Plus (Takara Biotech), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: BAT

value: male

value: 10 weeks

value: Flox


title: ZNF517_ChIPexo

value: Human embryonic kidney

value: Anti-HA :clone 16B12, Covance


title: AKO-BAT rep1

value: adipocyte-specific H1.2 knockout


title: Site D individual 14

value: tibia muscle

value: Wild type


title: DeWT_4b

value: seedling

value: wildtype

value: Rep 2


title: Site D individual 13

value: captured in chernobyl exclusion zone


title: AKO-iWAT rep2

source_name: iWAT

value: iWAT


title: Site D individual 2

value: exposed to radiocontamination


title: ZNF514_ChIPexo

value: transduced HEK293T cell line


title: ZNF563_ChIPexo


title: Flox-BAT rep1


title: DeWT_4a

value: 30 uM DEX

value: 4 days

value: Rep 1


title: ZNF473_ChIPexo


title: AKO-iWAT rep1

value: male

value: 10 weeks


title: Site D individual 11


title: ZNF470_ChIPexo

value: Human embryonic kidney


title: Site D individual 12


title: MoWT_12c

value: MOCK

value: 12 days

value: Rep 3


title: MoWT_12b


title: Flox-iWAT rep2

value: Flox


title: AKO-BAT rep2

value: BAT

value: adipocyte-specific H1.2 knockout


title: ZNF461_ChIPexo

value: Anti-HA :clone 16B12, Covance


title: MoWT_12a

value: seedling

value: wildtype


title: Site C individual 9

value: tibia muscle

value: Wild type

value: captured in chernobyl exclusion zone

value: exposed to radiocontamination


title: MoWT_4c

value: 4 days


title: Flox-iWAT rep1

value: iWAT

value: male


title: ZNF43_ChIPexo

value: transduced HEK293T cell line

value: Human embryonic kidney


title: Site C individual 8


title: scRNAseq_588_r1

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

institute: Novo Nordisk Foundation Center for Protein Research

description:
4487 cells
MCM2-R

data_processing:
3’ cell multiplexing data was converted with Cell Ranger (version 6.0.2) to acquire raw reads (cellranger mkfastq) and subsequently sparse matrices (cellranger multi) based on GENCODE vM23 transcriptome annotations.
Cells corresponding to doublets were identified with DoubletFinder (version 2.0.3) with the doublet formation rate retrieved from Cell Ranger’s estimates for homotypic doublets.
RNA velocity analyses of the 3’ cell multiplexing data was processed with velocyto (version 0.17.17) based on read alignments derived from Cell Ranger to acquire sparse matrices for both spliced and unspliced transcripts per sample. The resulting loom files were read with SeuratWrappers (version 0.3.0).
Standard processing for all samples included log-normalization and variable feature detection before and scaling, dimensionality reduction (i.e., PCA, UMAP) and cluster identification before and after CCA-based sample integration. Clustree (version 0.4.3) was used to optimise the resolution of detected clusters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: The combined velocity data is deposited as loom file type and Cell Ranger per sample processed files of barcodes.tsv.gz, features.tsv.gz and matrix.mtz.gz.

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5% CO2. DMEM was supplied with fetal bovine serum (15%), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using TrypLE. Around 36h before the experiment 1.5X10^5 cells/6-well WT, MCM2-2A#2 and MCM2-R#2 cells were seeded on 0.2% gelatin in serum/LIF medium.

extract_protocol:
Cells were dissociated with TrypLE (Invitrogen), resuspended in PBS + 0.04% BSA and passed through 100um cell strainer (pluriSelect) to reach homogeneous single cell suspension. Samples were automatically counted (LUNA-FX7™, Logos biosystems) and evaluated for viability and homogeneity, each sample was divided to two to increase the complexity of the cell multiplexing oligos in the final library. 1M cells were labelled with cell multiplexing oligo following the CellPlex kit (PN-1000261, 10X Genomics) protocol. Labelled samples and technical repeats were evenly pooled and recounted reaching ~ 1500 cells/ul with cell viability higher than 95% for loading at the chromium controller (10X Genomics).
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) was used following the manufacturer's protocol.


title: MoWT_4b

value: MOCK

value: Rep 2


title: MoWT_4a

value: Rep 1


title: Site C individual 7


title: ZNF436_ChIPexo


title: ZNF404_ChIPexo


title: scRNAseq_410_r2

description: 4454 cells


title: Site C individual 6


title: ZNF354C_ChIPexo


title: Electroporated cells EPZ

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end sequenced reads were trimmed for adaptor sequence, and aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). For every single cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus (Zeis et al., 2020). Number of UMIs was converted into transcript counts (Gruen et al., 2014).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Rdata files containing tab-delimited matrices

source_name: Neuronal cells

growth_protocol: Microinjected organotypic brain slices were cultured for 24 h as previously described (Taverna et al., 2012)

extract_protocol:
Labelled cells and progeny were isolated via FACS enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DOT1L inhibition with EPZ5676 (Pinometostat) or DMSO as control

value: Cerebral cortex

value: Embryonic day E14.5

value: wild type


title: scRNAseq_442_r2

description: 4908 cells


title: scRNAseq_442_r1_tech2

description: 5284 cells


title: ZNF347_ChIPexo

value: Anti-HA :clone 16B12, Covance


title: Electroporated cells Control


title: Site C individual 4


title: Site C individual 5


title: Microinjected cells EPZ rep 2


title: ZNF268_ChIPexo


title: Site C individual 3


title: scRNAseq_410_r1_tech1

description: 5370 cells

value: wildtype


title: scRNAseq_410_r1_tech2

description: 5357 cells


title: Microinjected cells Control rep 2


title: scRNAseq_442_r1_tech1

description: 5296 cells


title: Microinjected cells EPZ rep 1


title: Site C individual 2

value: tibia muscle


title: ZNF263_1_ChIPexo


title: Site C individual 1

value: Wild type


title: ZNF253_ChIPexo


title: RAW264.7 PNPO-OE

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse macrophage

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage

tag: construct

value: PNPO-OE


title: Site C individual 14

value: captured in chernobyl exclusion zone

value: exposed to radiocontamination


title: Microinjected cells Control rep 1

description: Sample 1 contains cells from both 24 h and 48 h organotypic slice culture experiments. Only cells from the 24 h time point were analysed.


title: ZNF23_ChIPexo


title: RAW264.7 EV

value: EV


title: A549, SCR, MEOX2

city: Tlalnepantla

first: Armas

middle: López

last: Leonel

state: Estado de México

address: Av. de los reyes

department: UBIMED

country: Mexico

institute: Universidad Nacional Autónoma de México

data_processing:
For the cleaning of adapter and quality readings, the parameters provided by default by Trim Galore version 0.6.7
For the alignment and quality analysis, BWA-MEM version 0.7.17, included in Galaxy was used against the hg19 GRCh37 human reference genome
The data was filtered considering a mapping quality of less than 20 (p>0.02) with the SAMtools version 1.8 tool
The significant peaks (Meox2 binding sites) of mapped reads were identified using the program ‘findPeaks’ from the software suite HOMER with the following parameters: false discovery rate = 0.001, Poisson p-value over input required = 1.00e-04, fold over input required = 4.00, maximum fold under expected unique positions for tags = 2.00, and normalization to 10 million mapped tags per experiment
The significant peaks of the aligned reads were identified with MACS version 2.1.1.20160309.6 with the parameters FDR=0.05, minimum mfold=5, maximum mfold=50 and band width=300
We used the web-based ChIP-Seq analysis tool ChIPseek to obtain the genomic annotation and visualization of Meox2 TFBSs.
Assembly: hg19 GRCh37
Supplementary files format and content: The bed files include Meox2 values in 100bp bins for each ChIP-seq sample. The bam files contain information about sequence reads after they have been aligned against a reference genome.

growth_protocol: RPMI-1640, 10% fetal bovine serum,  1X penicillin/streptomycin. Cells were cultured at 37oC at 5% CO2.

extract_protocol:
A549 cells were fixed with 1% formaldehyde for 10 minutes, then glycine at 0.125 M was added. After cellular lysis, chromatin was sonicated using a VCX130PB vibra cell (Sonics).
The DNA size profile was evaluated in a bioanalyzer 2100 (kit High Sensitivity DNA Reagent Agilent No. Cat. 50674626), for the libraries assemble the kit Truseq Chip de Illumina (No. Cat. IP-202-1012) was used, using a total of 10 ng.
Cutted DNA fragments were performed from 300 to 500 bp, the distribution of the amplified libraries were evaluated by TapeStation 4200 (kit High Sensitivity DNA Reagent Agilent Technologies No. Cat. 5067- 5585), the final loading concentration was of 1.5 pM and a 30% of control PhiX was included. For the sequenciation we used a kit Nextseq 500/550 High Output (150-cycles) Flow Cell (No. Cat. FC-404-202, 20024904).

treatment_protocol:
A549 Cells were seeded in 6 well plates until 70% confluence in RPMI-1640 without antibiotic and in fast conditions by 12-16 h. Transfection solutions were prepared according to the supplier´s instructions with plasmids for a control a scrambled (SCR) sequence (sc-1080062).
Cells were incubated with the transfection medium at growing conditions by 6 h. Subsequently, 1mL of RPMI-1640 medium supplemented with twice serum and antibiotics (2x) was added to each well and A549 cells were incubated for 24h in normal growing conditions.
The stable transfected (Negative Scramble) A549 lung cancer cell model was sustained for growth with puromycin selection medium at a concentration of 5mg/mL until use in subsequent assays.

value: Human lung cancer (adenocarcinoma)

value: MEOX2 (SantaCruz, sc-81971)


title: ZNF229_ChIPexo

value: transduced HEK293T cell line

value: Human embryonic kidney


title: Site C individual 13


title: 2020-42-set2_mRNA_library

city: Marseille

first: Timothée

middle: Jean-Rémi

last: Bigot

address: 27 Bd Jean Moulin

department: Equipe 2

data_processing:
Reads from the mRNA library were mapped to GRch38-2020-A transcripts and cells using CellRanger software (v5.0.0), giving 2020-42-set1_mRNA_barcodes.tsv.gz, 2020-42-set1_mRNA_features.tsv.gz and 2020-42-set1_mRNA_matrix.mtx.gz, 2020-42-set2_mRNA_barcodes.tsv.gz, 2020-42-set2_mRNA_features.tsv.gz and 2020-42-set2_mRNA_matrix.mtx.gz files.
Reads from the HTO library were processed with CITE-seq-count (v1.4.3), giving 2020-42-set1_HTO_barcodes.tsv.gz, 2020-42-set1_HTO_features.tsv.gz and 2020-42-set1_HTO_matrix.mtx.gz, 2020-42-set2_HTO_barcodes.tsv.gz, 2020-42-set2_HTO_features.tsv.gz and 2020-42-set2_HTO_matrix.mtx.gz files
Data was loaded using R (v4.1.2) in a Seurat (v4.1.0) object for further processing
Filtering : Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed. Cells with more than 8% of mitochondrial-associated genes among their expressed genes were also removed.
Demultiplexing :  We used HTO demux coupled with Souporcell (v2.0 ; https://github.com/wheaton5/souporcell) to assign each cells to its sample of origin; doublet cells and negative cells were removed.
Expression data were normalized using the Seurat R package NormalizeData function.
Expression data were scaled and centred using the Seurat R package ScaleData function. PCA calculation was done using Seurat R package RunPCA function. Clusters were defined using Seurat R package FindNeighbors and FindClusters.
Assembly: GRch38
Supplementary files format and content: tsv and mtx files

source_name: Blood

growth_protocol: Cells were cultured in StemSpan™ Serum-Free Expansion Medium II (SFEM II) supplemented with StemSpan™ Megakaryocyte Expansion Supplement (100X) for 6 (2020-42-set1) or 11 days (2020-42-set2).

extract_protocol: 10x Genomics Chromium Single-Cell 5’ protocol

value: Blood

value: CD34+ progenitors isolated from blood


title: Site C individual 11


title: IMQ_2d_3

first: Xueting

last: Liu

address: Changgangdong 250

institute: The Second Affiliated Hospital of Guangzhou Medical University

description: IMQ-induced group, biological rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Spinal cord_psoriasis

extract_protocol:
Cervical spinal cords were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Psoriasis-like dermatitis was induced by topically applying 50 mg of 5% imiquimod (IMQ) cream , or the same amount of control vehicle cream on the shaved skin on the back of the neck once a day for 2 consecutive days.

tag: strain background

tag: group

value: imiquimod (IMQ)-induced psoriasis model

value: Cervical spinal cord


title: 2020-42-set2_HTO_library

description: Anti-beta2 microglobuline and anti-CD298 antibodies tagged with hashtags oligonucleotides

library_source: other

molecule: protein


title: ZNF226_ChIPexo

value: Anti-HA :clone 16B12, Covance


title: IMQ_2d_2

description: IMQ-induced group, biological rep2


title: Site B individual 9

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.6.6
Mapping on the reference Transcriptom of Hyla orientalis with Bowtie2 and RSEM
RSEM results imported with tximport in R and analysed with DESeq2
Polymorphism analysis with GATK haplotypeCaller v 4.2.0.0
Assembly: Unpublished de novo transcriptom assembly of Hyla orientalis
Supplementary files format and content: vcf with variant SNP

extract_protocol:
Trizol extraction followed by column purification on Quick RNA Miniprep kit (Zymoreasearch)
Stranded mRNA kit (Illumina). Paired end with dual Index UD IDT (illumina)


title: ZNF221_ChIPexo


title: Site C individual 10


title: IMQ_2d_1

description: IMQ-induced group, biological rep1


title: 2020-42-set1_mRNA_library


title: IMQ_C3

description: control group, biological rep3

source_name: Spinal cord_control

value: Control


title: Site B individual 8

source_name: tibia muscle

value: tibia muscle


title: 2020-42-set1_HTO_library


title: ZNF136_ChIPexo


title: ZFP82_ChIPexo


title: IMQ_C2

description: control group, biological rep2


title: Site B individual 7

value: Wild type


title: Site B individual 6


title: ZFP57_ChIPexo


title: Site B individual 5


title: H9_WT_RP_3

first: Anders

middle: Henrik

last: Lund

address: Ole Maaløes Vej 5

institute: University of Copenhagen,BRIC

description: ribosome protected fragment RNA

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq (v2.20.0.422). Parameters: –barcode-mismatches 1 --create-fastq-for-index-reads --no-lane-splitting
Adaptor sequences were removed with cutadapt (v1.18) Parameters: -q 30,30 --minimum-length 20 --discard-untrimmed --trim-n -o
Reads derived from RPF and total RNA were aligned to known human rRNA and tRNA sequences with bowtie2 (v2.2.9). Mapped reads were discarded. Parameters: --local -D 20 -R 3 -N 1 -L 20 -i S,1,0.75
Cleaned reads were aligned to GRCh38.p12 (Ensembl v.97) with STAR (STAR-2.5.1a). Only reads mapping to HUGO approved genes were retained for downstream analysis. Parameters: --runMode alignReads –outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.075 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.95 --outSAMheaderCommentFile COfile.txt --outSAMattributes All --outSAMheaderHD @HD VN:1.4 SO:coordinate --genomeLoad NoSharedMemory --outSAMunmapped None  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM  --limitBAMsortRAM 60000000000 --chimSegmentMin 1 --chimOutType SeparateSAMold --twopassMode Basic outWigType wiggle
RPF read alignment files were filtered with samtools (v1.10) to retain only 28-31nt read lengths . No read length filtering was applied to the total RNA alignment files.
The transcript coordinate alignments files were converted into genomic coordinate alignments with RSEM. Commands: rsem-prepare-reference and rsem-tbam2gbam
A single canonical transcript representing each protein-coding gene was selected from Ensembl GRCh38 gtf file. FeatureCounts (v1.5.1) was used to generate counts of reads mapping to exons of these transcripts for total RNA and RPF. Parameters: i.exon: featureCounts -R  -t exon -g transcript_id -O -M -Q 0 --largestOverlap   ii.3UTR: featureCounts -R  -t three_prime_utr -g transcript_id -O -M -Q 0 --largestOverlap --fracOverlap 0.72  iii.5UTR: featureCounts -R  -t five_prime_utr -g transcript_id -O -M -Q 0 --largestOverlap --fracOverlap 0.53
RPF and total RNA alignment files were extracted to have only exon assigned reads in FeatureCounts. All alignments were converted to CPM normalized wig files with bamCoverage functionality of deeptools (v3.3.1).  Replicates of each library were merged with WiggleTools (v1.2.3) and converted to bigwig files with wigToBigWig (v4). Paremeters: bamCoverage –binSize 1 --normalizeUsing CPM  && wiggletools write mean && wigToBigWig
Assembly: GRCh38.p12
Supplementary files format and content: Exon spanning alignments of RPF and total RNA were converted to bigwig files with deeptools (v3.3.1). Replicates for each condition were CPM normalised individually. The Replicates from each condition were merged by calculating their mean coverage per base. For RPF bigwig files, only exon spanning 28-31nt reads were included. For total RNA bigwig files, no filtering for read length applied. Reads mapping to the canonical transcripts selected to represent each protein-coding are included in the bigwig files.

source_name: ribosome protected fragment RNA

growth_protocol: Cells were cultured in mTeSR™1 medium (Stem Cell Technologies #85850) on Matrigel (Corning #354277) and passaged with TryplE 8Lieffe Technologies 12563-011).

extract_protocol:
Three individual replicates for each of the two cell lines were collected. A single 15cm dish corresponding to one replicate was harvested at a time. For each replicate, cell media was aspirated and cells washed with ice-cold PBS. No cycloheximide pre-treatment was was performed. After thorough removal of the PBS, the dish was fully immersed in liquid nitrogen and placed on dry ice. For cell lysis, 1ml of 1x Mammalian Lysis Buffer (Illumina) containing 100 μg/ml cycloheximide was added dropwise to the dish which was then placed on wet ice. Cells were then scraped off to the lower portion of the dish and allowed to thaw in the lysis buffer. Lysate was homogenised by pipetting and triturated ten times through a 25-gauge needle. The lysate was then transferred to a DNA LoBind 1.5ml microfuge tube (Eppendorf) and incubated on ice for 5min. The lysate was cleared by centrifugation at 20000g, 4°C for 10 minutes and the supernatant transferred to a fresh microfuge tube. Aliquots of 100 and 200µl were prepared for each replicate, flash-frozen in liquid nitrogen and stored at −80°C until further use. Thereafter, the protocol for TruSeq Ribo Profile Mammalian (Illumina) was followed to generate total RNA and ribosome protected fragment RNA-seq libraries corresponding to 3 individual replicates from each of the two cell lines.
TruSeq Ribo Profile Mammalian (Illumina), with the modifications given in "extract protocol" above

value: wild type


title: ZFP37_ChIPexo

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads).
Reads with mapping quality lower than 10,  from the UCSC blacklist, or from a greylist derived from TI using GreyListChIP Bioconductor package were removed from the analysis.
Peaks were called using MACS v2.2.4 with default parameters except “--keep-dup all” and -q 0.01
Assembly: hg19
Supplementary files format and content: bedfile obtained for MACS

source_name: transduced HEK293T cell line

extract_protocol:
Chromatin was prepared by resuspending 3x107 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follow: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
Total inputs and chromatin immunoprecipitated samples were prepared for libraries using 10 ng of material. After end-repair and A-tailing, Illumina IDT indexes were ligated to the samples. Aliquots were tested in qPCR to determine the optimal number of PCR cycles needed to amplify each library without reaching saturation. Libraries were amplified with, size-selected using Ampure XP beads (Beckman Coulter), and always quality-checked on a Bioanalyzer DNA high sensitivity chip (Agilent) and quantified with a Qubit dsDNA HS assay kit (Qubit 2.0 Fluorometer, Invitrogen)


title: H9_WT_RP_1

description: ribosome protected fragment RNA


title: H9_52KO_RP_3

description: ribosome protected fragment RNA

value: SNORD52 knockout cells


title: Site B individual 4

value: captured in chernobyl exclusion zone


title: 2-4h embryo rescueHEBI Rep4

data_processing:
usegalaxy.eu
RNA-seq reads were mapped to the Drosophila melanogaster (dm6) genome assembly using STAR with default parameters. RNA-seq count tables were generated with featureCounts and differential expression analysis (DE) of HDAC3 shRNA vs. Control, shRNA-resistant rescueWT,  shRNA-resistant rescueY303F,  shRNA-resistant rescueK26A or shRNA-resistant rescueHEBI was performed using DEseq2.
Assembly: dm6
Supplementary files format and content: xlsx file for RNA-seq count table

source_name: Whole embryo

extract_protocol:
Embryos were homogenized in 300 µL TRIzol LS Reagent followed by total RNA purification using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch).
RNA libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina).

value: Whole embryo

value: tub-GAL4/shRNA HDAC3, shRNA-resistant rescueHEBI

tag: developmental stage

value: 2-4h after egg laying

value: rescueHEBI


title: Site B individual 3

value: exposed to radiocontamination


title: β-Gal

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.83 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbersmapped to each gene. And then   FPKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.83
Supplementary_files_format_and_content: FPKM

source_name: primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in DMEM medium supplemented with 5% FBS.

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary hepatocytes were infected with βGal and HuR adenoviruses overnight.

value: primary hepatocytes

tag: background strain

tag: overexpression

value: B-Gal


title: ZFP30_ChIPexo

tag: cell line

value: transduced HEK293T cell line

value: Human embryonic kidney

tag: genotype


title: ZNF140_ChIPexo


title: H9_52KO_RP_2

description: ribosome protected fragment RNA


title: ChIPexo_TI_sampled

value: mixed total input


title: HuR

value: HuR


title: Site B individual 2


title: 2-4h embryo rescueHEBI Rep2


title: 2-4h embryo rescueHEBI Rep3


title: H9_WT_RNA_3

description: total RNA

source_name: RNA


title: H9_52KO_RP_1

description: ribosome protected fragment RNA


title: Site B individual 1


title: AcmS_Rep3

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

country: Australia

institute: Macquarie University

data_processing:
Basecalling and adaptor sequence trimming were processed by commercial sequencing provider.
The sequence reads from the 6 RNA-Seq samples were aligned to the A. baumannii AB5075_UW reference genome and counted using EDGE-Pro (Estimated Degree of Gene Expression in Prokaryotic Genomes).
Differential gene expression between the parental and mutant samples were analysed using the DEseq2 R package.

organism: Acinetobacter baumannii

source_name: Bacterial planktonic cells grown in Müller Hinton broth

growth_protocol: Three independent A. baumannii parental AB5075_UW and AB00499(ABUW_0182-124:T26) mutant cultures were grown overnight in 5ml Müller Hinton broth at 37°C, with shaking. The overnight cultures were diluted 1:100 in MH and grown to mid-exponential phase cultures (15 mL, OD600~ 0.4- 0.6) at 37°C, with shaking.

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen) and DNA digestion was performed on the total RNA using DNaseI (TURBO DNA-freeTM kit, Invitrogen).
Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using TruSeq® stranded RNA preparation kit (Illumina, Inc., USA). The samples were then sequenced on Illumina NextSeq_500 (2x75bp high output flowcell) platform.

value: Tn mutant


title: H9_WT_RP_2

description: ribosome protected fragment RNA


title: 2-4h embryo rescueHEBI Rep1


title: AcmS_Rep2


title: H9_WT_RNA_2

description: total RNA


title: IMQ_C1

description: control group, biological rep1

value: Control

value: Cervical spinal cord


title: AcmS_Rep1


title: Site B individual 13

value: tibia muscle

value: Wild type


title: 2-4h embryo rescueK26A Rep4

value: tub-GAL4/shRNA HDAC3, shRNA-resistant rescueK26A


title: Site B individual 12

value: captured in chernobyl exclusion zone


title: Parental AB5075_UW_Rep3

value: Parental


title: H9_WT_RNA_1

description: total RNA

value: wild type


title: H9_52KO_RNA_3

description: total RNA

value: SNORD52 knockout cells


title: Site B individual 11

value: exposed to radiocontamination


title: H9_52KO_RNA_2

description: total RNA


title: Site B individual 10


title: Site A individual 9


title: H9_52KO_RNA_1

description: total RNA


title: 2-4h embryo rescueY303F Rep4

value: Whole embryo

value: tub-GAL4/shRNA HDAC3, shRNA-resistant rescueY303F

value: 2-4h after egg laying


title: Parental AB5075_UW_Rep1


title: 2-4h embryo rescueK26A Rep2


title: Site A individual 8


title: 2-4h embryo rescueY303F Rep3


title: Site A individual 7


title: 2-4h embryo rescueK26A Rep1


title: Site A individual 5


title: 2-4h embryo rescueY303F Rep2


title: iWAT6_3_IP

city: Wuhan

first: yangmian

last: yuan

state: --- Select a state ---

address: wuhan

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimgalore version 0.36 , and masked for low-complexity or low-quality sequence.
The clean reads were mapped to mouse genome (GRCm38) using STAR software (version 2.5.3a).
The MACS2 software (Version 2.1.1) was used for peak calling the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
bigWig files were generated using the deeptools 3.1.3 bamCoverage with the following setting -p 10 --normalizeUsing RPKM
Assembly: GRCm38
Supplementary files format and content: bigWig

growth_protocol: For normal conditions, 10 weeks-old mice were housed at 22 °C±2 °C

extract_protocol:
iWAT tissues were cut and fixed with 1% formaldehyde and stopped by adding glycine. Pellets were homogenized and resuspended in lysis buffer, and crosslinked chromatin was sheared into 200-500 bp fragments with Bioruptor Sonication System UCD-300 . 200 ug DNA from each sample were resuspended in digestion buffer containing H1.2 antibody plus protein G magnetic beads for overnight. Immune complexes were collected, washed, and eluted. The DNA-protein crosslinks were then incubated overnight at 65 °C for extracting DNA for qPCR analysis or high through-put sequencing.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for MGI（Catalog NO. NDM607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

treatment_protocol: For cold-exposure, 10 weeks-old mice were single-housed at 6 °C for 3 days

value: iWAT

value: WT

value: 6 C


title: iWAT6_2_IP


title: iWAT6_2


title: 2-4h embryo rescueK26A Rep3

first: Mattias

address: Svante Arrhenius väg 20C


title: iWAT6_3


title: Site A individual 3

first: olivier

address: Cadarache BP3


title: 2-4h embryo rescueWT Rep4

value: tub-GAL4/shRNA HDAC3, shRNA-resistant rescueWT

value: rescueWT


title: 2-4h embryo rescueY303F Rep1


title: Parental AB5075_UW_Rep2


title: ACLYERKi a

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.33, and then mapped to hg19 whole genome using hisat2-2.0.4
Raw counts were calculated using HtSeq-count
Differentially expressed genes were obtained using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample and edgeR output

source_name: Embryonic stem cell H9

extract_protocol: Poly-A mRNA was  enriched from between 1-10 µg of total RNA with oligo dT beads (Invitrogen). ~10-100 ng of poly-A mRNA recovered was used to construct multiplexed strand-specific RNA-seq libraries as per manufacturer’s instruction (NEXTflexTM Rapid Directional RNA-SEQ Kit, dUTP-Based, v2). Individual library quality was assessed with an Agilent 2100 Bioanalyzer and quantified with a QuBit 2.0 fluorometer before pooling for sequencing on a HiSeq 2000 (1x101 bp read). The pooled libraries were quantified using the KAPA quantification kit (KAPA Biosystems) prior to cluster formation.

treatment_protocol: Differentiation into definitive endoderm using RPMI/2%B27, Activin, CHIR99021, LY294002 +/- FGF2, SU5402 or TCS ERKi

value: Definitive endoderm-like

value: Basal differentiation media + ERKiII

value: Embryonic stem cell H9

tag: gender

value: Female


title: iWAT6_1_IP

tag: tissue


title: ACLYERKi b

tag: cell type


title: ACLYSU c

value: Basal differentiation media + SU5402


title: Site A individual 2

value: tibia muscle

value: Wild type

value: captured in chernobyl exclusion zone


title: ACLYSU b


title: iWAT6_1


title: ACLYSU a


title: iWAT22_2_IP


title: 2-4h embryo rescueWT Rep3

last: Mannervik

institute: Stockholm University


title: ACLYERKi c


title: Site A individual 22

last: ARMANT

institute: IRSN

value: exposed to radiocontamination


title: 2-4h embryo rescueWT Rep2

value: Whole embryo


title: Site A individual 21


title: ACLYF30 c

value: Definitive endoderm

value: Basal differentiation media + FGF2 (30 ng/ml)


title: 2-4h embryo rescueWT Rep1

value: 2-4h after egg laying


title: iWAT22_2

value: iWAT

value: WT


title: ACLYF30 b


title: Site A individual 20


title: 2-4h embryo shHDAC3 Rep4

value: tub-GAL4/shRNA HDAC3

value: HDAC3 shRNA


title: iWAT22_1_IP


title: Site A individual 17


title: 2-4h embryo shHDAC3 Rep3


title: iWAT22_1


title: ACLYF30 a


title: ACLY c

value: Basal differentiation media


title: Site A individual 16


title: 2-4h embryo shHDAC3 Rep2


title: ACLY b


title: Site A individual 15


title: Site A individual 14


title: Arabidopsis Input replicate 2

city: Changsha

first: Chongsheng

last: He

address: 27 Tianma road

institute: Hunan university

description: Input, rep2

data_processing:
Adapters were removed from reads with the AdapterRemoval tool with adapter sequence 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'.
Reads were then mapped against the Arabidopsis (TAIR10) or rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
Assembly: TAIR10 and IRGSP-1.0
Supplementary files format and content: bigwig files were generated using bedGraphToBigWig; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP.

source_name: 10-day-old seedlings

growth_protocol: Arabidopsis seedlings were grown on 1/2-strength Murashige and Skoog (MS) medium (1/2 MS) with 0.8% sucrose under long-day conditions (16 hr light/8 hr dark) at 21ºC ±2ºC. Oryza sativa L. ssp. japonica cultivar Nipponbare plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 mmol m-2 s -1.

extract_protocol:
Seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. ac4C IVT was spiked-in in a 1:5000 mass ratio. RNA was fragmented and isolated with IgG or ac4C antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.
acRIP-seq

tag: rip antibody

tag: variety

value: seedlings