title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, KCl, rep3

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University

description:
Library name: 7dGTP_KCL_rep3
Homo sapiens

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: -r SAMPLE.R1.fastq.gz -p SAMPLE.R2.fastq.gz --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAGC --adapter-min-overlap 1 --min-read-length 15  --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: GTP_KCL_rep1: NNNNNCGTGATNNNN, GTP_KCL_rep2: NNNNNTACAAGNNNN, GTP_KCL_rep3: NNNNNTTTCACNNNN, GTP_NaCL_rep1: NNNNNGCTCATNNNN, GTP_NaCL_rep2: NNNNNGGAACTNNNN, GTP_NaCL_rep3: NNNNNCCGGTGNNNN, 7dGTP_KCL_rep1: NNNNNTCAAGTNNNN, 7dGTP_KCL_rep2: NNNNNACATCGNNNN, 7dGTP_KCL_rep3: NNNNNGCCTAANNNN, 7dGTP_NaCL_rep1: NNNNNTAGTTGNNNN, 7dGTP_NaCL_rep2: NNNNNGATCTGNNNN, 7dGTP_NaCL_rep3: NNNNNCTGATCNNNN)
De-multiplexing oligonucleotides: using basic Bash commands and seqtk (v1.3), R1 reads of each sample were split into one FASTQ file per oligonucleotide per sample based on the first 15 bp of R2 reads (=oligonucleotide barcode), remove empty space characters in read ids
Per oligonucleotide: create STAR mapping index: STAR (v2.6.1b) with parameters: --runMode genomeGenerate --genomeDir OLIGOINDEX --genomeFastaFiles OLIGO.fa --runThreadN 4 --genomeSAindexNbases 2
Per oligonucleotide: map reads to OLIGOINDEX: STAR (v2.6.1b) with parameters: --runMode alignReads --genomeDir OLIGOINDEX --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --alignIntronMin 21 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 1001076135
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i OLIGO.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTH | sort -k1,1 -k2,2n > OLIGO.shifted1bp.bed
BED to bedGraph considering only 5' end positions of reads mapped to plus strand: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i OLIGO.shifted1bp.bed -g CHROMOLENGTH > OLIGO.plus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
To quantify the number of rG4s in the IVTs, a custom RTstop peak-calling approach was implemented to identify "RTstop peaks", i.e. 3-nt windows with RTstop signal above background. In brief, peak calling was performed independently for each buffer condition (KCl and NaCl), on the RTstop signal (read starts) summed across all three replicates per condition. To account for read start enrichment at the 5’ end of constructs lacking rG4 formation—i.e., when reverse transcription is not hindered by secondary structure—the first 18 nt of the 200-nt constructs were excluded from the seed position search. Subsequently, positions 19 to 200 were scanned for positions containing at least six stacked RTstop read starts, which were defined as seed sites. Seed sites were further processed using BindingSiteFinder (version 1.3.8) (PMID: 31751605) to generate 3-nt wide RTstop peaks, requiring that at least two out of three positions were supported by RTstop signal (bsSize = 3, minWidth = 1, minCrosslinks = 2, minCLSites = 1). Peaks from both conditions were then merged, and partial overlaps of peaks were resolved by resizing them to their center point, based on the maximum combined coverage.
To identify rG4s—i.e., RTstop peaks significantly reduced in NaCl condition—differential testing on the RTstop signal level at RTstop peaks between the conditions was performed using DESeq2 (version 1.37.2). Specifically, a condition-specific comparison between NaCl and KCl buffer conditions was conducted (alpha = 0.05, Benjamini-Hochberg correction). Prior to differential testing, constructs were filtered out based on the following quality criteria: (1) low expression (<100 normalized reads), (2) high variability in total reads per construct between conditions (adjusted P value < 0.05 in a separate DESeq2 test using the parameters altHypothesis = 'lessAbs' and lfcThreshold = 1). The resulting log2-transformed fold-changes (L2FC) were shrunken using the adaptive shrinkage method (‘ashr’). Significantly changing RTstop peaks (adjusted P value < 0.05) with a shrunken L2FC < 0 were considered as rG4, and constructs with at least one rG4 were labelled as rG4-containing. Finally, given that each tested transcript region was represented by four oligonucleotide constructs with distinct barcodes, only regions with two or more rG4-containing constructs were classified as rG4 regions (n=1,060), while a classified non-rG4 region (n=1,109) was not allowed to have a single construct labelled as rG4-containing. The remaining 831 transcript regions were inconsistent and removed from further analysis.
Assembly: GRCh38.p7
Supplementary files format and content: RTstop_oligonucleotides_info.xlsx: contains information on oligonucleotide library, including contruct ID, Ensembl gene ID and gene name, genomic coordinates and sequence of chosen region, and barcode; note that each region is represented by four oligonucleotides with different barcodes
Supplementary files format and content: RTstop_rG4_classification.xlsx: contains information on one representative oligonucleotide for each region that was classified as rG4-containing (n=1,060) or non-rG4-containing (n=1,109), including construct_ID, rG4 identification in RTstop, genomic coordinates and rG4 prediction (pqsfinder)

molecule: other

organism: synthetic construct

source_name: Synthetic oligonucleotides

extract_protocol:
1 µg RNA of the oligo library was used as a template for the reverse transcription with SuperScript III (Invitrogen). First, the RNA was mixed with 0.5 pmol of the RT primer (5’-GGATCCTGAACCGCT-3’) and 0.5 mM dNTPs in reverse transcription buffer (20 mM Tris-Cl pH 7.5, 150 mM KCl or 150 mM NaCl, 3 mM MgCl2) in a total reaction volume of 19.5 µL. The mixture was incubated at 80°C for 2 min, followed by an incubation at 25°C for 2 min. Then, 100 U of SuperScript III enzyme was added and the reaction was incubated for 10 min at 42°C. To hydrolyse the template RNA, 1.65 µL of 1 M NaOH solution was added, followed by an incubation at 98°C for 20 min. Addition of 20 µL 1M HEPES-NaOH pH 7.3 stopped the hydrolysis reaction. Then, the cDNA was isolated using a MyONE Silane bead clean-up following the iCLIP2 protocol (PMID: 31610236).
The library preparation was performed using the iCLIP2 protocol continuing with second adapter ligation to the 5’ end of the extracted cDNA (PMID: 31610236). The second adaptor was ligated to the 5’ end of the cDNAs on the beads. Then, the cDNA was purified via MyONE Silane beads and the library was amplified using a 6-cycle PCR and afterwards two times size-selected with ProNex beads. The samples were quality checked and profiled on a High Sensitivity D1000 ScreenTape using TapeStation 2200 (Agilent). After quantification with the Qubit dsDNA HS Assay Kit (Life technologies) the samples were pooled in an equimolar ratio. Sequencing was performed on a NextSeq 500 Mid Output Flowcell using paired-end sequencing with 150 cycles (Read 1: 141nt, Read 2: 25nt).

value: Synthetic oligonucleotides

tag: in vitro_transcription

tag: reverse transcription

value: KCl


title: S3KO_CD4_STAT3.203_rep1

status: Public on Apr 14 2026

type: SRA

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

country: USA

institute: University of Miami

description:
Library name: Villarino‐18253‐001_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

library_source: transcriptomic

data_processing:
bulk RNA-seq: FASTQ alignment with Tophat2
bulk RNA-seq: transcript assembly with cufflinks
bulk RNA-seq: Gene level read count data generated using htseq-count
scRNA-seq: FASTQ alignment, transcript assembly and gene-level counts matrix generated with cellRanger
scRNA-seq: multitagged cells selected using custom scrip and metadata assembled with Seurat
Assembly: bulk RNA-seq: mm10
Supplementary files format and content: bulk RNA-seq: Tab delimited text of RNA-seq gene-level expression count data
Supplementary files format and content: scRNA-seq: Tab delimited text of metadata for multi-tagged cells

molecule: polyA RNA

organism: Mus musculus

source_name: pooled LN and spleen

growth_protocol: 20-100K viable, GFP+ cells were sorted and cultured, then lysed and stored in Trizol

extract_protocol:
Total RNA isolated from TRIzol by phenol/chloroform extraction, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
For bulk RNA-seq, sequencing libraries were generated with NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs). For scRNA-seq , sequencing libraries were generated with 10X Chromium Single Cell 3' V3 chemistry kit.

treatment_protocol: 20-100K viable cells were sorted and cultured with IL-27, then lysed and stored in Trizol

tag: tissue

value: pooled LN and spleen

tag: cell line

value: CD4+ T cell

tag: cell type

value: Viable CD4+ GFP+ RV tranduced

tag: genotype

tag: treatment


title: S3KO_CD8_MigR1_rep3

description:
Library name: Villarino‐18253‐080_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, NaCl, rep1

city: Würzburg

country: Germany

description:
Library name: 7dGTP_NaCl_rep1
Homo sapiens

library_source: other

value: NaCl


title: Liver, DIO-MASH Vehicle 24 w, rep 3

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 16211

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38, ensembl release 96
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Liver

extract_protocol:
cDNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on the NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit V2 (#75 CYS, Illumina)
RNA-seq

treatment_protocol: Liver tissue were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL) or the RNAdvance Tissue Kit (Beckman-Coulter

value: Liver

value: DIO-MASH Vehicle

tag: time


title: 3-month, cerebellar cortex, heterozygous replicate 4

city: Cambridge

first: Sameer

last: Aryal

state: Massachusetts

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

description:
Library name: 12w-CC-HT4
3-mo_CC_HET_4

data_processing:
Reads were aligned to Gencode M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: Gencode M25 / GRCm38.p6
Supplementary files format and content: Comma-separated text files that includes raw counts (estimated by RSEM) for each sample.

source_name: Brain

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Srrm2 +/- mutant mice and wild-type littermates. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

value: Brain

value: Srrm2 +/-


title: 3-month, cerebellar cortex, heterozygous replicate 1

description:
Library name: 12w-CC-HT1
3-mo_CC_HET_1


title: RT-Stop Profiling, RNA oligo library, GTP, NaCl, rep3

description:
Library name: GTP_NaCl_rep3
Homo sapiens

value: GTP


title: Liver, Chow Vehicle 24 w, rep 4

description: Library name: 16204

value: Chow Vehicle


title: 3-month, cerebellar cortex, wild-type replicate 3

description:
Library name: 12w-CC-WT3
3-mo_CC_WT_3

value: Wild-type


title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, KCl, rep2

description:
Library name: 7dGTP_KCL_rep2
Homo sapiens


title: Liver, Semaglutide 24 w, rep 3

description: Library name: 16202

value: Semaglutide


title: Micromass derived bone marrow cells

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

country: China

institute: Sichuan University

description:
Library name: Sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sample quality control was conducted using the official Cell Ranger software (10x Genomics), which incorporates the STAR aligner for read mapping. Following alignment to the reference genome, key quality metrics—including the number of high-quality cells, the number of detected genes, and the genome mapping rate—were generated. These metrics provided a comprehensive assessment of data quality for each sample.
Assembly: Mouse mm10
Supplementary files format and content: Filtered gene expression matrix with genes in rows and cells in columns.

molecule: total RNA

source_name: Bone marrow

growth_protocol: The differentiated scl-progenitor cells were cultured as micromass under endochondral ossification medium. Then the micromass was subcutaneous transplanted to NCG mice for 3 weeks.

extract_protocol:
Bone tissue with mechanically and enzymatically digested
Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions(single cell 3' v2 protocol, 10x genomics).

treatment_protocol: no treatment

value: Bone marrow

value: 3 weeks

value: Bone marrow cells

value: NCG

value: Differentiation

tag: batch


title: S3KO_CD4_MigR1_rep1

description:
Library name: Villarino‐18253‐021_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: CD4+ T cell

value: Viable CD4+ GFP+ RV tranduced


title: S3KO_CD4_STAT3.203_rep2

description:
Library name: Villarino‐18253‐039_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, KCl, rep1

description:
Library name: 7dGTP_KCL_rep1
Homo sapiens

value: Synthetic oligonucleotides

value: KCl


title: RT-Stop Profiling, RNA oligo library, GTP, NaCl, rep2

description:
Library name: GTP_NaCl_rep2
Homo sapiens

value: NaCl


title: Cell line, Myc310, Cys deprived, rep 3

city: London

first: Josep

last: Tarrago-Celada

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: TAR6417A27

data_processing:
Alignment and quantification via nf-core RNAseq pipeline: nf-core version 3.10.1; Nextflow version 22.10.3; R version 4.2.2; using STAR and RSEM.
Differential gene expression analyses, performed using the the default methods of DESeq2, version 1.38.3
Ensembl gene IDs were associated with their common names according to AnnotationDbi, version 1.60.2
Assembly: GRCm38, release-95
Supplementary files format and content: Tab-delimited txt file. Contains the ensembl gene ID, entrez gene ID, gene symbol, and raw counts for each sample. Samples are listed by their sequencing ID, which begins "TAR6417A". Counts from multiple sequencing runs have been merged.

growth_protocol: Cells were seeded at 250,000 cells/well in 6-well plates, in DMEM:F12 1:1 (no glutamine, Gibco 21331-020), adding 10% FBS (Gibco 10270-106), 1% Glutamine (200 mM), 1% P/S, 1% HEPES, 0.1% Insulin, 0.1% Hydrocortisone, 0.01% mouse EGF. Incubation conditions were 37°C, 5% CO2.

extract_protocol:
RNA extraction was performed according to RNAeasy kit (QIAGEN 74104), including DNA digestion with DNAse I set (QIAGEN 79254).
mRNA was sequenced using the library NEBNext Ultra II Directional PolyA mRNA. Number of reads per sample was 25 million, and requested read length was 100. The run type was paired-end format, and the sequencing platform was a NovaSeq.

treatment_protocol: After 24h, media was changed to control or cysteine/cystine free media for 6 hours

value: Cys deprived


title: Liver, Semaglutide 24 w, rep 4

description: Library name: 16212

value: Liver


title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, NaCl, rep2

description:
Library name: 7dGTP_NaCl_rep2
Homo sapiens


title: 3-month, cerebellar cortex, heterozygous replicate 3

description:
Library name: 12w-CC-HT3
3-mo_CC_HET_3

value: Brain

value: Srrm2 +/-


title: Liver, DIO-MASH Vehicle 24 w, rep 2

description: Library name: 16201

value: DIO-MASH Vehicle


title: 3-month, cerebellar vermis, heterozygous replicate 2

description:
Library name: 12w-CV-HT2
3-mo_CV_HET_2


title: S3KO_CD4_MigR1_rep2

description:
Library name: Villarino‐18253‐038_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: RT-Stop Profiling, RNA oligo library, 7-deaza-GTP, NaCl, rep3

description:
Library name: 7dGTP_NaCl_rep3
Homo sapiens


title: Liver, Chow Vehicle 24 w, rep 2

description: Library name: 16184

value: Chow Vehicle


title: Cell line, Myc310, Cys  deprived, rep 2

description: Library name: TAR6417A26


title: Cell line, Myc310, Control, rep 2

description: Library name: TAR6417A23

value: Control


title: Liver, Semaglutide 24 w, rep 1

description: Library name: 16182

value: Semaglutide


title: RT-Stop Profiling, RNA oligo library, GTP, KCl, rep2

description:
Library name: GTP_KCL_rep2
Homo sapiens

value: GTP


title: E14 embryonic stem cell 56hr30c

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: 56hr30c

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software. Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1, parameters: --paired). Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to use overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.14.4 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. 2i_release: CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
Assembly: GRCm38
Supplementary files format and content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome> <position> <strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context>

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: E14 mESC were cultured in 2i+LIF media consisting out of N2B27 medium, composed out of DMEM/F12 (Life Technologies, 12634010) and Neurobasal (Life Technologies, 21103049) in a volume/volume (v/v) ratio 1:1, 0.1 mM 2-mercaptoethanol, 2 mM L-Glutamine, 1:200 v/v N2 (Life Technologies, 17502048) and 1:100 v/v B27 supplement (Life Technologies, 17504044), supplemented with 3 µM CHIR99021, 1 µM PD0325901 and 20 ng/ml of leukemia inhibitory factor (LIF) (all Department of Biochemistry, University of Cambridge). mESCs were cultured on tissue culture plastic pre-coated with 0.1 % gelatine in H2O. Cultures were passaged when approaching confluence (every 2 days). All cells were cultured in a humidified incubator at 37 °C in 5 % CO2 and 20 % O2. mESCs were subject to routine mycoplasma testing using the MycoAlert testing kit (Lonza) and tested negative. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium consisting of DMEM (Life Technologies, 10566-016), containing 15% Fetal Bovine Serum (FBS) (Gibco, 10270106), 1x non-essential amino acids (NEAA) (Life Technologies, 11140050), 0.1 mM 2-mercaptoethanol (Life Technologies, 31350-010), 2 mM L-Glutamine (Life Technologies, 25030-024), supplemented with 20 ng/ml of LIF (Department of Biochemistry, University of Cambridge).

extract_protocol:
2i_release: Cells were lysed by RLT plus lysis buffer (Qiagen) containing 0.5mM 2-mercaptoethanol. Total nucleic acid was purified from the lysate with RNAdvance magnetic beads (Beckman Coulter, A32649) using a Bravo Workstation pipetting robot (Agilent Technologies). BS-seq libraries were prepared from total nucleic acid using the bulk-cell method previously described (Smallwood et al., Nature Methods 11, 817-820) but with the following modifications: bisulfite conversion was carried out using the EZ Methylation Direct MagPrep kit (Zymo, D5044), with desulphonation and purification using magnetic beads, following the manufacturers’ instructions but with half volumes. Primers for first and second strand synthesis contained a 3’ random hexamer instead of a nonamer and biotin capture of first strand synthesis products was omitted, substituting an extra AMPure XP (Beckman Coulter, A63881) purification between second strand synthesis and PCR amplification. In order to avoid potential batch effects which could mask subtle differences between samples all libraries were prepared in parallel with the pre-PCR purification steps carried out using a Bravo Workstation pipetting robot (Agilent Technologies).
PBAT Bilsulfite-seq

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release

tag: collection timepoint


title: Cell line, Myc310, Control, rep 1

description: Library name: TAR6417A22


title: RT-Stop Profiling, RNA oligo library, GTP, KCl, rep1

description:
Library name: GTP_KCL_rep1
Homo sapiens


title: S3KO_CD4_N647D_rep2

description:
Library name: Villarino‐18253‐045_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen

value: CD4+ T cell


title: Cell line, MYAZ6_6g, Control, rep 3

description: Library name: TAR6417A18


title: Cell line, Myc310, Control, rep 3

description: Library name: TAR6417A24


title: Liver, Chow Vehicle 24 w, rep 6

description: Library name: 16224


title: RT-Stop Profiling, RNA oligo library, GTP, KCl, rep3

description:
Library name: GTP_KCL_rep3
Homo sapiens

value: Synthetic oligonucleotides


title: E14 embryonic stem cell 56hr30b

description: Library name: 56hr30b


title: Activated HIV-1 infected CD4+ T cells, donor F, biological replicate 3

city: Boca Raton

first: Sean

last: Paz

address: 777 Glades Road

department: Biomedical Sciences

institute: Florida Atlantic University

description: Library name: Inf_F

data_processing:
Read quality control was performed using FastQC.
Reads were aligned to the GRCh38 assembly of the human genome using HISAT2 running in a Galaxy environment.
Aligned reads were assembled into transcripts and quantified using the ENSEMBL reference human transcript assembly with CuffDiff2 running in a Galaxy environment.
Differential expression comparisons: (1) Naive CD4+ T cells vs. Activated CD4+ T cells; (2) Activated CD4+ T cells vs. Activated HIV-1 infected CD4+ T cells. Differentially expressed genes were prioritized by Log2 fold change and associated p-value.
Assembly: GRCh38
Supplementary files format and content: Excel workbook (DE Analysis_cuffdiff.xlsx): contains FPKM values per sample and log2 fold change, test statistic, p-value, and q-value for each gene across two comparisons: (1) Naive vs. Activated CD4+ T cells and (2) Activated vs. Activated HIV-1 infected CD4+ T cells. Separate sheets per donor (D, E, F) and combined DEF sheets are included.

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: CD4+ T cells were isolated from peripheral blood of 3 healthy donors by negative selection. Cells were maintained in RPMI-1640 supplemented with 10% FBS and antibiotics at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from CD4+ T cells for each of the three conditions across three biological replicates. Total RNA was DNase-treated and depleted of ribosomal RNA prior to library preparation.
cDNA libraries were generated using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Naive CD4+ T cells were activated for 5 days using plate-bound anti-CD3 and anti-CD28 antibodies with soluble IL-2. Activated cells were then either mock infected or infected at high MOI (MOI>1000) with HIV-1 NL4-3. RNA was extracted 5 days post-infection.

value: peripheral blood

value: CD4+ T cells

value: healthy donor

value: HIV-1 NL4-3 (MOI>1000), 5 days post-infection

value: Donor F


title: S3KO_CD4_Y640F_rep2

description:
Library name: Villarino‐18253‐040_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: Viable CD4+ GFP+ RV tranduced


title: E14 embryonic stem cell 56hr30a

description: Library name: 56hr30a


title: Liver, DIO-MASH Vehicle 24 w, rep 1

description: Library name: 16181

value: Liver

value: DIO-MASH Vehicle


title: E14 embryonic stem cell 53hr30c

description: Library name: 53hr30c


title: Cell line, MYAZ6_6g, Control, rep 1

description: Library name: TAR6417A16

value: Control


title: Activated HIV-1 infected CD4+ T cells, donor E, biological replicate 2

description: Library name: Inf_E

value: Donor E


title: Liver, Chow Vehicle 24 w, rep 3

description: Library name: 16194

value: Chow Vehicle


title: EB, WT rep, Rad21

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Trimming: trimgalore --stringency 2
Mapping : bowtie2
samtools view chr11
Removing duplicates : samtools rmdup
Generating bigwig tracks: deeptools -bs 20 --normalizeUsingRPKM
Assembly: mm9 or mm9 based custom genome
Supplementary files format and content: bigWig : (deeptools) bamCoverage converison of filtered fragments (duplicate-filtered fragments) from bam to bigwig,  (--binSize 20 --normalizeUsingRPKM)

source_name: EB

growth_protocol: EB: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker. Spleen: APH-treated spleens were dissociated and Ter119+ cells were selected.

extract_protocol:
For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 5-10*10^6 cells were lysed by incubation on ice in lysis buffer for 10 minutes. Chromatin was sonicated using the Bioruptor or Bioruptor pico to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 10 min, 4 ºC) and soluble material was diluted to 2 ml with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for CTCF (10 µl 07-729; Millipore) overnight. Chromatin incubation with Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions. Alternatively,  for Rad21 ChIPs, the above described agarose protocol was used with DSG+formaldehyde fixed samples, or a magnetic bead protocol was used with formaldehyde fixed samples. For the magnetic bead-based protocol, samples were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine for 5 minutes. Cells were lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) supplemented with Proteinase Inhibitor Cocktail (Roche, 11697498001) and chromatin was sonicated using the Bioruptor pico (Diagenode) to produce fragments of 200-500 bp. Chromatin was isolated using a Rad21 antibody (ab992) and Protein-G Dynabeads (Thermo Fisher) and washed three times with RIPA buffer (50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% Igepal CA-630, 0.7% sodium deoxycholate) and two times with Tris-EDTA (TE buffer with 50 mM NaCl). Precipitated chromatin was eluted in 1% SDS, 10 mM EDTA and 50 mM Tris-HCl. After decrosslinking and treatment with RNase A and proteinase K, DNA was purified using DNA Clean-up and Concentration kit.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: EB

value: Erythroid

value: WT

tag: antibody

value: Anti-Rad21, abcam, ab992

tag: protocol

value: Agarose


title: E14 embryonic stem cell 53hr30b

description: Library name: 53hr30b

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release


title: E14 embryonic stem cell 53hr30a

description: Library name: 53hr30a


title: Liver, Chow Vehicle 24 w, rep 1

description: Library name: 16174


title: EB, D3H2, Rev, Rad21

value: Reverse


title: E14 embryonic stem cell 51hr00c

description: Library name: 51hr00c


title: Cell line, MYAZ16_1e, Control, rep 3

description: Library name: TAR6417A52


title: EB, F2D3, Fwd, Rad21

value: Forward

value: Magnetic


title: E14 embryonic stem cell 51hr00b

description: Library name: 51hr00b


title: Liver, Semaglutide 24 w, rep 2

description: Library name: 16192

value: Semaglutide


title: RT-Stop Profiling, RNA oligo library, GTP, NaCl, rep1

description:
Library name: GTP_NaCl_rep1
Homo sapiens

value: Synthetic oligonucleotides

value: GTP

value: NaCl


title: Cell line, Myc310, Cys deprived, rep 1

description: Library name: TAR6417A25

value: Cys deprived


title: Cell line, MYAZ16_1e, Cys deprived, rep 1

description: Library name: TAR6417A13


title: Activated CD4+ T cells, donor D, biological replicate 1

description: Library name: Active_D

value: peripheral blood

value: CD4+ T cells

value: healthy donor

value: anti-CD3/anti-CD28/IL-2, 5 days

value: Donor D


title: E14 embryonic stem cell 50hr00b

description: Library name: 50hr00b


title: Naive CD4+ T cells, donor F, biological replicate 3

description: Library name: Naive_F

value: none (naive)

value: Donor F


title: Spleen, Rev C, Rad21

source_name: Spleen

value: Spleen

value: Erythroid

value: Anti-Rad21, abcam, ab992


title: EB, WT, Rad21

value: EB

value: WT


title: Activated HIV-1 infected CD4+ T cells, donor D, biological replicate 1

description: Library name: Inf_D

value: HIV-1 NL4-3 (MOI>1000), 5 days post-infection


title: E14 embryonic stem cell 50hr00a

description: Library name: 50hr00a

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release


title: Activated CD4+ T cells, donor F, biological replicate 3

description: Library name: Active_F


title: Cell line, MYAZ16_1e, Control, rep 1

description: Library name: TAR6417A10

value: Control


title: Spleen, Rev A rep, Rad21

value: Reverse

value: Agarose


title: E14 embryonic stem cell 49hr00c

description: Library name: 49hr00c


title: Naive CD4+ T cells, donor E, biological replicate 2

description: Library name: Naive_E

value: peripheral blood

value: CD4+ T cells

value: healthy donor

value: Donor E


title: Cell line, MYAZ16_1e, Cys deprived, rep 3

description: Library name: TAR6417A15

value: Cys deprived


title: EB, D3F3 rep Fwd, Rad21

value: Forward


title: Cell line, MYAZ16_1e, Cys deprived, rep 2

description: Library name: TAR6417A14


title: Spleen, Rev A, Rad21

value: Spleen

value: Erythroid

value: Magnetic


title: E14 embryonic stem cell 51hr00a

description: Library name: 51hr00a


title: Cell line, MYAZ12_3i_NDI1, Control, rep 3

description: Library name: TAR6417A9


title: Cell line, MYAZ12_3i_NDI1, Control, rep 2

description: Library name: TAR6417A8


title: E14 embryonic stem cell 49hr00a

description: Library name: 49hr00a


title: a549 cells,si-DLX6,1

city: JIANGSU

first: J

last: ff

address: JIANGSU NANJING

institute: Jiangsu Cancer Hospital

description:
Library name: Sample 3
HR99SEQ1_Si
processed data.xls

data_processing:
CLC Geomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CRCh38
Supplementary files format and content: FPKM values for each Sample

growth_protocol: a549 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trozol.1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: a549 cells were transfected with si-control or si-DLX6 RNA

value: Human Non-Small Cell Lung Cancer Cells

value: DLX6 knockdown

value: adipogenic differentiation


title: Spleen, Fwd C, Rad21

value: Anti-Rad21, abcam, ab992


title: a549 cells,si-control,1

description:
Library name: Sample 1
HR99_NC_1
processed data.xls

value: WT


title: Cell line, MYAZ12_3i_NDI1, Control, rep 1

description: Library name: TAR6417A7

value: Control


title: E14 embryonic stem cell 48hr00b

description: Library name: 48hr00b

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release


title: E14 embryonic stem cell 48hr00c

description: Library name: 48hr00c


title: E14 embryonic stem cell 50hr00c

description: Library name: 50hr00c


title: Activated CD4+ T cells, donor E, biological replicate 2

description: Library name: Active_E

value: peripheral blood

value: CD4+ T cells

value: anti-CD3/anti-CD28/IL-2, 5 days


title: E14 embryonic stem cell 48hr00a

description: Library name: 48hr00a


title: Cell line, MYAZ16_1e, Control, rep 2

description: Library name: TAR6417A11


title: CD11b+ cDC2, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep3

city: MADRID

first: Ignacio

last: Heras-Murillo

state: MADRID

address: c/Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contamination was removed from reads using Cutadapt v1.7.1.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.3.1.
Data were then processed with a pipeline that used Bioconductor package LIMMA for normalization (TMM method) and differential expression analysis.
Assembly: GRCm38 assembly, Ensembl genebuild 99
Supplementary files format and content: tab-delimited text files includes ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

extract_protocol:
Total RNA was harvested using the Rneasy Micro kit with DNAseI digestion (Qiagen) following the manufacturers’ instructions.
NEBNext Ultra II Directional RNA library Prep Kit for Illumina

treatment_protocol: 50 ug poly(I:C) LMW and 50 ug R848 or the control PBS were intravenously administered into 6-8-week old Uqcrqf/f or Itgax-Uqcrqf/f male or female mice and, after 1.5 hours, the spleen  was harvested and processed. To obtain a single cell suspension, spleens were incubated for 10 min at 37 °C with 0.25 mg/ml Liberase TL (Roche) and 50 μg/ml DNaseI (Sigma Aldrich),  squeezed through a 70 μm cell strainer (Corning) and spleen subjected for 5 min to Red Blood Cell Lysis Buffer (Sigma). Cells were then  subjected to positive selection of CD11c+ cells using CD11c MicroBeads UltraPure (Miltenyi Biotec), stained with fluorochrome-conjugeted antibodies and Fluorescence-Activated Cell Sorting (FACS) was used to collect cDC1s (MHCII+CD11c+CD8+CD11b-) and cDC2s (MHCII+CD11c+CD8-CD11b+) directly onto RLT buffer.

value: CD11b+ cDC2

value: Itgax-Uqcrqf/f


title: Cell line, MYAZ12_3i, Control, rep 3

description: Library name: TAR6417A21


title: Spleen, Fwd A, Rad21

value: Spleen

value: Forward

value: Agarose


title: Cell line, MYAZ12_3i, Control, rep 1

description: Library name: TAR6417A19


title: E14 embryonic stem cell 31hr30c

description: Library name: 31hr30c


title: Cell line, LM3, Control, rep 2

description: Library name: TAR6417A38


title: E14 embryonic stem cell 49hr00b

description: Library name: 49hr00b


title: a549 cells,si-control,2

description:
Library name: Sample 2
HR99_NC_2
processed data.xls

value: Human Non-Small Cell Lung Cancer Cells


title: wt3_R1R2

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: NG Capture-C
Based on Telenius et al. 2020 (bioRxiv)
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: mm9 or mm9 based custom genome
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: EB day 7

growth_protocol: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016) or the NuCapture-C protocol (Downes et al., 2020). A total of 3 - 10 x 106 ¬¬EB-derived CD71+ were processed per biological replicate and libraries of sufficient quality were used to capture .
5-10ug of each library was sheared using a Covaris S2. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a a Tapestation (Agilent Technologies). Libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs). Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each  library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation . The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

value: Erythroid

tag: selected cell surface marker


title: Cell line, LM3, Control, rep 3

description: Library name: TAR6417A39


title: E14 embryonic stem cell 31hr30a

description: Library name: 31hr30a


title: Cell line, LM3, Control, rep 1

description: Library name: TAR6417A37


title: E14 embryonic stem cell 31hr30b

description: Library name: 31hr30b


title: Naive CD4+ T cells, donor D, biological replicate 1

description: Library name: Naive_D

value: healthy donor

value: none (naive)

value: Donor D


title: wt3_HS3839


title: EB, D3F3 Fwd, Rad21

value: EB

value: Anti-Rad21, abcam, ab992

value: Magnetic


title: Spleen, Fwd B rep, Rad21


title: Spleen, Fwd A rep, Rad21


title: E14 embryonic stem cell 29hr30c

description: Library name: 29hr30c

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release


title: CD8+ cDC1, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep3

value: CD8+ cDC1


title: Spleen, Fwd B, Rad21


title: Cell line, MYAZ6_6g, Control, rep 2

description: Library name: TAR6417A17

value: Control


title: Cell line, MYAZ12_3i, Control, rep 2

description: Library name: TAR6417A53


title: wt2_R1R2


title: E14 embryonic stem cell 29hr30b

description: Library name: 29hr30b


title: CD8+ cDC1, Itgax-Uqcrqf/f, PBS, rep3

value: Itgax-Uqcrqf/f

value: PBS


title: Cell line, LM1, Cys deprived, rep 3

description: Library name: TAR6417A33

value: Cys deprived


title: E14 embryonic stem cell 27hr30c

description: Library name: 27hr30c


title: Cell line, LM2, Control, rep 2

description: Library name: TAR6417A35


title: wt2_HS4448


title: wt2_HS3839


title: CD11b+ cDC2, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep2

value: Spleen

value: CD11b+ cDC2


title: CD11b+ cDC2, Itgax-Uqcrqf/f, PBS, rep3


title: CD8+ cDC1, Uqcrqf/f, polyI:C+R848, 1.5h, rep3

value: Uqcrqf/f


title: a549 cells,si-DLX6,2

description:
Library name: Sample 4
HR99SEQ2_Si
processed data.xls

value: Human Non-Small Cell Lung Cancer Cells

value: DLX6 knockdown

value: adipogenic differentiation


title: CD8+ cDC1, Uqcrqf/f, PBS, rep3


title: wt1_R1R2

value: Erythroid


title: E14 embryonic stem cell 27hr30b

description: Library name: 27hr30b


title: Cell line, LM1, Cys deprived, rep 2

description: Library name: TAR6417A32


title: E14 embryonic stem cell 27hr30a

description: Library name: 27hr30a


title: CD11b+ cDC2, Itgax-Uqcrqf/f, PBS, rep2


title: wt1_HS4448


title: CD11b+ cDC2, Uqcrqf/f, polyI:C+R848, 1.5h, rep3


title: CD11b+ cDC2, Uqcrqf/f, polyI:C+R848, 1.5h, rep2


title: E14 embryonic stem cell 26hr30a

description: Library name: 26hr30a


title: wt3_HS4448


title: CD8+ cDC1, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep2


title: CD11b+ cDC2, Uqcrqf/f, PBS, rep3


title: Cell line, LM1, Control, rep 1

description: Library name: TAR6417A28


title: F2G6_R1R2_HS3839_Rev


title: E14 embryonic stem cell 25hr30c

description: Library name: 25hr30c


title: F2D3_R1R2_Fwd


title: E14 embryonic stem cell 29hr30a

description: Library name: 29hr30a


title: CD8+ cDC1, Itgax-Uqcrqf/f, PBS, rep2


title: Cell line, LM3_LM, Control, rep 3

description: Library name: TAR6417A51


title: F2D3_HS4448_Fwd


title: E14 embryonic stem cell 26hr30b

description: Library name: 26hr30b


title: CD8+ cDC1, Uqcrqf/f, polyI:C+R848, 1.5h, rep2


title: Cell line, LM2, Control, rep 1

description: Library name: TAR6417A34


title: CD11b+ cDC2, Uqcrqf/f, PBS, rep2


title: Cell line, LM1, Control, rep 2

description: Library name: TAR6417A29


title: F2G6_HS4448_Rev


title: Cell line, LM3_LM, Control, rep 1

description: Library name: TAR6417A49


title: D3H2_R1R2_Rev


title: Cell line, LM2_LM, Control, rep 3

description: Library name: TAR6417A48


title: CD11b+ cDC2, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep1


title: E14 embryonic stem cell 26hr30c

description: Library name: 26hr30c


title: E14 embryonic stem cell 25hr30b

description: Library name: 25hr30b


title: Cell line, LM2, Control, rep 3

description: Library name: TAR6417A36


title: D3H2_HS4448_Rev


title: D3F3_R1R2_Fwd


title: wt1_HS3839


title: Cell line, LM1, Cys deprived, rep 1

description: Library name: TAR6417A31


title: Cell line, LM1, Control, rep 3

description: Library name: TAR6417A30


title: E14 embryonic stem cell 24hr30c

description: Library name: 24hr30c


title: D3F3_HS4448_Fwd


title: CD8+ cDC1, Itgax-Uqcrqf/f, polyI:C+R848, 1.5h, rep1


title: CD11b+ cDC2, Uqcrqf/f, PBS, rep1


title: E14 embryonic stem cell 24hr30b

description: Library name: 24hr30b


title: Cell line, LM1_LM, Cys deprived, rep 3

description: Library name: TAR6417A45


title: D3F3_HS3839_Fwd


title: Cell line, LM1_LM, Cys deprived, rep 2

description: Library name: TAR6417A44


title: E14 embryonic stem cell 25hr00c

description: Library name: 25hr00c


title: D2H3_R1R2_Fwd


title: CD8+ cDC1, Uqcrqf/f, polyI:C+R848, 1.5h, rep1


title: Cell line, LM1_LM, Cys deprived, rep 1

description: Library name: TAR6417A43


title: Cell line, LM3_LM, Control, rep 2

description: Library name: TAR6417A50


title: F2D3_HS3839_Fwd


title: Cell line, LM2_LM, Control, rep 1

description: Library name: TAR6417A46


title: E14 embryonic stem cell 25hr30a

description: Library name: 25hr30a


title: MEV_80.9_Subway (Valencia)

city: Barcelona

first: Benjamin

last: Piña

address: Jordi Girona, 18

department: Environmental Chemistry

institute: IDAEA-CSIC

description: Library name: ABA38005

data_processing:
Image analysis, base calling, and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA software. More than 90% of the obtained reads mapped properly to the reference genome.
Assembly: Seqeucnes mapped to bwa.drerio.GRCz11 assembly
Supplementary files format and content: An xlsx file with two sheets: DB:  containing id_gene, gene_name, gene_type, and counts per library (a 25433x35 dataset). QC: Quality control of the sequences plus some extra description of the samples

organism: Danio rerio

source_name: 96-120 hpf embryo

growth_protocol: Adult zebrafish (Danio rerio) were maintained in fish water (FW, reverse-osmosis purified water containing 90 μg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4, pH 6.5) at 28 ± 1°C under a 12h:12h light:dark photoperiod. Zebrafish embryos were obtained by natural mating, collected embryos were maintained until 96 hpf (hours post-fertilization) in embryonic water (EW,  FW without added CaSO4) inside an incubator at 28°C (12:12 light:dark photoperiod).

extract_protocol:
Organic molecular compounds were  extracted from DGI filter a with a 10 mL mixture of dichloromethane: methanol (2:1 v/v) has been already described (Ricarte et al., 2025). Extracts were finally resuspended in methanol and stored at -20ºC.
RNA isolation, library preparation and RNA sequencing Total RNA was isolated from the pools of 10 zebrafish eleutheroembryos using TRizol (Invitrogen Life Technologies, Carlsbad, CA, USA) as described by the manufacturer. Extracted RNA was reconstituted in RNase-free water and assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies). Three high-quality RNA biological replicates per condition were sent for sequencing to the National Center for Genomic Analysis (CNAG, Barcelona, Spain). In all cases, RNA concentrations ranged between 50-200 ng·µL-1, free of DNA and with RNA integrity number (RIN) > 8.  Libraries for RNA-Seq were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500 ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to ensure the strand specificity. The blunt-ended double-stranded cDNA was 3´adenylated and Illumina indexed adapters (Illumina) were added by ligation. The ligation product was enriched through 15 PCR cycles, and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.  Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2x76bp. We generated on average 40 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina) following the manufacturer’s protocol.

treatment_protocol: Zebrafish exposure experiments followed the OECD Test Guideline 236 for zebrafish embryos, but limiting exposures to 24h, from 96 hpf to 120 hpf, with three replicas of ten embryos for each sample extract.

value: 96-120 hpf embryo

value: wt

value: NDGI80 rep 2


title: CD8+ cDC1, Uqcrqf/f, PBS, rep2


title: CD8+ cDC1, Uqcrqf/f, PBS, rep1


title: Cell line, LM1_LM, Control, rep 1

description: Library name: TAR6417A40


title: Cell line, LM1_LM, Control, rep 2

description: Library name: TAR6417A41


title: CD11b+ cDC2, Uqcrqf/f, polyI:C+R848, 1.5h, rep1


title: Jmjd1cWT 2h Rep3

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

description: Library name: N1390_WT_2h

data_processing:
Raw sequencing reads were aligned to mouse mm10 genome using STAR aligner
Assembly: mm10
Supplementary files format and content: gene_count_*.csv

extract_protocol:
Splenic FO B cells were sorted and stimulated with anti-IgM for 2 hours, then lysed in TRIzol for RNA extraction.
mRNA was isolated (10 to 50 ng) using the NEBNext poly(A) mRNA Magnetic Isolate Module and converted into libraries with the NEBNext Ultra RNA Library Prep kit (New England Biolabs).

value: FO B cells

value: primary cells

value: Jmjd1c WT

value: anti-IgM 2h


title: MEV_80.10_Subway (Valencia)

description: Library name: ABA38007

value: NDGI80 rep 3


title: APBW54.3_Airport (Barcelona, warm season)

description: Library name: ABA35108


title: f-4_WT_ATAC_FL

description: Genome-wide library of tagmented fragments

data_processing:
Trimming: trimgalore --stringency 2
Mapping : bowtie2
samtools view chr11
Removing duplicates : samtools rmdup
Generating bigwig tracks: deeptools -bs 20 --normalizeUsingRPKM
Genome_build: mm9 or mm9 based custom genome
Supplementary_files_format_and_content: bigWig : (deeptools) bamCoverage converison of filtered fragments (duplicate-filtered fragments) from bam to bigwig,  (--binSize 20 --normalizeUsingRPKM)

source_name: Fetal liver culture

growth_protocol: EB: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker. FL: E12.5 mouse fetal liver were dissected and cultured in StemPro medium (Invitrogen) supplemented with Epo (1 U/mL; Janssen, PL 00242/029), SCF (50 ng/mL; Peprotech, 250-03), dexamethasone (1 μM; Hameln, DEXA3.3) and 1× L-Glutamine (Invitrogen) for 6–7d to expand the erythroid progenitor population. If necessary cells were frozen at day 4 and after thawing expanded for a further 2-4 days. Cells were selected for Ter119.

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-75000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

tag: growth protocol

value: FL


title: Jmjd1cWT 2h Rep2

description: Library name: N1360_WT_2h


title: E14 embryonic stem cell 24hr30a

description: Library name: 24hr30a

value: embryonic stem cell

value: E14 embryonic stem cell

value: induction of 2i-release


title: E14 embryonic stem cell 25hr00a

description: Library name: 25hr00a


title: E14 embryonic stem cell 25hr00b

description: Library name: 25hr00b


title: D2H3_HS3839_Fwd


title: Alb-Cre; Fpn flox/flox, rep 1

city: Jeonju

first: Chang Yeob

last: Han

address: 20, Geonji-ro, Deokjin-gu

department: School of Pharmacy

country: South Korea

institute: Jeonbuk National University

description: Library name: LKO-HFD_1

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Assembly: mm10
Supplementary files format and content: Expression_Profile.mm10.gene.txt
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Liver tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

value: liver

tag: strain

tag: Sex

value: male

value: LKO (hepatocyte-specific Fpn KO)

value: Batch 1


title: Jmjd1cKO 2h Rep3

description: Library name: N1399_KO_2h

value: Spleen

value: Jmjd1c KO


title: g7_WT_FL_ATAC

value: Erythroid


title: g-4_Rev_FL_ATAC


title: TRBC28.9_Traffic road (Barcelona, cold season)

description: Library name: ABA37620

value: 96-120 hpf embryo

value: wt

value: NDGI28 rep 4


title: Jmjd1cKO 2h Rep2

description: Library name: N1378_KO_2h

value: FO B cells

value: primary cells


title: g-1_Rev_FL_ATAC


title: APBC48.1_Airport (Barcelona, cold season)

description: Library name: ABA35107


title: Cell line, LM2_LM, Control, rep 2

description: Library name: TAR6417A47

value: Control


title: Fpn flox/flox, rep 2

description: Library name: Litter-HFD_4

value: WT (Fpn f/f)


title: D2H3_HS4448_Fwd


title: MEV_80.8_Subway (Valencia)

description: Library name: ABA38004

value: NDGI80 rep 1


title: Jmjd1cWT 0h Rep2

description: Library name: N1360_WT_0h

value: Jmjd1c WT

value: anti-IgM 0h


title: CD11b+ cDC2,Itgax-Uqcrqf/f, PBS, rep1

value: CD11b+ cDC2

value: Itgax-Uqcrqf/f

value: PBS


title: 5-4_Fwd_FL_ATAC

value: FL


title: TRBC30.2_Traffic road (Barcelona, cold season)

description: Library name: ABA35105


title: D15 enriched NK cells_GEX_library 2

city: New York

first: Isaac

last: Jensen

state: NY

address: 701 West 168th St

institute: Columbia University

description:
Library name: DI03B_GEX
10x Genomics

data_processing:
ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo with default parameters.
Assembly: GRCm38
Supplementary files format and content: matrix files
Supplementary files format and content: tsv files

extract_protocol:
C57Bl/6 splenic NK cells were enriched by Miltenyi NK cell negative selection kit. All samples were stained with TotalSeq-C DNA Barcoded CD45.1 and CD45.2 antibodies. Each cohort composed 4 adults and 4 infants each individual mouse was labeled with TotalSeq-C DNA-Barcoded hashtags 1-4 (for adult or infant). Cells were washed and equilabrated and combined. Combined cell pool was then labeled with TotalSeq-C cocktail v1.0
CITE libraries were constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics) with a 5’ Feature Barcode Kit (10x Genomics) for antibody-derived tag (ADT) amplification according to the manufacturer’s instructions. The ADT library pool and scRNA-seq library pool were each sequenced on one lane of an S4 flow cell on an Illumina NovaSeq 6000 (~2.5 billion 2x100 bp reads per lane). Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto v0.46.2 in “BUS” mode

value: Spleen

value: NK cells

value: Mixed Sample (adult/infant) 15DPI


title: D3H2_HS3839_Rev

value: Erythroid


title: Alb-Cre; Fpn flox/flox, rep 3

description: Library name: LKO-HFD_8

value: liver

value: male

value: LKO (hepatocyte-specific Fpn KO)

value: Batch 1


title: Alb-Cre; Fpn flox/flox, rep 2

description: Library name: LKO-HFD_3


title: Jmjd1cWT 0h Rep1

description: Library name: N1352_WT_0h

value: FO B cells

value: primary cells


title: Jmjd1cKO 0h Rep3

description: Library name: N1399_KO_0h

value: Jmjd1c KO


title: APBC44.1_Airport (Barcelona, cold season)

description: Library name: ABA35106

value: 96-120 hpf embryo

value: wt


title: i-2_Fwd_FL_ATAC


title: TRBC28.7_Traffic road (Barcelona, cold season)

description: Library name: ABA37617

value: NDGI28 rep 2


title: EB_ATAC_wt_C

value: EB


title: Fpn flox/flox, rep 3

description: Library name: Litter-HFD_7

value: WT (Fpn f/f)


title: Jmjd1cKO 2h Rep1

description: Library name: N1350_KO_2h

value: anti-IgM 2h


title: TRBC26.8_Traffic road (Barcelona, cold season)

description: Library name: ABA37614

value: NDGI26 rep 3


title: Jmjd1cKO 0h Rep2

description: Library name: N1378_KO_0h

value: Spleen

value: anti-IgM 0h


title: D15 enriched NK cells_GEX_library 1

description:
Library name: DI03A_GEX
10x Genomics

value: NK cells

value: Mixed Sample (adult/infant) 15DPI


title: f-3_Rev_FL_ATAC

value: Erythroid

value: FL


title: Jmjd1cWT 2h Rep1

description: Library name: N1352_WT_2h

value: Jmjd1c WT


title: TRBC28.8_Traffic road (Barcelona, cold season)

description: Library name: ABA37618

value: NDGI28 rep 3


title: 5-2_wt_FL_ATAC


title: Jmjd1cWT 0h Rep3

description: Library name: N1390_WT_0h

value: FO B cells

value: primary cells


title: Fpn flox/flox, rep 1

description: Library name: Litter-HFD_2

value: liver

value: male

value: Batch 1


title: Jmjd1cKO 0h Rep1

description: Library name: N1350_KO_0h

value: Jmjd1c KO


title: TRBC28.3_Traffic road (Barcelona, cold season)

description: Library name: ABA35102

value: 96-120 hpf embryo

value: wt

value: NDGI28 rep 1


title: HABC38.9_Harbour (Barcelona, cold season)

description: Library name: ABA37632

value: NDGI38 rep 4


title: 5-1_Fwd_FL_ATAC


title: D7 enriched NK cells_ADT_library 1

description:
Library name: DI02A_ADT
10x Genomics

data_processing:
ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo with default parameters.
Assembly: GRCm38
Supplementary files format and content: matrix files
Supplementary files format and content: tsv files
Library strategy: CITE-seq

molecule: protein

value: Spleen

value: Mixed Sample (adult/infant) 7DPI


title: Cell line, LM1_LM, Control, rep 3

description: Library name: TAR6417A42

value: Control


title: D7 enriched NK cells_ADT_library 2

description:
Library name: DI02B_ADT
10x Genomics

value: NK cells


title: HABC38.7_Harbour (Barcelona, cold season)

description: Library name: ABA37630

value: NDGI38 rep 2


title: D15 enriched NK cells_ADT_library 2

description:
Library name: DI03B_ADT
10x Genomics

value: Mixed Sample (adult/infant) 15DPI


title: D7 enriched NK cells_GEX_library 2

description:
Library name: DI02B_GEX
10x Genomics


title: WT3_2h_IgG

description: Library name: WT3_2h_IgG

data_processing:
Reads were aligned to the mm10, and peaks were called using SEACR in stringent mode with IgG controls. DESeq2 was used for normalization and differential peak analysis. Pre-ranked GSEA was performed with clusterProfiler using KEGG and Reactome databases, and visualized with ComplexHeatmap, with p-values adjusted by Benjamini-Hochberg
Assembly: mm10
Library strategy: CUT&Tag

extract_protocol:
Sorted FO B cells were stimulated with anti-IgM for 2 h, washed, bound to ConA-coated beads (Bangs Laboratories), and incubated overnight with anti-H3K36me1 (Abcam), followed by anti-rabbit IgG secondary antibodies (Antibodies Online). Samples were incubated with the pA-Tn5 adapter complex (Epicypher) for 1 h at room temperature and subjected to tagmentation at 37°C.
DNA was extracted, PCR-amplified, and sequenced on an Illumina NextSeq 500 using the NextSeq 500/550 v2 kit.

value: Jmjd1c WT

value: anti-IgM 2h


title: TRBC26.7_Traffic road (Barcelona, cold season)

description: Library name: ABA37613

value: NDGI26 rep 2


title: HABC36.10_Harbour (Barcelona, cold season)

description: Library name: ABA38006

value: NDGI36 rep 4


title: CD8+ cDC1, Itgax-Uqcrqf/f, PBS, rep1

value: CD8+ cDC1

value: Itgax-Uqcrqf/f

value: PBS


title: D15 enriched NK cells_ADT_library 1

description:
Library name: DI03A_ADT
10x Genomics

value: primary cells


title: HABC38.8_Harbour (Barcelona, cold season)

description: Library name: ABA37631

value: 96-120 hpf embryo

value: wt

value: NDGI38 rep 3


title: TRBC26.3_Traffic road (Barcelona, cold season)

description: Library name: ABA35101

value: NDGI26 rep 1


title: D3F3_EB_Fwd_ATAC

value: Erythroid

value: EB


title: D2D6_Rev_EB_ATAC


title: WT3_2h_H3K9me2

description: Library name: WT3_2h_H3K9me2

value: Spleen

value: FO B cells


title: D0 enriched NK cells_ADT_library 1

description:
Library name: DI01A_ADT
10x Genomics

value: NK cells

value: Mixed Sample (adult/infant) uninfected


title: F2G6_Rev_ATAC_EB


title: TRBC26.9_Traffic road (Barcelona, cold season)

description: Library name: ABA37615

value: NDGI26 rep 4


title: D0 enriched NK cells_GEX_library 1

description:
Library name: DI01A_GEX
10x Genomics


title: WT1_2h_H3K9me2

description: Library name: WT1_2h_H3K9me2

value: Jmjd1c WT

value: anti-IgM 2h


title: D3H2_EB_Rev_ATAC


title: EB_ATAC_wt_B


title: D7 enriched NK cells_GEX_library 1

description:
Library name: DI02A_GEX
10x Genomics

value: Mixed Sample (adult/infant) 7DPI


title: D0 enriched NK cells_ADT_library 2

description:
Library name: DI01B_ADT
10x Genomics


title: aged mouse synovial cells

city: Guangzhou

first: Tao

last: Gui

address: Huangpu Ave

institute: Jinan University

description:
Library name: Sample 1
10x Genomics

data_processing:
Raw sequencing reads were processed to generate count matrices using the Cell Ranger pipeline (10X Genomics). Downstream analysis was performed using the Scanpy Python package (version 1.9.3). Principal component analysis (PCA) was performed on the integrated data using the top 30 principal components. Uniform Manifold Approximation and Projection (UMAP) was then used for dimensionality reduction and visualization of cell clusters. Cell clusters were identified using the Leiden algorithm with a resolution parameter of 0.5. Differentially expressed genes for each cluster were identified using the Wilcoxon rank-sum test. To investigate intercellular communication, we utilized the CellChat package (version 1.6.0). CellChat infers significant ligand-receptor interactions between cell populations based on gene expression data.
Assembly: GRCm38, mm10
Supplementary files format and content: Matrix files

source_name: synovial tissue

extract_protocol:
Primary synovial cells were isolated from the knee joints of 24‑month‑old wild‑type (WT) mice. The synovial tissues were carefully dissected, minced, and sequentially digested with 0.25% trypsin (Thermo Fisher, 25200072, USA) for 30 min, followed by type I collagenase (1 mg/mL, Thermo Fisher, 17100017, USA) for 45 min at 37 °C with constant agitation. The digestion was stopped by adding complete culture medium. The resulting cell suspension was filtered, centrifuged, and the pellet was resuspended in DMEM supplemented with 10% heat‑inactivated fetal bovine serum (FBS) and 1% penicillin–streptomycin (PS) for further use.
Library preparation was performed according to the manufacturer's instructions (Single Cell 3′ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel beads-in-emulsion (GEMs). The poly-A RNA from the cell lysate contained in each single GEM was reverse transcribed into cDNA, which incorporates an Illumina R1 primer sequence, a unique molecular identifier (UMI), and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and appropriately sized fragments were selected using SPRIselect reagent for subsequent library construction. During library construction, the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: synovial tissue

value: synovial cells

value: wild type


title: EB_ATAC_wt_A


title: F2D3_Fwd_EB_ATAC


title: HABC38.3_Harbour (Barcelona, cold season)

description: Library name: ABA35100

value: 96-120 hpf embryo

value: NDGI38 rep 1


title: WT1_2h_H3K9me1

description: Library name: WT1_2h_H3K9me1

value: primary cells


title: D15 enriched NK cells_ADT_library1

description:
Library name: DI002C_ADT
10x Genomics

extract_protocol:
C57Bl/6 splenic CD8 T cells were enriched by STEMCELL CD8 T cell negative selection kit. All samples were stained with TotalSeq-C DNA Barcoded CD45.1, CD45.2, Thy1.1, Thy1.2 antibodies. Individual mouse were labeled with TotalSeq-C DNA-Barcoded hashtags 1-5 (for adult or infant). Cells were washed and equilabrated and combined. Combined cell pool was then labeled with TotalSeq-C DNA-Barcoded KLRG1, CD127, CD4, CD8a.
CITE libraries were constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics) with a 5’ Feature Barcode Kit (10x Genomics) for antibody-derived tag (ADT) amplification according to the manufacturer’s instructions. The ADT library pool and scRNA-seq library pool were each sequenced on one lane of an S4 flow cell on an Illumina NovaSeq 6000 (~2.5 billion 2x100 bp reads per lane). Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto v0.46.2 in “BUS” mode

value: CD8 T cells


title: D0 enriched NK cells_GEX_library 2

description:
Library name: DI01B_GEX
10x Genomics


title: D7 enriched NK cells_ADT_library2

description:
Library name: DI002B_ADT
10x Genomics


title: D15 enriched NK cells_GEX_library1

description:
Library name: DI002C_GEX
10x Genomics


title: WT3_2h_H3K36me1

description: Library name: WT3_2h_H3K36me1


title: CTCF_ChIP_EB_Fwd_rep2_F2D3

description: Genome-wide library of Immunoprecipitated fragments

extract_protocol:
For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 5-107 cells were lysed by incubation on ice in lysis buffer for 10 minutes. Chromatin was sonicated using the Bioruptor or Bioruptor pico to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 10 min, 4 ºC) and soluble material was diluted to 2 ml with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for CTCF (10 µl 07-729; Millipore) overnight. Chromatin incubation with Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 1 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

value: Erythroid

tag: selected surface marker


title: CTCF_ChIP_EB_Fwd_rep1_D2H3

value: EB


title: KO3_2h_IgG

description: Library name: KO3_2h_IgG

value: Spleen

value: Jmjd1c KO


title: KO3_2h_H3K9me2

description: Library name: KO3_2h_H3K9me2

value: FO B cells


title: HABC36.7_Harbour (Barcelona, cold season)

description: Library name: ABA37627

value: wt

value: NDGI36 rep 2


title: D7 enriched NK cells_GEX_library2

description:
Library name: DI002B_GEX
10x Genomics


title: CTCF_ChIP_EB_WT_rep2


title: CTCF_ChIP_EB_Rev_rep1_D2D6


title: WT1_2h_H3K36me1

description: Library name: WT1_2h_H3K36me1

value: Jmjd1c WT


title: CT__11.2_Control (Vehicle)

description: Library name: ABA37599

value: none (vehicle) rep5


title: D2H3_Fwd_EB_ATAC


title: HABC36.2_Harbour (Barcelona, cold season)

description: Library name: ABA35099

value: NDGI36 rep 1


title: D7 enriched NK cells_ADT_library1

description:
Library name: DI002A_ADT
10x Genomics

value: Mixed Sample (adult/infant) 7DPI


title: CT__11.1_Control (Vehicle)

description: Library name: ABA37598

value: none (vehicle) rep4


title: HABC36.8_Harbour (Barcelona, cold season)

description: Library name: ABA37628

value: NDGI36 rep 3


title: KO3_2h_H3K9me1

description: Library name: KO3_2h_H3K9me1

value: anti-IgM 2h


title: CTCF_ChIP_EB_WT_rep1


title: KO3_2h_H3K36me1

description: Library name: KO3_2h_H3K36me1


title: WT1_2h_IgG

description: Library name: WT1_2h_IgG


title: CTCF_ChIP_FL_Rev_rep2_g-1

value: FL


title: CTCF_ChIP_EB_Rev_rep2_D3H2


title: D0 enriched NK cells_ADT_library1

description:
Library name: DI001_ADT
10x Genomics

value: primary cells

value: Mixed Sample (adult/infant) uninfected


title: CT__05.P_Control (Vehicle)

description: Library name: ABA35088

value: 96-120 hpf embryo

value: none (vehicle) rep2


title: CTCF_ChIP_FL_Rev_rep3_g-4

value: Erythroid


title: D0 enriched NK cells_GEX_library1

description:
Library name: DI001_GEX
10x Genomics

value: Spleen

value: CD8 T cells


title: KO2_2h_H3K9me2

description: Library name: KO2_2h_H3K9me2

value: FO B cells

value: Jmjd1c KO


title: Sensitive clinical isolate-TV1038, bio rep 2

status: Public on Apr 15 2026

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

description: Library name: TV1038-2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Trichomonas_vaginalis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: txid5722
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample

organism: Trichomonas vaginalis

source_name: trichomonad

growth_protocol: All T. vaginalis isolates were grown under anaerobic conditions using Diamond’s Trypticase-Yeast-Maltose (TYM) media.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions.
Pre-made library -- no library preparation performed

value: trichomonad

tag: phenotype

value: Sensitive

tag: group

value: clinical isolate


title: CT__04.P_Control (Vehicle)

description: Library name: ABA35086

tag: tissue

value: wt

value: none (vehicle) rep1


title: WT3_2h_H3K9me1

description: Library name: WT3_2h_H3K9me1

tag: cell line

value: Jmjd1c WT


title: CTCF_ChIP_FL_Rev_rep1_f3

tag: cell type


title: KO2_2h_H3K9me1

description: Library name: KO2_2h_H3K9me1

tag: genotype

value: anti-IgM 2h


title: ChiP Brn1-PK in HU60 in rad50delta cells

city: Montpellier

first: Mégane

last: Da Mota

address: 141 rue de la cardonille

country: France

institute: CNRS

data_processing:
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Assembly: sacCer3
Supplementary files format and content: Biwgiw files correspond to a ratio relative to Input or relative to G1 (gDNA)

organism: Saccharomyces cerevisiae

source_name: hydroxyurea 200mM fo 60min

growth_protocol: S. cerevisiae cells were grown in YPAD and released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea) for 60 min, or 90min or 120min

extract_protocol:
Yeast genomic DNA was prepared using standard protocol
For single-end experiment : Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols Sequencer: HiSeq4000 or for paired-end experiments : the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sequencer : NovaSeq 6000. Reads lenght: 50.

value: yeast cells

tag: treatment

value: S + HU 60


title: CTCF_ChIP_FL_Fwd_rep3_5-4

value: FL


title: KO2_2h_H3K36me1

description: Library name: KO2_2h_H3K36me1

value: primary cells


title: ChiP Brn1-PK in HU60 in WT cells


title: D7 enriched NK cells_GEX_library1

description:
Library name: DI02A_GEX
10x Genomics

value: Mixed Sample (adult/infant) 7DPI


title: BL__03.1_Control (Mock filter)

description: Library name: ABA35092

value: 96-120 hpf embryo

value: Mock filter rep2


title: All joint cells from rat with meniscus injury treated by 4PPBP for 2 weeks

first: Chang

middle: Hun

last: Lee

description:
Library name: sample2
10X Genomics

data_processing:
The scRNA-seq analysis was conducted in R (version 4.4.2) with a rigorously developed pipeline integrating multiple analytical tools. Raw count matrices were imported from H5 files, from which the Seurat objects were generated separately for each sample using Seurat (version 5.2.1). Quality control steps entailed filtering out cells with fewer than 200 or more than 6,000 detected features and with greater than 20% mitochondrial gene expression. Gene expression data were then globally normalized, and the top 2,000 variable genes were identified using a variance‐stabilizing transformation. Scaled data were subjected to principal component analysis (PCA). The number of principal components used in downstream analyses was determined via the elbow plot by identifying the inflection point at which additional principal components contributed only marginally to the variance. Doublet detection was performed using DoubletFinder (version 2.0.4) with an estimated doublet rate of approximately 7.5%, and only cells classified as singlets were retained. Following normalization and filtering, control and OP datasets were merged and batch‐corrected using Harmony (version 1.2.3) with the original sample identifier as the grouping variable. Clustering was conducted based on the optimal number of PCA components (as determined by the elbow plot) and subsequently visualized using both UMAP, produced via ggplot2 (version 3.5.1) and patchwork (version 1.3.0). Cell type annotation was initially performed via differential expression analysis using Seurat’s FindAllMarkers function (with a log₂ fold-change cutoff of 0.25 and a minimum percentage threshold of 25% for gene expression).
Supplementary files format and content: H5 files.

organism: Rattus norvegicus

source_name: knee joint

extract_protocol:
rats were euthanized by carbon dioxide inhalation at each time point. At 2 weeks post-op, cells were isolated from whole knee joint tissues, including synovium, ligament, infrapatellar fat pad, cartilage, and medial meniscus. The harvested tissues were minced, followed by 5 mg/ml collagenase I and IV in serum-free DMEM for 2.5 h at 37°. After enzymatic digestion, an equal volume of 10% FBS in DMEM was added to neutralize the enzymes. Suspended cells were transferred to a 100 µm strainer, centrifuged at 1,600 rpm, and rinsed 3 three times using PBS with 10% FBS. All cells from three animals per group were combined for scRNA-seq analysis.
Library construction and scRNA-seq were performed on the 10XGenomics platform.

value: knee joint

value: all joint cells

value: 4PPBP bioglue


title: BL__02.1_Control (Mock filter)

description: Library name: ABA35091

value: Mock filter rep1


title: ChiP Brn1-PK in G1 in WT cells

source_name: alpha-factor synchronization


title: All joint cells from rat with meniscus injury for 2 weeks

description:
Library name: sample1
10X Genomics


title: HABC32.3_Harbour (Barcelona, cold season)

description: Library name: ABA35098


title: BL__03.3_Control (Mock filter)

description: Library name: ABA35094

value: Mock filter rep3


title: sperm_3

status: Public on Apr 13 2026

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

institute: UPenn Perelman SOM and CHOP

description: Library name: sperm_3

data_processing:
RNA-sequencing Analysis. To exclude low-complexity libraries, single embryos were required to exhibit detectable expression in a minimum number of genes. Thresholds were selected separately for each developmental stage and dataset based on inspection of the distribution of detected genes per sample, using the inflection point preceding the major drop-off in library complexity. Stage-specific cutoffs ranged from 6000-8000 detected genes. Samples failing these criteria were excluded from downstream analyses. Raw gene-level counts were analyzed in R (v4.5.1) using DESeq2 (v1.48.2). Genes were retained if they achieved at least 2.5 counts per million (CPM) in at least 80% of samples within at least one treatment group. Genes failing these criteria were removed from downstream analysis. Differential expression was modeled using a negative binomial generalized linear model with batch (embryo collection date) as a variable and Wald tests were performed to assess differential expression between each treatment level and designated control group. Normalized counts and full differential expression statistics were exported for downstream analysis. Given the limited statistical power of single-embryo sequencing due to the nature of the experimental design, nominal p-values were used for candidate identification, while enrichment and pathway-level analyses incorporated multiple-testing correction.  Computational Analysis for REMORA-AGO. Raw FASTQ files were processed using an adaptation of the MARINE pipeline developed by the Yeo Lab. Adapter trimming and low-quality base removal were performed using Cutadapt, followed by per-sample quality assessment with FastQC. Trimmed reads were aligned to the Mus musculus reference genome (mm10) using STAR, retaining uniquely mapped reads for downstream analysis. Gene-level read quantification was performed using featureCounts. To detect RNA editing events, MARINE applied its internal A-to-I (A→G) editing identification module downstream of STAR alignment and filtered using the dbSNP database mm10 to remove any SNPs.  RNA editing quantification and normalization. Editing counts were aggregated by summing site-levels counts within each gene and genomic region (CDS, 3’UTR, or intron) for each sample. Region definitions and gene/region lengths were derived from the GENCODE mouse GTF (gencode.vM10). Transcript-level intervals were collapsed to gene-level unions by gene symbol. Intronic intervals were defined per gene as the gene body minus the union of annotated exons. For each sample, the number of RNA-seq alignments overlapping CDS, inferred 3’UTRs, or introns were quantified from genome-aligned BAM files using featureCounts in SAF mode, producing region-specific mapped-read denominators. Editing activity was normalized to region length and region-specific library depth by computing editing events per kilobase per million mapped reads (EPKM); EPKM=edit_counts×10^9/(〖mapped_reads〗_region×region_bp). The resulting gene-by-sample EPKM matrices for CDS, 3’UTR, and introns were used for downstream comparisons across experimental conditions.  Statistical identification of miRNA-directed RNA editing targets. To account for small differences in global editing activity across conditions given the nature of embryo microinjections, EPKM values were further normalized within each replicate by scaling to a total of one million, generating edits per million (EPM) values that represent the fraction of total editing attributable to each transcript. Per-gene RNA editing levels were quantified for each single embryo as editing events per million mapped reads (EPM). To stabilize variance and accommodate zero-inflated distributions, EPM values were transformed at the embryo level as log₂(EPM + 1). For each gene, the mean log₂(EPM + 1) was calculated separately across rABE_Ago embryos and rABE_Ago + miR-200c-3p embryos. The change in editing was defined as the difference in these means. Editing abundance was defined as the average of the two group means. These values were visualized in an MA-style plot to separate editing abundance from miR-200c-3p–induced editing shifts. Statistical significance was assessed per gene using an unpaired one-sided Wilcoxon rank-sum test comparing log₂(EPM+1) values between conditions. Genes were required to have data from at least three embryos per group to be tested. Given the limited power and inherent variability of single-embryo RNA-sequencing, nominal p-values were interpreted alongside effect size and reproducibility across embryos.
Assembly: MM10
Supplementary files format and content: xlsx spreadsheet with one tab per /comparison

source_name: 2-cell parthenote

growth_protocol: Male (8-12 weeks old) and female (5-7 weeks old) FVB/NJ mice were derived from breeders obtained from Jackson Laboratory (Strain #001800) and maintained in-house.  Mouse parthenogenesis and embryogenesis were performed as previously described9. Briefly, oocytes were isolated from superovulated females and activated to generate parthenotes using KSOM with 10 mM SrCl2, 4 mM EGTA, and 0.05 μg/mL cytochalasin B for 1 hour. In Vitro Fertilization was performed in HTF with 1 mM glutathione with capacitated sperm for 3 hours. Embryos were cultured in KSOM under standard conditions 37°C, 5% CO2, and 5% O2 until microinjection and to the indicated developmental stages. Detailed step-by-step procedures are available in Lee et al., STAR Protocols

extract_protocol:
For sperm RNA and embryo isolations for single embryo RNA-seq see Trigg and Conine et al. 2024
Small RNA sequencing from sperm was performed largely as previously described10. Briefly, total sperm RNA was isolated and size-selected for small RNAs. In contrast to the original protocol (18-40 nucleotides), libraries in this study were size-selected for 18-24 nucleotide fragments to enrich specifically for mature miRNAs. Libraries were prepared using a modified Illumina Tru-Seq small RNA library prep protocol and sequenced on an Illumina NextSeq 1000/2000 platform. Libraries were mapped and normalized to reads per million as described previously (Trigg and Conine 2024).  Single-embryo RNA-sequencing. Following microinjection, individual embryos were collected 28 hours (late 2-cell), 46 hours (4-cell), or 70 hours (compacted morula) post activation or fertilization in 5 μL of TCL buffer (Qiagen, Cat. No. 1070498) with 1% 2-mercaptoethanol. Samples were immediately placed in -80°C until all replicates were collected. Libraries were generated using the SMART-Seq protocol11. Briefly, lysed embryos were isolated using RNAClean-XP beads and polyadenylated RNA was reverse transcribed using Superscript II. cDNA was amplified and indexed using the Nextera XT kit and sequenced on an Illumina NextSeq 1000/2000 platform (paired-end 50 bp, ~5 million reads per sample). Reads were mapped against the Mus musculus (mm10) genome using RSEM.

treatment_protocol: Embryo Microinjection. Cytoplasmic microinjections were performed on parthenotes or embryos as described previously9, delivering ~53 fL of injection solution per embryo. For each experimental replicate, embryos were collected from ~5 females derived from one or two litters, pooled, and randomly assigned to all injection conditions to minimize litter-specific effects. Within each experimental day, all treatments groups were represented in parallel. Embryos were distributed to ensure approximately matched numbers per condition (typically ~8 embryos per group and embryonic stage per replicate), preventing confounding by collection date or maternal origin. At least 24 embryos per condition were collected across three independent biological replicates. In one experiment with high embryo yield and injection efficiency, sufficient embryos were obtained across two replicates to meet this threshold.

value: 2-cell parthenote


title: 102325_ago_only_2cell_4

description: Library name: 102325_ago_only_2cell_4


title: 102325_ago_only_2cell_5

description: Library name: 102325_ago_only_2cell_5


title: 102325_ago_only_2cell_22

description: Library name: 102325_ago_only_2cell_22


title: CTCF_ChIP_FL_Fwd_rep1_i2

value: Erythroid


title: 102325_ago_only_2cell_23

description: Library name: 102325_ago_only_2cell_23


title: 102325_ago_only_2cell_3

description: Library name: 102325_ago_only_2cell_3


title: 102325_ago_only_2cell_7

description: Library name: 102325_ago_only_2cell_7


title: Input

source_name: yeast cells

value: wild-type


title: KO2_2h_IgG

description: Library name: KO2_2h_IgG

value: Spleen

value: FO B cells

value: Jmjd1c KO


title: 102325_ago_only_2cell_21

description: Library name: 102325_ago_only_2cell_21


title: 102325_ago_only_2cell_17

description: Library name: 102325_ago_only_2cell_17


title: 102325_ago_only_2cell_9

description: Library name: 102325_ago_only_2cell_9


title: CT__07.P_Control (Vehicle)

description: Library name: ABA35090

value: wt

value: none (vehicle) rep3


title: 102325_ago_only_2cell_8

description: Library name: 102325_ago_only_2cell_8


title: 102325_ago_only_2cell_20

description: Library name: 102325_ago_only_2cell_20


title: 102325_ago_only_2cell_6

description: Library name: 102325_ago_only_2cell_6


title: 102325_ago_only_2cell_13

description: Library name: 102325_ago_only_2cell_13


title: sperm_2

description: Library name: sperm_2


title: 102325_ago_only_2cell_19

description: Library name: 102325_ago_only_2cell_19


title: 102325_ago_only_2cell_16

description: Library name: 102325_ago_only_2cell_16


title: 102325_ago_only_2cell_15

description: Library name: 102325_ago_only_2cell_15


title: CTCF_ChIP_FL_Fwd_rep2_5-1

value: FL


title: 102325_ago_only_2cell_12

description: Library name: 102325_ago_only_2cell_12


title: 102325_ago_only_2cell_10

description: Library name: 102325_ago_only_2cell_10


title: 102325_ago_only_2cell_14

description: Library name: 102325_ago_only_2cell_14


title: 102325_ago_only_2cell_11

description: Library name: 102325_ago_only_2cell_11


title: 102325_ago_mir465_2cell_8

description: Library name: 102325_ago_mir465_2cell_8


title: 102325_ago_only_2cell_1

description: Library name: 102325_ago_only_2cell_1


title: 102325_ago_mir465_2cell_7

description: Library name: 102325_ago_mir465_2cell_7


title: 102325_ago_mir465_2cell_4

description: Library name: 102325_ago_mir465_2cell_4


title: sperm_4

description: Library name: sperm_4


title: 102325_ago_mir465_2cell_9

description: Library name: 102325_ago_mir465_2cell_9


title: 102325_ago_mir465_2cell_5

description: Library name: 102325_ago_mir465_2cell_5


title: 102325_ago_mir465_2cell_6

description: Library name: 102325_ago_mir465_2cell_6


title: 102325_ago_mir465_2cell_29

description: Library name: 102325_ago_mir465_2cell_29


title: 102325_ago_only_2cell_2

description: Library name: 102325_ago_only_2cell_2


title: 102325_ago_mir465_2cell_24

description: Library name: 102325_ago_mir465_2cell_24


title: 102325_ago_mir465_2cell_20

description: Library name: 102325_ago_mir465_2cell_20


title: sperm_1

description: Library name: sperm_1


title: 102325_ago_mir465_2cell_25

description: Library name: 102325_ago_mir465_2cell_25


title: 102325_ago_mir465_2cell_21

description: Library name: 102325_ago_mir465_2cell_21


title: 102325_ago_mir465_2cell_23

description: Library name: 102325_ago_mir465_2cell_23


title: 102325_ago_mir465_2cell_22

description: Library name: 102325_ago_mir465_2cell_22


title: 102325_ago_mir465_2cell_2

description: Library name: 102325_ago_mir465_2cell_2


title: 102325_ago_mir465_2cell_28

description: Library name: 102325_ago_mir465_2cell_28


title: 102325_ago_mir465_2cell_19

description: Library name: 102325_ago_mir465_2cell_19


title: 102325_ago_mir465_2cell_18

description: Library name: 102325_ago_mir465_2cell_18


title: 102325_ago_mir465_2cell_17

description: Library name: 102325_ago_mir465_2cell_17


title: CT__11.3_Control (Vehicle)

description: Library name: ABA37600

value: none (vehicle) rep6


title: 102325_ago_mir465_2cell_16

description: Library name: 102325_ago_mir465_2cell_16


title: 102325_ago_mir465_2cell_15

description: Library name: 102325_ago_mir465_2cell_15


title: 102325_ago_mir465_2cell_11

description: Library name: 102325_ago_mir465_2cell_11


title: 102325_ago_mir465_2cell_12

description: Library name: 102325_ago_mir465_2cell_12


title: 102325_ago_mir465_2cell_13

description: Library name: 102325_ago_mir465_2cell_13


title: 102325_ago_mir465_2cell_10

description: Library name: 102325_ago_mir465_2cell_10


title: 102325_ago_mir465_2cell_1

description: Library name: 102325_ago_mir465_2cell_1


title: 102325_ago_mir200_2cell_9

description: Library name: 102325_ago_mir200_2cell_9


title: 102325_ago_mir200_2cell_6

description: Library name: 102325_ago_mir200_2cell_6


title: 102325_ago_mir200_2cell_8

description: Library name: 102325_ago_mir200_2cell_8


title: 102325_ago_mir465_2cell_14

description: Library name: 102325_ago_mir465_2cell_14


title: 102325_ago_mir200_2cell_5

description: Library name: 102325_ago_mir200_2cell_5


title: 102325_ago_mir200_2cell_7

description: Library name: 102325_ago_mir200_2cell_7


title: 102325_ago_mir200_2cell_27

description: Library name: 102325_ago_mir200_2cell_27


title: 102325_ago_mir200_2cell_3

description: Library name: 102325_ago_mir200_2cell_3


title: 102325_ago_mir200_2cell_26

description: Library name: 102325_ago_mir200_2cell_26


title: 102325_ago_mir200_2cell_4

description: Library name: 102325_ago_mir200_2cell_4


title: 102325_ago_only_2cell_18

description: Library name: 102325_ago_only_2cell_18


title: 102325_ago_mir200_2cell_25

description: Library name: 102325_ago_mir200_2cell_25


title: 102325_ago_mir200_2cell_23

description: Library name: 102325_ago_mir200_2cell_23


title: 102325_ago_mir200_2cell_21

description: Library name: 102325_ago_mir200_2cell_21


title: 102325_ago_mir200_2cell_24

description: Library name: 102325_ago_mir200_2cell_24


title: 102325_ago_mir200_2cell_22

description: Library name: 102325_ago_mir200_2cell_22


title: 102325_ago_mir200_2cell_2

description: Library name: 102325_ago_mir200_2cell_2


title: 102325_ago_mir200_2cell_19

description: Library name: 102325_ago_mir200_2cell_19


title: 102325_ago_mir200_2cell_18

description: Library name: 102325_ago_mir200_2cell_18


title: 102325_ago_mir200_2cell_16

description: Library name: 102325_ago_mir200_2cell_16


title: 102325_ago_mir200_2cell_13

description: Library name: 102325_ago_mir200_2cell_13


title: 102325_ago_mir200_2cell_15

description: Library name: 102325_ago_mir200_2cell_15


title: 102325_ago_mir200_2cell_12

description: Library name: 102325_ago_mir200_2cell_12


title: fzf1 cyanamide rep 1

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

country: Canada

institute: University Of British Columbia

description: Library name: fzf1-1+CY

data_processing:
Adapter sequences were removed from paired end FASTQ files using cutadapt (version 4.9), before aligning to the sacCer3 genome using BWA (version 0.7.17-r1188).
Samtools view (version 1.21) was used to retain uniquely mapping and properly paired reads with a Mapping Quality (MAPQ) score of 10 or higher.  Note the due to sequence similarity between DDI2 and DDI3, approximately 55% of reads mapping to these loci were discarded.
BAM files were converted to BED files using awk (version 20200816), and coverage tracks, representing reads per genome coverage (RPGC), were calculated using the Java Genomics Toolkit (https://github.com/timpalpant/java-genomics-toolkit) scripts, ngs.BaseAlignCounts and wigmath.Scale.
Assembly: sacCer3.fa
Supplementary files format and content: wig files normalized to genomic mean

growth_protocol: BY4741 wild-type and its isogenic fzf1∆::KanMX4 mutant were grown to log phase and treated with 20 mM cyanamide for 2 hours.

extract_protocol:
Cells were resuspended in spheroplast buffer, and 10% cross-linked Schizosaccharomyces pombe cells were added to each sample as a spike-in. Cells were treated with 2 mg of zymolyase for 15 mins at 25°C with rotation, then digested with 60 units of micrococcal nuclease (MNase) and 30 units of ExoIII for 11 minutes at 37°C. Residual proteins and RNAs were removed, and DNA was purified with a QIAGEN MinElute PCR Purification Kit.
Libraries were prepared with NEB DNA Ultra II kit, and sequenced on an Illumina NextSeq.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 15 minutes and quenched by glycine addition to a final concentration of 300 mM for 5 minutes. Pellets were washed three times with cold 10 mM Tris-Cl pH 7.5, 100 mM NaCl and then flash frozen.

value: MATa his3D1 leu2D0 met15D0 ura3D0 fzf1D::KanMX4

value: 20 mM CY for 2 hours


title: fzf1 cyanamide rep 2

description: Library name: fzf1-2+CY


title: 102325_ago_mir200_2cell_10

description: Library name: 102325_ago_mir200_2cell_10


title: 102325_ago_mir200_2cell_1

description: Library name: 102325_ago_mir200_2cell_1


title: fzf1 control rep 2

description: Library name: fzf1-2_CK


title: Wild type cyanamide rep 1

description: Library name: WT-1+CY

value: MATa his3D1 leu2D0 met15D0 ura3D0


title: 102325_abe_2cell_6

description: Library name: 102325_abe_2cell_6


title: 102325_abe_2cell_5

description: Library name: 102325_abe_2cell_5


title: 102325_abe_2cell_8

description: Library name: 102325_abe_2cell_8


title: Wild type cyanamide rep2

description: Library name: WT-2+CY


title: 102325_ago_mir200_2cell_14

description: Library name: 102325_ago_mir200_2cell_14