title: fiaj1, CHR, replicate 1

description: Library name: EM_Fiaj_CR_Rep1


status: Public on Jun 30 2026

type: SRA

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

description:
Library name: Short_plus72nt_mut5SS_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)

library_source: transcriptomic

data_processing:
Alignment (minimap2)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab/splicing_order)
Assembly: GRCh38
Supplementary files format and content: hg38_multi_introns_counts.txt: text files containing the number of reads with each possible read-level splicing status based on the introns spanned by the read

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNA extraction with Qiazol and isopropanol precipitation
See description field for each library

tag: cell line

tag: treatment

value: Transfection with short_plus72nt_mut5SS EIF4G2 minigene


title: SAMPLES21

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

country: China

institute: Ningxia University

description:
Library name: SAMPLES21
GZ_SA_1

data_processing:
Transcriptome sequencing generated 231.41 Gb clean data across the 32 samples, with at least 5.95 Gb clean data per sample and Q30 values above 96%. Raw reads were quality-filtered using fastp. Adapter sequences, reads without inserts, low-quality 3' bases, reads containing >10% ambiguous bases, and reads shorter than 20 bp after trimming were removed. Clean reads were aligned to the Ovis aries reference genome ARS-UI_Ramb_v2.0, obtained from Ensembl (https://mart.ensembl.org/Ovis_aries_rambouillet/Info/Index), using HISAT2. Mapping rates ranged from 80.08% to 97.88%. Gene and transcript abundance was quantified using RSEM and expressed as transcripts per million.
Assembly: Reference gene source: Ovis_aries; Reference genome version: ARS-UI_Ramb_v2.0; Reference genome source: https://mart.ensembl.org/Ovis_aries_rambouillet/Info/Index
Supplementary files format and content: Comma-Separated Values file

molecule: total RNA

organism: Ovis aries

source_name: Liver

extract_protocol:
Hypothalamus, pituitary, liver, and tail adipose tissue samples from four sheep per treatment were used for transcriptome sequencing, yielding 32 RNA-seq libraries in total. Total RNA was extracted using TRIzol reagent. Briefly, tissue samples were ground in liquid nitrogen and lysed in pre-cooled TRIzol reagent. Chloroform was added, and samples were centrifuged at 13000 g for 15 min at 4°C. The aqueous phase was transferred to a new tube, mixed with an equal volume of pre-cooled isopropanol, and incubated at room temperature for 10 min. RNA pellets were collected by centrifugation, washed with 75% ethanol, air-dried for 3-5 min, and dissolved in sterile 0.1% DEPC-treated water.
RNA concentration and purity were assessed using NanoDrop 2000, and RNA integrity was evaluated by agarose gel electrophoresis and an Agilent bioanalyzer. Stranded mRNA libraries were constructed using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer's protocol. Briefly, mRNA was enriched using oligo (dT) beads, fragmented, reverse-transcribed into cDNA, end-repaired, A-tailed, ligated to adapters, size-selected, PCR-amplified, and purified. Libraries were quantified using Qubit 4.0 and sequenced on an Illumina NovaSeq 6000 Plus platform.

tag: tissue

value: Liver


title: Female, DCT(early), control,96h, replicate 2

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

country: USA

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using salmon (0.14.10).
Assembly: Gencode (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include raw gene counts for each gene

organism: Mus musculus

source_name: Kidney

growth_protocol: Mice were fed with control diet before furosemide administration.

extract_protocol:
Microdissection of the tubules were performed at 9-11 am. The microdissected tubules were washed in PBS three times and lyzed in Trizon solution. Total RNA was extracted using Direct-zol RNA Microprep kit (ZYMO RESEARCH).
For library preparation, cDNA was synthesized using SMART-Seq HT Kit (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: For furosemide treatment, mice were fed with furosemide-containing diet for 12h , 24h, 48h, or 96h. Control diet-fed mice were prepared at each time point.

value: Kidney

tag: cell type

value: distal convoluted tubule cell

tag: genotype

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J

value: control diet


title: burb1, untreated, replicate 2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Library name: EM_Burb_Rep2

library_source: genomic

data_processing:
The quality of the raw EM-seq FASTQ reads was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were subsequently trimmed using Trim Galore v0.6.1.10 (with Cutadapt v4.6) and trimmed reads were reassessed using FastQC.
The adaptor trimmed reads were aligned and mapped to Homo sapiens GRCh38 with Bismark v0.24.2103  with modified trimming parameters optimised for EM-seq. The resulting BAM files were deduplicated and methylation calls were extracted using the Bismark deduplication and methylation extractor tools.
Quantitation of DNA methylation datasets was conducted using SeqMonk. The Bismark-generated methylation call coverage files (.cov files) were imported into SeqMonk. Read positions were generated with CpGs by filtering CpGs with a minimum threshold of 1 read count and grouped into windows containing 100 valid CpGs. The bisulphite methylation feature pipeline in SeqMonk was used to quantitate the CpG windows, with a minimum count of 1 read per CpG position and a minimum of 20 CpGs reads per window. This generated mean percentage methylation values for each window. Differential methylation analysis between incompetent and reset incompetent lines was performed using the EdgeR (for/rev) statistical filter in SeqMonk with a p-value<0.05 cut-off after Benjamimi and Hochberg correction with a minimum methylation difference threshold of 25%.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed DNA methylation dataset was generated from enzymatic methyl-sequencing (EM-seq) data following quality control, adapter trimming, alignment to the human reference genome (GRCh38), removal of duplicate reads, and extraction of methylation calls using Bismark v0.24.2 (https://pmc.ncbi.nlm.nih.gov/articles/PMC3102221/). The Bismark-generated methylation call coverage files (.cov files) were imported into SeqMonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Read positions were generated by filtering CpGs with a minimum threshold of 1 read count and grouped into windows containing 100 valid CpGs. The bisulphite methylation feature pipeline in SeqMonk was used to quantitate the CpG windows, with a minimum count of 1 read per CpG position and a minimum of 20 CpGs reads per window. This generated mean percentage methylation values for each window, producing a genome-wide quantitative methylation dataset. Each row represents a genomic window containing 100 CpGs and reports the genomic coordinates and mean percentage.  The genomic locations and the quantitated values for each sample were extracted from the SeqMonk output file.  The values were also rounded to 2 decimal places.
Library strategy: EM-seq

molecule: genomic DNA

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/ well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951) for at least 8 passages before the experiment was carried out.

extract_protocol:
hiPSCs or hESCs genomic DNA (gDNA) was extracted from isolated nuclei using the Monarch Spin gDNA Extraction Kit (NEB, #T3010S). gDNA concentration was quantified using a Nanodrop. 200ng of gDNA was fragmented to an average size of ~300bp using a Covaris E220 Sonicator with the following parameters: temperature 7°C, peak incident power 140W, duty factor 10%, cycles per burst 200, treatment time 80s.
The sheared gDNA was then used to prepare EM-seq libraries using the NEBNext Enzymatic Methyl-seq kit (NEB, #E7120S) following the manufacturer’s standard size library protocol. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 4 cycles. Size distribution and yield quantification of the libraries were tested using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626). Libraries were then multiplexed and sequenced (paired-end 150 bp) on a NovaSeq X Plus Series PE150 (Illumina) to a depth of a minimum 30 million reads per library.

value: human pluripotent stem cells

tag: batch


title: Fiaj1-CHR_H3K4me3_REP1

description:
Library name: Fiaj-CR_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the cutandrun pipeline (version 3.2.1), distributed by nf-core [doi: 10.5281/zenodo.2634132]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/cutandrun -r 3.2.1 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.config --blacklist ENCFF356LFX.txt --normalisation_mode CPM --use_control false --skip_heatmaps --outdir results -bg  These parameters generally adhered to the defaults set by the nf-core cutandrun pipeline.  Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to regions blacklisted by the ENCODE project [https://www.encodeproject.org/files/ENCFF356LFX/] were removed. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities, antibodies used, and how technical and biological replicates should be grouped together. The pipeline used the software SEACR (version 1.3)102 to identify peaks i.e genomic regions with a localised high abundance of mapped reads. SEACR was run using the default settings for the cutandrun pipeline, but no IgG control was provided.
Consensus peaks were identified separately for the H3K4me3 and the H3K27me3 antibodies. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained.  Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, the aligned reads BAM files generated by the nf-core cutandrun pipeline were imported into SeqMonk, along with a text-format list detailing peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the associated log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.
Library strategy: CUT&Tag

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951).

extract_protocol:
CUT&Tag was carried out using EpiCypher CUTANA™ CUT&Tag Protocol v 1.7. 120,000 cells per CUT&Tag experiment were harvested for nuclei extraction. The cell suspension was centrifuged for 3 minutes at 300 RCF at RT. The cell pellet was resuspended in 100 µl/sample of cold nuclei extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine (Sigma-Aldrich, 05292), 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor) and incubated on ice for 10 minutes, followed by centrifugation for 3 minutes at 600 RCF and 4°C. The nuclei pellet was resuspended in nuclei extraction buffer to achieve a final concentration of 1.2 million nuclei/ml and frozen at -80°C until library preparation. Upon thawing of the nuclei suspension, 100µl of the suspension (120,000 nuclei) was aliquoted to be used per CUT&Tag reaction.
Concavalin A (ConA) beads (EpiCypher, 21-1401) were transferred to a 1.5ml Eppendorf tube on a magnetic stand and washed twice with cold bead activation buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Beads and buffer were added at 11µl and 100µl per sample, respectively, and after washing, the beads were resuspended in a final volume of 11μl of buffer per sample. 10µl of ConA bead slurry was aliquoted into each sample tube of an 8-strip tube containing 100µl nuclei per tube for batch processing. The ConA bead and nuclei mixture was vortexed gently to mix and incubated at RT for 10 minutes. The tubes were placed on a magnetic stand and the supernatant removed. Each nuclei sample was resuspended in 50µl of cold Antibody150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2mM EDTA) containing primary antibody (anti-H3K27me3 (Active Motif; 39157; dilution 1:50), anti-H3K4me3 (Active Motif; 39160; dilution 1:50), anti-IgG negative control antibody (EpiCypher; 13-0042; dilution 1:50). Samples were then gently mixed and incubated overnight at 4°C on an orbital shaker. The next day, the tubes were placed on a magnet and the supernatant discarded. Each sample was resuspended in 50µl Digitonin150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin) containing 0.5μg of secondary antibody (anti-rabbit Epicypher; 13-0047) for 1 hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin150 buffer. The samples were then resuspended in 50µl Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin), and 1.25μl of CUTANA pAG-TN5 (EpiCypher, 15-1017) was added. Samples were then gently mixed and incubated for 1hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin300 buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin). The samples were then resuspended in 50 µl of Tagmentation buffer (Digitonin 300 Buffer, 10 mM MgCl2) and incubated for 1hr at 37°C in a thermocycler. Then the sample tubes were placed on a magnet and the supernatant discarded, the samples were then resuspended in 50µl TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA). The tubes were returned to the magnet and the supernatant removed, followed by addition of 5µl SDS release buffer (0.5M HEPES-NaOH pH 8.5, 10% SDS). The reaction mixture was vortexed on maximum speed for 10s and briefly centrifuged. The samples were then incubated on the thermocycler for 1hr at 58℃. The SDS was neutralised by the addition of 15µl SDS quench buffer (0.67% Triton-X 100), vortexed at maximum speed for 10s, and centrifuged briefly. The libraries were amplified using KAPA HiFi HotStart ReadyMix (Roche Diagnostics Ltd, KK2602). 25ul KAPA HiFi HotStart ReadyMix per CUT&Tag reaction (mastermix only) was incubated at 95℃ for 3 min and cooled to 22℃ in a thermocycler. 1μl of each of barcoded i5 and i7 primers (5μM stock) and 25µl of the previously heated mastermix was added to the DNA. PCR was conducted using the following programme: extension step at 72°C for 5 min, denaturation at 98°C for 45 s, 13-15 cycles (denaturation at 98°C for 10s and short extension at 60°C for 10s), and final extension at 72°C for 1 min. Amplified libraries were cleaned twice using 1X volume of AMPure XP Beads (Beckman Coulter; A63881) and resuspended in 15μl of 0.1X TE buffer. Size distribution and yield quantification of the CUT&Tag libraries were tested using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626). Libraries were then multiplexed and sequenced (paired-end 150 bp) on a NovaSeq X Plus Series PE150 (Illumina) to a depth of a minimum 10 million reads per replicate.

treatment_protocol: no treatment


title: Short_plus72nt_minigene_EIF4G2_DRS

description:
Library name: Short_plus72nt_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)

value: Transfection with short_plus72nt EIF4G2 minigene


title: SAMPLES20

description:
Library name: SAMPLES20
GZ_CON_4


title: Mut5SS_minigene_EIF4G2_DRS

description:
Library name: Mut5SS_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)

value: Transfection with mut5SS EIF4G2 minigene


title: burb1, untreated, replicate 1

description: Library name: EM_Burb_Rep1


title: Male, DCT(early), replicate 4

growth_protocol: Mice were fed with a normal diet with free access to water.


title: neurons,cK2c,week6,female,rep2

city: Philadelphia

first: Matthew

last: Edwards

state: PA

address: 450 Clinical Research Building

department: Genetics

institute: University of Pennsylvania School of Medicine

description: Library name: 4396

data_processing:
Read quality was assessed with FastQC (v0.11.7). Adapter sequences were trimmed with cutadapt (v5.0; Martin, 2011) in paired-end mode (minimum length 1; Nextera or Illumina adapters according to the library). Trimmed reads were aligned to the mouse genome (mm10) with STAR33 (v2.7.9a) using the Ensembl gene annotation (sjdbOverhang 99), retaining only uniquely mapped reads (outFilterMultimapNmax 1) with at most three mismatches (outFilterMismatchNmax 3). Alignments were sorted and indexed with SAMtools34 (v1.9). Gene-level counts were generated with featureCounts35 (Subread v2.0.3) against the same Ensembl annotation, counting properly paired fragments (-p -B -C) at a minimum mapping quality of 10 (-Q 10) on the reverse strand (-s 2). Fragments were summarized over transcript features (-t transcript) and aggregated by gene (-g gene_id), so that intronic reads from nuclear RNA were retained.
Assembly: mm10
Supplementary files format and content: Featurecount matricies (.txt) obtained as described in data processing

molecule: nuclear RNA

source_name: Cortex

extract_protocol:
RNA was extracted from sorted nuclei using the AllPrep DNA/RNA Kit (Qiagen #80204) according to manufacturer instructions with modifications to preserve nuclear RNA. RLT buffer was freshly supplemented with β-mercaptoethanol (Bio-rad #1610710) and lysates were passed through AllPrep DNA columns and then mixed 1:1 with 70% ethanol before binding to RNeasy columns on a vacuum manifold. Columns were washed with RW1 and RPE, dried by centrifugation, and RNA was eluted in RNase-free water. DNase treatment (37 µL DNase mix, 25 min, RT) was followed by ethanol precipitation with glycogen and sodium acetate.
Nuclear RNA-seq libraries were generated using the illumina Standard Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina # 20040529) and were indexed using the IDT for Illumina RNA UD Indexes Set A (Illumina # 20091655). Indexed Libraries were amplified by 12 cycles of PCR, followed by 1× AMPure XP cleanup. Libraries were quantified by Qubit fluorometry and size-checked using the Agilent High Sensitivity DNA Bioanalyzer assay.

value: Cortex

value: In vivo

value: Excitatory neurons

value: conditional kmt2c knockout

tag: age

tag: Sex

value: female


title: Female, DCT(early), control,96h, replicate 1


title: Del_int19-20_minigene_EIF4G2_DRS

description:
Library name: Del_int19-20_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)

value: Transfection with delta_int19-20 EIF4G2 minigene


title: Female, DCT(early), control, 48h, replicate 4


title: burb1, CHR, replicate 2

description: Library name: EM_Burb_CR_Rep2


title: SAMPLES18

description:
Library name: SAMPLES18
GZ_CON_2


title: Female, DCT(early), control, 48h, replicate 3


title: SAMPLES19

description:
Library name: SAMPLES19
GZ_CON_3


title: SAMPLES17

description:
Library name: SAMPLES17
GZ_CON_1


title: Female, DCT(early), control, 48h, replicate 2


title: burb1, CHR, replicate 1

description: Library name: EM_Burb_CR_Rep1


title: Long_minigene_EIF4G2_DRS_

description:
Library name: Long_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)

value: Transfection with long EIF4G2 minigene


title: sojd3, untreated, replicate 2

description: Library name: EM_Sojd_Rep2


title: SAMPLES16

description:
Library name: SAMPLES16
C_SA_4

source_name: Pituitary gland

value: Pituitary gland


title: SAMPLES15

description:
Library name: SAMPLES15
C_SA_3


title: Female, DCT(early), control, 24h, replicate 4


title: sojd3, untreated, replicate 1

description: Library name: EM_Sojd_Rep1


title: Short1_alt_RT-PCR_EIF4G2_ex15-19_rep1

description:
Library name: Short1_alt_RT-PCR_EIF4G2_ex15-19_rep1
RT-PCR of EIF4G2 exons 15 to 19 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Transfection with short_1_alt EIF4G2 minigene


title: sojd3, untreated, replicate 1, with control DNA spike ins provided by NEB in EMseq kit

description: Library name: EM_Sojd_Rep1_spike


title: Female, DCT(early), control, 48h, replicate 1


title: Long_alt_RT-PCR_EIF4G2_ex15-21_rep2

description:
Library name: Long_alt_RT-PCR_EIF4G2_ex15-21_rep2
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Transfection with long_alt EIF4G2 minigene


title: SAMPLES14

description:
Library name: SAMPLES14
C_SA_2


title: sojd3, CHR, replicate 2

description: Library name: EM_Sojd_CR_Rep2


title: SAMPLES13

description:
Library name: SAMPLES13
C_SA_1


title: Short1_alt_RT-PCR_EIF4G2_ex15-19_rep2

description:
Library name: Short1_alt_RT-PCR_EIF4G2_ex15-19_rep2
RT-PCR of EIF4G2 exons 15 to 19 followed by nanopore sequencing with Native Barcoding Kit 24 V14


title: SAMPLES12

description:
Library name: SAMPLES12
C_CON_4


title: sojd3, CHR, replicate 1

description: Library name: EM_Sojd_CR_Rep1


title: Long_alt_RT-PCR_EIF4G2_ex15-21_rep1

description:
Library name: Long_alt_RT-PCR_EIF4G2_ex15-21_rep1
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14


title: Female, DCT(early), control, 12h, replicate 4

value: Kidney


title: SAMPLES11

description:
Library name: SAMPLES11
C_CON_3


title: sojd3, CHR, replicate 1, with control DNA spike ins provided by NEB in EMseq kit

description: Library name: EM_Sojd_CR_Rep1_spike


title: Short1_RT-PCR_EIF4G2_ex15-19_rep1

description:
Library name: Short1_RT-PCR_EIF4G2_ex15-19_rep1
RT-PCR of EIF4G2 exons 15 to 19 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Transfection with short_1 EIF4G2 minigene


title: Female, DCT(early), control, 12h, replicate 3

value: distal convoluted tubule cell

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: Long_RT-PCR_EIF4G2_ex15-21_rep2

description:
Library name: Long_RT-PCR_EIF4G2_ex15-21_rep2
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14


title: SAMPLES10

description:
Library name: SAMPLES10
C_CON_2


title: hehd1, untreated, replicate 1

description: Library name: EM_Hehd_Rep1

value: human pluripotent stem cells


title: Female, DCT(early), control, 12h, replicate 2

value: control diet


title: SAMPLES8

description:
Library name: SAMPLES8
X_SA_4

source_name: Hypothalamus

value: Hypothalamus


title: hehd1, CHR, replicate 2

description: Library name: EM_Hehd_CR_Rep2


title: Female, DCT(early), control, 12h, replicate 1


title: Long_RT-PCR_EIF4G2_ex15-21_rep1

description:
Library name: Long_RT-PCR_EIF4G2_ex15-21_rep1
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14


title: NT_RT-PCR_EIF4G2_ex15-21_rep2

description:
Library name: NT_RT-PCR_EIF4G2_ex15-21_rep2
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Non-transfected cells


title: hehd1, CHR, replicate 1

description: Library name: EM_Hehd_CR_Rep1


title: SAMPLES7

description:
Library name: SAMPLES7
X_SA_3


title: Male, DCT(early), control, 96h, replicate 4


title: SAMPLES6

description:
Library name: SAMPLES6
X_SA_2


title: HEP3B, E389L, Rep 2

city: Chicago

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

institute: Northwestern University

description: Library name: pDA154_2

data_processing:
Base calling was performed using dorado/0.8.1 ‘basecaller rna004_130bps_sup@v5.1.0’. Reads were then aligned to the 45S rRNA reference using graphmap7 with settings ‘--mapq -1 -x sensitive -z 1 -K fastq --min-read-len 0 -A 6 -k 5’.
For re-squiggling, .pod5 files were first converted to blow5 files using blue-crab.
We ran nanoCEM8 with settings ‘current_events_magnifier f5c_re --rna --norm --pore rna004’ for every single modified position in 18S rRNA. This script extracts the dwell time, the Median intensity, the Mean intensity, and the Standard Deviation intensity around every single modified position with a window of +/-4 nucleotides for every single read.
Statistical differences in dwell time and the median intensity per position between conditions were obtained using a Wilcoxon test. 18S rRNA modification positions with significant differences within a ±2 window was extracted. Only positions reproducible across all comparisons were selected as confident sites.
Assembly: RNA45SN5 (NT_167214.1)
Supplementary files format and content: Processed data is a .csv file containing ReadID, Mean, STD, Median, Dwell time, Position, Group, and Folder.

growth_protocol: HEP3B cells were maintained in DMEM supplemented with 10% fetal bovine albumin (FBS) and 1% Penicillin/Streptomycin. All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Briefly, total RNA of 1 µg was ligated to 18S rRNA custom-ordered reverse transcription adapter with T4 DNA Ligase (New England Biolabs) at room temperature for 10 min. Ligated RNA was reverse transcribed with Induro® Reverse Transcriptase (New England Biolabs) at 60°C for 30 min, then inactivated at 70°C for 10 min. The mixture was cleaned using 1.8-fold CleanNGS (CleanNA) according to the manufacturer’s protocol. Reverse transcribed RNA (RT-RNA) was then ligated to an RNA Ligation Adapter (RLA) from the Direct RNA sequencing Kit (Oxford Nanopore, SQK-RNA004) at room temperature for 10 min, then purified with 0.4-fold CleanNGS (CleanNA). RNA library of 12 µl with 37.5 µl sequencing buffer and 25.5 µl library solution making 75 µl of final RNA library.

treatment_protocol: NAT10-FKBP cells were transduced with single mutants in the Helicase domain (K290A or E389L) for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1.

value: Liver

value: Hepatocellular Carcinoma

value: 100 nM dTAGV1 (24 hours)

value: Replicate 2


title: H9, untreated, replicate 2

description: Library name: EM_H9_Rep2


title: SAMPLES5

description:
Library name: SAMPLES5
X_SA_1


title: Male, DCT(early), control, 96h, replicate 2


title: HEP3B, E389L, Rep 1

description: Library name: pDA154_1

value: Replicate 1


title: Male, DCT(early), control, 96h, replicate 1


title: HEP3B, K290A, Rep 2

description: Library name: pDA123_2


title: feec2_untreated_rep2

description: Library name: feec2_rep_2

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the atacseq pipeline (version 2.1.2), distributed by nf-core [doi: 10.5281/zenodo.2634132].  The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/atacseq -r 2.1.2 --input batch2_samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --read_length 50 --trim_nextseq 20 --mito_name MT --blacklist blacklist/ENCFF356LFX.bed.chr_deleted.txt --aligner bowtie2 --deseq2_vst --outdir results -bg  These parameters generally adhere to the defaults set by the nf-core atacseq pipeline, except that Bowtie2 (version 2.4.4) was used as the aligner for the pipeline. Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to the mitochondrial chromosome or regions blacklisted by the ENCODE project were removed [https://www.encodeproject.org/files/ENCFF356LFX/]. The specified read trimming parameters (--trim_nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flowcell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how technical and biological replicates should be grouped together.
The nf-core atacseq pipeline used the software MACS2 (version 2.2.7.1) to identify peaks i.e genomic regions with a localised high abundance of mapped reads. MACS2 was run using the default settings for the atacseq pipeline. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained. Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, BAM files of the aligned reads generated by the nf-core atacseq pipeline were imported into SeqMonk, along with a text-format list detailing ATAC-seq peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the deduplicated raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak. A minimum threshold of -2 (log2-transformed counts per million reads) in any of the datasets was applied to remove consensus peaks with low count values.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the identity of the nearest gene (to within 2kb).  The files also provide the log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-seq kit (Active Motif 53150). Briefly, adherent cells were treated with Accutase to produce a single cell suspension. 100,000 cells per sample were pelleted, washed once in ice-cold PBS, resuspended in ATAC Lysis Buffer and then combined with Tagmentation Master Mix. The reaction was then incubated for 30min at 37°C with 800rpm agitation. Immediately after, the tagmented DNA was column-purified, eluted in a 35μL volume and PCR-amplified for 10 cycles with indexing primers to generate sequencing libraries. Library quality control was carried out with the Bioanalyzer High-Sensitivity DNA analysis kit (Agilent 5067-4626). Libraries were sequenced as paired end 50bp reads, on the Illumina NovaSeq platform at the Cancer Research UK Cambridge Institute Genomics Core Facility. Two biological replicates were collected from independent experiments.
Sequencing libraries were prepared from 100,000 cells per sample using the Active Motif ATAC-seq kit, following tagmentation of accessible chromatin regions for 30 minutes at 37°C, column purification of tagmented DNA, and PCR amplification for 10 cycles with indexing primers. Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit.


title: feec2_untreated_rep1

description: Library name: feec2_rep_1


title: Male, DCT(early), control, 48h, replicate 4


title: HEP3B, K290A, Rep 1

description: Library name: pDA123_1


title: deyz2_untreated_rep2

description: Library name: deyz2_rep_2


title: Male, DCT(early), control, 48h, replicate 3


title: HEP3B, NAT10-FKBP, Rep 2

description: Library name: FKBP_2


title: deyz2_untreated_rep1

description: Library name: deyz2_rep_1


title: HEP3B, NAT10-FKBP, Rep 1

description: Library name: FKBP_1


title: Male, DCT(early), control, 48h, replicate 2


title: SAMPLES1

description:
Library name: SAMPLES1
X_CON_1


title: Male, DCT(early), control, 48h, replicate 1


title: S6_BR.bulk_RNAseq

city: Phoenix

first: John

last: Fryer

email: jfryer@tgen.org, kolney@tgen.org

address: 445 N 5th St

institute: TGen

description:
Library name: S6_BR.FCHVC2VDRXY
paired-end bulkRNAseq

data_processing:
Samples were QC’d on the Agilent Tapestation, and bulk RNAseq libraries prepared with TruSeq stranded mRNA (cat # 20020594) and sequenced to a depth of ~50M paired-end reads on an Illumina NovaSeq S4 instrument at the Mayo Clinic Genome Sequencing Core. FASTQ files were trimmed for adapter content and polyA/polyG artifacts using BBDuk, part of the BBMap package (48).FastQC and MultiQC were used to assess read quality before and after trimming (49, 50). Trimmed reads were aligned to the Ensembl reference genome Sscrofa11.1 v107 using STAR 2.7.11b (51). Quantification estimates for each sample were obtained using STAR following the twopassMode alignment and quantMode to get the read counts for each geneID. A count matrix of gene rows by sample columns was created and read into R for analysis. Mitochondrially-encoded genes (MT-genes) were excluded during the normalization pipeline to prevent highly abundant mitochondrial transcripts from masking more subtle nuclear-encoded differential expressions, and only protein-coding genes were retained. Lowly expressed genes were removed from the analysis by keeping only genes with a count greater than or equal to one count per million (CPM) in all samples within at least one group, 13,692 protein coding genes were retained for downstream differential expression analysis. The edgeR package converted library sizes into effective library sizes using the Trimmed Mean of M-values (TMM) (52). Differential expression was performed using the limma/voom pipeline (53, 54). A model was created to compare E. coli and saline where each coefficient corresponds to a group mean and minutes from injection till the killing was added as a covariate. P-values were adjusted for multiple tests using the Benjamin-Hochberg correction, denoted as q-value. Specifically, the q-value is derived by adjusting the distribution of p-values across all tested genes to control the expected proportion of false positives among the set of significant findings. There is no fixed raw p-value cutoff that corresponds to q < 0.05. Instead, the effective p-value threshold depends on the overall p-value distribution. We used a logarithm base 2 of the fold change (log2FC) to denote the ratio of change between experimental and control animals. Genes were identified as differentially expressed when the absolute log2FC exceeded 1.0  and the q-value < 0.05. This strict criterion guarantees that the detected changes are not only statistically reliable after adjusting for multiple testing, but also biologically robust in magnitude.
Assembly: Ensembl reference genome Sscrofa11.1 v107
Supplementary files format and content: rds or txt file contains sample counts, gene information, and sample information

organism: Sus scrofa

source_name: brain

extract_protocol:
Brain (prefrontal cortex) samples were collected post-mortem and flash-frozen immediately at −80°C or fixed in formalin for subsequent analysis
A total of 0.5 grams of forebrain tissue was used to prepare total brain RNA from n = 4 E. coli pigs and n = 4 saline-treated pigs with the Qiagen RNeasy Mini Kit (cat # 74104). Samples were QC’d on the Agilent Tapestation, and bulk RNAseq libraries prepared with TruSeq stranded mRNA (cat # 20020594) and sequenced to a depth of ~50M paired-end reads on an Illumina NovaSeq S4 instrument at the Mayo Clinic Genome Sequencing Core.

treatment_protocol: Animals were group-housed with ad libitum access to water and Purina Lab Porcine Grower Diet 5084. Adult males were not included in these experiments as they are too large and aggressive for safe housing and handling. At experiment onset, anesthesia was induced with intramuscular glycopyrrolate (0.02 mg/Kg), telazol (5 mg/Kg), and xylazine (2 mg/Kg), followed by maintenance anesthesia with continuous isoflurane (1.5-2.5%). Once anesthetized, cannulas were surgically placed in the jugular vein and carotid artery for clinical monitoring and infusion procedures. A continuous i.v. infusion of E. coli (clinical isolate 41949 obtained from Brigham and Women’s Hospital, Crimson Biorepository) was initiated for a target dose of 1.2x10^9 colony forming units (CFU)/Kg over a maximum of 6 hours, while saline controls received an equivalent volume of 0.9% normal saline (1.00 mL/h). Time to euthanasia varied among pigs exposed to E. coli (199 – 362 minutes) due to individual differences in the progression of septic shock. In contrast, all saline control pigs were euthanized at 300 minutes, having exhibited no signs of organ dysfunction.

value: brain

value: female

value: Sus scrofa

value: Saline


title: cuhk2_untreated_rep2

description: Library name: cuhk2_rep_2


title: Short_1_minigene_EIF4G2_DRS

description:
Library name: Short_1_minigene_EIF4G2_DRS
Direct RNA nanopore sequencing (SQK-RNA004)


title: HEP3B, Control, Rep 2

description: Library name: WT_2

value: Parental


title: cuhk2_untreated_rep1

description: Library name: cuhk2_rep_1


title: S3_BR.bulk_RNAseq

description:
Library name: S3_BR.FCHVC2VDRXY
paired-end bulkRNAseq


title: Female, DCT(early), control, 24h, replicate 3

value: Kidney


title: Male, DCT(early), control, 24h, replicate 4

value: distal convoluted tubule cell


title: Female, DCT(early), control, 24h, replicate 2

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: Short1_RT-PCR_EIF4G2_ex15-19_rep2

description:
Library name: Short1_RT-PCR_EIF4G2_ex15-19_rep2
RT-PCR of EIF4G2 exons 15 to 19 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Transfection with short_1 EIF4G2 minigene


title: Female, DCT(early), control, 24h, replicate 1

value: control diet


title: sojd3_CHR_rep2

description: Library name: Part2_sojd3-CHR2_rep_2

value: human pluripotent stem cells


title: S2_BR.bulk_RNAseq

description:
Library name: S2_BR.FCHVC2VDRXY
paired-end bulkRNAseq


title: Male, DCT(early), control, 24h, replicate 3


title: K562, Day 12, Rep 3

description: Library name: NB14

data_processing:
POD5 files were base called and demultiplex using Dorado/0.5.33 with ‘dorado basecaller sup’ and ‘--kit-name SQK-NBD114-24’ settings.
p
Reads were aligned to a reference NAT10 sequence (NM_024662.3) using minimap2/2.244 ‘-ax map-ont’ and sorted and indexed using samtools/1.16.15. Then, we counted the occurrence of each variant at the specific residue using a custom python script. The output is the counts of each substitution per barcode per residue.
Counts were analyzed using DESeq2 in R/4.1.1 to compute log2 fold change values and an adjusted p-value threshold of 0.05.
Assembly: NAT10 sequence (NM_024662.3)
Supplementary files format and content: HEP3B_counts.csv contains counts of each substitution per barcode per residue for HEP3B cells.
Supplementary files format and content: K562_counts.csv contains counts of each substitution per barcode per residue for K562 cells.

source_name: Bone marrow

growth_protocol: HEP3B cells were maintained in DMEM supplemented with 10% fetal bovine albumin (FBS) and 1% Penicillin/Streptomycin, and K562 cells were maintained in RPMI supplemented with 10% Bovine Calf Serum (BCS). All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
DNA was isolated from sorted cells using GeneJET™ Genomic DNA Purification Kit (ThermoFisher Scientific) according to the manufacturer’s protocol. Exogenous NAT10 from isolated genomic DNA was amplified by PCR and ran on 1% agarose gel. The fragment of interest was gel extracted by GeneJET Gel Extraction Kit (ThermoFisher Scientific) following the manufacturer’s protocol.
Amplicons were end-prepped using NEBNext® Ultra™ II End Repair/dA-Tailing Module (New England Biolabs).  The end-prepped DNA was native barcode ligated using Native Barcoding Kit 24 V14 (Oxford Nanopore, SQK-NBD114.24) using Blunt/TA Ligase Master Mix (New England Biolabs) followed by purification with 0.4-fold AMPure XP Bead-Based Reagent (Beckman Coulter). The native barcoded samples were pooled and ligated to a native adaptor with Quick T4 DNA Ligase (New England Biolabs), and then the pooled ligated sample was cleaned with 0.4-fold AMPure XP Bead-Based Reagent (Beckman Coulter). The ligated pool was quantified using Qubit™ dsDNA Quantification Assay Kits (ThermoFisher Scientific). DNA pool of 12 µl was added to 37.5 µl sequencing buffer (SB) and 25.5 µl library solution (LIS), making a final volume of 75 µl.

treatment_protocol: NAT10FKBP cells (1 × 106) were transduced with a site-saturation mutagenesis library and incubated for 24 h. Three biological replicates of transduced cells were collected on Day 0 and Day 12 after treatment with 100 nM dTAGV1.

value: Bone marrow

value: Chronic Myelogenous Leukemia

value: 100 nM dTAGV1

value: Replicate 3


title: HEP3B, Control, Rep 1

description: Library name: WT_1

value: Liver

value: Hepatocellular Carcinoma

value: 100 nM dTAGV1 (24 hours)


title: hehd1, untreated, replicate 2

description: Library name: EM_Hehd_Rep2


title: sojd3_CHR_rep1

description: Library name: Part2_sojd3-CHR2_rep_1


title: SAMPLES9

description:
Library name: SAMPLES9
C_CON_1

value: Pituitary gland


title: S1_BR.bulk_RNAseq

description:
Library name: S1_BR.FCHVC2VDRXY
paired-end bulkRNAseq

value: brain

value: female

value: Sus scrofa


title: K562, Day 12, Rep 2

description: Library name: NB13

value: Replicate 2


title: Male, DCT(early), control, 24h, replicate 2

value: Kidney

value: distal convoluted tubule cell


title: sojd3_untreated_rep4

description: Library name: Part2_sojd3_rep_2


title: Male, DCT(early), control, 24h, replicate 1

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: K562, Day 12, Rep 1

description: Library name: NB12

value: Replicate 1


title: E8_BR.bulk_RNAseq

description:
Library name: E8_BR.FCHVC2VDRXY
paired-end bulkRNAseq

value: E coli


title: sojd3_untreated_rep3

description: Library name: Part2_sojd3_rep_1

value: human pluripotent stem cells


title: E6_BR.bulk_RNAseq

description:
Library name: E6_BR.FCHVC2VDRXY
paired-end bulkRNAseq


title: NT_RT-PCR_EIF4G2_ex15-21_rep1

description:
Library name: NT_RT-PCR_EIF4G2_ex15-21_rep1
RT-PCR of EIF4G2 exons 15 to 21 followed by nanopore sequencing with Native Barcoding Kit 24 V14

value: Non-transfected cells


title: K562, Day 0, Rep 3

description: Library name: NB11

value: Bone marrow

value: Chronic Myelogenous Leukemia

value: 100 nM dTAGV1


title: hehd1_CHR_rep2

description: Library name: Part2_hehd1-CHR2_rep_2


title: E4_BR.bulk_RNAseq

description:
Library name: E4_BR.FCHVC2VDRXY
paired-end bulkRNAseq


title: Male, DCT(early), control, 12h, replicate 4

value: control diet


title: Male, DCT(early), control, 12h, replicate 3


title: K562, Day 0, Rep 2

description: Library name: NB10


title: Male, DCT(early), control, 96h, replicate 3


title: hehd1_CHR_rep1

description: Library name: Part2_hehd1-CHR2_rep_1


title: E1_BR.bulk_RNAseq

description:
Library name: E1_BR.FCHVC2VDRXY
paired-end bulkRNAseq


title: H9, untreated, replicate 1

description: Library name: EM_H9_Rep1


title: Male, DCT(early), control, 12h, replicate 2


title: hehd1_untreated_rep4

description: Library name: Part2_hehd1_rep_2


title: K562, Day 0, Rep 1

description: Library name: NB09


title: Male, DCT(early), control, 12h, replicate 1


title: HEP3B, Day 12, Rep 3

description: Library name: NB06

value: Liver

value: Hepatocellular Carcinoma

value: Replicate 3


title: hehd1_untreated_rep3

description: Library name: Part2_hehd1_rep_1


title: SAMPLES4

description:
Library name: SAMPLES4
X_CON_4

value: Hypothalamus


title: Bend2 KO, zygSC, REC8, rep3

city: Beijing

first: Chunsheng

last: Han

address: No.5, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Paired-end reads were aligned with Bowtie2 using default parameters, and only uniquely mapping reads were retained for further analysis.
PCR duplicate reads were removed using Picard (v2.27.4) and Samtools (v1.3). Peak calling was executed using MACS2 (v2.2.7.1).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: testes

extract_protocol:
Cells were penetrated and incuated with primary antibodies at 4 ℃ overnight. Following incubation with secondary antibodies, the target DNA were digested by pA/G-Tn5 enzyme.
Fragments were purified and library amplification was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro instructions (Vazyme, TD904).

treatment_protocol: To characterize REC8-binding sites on the genome, all male pups were pipette-fed 100 μg/g body weight WIN 18,446 for 7 consecutive days from 2 days postpartum (P2). At P9, pups received an intraperitoneal injection of Retinoic acid (RA, 32 μg/g body weight) suspended in DMSO. At 7-, 8- and 9- days post-RA injection, we obtained mice with spermatogenesis synchronized to the preleptotene, leptotene, and zygotene stages, respectively. To describe the changes of REC8 binding sites in Bend2 KOmice, zygotene spermatocytes isolated by FACS from Bend2 WT and KO mice in Rec8 KI background whose spermatogenesis were synchronized to zygotene stages. The testicular cells were digested by two-step method using 1mg/ml collagenase I and 0.025 % trypsin-EDTA.

value: testes

value: zygotene spermatocytes

value: Bend2 KO, Rec8 KI

tag: strain

value: spermatogenesis synchronization and FACS

tag: developmental stage

tag: chip antidodies

value: HA


title: HEP3B, Day 12, Rep 2

description: Library name: NB05

value: Replicate 2


title: fiaj1_CHR_rep2

description: Library name: Part2_fiaj1-CHR2_rep_2


title: HEP3B, Day 12, Rep 1

description: Library name: NB04

value: Replicate 1


title: Bend2 KO, zygSC, REC8, rep2


title: A549-shLDOC1-H2BK120R (2)

type: RNA

city: Zhunan Town, Miaoli County

first: Pin

middle: Feng

last: Hung

state: Taiwan, ROC

address: 35, Keyan Road

department: Cancer research

country: Taiwan

institute: National Health Research Institutes

description: an LDOC1-depleted A549 cell line expressing muant H2BK120R rep2

hyb_protocol: Samples were hybridized with Clariom™ S Assay, human Arrays (Applied Biosystems) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Applied Biosystems)

data_processing:
Data were processed usingTranscriptome Analysis Console (TAC) Software which normalizes array signals using MAS5 algorithm.
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.mps

label: biotin

source_name: NSCLC tumor

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Applied Biosystems) and then fragmented and labeled with the WT Terminal Labeling Kit (Applied Biosystems).

growth_protocol: All A549-derived cell sublines, including A549-shLDOC1 and A549-H2BK120R, and their corresponding control  cell lines were maintained in DMEM (high glucose) medium supplemented with 10% FBS, penicillin (100 U/mL), streptomycin (100 μg/mL) and puromycin (5μg/mL). ed 5% CO2 incubator.

extract_protocol: Total RNA were extracted from cultured cells with more than 90% confluency using RNeasy Mini-kit (Qiagen, MD, USA) followed the manufacturer’s protocol.

treatment_protocol: Not applicable

tag: tumor type

value: NSCLC

tag: shRNA


title: A549-shLDOC1-V (1)

description: a vector control cell line of A549-shLDOC1-H2BK120R rep1


title: SAMPLES3

description:
Library name: SAMPLES3
X_CON_3


title: A549-shLDOC1-V (2)

description: a vector control cell line of A549-shLDOC1-H2BK120R rep2


title: fiaj1_CHR_rep1

description: Library name: Part2_fiaj1-CHR2_rep_1

value: human pluripotent stem cells


title: HEP3B, Day 0, Rep 3

description: Library name: NB03


title: Bend2 KO, zygSC, REC8, rep1


title: daf-16(mu86);daf-2(e1370);htz-1(bon101), the first day of young adult, rep 4

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

description: Library name: Sample24

data_processing:
Sequencing was executed in PE75 on a NextSeq 2000 System (Illumina) with a NextSeq 2000 P4 XLEAP-SBS™ Reagent Kit (300 Cycles) chemistry.
Raw sequencing data were demultiplexed using bcl2fastq2 v2.20 and aligned against C. elegans reference genome (Ensembl release 109) using Kallisto v048.0.
Assembly: WBcel235
Supplementary files format and content: csv file includes normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematodes were grown on OP-50-1 E. coli at 20℃.

extract_protocol:
Young adult worms were collected and dissolved in 1ml Trizol (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen).
Libraries were prepared using SMART-Seq2 protocol (Picelli et al., 2014).

value: whole animal


title: Bend2 WT, zygSC, REC8, rep3

value: Bend2 WT, Rec8 KI


title: fiaj1_untreated_rep4

description: Library name: Part2_fiaj1_rep_2


title: HEP3B, Day 0, Rep 2

description: Library name: NB02

value: 100 nM dTAGV1


title: fiaj1_untreated_rep3

description: Library name: Part2_fiaj1_rep_1


title: daf-2(e1370);htz-1(bon101), the first day of young adult, rep 4

description: Library name: Sample23


title: Bend2 WT, zygSC, REC8, rep2


title: HEP3B, Day 0, Rep 1

description: Library name: NB01


title: A549-shLDOC1-H2BK120R (1)

description: an LDOC1-depleted A549 cell line expressing muant H2BK120R rep1


title: htz-1(bon101), the first day of young adult, rep 4

description: Library name: Sample22


title: burb1_CHR_rep2

description: Library name: Part2_burb1-CHR2_rep_2


title: SAMPLES2

description:
Library name: SAMPLES2
X_CON_2


title: Bend2 WT, zygSC, REC8, rep1


title: Rabbit_IgG_CS27295_48h_HeLa_Rep2

city: Berlin

first: Konrad

middle: Jakub

last: Chudzik

address: Hannoversche Str. 28

institute: MDC-BIMSB

description: Library name: Rabbit_IgG_CS27295_48h_HeLa_Rep2

data_processing:
Sequencing adapters were trimmed using Trim Galore (v0.6.4) with the options --paired --nextera. Trimmed reads were aligned to the mouse genome (mm10) for rod cells or the human genome (hg38) for HeLa cells using Bowtie2 (v2.3.5.1) with --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000. Aligned reads were filtered for mapped, paired-end reads (MAPQ ≥ 20) using samtools (v1.10) with view -f 2 -q 20 and then sorted. ENCODE blacklisted regions were removed using bedtools (v2.29.2) with intersect -v.
Normalized coverage tracks (bigWig) were generated with deepTools2 (v3.4.1) using a bin size of 10 bp, read extension (-e), and CPM normalization, ignoring chrX and chrY. For merged tracks, FASTQ files were concatenated from biological replicates. To visualize enrichment relative to matched IgG controls, log2 ratio tracks were generated using deepTools bigwigCompare (v3.4.1). Analogous 20 kb binned subtraction bedGraphs were used as input for domain calling.
Domain calling was performed as previously described (Kefalopoulou et al., 2025) with minor changes in parameters. Specifically, 20 kb binned log2 matrices were binarized: bins above a signal threshold were considered positive (within domain) and below as negative. Adjacent segments separated by gaps ≤200 kb were merged, and regions smaller than 100 kb were removed. To evaluate biological replicate consistency, consensus domains were defined using bedtools intersect (v2.29.2). Consensus regions were used for all subsequent downstream analyses.
To characterize signal distribution across distinct chromatin environments, the genome was segmented into four categories based on the presence or absence of LMNB1 and ab1220 consensus domains: LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, and LMNB1−/ab1220−, using bedtools intersect and subtract (v2.29.2).
Assembly: mm10/hg38
Supplementary files format and content: bigWig (.bw): per-replicate CPM-normalized coverage tracks (10 bp bins, chrX/Y excluded), generated from blacklist-filtered alignments with deepTools2. Merged log2 ratio bigWigs (vs matched IgG, replicate-pooled) are provided as series-level supplementary files for visualization.
Supplementary files format and content: bedGraph (.bedgraph): per-replicate log2 ratio of signal vs matched IgG control, binned at 20 kb. Used as input for domain calling.
Supplementary files format and content: BED (.bed): per-replicate domain calls from the binarized 20 kb log2 bedGraphs (".bedgraph.bed"). Series-level supplementary BEDs include consensus domains per condition (intersection of biological replicates) and four genome-segmentation tracks (LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, LMNB1−/ab1220−)
Library strategy: CUT&Tag

source_name: HeLa

growth_protocol: All mice were housed in a centrally controlled environment with a 12 h light and 12 h dark cycle, temperature of 20-22.2°C, and humidity of 30–50%. All mice had access to food and water ad libitum. Bedding, food and water were routinely changed. All experiments involving animals were carried out following institutional guidelines as approved by LaGeSo Berlin and following the Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. Biological replicates represent samples collected independently from different animals.  HeLa cells were cultured in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO₂, and routinely tested for Mycoplasma contamination. Biological replicates represent HeLa cells grown independently from separate cryovials.

extract_protocol:
HeLa cells were collected using TrypLE (Gibco, 12604021) and following centrifugation (5 min, 300g, RT), resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5 (Jena Bioscience, BU10675), 150 mM NaCl (Invitrogen, AM9760G), 0.5 mM spermidine (Sigma, S0266), 10 mM sodium butyrate (Sigma Aldrich, B5887), 1 mM PMSF (Thermo Scientific, 36978), Protease Inhibitor Cocktail (Roche, 04693132001)) and quantified using EVE automatic cell counter (NanoEntek). For sampling rod cells, retinas from 2-month-old NRL-GFP mice were dissociated using the Papain Dissociation System (Worthington, #130-094-802). Four retinas from two mice were used for one biological replicate. Briefly, retinas were dissociated in papain solution for 60 min at 37°C, while shaking at 700 rpm. Afterwards, retinas were triturated with a 1 ml micropipette and transferred to a new tube containing a mix of EBSS, DNase and albumin-ovomucoid inhibitor. Cell suspensions were triturated again with a glass Pasteur pipette ten times until tissue fragments were no longer visible. Finally, 250 µl of EBSS/albumin-ovomucoid inhibitor was added, and the single-cell suspension was cleared of cell clumps by filtration (pluriStrainer Mini 70 μm). FACS sorting of single cells was performed on the BD FACS Aria II or Aria III Cell Sorter System with sample and plate cooling at 4°C. Forward-side scatter gating was used to eliminate debris and identify intact cells, and GFP intensity was used to specifically isolate rod cells. Single cells were sorted into 15 ml falcons pre-coated with BSA and containing 5 ml of wash buffer for approximately 1 h. After sorting, rod cells were quantified using a haemocytometer. For each CUT&Tag reaction, 11 μl Concanavalin A beads (BioMag, 86057) were equilibrated twice with 100 μl and then concentrated in 11 μl of binding buffer (20 mM HEPES pH 7.5, 10 mM KCl (Invitrogen, AM9640G), 1 mM CaCl₂ (Merck, 102382), 1 mM MnCl₂ (Thermo, J63150.AD)). 100,000 cells were then bound to the beads by incubating for 10 min at RT with rotation. Beads were subsequently separated on a magnet and resuspended in 100 μl CUT&Tag Antibody buffer (Wash buffer with 0.05% Digitonin (Millipore, 30410) and 2 mM EDTA (Invitrogen, 15575-038)). Subsequently, 1 μl of primary antibody or IgG control was added and incubated on a rotator overnight (15 h) or for 48 h at 4°C. After magnetic separation, beads were resuspended in 100 μl of Dig-wash buffer containing 1 μl of matching secondary antibody (Abcam, ab46540 for mouse; Antibodies-online, ABIN101961 for rabbit) and incubated for 1 h at 4°C with rotation. Following three washes with CUT&Tag Dig-wash buffer (Wash buffer with 0.05% Digitonin), beads were resuspended in 100 μl CUT&Tag Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with a 1:250 dilution of homemade 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1 h at 4°C with rotation, beads were washed four times with Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer with 10 mM MgCl₂ (Invitrogen, AM9530G)). Homemade spike-in-AmpR was added to the tagmentation buffer at a final concentration of 33.6 fM (Li et al., 2021). Tagmentation was performed for 1 h at 37°C and subsequently stopped by adding 2.25 μl EDTA, 2.75 μl 10% SDS (Invitrogen, 15553-035) and 0.5 μl Proteinase K (Invitrogen, 25530049). DNA fragments were solubilized for 16 h at 55°C followed by 30 min at 70°C to inactivate residual Proteinase K. DNA fragments were finally purified and eluted with 25 μl of elution buffer (Zymo, D5205).
NGS libraries were generated by PCR amplifying the CUT&Tag DNA fragments with barcoded i5 and i7 primers (Buenrostro et al., 2015) as described previously (Gjaltema et al. 2022). Briefly, DNA fragments with Nextera barcoded HPLC grade primers were loaded with NEBNext HiFi 2x PCR Master Mix (New England BioLabs, M0541S) into a thermocycler for 5 min at 72 °C, 30 sec at 98 °C, 10 sec at 98 °C, 10 sec at 63 °C (14 Cycles for steps 3-4) and 1 min at 72°C. Following PCR, 1x volume of Ampure XP beads (Beckman Coulter) were mixed with the NGS libraries and incubated at RT for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol, and the libraries were eluted with Tris-HCL, pH 8.0 (Roth, 9090.3). The quality of the purified NGS libraries was assessed with the D5000 tapestation (Agilent Technologies).

value: HeLa

value: cervical adenocarcinoma epithelial cells

value: wild-type

tag: time

tag: chip antibody

value: Rabbit IgG (CS27295, Cell Signaling)

tag: strain background

value: human cervical adenocarcinoma (ATCC CCL-2)


title: burb1_CHR_rep1

description: Library name: Part2_burb1-CHR2_rep_1


title: daf-16(mu86);daf-2(e1370), the first day of young adult, rep 4

description: Library name: Sample21


title: zygSC, REC8, rep2

value: testes

value: testicular cells

value: Rec8 KI

value: spermatogenesis synchronization


title: burb1_untreated_rep4

description: Library name: Part2_burb1_rep_2


title: daf-2(e1370), the first day of young adult, rep 4

description: Library name: Sample20


title: Rabbit_IgG_CS27295_48h_HeLa_Rep1

description: Library name: Rabbit_IgG_CS27295_48h_HeLa_Rep1


title: zygSC, REC8, rep1

value: zygotene spermatocytes

value: HA


title: burb1_untreated_rep3

description: Library name: Part2_burb1_rep_1


title: Rabbit_IgG_CS27295_HeLa_Rep2

description: Library name: Rabbit_IgG_CS27295_HeLa_Rep2


title: lepSC, REC8, rep2

value: leptotene spermatocytes


title: wt(N2), the first day of young adult, rep 4

description: Library name: Sample19


title: Rabbit_IgG_CS27295_HeLa_Rep1

description: Library name: Rabbit_IgG_CS27295_HeLa_Rep1


title: sojd3_untreated_rep2

description: Library name: Part1_sojd3_rep_2


title: daf-16(mu86);daf-2(e1370);htz-1(bon101), the first day of young adult, rep 3

description: Library name: Sample18


title: lepSC, REC8, rep1


title: sojd3_untreated_rep1

description: Library name: Part1_sojd3_rep_1


title: plpSC, REC8, rep2

value: preleptotene spermatocytes


title: daf-2(e1370);htz-1(bon101), the first day of young adult, rep 3

description: Library name: Sample17


title: Mouse_IgG_CS68860_48h_HeLa_Rep2

description: Library name: Mouse_IgG_CS68860_48h_HeLa_Rep2

value: Mouse IgG (CS68860, Cell Signaling)


title: Mouse_IgG_CS68860_48h_HeLa_Rep1

description: Library name: Mouse_IgG_CS68860_48h_HeLa_Rep1


title: kolf2_untreated_rep2

description: Library name: Part1_kolf2_rep_2

value: human pluripotent stem cells


title: plpSC, REC8, rep1


title: htz-1(bon101), the first day of young adult, rep 3

description: Library name: Sample16

value: whole animal


title: Mouse_IgG_CS68860_HeLa_Rep2

description: Library name: Mouse_IgG_CS68860_HeLa_Rep2


title: kolf2_untreated_rep1

description: Library name: Part1_kolf2_rep_1


title: lepSC, ATAC, rep2

data_processing:
Paired-end reads were aligned with Bowtie2 using default parameters, and only uniquely mapping reads were retained for further analysis.
PCR duplicate reads and mitochondrial genome were removed using Picard (v2.27.4) and Samtools (v1.3). Peaks were determined with the software MACS2 (v2.2.7.1) at the significance level q < 0.05.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Cells were lysed and nucleus were incubated with Tn5 reaction mix.
Fragments were purified and library amplification was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme).

value: wildtype

value: Hoechst 33342 staining and FACS


title: Mouse_IgG_CS68860_HeLa_Rep1

description: Library name: Mouse_IgG_CS68860_HeLa_Rep1

value: HeLa

value: cervical adenocarcinoma epithelial cells


title: lepSC, ATAC, rep1


title: daf-2(e1370), the first day of young adult, rep 3

description: Library name: Sample14


title: wt(N2), the first day of young adult, rep 3

description: Library name: Sample13


title: H3K9me2_CMA317_48h_HeLa_Rep2

description: Library name: H3K9me2_CMA317_48h_HeLa_Rep2

value: wild-type

value: H3K9me2 (CMA317, Diagenode)


title: BMDMs LPS+PA-BSAl 3

city: Shanghai

first: An

last: Lao

state: Shanghai

address: Xin Hua Hospital

institute: Xin Hua Hospital, Shanghai Jiao Tong University 9 School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) 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, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Bone marrow

value: BMDMs

value: Macrophage

value: WT

value: LPS+PA-BSA


title: hehd1_untreated_rep2

description: Library name: Part1_hehd1_rep_2


title: HUES8_untreated_rep1

description: Library name: Part1_HUES8_rep_1


title: daf-16(mu86);daf-2(e1370);htz-1(bon101), the first day of young adult, rep 2

description: Library name: Sample12


title: H3K9me2_CMA317_48h_HeLa_Rep1

description: Library name: H3K9me2_CMA317_48h_HeLa_Rep1

value: human cervical adenocarcinoma (ATCC CCL-2)


title: BMDMs LPS+PA-BSA 2


title: hehd1_untreated_rep1

description: Library name: Part1_hehd1_rep_1


title: H3K9me2_CMA317_HeLa_Rep2

description: Library name: H3K9me2_CMA317_HeLa_Rep2


title: daf-2(e1370);htz-1(bon101), the first day of young adult, rep 2

description: Library name: Sample11


title: BMDMs LPS+PA-BSA 1


title: H3K9me2_CMA317_HeLa_Rep1

description: Library name: H3K9me2_CMA317_HeLa_Rep1


title: H9_untreated_rep2

description: Library name: Part1_H9_rep_2


title: htz-1(bon101), the first day of young adult, rep 2

description: Library name: Sample10


title: BMDMs control 3

value: Control


title: H9_untreated_rep1

description: Library name: Part1_H9_rep_1


title: H3K9me2_AM39239_48h_HeLa_Rep2

description: Library name: H3K9me2_AM39239_48h_HeLa_Rep2

value: H3K9me2 (AM39239, Active Motif)


title: daf-16(mu86);daf-2(e1370), the first day of young adult, rep 2

description: Library name: Sample9


title: BMDMs control 2


title: H1_untreated_rep2

description: Library name: Part1_H1_rep_2


title: H3K9me2_AM39239_48h_HeLa_Rep1

description: Library name: H3K9me2_AM39239_48h_HeLa_Rep1


title: daf-2(e1370), the first day of young adult, rep 2

description: Library name: Sample8


title: BMDMs control 1


title: H3K9me2_AM39239_HeLa_Rep2

description: Library name: H3K9me2_AM39239_HeLa_Rep2


title: H1_untreated_rep1

description: Library name: Part1_H1_rep_1


title: wt(N2), the first day of young adult, rep 2

description: Library name: Sample7


title: IR+HSO group

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

library_source: transcriptomic single cell

data_processing:
Cellranger
Assembly: Mmu_GRCm39
Supplementary files format and content: Sparse matrix consisting of a barcode file, a feature file and a matrix file

source_name: Spleen

extract_protocol:
Spleens were ground into single-cell suspensions for scRNA-seq.
10x Genomics

value: Spleen

value: irradiated at 8.5 Gy and administered with HSO


title: H3K9me2_AM39239_HeLa_Rep1

description: Library name: H3K9me2_AM39239_HeLa_Rep1


title: IR group

value: irradiated at 8.5 Gy and administered with colvent control


title: H3K9me2_ab1220_HeLa_Rep2

description: Library name: H3K9me2_ab1220_HeLa_Rep2

value: H3K9me2 (ab1220, Abcam)


title: fiaj1_untreated_rep1

description: Library name: Part1_fiaj1_rep_1

value: human pluripotent stem cells


title: Control group

value: no irradiation


title: burb1_untreated_rep2

description: Library name: Part1_burb1_rep_2


title: htz-1(bon101), the first day of young adult, rep 1

description: Library name: Sample4

value: whole animal


title: CDAA-KO-06

city: Bethesda

first: Yaron

last: Rotman

address: 10 Center Drive, 10/10N248C

department: Liver Diseases Branch

institute: NIDDK

data_processing:
Transcriptomic analysis was performed using Partek Flow software (version 10.0).
Raw data were quality checked and trimmed (Phred score <30), then aligned to the mus musculus (mm10) reference genome using STAR (version 2.7.3a).
Transcripts were quantified and annotated using Ensembl (release 100).
Differential gene expression was examined using DESeq2 (version 1.14.1) R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: liver

extract_protocol:
Total RNA samples were extracted from 25-100 mg mouse liver tissues using TRIzol Reagent followed by purification process using RNeasy mini-Kit (QIAGEN, 74106) and RNase-free DNase set (QIAGEN, 79256).
Sequencing libraries were constructed from 1 µg total RNA using “Protocol for use with NEBNext® Globin & rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina”.

treatment_protocol: 8-10 week-old WT and Hsd17b13-KO mice were fed with CDAA-HFD for 12 weeks

value: liver

value: CDAA-HFD


title: LaminB1_ab16048_HeLa_Rep2

description: Library name: LaminB1_ab16048_HeLa_Rep2

value: HeLa

value: cervical adenocarcinoma epithelial cells

value: wild-type

value: LaminB1 (ab16048, Abcam)


title: CDAA-KO-05


title: LaminB1_ab16048_HeLa_Rep1

description: Library name: LaminB1_ab16048_HeLa_Rep1


title: IFNg Ax 500 sample12

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

description: Library name: IFNg_Ax_500_sample12

data_processing:
Data was processed using Cell Ranger 3.1.0 (10x Genomics), reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference). Data was processed using Scanpy 1.10.4, and multisample integration was performed with scvi-tools 1.3.0. The scVI model was constructed on 2000 HVGs with the hyperparameters n_layers = 2, dropout_rate = 0.2, and n_latent = 10, and were trained using the settings max_epochs = 400, check_val_every_n_epoch = 2, and early_stopping = True. Default hyperparameters and settings were used otherwise. An initial round of Leiden clustering using the function sc.tl.leiden was performed on the integrated BAL object with a resolution of 1. Clusters characterized by low number of detected genes and transcripts and high percentage of mitochondrial genes were removed.
Assembly: GRCh38.84
Supplementary files format and content: Tab-separated values file and matrix file

source_name: lung

extract_protocol:
BALF samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 rcf for 10 min at 4°C, followed by hypotonic erythrocyte lysis using 1 ml of PharmLyse solution (BD) for 2 min, followed by another wash with 10 ml of 0.5% BSA in PBS and centrifugation. Cell pellet was resuspended in 0.5% BSA in PBS at the final concentration 1000 cells/ul. Cell concentration and viability were determined using K2 Cellometer (Nexcelom) with AO/PI reagent and cells were loaded on 10x Genomics Chip A with Chromium Single Cell 3′ V2 gel beads and reagents (10x Genomics) aiming to capture 5,000–7,000 cells per library.
Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000052_RevB). BAL sample processing for scRNA-seq using “FACS” protocol: BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine orange (AO)/Propidium iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always < 5 × 107 cells/ ml and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio.

value: lung

tag: agent

value: IFNg Auxora 500 nM


title: daf-2(e1370), the first day of young adult, rep1

description: Library name: Sample2


title: IFNg Ax 500 sample11

description: Library name: IFNg_Ax_500_sample11


title: PRAISE-seq-HEK293T-nontreated-Ctrl2

city: Shanghai, P.R. China

first: weiying

last: meng

address: 1239 Siping Road, Shanghai, P.R. China

institute: Tongji University

description: Library name: PRAISE-seq-HEK293T-nontreated-Ctrl2

data_processing:
To identify Ψ modification sites, the PRAISE sequencing data from HEK293T and HuCCT1 cells, together with  sequencing data  were analyzed using BASAL. Analysis was conducted with parameters ‘-M T:-’. Candidate Ψ sites were further filtered based on the following stringent criteria: (i) deletion rate > 5% in treated samples; (ii) frequency of the ‘convert-to’ bases (deletions in this case) > 3 in treated samples; (iii) deletion rate < 1% in control samples; (iv) sequencing depth > 10 in both treated and control samples; (v) the deletion rates in treated samples were > 1.5-fold of the deletion rates in control samples or met statistical significance (FDR < 0.05), and the candidate sites were detected in all biological replicates.
Assembly: hg38
Supplementary files format and content: txt file containing raw counts s for each sample.

extract_protocol:
PRAISE-seq Pre-mRNA purification:Ribosomal RNA was depleted using the Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, N406) according to the manufacturer's protocol. Sulfite/bisulfite treatment:The 85% sulfite/15% bisulfite solution was prepared freshly by adding 2.58 g of potassium sulfite (Aladdin, P112413) and 0.3 g sodium bisulfite (Oxoid, 10019018) to 8 ml of RNase-free water and the solution was vortexed to clear (pH value is ~7.5). The 100 mM hydroquinone was prepared freshly by adding 11.01 mg of hydroquinone (Oxioid, 10011317) to 1 ml of RNase-free water. For sulfite/bisulfite treatment, 5 µl of RNA fragments was dissolved in 50 µl sulfite/bisulfite solution, which is a 100:1 mixture of 85% sulfite/15% bisulfite solution and 100 mM hydroquinone, and subjected to heat incubation at 70 °C for 5 h. The reaction mixture was purified by passing it through Spin Column (Sangon, B518688). Desulfonation:Purified RNA was transferred to a new 1.5 ml nuclease-free tube and adjusted to 100 μl with RNase-free water, then incubated with an equal volume of 1 M Tris–HCl (pH 9.0) at 75 °C for 30 min. The reaction was then immediately stopped by chilling on ice and ethanol precipitation. Add a coprecipitant (Takara, 9094) to aid in precipitation during the settling process. After ethanol precipitation, the RNA was resuspended in 10 µl of RNase-free water, and the concentration of RNA was quantified by Qubit RNA HS Assay Kit (Invitrogen, Q33231). Take 50 ng RNA (~1 µl) as ‘treated’ sample for subsequent library construction.
Library construction:‘Treated’ RNA sample and ‘untreated’ RNA sample were subjected to library construction. For first-strand cDNA synthesis, Maxima H minus Reverse Transcriptase (Thermo Fisher, K1651) was used. Second, we used RNase H to remove mRNA (Thermo Fisher, EN0201) and finally, for second-strand cDNA synthesis, VATHS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme, NR606) was used. Twelve cycles were used for untreated and treated RNA in the second round of PCR. High-throughput sequencing was performed on the Illumina xplus system.

tag: cell line


title: wt(N2), the first day of young adult, rep 1

description: Library name: Sample1


title: daf-16(mu86);daf-2(e1370), the first day of young adult, rep1

description: Library name: Sample3


title: CDAA-KO-03

tag: treatment


title: PRAISE-seq-HEK293T-nontreated-Ctrl1

description: Library name: PRAISE-seq-HEK293T-nontreated-Ctrl1


title: IFNg Ax 500 sample10

description: Library name: IFNg_Ax_500_sample10

tag: tissue


title: seedlings_C2_pifq_ZT1.5_R1

city: York

first: Gina

last: Vong

address: Wentworth Way

department: Biology

institute: University of York

description: Library name: P95

data_processing:
fastq files were merged across lanes
Illumina adaptors were trimmed with Trim_Galore/0.6.10-GCCcore-11.3.0 --clip_R1 12 --clip_R2 12
Reads were mapped using Salmon/1.10.0-GCC-11.3.0
quantified reads were processed into abundance, counts and length tables using tximport v.1.34.0 in R v.4.5
Assembly: AtRTD3
Supplementary files format and content: Salmon quant output for each sample.
Supplementary files format and content: abundance_table_salmon.txt, counts_table_salmon.txt and length_table_salmon.txt are tab separated tables containing gene expression data for TPM, counts and read leangths respectively. Each row is a gene and each column is a sample.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface sterilised and plated on 1xMS plates with 1% sucrose and 3% agar, in clusters of ~50 seeds. We stratified 3 genotypes of Arabidopsis thaliana (col-0, elf3-1, pifq) seeds at 4C for 3 days. To initiate germination, we exposed all plates to 24h continuous light with blue, red, far-red LEDs at 1:1:1 ratio. We grew the seedlings (on plates) in Snijders (Tilburg, Netherlands) MC1750 growth chamber at 22C and 60% room humidity under 4 light regimes: a) linear dawn; b) extreme dawn; c) 8h photoperiod control; d) 7h photoperiod control. After 7 days of growth, the seedlings were sampled every 30 mins from ZT-0.5 to ZT3 (i.e. 8 timepoints) for 2 replicates of  RNA-seq transcriptome analysis.

extract_protocol:
RNA was extracted using the Omega BioTek EZNA Plant RNA kit, following their protocols
NEBNext Ultra II Directional Library Prep Kit for Illumina, with NEBNext ploy(A) magnetic isolation

treatment_protocol: a) linear dawn (T1): blue, red and far red lights with a 1:1:1 ratio which increased in irradiance stepwise every 10 minutes, for 2h until a maximum PAR of 27.8 umol m-2 s-1. The maximum was sustained for a further 6h before lights turned off. b) extreme dawn (T2): using the same blue, red, far red light settings as the linear dawn treatment, but increasing the slope of the red channel and starting that 0.5h later than the other channels. This resulted in a <1 ratio initially (red relative to the other channels) but increasing as time progressed until the maximum PAR of 27.8 umol m-2 s-1. At the maximum, the B:R:FR ratio was 1:1:1 and was sustained for a further 6h before lights turned off. c) 8h control (C1): on/off square wave 8h photoperiod, with B:R:FR ratios at 1:1:1 d) 7h contro (C2)l: on/off square wave 7h photoperiod, with B:R:FR ratios at 1:1:1

value: seedling

value: pifq


title: PAR-CLIP-seq-HEK293T-SMD2IP-3

description: Library name: PAR-CLIP-seq-HEK293T-SMD2IP-3

data_processing:
For PAR-CLIP, only R1 reads from paired-end sequencing were used for data analysis. Adapter trimming and quality filtering were performed using Trim Galore (v0.6.10; https://github.com/FelixKrueger/TrimGalore) with the parameters “--clip R1 3 -a A{10} --max n 0.1 --length 15”. Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.5.1) with default settings. Resulting SAM files were processed with PARalyzer (v1.5) for peak calling using default parameters.{Corcoran, 2011 #917} Peaks significantly enriched relative to input controls were retained for downstream analyses.
Assembly: hg38
Supplementary files format and content: txt file containing raw counts s for each sample.

source_name: cell line

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, C11995500CP) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S; BasalMedia, S110JV)，HuCCT1 cells were maintained in RPMI-1640 medium (ThermoFisher, C11875500BT) supplemented with 10% FBS and 1% P/S. All cell lines were incubated at 37°C in a humidified atmosphere with 5% CO2. Cells were passaged every 2-3 days when they reached approximately 90% confluency.

extract_protocol:
PAR-CLIP 4SU treatment and UV crosslinking:Add 4SU (MCE, HY-W011793) to final conc. of 200 uM to culture medium, 37℃, 14 hr. For each 15 cm plate, remove medium and wash twice with 5 ml ice-cold PBS. Then place the plate on ice, 365 nm, 1500*100 uJ/cm2, crosslink twice. Collect cells in 2 ml ice-cold PBS. Centrifuge to collect cell pellet. Finally freezing with liquid nitrogen. Lysate preparation:Thaw cell pellet on ice, add 2 times vol lysis buffer containing 50 mM HEPES (pH 7.5), 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail, mix well, incubate on ice for 10min with periodic perturbation. Then Cells were lysed by sonication with 6 cycles of 5 seconds on / 5 seconds off at 30% amplitude, while keeping samples on ice to prevent overheating. Centrifuge 15000g for 15min 4℃ to collect supernatant. IP:Add Monoclonal anti-FLAG ®M2（Sigma-Aldrich，F3165）to cleared lysate. Rotate for 4h at 4℃. Prepare Protein A/G Magnetic Beads by washing twice with IP-wash buffer containing 50 mM HEPES-KOH (pH 7.5), 300 mM KCl, 0.05% (v/v) NP40, complete EDTA-free protease inhibitor cocktail. Then add beads to lysate, rotate for 3h at 4℃. 2nd RNase T1 digestion:Resuspend beads in 1 vol of IP wash buffer containing 50 mM HEPES-KOH( pH 7.5), 300 mM KCl, 0.05% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail, add RNase T1 (Thermo Fisher，EN0541) to a final conc. of 10U/μl and incubate for 8min at 22℃, then chill reaction on ice for 5min. Wash beads 3 times in High Salt Buffer containing 50 mM HEPES-KOH(pH 7.5), 500 mM KCl, 0.05% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail. Then change to new tube during the last wash. Dephosphorylation:Wash beads once with Dephosphorylation buffer containing 50 mM Tris-HCl (pH 7.9), 100 mM NaCl, 10 mM MgCl2, 1 mM DTT, then resuspend in 1volumn of commercial dephosphorylation buffer (beads volume). Add Quick CIP (NEB, M0525V) to final concentration of 0.5U/μl, incubate for 15min at 37℃ (remove 5’P).
Library construction:Total RNA was extracted using TRIzol™ reagent according to the manufacturer’s instructions. RNA-seq library preparation was conducted using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s protocol.

treatment_protocol: Total RNA was extracted from HEK293T or other cell lines using TRIzol™ reagent (Thermo Scientific, 15596018) following the manufacturer’s instructions.

value: cell line

tag: cell type


title: WT, sham, rep4

city: izunokuni mifuku

first: takahisa

last: shimoda

state: Shizuoka

country: Japan

institute: Asahi Kasei Pharma

description: Library name: sample4

data_processing:
Sequencing was conducted on the Illumina NovaSeq platform in paired-end mode (150 bp × 2) (performed by Takara Bio, Shiga, Japan).
Raw sequencing reads were subjected to quality control using fastp (v0.22.0).
High-quality reads were aligned to the rat reference genome (mRatBN7.2) using STAR aligner (v2.7.9a).
Gene-level counts and transcripts per million (TPM) were calculated using RSEM (v1.3.1).
Assembly: mRatBN7.2
Supplementary files format and content: CSV (Comma-Separated Values) file includes raw counts for each sample

organism: Rattus norvegicus

source_name: spinal dorsal horn

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (Catalog # NEB #T2110, New England Biolabs, Ipswich, MA, USA) .
Total RNA was processed for sequencing using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: spinal dorsal horn


title: daf-16(mu86);daf-2(e1370), the first day of young adult, rep 3

description: Library name: Sample15

tag: genotype


title: CDAA-KO-02


title: Hehd1_organoids_Day20

description:
Library name: Hehd1_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the rnaseq pipeline (version 3.12.0), distributed by nf-core [doi: https://zenodo.org/records/7998767]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io]. The following command was used to execute the pipeline:  nextflow run nf-core/rnaseq -r 3.12.0 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --extra_trimgalore_args '--nextseq 20' --outdir results --deseq2_vst -bg  These parameters generally adhere to the defaults set by the nf-core rnaseq pipeline. That pipeline release used STAR (version 2.7.9a) as the aligner, mapping reads to the human reference genome (GRCh38 / release 102). The specified read trimming parameter (--nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flow cell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how any technical and biological replicates should be grouped together. The nf-core rnaseq pipeline produces quantitated expression values for every gene for each sample, reporting raw counts and TPM values. These expression matrices were used in subsequent analyses.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the TPM expression values for each gene, segmented by biological replicate.  These data were produced by the nf-core rnaseq pipeline.

extract_protocol:
700,000 hiPSCs or hESCs were used for RNA extraction for each biological replicate. Cells were washed once with 1ml Dulbecco's Phosphate Buffered Saline (DPBS) and harvested using 500µl Accutase (StemCell Technologies, 07922) for 3 minutes at 37°C. Dissociated cells were then collected with 5ml of corresponding hPSC medium and centrifuged for 3 min at 400 RCF at RT. Supernatant was aspirated and the cells were resuspended in 1ml cold DPBS. RNA extraction from hiPSCs/hESCs was conducted using the Monarch Total RNA Miniprep Kit (NEB T2010S) according to the manufacturer’s protocol, with DNase I treatment used to enzymatically remove residual gDNA. RNA concentration was quantified using Nanodrop and the RNA Integrity Number (RIN) was assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on Agilent 2100 Bioanalyzer (Agilent). A RIN value of >7 was deemed to be of good quality and used for downstream RNA-seq library processing. The isolated RNA was frozen and stored at -80°C until RNA-seq library preparation.
RNA-seq library preparation was performed on the isolated RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module, which isolated mRNA from total RNA (100ng input) by poly(A)-enrichment. RNA-seq libraries were subsequently prepared from the isolated mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L), and the NEBNext Multiplex Oligos from Illumina (Index Primers Set 1, 2, 3 and 4, NEB, E7335S, E7500S, E7710S, E7730S), following the manufacturer’s protocols. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 12 cycles. Size distribution and yield quantification of the RNA-seq libraries were assessed using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626).


title: HUES8_untreated_rep2

description: Library name: Part1_HUES8_rep_2

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the atacseq pipeline (version 2.1.2), distributed by nf-core [doi: 10.5281/zenodo.2634132].  The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/atacseq -r 2.1.2 --input batch2_samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --read_length 50 --trim_nextseq 20 --mito_name MT --blacklist blacklist/ENCFF356LFX.bed.chr_deleted.txt --aligner bowtie2 --deseq2_vst --outdir results -bg  These parameters generally adhere to the defaults set by the nf-core atacseq pipeline, except that Bowtie2 (version 2.4.4) was used as the aligner for the pipeline. Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to the mitochondrial chromosome or regions blacklisted by the ENCODE project were removed [https://www.encodeproject.org/files/ENCFF356LFX/]. The specified read trimming parameters (--trim_nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flowcell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how technical and biological replicates should be grouped together.
The nf-core atacseq pipeline used the software MACS2 (version 2.2.7.1) to identify peaks i.e genomic regions with a localised high abundance of mapped reads. MACS2 was run using the default settings for the atacseq pipeline. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained. Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, BAM files of the aligned reads generated by the nf-core atacseq pipeline were imported into SeqMonk, along with a text-format list detailing ATAC-seq peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the deduplicated raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak. A minimum threshold of -2 (log2-transformed counts per million reads) in any of the datasets was applied to remove consensus peaks with low count values.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the identity of the nearest gene (to within 2kb).  The files also provide the log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-seq kit (Active Motif 53150). Briefly, adherent cells were treated with Accutase to produce a single cell suspension. 100,000 cells per sample were pelleted, washed once in ice-cold PBS, resuspended in ATAC Lysis Buffer and then combined with Tagmentation Master Mix. The reaction was then incubated for 30min at 37°C with 800rpm agitation. Immediately after, the tagmented DNA was column-purified, eluted in a 35μL volume and PCR-amplified for 10 cycles with indexing primers to generate sequencing libraries. Library quality control was carried out with the Bioanalyzer High-Sensitivity DNA analysis kit (Agilent 5067-4626). Libraries were sequenced as paired end 50bp reads, on the Illumina NovaSeq platform at the Cancer Research UK Cambridge Institute Genomics Core Facility. Two biological replicates were collected from independent experiments.
Sequencing libraries were prepared from 100,000 cells per sample using the Active Motif ATAC-seq kit, following tagmentation of accessible chromatin regions for 30 minutes at 37°C, column purification of tagmented DNA, and PCR amplification for 10 cycles with indexing primers. Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit.

tag: batch


title: Cuhk2_organoids_Day20

description:
Library name: Cuhk2_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: IFNg Ax 500 sample9

description: Library name: IFNg_Ax_500_sample9


title: seedlings_C1_pifq_ZT3_R2

description: Library name: P88


title: CDAA-KO-01


title: PAR-CLIP-seq-HEK293T-SMD2IP-2

description: Library name: PAR-CLIP-seq-HEK293T-SMD2IP-2


title: IFNg Ax 500 sample7

description: Library name: IFNg_Ax_500_sample7


title: seedlings_C1_pifq_ZT2.5_R2

description: Library name: P87


title: CDAA-WT-06

value: Wildtype


title: PAR-CLIP-seq-HEK293T-SMD2IP-1

description: Library name: PAR-CLIP-seq-HEK293T-SMD2IP-1


title: IFNg Ax 50 sample12

description: Library name: IFNg_Ax_50_sample12

value: IFNg Auxora 50 nM


title: CDAA-WT-05


title: PAR-CLIP-seq-HEK293T-Input-1

description: Library name: PAR-CLIP-seq-HEK293T-Input-1


title: seedlings_C1_pifq_ZT2_R2

description: Library name: P86


title: IFNg Ax 50 sample11

description: Library name: IFNg_Ax_50_sample11


title: seedlings_C1_pifq_ZT1.5_R2

description: Library name: P85


title: CDAA-WT-04