title: Spirodela polyrhiza, Stipe region, replicate 3

description:
Library name: Spirodela_Stipe_3
RNA-seq of Spirodela Stipe region, biological replicate 3


title: fr23588432

status: Public on Apr 14 2026

type: SRA

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Library name: fr23588432

library_source: transcriptomic

data_processing:
Binary base call output was converted to fastq files using bclconvert
Fastq files were normalized to transcript per million by Hartwig Medical Foundation's isofox algorithm
the normalized count data were corrected for RIN value (continuous covariate) using the ‘removeBatchEffect’ (limma package, R)
Assembly: ch37
Supplementary files format and content: text file contains isofox-normalized count data for each sample
Supplementary files format and content: reference genome: ensh37 , version 75, log2 transformed

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Tumor RNA was isolated from 40x10um slides according to the protocol of Qiagen AllPrep DNA/RNA/miRNA kit 50 (80224). 50-100 ng RNA was used as input
RNA was fragmented to a targeted fragment length of 300bp.
Library preparation was performed with KAPA RNA HyperPrep Kit with RiboErase (Human/Mouse/Rat) (Roche).

tag: tissue

value: Pancreatic ductal adenocarcinoma


title: fr23588426

description: Library name: fr23588426


title: Spirodela polyrhiza, Basal region, replicate 4

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

description:
Library name: Spirodela_Basal_4
RNA-seq of Spirodela Basal region, biological replicate 4

data_processing:
Salmon v1.10.0
Reads were pseudo-aligned and quantified using Salmon v1.10.0 with --validateMappings against a gentrome index built from the species-specific reference transcriptome and genome as decoys.
TPM values were extracted from Salmon quant.sf output files and assembled into gene x sample matrices.
Genes were filtered to remove those where max organ-averaged TPM was not at least 2.0 in at least one organ.
Assembly: Lemna minor: Le_minor_7210-REF-CSHL-1.0 (lemna.org); Spirodela polyrhiza: Sp_polyrhiza_9509-REF-OXFORD-3.0 (lemna.org); Colocasia esculenta (cngdb.com)
Supplementary files format and content: CSV files containing TPM (Transcripts Per Million) values for each gene across all samples per species

molecule: polyA RNA

organism: Spirodela polyrhiza

source_name: Basal

extract_protocol:
Duckweed samples: Samples were recovered from RNAlater by sieving through 70uM cell strainers, blotted from underneath with tissue paper to remove excess RNAlater, and snap frozen. Samples were ground on liquid nitrogen in 1.5ml Eppendorf tubes with plastic pestles. RNA was extracted using a RNeasy UCP Micro Kit (Qiagen) as per manufacturer's instructions.
Taro leaf-derived tissue (Apical, Basal regions): Tissue was ground to fine powder using a mortar and pestle on liquid nitrogen. 3 replicate aliquots of approximately 100mg were taken, added to 450ul buffer RLT and snap frozen. RNA extraction was performed on a single aliquot using the RNeasy Mini Kit (Qiagen) as per manufacturer's instructions with an additional RPE wash step.
Taro sheath and petiole tissue: Tissue was ground to fine powder using a mortar and pestle on liquid nitrogen. 3 replicate aliquots of approximately 100mg were taken, added to 450ul buffer RLT and snap frozen. All three aliquots were extracted using the RNeasy Mini Kit (Qiagen), then pooled and cleaned up using the RNeasy PowerClean Pro Cleanup Kit as per manufacturer's instructions.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies). Library preparation and sequencing were performed by Novogene. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. After adenylation of 3' ends, adaptors with hairpin loop structure were ligated. Library fragments of 370-420 bp were purified with AMPure XP system (Beckman Coulter). PCR was performed with Phusion High-Fidelity DNA polymerase. Clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Libraries were sequenced on an Illumina NovaSeq platform generating 150 bp paired-end reads.

value: Basal

tag: strain


title: fr23588431

description: Library name: fr23588431


title: Spirodela polyrhiza, NodeTract region, replicate 4

description:
Library name: Spirodela_NodeTract_4
RNA-seq of Spirodela NodeTract region, biological replicate 4

source_name: NodeTract

value: NodeTract


title: Spirodela polyrhiza, NodeTract region, replicate 1

description:
Library name: Spirodela_NodeTract_1
RNA-seq of Spirodela NodeTract region, biological replicate 1


title: fr23588424

description: Library name: fr23588424


title: fr23588427

description: Library name: fr23588427


title: fr23588425

description: Library name: fr23588425


title: Spirodela polyrhiza, Basal region, replicate 3

description:
Library name: Spirodela_Basal_3
RNA-seq of Spirodela Basal region, biological replicate 3


title: fr23588435

description: Library name: fr23588435


title: Spirodela polyrhiza, Basal region, replicate 2

description:
Library name: Spirodela_Basal_2
RNA-seq of Spirodela Basal region, biological replicate 2


title: Spirodela polyrhiza, Stipe region, replicate 1

description:
Library name: Spirodela_Stipe_1
RNA-seq of Spirodela Stipe region, biological replicate 1

source_name: Stipe

value: Stipe


title: fr23588421

description: Library name: fr23588421


title: Spirodela polyrhiza, Basal region, replicate 1

description:
Library name: Spirodela_Basal_1
RNA-seq of Spirodela Basal region, biological replicate 1


title: fr23588423

description: Library name: fr23588423


title: fr23588420

description: Library name: fr23588420


title: Spirodela polyrhiza, LowerWall region, replicate 4

description:
Library name: Spirodela_LowerWall_4
RNA-seq of Spirodela LowerWall region, biological replicate 4

source_name: LowerWall

value: LowerWall


title: Spirodela polyrhiza, NodeTract region, replicate 3

description:
Library name: Spirodela_NodeTract_3
RNA-seq of Spirodela NodeTract region, biological replicate 3


title: Spirodela polyrhiza, LowerWall region, replicate 3

description:
Library name: Spirodela_LowerWall_3
RNA-seq of Spirodela LowerWall region, biological replicate 3


title: fr23588418

description: Library name: fr23588418


title: fr23588419

description: Library name: fr23588419


title: Spirodela polyrhiza, NodeTract region, replicate 2

description:
Library name: Spirodela_NodeTract_2
RNA-seq of Spirodela NodeTract region, biological replicate 2


title: Spirodela polyrhiza, LowerWall region, replicate 2

description:
Library name: Spirodela_LowerWall_2
RNA-seq of Spirodela LowerWall region, biological replicate 2


title: fr23588417

description: Library name: fr23588417


title: Spirodela polyrhiza, LowerWall region, replicate 1

description:
Library name: Spirodela_LowerWall_1
RNA-seq of Spirodela LowerWall region, biological replicate 1


title: fr23588415

description: Library name: fr23588415


title: fr23588412

description: Library name: fr23588412


title: fr23588413

description: Library name: fr23588413


title: Spirodela polyrhiza, Apical region, replicate 1

description:
Library name: Spirodela_Apical_1
RNA-seq of Spirodela Apical region, biological replicate 1

source_name: Apical

value: Apical


title: Spirodela polyrhiza, Apical region, replicate 4

description:
Library name: Spirodela_Apical_4
RNA-seq of Spirodela Apical region, biological replicate 4


title: fr23588410

description: Library name: fr23588410


title: fr23588407

description: Library name: fr23588407


title: fr23588402

description: Library name: fr23588402


title: fr23588400

description: Library name: fr23588400


title: fr23588409

description: Library name: fr23588409


title: fr23588403

description: Library name: fr23588403


title: fr23588396

description: Library name: fr23588396


title: fr23588397

description: Library name: fr23588397


title: fr23588416

description: Library name: fr23588416


title: fr23588405

description: Library name: fr23588405


title: GCR clone 14 from the strain with deleted SPLTRA11-SPLTRA12

city: Atlanta

first: Kirill

middle: S

last: Lobachev

state: GA

address: 315 Ferst Drive

department: School of Biological Sciences

country: USA

institute: Georgia Institute of Technology

description: Library name: LTR-d C11

library_source: genomic

data_processing:
CLC Genomic Workbench 25.0.1
Chromosomal read coverage computation and plotting were performed using an in-house Python script
Assembly: Reads were mapped to the reference sequence ASM294v2.62
Supplementary files format and content: Detailed per-base coverage information presented as tsv files

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: strain

extract_protocol:
Genomic DNA was extracted  using the YeaStar Genomic DNA kit (Zymo research)
fragmenting DNA, repairing ends, adding A-tails, ligating adapters, and PCR amplification, optimized for Illumina platforms

value: strain

tag: genotype


title: fr23588408

description: Library name: fr23588408


title: fr23588399

description: Library name: fr23588399


title: Spirodela polyrhiza, Apical region, replicate 3

description:
Library name: Spirodela_Apical_3
RNA-seq of Spirodela Apical region, biological replicate 3


title: fr23588404

description: Library name: fr23588404


title: Spirodela polyrhiza, Apical region, replicate 2

description:
Library name: Spirodela_Apical_2
RNA-seq of Spirodela Apical region, biological replicate 2


title: fr23588401

description: Library name: fr23588401


title: Splenic cDC1, Uqcfqf/f, rep2

type: genomic

city: MADRID

first: Ignacio

last: Heras-Murillo

state: MADRID

address: c/Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: DNA methylation data quality control was conducted with Sesame R package, and proceeded as in PMID: 35873672. Exploratory and inferential analyses were conducted with functions in shinyÉPICO application (PMID: 33416853), which relies on functions from the minfi (PMID: 24478339), lumi (PMID: 18467348), and limma (PMID: 25605792) R libraries, among others.

label: Cy3 and Cy5

organism: Mus musculus

source_name: Spleen

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was harvested using the DNA mini kit (Qiagen). Then, DNA was bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research). Infinium Methylation BeadChip arrays (Illumina) were used to analyze DNA methylation, following the manufacturer’s instructions

treatment_protocol: The spleen from 6-8 week old Uqcrqf/f or Itgax-Uqcrqf/f male or female mice  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+).

value: Spleen

tag: cell type

value: Uqcrqf/f


title: GCR clone 12 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C10


title: fr23588394

description: Library name: fr23588394


title: fr23588395

description: Library name: fr23588395


title: fr23588388

description: Library name: fr23588388


title: fr23588387

description: Library name: fr23588387


title: fr23588391

description: Library name: fr23588391


title: GCR clone1 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C6


title: fr23588393

description: Library name: fr23588393


title: fr23588389

description: Library name: fr23588389


title: GCR clone 7 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C3


title: GCR clone 13 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C7


title: GCR clone 8 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C4


title: GCR clone 6 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C2


title: GCR clone 4 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C8


title: fr23588392

description: Library name: fr23588392


title: GCR clone 9 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C9


title: GCR clone 10 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C5


title: Splenic cDC2, Uqcfqf/f, rep2


title: GCR clone 2 from the strain with deleted SPLTRA11-SPLTRA12

description: Library name: LTR-d C1


title: fr23588386

description: Library name: fr23588386


title: fr23588384

description: Library name: fr23588384


title: GCR clone 4 from the wild type strain

description: Library name: WT C13

value: Wilde-type


title: GCR clone14 from the wild type strain

description: Library name: WT C11


title: fr23588381

description: Library name: fr23588381


title: fr23588376

description: Library name: fr23588376


title: GCR clone 11 from the wild type strain

description: Library name: WT C8


title: GCR clone 10 from the wild type strain

description: Library name: WT C7


title: fr23588375

description: Library name: fr23588375


title: fr23588372

description: Library name: fr23588372


title: Splenic cDC2, Itgax-Uqcfqf/f , rep1

value: Itgax-Uqcrqf/f


title: Splenic cDC1, Uqcfqf/f, rep 1


title: Splenic cDC2, Itgax-Uqcfqf/f, rep2


title: GCR clone 8 from the wild type strain

description: Library name: WT C6


title: GCR clone 1 from the wild type strain

description: Library name: WT C1


title: fr23588371

description: Library name: fr23588371


title: Splenic cDC1, Uqcfqf/f, rep3


title: Splenic cDC2, Uqcfqf/f, rep3


title: Splenic cDC1, Itgax-Uqcfqf/f, rep1


title: fr23588385

description: Library name: fr23588385


title: fr23588377

description: Library name: fr23588377


title: fr23588380

description: Library name: fr23588380


title: Splenic cDC2, Itgax-Uqcfqf/f, rep3


title: Splenic cDC1, Itgax-Uqcfqf/f , rep2


title: fr23588373

description: Library name: fr23588373


title: Splenic cDC1, Itgax-Uqcfqf/f, rep3


title: GCR clone 2 from the wild type strain

description: Library name: WT C2


title: GCR clone 6 from the wild type strain

description: Library name: WT C4


title: RNA seq of Wickerhamomyces anomalus in 64h, biol repl3

city: Zhengzhou

first: Zhifei

last: Chen

state: Hunan

address: No. 16, Yulin South Road

country: China

institute: Technology Center for China Tobacco Henan Industrial Limited Company

description:
Library name: 64hc
Column name in gene_count.xls: 64hc

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GCF_001661255.1
Supplementary files format and content: xls file includes gene counts for all Sample

organism: Wickerhamomyces anomalus

source_name: Whole fermentation broth

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Whole fermentation broth


title: fr23588368

description: Library name: fr23588368


title: Splenic cDC2, Uqcfqf/f, rep1


title: RNA seq of Wickerhamomyces anomalus in 64h, biol repl2

description:
Library name: 64hb
Column name in gene_count.xls: 64hb


title: fr23588365

description: Library name: fr23588365


title: fr23588370

description: Library name: fr23588370


title: GCR clone 5 from the wild type strain

description: Library name: WT C3


title: RNA seq of Wickerhamomyces anomalus in 64h, biol repl1

description:
Library name: 64ha
Column name in gene_count.xls: 64ha


title: fr23588364

description: Library name: fr23588364


title: GCR clone 3 from the wild type strain

description: Library name: WT C12


title: RNA seq of Wickerhamomyces anomalus in 48h, biol repl2

description:
Library name: 48hb
Column name in gene_count.xls: 48hb


title: GCR clone13 from the  wild type strain

description: Library name: WT C10


title: fr23588383

description: Library name: fr23588383


title: fr23588362

description: Library name: fr23588362


title: fr23588363

description: Library name: fr23588363


title: GCR clone 12 from the wild type strain

description: Library name: WT C9


title: RNA seq of Wickerhamomyces anomalus in 48h, biol repl1

description:
Library name: 48ha
Column name in gene_count.xls: 48ha


title: fr23588379

description: Library name: fr23588379


title: RNA seq of Wickerhamomyces anomalus in 32h, biol repl3

description:
Library name: 32hc
Column name in gene_count.xls: 32hc


title: fr23588360

description: Library name: fr23588360


title: RNA seq of Wickerhamomyces anomalus in 32h, biol repl2

description:
Library name: 32hb
Column name in gene_count.xls: 32hb


title: fr23588359

description: Library name: fr23588359


title: RNA seq of Wickerhamomyces anomalus in 16h, biol repl3

description:
Library name: 16hc
Column name in gene_count.xls: 16hc


title: fr23588357

description: Library name: fr23588357


title: fr23588356

description: Library name: fr23588356


title: fr23588358

description: Library name: fr23588358


title: fr23588352

description: Library name: fr23588352


title: RNA seq of Wickerhamomyces anomalus in 16h, biol repl1

description:
Library name: 16ha
Column name in gene_count.xls: 16ha


title: RNA seq of Wickerhamomyces anomalus in 0h, biol repl3

description:
Library name: 0hc
Column name in gene_count.xls: 0hc


title: 1-month, Striatum, heterozygous replicate 5

city: Cambridge

first: Sameer

last: Aryal

state: Massachusetts

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

description:
Library name: P28-STR-HET5
1month-STR-HET5

library_source: transcriptomic single cell

data_processing:
For striatum samples, the 10X Genomics Cell Ranger v7.2.0 84 pipeline was used to align reads from snRNA-seq to a version of the mouse mm10 reference transcriptome that includes introns (refdata-gex-mm10-2020-A, 10X Genomics). The –chemistry=SC3Pv3 and –include-introns=TRUE flags were used in addition to default parameters for Cell Ranger count. For PFC samples, Cell Ranger v3.0.2 was used with the same reference transcriptome.
Ambient RNA removal was performed on striatum samples using CellBender v0.3.0.
Assembly: refdata-gex-mm10-2020-A (10X Genomics)
Supplementary files format and content: H5 files contain filtered cells, the barcodes, features, and the count matrix together in one HDF5 file for each sample and brain region.

molecule: nuclear RNA

source_name: Striatum

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Srrm2 +/- mutant mice and wild-type littermates.Nuclei were purified by dissociating dissected brain tissue in a 1% Triton-X based buffer, followed by FACS enrichment.
Libraries were prepared using 10X Genomics v3 (Single Cell 3') kit, using manufacturer's instructions. cDNA fragment sizes were analyzed using High Sensitivity DNA chips (Agilent), a 10 nM normalized library was pooled, and sequencing performed on a NovaSeq S2 (Illumina) with 28 and 75 bases for reads 1 and 2 and 10 bases each for index reads 1 and 2.

value: Brain

value: Striatum

value: Srrm2 +/-


title: fr23588367

description: Library name: fr23588367


title: fr23588350

description: Library name: fr23588350


title: 1-month, Striatum, heterozygous replicate 6

description:
Library name: P28-STR-HET6
1month-STR-HET6


title: fr23588344

description: Library name: fr23588344


title: RNA seq of Wickerhamomyces anomalus in 16h, biol repl2

description:
Library name: 16hb
Column name in gene_count.xls: 16hb


title: fr23588355

description: Library name: fr23588355


title: fr23588348

description: Library name: fr23588348


title: 1-month, Striatum, wild-type replicate 4

description:
Library name: P28-STR-WT4
1month-STR-WT4

value: Wild-type


title: GCR clone 7 from the wild type strain

description: Library name: WT C5


title: 1-month, Striatum, heterozygous replicate 2

description:
Library name: P28-STR-HET2
1month-STR-HET2


title: 1-month, Striatum, heterozygous replicate 1

description:
Library name: P28-STR-HET1
1month-STR-HET1


title: DOGMA-plex CT library 28

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

institute: New York University

description:
Library name: DOGMA-plex CT library 28
CT

data_processing:
Fastqs were generated using CellRanger-arc mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-arc or cellranger count for the hg38 reference genome
For ADT, HTO and CT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Assembly: hg38
Supplementary files format and content: Per-barcode count abundance for the protein and viral barcode count data including the scRNA and scMultiome singlecell QC metrics; barcoded accessible chromatin fragments and transcripts per library

source_name: primary T cells

extract_protocol:
Digitonin lysis for DOGMA-seq and standard 10x Genomics protocol for scRNA-seq
DOGMA-seq libraries were constructed according to previously described protocols (Mimitou et al, 2021). icCITE-seq libraries were constructed as described previously (Chen et al., 2025) and CITE tags were prepared as described in CITE-seq protocols (Stoeckius et al, 2017). Viral barcodes were amplified by two rounds of DialOut PCR adapted from Perturb-CITE-seq (Frangieh et al., 2021).

value: primary T cells


title: 1-month, Striatum, wild-type replicate 3

description:
Library name: P28-STR-WT3
1month-STR-WT3


title: 1-month, Striatum, wild-type replicate 2

description:
Library name: P28-STR-WT2
1month-STR-WT2


title: 1-month, Striatum, wild-type replicate 5

description:
Library name: P28-STR-WT5
1month-STR-WT5


title: fr23588343

description: Library name: fr23588343

value: Pancreatic ductal adenocarcinoma


title: 1-month, Striatum, wild-type replicate 1

description:
Library name: P28-STR-WT1
1month-STR-WT1


title: fr23588354

description: Library name: fr23588354


title: 1-month, Prefrontal Cortex, heterozygous replicate 6

description:
Library name: P28-PFC-HET6
1month-PFC-HET6

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: 1-month, Striatum, heterozygous replicate 3

description:
Library name: P28-STR-HET3
1month-STR-HET3


title: DOGMA-plex CT library 27

description:
Library name: DOGMA-plex CT library 27
CT


title: DOGMA-plex CT library 25

description:
Library name: DOGMA-plex CT library 25
CT


title: RNA seq of Wickerhamomyces anomalus in 0h, biol repl1

description:
Library name: 0ha
Column name in gene_count.xls: 0ha


title: 1-month, Prefrontal Cortex, heterozygous replicate 5

description:
Library name: P28-PFC-HET5
1month-PFC-HET5


title: DOGMA-plex CT library 22

description:
Library name: DOGMA-plex CT library 22
CT


title: 1-month, Prefrontal Cortex, heterozygous replicate 4

description:
Library name: P28-PFC-HET4
1month-PFC-HET4


title: DOGMA-plex CT library 23

description:
Library name: DOGMA-plex CT library 23
CT


title: DOGMA-plex CT library 24

description:
Library name: DOGMA-plex CT library 24
CT


title: 1-month, Prefrontal Cortex, heterozygous replicate 1

description:
Library name: P28-PFC-HET1
1month-PFC-HET1


title: RNA seq of Wickerhamomyces anomalus in 32h, biol repl1

description:
Library name: 32ha
Column name in gene_count.xls: 32ha


title: 1-month, Prefrontal Cortex, heterozygous replicate 2

description:
Library name: P28-PFC-HET2
1month-PFC-HET2


title: DOGMA-plex CT library 20

description:
Library name: DOGMA-plex CT library 20
CT


title: Colocasia esculenta, Sheath region, replicate 2

description:
Library name: Taro_Sheath_2
RNA-seq of Taro Sheath region, biological replicate 2

organism: Colocasia esculenta

source_name: Sheath

value: Sheath


title: fr23588369

description: Library name: fr23588369


title: 1-month, Prefrontal Cortex, wild-type replicate 6

description:
Library name: P28-PFC-WT6
1month-PFC-WT6


title: fr23588351

description: Library name: fr23588351


title: DOGMA-plex CT library 19

description:
Library name: DOGMA-plex CT library 19
CT


title: Colocasia esculenta, Basal region, replicate 4

description:
Library name: Taro_Basal_4
RNA-seq of Taro Basal region, biological replicate 4

value: Basal


title: 1-month, Prefrontal Cortex, wild-type replicate 5

description:
Library name: P28-PFC-WT5
1month-PFC-WT5


title: RNA seq of Wickerhamomyces anomalus in 0h, biol repl2

description:
Library name: 0hb
Column name in gene_count.xls: 0hb


title: 1-month, Striatum, heterozygous replicate 4

description:
Library name: P28-STR-HET4
1month-STR-HET4


title: Colocasia esculenta, Basal region, replicate 3

description:
Library name: Taro_Basal_3
RNA-seq of Taro Basal region, biological replicate 3


title: DOGMA-plex CT library 18

description:
Library name: DOGMA-plex CT library 18
CT


title: Colocasia esculenta, Basal region, replicate 2

description:
Library name: Taro_Basal_2
RNA-seq of Taro Basal region, biological replicate 2


title: RNA seq of Wickerhamomyces anomalus in 48h, biol repl3

description:
Library name: 48hc
Column name in gene_count.xls: 48hc


title: Colocasia esculenta, Basal region, replicate 1

description:
Library name: Taro_Basal_1
RNA-seq of Taro Basal region, biological replicate 1


title: 1-month, Prefrontal Cortex, wild-type replicate 4

description:
Library name: P28-PFC-WT4
1month-PFC-WT4


title: 1-month, Prefrontal Cortex, wild-type replicate 3

description:
Library name: P28-PFC-WT3
1month-PFC-WT3


title: DOGMA-plex CT library 17

description:
Library name: DOGMA-plex CT library 17
CT


title: fr23588353

description: Library name: fr23588353


title: Colocasia esculenta, Petiole region, replicate 6

description:
Library name: Taro_Petiole_6
RNA-seq of Taro Petiole region, biological replicate 6

source_name: Petiole

value: Petiole


title: DOGMA-plex CT library 16

description:
Library name: DOGMA-plex CT library 16
CT


title: fr23588345

description: Library name: fr23588345


title: fr23588346

description: Library name: fr23588346


title: 1-month, Striatum, wild-type replicate 6

description:
Library name: P28-STR-WT6
1month-STR-WT6


title: Colocasia esculenta, Petiole region, replicate 5

description:
Library name: Taro_Petiole_5
RNA-seq of Taro Petiole region, biological replicate 5


title: 1-month, Prefrontal Cortex, wild-type replicate 2

description:
Library name: P28-PFC-WT2
1month-PFC-WT2


title: DOGMA-plex CT library 26

description:
Library name: DOGMA-plex CT library 26
CT


title: Colocasia esculenta, Petiole region, replicate 4

description:
Library name: Taro_Petiole_4
RNA-seq of Taro Petiole region, biological replicate 4


title: Colocasia esculenta, Petiole region, replicate 3

description:
Library name: Taro_Petiole_3
RNA-seq of Taro Petiole region, biological replicate 3


title: DOGMA-plex CT library 15

description:
Library name: DOGMA-plex CT library 15
CT


title: 1-month, Prefrontal Cortex, wild-type replicate 1

description:
Library name: P28-PFC-WT1
1month-PFC-WT1


title: fr23588347

description: Library name: fr23588347


title: DOGMA-plex CT library 12

description:
Library name: DOGMA-plex CT library 12
CT


title: fr23588349

description: Library name: fr23588349


title: Colocasia esculenta, Apical region, replicate 1

description:
Library name: Taro_Apical_1
RNA-seq of Taro Apical region, biological replicate 1

value: Apical


title: 1-month, Prefrontal Cortex, heterozygous replicate 3

description:
Library name: P28-PFC-HET3
1month-PFC-HET3


title: DOGMA-plex CT library 14

description:
Library name: DOGMA-plex CT library 14
CT


title: DOGMA-plex CT library 9

description:
Library name: DOGMA-plex CT library 9
CT


title: Splenic cDC1, Itgax-Uqcfqf/f , rep2

data_processing:
Reads were trimmed to remove adapter contaminants and filtered out based on quality using TrimGalore.
Then, reads were aligned to the reference genome GRCm38/MM10 using Bowtie2, and properly aligned reads were filtered out according to a mapping quality greater than 30, not being aligned to mitochondrial DNA, and not being aligned to the ENCODE blacklist of problematic genomic regions.
Duplicated reads were removed and only those with a fragment size greater than 120pb (nucleosome-free regions) were kept for downstream analyses.
Peak calling was performed using Genrich with ATAC-seq mode, and finally DiffBind was used to calculate and normalize the consensus peak set, and to identify differentially accessible regions (DARs) in pair-wise contrasts using EdgeR as analysis method.
Assembly: GRCm38/MM10 using Bowtie2
Supplementary files format and content: narrowPeak

extract_protocol:
5 x 104 cDC1s or cDC2s were lysed by spinning at 500 x g for 20 minutes at 4°C in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei pellets were resuspended in the transposase reaction mix (including 2 ml Transposase (Illumina)) and the transposition reaction was carried out for 1 h at 37 ºC. Then, samples were purified using PCR Minelute kit (Qiagen) following the manufacturer’s instruction.
Libraries were generated by PCR using the NEBNext High-Fidelity PCR Master Mix (New England Biolabs) and the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute for 12 cycles. PCR product was purified using PCR Minelute kit (Qiagen) and SPRI beads-based size selection carried out using AMPure XP (Beckman). Libraries size and quality were assessed using a 2100 Bioanalyzer instrument (Agilent).


title: Splenic cDC2, Itgax-Uqcfqf/f, rep2


title: Colocasia esculenta, Petiole region, replicate 2

description:
Library name: Taro_Petiole_2
RNA-seq of Taro Petiole region, biological replicate 2


title: Splenic cDC2, Uqcfqf/f, rep2


title: DOGMA-plex CT library 13

description:
Library name: DOGMA-plex CT library 13
CT


title: Colocasia esculenta, Petiole region, replicate 1

description:
Library name: Taro_Petiole_1
RNA-seq of Taro Petiole region, biological replicate 1


title: Colocasia esculenta, Apical region, replicate 3

description:
Library name: Taro_Apical_3
RNA-seq of Taro Apical region, biological replicate 3


title: Colocasia esculenta, Apical region, replicate 4

description:
Library name: Taro_Apical_4
RNA-seq of Taro Apical region, biological replicate 4


title: CNL_LDR_100mGy_rep5

city: Ottawa

first: Seung-Hwan

last: Lee

state: Ontario

address: 451 Smyth Road

department: Biochemistry, Immunology and Microbiology

country: Canada

institute: University of Ottawa

description:
Library name: C6
Column Name in TPM_Matrix.csv => C6

data_processing:
FASTQ files were pseudo-aligned to the mouse transcriptome assembly (mm10) using Kallisto (v.0.46.1). Gene-level quantification was performed with Tximport (v1.32.0).
Assembly: mm10
Supplementary files format and content: tximport$abundance exported as .csv

extract_protocol:
RNA was extracted from isolated splenocytes using Trizol (Thermofisher). RNA integrity was ensured with a minimum RIN cut-off of 6.5.
6 RNA samples per radiation condition were submitted for sequencing. 3 Samples (A3, B2, and C1) did not pass quality control. Samples with proper quality metrics proceeded. Poly-A enriched stranded cDNA libraries were generated and subjected to 100 bp paired-end sequencing on a NovaSeq6000 at Genome Quebec (Montreal, Canada).

treatment_protocol: Whole-body gamma irradiation was administered using a Nordion (Ottawa, Ontario, Canada) Gammabeam 150C irradiator equipped with a Cobalt-60 source. The irradiation was continuous for 7 days in the pathogen-free irradiation hall of the CNL. Treatment groups were positioned at varying distances from the irradiator to achieve different dose rate exposures. Mice receiving a cumulative dose of 10 mGy (n=6) received an average dose rate of 0.0614mGy/hr. Mice receiving a cumulative dose of 100 mGy (n=6) received an average dose rate of 0.625mGy/hr. The positioning ensured the beam targeted the mid-level of each cage, centered between the two cages. Dosimetry was performed using an Exradin A8 ion chamber and a Supermax electrometer. Control mice (n=6) were housed separately in a conventional animal room.

value: bulk splenocytes

tag: treatment

value: 100 mGy chronic LDR gamma irradiation


title: CNL_LDR_100mGy_rep4

description:
Library name: C5
Column Name in TPM_Matrix.csv => C5

value: Spleen


title: CNL_LDR_10mGy_rep4

description:
Library name: B5
Column Name in TPM_Matrix.csv => B5

value: 10 mGy chronic LDR gamma irradiation


title: Colocasia esculenta, Apical region, replicate 2

description:
Library name: Taro_Apical_2
RNA-seq of Taro Apical region, biological replicate 2


title: CNL_LDR_100mGy_rep3

description:
Library name: C4
Column Name in TPM_Matrix.csv => C4


title: Splenic cDC2, Itgax-Uqcfqf/f, rep3

value: Itgax-Uqcrqf/f


title: DOGMA-plex CT library 21

description:
Library name: DOGMA-plex CT library 21
CT


title: CNL_LDR_10mGy_rep3

description:
Library name: B4
Column Name in TPM_Matrix.csv => B4


title: Colocasia esculenta, Sheath region, replicate 1

description:
Library name: Taro_Sheath_1
RNA-seq of Taro Sheath region, biological replicate 1


title: Colocasia esculenta, Sheath region, replicate 3

description:
Library name: Taro_Sheath_3
RNA-seq of Taro Sheath region, biological replicate 3


title: CNL_LDR_10mGy_rep2

description:
Library name: B3
Column Name in TPM_Matrix.csv => B3


title: Splenic cDC2, Uqcfqf/f, rep3

value: Uqcrqf/f


title: DOGMA-plex CT library 10

description:
Library name: DOGMA-plex CT library 10
CT


title: DOGMA-plex CT library 5

description:
Library name: DOGMA-plex CT library 5
CT


title: Splenic cDC2, Itgax-Uqcfqf/f , rep1


title: Splenic cDC2, Uqcfqf/f, rep1


title: Splenic cDC1, Uqcfqf/f, rep 1


title: Day 7 Blastocyst TE 11

city: Lone Tree

first: Mary

middle: E

last: Haywood

state: CO

address: 10290 RidgeGate Circle

department: Genetics

institute: CCRM

description: Library name: D7-TE-11_run2

data_processing:
FASTQ files were aligned to the hg38 genome using GSNAP version 2019-03-15 and the following command: gsnap --dir=${GENOMED} --db=GRCh38 --use-splicing=Homo_sapiens.GRCh38.96.chr.splicesites --max-mismatches=0.04 -i2 -n2 -Q --gunzip --force-xs-dir -B2 -t10 --read-group-id=${OUTPUT_SAM} --read-group-name=${OUTPUT_SAM} --read-group-library=${OUTPUT_SAM} --read-group-platform=illumina -A sam ${INPUT_FASTQ} > ${OUTPUT_SAM}
SAM files were sorted and output as BAM files
Reads were mapped with featureCounts in subread 1.6.2 using the following command: featureCounts -s 0 -t gene -g gene_id -a ${INPUT_GTF} -o ${OUTPUT_COUNTS} ${INPUT_BAM}
Assembly: hg38
Supplementary files format and content: Each count text file contains the output from featureCounts. This includes an Ensembl gene name, chromosome, start position, stop position, strand, length, and count for a given sample.

source_name: Blastocyst

growth_protocol: Routine IVF protocols reaching blastocyst stage on Day 5 or Day 7

extract_protocol:
RNA isolation was completed using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
cDNA conversion and library preparation was completed using the NEBNext Single Cell/Low input RNA library prep kit (New England Biolabs)

treatment_protocol: Surplus cryopreserved donated Day 5 and Day 7 blastocysts were warmed and mechanically separated into ICM and TE portions

value: Blastocyst

tag: cell line

value: Day 7 of preimplantation development

value: trophectoderm

tag: batch

value: run 2


title: Splenic cDC1, Uqcfqf/f, rep2


title: DOGMA-plex CT library 6

description:
Library name: DOGMA-plex CT library 6
CT

value: primary T cells


title: CNL_LDR_10mGy_rep1

description:
Library name: B1
Column Name in TPM_Matrix.csv => B1; Raw FASTQ R1 file is irretrievably lost due to storage failure at the Digital Research Alliance of Canada HPC. Processed data retained.


title: Splenic cDC1, Itgax-Uqcfqf/f, rep1


title: Day 7 Blastocyst TE 7

description: Library name: D7-TE-7_run5

value: run 5


title: DOGMA-plex CT library 11

description:
Library name: DOGMA-plex CT library 11
CT


title: CNL_LDR_10mGy_rep5

description:
Library name: B6
Column Name in TPM_Matrix.csv => B6; Raw FASTQ files irretrievably lost due to storage failure at the Digital Research Alliance of Canada HPC. Processed data retained.


title: Splenic cDC1, Uqcfqf/f, rep3


title: Day 7 Blastocyst TE 10 FAILED RUN

description: Library name: D7-TE-10_run4

value: run 4


title: DOGMA-plex CT library 4

description:
Library name: DOGMA-plex CT library 4
CT


title: CNL_LDR_UT_rep5

description:
Library name: A6
Column Name in TPM_Matrix.csv => A6

value: untreated (0 mGy LDR)


title: Day 7 Blastocyst TE 9

description: Library name: D7-TE-9_run5


title: Day 7 Blastocyst TE 9 FAILED RUN

description: Library name: D7-TE-9_run4


title: Day 7 Blastocyst TE 2

description: Library name: D7-TE-2_run1

value: run 1


title: DOGMA-plex CT library 1

description:
Library name: DOGMA-plex CT library 1
CT


title: DOGMA-plex CT library 7

description:
Library name: DOGMA-plex CT library 7
CT


title: CNL_LDR_UT_rep2

description:
Library name: A2
Column Name in TPM_Matrix.csv => A2


title: Day 7 Blastocyst TE 10

description: Library name: D7-TE-10_run5


title: DOGMA-plex CT library 3

description:
Library name: DOGMA-plex CT library 3
CT


title: CNL_LDR_UT_rep4

description:
Library name: A5
Column Name in TPM_Matrix.csv => A5


title: Day 7 Blastocyst TE 7 FAILED RUN

description: Library name: D7-TE-7_run4


title: DOGMA-plex CT library 2

description:
Library name: DOGMA-plex CT library 2
CT


title: DOGMA-plex HTO library 27

description:
Library name: DOGMA-plex HTO library 27
HTO


title: Day 7 Blastocyst TE 6

description: Library name: D7-TE-6_run3

value: run 3


title: DOGMA-plex CT library 8

description:
Library name: DOGMA-plex CT library 8
CT


title: CNL_LDR_UT_rep3

description:
Library name: A4
Column Name in TPM_Matrix.csv => A4


title: CNL_LDR_100mGy_rep2

description:
Library name: C3
Column Name in TPM_Matrix.csv => C3


title: Day 7 Blastocyst ICM 10 FAILED RUN

description: Library name: D7-ICM-10_run4

value: inner cell mass


title: Spleen, infected, 75days, KO

city: Beijing

first: Xiaonan

last: Ma

address: NO.30 Shuangqing Road

institute: Tsinghua University

description: Library name: Sample_4

data_processing:
The CeleScope (v1.9.0) pipeline was used for scRNA-seq data alignment and quantification.
The generated data files, including aligned and filtered reads, barcodes, and unique molecular identifiers, were processed using Seurat (v4.3.0) for further analysis.
Four groups of cells were merged for standard processing, including filtering of those genes <200 or >3000, and those cells with mitochondrial gene proportions larger than 10%. The cluster proportions were calculated by dividing the cells of each cluster to the total cells. Cluster-specific genes were identified using FindAll-Markers (log FC threshold = 0.25) function.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files for each Sample
Supplementary files format and content: Matrix files in mtx format for each Sample

source_name: spleen

extract_protocol:
Thy1.1+ sgNTC or sgUbe2f transduced Cas9 P14 cells were transferred into Cas9 mice followed by LCMV Armstrong infection one day after cell transfer. 15 days or 75 days post-infection, CD8+Thy1.1+ transferred control T cells or UBE2F-deficient T cells were sorted by flow cytometry with a purity > 95% from the spleens of recipient mice.
The single-cell suspensions were directly loaded onto a microfluidic chip (GEXSCOPE Single Cell RNA-seq Kit, Singleron Biotechnologies) and processed for scRNA-seq library preparation according to the manufacturer’s protocol.

value: spleen

value: CD8 T cell

value: UBE2F KO

value: LCMV-Armstrong infection


title: Day 7 Blastocyst TE 3

description: Library name: D7-TE-3_run2


title: Day 7 Blastocyst ICM 9 FAILED RUN

description: Library name: D7-ICM-9_run4


title: Day 7 Blastocyst ICM 7

description: Library name: D7-ICM-7_run5


title: Spleen, infected, 75days, WT

description: Library name: Sample_3

value: WT


title: Day 7 Blastocyst TE 1

description: Library name: D7-TE-1_run1


title: Day 7 Blastocyst ICM 6

description: Library name: D7-ICM-6_run3


title: CNL_LDR_UT_rep1

description:
Library name: A1
Column Name in TPM_Matrix.csv =>  A1

value: Spleen

value: bulk splenocytes


title: Day 7 Blastocyst ICM 10

description: Library name: D7-ICM-10_run5

value: Blastocyst

value: Day 7 of preimplantation development


title: DOGMA-plex HTO library 25

description:
Library name: DOGMA-plex HTO library 25
HTO


title: DOGMA-plex HTO library 26

description:
Library name: DOGMA-plex HTO library 26
HTO


title: DOGMA-plex HTO library 24

description:
Library name: DOGMA-plex HTO library 24
HTO


title: Day 7 Blastocyst ICM 3

description: Library name: D7-ICM-3_run2

value: run 2


title: DOGMA-plex HTO library 23

description:
Library name: DOGMA-plex HTO library 23
HTO

value: primary T cells


title: Spleen, infected, 15days, KO

description: Library name: Sample_2


title: Spleen, infected, 15days, WT

description: Library name: Sample_1


title: mKO soleus rep2

city: Tochigi

first: Yasuhiro

last: Horibata

address: 880 Kitakobayashi

country: Japan

institute: Dokkyo Medical University

description: Library name: KO_2

data_processing:
CLC Genomics Workbench (v23.0.2)
Assembly: GRCm39
Supplementary files format and content: Processed data files contain raw gene counts for each sample in tab-delimited text format.

source_name: soleus

extract_protocol:
Total RNA was purified using the Maxwell RSC simply RNA Tissue Kit (Promega).
RNA-seq libraries were prepared from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

value: soleus

value: mKO


title: Day 7 Blastocyst ICM 2

description: Library name: D7-ICM-2_run1


title: Splenic cDC1, Itgax-Uqcfqf/f, rep3

value: Itgax-Uqcrqf/f


title: Day 7 Blastocyst ICM 11

description: Library name: D7-ICM-11_run2


title: Day 5 Blastocyst TE 10

description: Library name: D5-TE-10_run5

value: Day 5 of preimplantation development

value: trophectoderm

value: run 5


title: DOGMA-plex HTO library 22

description:
Library name: DOGMA-plex HTO library 22
HTO


title: Day 7 Blastocyst ICM 9

description: Library name: D7-ICM-9_run5

value: inner cell mass


title: Day 5 Blastocyst TE 6

description: Library name: D5-TE-6_run3

value: run 3


title: Day 5 Blastocyst TE 10 FAILED RUN

description: Library name: D5-TE-10_run4

value: run 4


title: mKO soleus rep3

description: Library name: KO_3


title: Day 5 Blastocyst TE 9

description: Library name: D5-TE-9_run3


title: DOGMA-plex HTO library 21

description:
Library name: DOGMA-plex HTO library 21
HTO


title: Day 5 Blastocyst TE 11

description: Library name: D5-TE-11_run2


title: CNL_LDR_100mGy_rep1

description:
Library name: C2
Column Name in TPM_Matrix.csv => C2

value: 100 mGy chronic LDR gamma irradiation


title: DOGMA-plex HTO library 19

description:
Library name: DOGMA-plex HTO library 19
HTO


title: mKO soleus rep1

description: Library name: KO_1


title: Day 7 Blastocyst ICM 7 FAILED RUN

description: Library name: D7-ICM-7_run4


title: WT soleus rep2

description: Library name: Control_2

value: WT


title: WT soleus rep1

description: Library name: Control_1


title: DOGMA-plex HTO library 20

description:
Library name: DOGMA-plex HTO library 20
HTO


title: Day 5 Blastocyst ICM 10

description: Library name: D5-ICM-10_run5


title: Day 5 Blastocyst ICM 10 FAILED RUN

description: Library name: D5-ICM-10_run4


title: DOGMA-plex HTO library 18

description:
Library name: DOGMA-plex HTO library 18
HTO


title: CCI_WT_5

city: Daegu

first: Myungin

last: Baek

address: Techno jungang Daero 333

department: Department of Brain Sciences

country: South Korea

institute: DGIST (Daegu Gyeongbuk Institute of Science and Technology)

description: Library name: sample17

data_processing:
Image analysis was performed using the NovaSeq 6000 Control Software (v1.8.2), and base calling data were demultiplexed using bcl2fastq (v2.20.0.422), generating FASTQ files.
Assembly: Raw sequencing reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner (version 2.7.11a).
Supplementary files format and content: tab-delimited csv files including raw counts for each sample

source_name: lumbar

extract_protocol:
PicoPure™ RNA Isolation Kit
SMART-Seq v4 Ultra Low Input RNA Kit.

value: DRGs

value: lumbar

tag: lumbar region

value: CCI

value: day 30


title: Day 7 Blastocyst ICM 1

description: Library name: D7-ICM-1_run1

value: Blastocyst

value: Day 7 of preimplantation development

value: run 1


title: Day 5 Blastocyst TE 3

description: Library name: D5-TE-3_run2

value: run 2


title: Day 5 Blastocyst ICM 7

description: Library name: D5-ICM-7_run3


title: WT soleus rep3

description: Library name: Control_3

value: soleus


title: DOGMA-plex HTO library 15

description:
Library name: DOGMA-plex HTO library 15
HTO

value: primary T cells


title: Day 5 Blastocyst ICM 3

description: Library name: D5-ICM-3_run2

value: Day 5 of preimplantation development


title: Day 5 Blastocyst TE 2

description: Library name: D5-TE-2_run2

value: trophectoderm


title: Day 5 Blastocyst TE 1

description: Library name: D5-TE-1_run1


title: Day 5 Blastocyst ICM 2

description: Library name: D5-ICM-2_run1

value: inner cell mass


title: CCI_WT_4

description: Library name: sample16


title: cvsR, Pellet Rep3

city: Athens

first: Brian

middle: Howard

last: Kvitko

address: 120 Carlton St.

department: Plant Pathology

institute: University of Georgia

description: Library name: sample18

data_processing:
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations.
Paired-end 150-nt reads were sequenced using the Nova-seq platform (Illumina, San Diego, CA).
Reads were quality trimmed using Trimmomatic
Trimmed sequences were mapped to the RefSeq P. syringae pv. tomato DC3000 genome (NC_004278.1, NC_004632.1, NC_004633.1), using Bowtie2
Assembly: NC_004278.1, NC_004632.1, NC_004633.1
Supplementary files format and content: csv. file contains normalied reads count table at each locus and raw reads from instrument are provided in fastq.gz format.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: in vitro

growth_protocol: Pseudomonas syringae pv. tomato DC3000 (wildtype and cvsR mutant) was streaked from a single colony onto King’s B media and grown overnight at room temperature. Bacterial inoculum was smeared into a lawn using liquid media and incubated overnight at room temperature. For individual inoculations, bacteria were harvested from plates, suspended in 0.25 mM MgCl2, and diluted to an OD600 of 0.8 (~1X10^9 CFU/mL)

extract_protocol:
At 5 hpi, leaves from each treatment were harvested by cutting at the leaf blade junction. Briefly, 80-100 leaves were arranged on four sheets of parafilm, rolled and inserted into the barrels of four 20-ml syringes. An ice-cold RNA stabilizing buffer (Invitrogen) was poured into each syringe, which was sealed and vacuum infiltrated at 95 kPa for 2 min, followed by a slow release of the vacuum. The RNA stabilizing buffer was spun out from apoplast at 1000× g for 10 min at 4°C to isolate bacterial RNA. The flow-through was pooled for each biological replicate form each treatment and was concentrated by syringe filtration, using a 0.20-μm Micropore membrane (Millipore). Filters were placed in homogenization tubes, were flash frozen in liquid nitrogen, and were stored at −80°C for RNA extraction.The filter membranes were homogenized in Trizol reagent (Thermo Fisher Scientific, Waltham, MA) for 1 min at 1,750 Hz, using a Geno/Grinder (Thermo Fisher Scientific, Waltham, MA) followed by the chloroform-ethanol isolation from manufacture (TRIzol™ Reagent User Guide, Pub. No. MAN0001271 D). For in vitro samples, 1 ml of the 1 × 109 CFU/ml bacterial inoculum in 0.25 mM MgCl2 was pelleted and RNA was extracted followed by the same procedure above.
The plant samples were depleted of rRNA using the QIAseq FastSelect –rRNA Plant Kit (Qiagen, Germantown, MD) and bacteria samples were depleted of rRNA using the QIAGEN FastSelect rRNA HMR Kit.

treatment_protocol: Four marked leaves each on plants (80-100 leaves per strains per treatment) were treated with either 1 mM flg22 in 0.1% DMSO or with 0.1% DMSO (mock) by infiltration with a 1 mL blunt syringe on the abaxial surface. Plants were kept uncovered in the growth room for 16 hours prior to bacterial inoculation.

value: in vitro

value: cvsR knockout

value: pellet


title: Day 5 Blastocyst ICM 1

description: Library name: D5-ICM-1_run1


title: Day 5 Blastocyst ICM 9

description: Library name: D5-ICM-9_run3

value: run 3


title: Day 5 Blastocyst ICM 11

description: Library name: D5-ICM-11_run2


title: DOGMA-plex HTO library 16

description:
Library name: DOGMA-plex HTO library 16
HTO


title: DOGMA-plex HTO library 28

description:
Library name: DOGMA-plex HTO library 28
HTO


title: cvsR, Pellet Rep2

description: Library name: sample17


title: CCI_WT_1

description: Library name: sample13

value: DRGs

value: WT


title: cvsR, Pellet Rep1

description: Library name: sample16


title: DOGMA-plex HTO library 12

description:
Library name: DOGMA-plex HTO library 12
HTO


title: Day 5 Blastocyst ICM 6

description: Library name: D5-ICM-6_run3


title: CCI_WT_2

description: Library name: sample14

value: lumbar

value: CCI


title: DOGMA-plex HTO library 13

description:
Library name: DOGMA-plex HTO library 13
HTO


title: wildtype, Pellet Rep2

description: Library name: sample14


title: wildtype, Pellet Rep3

description: Library name: sample15


title: CCI_WT_3

description: Library name: sample15

value: day 30


title: CCI_KO_4

description: Library name: sample12

value: KO


title: Day 5 Blastocyst TE 7

description: Library name: D5-TE-7_run3

value: Blastocyst


title: CCI_KO_3

description: Library name: sample11


title: DOGMA-plex HTO library 10

description:
Library name: DOGMA-plex HTO library 10
HTO


title: wildtype, Pellet Rep1

description: Library name: sample13


title: cvsR, flg22 Rep3

description: Library name: sample12

source_name: plant

value: plant

value: leaf


title: cvsR, flg22 Rep1

description: Library name: sample10


title: cvsR, Mock Rep1

description: Library name: sample7

value: mock


title: Sham_WT_4

description: Library name: sample8

value: Sham


title: wildtype, flg22 Rep3

description: Library name: sample6


title: DOGMA-plex HTO library 7

description:
Library name: DOGMA-plex HTO library 7
HTO

value: primary T cells


title: Sham_WT_3

description: Library name: sample7


title: wildtype, flg22 Rep1

description: Library name: sample4


title: DOGMA-plex HTO library 6

description:
Library name: DOGMA-plex HTO library 6
HTO


title: wildtype, flg22 Rep2

description: Library name: sample5


title: wildtype, Mock Rep3

description: Library name: sample3


title: DOGMA-plex HTO library 14

description:
Library name: DOGMA-plex HTO library 14
HTO


title: DOGMA-plex HTO library 9

description:
Library name: DOGMA-plex HTO library 9
HTO


title: wildtype, Mock Rep2

description: Library name: sample2


title: cvsR, Mock Rep2

description: Library name: sample8


title: Sham_WT_1

description: Library name: sample5


title: HC5-H

city: Guangzhou

first: Huan

last: Dong

state: Guangdong

address: No. 58, Zhongshan Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University First Affiliated Hospital

description:
Library name: Sample11
HC5-H

data_processing:
Raw reads were filtered to remove the adaptor by cutadapt (v2.10). Reads were aligned to the human Ensemble genome GRCh38 using STAR (v2.7.3a). We use featureCounts (v1.6.3; https://subread.sourceforge.net/featureCounts.html) to perform quantification on the mapped sequences. The differential expression analysis was performed with the DESeq2 (v1.18.1).
Assembly: hg38
Supplementary files format and content: xlsx fles include FPKM values for each Sample

source_name: Plasma

growth_protocol: Whole blood specimens were collected using disposable EDTA-containing vacuum blood collection tubes, and subjected to separation within 2 hours post-collection via centrifugation at 700g for 20 minutes in a 4℃ refrigerated centrifuge.

extract_protocol:
Each sample was lysed thoroughly by adding Magzol LS Reagent (Magen, catalog no. 110200) at a 3:1 volume ratio (reagent to plasma). Total RNA was subsequently isolated and purified using the phenol-chloroform extraction protocol.
Library preparation using the EpiTM mini longRNA-seq kit: Add 5X RT Buffer and rRNA Probe to fragmented RNA to remove ribosomal RNA; after rRNA removal, add RT primer, TSO primer, RT IV Enzyme, RNase Inhibitor, and EPI RT Enhancer, react at 42°C for 90 minutes and at 70°C for 15 minutes to inactivate the enzyme, synthesizing the first-strand cDNA according to the SMART principle; after magnetic bead purification, add EPI HiFi Amplification MIX and index primers for PCR amplification to enrich library fragments, purify fragments with magnetic beads, perform a second round of PCR amplification to further enrich the obtained fragments, and purify DNA library fragments with magnetic beads; sequencing is performed using the Genmai SURFSeq 5000 high-throughput sequencing platform in PE150 sequencing mode.

value: Plasma

tag: disease state

value: healthy


title: DOGMA-plex HTO library 8

description:
Library name: DOGMA-plex HTO library 8
HTO


title: HC3-H

description:
Library name: Sample9
HC3-H


title: cvsR, flg22 Rep2

description: Library name: sample11

value: cvsR knockout


title: CCI_KO_2

description: Library name: sample10


title: Sham_WT_2

description: Library name: sample6


title: HC2-H

description:
Library name: Sample8
HC2-H


title: cvsR, Mock Rep3

description: Library name: sample9


title: DOGMA-plex HTO library 3

description:
Library name: DOGMA-plex HTO library 3
HTO


title: DOGMA-plex HTO library 5

description:
Library name: DOGMA-plex HTO library 5
HTO


title: DOGMA-plex HTO library 2

description:
Library name: DOGMA-plex HTO library 2
HTO


title: DOGMA-plex HTO library 17

description:
Library name: DOGMA-plex HTO library 17
HTO


title: HC1-H

description:
Library name: Sample7
HC1-H


title: Sham_WT_5

description: Library name: sample9


title: Sham_KO_2

description: Library name: sample2


title: HC6-H

description:
Library name: Sample12
HC6-H


title: DOGMA-plex HTO library 1

description:
Library name: DOGMA-plex HTO library 1
HTO


title: RA4-H

description:
Library name: Sample4
RA4-H

value: rheumatoid arthritis


title: Sham_KO_4

description: Library name: sample4


title: RA5-H

description:
Library name: Sample5
RA5-H


title: DOGMA-plex ADT library 28

description:
Library name: DOGMA-plex ADT library 28
ADT


title: RA3-H

description:
Library name: Sample3
RA3-H


title: P8w PTHrP-mCherry+ scRNA-seq

city: Houston

first: Taishi

last: Komori

state: TX

address: 7500 Cambridge St #1210

institute: The University of Texas Health School of Dentistry

description: Library name: Sample_3

data_processing:
Raw BCL converted to FASTQ (Illumina bcl-convert). Reads processed with Cell Ranger count v6.1.2 (10x Genomics) using default settings; introns not included.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Molars

extract_protocol:
Mandibular molars were dissected and enzymatically dissociated. Single-cell suspensions were filtered (70 µm) and resuspended in DPBS/1% FBS. PTHrP-mCherry⁺ cells were isolated by FACS (BD FACSAria III; 407/488/561/633 nm; 100-µm nozzle) directly into ice-cold buffer.
Single-cell libraries were prepared with the 10x Genomics Chromium Single Cell 3’ kit (v3.1) following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000.

value: Molars

value: PTHrP-mCherry+ cementoblasts and precursors

value: Pthrp-mCherry knock-in


title: DOGMA-plex HTO library 11

description:
Library name: DOGMA-plex HTO library 11
HTO


title: RA2-H

description:
Library name: Sample2
RA2-H


title: wildtype, Mock Rep1

description:
Library name: sample1
column name in processed raw count Count.csv

value: WT


title: RA1-H

description:
Library name: Sample1
RA1-H


title: P25 PTHrP-mCherry+ scRNA-seq

description: Library name: Sample_2


title: DOGMA-plex HTO library 4

description:
Library name: DOGMA-plex HTO library 4
HTO


title: HC6-P

description:
Library name: Sample12
HC6-P_all

data_processing:
Small RNA sequences were annotated using the software SPORTS1.1 with one mismatch tolerance (parameter setting: -M 1). The tsRNAs were annotated based on both pre-tRNA and mature tRNA sequences. Mature tRNA sequences were derived from the GtRNAdb and mitotRNAdb sequences
Assembly: hg38
Supplementary files format and content: xls fles include RPM values for each Sample

growth_protocol: Whole blood was collected in EDTA anticoagulant tubes. Within two hours of collection, the tubes were gently inverted 8-10 times and centrifuged at 700 × g for 20 minutes at 4°C. The plasma supernatant was then aliquoted into sterile cryovials  and stored at -80°C.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (1 ml; Invitrogen; 15596018). Small RNAs of 15–50 nucleotides was selected.
The RNA segment was fractionated using PAGE, then a 15- to 45-nucleotide stripe was selected and purified. Adapter ligation and library amplification were performed using the QIAseq® miRNA Library Kit (QIAGEN; 331505). The amplified libraries were sequenced on Next-Generation Sequencing (NGS) platform.


title: DOGMA-plex ADT library 26

description:
Library name: DOGMA-plex ADT library 26
ADT


title: HC4-P

description:
Library name: Sample10
HC4-P_all


title: P15 PTHrP-mCherry+ scRNA-seq

description: Library name: Sample_1


title: HC2-P

description:
Library name: Sample8
HC2-P_all


title: HC3-P

description:
Library name: Sample9
HC3-P_all


title: Splenic cDC1, Uqcfqf/f, rep 3

description:
Library name: IH_12
Bisulfite-converted DNA

data_processing:
Reads were trimmed to remove adapter contaminants and filtered out based on quality using TrimGalore (v0.6.10) and aligned to the reference genome GRCm38/MM10 using BSMAP (v2.9).
The only uniquely mapped reads are selected to sort, index and PCR duplicates are removed with SAMBAMBA (v0.5.9). The methylation ratio of every single cytosine location is extracted from the mapping results using BSMAP. The results of the coverage profiles were calculated as "# of C / effective CT counts" for each cytosine in CpG, CHH and CHG.
Assembly: GRCm38/MM10 using BSMAP
Supplementary files format and content: Methylation profile (CpG site in each chromosome)

extract_protocol:
Genomic DNA was harvested using the DNA Micro kit (Qiagen).
Subsequent analysis was carried out by Macrogen NGS Service. Briefly, genomic DNA is bisulfite-treated, then sequentially adapter-tailed, extended, ligated, and amplified by indexing PCR to generate full-length libraries, with bead-based clean-ups at each step to remove small fragments and adjust buffer conditions.

treatment_protocol: The spleen from 6-8 week old Uqcrqf/f,  Itgax-Uqcrqf/f, Uqcrqf/f AOX-Rosa26 or Itgax-Uqcrqf/f AOX-Rosa26 male or female mice  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-).

value: Spleen

value: Uqcrqf/f


title: HC5-P

description:
Library name: Sample11
HC5-P_all


title: HC1-P

description:
Library name: Sample7
HC1-P_all


title: Splenic cDC1, Itgax-Uqcfqf/f , rep3

description:
Library name: IH_11
Bisulfite-converted DNA

value: Itgax-Uqcrqf/f


title: DOGMA-plex ADT library 24

description:
Library name: DOGMA-plex ADT library 24
ADT


title: DOGMA-plex ADT library 23

description:
Library name: DOGMA-plex ADT library 23
ADT


title: DOGMA-plex ADT library 25

description:
Library name: DOGMA-plex ADT library 25
ADT


title: RA5-P

description:
Library name: Sample5
RA5-P_all


title: Splenic cDC1, Uqcfqf/f AOX-Rosa26, rep 3

description:
Library name: IH_10
Bisulfite-converted DNA

value: Uqcrqf/f AOX-Rosa26


title: RA4-P

description:
Library name: Sample4
RA4-P_all


title: DOGMA-plex ADT library 22

description:
Library name: DOGMA-plex ADT library 22
ADT


title: RA6-P

description:
Library name: Sample6
RA6-P_all


title: Sham_KO_3

description: Library name: sample3

value: DRGs

value: lumbar

value: KO

value: day 30


title: RA6-H

description:
Library name: Sample6
RA6-H


title: Splenic cDC1, Itgax-Uqcfqf/f AOX-Rosa26 , rep3

description:
Library name: IH_09
Bisulfite-converted DNA

value: Itgax-Uqcrqf/f AOX-Rosa26


title: RA2-P

description:
Library name: Sample2
RA2-P_all

value: Plasma


title: DOGMA-plex ADT library 21

description:
Library name: DOGMA-plex ADT library 21
ADT

value: primary T cells


title: RA1-P

description:
Library name: Sample1
RA1-P_all


title: HC4-H

description:
Library name: Sample10
HC4-H

value: healthy


title: Splenic cDC1, Itgax-Uqcfqf/f AOX-Rosa26 , rep2

description:
Library name: IH_08
Bisulfite-converted DNA


title: DOGMA-plex ADT library 20

description:
Library name: DOGMA-plex ADT library 20
ADT


title: Sham_KO_1

description: Library name: sample1

value: Sham


title: P2024_123 Ileum,  rep15

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description: Library name: 2024_123

data_processing:
FastQC (version 0.12.1) and MultiQC (version 1.25.2) were used for quality control of raw paired-end fastq files.
Illumina's adaptors as well as low quality reads were trimmed out using TrimGalore (version 0.39)
Transcript quantification was performed using Salmon (version 1.10.3) on trimmed fastqs against GENCODE V47 transcript reference database (assembly GRCh38)
Quantified transcripts were imported in R (version 4.4.0) using the package tximport (version 1.24.0)
Count data handling and differential analysis were performed using the package DESeq2 (version 1.36.0)
Genes were pre-filtered out if they expressed (count > 0) in less than 60% of samples of 1 group.
Assembly: GENCODE 47/GRCh38
Supplementary files format and content: tab delimited transcript quantification (Salmon output)

source_name: Ileum

extract_protocol:
Biopsies samples were stored in RNAlater™ solution. They were first mechanically dissociated to obtain a single-cell suspension, then processed for total RNA extraction using the RNeasy® Kit (Qiagen), following the manufacturer’s protocol. Each RNA sample was eluted in 20μl elution buffer and stored in low-binding tubes. The quality control of the extracted RNA was performed using micro-electrophoresis on the 4200 Tapestation system (Agilent®). RNA samples were stored at a temperature below −80°C.
RNA-seq libraries were constructed from a standardized input of 250 ng of total RNA per sample. Libraries were prepared according to the manufacturer's instructions for the Takara SMARTer Stranded Total RNA Sample Prep Kit (634876, Takara Bio USA). Quality control of the RNA-seq libraries was performed using micro-electrophoresis on the 4200 Tapestation system (Agilent®). RNA-seq data were generated using an Illumina NovaSeq X with a 200 bp paired-end read format, targeting 50 million reads per sample.

value: Ileum


title: P2024_122 Rectum,  rep14

description: Library name: 2024_122

source_name: Rectum

value: Rectum


title: DOGMA-plex ADT library 18

description:
Library name: DOGMA-plex ADT library 18
ADT


title: P2024_119 Ileum,  rep13

description: Library name: 2024_119


title: DOGMA-plex ADT library 19

description:
Library name: DOGMA-plex ADT library 19
ADT


title: P2024_118 Ileum,  rep12

description: Library name: 2024_118


title: P2024_121 Ileum,  rep14

description: Library name: 2024_121


title: DOGMA-plex ADT library 17

description:
Library name: DOGMA-plex ADT library 17
ADT


title: DOGMA-plex ADT library 27

description:
Library name: DOGMA-plex ADT library 27
ADT


title: Splenic cDC1, Itgax-Uqcfqf/f AOX-Rosa26 , rep1

description:
Library name: IH_04
Bisulfite-converted DNA

source_name: Spleen


title: P2024_115 Ileum,  rep11

description: Library name: 2024_115


title: DOGMA-plex ADT library 16

description:
Library name: DOGMA-plex ADT library 16
ADT


title: P2024_114 Colon,  rep7

description: Library name: 2024_114

source_name: Colon

value: Colon


title: P2024_113 Rectum,  rep12

description: Library name: 2024_113


title: P2024_112 Rectum,  rep11

description: Library name: 2024_112


title: DOGMA-plex ADT library 15

description:
Library name: DOGMA-plex ADT library 15
ADT


title: P2024_111 Ileum,  rep10

description: Library name: 2024_111


title: Splenic cDC1, Uqcfqf/f, rep 1

description:
Library name: IH_03
Bisulfite-converted DNA


title: Splenic cDC1, Uqcfqf/f AOX-Rosa26, rep 1

description:
Library name: IH_01
Bisulfite-converted DNA


title: Splenic cDC1, Uqcfqf/f AOX-Rosa26, rep 2

description:
Library name: IH_07
Bisulfite-converted DNA


title: DOGMA-plex ADT library 13

description:
Library name: DOGMA-plex ADT library 13
ADT


title: P2024_110 Ileum,  rep9

description: Library name: 2024_110


title: DOGMA-plex ADT library 14

description:
Library name: DOGMA-plex ADT library 14
ADT


title: P2024_107 Rectum,  rep10

description: Library name: 2024_107


title: DNase-seq_DN3_GATA3_WT_rep1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Library name: DNase-seq_DN3_GATA3_WT_rep1

data_processing:
All bioinformatics analyses were performed using mouse (mm10) and human (hg38) reference genomes annotated by GENCODE (M21 and V30, respectively) (Frankish, et al., 2019).  DNase-seq were processed from raw reads into reads-per-million (RPM)-normalized bigWig tracks following established pipelines (Cao, et al., 2023; Cui, et al., 2023). Briefly, sequencing reads were mapped using Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012), retaining only non-redundant reads with MAPQ ≥ 10 for downstream analyses. Peak calling was performed using the cLoops2 callPeaks module (Cao, et al., 2022) with pooled replicates and assay-specific parameters: DNase-seq (-eps 75,150 -minPts 10,20 -sen). Genome-browser-style visualizations were generated using the cLoops2 plotting module (5), and averaged tracks from biological replicates were produced using the bigwigCompare function from deepTools2 (Ramirez, et al., 2016).
Assembly: mm10
Supplementary files format and content: BigWig files containing signals normalized as reads per million (RPM)

source_name: thymus

extract_protocol:
The GATA3-fl/fl-CreERT mice were treated with or without tamoxifen for 3 days. To sort DN3 T cells, single cell suspension was prepared from thymus and CD4/CD8 T cells were labeled with unlabeled anti-CD4 and anti-CD8 antibody. BioMag Goat anti-rat IgG beads from QIAGEN were added and bead-bound CD4/CD8 T cells were removed. The remaining cells were stained with linage markers (anti-CD4, CD8a, TCR gamma/delta, CD19, B220, Gr-1, CD11b, CD11c, Nk1.1 and Ter119) and anti-CD3, CD44, CD25. DN3 T subset were sorted as linage-CD3-CD44-CD25+.     The primary fibroblasts were isolated from mice ear in WT and BRG1-AID mice. In brief, the ear was cut into 1 ~ 3 mm pieces, incubated with 0.25% trypsin–EDTA solution for 30 min at 37 °C, neutralized by culture medium with FBS and then plated on 6 well plate with coverslip on it. Fibroblasts will migrate from tissues during the 3 ~ 5-day culture period. After reaching the appropriate confluence, tissues will be removed and primary fibroblasts will be passaged and maintained in DMEM medium (high glucose) containing 10% fetal bovine serum.  For plasmid transfection in fibroblasts, 20 μg plasmid DNA was used for each 10 cm dish using a combination of two commercial reagents, Lipofectamine LTX (Cat. No. 15338100) and FuGENE HD (Cat. No. E2311) with the ratio of 1:1. The auxin was added 24 h later after transfection and incubated for 8 ~ 10 h. Then, the live fibroblasts were sorted for further experiments.
DNase-seq assays were performed as described previously. Briefly, 10,000 cells from each group were collected by FACS sorting and fixed in 1% formaldehyde for 10min at RT. The fixation was stopped by glycine and washed twice by PBS buffer. DNase I was added to each sample and incubated at 37 °C for 1 min. Reactions were stopped by adding stop buffer (10 mM Tris-HCl, 10 mM NaCl, 0.1% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 65 °C overnight, and DNAs were purified by using MinElute reaction cleanup kit following the manufacturer’s protocol. DNase-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For fibroblasts, equal amount of human 293T cells were added as spike in before DNase treatment.

value: thymus

value: GATA3 fl/fl Cre-ERT

value: GATA3 KO


title: DNase-seq_DN3_GATA3_WT_rep2

description: Library name: DNase-seq_DN3_GATA3_WT_rep2


title: DOGMA-plex ADT library 12

description:
Library name: DOGMA-plex ADT library 12
ADT

source_name: primary T cells


title: P2024_106 Rectum,  rep9

description: Library name: 2024_106


title: DOGMA-plex ADT library 11

description:
Library name: DOGMA-plex ADT library 11
ADT


title: DNase-seq_DN3_GATA3_KO_rep2

description: Library name: DNase-seq_DN3_GATA3_KO_rep2


title: P2024_103 Ileum,  rep7

description: Library name: 2024_103


title: P2024_102 Ileum,  rep6

description: Library name: 2024_102


title: DNase-seq_DN3_GATA3_KO_rep1

description: Library name: DNase-seq_DN3_GATA3_KO_rep1


title: P2024_108 Ileum,  rep8

description: Library name: 2024_108


title: DOGMA-plex ADT library 9

description:
Library name: DOGMA-plex ADT library 9
ADT


title: RA3-P

description:
Library name: Sample3
RA3-P_all


title: 1-month, thalamus, wild-type replicate 5

description:
Library name: P28-TH-WT5
1-mo_TH_WT_5

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: Wild-type


title: P2024_100 Rectum,  rep7

description: Library name: 2024_100


title: DOGMA-plex ADT library 10

description:
Library name: DOGMA-plex ADT library 10
ADT


title: P2024_098 Rectum,  rep6

description: Library name: 2024_098


title: P2024_120 Colon,  rep9

description: Library name: 2024_120


title: Splenic cDC1, Uqcfqf/f, rep 2

description:
Library name: IH_06
Bisulfite-converted DNA

value: Spleen

value: Uqcrqf/f


title: P2024_116 Colon,  rep8

description: Library name: 2024_116


title: 1-month, thalamus, wild-type replicate 4

description:
Library name: P28-TH-WT4
1-mo_TH_WT_4


title: P2024_099 Colon,  rep14

description: Library name: 2024_099


title: 1-month, thalamus, wild-type replicate 3

description:
Library name: P28-TH-WT3
1-mo_TH_WT_3


title: P2024_096 Colon,  rep11

description: Library name: 2024_096


title: P2024_095 Rectum,  rep5

description: Library name: 2024_095


title: DOGMA-plex ADT library 7

description:
Library name: DOGMA-plex ADT library 7
ADT


title: P2024_109 Colon,  rep6

description: Library name: 2024_109


title: Splenic cDC1, Itgax-Uqcfqf/f , rep1

description:
Library name: IH_02
Bisulfite-converted DNA

value: Itgax-Uqcrqf/f


title: DOGMA-plex ADT library 6

description:
Library name: DOGMA-plex ADT library 6
ADT


title: Splenic cDC1, Itgax-Uqcfqf/f , rep2

description:
Library name: IH_05
Bisulfite-converted DNA


title: DOGMA-plex ADT library 4

description:
Library name: DOGMA-plex ADT library 4
ADT


title: P2024_104 Colon,  rep4

description: Library name: 2024_104


title: P2024_097 Colon,  rep12

description: Library name: 2024_097


title: P2024_089 Ileum,  rep4

description: Library name: 2024_089


title: DOGMA-plex ADT library 3

description:
Library name: DOGMA-plex ADT library 3
ADT


title: 1-month, thalamus, heterozygous replicate 4

description:
Library name: P28-TH-HT4
1-mo_TH_HET_4

value: Srrm2 +/-


title: P2024_090 Ileum,  rep5

description: Library name: 2024_090


title: P2024_088 Rectum,  rep3

description: Library name: 2024_088


title: P2024_105 Colon,  rep5

description: Library name: 2024_105


title: DOGMA-plex ADT library 2

description:
Library name: DOGMA-plex ADT library 2
ADT


title: P2024_086 Rectum,  rep1

description: Library name: 2024_086


title: P2024_094 Colon,  rep10

description: Library name: 2024_094


title: 1-month, thalamus, heterozygous replicate 5

description:
Library name: P28-TH-HT5
1-mo_TH_HET_5


title: DOGMA-plex ADT library 1

description:
Library name: DOGMA-plex ADT library 1
ADT


title: P2024_092 Rectum,  rep4

description: Library name: 2024_092


title: P2024_083 Colon,  rep2

description: Library name: 2024_083


title: P2024_117 Rectum,  rep13

description: Library name: 2024_117


title: DOGMA-plex GEX library 28

description:
Library name: DOGMA-plex GEX library 28
RNA


title: P2024_081 Colon,  rep1

description: Library name: 2024_081


title: DOGMA-plex GEX library 27

description:
Library name: DOGMA-plex GEX library 27
RNA


title: DMSO_WGBS

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: DMSO_WGBS

data_processing:
The Illumina adapters and low-complexity adapters were removed from the reads using Trim Galore! (version 0.6.7), cutadapt (version 4.1), and an in-house bash script.
Then the reads were mapped to the human genome hg38 using the bisulfite converted read mapper Bismark (version v0.16.3) and Bowtie2 (version 2.1.0).
Methylation percentages for CpG sites were calculated using the bismark_methylation_extractor script from Bismark and an in-house Perl script. CpG sites with read coverage ≥ 10x were considered as qualified for further analysis.
Assembly: hg38
Supplementary files format and content: Methylation percentages for CpG sites with read coverage ≥10x, formatted for methylKit input (chrBase, chr, base, strand, coverage, freqC [methylation percentage], freqT).

growth_protocol: HUDEP-2 cells were maintained in expansion medium (StemSpanTM SFEM, STEMCELL #09650) supplemented with 50 ng/mL stem cell factor (SCF) (STEMCELL #78062), 1 μg/mL doxycycline (Sigma-Aldrich #D9891), 0.4 μg/mL dexamethasone (Sigma-Aldrich #D4902), 3 IU/mL erythropoietin (STEMCELL #78007), 2% penicillin–streptomycin (Gibco #15140148), and 1% L-glutamine (STEMCELL #07100). Cells were expanded for 3-4 days. Erythroid differentiation medium (EDM) consisted of Iscove’s Modified Dulbecco’s Medium (IMDM) (Sigma-Aldrich #51471C) supplemented with 330 μg/mL holo-transferrin (Sigma-Aldrich #T0665), 10 μg/mL insulin (Sigma-Aldrich #I9278), 2 IU/mL heparin (Sigma-Aldrich #H3149), 5% fetal bovine serum (FBS) (Sigma-Aldrich #F4135), 3 IU/mL erythropoietin, 2% penicillin–streptomycin and 1% L-glutamine. For stage 2 (differentiation-growth, 4 days), EDM was further supplemented with 100 ng/mL SCF and 1 μg/mL doxycycline. For stage 3 (differentiation-maturation, 2 days), EDM contained only 1 μg/mL doxycycline. All cultures cells were maintained at 37°C with 5% CO2.

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA Mini Kit (Invitrogen #K182001). Between 10–100 ng of genomic DNA was mixed with 0.5% lambda DNA and subjected to bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research #5031).
Bisulfite-converted DNA was used to prepare sequencing libraries with the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences #30024).

treatment_protocol: Compounds in 0.1% DMSO (final) were added in fresh medium beginning at expansion stage and continued through stages of differentiation-growth and differentiation-maturation.

value: human erythrocyte precursor

value: HUDEP-2 cells normally express adult hemoglobin

value: DMSO

tag: differentiation status

value: differentiated


title: 1-month, striatum, wild-type replicate 5

description:
Library name: P28-ST-WT5
1-mo_ST_WT_5


title: 1-month, thalamus, wild-type replicate 2

description:
Library name: P28-TH-WT2
1-mo_TH_WT_2


title: DOGMA-plex GEX library 26

description:
Library name: DOGMA-plex GEX library 26
RNA

value: primary T cells


title: P2024_093 Colon,  rep13

description: Library name: 2024_093


title: 1-month, thalamus, wild-type replicate 1

description:
Library name: P28-TH-WT1
1-mo_TH_WT_1


title: DOGMA-plex ADT library 5

description:
Library name: DOGMA-plex ADT library 5
ADT


title: DNMT1_WGBS

description: Library name: DNMT1_WGBS

value: treated HUDEP-2 cells increased expression of fetal hemoglobin


title: P2024_101 Rectum,  rep8

description: Library name: 2024_101

value: Rectum


title: P2024_091 Colon,  rep3

description: Library name: 2024_091

value: Colon


title: 1-month, striatum, wild-type replicate 4

description:
Library name: P28-ST-WT4
1-mo_ST_WT_4


title: 1-month, thalamus, heterozygous replicate 1

description:
Library name: P28-TH-HT1
1-mo_TH_HET_1


title: 1-month, thalamus, heterozygous replicate 3

description:
Library name: P28-TH-HT3
1-mo_TH_HET_3


title: P2024_087 Rectum,  rep2

description: Library name: 2024_087


title: P2024_085 Ileum,  rep3

description: Library name: 2024_085

value: Ileum


title: DOGMA-plex ADT library 8

description:
Library name: DOGMA-plex ADT library 8
ADT


title: P2024_082 Ileum,  rep1

description: Library name: 2024_082


title: P2024_084 Ileum,  rep2

description: Library name: 2024_084


title: 1-month, striatum, wild-type replicate 3

description:
Library name: P28-ST-WT3
1-mo_ST_WT_3


title: Control9

description:
Library name: Sample19
C9

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequencing quality are examined by FastQC (pass Illumina quality filter),  and reads were trimmed 5 ,3-adaptor bases by cutadapt.
The expression profiling of tRF & tiRNA  were calculated based on counts of reads mapped.
Reads were aligned allowing for 1 mismatch only to the mature tRNA sequences,  then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Differential expression analysis of tRF&tiRNAs between groups was performed using edgeR. For differentially expressed tRF&tiRNAs were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1
Assembly: GRCh38
Supplementary files format and content: the CPM value of detected tRF&tiRNA for each sample

source_name: Serum

growth_protocol: Venous blood samples obtained after overnight fasting were aseptically processed(centrifugation at 1000 × g for 10 min at 4 °C) to obtain serum, which was then stored at −80 °C. Serum samples were collected from 10 gout patients and 10 HCs.

extract_protocol:
Serum RNA was extracted using TRIzol LS reagent (Cat#10296028, Invitrogen, USA) according to the manufacturer’s protocol. Briefly, 0.25 ml serum was added to a 1.5 ml tube mixed with 0.75 ml TRIzol LS reagent and swirled. The mixtures were incubated on ice for 2 h with occasional vortexing to ensure the serum was completely cracked. Then, 0.2 ml chloroform was added to the mixtures, vortexed, and incubated at room temperature for 10 min. The samples were centrifuged at 12,000×g for 15 min at 4 °C. Next, the aqueous phase was collected into a tube filled with an equal volume of isopropanol. Then, the mixtures were gently mixed with 1.5 μl glycogen (Cat#10901393001, Roche, Switzerland) and refrigerated at −80 °C for at least 30 min to precipitate RNA. The mixture was centrifuged at 12,000×g for 30 min at 4 °C, and the pellet was washed with 75% cold ethanol twice. Finally, the RNA pellet was dissolved in 10 μl of RNase-free water after being dried and stored at −80 °C.
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3-aminoacyl (charged) deacylation to 3-OH for 3-adaptor ligation, 3-cP(2,3-cyclic phosphate) removal to 3-OH for 3-adaptor ligation, 5-OH(hydroxyl group) phosphorylation to 5-P for 5-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Then pretreated total RNA was used to prepare the sequencing library in the following steps: 1) 3-adapter ligation; 2) 5-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturer sinstructions.

value: Serum


title: EED_WGBS

description: Library name: EED_WGBS

value: EED-inhibitor


title: Femur, Sham1

city: Fuzhou

first: tianpeng

last: dai

address: No. 1 Qiuyang Road, Shangjie Town, Minhou County

department: College of Orthopedics and Traumatology

institute: Fujian University of Traditional Chinese Medicine

description: Library name: Sham1

data_processing:
CLC Genomics 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 mRatBN7.2  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: mRatBN7.2
Supplementary files format and content: tab-delimited text files include FPKM value and gene count for each Sample

organism: Rattus norvegicus

source_name: Femur

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Femur

value: Sham group:Intact rat femur, 7 days post-sham surgery.


title: Control10

description:
Library name: Sample20
C10


title: Femur, GPI1

description: Library name: GPI1

value: GPI group:Intact rat femur, 7 days post-distal femoral growth plate injury.


title: Femur, GPI2

description: Library name: GPI2


title: Femur, GMTT3

description: Library name: GMTT3

value: GMTT group:Rat femur with intact growth plate, 7 days post-injury and GMTT hydrogel treatment.


title: Control8

description:
Library name: Sample18
C8


title: DOGMA-plex GEX library 25

description:
Library name: DOGMA-plex GEX library 25
RNA

data_processing:
Fastqs were generated using CellRanger-arc mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-arc or cellranger count for the hg38 reference genome
For ADT, HTO and CT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Assembly: hg38
Supplementary files format and content: Per-barcode count abundance for the protein and viral barcode count data including the scRNA and scMultiome singlecell QC metrics; barcoded accessible chromatin fragments and transcripts per library

extract_protocol:
Digitonin lysis for DOGMA-seq and standard 10x Genomics protocol for scRNA-seq
DOGMA-seq libraries were constructed according to previously described protocols (Mimitou et al, 2021). icCITE-seq libraries were constructed as described previously (Chen et al., 2025) and CITE tags were prepared as described in CITE-seq protocols (Stoeckius et al, 2017). Viral barcodes were amplified by two rounds of DialOut PCR adapted from Perturb-CITE-seq (Frangieh et al., 2021).


title: Femur, Sham3

description: Library name: Sham3


title: NonDiff_WGBS

description: Library name: NonDiff_WGBS

value: untreated

value: non-differentiated


title: 1-month, striatum, heterozygous replicate 4

description:
Library name: P28-ST-HT4
1-mo_ST_HET_4

value: Brain

value: Srrm2 +/-


title: DOGMA-plex GEX library 23

description:
Library name: DOGMA-plex GEX library 23
RNA


title: Femur, Sham2

description: Library name: Sham2


title: 1-month, striatum, wild-type replicate 2

description:
Library name: P28-ST-WT2
1-mo_ST_WT_2

value: Wild-type


title: Control7

description:
Library name: Sample17
C7


title: 1-month, thalamus, heterozygous replicate 2

description:
Library name: P28-TH-HT2
1-mo_TH_HET_2


title: Femur, GPI3

description: Library name: GPI3


title: 1-month, striatum, heterozygous replicate 5

description:
Library name: P28-ST-HT5
1-mo_ST_HET_5


title: DOGMA-plex GEX library 18

description:
Library name: DOGMA-plex GEX library 18
RNA


title: 1-month, striatum, wild-type replicate 1

description:
Library name: P28-ST-WT1
1-mo_ST_WT_1


title: Femur, GMTT2

description: Library name: GMTT2


title: DOGMA-plex GEX library 22

description:
Library name: DOGMA-plex GEX library 22
RNA


title: Control4

description:
Library name: Sample14
C4


title: 1-month, striatum, heterozygous replicate 3

description:
Library name: P28-ST-HT3
1-mo_ST_HET_3


title: Control6

description:
Library name: Sample16
C6


title: Femur, GMTT1

description: Library name: GMTT1


title: Control3

description:
Library name: Sample13
C3


title: 1-month, somatosensory cortex, wild-type replicate 5

description:
Library name: P28-SSC-WT5
1-mo_SSC_WT_5


title: DOGMA-plex GEX library 19

description:
Library name: DOGMA-plex GEX library 19
RNA


title: DOGMA-plex GEX library 21

description:
Library name: DOGMA-plex GEX library 21
RNA


title: Control1

description:
Library name: Sample11
C1


title: DOGMA-plex GEX library 20

description:
Library name: DOGMA-plex GEX library 20
RNA


title: 1-month, somatosensory cortex, wild-type replicate 4

description:
Library name: P28-SSC-WT4
1-mo_SSC_WT_4


title: DOGMA-plex GEX library 15

description:
Library name: DOGMA-plex GEX library 15
RNA


title: Gout10

description:
Library name: Sample10
T10

tag: gender

value: male

tag: age

tag: sua(μmol/l)

tag: ast(u/l)

tag: alt(u/l)

tag: crea(μmol/l)

tag: crp(mg/l)


title: 1-month, somatosensory cortex, wild-type replicate 3

description:
Library name: P28-SSC-WT3
1-mo_SSC_WT_3

tag: tissue


title: Gout9

description:
Library name: Sample9
T9


title: DOGMA-plex GEX library 17

description:
Library name: DOGMA-plex GEX library 17
RNA

value: primary T cells


title: Gout6

description:
Library name: Sample6
T6


title: 1-month, somatosensory cortex, wild-type replicate 1

description:
Library name: P28-SSC-WT1
1-mo_SSC_WT_1


title: Gout3

description:
Library name: Sample3
T3


title: 1-month, striatum, heterozygous replicate 2

description:
Library name: P28-ST-HT2
1-mo_ST_HET_2


title: 1-month, somatosensory cortex, heterozygous replicate 5

description:
Library name: P28-SSC-HT5
1-mo_SSC_HET_5


title: Control2

description:
Library name: Sample12
C2


title: DOGMA-plex GEX library 11

description:
Library name: DOGMA-plex GEX library 11
RNA


title: 1-month, somatosensory cortex, heterozygous replicate 4

description:
Library name: P28-SSC-HT4
1-mo_SSC_HET_4


title: Gout2

description:
Library name: Sample2
T2


title: DOGMA-plex GEX library 24

description:
Library name: DOGMA-plex GEX library 24
RNA


title: DOGMA-plex GEX library 10

description:
Library name: DOGMA-plex GEX library 10
RNA


title: in vitro iCLIP, RNA oligo library, 7-deaza-GTP RNA, rep4

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

description: Library name: 7dGTP_rep4

library_source: other

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_rep1: NNNNNCGTACGNNNN, GTP_rep2: NNNNNTACAAGNNNN, GTP_rep3: NNNNNTCAAGTNNNN, GTP_rep4: NNNNNGCTCATNNNN, 7dGTP_rep1: NNNNNAGGAATNNNN, 7dGTP_rep2: NNNNNCCGGTGNNNN, 7dGTP_rep3: NNNNNATTGGCNNNN, 7dGTP_rep4: NNNNNACATCGNNNN)
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)
Assembly: GRCh38.p7
Supplementary files format and content: invitro_iCLIP_read_counts.xlsx: table shows number of HNRNPH in vitro crosslink events (sum of bigWig) per oligonucleotide per condition and replicate; genomic range, Ensembl gene ID and gene name are given for each oligonucleotide
Library strategy: iCLIP

molecule: other

source_name: Synthetic oligonucleotides

extract_protocol:
Recombinant MBP-HNRNPH1 was incubated with the radioactively labelled RNA libraries and UV-crosslinked at 254 nm with 250 mJ/cm2. The protein-RNA complexes were separated using an SDS-PAGE and transferred to a nitrocellulose membrane. The RNA was extracted from the protein-RNA complexes using proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. The protocol for the RNA extraction from the nitrocellulose membrane was taken from the iCLIP2 protocol (PMID: 31610236).
The library preparation followed the iCLIP2 protocol (PMID: 31610236). In brief, the RNA was reversely transcribed to cDNA using an RT primer against the L3-App linker that was included at the 3’ end of each oligo on the sequence level. After MyONE Silane bead clean up to purify the cDNA, the 5’ linker was ligated to the cDNA. The cDNA was amplified using a 6-cycle PCR and 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


title: in vitro iCLIP, RNA oligo library, 7-deaza-GTP RNA, rep3

description: Library name: 7dGTP_rep3


title: Control5

description:
Library name: Sample15
C5


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

description:
Library name: P28-SSC-HT3
1-mo_SSC_HET_3


title: 1-month, striatum, heterozygous replicate 1

description:
Library name: P28-ST-HT1
1-mo_ST_HET_1


title: 1-month, somatosensory cortex, wild-type replicate 2

description:
Library name: P28-SSC-WT2
1-mo_SSC_WT_2


title: Gout8

description:
Library name: Sample8
T8


title: DOGMA-plex GEX library 14

description:
Library name: DOGMA-plex GEX library 14
RNA


title: DOGMA-plex GEX library 9

description:
Library name: DOGMA-plex GEX library 9
RNA


title: Gout5

description:
Library name: Sample5
T5


title: DOGMA-plex GEX library 13

description:
Library name: DOGMA-plex GEX library 13
RNA


title: in vitro iCLIP, RNA oligo library, 7-deaza-GTP RNA, rep2

description: Library name: 7dGTP_rep2


title: Gout4

description:
Library name: Sample4
T4


title: 1-month, somatosensory cortex, heterozygous replicate 2

description:
Library name: P28-SSC-HT2
1-mo_SSC_HET_2


title: in vitro iCLIP, RNA oligo library, 7-deaza-GTP RNA, rep1

description: Library name: 7dGTP_rep1


title: DOGMA-plex GEX library 12

description:
Library name: DOGMA-plex GEX library 12
RNA


title: DOGMA-plex GEX library 8

description:
Library name: DOGMA-plex GEX library 8
RNA


title: in vitro iCLIP, RNA oligo library, GTP RNA, rep4

description: Library name: GTP_rep4


title: in vitro iCLIP, RNA oligo library, GTP RNA, rep3

description: Library name: GTP_rep3


title: 1-month, somatosensory cortex, heterozygous replicate 1

description:
Library name: P28-SSC-HT1
1-mo_SSC_HET_1


title: in vitro iCLIP, RNA oligo library, GTP RNA, rep2

description: Library name: GTP_rep2


title: DOGMA-plex GEX library 16

description:
Library name: DOGMA-plex GEX library 16
RNA


title: in vitro iCLIP, RNA oligo library, GTP RNA, rep1

description: Library name: GTP_rep1


title: DOGMA-plex GEX library 7

description:
Library name: DOGMA-plex GEX library 7
RNA