title: IgG_2

description: Library name: IgG_2

value: RIP-seq by IgG in BMP4-treated, BOLL-overexpressing OLCs.


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: 0614N-YM2

status: Public on Apr 15 2026

type: SRA

city: Gainesville

first: Jaimar

last: Rincon

state: FL

address: 1600 SW Archer Road

department: Departament of Surgery

country: USA

institute: University of Florida

description:
Library name: 0614N-YM2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger Single-Cell Software v 7.0.1 (10X Genomics) was used to obtain FASTQ files from the Illumina base call files. The reads were aligned to the mm10 mouse transcriptome reference using “intronic reads included” mode, with an expected cell count of 10,000, and transcript expression was quantified at the single-cell level, generating gene-cell count matrices.
The Cell Ranger generated count matrices were imported into R (v4.3.2) and analyzed using the Seurat (v5.0.1) package (PMID: 37231261). Quality control (QC) steps were applied to remove low-quality cells (cells expressing > 10% mitochondrial transcripts or number of unique genes < 200) and doublets (number of unique genes > 6000). Gene expression data were log normalized and scaled. Principal Component Analysis (PCA) was performed based on the top 2,000 most variable genes. To account for batch effects across different samples, data integration was performed using the Harmony (v1.2.0) package (PMID: 31740819), using the top 50 principal components (PCs) to align datasets and reduce batch-specific variations. A shared nearest neighbor graph was constructed using 30 nearest neighbors based on the top 30 PCs. Further, cell clusters were detected based on the Louvain algorithm and were visualized in Uniform Manifold Approximation and Projection (UMAP) embeddings computed from the top 30 PCs.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed single-cell RNA-seq data are provided in HDF5 format (.h5) as generated by the Cell Ranger pipeline. Each file contains the filtered gene-cell expression matrices, along with associated barcodes and gene annotations output by Cell Ranger.

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Splenocytes were obtained and counts were quantified using Cellometer™ Auto 2000 Cell Viability Counter (Nexcelom Bioscience, Lawrence, MA). A million cell concentrations with a minimum of 85% cell viability were obtained for scRNASeq using Chromium X instrument (10X Genomics, Pleasonton, CA).
Libraries were prepared with the 10X’s Chromium Next GEM Single Cell 5’ v2 kit profiling 10,000 cells per sample. To ensure quality during library preparation RNA integrity and dsDNA insert were assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and Qubit 4 (Invitrogen, Carlsbad, CA). Final concentration of the library pool was measured with the NEBNext Library Quant Kit (New England Biolabs, Ipswich, MA). Libraries were sequenced at a minimum depth of 20,000 read pairs per cell on an Illumina Novaseq X plus Platform (Illumina, San Diego, CA).

treatment_protocol: Naïve and septic, young adult (3-4 months) and older adult (18-24 months) female and male C57BL/6 (B6) mice were used for all studies. Sepsis was induced using the cecal ligation and puncture with daily chronic stress (CLP+DCS) as published model. Seven days post- CLP+DCS (CLP+DCS 7d) animals were euthanized to harvest splenocytes.

tag: tissue

value: spleen

tag: strain

value: B6 strain

tag: cell type

value: splenocytes

tag: Sex

value: Male

tag: age

value: 3-4 months

tag: disease group

value: Naive


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: 0614S7-OM1

description:
Library name: 0614S7-OM1
10X Genomics

value: 18-24 months

value: Sepsis (CLP+7dDCS)


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 0606-N-OM2

description:
Library name: 0606-N-OM2
10X Genomics


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 0614N-OM1

description:
Library name: 0614N-OM1
10X Genomics


title: Callus, 7DAC, replicate 1

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
RNA-seq_raw_counts.tsv
RNA-seq_TPM_normalized.tsv

library_source: transcriptomic

data_processing:
Reads were mapped to TAIR10 reference genome using STAR (v2.7.10a) with “--pOverlapNbasesMin 12 --peOverlapMMp 0.1 --twopassMode Basic” options.
Raw counts were obtained from STAR (v2.7.10a) with "--quantMode GeneCounts" option.
RSEM (v1.3.1) was used to quantify transcript abundance to obtain TPM values.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values file includes raw counts for each sample
Supplementary files format and content: Tab-separated values file includes TPM values for each sample

organism: Arabidopsis thaliana

source_name: leaf explant-derived callus

extract_protocol:
Total RNA was extracted from calli using TransZol Up according to the manufacturer’s recommendations.
RNA-seq libraries were constructed from 1 μg total RNA using the TruSeq RNA library kit.

value: leaf explant-derived callus

tag: genotype


title: Pten;Trp53-knockout, sgMettl14, Tumor1

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
29046_T1_PPsgMettl14
tpm_values_CRISPR_samples.txt

data_processing:
Real-time base call (.bcl) files were converted to FASTQ files using Illumina bcl2fastq conversion software. Following Nextera adaptor trimming, sequencing reads were pseudoaligned and quantified using kallisto quant with the house mouse genome (mm10) used as a transcriptome index.
Assembly: mm10
Supplementary files format and content: tab-delimited text file provides TPM counts for each CRISPR sample.
Supplementary files format and content: tab-delimited text file provides TPM counts for each ORF sample.

source_name: mammary tumor

growth_protocol: Animal husbandry, ethical handling of mice, and all approved animal work was carried out according to guidelines approved by the Canadian Council on Animal Care and under protocols approved by the Centre for Phenogenomics Animal Care Committee (26-0272H).

extract_protocol:
RNA was extracted from approximately 3 x 105 freshly isolated, viable, nucleated FACS-purified tumor cells using the Quick-RNA Microprep Kit (R1050, Zymoresearch Inc.) according to manufacturer’s instructions. RNA was then treated with the kit-provided DNase I (R1050, Zymoresearch Inc.).
RNA quality was assessed using an Agilent 2100 Bioanalyzer. All RNA samples passed the quality control threshold of an RNA integrity number (RIN) score of >8.0. Full length cDNA libraries were generated from high quality total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634890, TaKaRa) according to manufacturer’s instructions. The quantity and quality of the purified full-length cDNA were measured by Qubit dsDNA High Sensitivity Assay kit (Q32851, ThermoFisher Scientific) and Agilent 2100 Bioanalyzer, respectively. The final barcoded sequencing libraries were prepared from full length cDNA using Nextera XT Library Prep Kit (FC-131-1024, Illumina) according to manufacturer’s instructions. The barcoded cDNA library quality was checking using an Agilent 2100 Bioanalyzer for fragment size and quantified by qRT-PCR on a BioRad CFX96 Touch Real-Time PCR Detection System (BioRad). Quality checked libraries were then loaded onto an Illumina NovaSeq 6000 running PE150 cycles.

treatment_protocol: To deliver lentivirus directly into the mammary gland, a noninvasive injection method was used that selectively transduces the mammary epithelium of female mice. The third and fourth inguinal mammary glands of female mice were injected between eight and twenty weeks of age, with age at time of injection matched between groups across all experiments. Lentiviruses were diluted to 1 x 107 pfu/mL in PBS and 10% (v/v) of Fast-Green dye for a total injection volume of 10 µL per mammary gland and injected using a pulled glass micropipette.

value: mammary tumor


title: 1_MG_ColIVInh

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Library name: 105193-001-001

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and BclConvert v3.10.5
Quality control was performed using FastQC (version 0.11.9). Adapter sequences were trimmed using fastp (version 0.23.2).
Reads were mapped to the human GRCh38.p13 genome using STAR2 (version 2.7.10) on default settings. Feature counts of reads mapped to genes were determined using HTSeq (version 2.0.2).
Resulting counts were analyzed separately using R (version 4.3.1) and Bioconductor.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts of each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: MG

extract_protocol:
Total RNA was isolated with the RNeasy MicroKit according to the manufacturer’s instructions (Qiagen).
The NEBNext Low Input RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Low Inputr RNA Library Prep Kit for Illumina" (NEB #E6420S/L).

tag: donor

value: MG

tag: treatment

value: ColIVInh

tag: cell number

tag: diagnosis

value: AD

tag: batch


title: Cortex_FP19_24-hours

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: Library name: 3

data_processing:
Adapters were trimmed and low-quality reads (N20 threshold) were filtered using a custom quality control pipeline. FASTQC was used to evaluate read quality metrics.
Trimmed reads were mapped to mature miRNAs in miRBase v21 using Bowtie v1.0.0, allowing one mismatch.
Reads were also mapped to the mm9 reference genome (UCSC) for validation. Only reads mapping to annotated miRNAs were retained.
Read counts were normalized using TMM (Trimmed Mean of M-values) via edgeR (Bioconductor).
Differential expression was assessed using two-way ANOVA across dose and timepoint groups. PCA and clustering were used for exploratory analysis.
Assembly: Mus musculus mm9 (UCSC)
Supplementary files format and content: Processed data includes normalized miRNA counts for each sample across cortex, heart, and lung tissues. File format: .xlsx  with miRNAs as rows and samples as columns.

source_name: Cortex

growth_protocol: Adult male SKH-1 Elite mice (Charles River, strain code 477) were housed in standard vivarium conditions with food and water provided ad libitum. All procedures were conducted in AAALAC-accredited facilities under IACUC-approved protocols.

extract_protocol:
Tissues were homogenized in TRIzol Reagent (Invitrogen) and total RNA, including small RNAs, was extracted using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol. RNA quality was assessed using NanoDrop, Qubit, and Agilent Tapestation 2200.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit. 3′ and 5′ adapters were ligated to RNA, followed by reverse transcription, PCR amplification, and gel-based size selection. Libraries were pooled and sequenced on an Illumina NextSeq 500 to generate 50 bp single-end reads.

treatment_protocol: Mice were administered subcutaneous fentanyl citrate at one of three doses: HNLD (62 mg/kg), LD10 (110 mg/kg), or LD50 (135 mg/kg). Sham controls received vehicle only. Mice were euthanized at 0h (40 min), 6h, 24h, or 7d post-injection for tissue collection.

value: Cortex

value: SKH-1 Elite

tag: dose

tag: timepoint

value: 24 hours


title: Pten;Trp53-knockout, sgMettl14, Tumor4

description:
24127_T2_PPsgMettl14
tpm_values_CRISPR_samples.txt


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 0612N-OF1

description:
Library name: 0612N-OF1
10X Genomics

value: Female


title: Pten;Trp53-knockout, sgCsnk1a1, Tumor4

description:
24138_T1_PPsgCsnk1a1
tpm_values_CRISPR_samples.txt


title: BOLL_2

city: Fuzhou

first: Ying

last: Li

state: Fujian

address: No. 2, Xueyuan Road, University Town

country: China

institute: Fuzhou University

description: Library name: BOLL_2

data_processing:
Adapter trimming and quality filtering used Trimmomatic v0.36 to remove low-quality bases and adapters.
All datasets (RIP-seq and T&T-seq) were aligned to the human reference genome (hg38) using HISAT2 v2.1.0.
Reads were assembled and quantified by featureCounts (v1.6.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: human embryonic stem cell

growth_protocol: H9 human embryonic stem cells (hESCs) were maintained in Knockout DMEM supplemented with 20% Knockout Serum Replacement (KSR), 25 μg/mL basic fibroblast growth factor (bFGF), 1× Penicillin-Streptomycin, 1× GlutaMAX, and 1× Non-Essential Amino Acids (NEAA), cultured on mitomycin-C-inactivated mouse embryonic fibroblast (MEF) feeder layers in a humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
For T&T-seq transcriptome RNA extraction, 100,000 oocyte-like cells (OLCs) were lysed in 2 μL aliquot, mixed with 1 mL TRIzol Reagent (Invitrogen #15596026), vortexed, incubated 5 min at RT, followed by chloroform addition (200 μL), centrifugation (12,000 × g, 15 min, 4°C), isopropanol precipitation (500 μL, 10 min RT), ethanol wash (75%), and resuspension in 11 μL nuclease-free water for storage at -80°C. For T&T-seq translatome RNA extraction, 8 μL lysate from 100,000 OLCs underwent ribosome capture using RiboLace Beads (Immagina) with 70-min rotation at 4°C, washed twice with W-Buffer, dissociated in 1% SDS + Proteinase K (37°C, 30 min), then extracted identically to transcriptome RNA including TRIzol/chloroform separation and overnight ethanol precipitation before resuspension. For RIP-seq RNA extraction, 1,000,000 OLCs were lysed in RIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) with protease/RNase inhibitors, precleared with Protein G Dynabeads (Thermo #10004D), immunoprecipitated with 5 μg BOLL antibody (Proteintech #13720-1-AP) overnight at 4°C followed by 4-h bead binding, washed four times with lysis buffer, resuspended in 1 mL TRIzol for RNA isolation via chloroform/isopropanol method, and eluted in 20 μL nuclease-free water. All RNA extracts were stored at -80°C pending library construction.
RNA libraries for T&T-seq and RIP-seq were prepared using SMART-Seq2 library construction strategy.

treatment_protocol: H9 hESCs were seeded at 50% confluency on Matrigel-coated plates and pretreated with 50 ng/mL BMP4 in differentiation medium for 1 hour prior to transduction with BOLL-overexpressing lentivirus (or p2k7 empty vector control) for 24 hours, followed by medium replacement, blasticidin selection (2 μg/mL for 3 days), and continued culture in differentiation medium until analysis at day 6 post-transduction.

value: human embryonic stem cell

value: RIP-seq by BOLL antiboidy in BMP4-treated, BOLL-overexpressing OLCs.


title: Pten;Trp53-knockout, sgMettl14, Tumor2

description:
29048_T1_PPsgMettl14
tpm_values_CRISPR_samples.txt


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: 0606-S-OF2

description:
Library name: 0606-S-OF2
10X Genomics

value: spleen

value: B6 strain

value: splenocytes


title: Pten;Trp53-knockout, sgMettl14, Tumor3

description:
24126_T3_PPsgMettl14
tpm_values_CRISPR_samples.txt


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 0606-N-OF2

description:
Library name: 0606-N-OF2
10X Genomics

value: Naive


title: NT_3

city: Kodaira

first: Lili

last: Quan

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: National Institute of Neuroscience

country: Japan

institute: National Center of Neurology and Psychiatry

description:
Library name: NT_3
Etching_raw_count.tsv

data_processing:
The generated reads were mapped to the rat reference genome (Rn6) or human reference genome (hg19) using TopHat (version 2.1.1) after adapter trimming by Trimmomatic.
Assembly: Rn6, hg19
Supplementary files format and content: Etching_raw_count.tsv
Supplementary files format and content: Dimemorfan_raw_count.tsv

organism: Rattus norvegicus

source_name: Rat prefrontal cortex

extract_protocol:
Total RNA was isolated from rat primary oligodendrocytes or iPSC-derived oligodendrocytes using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Full-length cDNA was synthesized from total RNA using a SMART-Seq stranded (TaKaRa) according to manufacturer instructions. An Illumina library was prepared using a Nextera XT DNA Library Prep Kit (Illumina) according to SMART-seq kit instructions. Sequencing was performed using an Illumina NovaSeq 6000 sequencer (Illumina) in the 101-base single end mode for rat samples and DNBSEQ-G400 sequencer (MGI) in a single-end mode (150 bp) for human samples.

value: Rat prefrontal cortex

tag: cell line

value: primary cell

value: oligodendrocytes


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: 0606-S-OF1

description:
Library name: 0606-S-OF1
10X Genomics

value: 18-24 months

value: Sepsis (CLP+7dDCS)


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 0606-N-OM1

description:
Library name: 0606-N-OM1
10X Genomics

value: Male


title: IgG_1

description: Library name: IgG_1

value: RIP-seq by IgG in BMP4-treated, BOLL-overexpressing OLCs.


title: Atrxn_SMC1

city: Houston

first: Anand

last: Singh

address: 1901 East Road

institute: MD Anderson Cancer Center

description: Library name: Atrxn_SMC1

library_source: genomic

data_processing:
Generated CUT&Tag data underwent quality-control measures using the FASTQC tool and was aligned to the mm9 reference genome with Bowtie2 (version 2.4.5).
BAM files were filtered and Gene annotations were performed using BED files subjected to GREAT (version 4) analysis with Basal plus extension parameters (Proximal: 5kb upstream, 1kb downstream, plus distal up to 1000kb), followed by pathway prediction analysis using Enrichr.
Assembly: mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: brain

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

extract_protocol:
500,000 cells were washed with 1X Wash Buffer and incubated with Concanavalin A Beads for 30 minutes. Cells were incubated overnight at 4°C using 1ug of anti-SMC1 (Thermo, Cat # A300-055A) with orbital mixing. The following day, the cells were washed using 1X Wash Buffer containing Protease Inhibitory Cocktail and Digitonin and incubated with Guinea Pig Anti-Rabbit secondary antibody, followed by Tn5 transposomes and Tagmentation procedures.
DNA was eluted using column filters and libraries constructed using i7 and i5 indexing primers, following PCR conditions. Eluted libraries were assessed for quality using a Bioanalyzer and subjected to Nextseq500 MID-300 using 75 bp pair-end read format at the MDACC-ATGC facility.

value: brain

value: Primary cell line

value: Neuroepithelial progenitor cell

value: Control

tag: antibody


title: Pten;Trp53-knockout, sgCsnk1a1, Tumor3

description:
24135_T3_PPsgCsnk1a1
tpm_values_CRISPR_samples.txt

value: mammary tumor


title: RNA_Control_2

description: Library name: RNA_Control_2

value: human embryonic stem cell

value: Transcriptome sequencing of spontaneously differentiated hESCs.


title: BOLL_1

description: Library name: BOLL_1

value: RIP-seq by BOLL antiboidy in BMP4-treated, BOLL-overexpressing OLCs.


title: B16F0, no NK, rep1

city: Palo Alto

first: Ravi

last: Dinesh

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University

description: Library name: B16F0_noNK_R2

data_processing:
Sequencing data was deconvoluted with the bcl2fastq function (illumina) and MAGeCK was used to produce ranks based on robust rank aggregation (RRA) scores comparing the NK and no NK conditions.
Assembly: hg38, mm39
Supplementary files format and content: MAGeCK count files
Library strategy: CRISPR Screen

growth_protocol: B16F0 cells were grown in DMEM (Corning #10-101-CV) supplemented with 1% Pen-Strep (Gibco 15-140-122), 1% NEAA (Cyclone #SH30238.01) and 10% FBS (BenchMark) at 37oC. K562 cells were grown in RPMI (Corning #10-104-CV) supplemented with 1% Pen-Strep, 1% NEAA, and 10% FBS at 37oC. HGC-27 cells were grown Eagle’s Minimum Essential Medium (Quality Biological #112-016-101CS) supplemented with 1% Pen-Strep, 1% NEAA, and 10% FBS at 37oC. YAC-1 cells were grown in NK media: RPMI supplemented with 1%  Pen-Strep, 1% NEAA, 1 mM sodium pyruvate (Thermo Scientific #11-360-070), 10 mM HEPES (Cytiva #SH30237.01), and 55 nM 2-mercaptoethanol (Fisher #21985023). Primary NK cells were isolated from thawed PBMCs using the Easy Sep NK cell Isolation Kit (StemCell Technologies #17955) according to manufacturer’s protocol.  Isolated NK cells were reconstituted at a density of 1-1.5 x 106 cells/mL of CTS NK-Xpander Medium (Thermo Scientific #A5019001) supplemented with 5% Immune Cell Serum Replacement (Thermo Scientific #A2596101) and containing NK Cell Activation/Expansion beads (Miltenyi Biotec #130-094-483) with 1000 IU IL-2 and 20 ng/mL IL-15 (NIH NCI BRB Preclinical Repository) for six days with additional media added on Day 3. On day 6, activation/expansion beads were removed with an EasySep magnet (Stem Cell #18000) and  allowed to expand further in NK media. After isolation NK cells were grown in 1000 IU IL-2 and 20 ng/mL IL-15 and used on day 10-14 post-isolation for all in vitro and in vivo experiments.

extract_protocol:
Surviving cancer cells from both NK and no NK conditions were collected and sorted by FACS for GFP+/mcherry+ cells. The cells were pelleted at 300 x g for 5 min, the supernatant removed, and stored in -80C for further processing.  Genomic DNA was isolated using Quick-DNA Midiprep Plus Kit (Zymo Research #D4075).
gRNA sequences were amplified from genomic DNA using the NEBNExt High-Fidelity 2X PCR Master Mix (NEB #M0541) with 50 uL reaction volumes and 2.5 ug of DNA per reaction and mixed staggered primers (Forward Primer: 5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT[Stagger, 0-7nt]TTGTGGAAAGGACGAAACACC-3’ Reverse Primer: 5’-CAAGCAGAAGACGGCATACGAGAT [8nt-barcode]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTACTATTCTTTCCCCTGCACTGT-3’). PCR reactions were pooled and column purified using Monarch PCR and DNA Cleanup Kit (NEB #T1030S). A fraction of the eluate was run on a gel, the band corresponding to the library amplicon excised, and then column purified. Amplified products were quantified using the Qubit 1X dsDNA HS Assay (Thermo Scientific #Q33230), normalized by concentration and sequenced on an Illumina NextSeq using 500/550 v2.5 kits at 1000X coverage per gRNA.

treatment_protocol: Cancer cells were co-cultured with or without NK cells for 24 hrs in the presence of IL-2 and IL-15 at an effector/target ratio that led to ~90% killing.

value: melanoma

value: no NK cells


title: Pten;Trp53-knockout, sgCsnk1a1, Tumor1

description:
29023_T1_PPsgCsnk1a1
tpm_values_CRISPR_samples.txt


title: RNA_Control_1

description: Library name: RNA_Control_1


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 0606-N-OF1

description:
Library name: 0606-N-OF1
10X Genomics

value: spleen

value: B6 strain

value: splenocytes

value: Female

value: Naive


title: Atrxp_SMC1

description: Library name: Atrxp_SMC1


title: YAC-1, NK, rep2

description: Library name: YAC1_NK_R2

value: lymphoma

value: Co-culture with NK cells


title: Pten;Trp53-knockout, sgFbxw7, Tumor4

description:
24125_T1_PPsgFbxw7
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, sgCsnk1a1, Tumor2

description:
29025_T2_PPsgCsnk1a1
tpm_values_CRISPR_samples.txt


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 042623NOM

description:
Library name: 042623NOM
10X Genomics

value: Male

value: 18-24 months


title: Pten;Trp53-knockout, sgFbxw7, Tumor3

description:
24124_T1_PPsgFbxw7
tpm_values_CRISPR_samples.txt


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: 042623S7OM

description:
Library name: 042623S7OM
10X Genomics

value: Sepsis (CLP+7dDCS)


title: B16F0, NK, rep1

description: Library name: B16F0_NK_R2


title: YAC-1, no NK, rep2

description: Library name: YAC1_noNK_R2


title: YAC-1, no NK, rep1

description: Library name: YAC1_noNK_R1


title: RNA_LIVER_ICR_ND-3

city: Shanghai

first: Wang

last: E

address: 280 South Chongqing Road

department: Department of Laboratory Animal Science

institute: Shanghai Jiaotong University School of Medicine

data_processing:
fastp software (v0.23.4)
High-quality reads were aligned to the reference genome using HISAT2 software (v2.2.1).
Gene level raw counts were obtained as mRNA expression profiles using featureCount software (v2.0.6).
Fold change (FC) and P-value between the two sets of samples were normalised and calculated using edgeR software (v4.0.16).
After getting differentially expressed (DE) mRNAs by filtering FC and P-value, the DE mRNAs were used for GO functional analysis and KEGG pathway analysis.
Assembly: mm39
Supplementary files format and content: excel file includes raw counts and RPKM values for each sample

source_name: liver

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA), and subjected to mRNA isolation using GenSeq® mRNA Purification Kit (GenSeq, Inc., Shanghai, China).
The mRNA was fragmented into ~300nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries.

value: liver

value: WT

value: ND


title: RNA_BOLL_2

description: Library name: RNA_BOLL_2

value: human embryonic stem cell

value: hESCs treated with BMP4 and BOLL overexpresssion after 6-day differentiation, genarated OLCs and conducted to transcriptome sequencing.


title: Ribo_Control_2

description: Library name: Ribo_Control_2

data_processing:
Adapter trimming and quality filtering used Trimmomatic v0.36 to remove low-quality bases and adapters.
All datasets (RIP-seq and T&T-seq) were aligned to the human reference genome (hg38) using HISAT2 v2.1.0.
Reads were assembled and quantified by featureCounts (v1.6.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample
Library strategy: Ribo-Seq

value: Translatome sequencing of ribosome-associated RNA from hESCs after 6 days of spontaneous differentiation.


title: RNA_LIVER_ICR_ND-2


title: Pten;Trp53-knockout, sgFbxw7, Tumor1

description:
24118_T1_PPsgFbxw7
tpm_values_CRISPR_samples.txt

value: mammary tumor


title: RNA_LIVER_ICR_ND-1


title: RNA_BOLL_1

description: Library name: RNA_BOLL_1


title: RNA_LIVER_ICR_CDHFD-3

value: CDAHFD


title: Ribo_Control_1

description: Library name: Ribo_Control_1


title: Pten;Trp53-knockout, sgFbxw7, Tumor2

description:
24122_T1_PPsgFbxw7
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, sgTigre, Tumor2

description:
29041_T1_PPsgTigre
tpm_values_CRISPR_samples.txt

value: sgSHL


title: YAC-1, NK, rep1

description: Library name: YAC1_NK_R1


title: s81

city: Boston

first: Perrie

last: O'Tierney-Ginn

state: MA

address: 800 Washington St

institute: Tufts Medical Center

description: Library name: s81

data_processing:
Raw .bcl files were converted to fastq format and demultiplexed using Illumina bcl2fastq 2.17 software (1 mismatch allowed). Six outlier samples were removed by PCA.
Assembly: GRCh38
Supplementary files format and content: CSV file contains count data for all samples.

source_name: placenta

extract_protocol:
Total RNA was extracted from ~50 mg placental tissue using TRIzol reagent following manufacturer's protocol. RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer (RIN>7).
Libraries were prepared using NEBNext Ultra II RNA Library Prep with polyA selection. mRNA was enriched with Oligo d(T) beads, fragmented at 94 degrees C for 15 min, converted to cDNA, end-repaired, adenylated, adapter-ligated, and PCR-amplified. Libraries were validated on Agilent TapeStation and quantified by Qubit and qPCR.

value: placenta

tag: maternal age

tag: gestational age

tag: gender

value: male

tag: neonatal percent_fat

tag: maternal prebmi

tag: maternal latebmi

tag: paternal bmi


title: Pten;Trp53-knockout, sgTigre, Tumor1

description:
29040_T4_PPsgTigre
tpm_values_CRISPR_samples.txt

tag: tissue

tag: genotype


title: s9

description: Library name: s9

value: female


title: RNA_LIVER_ICR_CDHFD-2

tag: treatment


title: Ribo_BOLL_2

description: Library name: Ribo_BOLL_2

tag: cell type

value: hESCs treated with BMP4 and BOLL overexpresssion after 6-day differentiation, genarated OLCs and conducted to translatome sequencing.


title: Ribo_BOLL_1

description: Library name: Ribo_BOLL_1


title: s74

description: Library name: s74


title: s86

description: Library name: s86


title: Pten;Trp53-knockout, sgHipp11, Tumor2

description:
24115_T2_PPsgHipp11
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, sgHipp11, Tumor1

description:
24114_T1_PPsgHipp11
tpm_values_CRISPR_samples.txt


title: s72

description: Library name: s72


title: vU1.8 IP (merge of three independent pulldowns)

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

description: Library name: Sample 13

data_processing:
Paired-end reads of total RNA-seq data and pulldown experiments in IPS cells were mapped with the STAR1 software version 2.7.3a with the default setting, quantified with htseq-count2 software version 0.12.4 and vU1KO IPS data were normalized with the RUVs method in RUVseq. VU1 pulldown targets were quantified with noise-seq. Differential gene expression between WT and KO was quantified with the R package DEseq2 version 1.34.0 using the default Wald test. We defined genes whose adjusted p-value < 0.05 as significantly differentially expressed genes (DEGs) in IPS data and whose absolute log2 fold change > 0.6 and adjusted p-value < 0.05 in HEK293 data.
RNA splicing events were quantified and compared using whippet with probability cutoff > 0.9 and |deltapsi| > 0.1. Functional isoform switches were detected with R package isoformSwitchAnalysis.
The RSSs were quantified using the method described in (Zhang et al., 2018) but searching YAGNN instead of AGGT as the rss motif and filtering out the RSSs detected in the polyA-enriched RNAseq as false positive, normalized with all junction reads connecting the 3’ of their upstream exons and compared using t-test with the p-value cutoff of 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: The .txt files contain raw counts of reads mapped to each gene.
Supplementary files format and content: The .psi.gz files are compressed files containing the percentage of splicing in of each node such as exons, introns, and transcripional start or end sites.
Supplementary files format and content: The .junc files contain counts of recursive spliced genome regions at the last column.

source_name: human iPSc

extract_protocol:
RNAs were extracted using the standard TriZol/chlorofom (acidic pH) approach and underwent quality control for integrity and size distribution
Standard Illumina-compatible library preparation procedures were followed, in all cases ribodepletion followed by random-hexamer-based reverse transcription to generate cDNA pools for sequenciing; strand-specific information was maintained during these preps.

value: human iPSc

value: wild type

value: vU1.8 IP


title: vU1.3 IP (merge of three independent pulldowns)

description: Library name: Sample 12

value: vU1.3 IP


title: GFP exposed 2

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description: Library name: GFP_exposed 2

data_processing:
fastqc version v0.11.9, STAR version 2.7.10a_alpha_220818, featureCounts version 2.0.6 and R version 4.4.2
fastq files were mapped using STAR and generated raw read using featureCounts.
Assembly: Zebrafish reference genome: Danio rerio (GRCz11)
Supplementary files format and content: STAR_counts.xlsx contain raw read counts

organism: Danio rerio

source_name: Zebrafish Embryo

growth_protocol: Animal husbandry guidelines for all zebrafish studies were designed, reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Mississippi Medical Center (IACUC #: 2024-1362). In accordance with IUCUC standardized protocols, embryos generated from the AB wildtype, CB1 receptor knockout (CB1-KO), CB2 receptor knockout (CB12-KO) (Liu et al., 2016) and sp7-eGFP transgenic zebrafish (DeLaurier et al., 2010) strains were raised in E3 medium under at 28.5°C.

extract_protocol:
WIN 55,212-2 (WIN), bisphenol A (BPA), bisphenol S (BPS), and 3,3’,5,5’-tetrabromobisphenol A (TBBPA) were dissolved in dimethyl sulfoxide (DMSO) in a stock solution of 10 mM. BPA, BPS and TBBPA were further diluted to 10 μM as an intermediate stock solution. Both the 10 mM and 10 μM solutions were stored at -20°C. Embryos were placed into 25 mL of E3 media in 50 mL tubes. Appropriate chemical volumes were added directly into the medium to get exposure concentrations of 120 or 200 nM for each bisphenol, and 108 or 180 nM for WIN. Additionally, suboptimal co-treatments of each bisphenol (120 nM) and WIN (108 nM) were used as well. Next, the embryos were placed back into the 28.5 °C incubator until time of fixation. Bisphenols A, S, and TBBPA were purchased from Sigma-Aldrich (St. Louis, MO, USA), and WIN was purchased from Cayman Chemicals (Ann Arbor, MI, USA). According to the literature, all chemical treatments are within normal exposure range.
Embryos from the sp7-GFP transgenic line were exposed to 200 nM BPA for 24 hpf to 4 dpf (N = 400 embryos) and run against a control group at 4 dpf (N = 400 embryos). As EGPF takes longer than sp7 in situ to be detected in the opercle we slightly shifted our analysis time point and performed all transcriptomic analysis at 4 dpf. At 4d pf, the embryos were transferred 1.5 mL microcentrifuge tubes, and as much E3 was removed as possible without damaging the embryos. Before moving forward, the centrifuge was pre-cooled to 4°C (all centrifugation steps need to be performed at 4°C). Next, 150 μL of collagenase solution was added to dissociate the embryos in each tube, and they were placed an incubator at 30°C, with mild shaking, for 10 minutes. Following successful dissociation, a STOP solution (1.2 mL PBS w/ 10% FBS) was added to halt the dissociation step. Once cooled, set centrifuge to 700xg, spin for 5 minutes at 4°C, aspirate supernatant, and resuspend in 1 mL PBS with 2% FBS. Add 1 μL of DAPI. Next, Fluorescence-Activated Cell Sorting (FACS) was performed to sort all cells expressing sp7-GFP (only osteoblasts would express GFP at this stage), and the cells were sorted into 350 μL of RNA lysis buffer. RNA extraction was carried out to transport samples safely. The steps involved with dissociation, FACS, and RNA extraction (ZYMO Quick RNA MicroPrep Kit cat no. R1050) were performed by the Williamson, Clements Lab at St. Jude Children’s Research Hospital. The RNA samples of the Control 4 dpf and the 200 nM BPA treatment were sent to the University of Mississippi Medical Center Molecular and Genomics Core Facility (www.umc.edu/genomicscore) for bulk quality control (QC) RNA-seq analysis. Reads were sequenced using the Illumina NextSeq 500 platform, and the Illumina BaseSpace Cloud Computing Program was used to assess the quality of sequenced reads.

value: Zebrafish Embryo

value: embryonnic osteoblasts

tag: sample group

value: GFP exposed

value: SP7 positive cells


title: RNA_LIVER_C57_ND-2

value: liver

value: WT

value: ND


title: GFP exposed 3

description: Library name: GFP_exposed 3

treatment_protocol: WIN 55,212-2 (WIN), bisphenol A (BPA), bisphenol S (BPS), and 3,3’,5,5’-tetrabromobisphenol A (TBBPA) were dissolved in dimethyl sulfoxide (DMSO) in a stock solution of 10 mM. BPA, BPS and TBBPA were further diluted to 10 μM as an intermediate stock solution. Both the 10 mM and 10 μM solutions were stored at -20°C. Embryos were placed into 25 mL of E3 media in 50 mL tubes. Appropriate chemical volumes were added directly into the medium to get exposure concentrations of 120 or 200 nM for each bisphenol, and 108 or 180 nM for WIN. Additionally, suboptimal co-treatments of each bisphenol (120 nM) and WIN (108 nM) were used as well. Next, the embryos were placed back into the 28.5 °C incubator until time of fixation. Bisphenols A, S, and TBBPA were purchased from Sigma-Aldrich (St. Louis, MO, USA), and WIN was purchased from Cayman Chemicals (Ann Arbor, MI, USA). According to the literature, all chemical treatments are within normal exposure range.


title: RNA_LIVER_ICR_CDHFD-1

value: CDAHFD


title: s505

description: Library name: s505


title: GFP exposed 1

description: Library name: GFP_exposed 1


title: s485

description: Library name: s485


title: RNA_LIVER_C57_ND-1


title: GFP control 3

description: Library name: GFP_control 3

value: GFP control


title: vU1.8KO, replicate 3

description: Library name: Sample 9

value: vU1.8 knockout


title: RNA_LIVER_C57_ND-3


title: control, IP

description: Library name: Sample 11

value: control IP


title: RNA_LIVER_C57_CDHFD-3


title: s493

description: Library name: s493

value: placenta

value: male


title: s481

description: Library name: s481

value: female


title: vU1.8KO, replicate 2

description: Library name: Sample 8

value: human iPSc


title: RNA_LIVER_C57_CDHFD-2


title: vU1.8KO, replicate 4

description: Library name: Sample 10


title: HLF siSBNO1#2 replicate 1

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: HLF were transfected with siSBNO1#2 targeting human SBNO1, replicate 1

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data was analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of Human Clariom D from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: HLF cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HLF cells were cultured in Dulbecco’s Modified Eagle’s Medium.

extract_protocol: Total RNA was extracted using the Macherey-Nagel RNA Extraction Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions.

treatment_protocol: siRNA-mediated knockdown was performed using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.

value: liver cancer cell line


title: GFP control 2

description: Library name: GFP_control 2


title: Pleural_LTS_5day_rep15

city: River Forest

first: Robert

middle: J

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

hyb_protocol: We used the Aplysia Tellabs Array (ATA: GEO: GPL18666) to characterize changes in gene expression persisting 5 days after long-term sensitization training.  The array was designed using the UniGene clustering of Aplysia ESTs (build 9, July 2011, ftp://ftp.ncbi.nih.gov/repository/UniGene/Aplysia_californica/) and includes 2-3 probes designed for each of the 24,702 distinct EST clusters identified by Unigene, 15 Aplysia mRNAs deposited in GenBank between the Unigene build and the design of the array, and 1,432 orphaned probes from two previous Aplysia microarray designs (the Aplysia Discovery Array (GEO:GPL3635) and the updated Aplysia Annotated Array (GEO: GPL13815/GPL17112)).  Thus, the ATA design includes 26,149 distinct probes representing all known sources of Aplysia californica ESTs and mRNAs at the time of design (January 2012).   Based on estimates from previous microarray designs (Moroz et al. 2006), the ATA should cover >50-60% of all neurally-expressed transcripts.  Complete details on the ATA design are in Herdegen et al. (Herdegen et al. 2014b).  Microarray processing was completed by Mogene Inc. (St. Louis, MO).  A two-color approach was used with each array hybridized to a sample from a trained or untrained animal.  In half of cases, trained samples were hybridized with Cy3 and controls to Cy5; the other half we dye-swapped.    Sample integrity was determined by Bioanalyzer RNA 6000, Pico total RNA protocol.  300ng of total RNA was amplified and labeled with Cy3 or Cy5 using the Agilent Quick Amp Two-Color Labeling Kit. Dye incorporation and yield was determined by Nanodrop.  Samples were hybridized to the microarray slide at 65C and 10rpm for 17 hours.  Slides were scanned on an Agilent C scanner at 3µm resolution.  Data was extracted using Agilent Feature Extraction software, v. 11.5.  All labeling and post-labeling processing was carried out in an ozone regulated environment, monitored at < 5ppb.

scan_protocol: Slides were scanned on an Agilent C scanner at 3um resolution.  Data was extracted using Agilent Feature Extraction software, v. 11.5.

data_processing:
Microarray data was analyzed using limma (Smyth 2005; Ritchie et al. 2015a) from the Bioconductor suite of tools (Gentleman et al. 2004) for R (Ihaka and Gentleman 1996).   Median expression values were analyzed (Zahurak et al. 2007).  These were corrected for background using the normexp+offset algorithm recommended for Agilent microarrays by Ritchie et al. (Ritchie et al. 2007).  An offset of 30 was selected based on inspection of MA Plots (Supplemental Figure 2).  Expression was then normalized using the loess function (Smyth and Speed 2003).  Where multiple probes were used to measure the same EST or mRNA, these were averaged.  Finally, trained and control expression were compared using an empirical Bayes-moderated t-test (Smyth 2004).  Statistical significance was calculated using Benjamini-Hochberg correction for multiple comparisons to maintain a 5% overall false-discovery rate (Benjamini and Hochberg 1995).  We used the treat function from limma (McCarthy and Smyth 2009) to conduct a stringent test for significant regulation.  Specifically, rather than use a null hypothesis of no regulation, we tested for regulation statistically distinguishable from at least a 10% change in expression in either direction.  We have previously found that using this type of high-stringency criterion yields very strong predictive validity in independent qPCR (Herdegen et al. 2014b; Holmes et al. 2014).   For this analyiss, we first tested for regulation in the set of 1,252  transcripts known to be regulated 24 hours after training (Conte et al., 2017).  Then we tested for unique regulation in the remaining transcripts.  We also explored the completeness of the gene list using the approach developed by Langaas et al. (2005), which is implemented in limma via the propTrueNull function (Ritchie et al. 2015b).  We also explored the degree of relationship between the regulation observed 7 days after training with what we have previoulsy observed 1 day after training (Conte et al., 2017).  Specifically, we examined both the correlation between raw log-fold-change scores and the correlation once these scores are adjusted for potential measurement error using the genuine association of gene-expression profiles (genas) function in limma (Ritchie et al. 2015b)
loess normalized log2 ratio (trained/untrained)

organism: Aplysia californica

source_name: Control

label_protocol: A two-color approach was used with each array hybridized to a trained (Cy5) or untrained (Cy3) sample.  Sample integrity was determined by Bioanalyzer RNA 6000, Pico total RNA protocol.  300ng of total RNA was amplified and labeled with Cy3 or Cy5 using the Agilent Quick Amp Two-Color Labeling Kit. Dye incorporation and yield was determined by Nanodrop.

growth_protocol: Animals (75-125g) were obtained from the RSMAS National Resource for Aplysia (Miami, FL) and maintained at 16o C in one of two 90-gallon aquariums with continuously circulating artificial sea water (Instant Ocean, Aquarium Systems Inc.).  Animals were separately housed in rectangular colanders (11.5cm wide, 16.5cm long, 7.3cm deep), fed dried seaweed twice a week, and maintained on a 12 hr light-dark cycle.  2 days prior to any experimental testing, animals were fed to satiation and then food deprived through the remainder of the study.

extract_protocol: We compared gene expression from pleural ganglia on the trained vs. untrained side of the animal.  Samples from two animals trained on opposite sides were pooled.  This was done to control for lateralized gene expression.  To analyze transcription, pleural ganglia RNA was isolated immediately after the 5-day post-tests, a time-point at which recall had partly but not fully decayed .  Briefly, animals were anesthetized with an injection of isotonic MgCl2 (50% of body weight), and an incision was then made along the ventral midline to expose the CNS.  As dissection can alter gene expression (Alberini et al. 1994), we extracted ganglia rapidly (< 5 minutes per animal) and transferred them immediately to Trizol (Invitrogen, Carlsbad CA) for homogenization.    Tissue was homogenized using the Bullet Blender (NextAdvance, Averill Park, NY) and RNA extracted using Direct-Zol Mini RNA Kit (Zymo, Irvine, CA). Quantity and quality of RNA was assessed using the NanoDrop 1000 (Thermo Scientific, Wilmington, DE).

treatment_protocol: A one-day long-term sensitization training protocol was used, adapted from Wainwright et al. (2002) as previously described (Bonnick et al. 2012; Herdegen et al. 2014b, 2014a)  Training consisted of 4 rounds of noxious shock applied at 30 minute intervals to one side of the body with a hand-held electrode.  Each round of shock consisted of 10 pulses (60Hz biphasic) of 500ms duration at a rate of 1hz and an amplitude of 90mA.  During the course of each shock, the stimulating electrode was slowly moved from anterior (just behind neck) to posterior (just in front of tail) and back to cover nearly the entire surface of that side of the body.  Side of training was counterbalanced.  One of the advantages of this training protocol is that both the induction and expression of sensitization is restricted to one side of the body (Antzoulatos and Byrne 2007; Antzoulatos et al. 2006; Cleary et al. 1998; Scholz and Byrne 1987; Wainwright et al. 2002), enabling each animal to serve as its own control (trained vs. untrained sides).'

value: Pleural ganglia

source_name: Trained


title: RNA_LIVER_C57_CDHFD-1


title: vU1.8KO, replicate 1

description: Library name: Sample 7


title: AGM99

city: Cincinnati

first: Yunguan

last: Wang

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: Library name: AGM99

data_processing:
Reads were aligned to reference (GRCh38) with ‘STAR’ (v2.7.2b)
Gene counts were quantified with ‘FeatureCounts’ (v1.6.4)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count per sample

source_name: Liver

extract_protocol:
RNA was isolated from liver biopsy samples from patients in the AILD cohort with the MiRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
Sequencing was performed by the University of Cincinnati DNA Core Center using 100 base pair, pair end reads at a depth of 50  million reads.

value: Liver

value: PSC


title: Pleural_LTS_5day_rep16


title: GFP control 1

description: Library name: GFP_control 1

value: Zebrafish Embryo

value: embryonnic osteoblasts


title: s476

description: Library name: s476


title: s479

description: Library name: s479


title: FACS-sorted -0.8flt1:RFP+/ cxcr4a:YFP+ replicate 2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: danRer11
Supplementary files format and content: library size normlaized counts

source_name: coronary endothelial cells

extract_protocol:
RNA was extracted using miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-free DNase set, Qiagen) to avoid contamination by genomic DNA.
Approx. 5ng of total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Clontech) for cDNA pre-amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

treatment_protocol: The ventricle were cryoinjured and extracted at 7 dpci to sort regenerating and non-regenerating coronary endothelial cells

value: coronary endothelial cells

value: cryoinjured


title: s473

description: Library name: s473


title: control, replicate 1

description: Library name: Sample 1

value: wild type


title: Pleural_LTS_5day_rep13


title: FACS-sorted -0.8flt1:RFP+/ cxcr4a:YFP+ replicate 1

value: WT


title: FACS-sorted -0.8flt1:RFP+/cxcr4a:YFP- repilcate 1


title: AGM97

description: Library name: AGM97


title: Pleural_LTS_5day_rep14


title: AGM98

description: Library name: AGM98

value: AIH


title: FACS-sorted -0.8flt1:RFP+/cxcr4a:YFP- replicate 2


title: s468

description: Library name: s468


title: AGM96

description: Library name: AGM96


title: s466

description: Library name: s466


title: HGC27, no NK, rep4

description: Library name: HGC27_noNK_R4

value: gastric carcinoma

value: no NK cells


title: Pleural_LTS_5day_rep11


title: s459

description: Library name: s459

value: placenta


title: Pleural_LTS_5day_rep10


title: Pleural_LTS_5day_rep12


title: s450

description: Library name: s450

value: male


title: s441

description: Library name: s441

value: female


title: HGC27, NK, rep4

description: Library name: HGC27_NK_R4

value: Co-culture with NK cells


title: Pleural_LTS_5day_rep9


title: AGM76

description: Library name: AGM76


title: AGM77

description: Library name: AGM77

value: ASC


title: AGM75

description: Library name: AGM75


title: Pleural_LTS_5day_rep8

value: Pleural ganglia


title: HGC27, NK, rep3

description: Library name: HGC27_NK_R3


title: s448

description: Library name: s448


title: AGM74

description: Library name: AGM74

value: Liver


title: Pleural_LTS_5day_rep6


title: s43

description: Library name: s43


title: s440

description: Library name: s440


title: HGC27, no NK, rep3

description: Library name: HGC27_noNK_R3


title: s428

description: Library name: s428


title: AGM71

description: Library name: AGM71


title: HGC27, no NK, rep2

description: Library name: HGC27_noNK_R2


title: Pleural_LTS_5day_rep7


title: HGC27, NK, rep1

description: Library name: HGC27_NK_R1


title: Pleural_LTS_5day_rep4


title: AGM262

description: Library name: AGM262


title: HGC27, NK, rep2

description: Library name: HGC27_NK_R2


title: Pleural_LTS_5day_rep3


title: AGM73

description: Library name: AGM73

value: PSC


title: HGC27, no NK, rep1

description: Library name: HGC27_noNK_R1


title: Pleural_LTS_5day_rep5


title: AGM260

description: Library name: AGM260


title: s42

description: Library name: s42


title: s407

description: Library name: s407


title: AGM261

description: Library name: AGM261


title: AGM263

description: Library name: AGM263


title: s378

description: Library name: s378


title: Pleural_LTS_5day_rep1


title: s390

description: Library name: s390


title: s361

description: Library name: s361


title: K562, no NK, rep2

description: Library name: K562_noNK_R2

value: acute myeloid leukemia


title: K562, no NK, rep3

description: Library name: K562_noNK_R3


title: Pleural_LTS_5day_rep2


title: s363

description: Library name: s363


title: BulkRNA_md>TRPV1_TNM3

city: Institute

first: Gerardo

last: Flores-Iga

state: West Virginia

address: Integrated Research and Extension Building

department: Biology

institute: West Virginia State University

description: Library name: TNM3

data_processing:
FastQC
Trimmomatic
STAR-HTSeq
Assembly: Drosophila_melanogaster.BDGP6.46
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Brain

value: Capsaicin


title: K562, NK, rep3

description: Library name: K562_NK_R3


title: BulkRNA_md>TRPV1_TNM2

description: Library name: TNM2


title: AGM26

description: Library name: AGM26


title: AGM258

description: Library name: AGM258


title: K562, NK, rep2

description: Library name: K562_NK_R2


title: K562, no NK, rep1

description: Library name: K562_noNK_R1


title: AGM255

description: Library name: AGM255


title: AGM257

description: Library name: AGM257


title: s356

description: Library name: s356


title: s349

description: Library name: s349


title: BulkRNA_md>TRPV1_TNM1

description: Library name: TNM1


title: K562, NK, rep1

description: Library name: K562_NK_R1


title: s343

description: Library name: s343


title: AGM253

description: Library name: AGM253


title: s353

description: Library name: s353


title: H929 multiple myeloma celll line with gN1E GapmeR replicate C

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: H929-gN1E-C

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed with featureCounts (v1.6.4) to obtain raw read counts. For gene expression analysis, we applied the voom/limma pipeline. Genes with fewer than 10 reads in more than 95% of samples were excluded to reduce background noise. Normalization was conducted using the trimmed mean of M-values (TMM) method to account for differences in library size and reduce technical variability. The data were then transformed using voom, which converts raw counts into log2 counts per million (log2-CPM) and assigns precision weights to each observation. Differential expression analysis was performed using these transformed values, and P values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method. Differential expressed genes were selected at 10% FDR adjusted p-value and 1.5 fold change cut off values.
Assembly: hg38
Supplementary files format and content: counts.txt

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer’s instructions. The purity and concentration of total RNA was determined by the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). The ratios of absorption (260 nm/280 nm) of all samples were between 1.8 and 2.0.
Before library preparation, RNA concentration was evaluated through Qubit™ RNA Broad Range Assay Kit (Invitrogen, Walthman, MA, USA) while RNA quality was established on 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA) using RNA Screen tape kit (Agilent Technologies, Santa Clara, CA, USA). According to the TruSeq Stranded Total RNA (San Diego, CA, USA) protocol, 500 ng of RNA for each sample with RIN value between 9 and 10, were used for RNA sequencing. Final libraries with optimal quality and quantity criteria, assessed by D1000 Screen tape kit (Agilent Technologies) and by Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen), respectively, were run on NextSeq 500 sequencer (Illumina) using a 2 × 150 high-output flow cell with 8 samples/run.

treatment_protocol: NEAT1 knock-down (KD) with specific GapmeR at 48h was obtained by gymnosis.

value: Multiple myeloma cell line

value: gN1E GapmeR


title: H929 multiple myeloma celll line with gN1E GapmeR replicate A

description: Library name: H929-gN1E-A


title: BulkRNA_md>TRPV1_TNF3

description: Library name: TNF3


title: H929 multiple myeloma celll line with SCR GapmeR replicate C

description: Library name: H929-SCR-C

value: SCR GapmeR


title: AGM254

description: Library name: AGM254


title: H929 multiple myeloma celll line with SCR GapmeR replicate B

description: Library name: H929-SCR-B


title: s34

description: Library name: s34


title: H929 multiple myeloma celll line with SCR GapmeR replicate A

description: Library name: H929-SCR-A


title: AGM25

description: Library name: AGM25


title: BulkRNA_md>TRPV1_TNF2

description: Library name: TNF2


title: H929 multiple myeloma celll line with gN1E GapmeR replicate B

description: Library name: H929-gN1E-B


title: s331

description: Library name: s331


title: AGM248

description: Library name: AGM248


title: BulkRNA_md>TRPV1_TNF1

description: Library name: TNF1


title: BulkRNA_md>TRPV1_TCF3

description: Library name: TCF3

value: Control


title: s330

description: Library name: s330


title: s329

description: Library name: s329


title: AGM252

description: Library name: AGM252


title: AGM246

description: Library name: AGM246


title: BulkRNA_md>TRPV1_TCM3

description: Library name: TCM3


title: s328

description: Library name: s328


title: BulkRNA_md>TRPV1_TCF1

description: Library name: TCF1


title: BulkRNA_md>TRPV1_TCM2

description: Library name: TCM2


title: AGM250

description: Library name: AGM250

value: AIH


title: s333

description: Library name: s333


title: s341

description: Library name: s341


title: BulkRNA_BerlinK_NBM3

description: Library name: NBM3

value: BerlinK


title: AGM24

description: Library name: AGM24


title: s323

description: Library name: s323

value: placenta


title: LP1 multiple myeloma celll line with SCR GapmeR replicate D

description: Library name: LP1-SCR-D


title: BulkRNA_md>TRPV1_TCM1

description: Library name: TCM1


title: BulkRNA_BerlinK_NBM1

description: Library name: NBM1


title: LP1 multiple myeloma celll line with gN1E GapmeR replicate B

description: Library name: LP1-gN1E-B


title: LP1 multiple myeloma celll line with gN1E GapmeR replicate D

description: Library name: LP1-gN1E-D


title: BulkRNA_md>TRPV1_TCF2

description: Library name: TCF2


title: BulkRNA_BerlinK_NBM2

description: Library name: NBM2


title: LP1 multiple myeloma celll line with gN1E GapmeR replicate A

description: Library name: LP1-gN1E-A


title: AGM22

description: Library name: AGM22


title: s314

description: Library name: s314

value: male


title: LP1 multiple myeloma celll line with SCR GapmeR replicate A

description: Library name: LP1-SCR-A


title: AGM23

description: Library name: AGM23


title: s31

description: Library name: s31


title: s325

description: Library name: s325


title: AGM19

description: Library name: AGM19


title: AMO1 multiple myeloma celll line with gN1E GapmeR replicate C

description: Library name: AMO1-gN1E-C


title: BulkRNA_BerlinK_CBM3

description: Library name: CBM3


title: LP1 multiple myeloma celll line with SCR GapmeR replicate B

description: Library name: LP1-SCR-B


title: s303

description: Library name: s303


title: AGM18

description: Library name: AGM18


title: s315

description: Library name: s315

value: female


title: AGM21

description: Library name: AGM21


title: AMO1 multiple myeloma celll line with gN1E GapmeR replicate D

description: Library name: AMO1-gN1E-D


title: BulkRNA_BerlinK_NBF3

description: Library name: NBF3


title: s3

description: Library name: s3


title: BulkRNA_BerlinK_CBM1

description: Library name: CBM1


title: AGM174

description: Library name: AGM174


title: AGM175

description: Library name: AGM175


title: AGM20

description: Library name: AGM20


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate D

description: Library name: AMO1-SCR-D


title: BulkRNA_BerlinK_CBF3

description: Library name: CBF3


title: BulkRNA_BerlinK_NBF1

description: Library name: NBF1


title: BulkRNA_BerlinK_CBM2

description: Library name: CBM2


title: AMO1 multiple myeloma celll line with gN1E GapmeR replicate A

description: Library name: AMO1-gN1E-A


title: s280

description: Library name: s280


title: AGM172

description: Library name: AGM172


title: s307

description: Library name: s307


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate A

description: Library name: AMO1-SCR-A


title: AGM176

description: Library name: AGM176


title: AMO1 multiple myeloma celll line with SCR GapmeR replicate C

description: Library name: AMO1-SCR-C


title: BulkRNA_BerlinK_NBF2

description: Library name: NBF2


title: BulkRNA_BerlinK_CBF1

description: Library name: CBF1


title: s29

description: Library name: s29


title: BulkRNA_BerlinK_CBF2

description: Library name: CBF2


title: 252800524068_2_2_FP95L_0_hour_(40_mins_post)

hyb_protocol: Hybridizations were performed using Agilent SurePrint G3 Mouse GE 8x60K microarrays following Agilent's Two-Color Microarray-Based Gene Expression protocol.

scan_protocol: Arrays were scanned using Agilent SureScan Microarray Scanner and features were extracted using Agilent Feature Extraction Software (v10.7).

data_processing: Data were processed using Feature Extraction Software. Log2 transformation and quantile normalization were applied where applicable.

source_name: Agilent Universal Mouse Reference RNA

label_protocol: Purified RNA samples were labeled with Cy5 using the Agilent Low Input Quick Amp Labeling Kit. The reference RNA was labeled with Cy3.

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent and miRNeasy Mini Kit (QIAGEN) following the manufacturer's instructions. Quality was assessed using NanoDrop, Qubit, and Tapestation 2200.

tag: time point

value: Sham

source_name: Lungs

value: Fentanyl

value: Lungs


title: AGM173

description: Library name: AGM173

value: Liver


title: s275

description: Library name: s275


title: s274

description: Library name: s274


title: AGM171

description: Library name: AGM171


title: s270

description: Library name: s270


title: AGM17

description: Library name: AGM17

value: PSC


title: s269

description: Library name: s269


title: AGM170

description: Library name: AGM170


title: 252800524068_2_4_FPB2L_6_hours


title: s272

description: Library name: s272


title: Spleen, infected, 14days, CKO repeat

city: Beijing

first: Xiaonan

last: Ma

address: NO.30 Shuangqing Road

institute: Tsinghua University

description: Library name: Sample_8

data_processing:
Raw FASTQ files from sequencing were aligned to the reference genome and reference gene set using HISAT/Bowtie2. Genes with a false discovery rate (FDR) < 0.05 and a log fold change > 0.58 or < −0.58 were considered differentially expressed.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files 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. 14 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. RNA was isolated and purified using the TIANGEN RNAprep Pure Cell/Bacteria Kit.
The RNA samples were sent to the Beijing Genomics Institute (BGI) for library preparation and RNA sequencing on a DNBseq platform.

value: spleen

value: CD8 T cell

value: UBE2F KO

value: LCMV-Armstrong infection


title: 252800524068_2_3_FP96L_0_hour_(40_mins_post)


title: AGM168

description: Library name: AGM168

value: ASC


title: AGM167B

description: Library name: AGM167B


title: s267

description: Library name: s267


title: Spleen, infected, 14days, CKO

description: Library name: Sample_7


title: Spleen, infected, 14days, WT

description: Library name: Sample_5

value: WT


title: Spleen, infected, 14days, WT repeat

description: Library name: Sample_6


title: AGM164

description: Library name: AGM164


title: 252800524068_1_4_FP93L_24_hours


title: 252800524068_2_1_FP94L_24_hours


title: AGM166B

description: Library name: AGM166B


title: 252800524068_1_2_FP91L_24_hours


title: 252800524068_1_3_FP92L_24_hours


title: s258

description: Library name: s258


title: 5xFAD

city: Baltimore

first: Yongqing

last: Liu

state: MARYLAND

address: 725 N Wolfe Street, WBSB 216

department: Physiology

institute: Johns Hopkins University

description:
Library name: AD
10x OCM
GEM2 contains AD and AD_cKO group. AD with OCM Barcode ID (OB1 and  OB2)

data_processing:
Raw sequencing data were processed with Cell Ranger (v10.0.0) against the mm39 reference. scRNA-seq analyses were conducted in R (v4.3.1) using Seurat (v5.4.0). Filtered gene-barcode count matrices from four experimental groups were generated by Cell Ranger and then processed and integrated in Seurat. Cells expressing fewer than 200 genes and genes detected in fewer than 3 cells were excluded; additional filtering removed cells with detected genes <200 or >6,000, total UMI counts <500 or >50,000, or mitochondrial reads ≥10%. Data were normalized with LogNormalize; 2,000 highly variable genes were selected via variance-stabilizing transformation (vst); and datasets were integrated by canonical correlation analysis (CCA). Principal component analysis (PCA) was computed (50 PCs), and the top 20 PCs were used to construct a shared nearest neighbor (SNN) graph for Louvain clustering; visualizations were generated with Uniform Manifold Approximation and Projection (UMAP). Microglia were identified by canonical markers Cx3cr1, P2ry12, Tmem119, and Hexb; non-microglia clusters were removed and UMAP was recomputed on the microglia subset. Differential expression was assessed using the Wilcoxon rank-sum test with thresholds of |log2FC| > 1, adjusted p < 0.05, and expression in >0.5% of cells in both groups. Dot plots were generated in R using ggplot2 (v4.0.2) from per-condition summaries computed with dplyr (v1.2.0). Volcano plots were generated with ggplot2 (v4.0.2) from Seurat FindMarkers outputs, with selected genes labeled using ggrepel (v0.9.6).
Assembly: mm39
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX) include barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
For FACS-based separation, Single cell suspension from 7-month-old mouse brain were stained with fluorophore-conjugated antibodies against CD11b (BioLegend, #101256) and CD45 (BioLegend, #103116) and subsequently sorted using a SONY MA900 cell sorter. Vybrant DyeCycle violet (Invitrogen, R37172) was used to identify living cells.
10x Genomics Chromium GEM-X Universal 3' Gene Expression v4 4-plex On-Chip Multiplexing (OCM) kit (CG000768, Rev A)

value: Brain

value: FACS-sorted microglia


title: 5xFAD; Kat7_cKO

description:
Library name: AD_cKO
10x OCM
GEM2 contains AD and AD_cKO group. AD_cKO with OCM Barcode ID (OB3 and  OB4)

value: 5xFAD; Kat7_cKO


title: 252800524068_1_1_FP88L_0_hour_(40_mins_post)

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

institute: WRAIR


title: s26

description: Library name: s26

value: placenta


title: AGM162

description: Library name: AGM162

value: AIH


title: s252

description: Library name: s252

value: male


title: LPS_KO_H3K14ac

description: Library name: LPS_KO_H3K14ac

data_processing:
Raw sequencing reads were trimmed using Cutadapt 5.0 (https://cutadapt.readthedocs.io/en/stable/). Trimmed reads were then aligned to the mouse reference genome mm10 with the Spike-in sequence using Bowtie2 (version 2.3.5.1). Bam files with low-quality reads were filtered and duplicates were removed using Samtools v1.18. Reads were then normalized to Spike-in using Bedtools v2.31.0. Peaks were then called with SEACR v1.3. Differential peak analysis was analyzed by MAnorm2 and annotated by CHIPseeker with a p<0.05 cutoff.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: BV2 cells

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for for Illumina Pro (TD904, Vazyme) according to the manufacturer’s instructions. In brief, BV2 cells were collected and counted same number for each group. Nuclei were isolated from BV2 cells and bounded to Concanavalin A (ConA)-coated beads. Subsequently, Nuclei were resuspended in antibody buffer and incubated with primary antibodies against H3K14ac (rabbit, Cell Signaling Technology, #7627), H3K4me3 (rabbit, Cell Signaling Technology, #9751) and IgG (rabbit, Cell Signaling Technology, #66362) at 4 °C overnight. On the next day, samples were incubated with goat anti-rabbit secondary antibodies (1:50, Cell Signaling Technology, #35401). The samples were incubated with pA/G-Tn5 transposase. After transposon activation and fragmentation, 0.5 pg Spike-in DNA was added to each sample and total DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed with TruePrep Index Kit V2 for Illumina (TD202, Vazyme) and VAHTS DNA Clean Beads (N411, Vazyme) were used for purification steps.

value: BV2 cells

value: Immortalized Microglia

value: KO

value: LPS


title: Kat7_cKO

description:
Library name: cKO
10x OCM
GEM1 contains WT and cKO group. cKO with OCM Barcode ID (OB3 and  OB4)


title: s243

description: Library name: s243


title: 252800524062_2_3_FP23L_24_hours

value: Sham

value: Fentanyl

value: Lungs


title: s227

description: Library name: s227

value: female


title: AGM161

description: Library name: AGM161

value: Liver


title: AGM163

description: Library name: AGM163

value: ASC


title: s223

description: Library name: s223


title: LPS_WT_H3K14ac

description: Library name: LPS_WT_H3K14ac

value: WT


title: 252800524062_2_4_FP24L_7_days


title: AGM160

description: Library name: AGM160


title: WT

description:
Library name: WT
10x OCM
GEM1 contains WT and cKO group. WT with OCM Barcode ID (OB1 and  OB2)

value: Brain


title: s211

description: Library name: s211


title: AGM16

description: Library name: AGM16


title: KO_H3K14ac

description: Library name: KO_H3K14ac

value: PBS


title: 252800524062_2_2_FP22L_6_hours


title: s210

description: Library name: s210


title: AGM159

description: Library name: AGM159


title: WT_H3K14ac

description: Library name: WT_H3K14ac


title: 252800524062_2_1_FP21L_0_hour_(40_mins_post)


title: 252800524062_1_3_FP19L_24_hours


title: 252800524062_1_4_FP20L_0_hour_(40_mins_post)


title: H3K4me3

description: Library name: H3K4me3


title: s198

description: Library name: s198


title: 252800524062_1_2_FP17L_7_days


title: AGM158

description: Library name: AGM158


title: s19

description: Library name: s19


title: IgG

description: Library name: IgG


title: s18

description: Library name: s18


title: LPS_Kat7_KO rep2

description: Library name: LPS_K7_KO_2

data_processing:
The raw sequencing data were aligned to the mouse preference genome (GRCm39, mm39) using HISAT2 (v2.0.5). Reads on each GENCODE annotated gene were counted using HTSeq, and then differential gene expression analysis was performed using DESeq2 R package.
Assembly: mm39
Supplementary files format and content: xls
Supplementary files format and content: excel with gene counts

extract_protocol:
Three biological replicates were sequenced per group. For each sample, RNA was extracted from BV2 cells with TRIzol reagents (Invitrogen). BV2 cells are treated with or without LPS for 6 hours.
NEBNext Ultra II RNA Library Prep Kit


title: LPS_Kat7_KO rep1

description: Library name: LPS_K7_KO_1


title: AGM157

description: Library name: AGM157


title: LPS_Kat7_KO rep3

description: Library name: LPS_K7_KO_3


title: AGM156

description: Library name: AGM156


title: LPS_WT rep3

description: Library name: LPS_WT_3


title: 252800524062_1_1_FP16L_7_days


title: s141

description: Library name: s141


title: AGM15

description: Library name: AGM15

value: PSC


title: AGM155

description: Library name: AGM155


title: s193

description: Library name: s193

value: placenta


title: AGM154

description: Library name: AGM154


title: s139

description: Library name: s139


title: LPS_WT rep2

description: Library name: LPS_WT_2


title: AGM14

description: Library name: AGM14


title: s137

description: Library name: s137


title: 252800524053_2_4_FPB2L_6_hours


title: 252800524053_2_1_FP94L_24_hours


title: LPS_WT rep1

description: Library name: LPS_WT_1


title: 252800524053_1_4_FP93L_24_hours


title: 252800524053_2_2_FP95L_0_hour_(40_mins_post)


title: 252800524053_1_3_FP92L_24_hours


title: AGM136

description: Library name: AGM136


title: 252800524053_2_3_FP96L_0_hour_(40_mins_post)


title: s131

description: Library name: s131


title: AGM135

description: Library name: AGM135


title: Kat7_KO rep3

description: Library name: K7_KO_3


title: 252800524053_1_2_FP30L_0_hour_(40_mins_post)


title: Kat7_KO rep2

description: Library name: K7_KO_2


title: s13

description: Library name: s13


title: WT rep3

description: Library name: WT_3


title: s132

description: Library name: s132


title: s127

description: Library name: s127


title: AGM133

description: Library name: AGM133


title: AGM132

description: Library name: AGM132


title: s129

description: Library name: s129


title: AGM13

description: Library name: AGM13


title: Kat7_KO rep1

description: Library name: K7_KO_1


title: 252800524046_2_3_FP86L_6_hours


title: 252800524046_2_4_FP87L_0_hour_(40_mins_post)


title: s120

description: Library name: s120


title: WT rep2

description: Library name: WT_2


title: AGM100

description: Library name: AGM100

value: AIH


title: s112

description: Library name: s112

value: male


title: WT rep1

description: Library name: WT_1

value: BV2 cells


title: 252800524046_2_2_FP85L_6_hours


title: 252800524046_2_1_FP84L_7_days


title: Zeb1Prx1 MSC rep3

city: NanJing

first: Chuyue

last: Pan

address: 639 Longmian Ave.

institute: China Pharmaceutical University

description:
Library name: KO_rep3
Primary MSCs from Zeb1Prx1 mice

data_processing:
Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include read counts (or FPKM) values for each Sample.

source_name: compact bone

extract_protocol:
The femurs and tibias were excised into bone chips and digested for 1 h with collagenase Ⅱ. Bone chips were then cultured in α-MEM supplemented with 10% FBS at 37 °C in a 5% CO2 incubator. Cells were sorted by GFP fluorescent signal to isolate Prx1+ MSCs
PCR products were purified by AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. A TruSeq PE Cluster Kit v3-cBot-HS (Illumina) was used to cluster the index-coded samples. 150 bp paired-end reads were generated on an Illumina Novaseq platform.

value: compact bone

value: Prx1+ MSCs

value: Prx1-Cre+; ROSA-YFP; Zeb1fl/fl

value: untreated


title: s104

description: Library name: s104


title: shTDP-43shDCPS_6h_rep3

first: Shuying

last: Sun

address: Hunterian 205

institute: jhmi

description: Library name: YY117

data_processing:
Raw reads were trimmed using trim-galore (version 0.6.7) and aligned to human genome and transcriptome (hg38) using HISAT2 (version 2.2.1)
Cleaned reads were mapped to human GRCh38/hg38 and ERCC spike-in (Thermo Fisher Scientific, Cat. No. 4456740), seperately.
The number of unique reads mapped to GENCODE (https://www.gencodegenes.org/, version 38) annotated genes were counted using subread (version 2.0.1).
Raw reads were normalized by linear regression fitting of the RNA ERCC spike-in.
Assembly: GRCh38/hg38
Supplementary files format and content: txt file of raw reads quantified by subread (version 2.0.1) and used for DEseq2
Supplementary files format and content: txt file of reads normalized to ERCC spike-in reads

growth_protocol: Classic Neuronal Medium

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher), and RNA concentrations were determined with the Qubit RNA HS Assay Kit on a Qubit 4.0 Fluorometer
Libraries were prepared according to protocol accompanying the NEBNext® Ultra™ II Directional RNA Library Prep Kit (Cat. No. E7765) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: Cells were transduced with shCTR or shTDP-43 for 8 days, and transduced with shCTR or shDCPS for 6 days. Cells were treated with 5μg/μL Actinomycin D for 0h, 3h, or 6h before harvesting.

value: Day 14 neuron

value: TDP-43 and DCPS double knockdown, actD treated for 6h

tag: batch


title: shTDP-43shDCPS_6h_rep1

description: Library name: YY115


title: Zeb1Prx1 MSC rep1

description:
Library name: KO_rep1
Primary MSCs from Zeb1Prx1 mice


title: WT MSC rep3

description:
Library name: WT_rep3
Primary MSCs from WT mice

value: Prx1-Cre+; ROSA-YFP; Zeb1wt/wt


title: shTDP-43shDCPS_3h_rep2

description: Library name: YY113

value: TDP-43 and DCPS double knockdown, actD treated for 3h


title: s1

description: Library name: s1

value: female


title: s100

description: Library name: s100


title: WT MSC rep2

description:
Library name: WT_rep2
Primary MSCs from WT mice


title: WT MSC rep1

description:
Library name: WT_rep1
Primary MSCs from WT mice


title: shTDP-43shDCPS_6h_rep2

description: Library name: YY116


title: shTDP-43shDCPS_3h_rep3

description: Library name: YY114


title: 252800524046_1_3_FP82L_7_days

value: Sham

value: Fentanyl

value: Lungs


title: 252800524046_1_1_FP78L_6_hours


title: 252800524046_1_4_FP83L_7_days


title: shTDP-43shDCPS_0h_rep3

description: Library name: YY111

value: TDP-43 and DCPS double knockdown, actD treated for 0h


title: T cells from Foxp3Cre DKO-severe and WT, HTO

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

description:
Library name: Foxp3Cre DKO-severe and WT, HTO
Hashtag-derived oligonucleotide (HTO)
HTO library: R1 file contains cell barcode and UMI; R2 file contains hashtag antibody derived tag reads

library_source: other

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting and aggregation of sequencing runs were performed using the Cell Ranger analysis pipeline (v.7.1.0) and the mouse reference genome mm10. Downstream analysis was performed using the R package Seurat
Assembly: mm10
Supplementary files format and content: Raw counts in MEX format.

molecule: protein

source_name: spleen and peripheral lymph nodes

extract_protocol:
Samples were processed per the manufacturer’s protocol using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genimics)
Sample sequencing was conducted at the La Jolla Institute sequencing core on an Illumina Novaseq 6000 sequencer using a 100-bp kit. Samples were sequenced using a 28|10|10|90 run configuration.

value: spleen and peripheral lymph nodes

value: splenocytes and lymphocytes

value: Foxp3Cre Tet2/3 flox/flox (DKO-severe), Foxp3Cre WT

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 (WT), TotalSeq-B0302 anti-mouse Hashtag 2 (DKO)


title: TC71_shSA2_1_Fli1

city: Ann Arbor

first: Abhijit

last: Parolia

state: MI

address: 1500 E Medical Center Dr

institute: Michigan Medicine

description: Library name: TC71_shSA2_1_Fli1

data_processing:
ChIP-Seq analysis was carried out by first assessing reads and performing trimming using Trimmomatic version 0.39 (settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Paired end reads were aligned to hg38 (GRCh38) human genome reference using bwa (“bwa mem” command with options -5SP -T0, version 0.7.17-r1198-dirty). Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates). Peak calling was performed using MACS2 using narrowpeak setting  for narrow peaks and a second set for broad peaks (eg H3K27Ac, --broad -B --cutoff-analysis --broad-cutoff 0.05 --max-gap 500). Finally, bedtools was used to remove blacklisted regions of the genome from the peaks list (Encode’s exclusion list ENCFF356LFX.bed). UCSC’s tool wigtoBigwig was used for conversion to bigwig formats.
Assembly: hg38
Supplementary files format and content: beds for peaks, blacklist removed
Supplementary files format and content: bigwig signal files

source_name: Bone/soft tissue

growth_protocol: Ewing sarcoma cells (A673, TC71) were grown in DMEM and IMDM media with 10% FBS and Penicillin/Streptomycin respectively.

extract_protocol:
Diagenode iDeal ChIP-seq kit for Transcription Factors / Histones
Chromatin immunoprecipitation experiments were carried out using the Ideal ChIP-seq Kit for Transcription Factors or Histones (Diagenode) as per the manufacturer’s protocol. Chromatin from 2 × 106 cells (for transcription factors) and 1x106 cells (for histones) was used for each ChIP reaction with 4 or 2  μg of the target protein antibody respectively. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 8 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode) using the standard protocol. Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: Cells were stably transduced with lentivirus containing non-targeting shRNA or STAG2 shRNA. Cells were treated with doxycycline prior to performing ChIP-seq to induce loss of STAG2. For CRISPR knockout lines, cells were transfected with control or STAG2-targeting guide RNAs. Chromatin immunoprecipitation (ChIP) experiments were performed using the Ideal ChIP-seq kit for transcription factors (Diagenode) per the manufacturer’s protocol.

value: Bone/soft tissue

tag: cell line

value: Ewing Sarcoma

tag: Sex

value: Male

value: TC71 cells were stably transduced with lentivirus containing STAG2-targeting shRNA.


title: 252800524045_2_4_FP77L_6_hours


title: 252800524046_1_2_FP81L_7_days


title: shTDP-43shDCPS_3h_rep1

description: Library name: YY112

value: Day 14 neuron


title: TC71_shSA2_2_Fli1

description: Library name: TC71_shSA2_2_Fli1


title: A673_shSTAG2_2_FLI1

description: Library name: A673_shSTAG2_2_FLI1

value: Female

value: A673 cells were stably transduced with lentivirus containing STAG2-targeting shRNA#2.


title: 252800524045_2_2_FP73L_6_hours


title: shTDP-43shDCPS_0h_rep2

description: Library name: YY110


title: TC71_shNT_Fli1

description: Library name: TC71_shNT_Fli1

value: TC71 cells were stably transduced with lentivirus containing non-targeting shRNA.


title: 252800524045_2_3_FP74L_0_hour_(40_mins_post)

value: Sham


title: A673_shSTAG2_1_H3K27Ac

description: Library name: A673_shSTAG2_1_H3K27Ac

value: A673 cells were stably transduced with lentivirus containing STAG2-targeting shRNA#1.


title: shTDP-43shDCPS_0h_rep1

description: Library name: YY109


title: 252800524045_2_1_FP72L_6_hours

value: Fentanyl

value: Lungs


title: CD4+ YFP(FOXP3)- T cells from DKO-severe4

description: Library name: DKO-severe-4

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR version 2.7.11 with the parameters -outFilterMultimapNmax 1 -alignIntronMin 20 -twopassMode Basic -outBAMcompression 10 -alignSJoverhangMin 8 -alignSJDBoverhangMin 1 -outFilterType BySJout -outSJfilterReads Unique -outFilterMismatchNoverReadLmax 0.04 to analyze gene expression.
HT-Seq was used to quantify the gene expression levels using the options htseq-count --stranded reverse. Genes with at least ten read counts in one condition were kept for further analysis.
Normalization and differential expression analyses were performed using DESEq2.
Assembly: mm10
Supplementary files format and content: For visualization of the data, we generated tracks using Deeptools version 3.5.1, with the option bamCoverage.

extract_protocol:
Total RNA was isolated from CD4+ YFP(FOXP3)- T cells from pooled spleen and peripheral lymph nodes (cervical and inguinal) from Foxp3Cre WT mice and Foxp3-Cre Tet2/3fl/fl mice (14-weeks-old) using Direct-zol RNA microprep (Zymo, #R2060).
RNA-sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7760, #7765) according to the manufacture’s protocol

value: spleen and peripheral lymph nodes

value: Foxp3Cre Tet2/3 flox/flox (DKO-severe)


title: A673_shSTAG2_1_FLI1

description: Library name: A673_shSTAG2_1_FLI1


title: CD4+ YFP(FOXP3)- T cells from DKO-severe3

description: Library name: DKO-severe-3

value: splenocytes and lymphocytes


title: A673_shNC_STAG2

description: Library name: A673_shNC_STAG2

value: A673 cells were stably transduced with lentivirus containing non-targeting shRNA.


title: T cells from Foxp3Cre DKO-severe and WT, mRNA

description:
Library name: Foxp3Cre DKO-severe and WT, mRNA
polyA RNA
GEX library: R1 file contains cell barcode and UMI; R2 file contains transcript

value: Foxp3Cre Tet2/3 flox/flox (DKO-severe), Foxp3Cre WT

value: mRNA


title: shTDP-43shCTR_6h_rep3

description: Library name: YY108

value: TDP-43 knockdown, actD treated for 6h


title: CD4+ YFP(FOXP3)- T cells from DKO-severe2

description: Library name: DKO-severe-2


title: 252800524045_1_4_FP71L_0_hour_(40_mins_post)


title: shTDP-43shCTR_6h_rep1

description: Library name: YY106


title: A673_shNC_RAD21

description: Library name: A673_shNC_RAD21

value: Bone/soft tissue

value: Ewing Sarcoma


title: CD4+ YFP(FOXP3)- T cells from DKO-severe1

description: Library name: DKO-severe-1


title: shTDP-43shCTR_3h_rep3

description: Library name: YY105

value: Day 14 neuron

value: TDP-43 knockdown, actD treated for 3h


title: CD4+ YFP(FOXP3)- T cells from DKO-moderate4

description: Library name: DKO-moderate-4

value: Foxp3Cre Tet2/3 flox/flox (DKO-moderate)


title: shTDP-43shCTR_6h_rep2

description: Library name: YY107


title: A673_shNC_H3K27Ac

description: Library name: A673_shNC_H3K27Ac

value: Female


title: shTDP-43shCTR_3h_rep2

description: Library name: YY104


title: shTDP-43shCTR_3h_rep1

description: Library name: YY103


title: CD4+ YFP(FOXP3)- T cells from DKO-moderate3

description: Library name: DKO-moderate-3


title: 252800524044_2_4_FP66L_24_hours

value: Sham


title: AGM247

description: Library name: AGM247

value: Liver

value: AIH


title: 252800524045_1_1_FP67L_0_hour_(40_mins_post)

value: Fentanyl

value: Lungs


title: A673_shNC_H3K4me1

description: Library name: A673_shNC_H3K4me1


title: 252800524044_2_2_FP63L_24_hours


title: 252800524045_1_2_FP68L_6_hours


title: A673_shNC_CTCF

description: Library name: A673_shNC_CTCF


title: A673_shNC_FLI1

description: Library name: A673_shNC_FLI1


title: 252800524044_2_3_FP64L_24_hours


title: CD4+ YFP(FOXP3)- T cells from DKO-moderate1

description: Library name: DKO-moderate-1

value: spleen and peripheral lymph nodes


title: 252800524045_1_3_FP69L_0_hour_(40_mins_post)


title: shTDP-43shCTR_0h_rep2

description: Library name: YY101

value: TDP-43 knockdown, actD treated for 0h


title: CD4+ YFP(FOXP3)- T cells from WT4

description: Library name: Foxp3Cre WT-4

value: splenocytes and lymphocytes

value: Foxp3Cre WT


title: shTDP-43shCTR_0h_rep3

description: Library name: YY102


title: CD4+ YFP(FOXP3)- T cells from DKO-moderate2

description: Library name: DKO-moderate-2


title: 252800524044_2_1_FP62L_24_hours


title: CD4+ YFP(FOXP3)- T cells from WT3

description: Library name: Foxp3Cre WT-3


title: shTDP-43shCTR_0h_rep1

description: Library name: YY100


title: A673_sgSA2_FLI1

description: Library name: A673_sgSA2_FLI1

value: A673 cells were treated with STAG2-targeting guide RNA


title: shCTRshCTR_6h_rep3

description: Library name: YY90

value: control with shCTR transduction, actD treated for 6h


title: 252800524044_1_4_FP61L_7_days


title: vU1.3KO, replicate 3

description: Library name: Sample 6

data_processing:
Paired-end reads of total RNA-seq data and pulldown experiments in IPS cells were mapped with the STAR1 software version 2.7.3a with the default setting, quantified with htseq-count2 software version 0.12.4 and vU1KO IPS data were normalized with the RUVs method in RUVseq. VU1 pulldown targets were quantified with noise-seq. Differential gene expression between WT and KO was quantified with the R package DEseq2 version 1.34.0 using the default Wald test. We defined genes whose adjusted p-value < 0.05 as significantly differentially expressed genes (DEGs) in IPS data and whose absolute log2 fold change > 0.6 and adjusted p-value < 0.05 in HEK293 data.
RNA splicing events were quantified and compared using whippet with probability cutoff > 0.9 and |deltapsi| > 0.1. Functional isoform switches were detected with R package isoformSwitchAnalysis.
The RSSs were quantified using the method described in (Zhang et al., 2018) but searching YAGNN instead of AGGT as the rss motif and filtering out the RSSs detected in the polyA-enriched RNAseq as false positive, normalized with all junction reads connecting the 3’ of their upstream exons and compared using t-test with the p-value cutoff of 0.05.
Assembly: GRCh38/hg38
Supplementary files format and content: The .txt files contain raw counts of reads mapped to each gene.
Supplementary files format and content: The .psi.gz files are compressed files containing the percentage of splicing in of each node such as exons, introns, and transcripional start or end sites.
Supplementary files format and content: The .junc files contain counts of recursive spliced genome regions at the last column.

extract_protocol:
RNAs were extracted using the standard TriZol/chlorofom (acidic pH) approach and underwent quality control for integrity and size distribution
Standard Illumina-compatible library preparation procedures were followed, in all cases ribodepletion followed by random-hexamer-based reverse transcription to generate cDNA pools for sequenciing; strand-specific information was maintained during these preps.

value: human iPSc

value: vU1.3 knockout


title: 252800524044_1_3_FP60L_7_days


title: A673_sgNC_FLI1

description: Library name: A673_sgNC_FLI1

value: Bone/soft tissue

value: Ewing Sarcoma

value: A673 cells were treated with non-targeting guide RNA


title: CD4+ YFP(FOXP3)- T cells from WT2

description: Library name: Foxp3Cre WT-2


title: 252800524044_1_1_FP58L_24_hours


title: vU1.3KO, replicate 2

description: Library name: Sample 5


title: vU1.3KO, replicate 1

description: Library name: Sample 4


title: CD4+ YFP(FOXP3)- T cells from WT1

description: Library name: Foxp3Cre WT-1


title: 252800524044_1_2_FP59L_7_days


title: shCTRshCTR_6h_rep1

description: Library name: YY88

value: Day 14 neuron


title: shCTRshCTR_6h_rep2

description: Library name: YY89


title: control, replicate 3

description: Library name: Sample 3

value: wild type


title: control, replicate 2

description: Library name: Sample 2


title: shCTRshCTR_3h_rep2

description: Library name: YY86

value: control with shCTR transduction, actD treated for 3h


title: Mus musculus male 3

city: Memphis

first: Troy

last: Camarata

state: TN

address: 1003 Monroe Avenue

department: Biomedical Sciences

institute: Baptist University College of Osteopathic Medicine

description:
Library name: M3
Mouse_Individual_Methylation.xlsx

data_processing:
Sequence quality and adapter trimming were performed using Fastqc and Fastp.
Sequence reads were aligned to the mouse or red-eared slider genome using Bismark.
Methylated cytosines were determined using MethyKit R package. MethylKit performed a Fisher’s test on the pooled sample and control groups, and an FDR-corrected P value threshold of ≤0.05 was considered significant for identifying differentially methylated cytosines (DMCs).
Assembly: T. scripta elegans: CAS_Tse_1.0; M. musculus: GRCm38
Supplementary files format and content: Quality control statistics for all sequenced samples in worksheet files
Supplementary files format and content: Genomic location, base calling, gene ID, reference ID, methylation location for each sample in worksheet files

source_name: adult kidney cortex

extract_protocol:
Genomic DNA was extracted using the Monarch Genomic DNA Extraction Kit (New England Biolabs) following manufacturer’s instructions including proteinase K and RNase A incubations. For mice, outer cortical tissue was dissected in cold PBS followed by genomic DNA extraction. For adult turtle kidneys, surface convolutions or medullary tissue were dissected in cold PBS followed by extraction of genomic DNA.
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treatedto generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, whilemethylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. Thelibrary was ready after size selection and PCR amplification.

value: adult kidney cortex

value: male

value: Mixed

value: WT

tag: tissue type

value: Manual dissected cortical tissue


title: shCTRshCTR_3h_rep3

description: Library name: YY87


title: Mus musculus male 5

description:
Library name: M5
Mouse_Individual_Methylation.xlsx


title: sibling biol rep2

city: Guangzhou

first: Zhibin

last: Huang

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

description:
Library name: sample4
sib rep2

data_processing:
Raw sequencing data underwent stringent quality control using fastp (v0.23.2). The cleaned reads were then aligned to the Danio rerio GRCz11 reference genome using STAR (v2.7.10a) with standard parameters. Gene-level read counts were generated using FeatureCounts (v2.0.1). The count matrix was input into R (v4.2.2) and analyzed with DESeq2 (v1.26.0) for normalization, identification of differentially expressed genes (DEGs), and sample-to-sample distance analysis. Functional enrichment analysis of KEGG pathways and Gene Ontology (GO) terms was performed on the significant DEGs using the R package ClusterProfiler (v4.6.2), with results visualized graphically.
Assembly: GRCz11
Supplementary files format and content: raw gene counts of tubgcp6 mutant and sibling countrol

source_name: whole embryos

growth_protocol: Zebrafish embroys were maintained in egg water in 28 °C till 7 dpf for sacrification.

extract_protocol:
Embryos from tubgcp6+/- intercrosses were genotyped at 7 dpf to identify mutants and  siblings. Then, total RNA was extracted from tubgcp6 mutants and their siblings using Trizol reagent (15596026, Invitrogen) according to the manufacturer’s instructions.
The RNA sequencing libraries were constructed by NEBNext® UltraTM RNA Library Prep Kit for Illumina® RNA (NEB; E7770)  according to the manufacturer’s instructions.

treatment_protocol: The embryos underwent no further treatment.

value: whole embryos

tag: strain

value: AB

tag: developmental stage

value: 7 dpf

value: sibling