title: IPSC-microglia, AD20, sncRNA

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

description:
Library name: S20_CN
small RNAseq of sample 20 (CN)

data_processing:
To analyze the seq data, adaptor sequences were first removed using Cutadapt and reads with a length of more than 15 bp were extracted. We further filtered out RNAs with counts <10 and all rRNA sequences, using the remaining reads as the cleaned input. In terms of the mapping databases, we prepared mRNA database downloaded from UCSC genome browser, extracted sequences with NM accession, and added official gene symbols after the RefSeq accession number. For small RNA database, we prepared tRF5 and tRF3 databases using the identical sequences derived from different tRNAs (sequences downloaded from tRNA genes using the Table Browser of the UCSC genome browser). We also prepared tRF1 sequences using the genome locations of tRNAs. Our inhouse small RNA database includes (1) these tRFs, (2) miR/snoR sequences downloaded from the UCSC genome browser, and (3) piRNA sequences downloaded from piRBase. The cleaned input reads were mapped to our in-house small RNA database using bowtie2 (v2.4.1), allowing two mismatches (option N-1). After we mapped the cleaned input reads to the small RNA database, the unmapped sequences were then mapped to the hg38 genome using the bowtie2 pre-built index (GRCh38_noalt_as) to detect all human sequences.
Assembly: hg38
Supplementary files format and content: csv file include raw counts mapping to mRNAs for all samples
Supplementary files format and content: csv file include raw counts mapping to sncRNAs for all samples

source_name: Human IPSC-derived microglia cells

growth_protocol: Induced pluripotent stem cells were obtained from the Coriell Institute and cultured in mTeSR Plus medium on Matrigel-coated 6-well plates. Induced pluripotent stem cells were differentiated into HPCs using the STEMdiff Hematopoietic Kit following the manufacturer’s instructions. Non-adherent cells harvested on Day 12 were confirmed as HPCs and used immediately for microglial differentiation. Hematopoietic progenitor cells were further differentiated using the STEMdiff Microglia Differentiation Kit and matured with the STEMdiff Microglia Maturation Kit, per the manufacturer’s protocol. On Day 12, cells were collected by centrifugation, resuspended in 2 mL fresh Differentiation Medium, and replated onto Matrigel-coated 6- well plates; medium was topped up every other day. On Day 24, cells were again collected, resuspended in Microglia Maturation Medium, and seeded onto Matrigel-coated 6-well plates. They were then fed every other day for an additional 6 days to complete maturation.

extract_protocol:
After 6 days of maturation, iPSC-derived microglia (iMG) cells were harvested, and RNA was extracted using TRIzol Reagent with the PureLink RNA Mini Kit, according to the manufacturer’s instructions. In brief, after adding chloroform and phase separation, the aqueous phase containing RNA was transferred to the Spin Cartridge provided in the kit.
RNA samples were submitted to RealSeq Biosciences (Santa Cruz, CA) for library preparation and RNA sequencing. Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Kit with 8 uL of total RNA input and 13 PCR cycles. Libraries were pooled at equal concentrations and profiled using a DNA Tapestation and dsDNA High Sensitivity Qubit assay before sequencing on the Singular G4 platform. We further examined small noncoding RNA (sncRNA) expression in iMGs from sporadic AD and healthy controls, using T4 PNKsncRNA-seq, a modified sequencing method designed to overcome barcode ligation biases inherent in standard library preparations. Many sncRNAs, including tRFs, lack 3’-hydroxyl ends required for efficient barcode ligation, leading to their underrepresentation in conventional methods (Wu et al., 2022). Therefore, before sncRNA seq, we pretreated RNAs with T4-PNK to make sncRNAs homogeneously with 3’-hydroxyl ends. In brief, 15 mL of RNAs was pretreated with 10 units of T4 PNK (New England Biolabs, Ipswich, MA) in a final reaction volume of 50 mL. After incubating them at 37 _x000E_C for 30 min, followed by heat inactivation at 65 C for 20 min, the treated RNAs were purified into 15 mL of nuclease-free water using the Zymo RNA Clean and Concentrator-5 kit, following the small RNA enrichment protocol according to the manufacturer’s instructions. RealSeq-Biofluids libraries were then prepared using 10 mL of treated RNA input and 20 PCR cycles. Libraries were pooled at equal concentrations and profiled using a DNA Tapestation and dsDNA High Sensitivity Qubit assay before sequencing on the NextSeq 550 platform.

value: Human IPSC-derived microglia cells


title: sample_75

status: Public on Jun 18 2026

type: genomic

city: Tampere

first: Keijo

last: Viiri

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

description: GFDd

hyb_protocol: Aliquots of 1 µg of DNA were subjected to bisulfite conversion, and 4 µl of bisulfite-converted DNA underwent whole-genome application, enzymatic fragmentation, and hybridization onto the MethylationEPIC BeadChip (EPICv2).

scan_protocol: The arrays were scanned using the iScan system (Illumina, San Diego, CA, USA).

data_processing:
The DNA methylation data was pre-processed using the default meffil pipeline, with a p-value threshold of 0.05. Probes that failed quality control (QC) were removed from further analysis. One saple was removed from processed data afte QC
Average Beta values

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC version 2 BeadChip at Helmholtz Zentrum, Munich, Germany

extract_protocol: Genomics DNA was extracted from whole blood samples with Chemagic 360 robot with CMG-1091 kit (Revvity, Waltham, MA, USA) in combination with chemagic™ DNA Blood 400 kit H96 (Cat. No. CMG-1091), following the manufacture’s protocol (VD190913.che).

tag: tissue

value: Whole blood

tag: treatment

value: drug

tag: age

tag: Sex

value: F

tag: timepoint

value: baseline


title: Sprague–Dawley rats, Saline Control2

type: SRA

city: Kunming

first: Kang

last: Luo

state: Yunnan

address: No. 1168, Chunrong West Road, Yuhua Street, Chenggong District, Kunming,

country: China

institute: Kunming Medical University

description: Library name: C82

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to
the manufacturer’s instructions. After cluster generation, the library preparations were
sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were
generated.
Assembly: mm10
Supplementary files format and content: RNAseq_counts_matrix.csv
Supplementary files format and content: RNAseq_counts_matrix.csv

molecule: total RNA

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 µg RNA oftotal RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM.RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Heart

tag: genotype

value: WT

value: subcutaneous injection of equal volume of saline for 7 consecutive days


title: sample_74

description: PGCp

value: placebo

value: challenge


title: IPSC-microglia, AD19, sncRNA

country: USA

description:
Library name: S19_CN
small RNAseq of sample 19 (CN)

tag: cell type


title: Sprague–Dawley rats, Saline Control1

description: Library name: C81


title: IPSC-microglia, AD18, sncRNA

description:
Library name: S18_AD
small RNAseq of sample 18 (AD)


title: KD4

city: Shenzhen

first: Qixin

last: Xu

state: Guangdong

address: No. 4009, Xinzhou Road, Futian District, Shenzhen, Guangdong Province

institute: Women and Children's Medical Center

description: Library name: Sample8

data_processing:
The image data of sequencing fragments measured by high-throughput sequencer were converted into sequence data (reads) by CASAVA base recognition. The file is in fastq format, which mainly contains the sequence information of sequencing fragments and the corresponding sequencing quality information.
The raw data obtained by sequencing contained a small number of reads with sequencing adapter or low sequencing quality, and the reads with adapter were removed. reads containing N(N means that the base information could not be determined) were removed. Low-quality reads(the number of bases with Qphred<=5 accounted for more than 50% of the entire read length) were removed
fragments were randomly interrupted, and the clean reads after quality control were aligned to the reference genome
According to the position information of gene alignment on the reference genome, the number of reads covered from the start to the end of each gene (including the newly predicted gene) was counted.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: csv files include FPKM value for each sample

extract_protocol:
Total RNA was isolated using RNA Extraction Kit (MACHEREY NAGEL)
mRNA was enriched from total RNA using Oligo dT magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, addition of an A-tail, linker ligation, fragment selection, amplification, and purification, the library is ready

treatment_protocol: HTR-8/SVneo trophoblast cells were cultured in 10% Fetal Bovine Serum (Gibco, 1640 medium) with 1% penicillin/streptomycin (Thermo Fisher). To establish a stable CLOCK knockdown line, 293T cells were used to package CLOCK knockdown lentivirus, which was then used to infect HTR-8/SVneo cells. Lentiviral particles were packaged using Tat, Gag, Vsvg, and Rev plasmids for stable CLOCK knockdown. Transfection efficiency was evaluated by green fluorescence, and puromycin was applied to select for cells lacking fluorescence.

tag: cell line

value: Trophoblast


title: IPSC-microglia, AD17, sncRNA

description:
Library name: S17_AD
small RNAseq of sample 17 (AD)


title: TCF7L2 KD, NEP, shRNA1, replicate1, reseq

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

description:
Library name: TCF7L2-NEP-1-3-2
Mercurius High Sensitivity BRB-seq kit

data_processing:
Samples with greater than 2e6 total counts were kept for  analysis. Counts and metadata tables were combined into a single dataset using DESeq2 (v1.36.0). For all-sample comparison using PCA, VST-normalized counts were extracted and batch corrected using the limma (v3.54.2) removeBatchEffect() function. For heatmap plotting, the size-factor normalized counts were extracted and used. For differential expression testing, the counts matrices were subset to only include either NEP or NMP data before generating the DESeq object using a ‘ ~ batch + KD_Gene’ design. The lists of differentially expressed genes were filtered to only include genes that crossed the significance threshold in 1 or 2 samples.
Assembly: human GRCh38
Supplementary files format and content: Processed data files consist of demultiplexed single-sample raw gene counts produced from STAR.

extract_protocol:
RNA was extracted using an RNeasy Plus Miniprep Kit (Qiagen) according to manufacturers directions. RNA was quantified on a nanodrop to confirm quality prior to library creation.
Bulk RNA libraries were generated using a Mercurius High Sensitivity BRB-seq Kit (Alithea Genomics) using ~200 ng of RNA per sample according to the manufacturers directions. All samples were pooled after reverse transcription and final libraries were quantified using a Qubit dsDNA HS kit and BioAnalyzer. Libraries were sequenced on a single lane of an Illumina NovaSeq X using paired end sequencing. Samples were aligned using STAR (v2.7.11b) according to the kit directions. Samples were further demultiplexed using BRB-seqTools (v1.6.1) into single-sample .fastq files.

treatment_protocol: Lentiviral supernatant was added to stem cell cultures for 48 hours, then selected for using puromycin (0.5 ug/mL). NEP progenitors were achieved by treating stem cells with dual SMAD inhibition in mTeSR Plus media for 5 days. NMP progenitors were differentiated by exchanging mTeSR Plus media for E6 for 24 hours, followed by the addition of 20 ng/mL bFGF for 24 hours, and finally 20 ng/mL bFGF, 3 uM CHIR99021, and 10 uM SB431542 for 48 hours. After NEP or NMP treatment, both populations were differentiated under identical conditions in neural induction media (DMEM:F12 supplemented with N2, NEAA, L-glut, and PenStrep at 1x concentration and 2 ug/mL heparin and 0.4 ug/mL ascorbic acid). For the first 48 hours after NEP or NMP treatment, NIM was supplemented with 10 ng/mL BDNF and 100 nM retinoic acid. This was followed by 12 days of NIM supplemented with 10 ng/mL BDNF, 1 uM DAPT, 100 nM retinoic acid, and 300 nM purmorphamine. At the final day 19 time point, neurons were lysed in wells with RLT buffer supplemented with betamercaptoethanol and frozen at -80 until use.

value: hPSC-derived neuron

value: TCF7L2 KD; NEP


title: KD3

description: Library name: Sample7


title: sample_71

description: GFDp


title: IPSC-microglia, AD15, sncRNA

description:
Library name: S15_AD
small RNAseq of sample 15 (AD)


title: PAX5 KD, NMP, shRNA2, replicate2

description:
Library name: PAX5-NMP-2-2
Mercurius High Sensitivity BRB-seq kit

value: PAX5 KD; NMP


title: KD2

description: Library name: Sample6


title: sample_70

description: PGCp

value: M


title: IPSC-microglia, AD22, RNA

description:
Library name: R22_CN
Singular G4, total RNAseq of sample 22 (CN)


title: PAX5 KD, NMP, shRNA2, replicate1

description:
Library name: PAX5-NMP-2-1
Mercurius High Sensitivity BRB-seq kit


title: KD1

description: Library name: Sample5


title: TCF7L2 KD, NEP, shRNA2, replicate1

description:
Library name: TCF7L2-NEP-2-1
Mercurius High Sensitivity BRB-seq kit


title: TCF7L2 KD, NEP, shRNA1, replicate2

description:
Library name: TCF7L2-NEP-1-4
Mercurius High Sensitivity BRB-seq kit


title: IPSC-microglia, AD20, RNA

description:
Library name: R20_CN
Singular G4, total RNAseq of sample 20 (CN)


title: sample_73

description: GFDp


title: TCF7L2 KD, NEP, shRNA1, replicate1

description:
Library name: TCF7L2-NEP-1-3
Mercurius High Sensitivity BRB-seq kit


title: CON4

description: Library name: Sample4


title: PAX5 KD, NMP, shRNA1, replicate2

description:
Library name: PAX5-NMP-1-2
Mercurius High Sensitivity BRB-seq kit


title: sample_68

description: PGCd


title: sample_72

description: PGCp


title: IPSC-microglia, AD19, RNA

description:
Library name: R19_CN
Singular G4, total RNAseq of sample 19 (CN)


title: PAX5 KD, NMP, shRNA1, replicate1

description:
Library name: PAX5-NMP-1-1
Mercurius High Sensitivity BRB-seq kit


title: CON3

description: Library name: Sample3


title: sample_67

description: GFDd


title: IPSC-microglia, AD18, RNA

description:
Library name: R18_AD
Singular G4, total RNAseq of sample 18 (AD)


title: PAX5 KD, NEP, shRNA2, replicate2

description:
Library name: PAX5-NEP-2-2
Mercurius High Sensitivity BRB-seq kit

value: PAX5 KD; NEP


title: CON2

description: Library name: Sample2


title: sample_66

description: PGCp


title: sample_69

description: GFDp


title: IPSC-microglia, AD17, RNA

description:
Library name: R17_AD
Singular G4, total RNAseq of sample 17 (AD)


title: PAX5 KD, NEP, shRNA2, replicate1

description:
Library name: PAX5-NEP-2-1
Mercurius High Sensitivity BRB-seq kit


title: sample_65

description: GFDp


title: CON1

description: Library name: Sample1


title: IPSC-microglia, AD15, RNA

description:
Library name: R15_AD
Singular G4, total RNAseq of sample 15 (AD)


title: PAX5 KD, NEP, shRNA1, replicate2

description:
Library name: PAX5-NEP-1-4
Mercurius High Sensitivity BRB-seq kit


title: siJAB1-3

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

description: Library name: sample6

data_processing:
A quality control phase validated the sequencing data, and R packages such as DESeq2, clusterProfiler, and ggplot2 were used for analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% FBS and incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For 48 hours, siRNA JAB1 was transfected into MDA-MB-231 cells. Following the manufacturer's instructions, total RNA was extracted using the TRIzol reagent (Roche, Penzberg, Germany). For mRNA library creation and sequencing, the product was shipped to the Annoroad Gene Technology (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Transfect control and JAB1-targeting siRNA into MDA-MB-231 cells.

value: Triple-negative breast cancer (TNBC)

value: JAB1 knock down


title: Bovine uterine gland, EGF, MCol, Day5, rep 3

city: Okayama

first: Yosuke

last: Sugino

address: 1-1-1, Tsushimanaka, Kita-Ku

country: Japan

institute: Okayama University

description:
Library name: EGF_MCOL_8
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_MCOL_8

data_processing:
Sequencing data were processed using CLC Genomics Workbench version 25.0.1 (Qiagen). Adapter sequences, low-quality reads, and ambiguous reads were trimmed using default parameters. Trimmed reads were then mapped to the bovine reference genome (ARS-UCD2.0) using default parameters.
Assembly: ARS-UCD2.0
Supplementary files format and content: csv files include raw total count values for each sample
Supplementary files format and content: csv files include TPM values for each sample

organism: Bos taurus

source_name: uterine gland

growth_protocol: Bovine uterine gland fragments were embedded in Matrigel and cultured for 5 days in DMEM/F12 supplemented with bovine serum albumin (BSA), ascorbic acid, transferrin, sodium selenite, and insulin, under humidified conditions with 5% CO2 at 38.5℃.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) and stored at -80℃ until further processing.
RNA libraries for RNA sequencing were prepared using the SMART-Seq HT PLUS Kit (Takara) according to the manufacturer’s instructions.

treatment_protocol: Uterine gland fragments were cultured with or without EGF. In addition, under EGF-supplemented conditions, fragments were cultured in Matrigel either supplemented with type I collagen (MCol) or without collagen (M).

value: uterine gland

value: epithelial cells

value: EGF, collagen


title: sample_63

description: GFDd

value: Whole blood

value: drug

value: baseline


title: siJAB1-2

description: Library name: sample5


title: PAX5 KD, NEP, shRNA1, replicate1

description:
Library name: PAX5-NEP-1-3
Mercurius High Sensitivity BRB-seq kit


title: Bovine uterine gland, EGF, M, Day5, rep 3

description:
Library name: EGF_M_7
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_M_7

value: EGF


title: ONECUT2 KD, NMP, shRNA2, replicate2

description:
Library name: ONECUT2-NMP-2-2
Mercurius High Sensitivity BRB-seq kit

value: ONECUT2 KD; NMP


title: sample_60

description: PGCp

value: placebo

value: challenge


title: sample_64

description: PGCd


title: Bovine uterine gland, EGF, MCol, Day5, rep 2

description:
Library name: EGF_MCOL_4
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_MCOL_4


title: ONECUT2 KD, NMP, shRNA2, replicate1

description:
Library name: ONECUT2-NMP-2-1
Mercurius High Sensitivity BRB-seq kit

value: hPSC-derived neuron


title: siJAB1-1

description: Library name: sample4


title: siNC-3

description: Library name: sample3

value: WT


title: sample_59

description: GFDp


title: ONECUT2 KD, NMP, shRNA1, replicate2

description:
Library name: ONECUT2-NMP-1-2
Mercurius High Sensitivity BRB-seq kit


title: Bovine uterine gland, EGF, M, Day5, rep 2

description:
Library name: EGF_M_3
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_M_3


title: sample_56

description: PGCd


title: siNC-2

description: Library name: sample2


title: Bovine uterine gland, EGF, MCol, Day5, rep 1

description:
Library name: EGF_MCOL_2
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_MCOL_2


title: ONECUT2 KD, NMP, shRNA1, replicate1

description:
Library name: ONECUT2-NMP-1-1
Mercurius High Sensitivity BRB-seq kit


title: sample_55

description: GFDd


title: siNC-1

description: Library name: sample1


title: Bovine uterine gland, EGF, M, Day5, rep 1

description:
Library name: EGF_M_1
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: EGF_M_1


title: ONECUT2 KD, NEP, shRNA2, replicate2

description:
Library name: ONECUT2-NEP-2-2
Mercurius High Sensitivity BRB-seq kit

value: ONECUT2 KD; NEP


title: WT, Replicate 1

city: Frankfurt am Main

first: Remus

middle: Richard Elrik

last: Rosenkranz

address: Max-von-Laue-Str. 9

country: Germany

institute: Goethe University Frankfurt

description: Library name: 20103R-01-01

data_processing:
Raw reads were mapped against the tomato reference genome (S. lycopersicum cv. Heinz 1706, genome build 4.0; ITAG 4.0) in a splice-aware manner using Star (Galaxy version 2.7.8a) with default settings, except for the following changes: --genomeSAindexNbases 14, --sjdbGTFfile ITAG4.0_gene_models.gff, -- sjdbOverhang 149, --chimOutType don’t report, --outFilterType yes, --outFilterMultimapNmax 1, -- outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.05.
Reads per gene were counted using htseq-count (Galaxy version 0.9.1) with the following settings: --mode union. –stranded no, --minaqual 10, --type gene, --idattr ID
Read counts per gene (ITAG 4.0 annotation) are deposited as processed data.
Assembly: Tomato Genome version SL4.0
Supplementary files format and content: tab-delimited text files contain read counts for each sample

organism: Solanum lycopersicum

source_name: Ovary

extract_protocol:
Total RNA was isolated using TriZol (Invitrogen) followed by DirectZol (Zymo Research)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II non-directional RNA Library Kit with polyA selection

value: Ovary

value: control


title: Whole Exosome seq, iPS cells, MECP2[R306C] mutation

city: Cambridge

first: Tatsuya

last: Osaki

state: MA

address: 43 Vassar street, 46-6227

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

description:
Library name: WES_Rett_patient-derived_iPSC_R306C
Variant Call Format (VCF), Compressed Reference-oriented Alignment Map (CRAM)

library_source: genomic

data_processing:
Fastq files were combined and aligned with STAR 2.0.4b Variant of mutations were computed with samtools.
Assembly: GRCh37/hg19
Supplementary files format and content: Variant Call Format (VCF)
Supplementary files format and content: Compressed Reference-oriented Alignment Map (CRAM)

growth_protocol: All hiPS cells were maintained on Matrigel-coated 6-well plates in mTeSR Plus medium (STEMCELL Technologies) with 10 μM Y-23632 (Rock inhibiter, STEMCELL Technologies) for the first day after each passage and subcultured every 5–7 days using ReLeSR reagent (STEMCELL Technologies).

extract_protocol:
genomic DNA was isolated from the cells from 2D culture using DNeasy Kit (Qiagen) following manufacture protocol.
Whole exome sequencing was performed (Germline Whole Exome Sequencing (WES) v6.0., 2 x 150 bp reads, Broad Institute).SNVs and indels were characterized by mapping on the reference genome (GRCh37/hg19).

value: Female

value: iPS cells

tag: replicate

value: biol rep1


title: sample_54

description: PGCd

value: F


title: ONECUT2 KD, NEP, shRNA2, replicate1

description:
Library name: ONECUT2-NEP-2-1
Mercurius High Sensitivity BRB-seq kit


title: Bovine uterine gland, Control, M, Day5, rep 3

description:
Library name: CONT_M_4
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: CONT_M_4

value: uterine gland

value: epithelial cells

value: Control


title: Whole Exosome seq, iPS cells, isogenic control for MECP2[R306C]

description:
Library name: WES_isogenic_control_iPSC_for_R306C
Variant Call Format (VCF), Compressed Reference-oriented Alignment Map (CRAM)


title: sample_53

description: GFDd

value: Whole blood

value: drug

value: baseline


title: Bovine uterine gland, Control, M, Day5, rep 2

description:
Library name: CONT_M_2
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: CONT_M_2


title: ONECUT2 KD, NEP, shRNA1, replicate2

description:
Library name: ONECUT2-NEP-1-4
Mercurius High Sensitivity BRB-seq kit


title: Whole Exosome seq,iPS cells, MECP2[V247X] mutation

description:
Library name: WES_Rett_patient-derived_iPSC_V247X
Variant Call Format (VCF), Compressed Reference-oriented Alignment Map (CRAM)


title: Bovine uterine gland, Control, M, Day5, rep 1

description:
Library name: CONT_M_1
Column name in raw_totalcounts_all_samples.csv, and TPM_all_samples.csv: CONT_M_1


title: Whole Exosome seq, iPS cells, isogenic control for MECP2[V247X]

description:
Library name: WES_isogenic_control_iPSC_for_V247X
Variant Call Format (VCF), Compressed Reference-oriented Alignment Map (CRAM)


title: sample_52

description: PGCp

value: placebo


title: KLF12 KD, NMP, shRNA2, replicate2

description:
Library name: KLF12-NMP-2-2
Mercurius High Sensitivity BRB-seq kit

value: KLF12 KD; NMP


title: sample_51

description: GFDp


title: Tau injected acetate diet 3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: Library name: Tau_ace_3

data_processing:
Demultiplexing: sequencing data was demultiplexed using native applications on BaseSpace.
Alignment: STAR v2.5.2a (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Bam conversion: samtools v1.1 (view -bS)
Gene quantitation: HTSeq v0.9.1 (-f sam -r pos -s reverse -t exon -i gene_id); Refseq annotations
Differential gene expression and adjustments were performed using DESeq2. The design consisted of 4 conditions (PBS injection + control diet; PBS + acetate diet; Tau injection + control diet; Tau injection + acetate diet.)
Assembly: GRCm38
Supplementary files format and content: txt table containing raw gene counts (one per sample)

molecule: polyA RNA

organism: Mus musculus

source_name: dorsal hippocampus

growth_protocol: Mice were housed on a 12/12h light/dark cycle (7 am to 7 pm), with food and water provided ad libitum.

extract_protocol:
Mice were sacrified 24 hours after remote recall. Brains were snap frozen in liquid nitrogen to preserve mRNA quality. After thawing in ice-cold PBS, brains were sectioned using a brain matrix into 1mm-thick coronal slices.  Dorsal hippocampi were dissected from the right hemisphere at approximately Bregma -1.25-2.25 and homogenized in Trizol. RNA was isolated using Trizol-chloroform extraction and quantified using a Qubit flurometer and RNA HS reagents.
RNAseq libraries were prepared using 300 ng of total RNA. mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation module (NEB#E7490), fragmented to ~200 nt, and converted to libraries using the NEB Ultra II Directional RNA Library Prep Kit (E7760). Samples were barcoded with NEBNext Multiplex Oligos (E7335, E7500) assessed for quality using a bioanalyzer DNA 1000 chip and quantified using a NEBnext Library quant kit (E7630)

treatment_protocol: Tau protein was purified in the following way: 6–14 g of frontal cortical gray matter from AD patients was homogenized using a Dounce homogenizer in nine volumes (v/w) of high-salt buffer (10 mM Tris-HCl, pH 7.4, 0.8 M NaCl, 1 mM EDTA, and 2 mM dithiothreitol [DTT], with protease inhibitor cocktail, phosphatase inhibitor, and PMSF) with 0.1% sarkosyl and 10% sucrose added and centrifuged at 10,000 g for 10 min at 4°C. Pellets were reextracted once or twice using the same buffer conditions as the starting materials, and the supernatants from all two to three initial extractions were filtered and pooled. Additional sarkosyl was added to the pooled low-speed supernatant to reach 1%. After 1h nutation at room temperature, samples were centrifuged again at 300,000 g for 60 min at 4°C. The resulting sarkosyl-insoluble pellets, which contain pathological Tau, were washed once in PBS and then resuspended in PBS (∼100 μl/g gray matter) by passing through 27-G 0.5-in needles. The resuspended pellets were further purified by a brief sonication (20 pulses at ∼0.5 s/pulse) using a hand-held probe (QSonica) followed by centrifugation at 100,000 g for 30 min at 4°C, whereby the majority of protein contaminants were partitioned into the supernatant, with 60–70% of tau remaining in the pellet fraction. The pellets were resuspended in PBS at one fifth to one half of the precentrifugation volume, sonicated with 20–60 short pulses (∼0.5 s/pulse), and spun at 10,000 g for 30 min at 4°C to remove large debris. The final supernatants were used in the study and referred to as AD Tau.  6 months old male and female WT and ACSS2 KO mice were anaesthetized with isoflurane gas (1–5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. Artificial tears were applied to eyes to ensure sufficient lubrication. Animals received an injection of bupivacaine (2.5 mg kg−1) for local anaesthesia before the skin was disinfected with betadine solution and the skull exposed with a short incision using sterile surgical equipment. A small hole (about 0.5 mm) was drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with AD Tau lysate was inserted into the right dorsal hippocampus and slowly removed following injection of 1 ug Tau (AP, − 2.5 mm; DV, − 1.4 mm; ML, + 2 mm from bregma). All animals received a single dose of subcutaneous meloxicam (5 mg/kg) as analgesia at induction and one dose per day for two days postoperatively as needed. To allow sufficient time for the development of AD-like pathology, mice underwent behavioral or molecular characterization 6 months post-injection.

tag: strain

value: dorsal hippocampus

tag: diet

value: high acetate diet (LabDiet 5001 with 5% Na-acetate )

value: AD-Tau injection (1 ug, unilateral)

value: male


title: KLF12 KD, NMP, shRNA2, replicate1

description:
Library name: KLF12-NMP-2-1
Mercurius High Sensitivity BRB-seq kit

value: hPSC-derived neuron


title: S7_ChP_Ctrl

city: Boston

first: Maria

last: Lehtinen

address: 300 Longwood Ave, Mailcode Bch3400

institute: Boston Children's Hospital

description: Library name: S7

data_processing:
Novogene aligned with STAR2
Reads were quantified with featurecounts 2.0.8
Assembly: GRCh39
Supplementary files format and content: tab delimited text file with each sample as a column

source_name: Choroid Plexus

extract_protocol:
Qiagen RNAEasy miniprep
, total RNA extracted from ChP tissue was submitted to Novogene for library preparation with poly A selection and mRNA directional sequencing

value: Choroid Plexus


title: sample_50

description: PGCd

value: M

value: challenge


title: Tau injected acetate diet 2

description: Library name: Tau_ace_2


title: tongue4_day2_untreated

city: Chicago

first: Hoang Anh

middle: V

last: Tran

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

description: Library name: Sample T16

data_processing:
[Sample T1-T16] The methods of the previously published pipeline (PMID 30559359) were used with some modifications. Raw paired-end sequence reads of 75 or 100 nucleotides were processed by Illumina-utils (PMID 23799126). Inserts contained a 7 nucleotide sample barcode and a random 6 nucleotide unique molecular identifier (UMI). Given that tRNA molecules range in length from 74-96 nucleotides, forward and reverse 100 nucleotide reads fully covered some tRNA sequences and partially overlapped for others. We upgraded the Illumina-utils ‘iu-merge-pairs’ command to merge both fully and partially overlapping reads, while trimming overhanging adapter sequences in the case of more than full overlap (the command line flag, ‘--marker-gene-stringent’, enables consideration of full as well as partial overlap). We minimized erroneous base calls, important for our analysis of modification-induced mutations, by retaining reads that matched with zero mismatches in the overlapping region (option ‘--max-num-mismatches 0’)
[Sample T1-T16] The procedure for de novo profiling of full-length and fragmentary tRNA reads introduced in tRNA-seq-tools (PMID 30559359) was modified as follows. tRNA structural features were identified from the 3’ end of the read. The minimum criteria for tRNA identification were the correct distance to the 7 canonically conserved nucleotides in the T arm, of which 5 must be found, and base pairing in of the T stem. A full-length read must contain a base-paired acceptor stem and all features in between.
[Sample S1-S24] Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to a curated Streptococcus mutans tRNA, rRNA and reference genome.
[Sample S1-S24] The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: [Sample T1-T16] tRNA sequences were taxonomically annotated by using the Global Alignment for Sequence Taxonomy (GAST) tool (PMID 19023400) to search a set of reference tRNA sequences that tRNAscan-SE (v1.3.1) (PMID 9023104) identified from 4,235 gold-standard bacterial genomes (non-endosymbiont genomes with an assembly level of “chromosome”) stored in the Ensembl Genomes 2016 database (PMID 26553803).
Assembly: [Sample S1-S24] ASM746v2
Supplementary files format and content: [Sample T1-T16] .tsv files with family taxonomy and tRNA anticodon counts per sample
Supplementary files format and content: [Sample S1-S24] .tsv files with gene name and abundance per sample
Supplementary files format and content: [Sample S1-S24] .sam.tsv files with mutation, deletion, coverage for each gene position per sample

source_name: tongue dorsum scraping

growth_protocol: [Sample S1-S24] S. mutans strains were cultured in Brain Heart Infusion Broth without Dextrose (BHI-D; Alpha Biosciences) at 37°C.

extract_protocol:
[Sample T1-T16] The tongue dorsum scrapings were combined with RNAlater Stabilization solution (Invitrogen) and stored at −80°C. For extraction, RNAlater was first removed by centrifugation. Pelleted material was lysed in 0.3M NaOAc/HOAc,10mM EDTA, pH 4.8 with an equal volume of acetate-saturated phenol:chloroform pH 4.5 (Invitrogen). After addition of 1.0 mm glass lysing beads (Bio-Spec Products) in a 1:1 ratio (bead:sample weight), samples were placed in a reciprocating bead beater (Mini-Beadbeater-16, Bio-Spec Products) for two 1-min intervals on maximum intensity. Samples were centrifuged before re-extraction and isopropanol precipitation of total RNA. Pellets were washed with 75% ethanol before resuspension in an acid-buffered elution buffer (10mM NaOAc, 1mM EDTA, pH 4.8). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
[Sample S1-S24] RNA was isolated using the Quick-RNA Fungal/Bacterial Microprep Kit (Zymo) and treated with DNAse I according to the DNAfree kit (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
MSR-seq (PMID 35513407)
[Sample T1-T16] Standard MSR-seq protocol was used with additional chemical treatment. Specifically, after the first ligation and streptavidin bead binding of all CHO, samples were split in two: one mock-treated, and the other subjected to AlkB demethylase reaction (PMID 35513407).

treatment_protocol: [Sample S1-S24] A starter culture for each strain was thawed, resuspended in BHI-D, and used to inoculate BHI-D or BHI-D + 0.15% glucose before incubation. Cells were harvested by centrifugation at 1 h and at early stationary phase (3 h for BHI-D, or 6.5 h for BHI-D + 0.15% glucose).

value: tongue dorsum scraping

value: untreated


title: KLF12 KD, NMP, shRNA1, replicate2

description:
Library name: KLF12-NMP-1-2
Mercurius High Sensitivity BRB-seq kit


title: tongue4_day2_demethylase

description: Library name: Sample T15

value: demethylase


title: sample_49

description: GFDd


title: Tau injected acetate diet 1

description: Library name: Tau_ace_1


title: KLF12 KD, NMP, shRNA1, replicate1

description:
Library name: KLF12-NMP-1-1
Mercurius High Sensitivity BRB-seq kit


title: tongue4_day1_untreated

description: Library name: Sample T14


title: Tau injected control diet 3

description: Library name: Tau_cont_3

value: control diet (standard chow - TestDiet)


title: KLF12 KD, NEP, shRNA2, replicate2

description:
Library name: KLF12-NEP-2-2
Mercurius High Sensitivity BRB-seq kit

value: KLF12 KD; NEP


title: sample_47

description: GFDp

value: Whole blood

value: F


title: sample_48

description: PGCp

value: placebo


title: tongue4_day1_demethylase

description: Library name: Sample T13


title: Tau injected control diet 2

description: Library name: Tau_cont_2


title: KLF12 KD, NEP, shRNA2, replicate1

description:
Library name: KLF12-NEP-2-1
Mercurius High Sensitivity BRB-seq kit


title: sample_44

description: PGCd

value: drug


title: Tau injected control diet 1

description: Library name: Tau_cont_1

value: dorsal hippocampus


title: tongue3_day2_untreated

description: Library name: Sample T12


title: sample_43

description: GFDd

value: baseline


title: KLF12 KD, NEP, shRNA1, replicate2

description:
Library name: KLF12-NEP-1-4
Mercurius High Sensitivity BRB-seq kit


title: tongue3_day2_demethylase

description: Library name: Sample T11


title: C_4

city: Pamplona

first: Josune

last: Orbe

address: Avenida Pio XII 55

country: Spain

institute: CIMA

description: Library name: 13_S13

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR 2.7.9a with default parameters.
UMI deduplication was performed using UMI-tools v1.0.0
featureCounts v1.6.0 software and Gencode v47 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Plasma EVs

extract_protocol:
EVs were isolated by centrifugation at 20.000 xg during 70 min from frozen  citrate  plasma samples at -80°C after double centrifugation (10 min 2000 xg and 15 min 2500 xg)
Plasma EVs were resuspended in 100 μL of lysis/binding Buffer (Invitrogen). RNA transcripts were captured with dynabeads oligo (dT) (Invitrogen) and reverse transcribed. RNA samples underwent a linear amplification by in vitro transcription followed by a fragmentation into 250–350 bp. Partial Illumina adaptor sequences were used, and a second reverse transcription reaction was performed. Full Illumina adaptor sequences were successfully added and the libraries sequenced (NextSeq 2000, Illumina)

value: Plasma EVs

tag: batch


title: PBS injected acetate diet 3

description: Library name: PBS_ace_3

value: high acetate diet (LabDiet 5001 with 5% Na-acetate )

value: PBS injection (unilateral)

value: male


title: tongue3_day1_untreated

description: Library name: Sample T10


title: sample_40

description: PGCd


title: PBS injected acetate diet 2

description: Library name: PBS_ace_2


title: CTL, NMP, replicate3

description:
Library name: CTL-NMP-3
Mercurius High Sensitivity BRB-seq kit

value: hPSC-derived neuron

value: CTL; NMP


title: sample_39

description: GFDd


title: PBS injected acetate diet 1

description: Library name: PBS_ace_1


title: tongue3_day1_demethylase

description: Library name: Sample T9

value: tongue dorsum scraping


title: CTL, NMP, replicate2

description:
Library name: CTL-NMP-2
Mercurius High Sensitivity BRB-seq kit


title: tongue2_day2_untreated

description: Library name: Sample T8

value: untreated


title: sample_36

description: PGCp

value: challenge


title: CTL, NMP, replicate1

description:
Library name: CTL-NMP-1
Mercurius High Sensitivity BRB-seq kit


title: tongue2_day2_demethylase

description: Library name: Sample T7

value: demethylase


title: sample_35

description: GFDp


title: PBS injected control diet 3

description: Library name: PBS_cont_3

value: control diet (standard chow - TestDiet)


title: PBS injected control diet 2

description: Library name: PBS_cont_2


title: CTL, NEP, replicate3

description:
Library name: CTL-NEP-3
Mercurius High Sensitivity BRB-seq kit

value: CTL; NEP


title: SiHa PR-3

city: Guangzhou

first: Li

last: Yuan

address: 58, Zhongshan 2nd road

institute: sun yat-sen university

description: Library name: Sample 3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: SiHa cells

growth_protocol: Uterine smooth muscle (2.0 × 0.5 × 0.5 cm3) was cut from the site of incision at the lower edges of the uterus during cesarean section. Samples were then washed three times with ice-cold sterile phosphate-buffered saline(PBS), and then stored in liquid nitrogen.

extract_protocol:
mRNA libraries were prepared for sequencing using standard Illumina protocols
mRNA-Seq

treatment_protocol: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.

value: SiHa cells

value: cervical cancer cells


title: sample_34

description: PGCd

value: Whole blood

value: drug

value: M


title: tongue2_day1_untreated

description: Library name: Sample T6


title: KLF12 KD, NEP, shRNA1, replicate1

description:
Library name: KLF12-NEP-1-3
Mercurius High Sensitivity BRB-seq kit

value: KLF12 KD; NEP


title: tongue2_day1_demethylase

description: Library name: Sample T5


title: sample_33

description: GFDd

value: baseline


title: CTL, NEP, replicate2

description:
Library name: CTL-NEP-2
Mercurius High Sensitivity BRB-seq kit


title: CTL, NEP, replicate1

description:
Library name: CTL-NEP-1
Mercurius High Sensitivity BRB-seq kit


title: PBS injected control diet 1

description: Library name: PBS_cont_1

value: dorsal hippocampus

value: PBS injection (unilateral)


title: tongue1_day2_untreated

description: Library name: Sample T4


title: sample_32

description: PGCd

value: F


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 3

type: RNA

city: Xi'an

first: Xuan

last: Li

address: 145, Changlexi Road

institute: School of Stomatology, Fourth Military Medical University

description: lncRNA expression data from PDLSC

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software.

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 3

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA samples utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Total RNA extracted from PDLSCs incubated in cementoblastic medium with inflammatory cytokines (Infla group) or cementoblastic medium with inflammatory cytokines and 5 μM melatonin (Infla + Mel group) (n = 3) using TRIzol reagent (Invitrogen).

treatment_protocol: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), or Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel).

value: periodontal ligament stem cells (PDLSCs)


title: sample_31

description: GFDd


title: tongue1_day2_demethylase

description: Library name: Sample T3

value: tongue dorsum scraping


title: CREB5 KD, NMP, shRNA2, replicate2

description:
Library name: CREB5-NMP-2-2
Mercurius High Sensitivity BRB-seq kit

value: hPSC-derived neuron

value: CREB5 KD; NMP


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 2

description: lncRNA expression data from PDLSC

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 2


title: tongue1_day1_untreated

description: Library name: Sample T2

value: untreated


title: CREB5 KD, NMP, shRNA2, replicate1

description:
Library name: CREB5-NMP-2-1
Mercurius High Sensitivity BRB-seq kit


title: sample_30

description: PGCd

value: challenge


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 1

description: lncRNA expression data from PDLSC

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel), 7 days, replicate 1


title: CREB5 KD, NMP, shRNA2, replicate1, reseq

description:
Library name: CREB5-NMP-2-1-2
Mercurius High Sensitivity BRB-seq kit


title: sample_29

description: GFDd


title: tongue1_day1_demethylase

description: Library name: Sample T1

value: demethylase


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 3

description: lncRNA expression data from PDLSC

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 3


title: CREB5 KD, NMP, shRNA1, replicate2

description:
Library name: CREB5-NMP-1-2
Mercurius High Sensitivity BRB-seq kit


title: hPDC-derived organoid_rep3

city: Leuven

first: Liuqi

last: Peng

state: BELGIUM

address: Janseniusstraat 45, B0204

country: Belgium

institute: KU Leuven

description:
Library name: GC157369
Organoid from hPDC cultured for 21 days

data_processing:
Raw sequencing reads were quality-checked with FastQC v0.11.7. Adapter sequences were trimmed using Trimmomatic v0.39.
Splice-aware alignment to the human reference genome (hg38) and transcriptome was performed using HISAT2 with default settings.
Gene-level quantification of uniquely mapped reads was conducted with Feature Counts from subread package, using strand-specificity (-s 1) and gene symbols for annotation (-g gene_name).
Differential expression analysis was performed using DESeq2 in R, filtering low-expression genes (mean counts < 10) and excluding mitochondrial/ribosomal genes. Adjusted p-values were calculated using the Benjamini-Hochberg procedure to control the false discovery rate (FDR < 0.05). Gene ontology analysis was performed by utilizing the EnrichR package in R.
Assembly: hg38
Supplementary files format and content: text file include raw counts with genes in rows and samples in columns.

source_name: in vitro differentiated cartilage

growth_protocol: For iChon, hAC, and hPDC organoids: Cells were cultured for 21 days in defined chondrogenic differentiation medium in AggreWell™800 plates under standard conditions (37°C, 5% CO₂, 95% humidity), with medium changes twice per week. For iChonMass: iPSC-derived cartilage nodules were cultured in CM1 medium for up to 8 weeks in suspension to allow 3D maturation.

extract_protocol:
Total RNA was extracted from organoids using the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. iChonMass samples were preprocessed using mechanical homogenization with Precellys lysing kits. RNA integrity and purity were assessed by NanoDrop prior to library preparation.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit, following the manufacturer’s protocol.

treatment_protocol: No additional treatments were applied. The samples reflect baseline transcriptional states of the three different cell populations after 21 days of differentiation and 3D aggregation.

value: in vitro differentiated cartilage

value: primary cells

value: periosteum-derived progenitor

value: WT

value: chondrogenic differentiation


title: sample_28

description: PGCd

value: Whole blood

value: drug


title: CREB5 KD, NEP, shRNA2, replicate2

description:
Library name: CREB5-NEP-2-2
Mercurius High Sensitivity BRB-seq kit

value: CREB5 KD; NEP


title: hPDC-derived organoid_rep2

description:
Library name: GC157368
Organoid from hPDC cultured for 21 days


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 2

description: lncRNA expression data from PDLSC

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 2


title: PDLSCs Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 1

description: lncRNA expression data from PDLSC

source_name: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), 7 days, replicate 1


title: sample_27

description: GFDd

value: baseline


title: Lung, LPS+CQMUH-011, rep4

first: Yaling

address: Jinsui Road 9

institute: Guangzhou Women and Children's Medical center

description:
Library name: Sample 11
Column names in raw_counts_All_Samples.xlsx: LPS-011-4

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: OryCun2.0
Supplementary files format and content: TXT file contain counts for each sample

organism: Oryctolagus cuniculus

source_name: Lung

extract_protocol:
lung tissue cells RNA was harvested using Trizol reagent. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard DNBSEQ-T7 protocols

value: Lung

value: LPS at 50mg/kg+CQMUH011 at 675ug/kg


title: CREB5 KD, NEP, shRNA2, replicate1

description:
Library name: CREB5-NEP-2-1
Mercurius High Sensitivity BRB-seq kit


title: hPDC-derived organoid_rep1

description:
Library name: GC157367
Organoid from hPDC cultured for 21 days


title: sample_26

description: PGCp

source_name: Whole blood

value: placebo

value: F


title: Lung, LPS+CQMUH-011, rep3

description:
Library name: Sample 10
Column names in raw_counts_All_Samples.xlsx: LPS-011-3


title: CREB5 KD, NEP, shRNA1, replicate2

description:
Library name: CREB5-NEP-1-4
Mercurius High Sensitivity BRB-seq kit

value: hPSC-derived neuron


title: hiPSC-derived iChonMass_rep3

description:
Library name: GC157366
8-week chondrogenic differentiated iChonMass nodules form iPSCs

value: iPSC-derived cartilage nodules


title: sample_25

description: GFDp


title: Lung, LPS+CQMUH-011, rep2

description:
Library name: Sample 9
Column names in raw_counts_All_Samples.xlsx: LPS-011-2


title: CREB5 KD, NEP, shRNA1, replicate2, reseq

description:
Library name: CREB5-NEP-1-4-2
Mercurius High Sensitivity BRB-seq kit


title: sample_24

description: PGCp

value: M

value: challenge


title: hiPSC-derived iChonMass_rep2

description:
Library name: GC157365
8-week chondrogenic differentiated iChonMass nodules form iPSCs

value: in vitro differentiated cartilage


title: Lung, LPS+CQMUH-011, rep1

description:
Library name: Sample 8
Column names in raw_counts_All_Samples.xlsx: LPS-011-1


title: hiPSC-derived iChonMass_rep1

description:
Library name: GC157364
8-week chondrogenic differentiated iChonMass nodules form iPSCs


title: CREB5 KD, NEP, shRNA1, replicate1

description:
Library name: CREB5-NEP-1-3
Mercurius High Sensitivity BRB-seq kit


title: sample_23

description: GFDp


title: Lung, LPS, rep4

description:
Library name: Sample 7
Column names in raw_counts_All_Samples.xlsx: LPS-4

value: LPS at 50mg/kg


title: Cas9_Screening_Library_R3

city: Odense M

first: Sanjeeb

middle: Kumar

last: Sahu

address: CAMPUSVEJ 55

department: Department of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

description: Enriched synthetic construct incorporated to genomic DNA

data_processing:
To identify gRNA that are enriched in the CRISPR library compared to control, we established an in-house computational pipeline. First, we removed the adaptors to get only the gRNA sequence from the FASTQ files. As the gRNAs are short fragments, we used Bowtie2(Langmead and Salzberg, 2012) for alignment using modified parameters of -p 10 -L 8. The aligned BAM files were converted to bed files and aligned reads were filtered to identify only those reads with the valid PAM sequence. The gRNAs from all libraries were collated together in a master gRNA file. Next, we used intersectBed function from BEDTools to calculate read coverage over all gRNA using aligned BAM files(Quinlan and Hall, 2010). The coverage files over all gRNA were merged together to create a coverage matrix. The coverage matrix was imported into R for further analysis. To normalize for library depth, we calculated CPM for all gRNAs. Enriched gRNA were identified using a 2 fold change compared to control libraries and a minimum of 2 CPM value. To map gRNAs to genes, we aggregated all enriched gRNA mapping to genes and mean enrichment value of all gRNAs was assigned to each gene. Genes were then ranked based on Z-Score in across replicates.
Assembly: hg19
Supplementary files format and content: Matrix table with raw counts for each enriched guideRNA in various samples
Library strategy: CRISPR screening

source_name: Primary cell

extract_protocol:
12 days post guide RNA transduction via lentivirus, cell were sorted for BFP (with guide RNA) and high GFP (severe SASP activity) and DNA was isolated from them for downstream processing. Then by targeted PCR cells harbouring guideRNa were amplified.
By targeted PCR, cells harbouring guideRNAs were PCR amplified. Primer used for the amplication contains Illumina barcode and the PCR products were quantified and sequenced using MiSeq

treatment_protocol: We used human primary lung fibroblasts (IMR90) for our in vitro screening.  IMR90 mimics most contexts of cellular and molecular alteration observed during senescence in human aging. We generated cells expressing the Cas9 enzyme (selected with Blasticidin) and the fluorescent SASP reporter (MIR146A-GFP) in early passage cells. We transduce these cells with lentiviral pool containing guide RNA library in very low multiplicity of infection (MOI) to achieve one guide RNA per cell or no guide RNA. Five days post transduction we add Puromycin (express under control of SASP reporter) to depletes cells not inducing SASP. Finally, 12 days post guide RNA transduction cell were sorted for BFP (with guide RNA) and high GFP (severe SASP activity) and DNA was isolated from them for downstream processing.

value: Primary cell

value: Lung fibroblast

value: Normal cell


title: iChon-derived organoid_rep3

description:
Library name: GC157363
Organoid from iChon single cells derived from iChonMass disossiation and cultured for 21 days

value: iPSC-derived organoid

value: WT

value: chondrogenic differentiation


title: sample_22

first: Keijo

institute: Tampere University

description: PGCp

data_processing:
The DNA methylation data was pre-processed using the default meffil pipeline, with a p-value threshold of 0.05. Probes that failed quality control (QC) were removed from further analysis. One saple was removed from processed data afte QC
Average Beta values

extract_protocol: Genomics DNA was extracted from whole blood samples with Chemagic 360 robot with CMG-1091 kit (Revvity, Waltham, MA, USA) in combination with chemagic™ DNA Blood 400 kit H96 (Cat. No. CMG-1091), following the manufacture’s protocol (VD190913.che).

value: Whole blood


title: Lung, LPS, rep3

description:
Library name: Sample 6
Column names in raw_counts_All_Samples.xlsx: LPS-3

value: Lung


title: Cas9_Screening_Library_R2


title: iChon-derived organoid_rep2

description:
Library name: GC157362
Organoid from iChon single cells derived from iChonMass disossiation and cultured for 21 days


title: Lung, LPS, rep2

description:
Library name: Sample 5
Column names in raw_counts_All_Samples.xlsx: LPS-2


title: sample_21

description: GFDp

value: baseline


title: Cas9_Screening_Library_R1


title: iChon-derived organoid_rep1

description:
Library name: GC157361
Organoid from iChon single cells derived from iChonMass disossiation and cultured for 21 days


title: sample_20

description: PGCd

value: drug


title: Lung, LPS, rep1

description:
Library name: Sample 4
Column names in raw_counts_All_Samples.xlsx: LPS-1


title: Control_Library_R2


title: hAC-derived organoid_rep3

description:
Library name: GC157360
Organoid from hAC single cells cultured for 21 days

value: primary cells

value: articular chondrocytes


title: Lung, Saline, rep3

description:
Library name: Sample 3
Column names in raw_counts_All_Samples.xlsx: NS-3

value: Saline


title: sample_19

description: GFDd

value: M


title: Control_Library_R1


title: hAC-derived organoid_rep2

description:
Library name: GC157359
Organoid from hAC single cells cultured for 21 days


title: sample_18

description: PGCd

value: F

value: challenge


title: Lung, Saline, rep2

description:
Library name: Sample 2
Column names in raw_counts_All_Samples.xlsx: NS-2


title: K1 cell, irradiated4

city: Shanghai

first: Xiaotong

last: Qiu

address: 301 yanchang road

institute: Tongji University school of medicine

description: Library name: L1EHH1601581-rad4

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.The mapped reads of each sample were assembled byStringTie inareference-basedapproach.
To identify DEGs(differentialexpressiongenes)betweentwodifferentsamples, the expression level of each transcriptwas calculated according to the transcripts permillion reads (TPM)method. RSEM as used to quantifygene abundances. Essentially, differential expression analysiswas performedusing theDESeq2 or DEGseq.DEGs with|log2FC|≧1 and FDR＜0.05(DESeq2) or FDR＜0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ＜ 0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and Python scipy software, respectively.
All the alternative splice events that occurred in our sample were identified by using recently releases program  rMATS. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered,  and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention  events.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: deseq2 files include counts and TPM values for each Sample

extract_protocol:
TotalRNAwasextractedfromthetissueusingTRIzol®Reagentaccordingthemanufacturer’s instructions. ThenRNAqualitywasdeterminedby5300Bioanalyser (Agilent)andquantifiedusingtheND-2000(NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0,>1μg)wasusedtoconstructsequencinglibrary
RNApurification, reverse transcription, library construction and sequencingwereperformed at Shanghai MajorbioBio-pharmBiotechnologyCo.,Ltd. (Shanghai,China)accordingtothemanufacturer’sinstructions.The RNA-seqtranscriptomelibrariywaspreparedfollowingIllumina®StrandedmRNAPrep,Ligation(SanDiego, CA) using1μgof totalRNA. Shortly,messengerRNAwas isolatedaccording topolyAselectionmethodby oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNAwas synthesizedusing a SuperScript double-stranded cDNAsynthesis kit (Invitrogen, CA)with randomhexamer primers.ThenthesynthesizedcDNAwassubjectedtoend-repair,phosphorylationandadapteradditionaccording to libraryconstructionprotocol.Librariesweresizeselectedfor cDNAtarget fragmentsof300bpon2%Low RangeUltraAgarosefollowedbyPCRamplifiedusingPhusionDNApolymerase(NEB)for15PCRcycles.After quantifiedbyQubit4.0,thesequencinglibrarywasperformedonNovaSeqXPlusplatform(PE150)usingNovaSeq ReagentKit.（NovaSeq）ORthesequencinglibrarywasperformedonDNBSEQ-T7platform(PE150) usingDNBSEQ-T7RSReagentKit(FCLPE150)version3.0.

value: human thyroid cancer cell

value: irradiation


title: hAC-derived organoid_rep1

description:
Library name: GC157358
Organoid from hAC single cells cultured for 21 days

value: in vitro differentiated cartilage


title: sample_17

city: Tampere

last: Viiri

address: Arvo Ylpön katu 34

description: GFDd


title: Lung, Saline, rep1

description:
Library name: Sample 1
Column names in raw_counts_All_Samples.xlsx: NS-1


title: sample_16

description: PGCp

value: placebo


title: K1 cell, irradiated3

description: Library name: L1EHH1601580-rad3


title: HacaT cell, high glucose+rFGF4, C-FOS, ChIP

city: Wenzhou

first: Zhiming

last: Zhang

address: Chashan Campus of Wenzhou Medical University

institute: Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

description: Library name: HacaT cell, high glucose+rFGF4, ChIP

data_processing:
Raw data quality control: FASTQ files were assessed with FastQC (v0.11.9). Adapter sequences were trimmed using Cutadapt (v3.4) with parameters.
Read alignment:Trimmed reads were aligned to the human reference genome GRCh38/hg38 using Bowtie2 (v2.4.2) with  BWA-MEM. Only uniquely mapped reads with mapping quality ≥ 30 were retained using SAMtools (v1.10).
Duplicate removal: PCR duplicates were removed using Picard MarkDuplicates (v2.23.8).
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigWig

source_name: cell culture

extract_protocol:
HaCaT cells were crosslinked with 1% formaldehyde for 10 min at room temperature, and the reaction was quenched with 125 mM glycine. Cells were lysed and chromatin was sheared to 200-600 bp using a sonicator. Immunoprecipitation was performed using antibody against  (anti-C-FOS, CST 31254S). Antibody-chromatin complexes were captured by protein A/G magnetic beads, washed, and eluted. Crosslinking was reversed overnight at 65°C, and DNA was purified by phenol-chloroform extraction or spin columns. Purified ChIP DNA was used for library preparation.
20-100 ng of ChIP DNA or input DNA was used as starting material. The DNA was mixed with Endprep Mix (Twist) in a 60 μL reaction and incubated in a thermal cycler: 30°C for 20 min, 72°C for 20 min, then hold at 4°C. To the dA-tailed DNA (60 μL), 30 μL Ligation Enhancer, 5 μL Fast T4 DNA Ligase, and 5 μL DNA Adapter (Twist) were added. The reaction was incubated at 20°C for 15 min. 60 μL of Hieff NGS® DNA Selection Beads (0.6× bead-to-sample ratio) were added, incubated at room temperature for 5 min, and placed on a magnetic stand. Beads were washed twice with 200 μL of 80% ethanol and air-dried. DNA was eluted in 21 μL ddH2O, and 20 μL of eluate was recovered. The eluted ligated DNA (20 μL) was mixed with 25 μL of 2× Amplification Mix and 5 μL of Primer Mix (Twist). PCR was performed: 98°C for 1 min; 7 cycles of 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; final extension 72°C for 5 min; hold at 4°C. The amplified library was purified using 0.9× Hieff NGS® DNA Selection Beads (0.9× bead-to-sample ratio) following the same washing and elution protocol. The final library was eluted in 20 μL ddH2O. Library concentration was measured by Qubit 4.0 (Thermo Fisher) and fragment size distribution was assessed by 1% agarose gel electrophoresis or Bioanalyzer. Libraries were sequenced on an Illumina NovaSeq X Plus instrument with paired-end 150 bp reads (or as per actual run parameters).

value: cell culture

value: HaCaT

value: Human keratinocyte


title: siZNF512B_R2

data_processing:
Sequencing was performed with Illumina, HiSeq 4000 SR50 for Single-End, 50-cycle.
The reads were aligned to the human genome (hg38) using TopHat (version 2.0.9) with the default options. After library size normalization using DESeq, expression was quantified and expressed in reads/kilobase of transcript per million mapped reads (RPKM) using cufflink (version 2.1.1). Differential expression analysis was performed using the DESeq package with an FDR cutoff of 0.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Human primary lung fibroblast IMR90 cells obtained from ATCC and were cultured in DMEM(Gibco), 10% FBS(Gibco), 1% penicillin/streptomycin (Invitrogen), along with 1x Glutamax (Invitrogen) and Non-Essential amino acids (Invitrogen).All cells were cultured at 37°C with 7% CO2 in a humid incubator. Cells were split at regular intervals when they reached around 70% confluency and the medium was changed every 2 days.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for poly A purification followed by the construction of sequencing libraries.
Total RNA was extracted with Invitrogen PureLink RNA Mini Kit. Extracted RNA was quantified at OD260 nm with a ND-1000 spectrophotometer (Nanodrop Technology) and quality of the RNA was assessed with the RNA 6000 LabChip kit using a Bioanalyzer 2100 (Agilent Technologies). Poly-A RNA isolation and Library Preparation was done by using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® as per manufacture’s instruction.

treatment_protocol: For all siRNA-mediated knockdown experiments, cells were seeded at the same starting density and transfected every second day with ON-TARGET plus single siRNAs or SMART pool siRNAs (i.e., a mixture of 4 siRNAs provided as a single reagent) (Dharmacon), and Lipofectamine RNAiMAX (Invitrogen, 13778-150) was used according to the manufacturer’s instructions.

value: Primary cell

value: Lung fibroblast

value: ZNF512B knock down

value: no treatment


title: K1 cell, irradiated2

description: Library name: L1EHH1601579-rad2

value: WT


title: siZNF512B_R1


title: sample_15

description: GFDp

value: Whole blood

value: baseline


title: HacaT cell, high glucose, C-FOS, ChIP

description: Library name: HacaT cell, high glucose, ChIP


title: K1 cell, irradiated1

description: Library name: L1EHH1601578-rad1


title: siControl_R2

value: Control IMR90


title: sample_14

description: PGCd

value: drug

value: F


title: K1 cell, Control4

description: Library name: L1EHH1601577-ctrl4

value: human thyroid cancer cell

value: untreated


title: siControl_R1


title: HacaT cell, low glucose, C-FOS, ChIP

description: Library name: HacaT cell, low glucose, ChIP


title: sample_13

description: GFDd


title: iPSC-derived oligodendrocytes nanofiber_rep3

city: Kyoto

first: Haruhisa

last: Inoue

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: Library name: Sample6

data_processing:
Raw BCL data were converted to FASTQ files using bcl2fastq2 v2.20 (Illumina). Read mapping and gene quantification were performed using the DRAGEN Bio-IT Platform v4.3.6 (Illumina) against the GRCh38 reference genome and annotation (GENCODE release 39).
Assembly: GRCh38 (GENCODE release 39)
Supplementary files format and content: tab-delimited text file includes raw counts and TPM for each Sample

source_name: 201B7 iPSC

growth_protocol: Human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs) were differentiated into oligodendrocytes. NPCs were seeded onto conventional 2D culture plates or onto nanofiber plates. Cells were cultured in differentiation medium containing growth factors including IGF-I, PDGF-AA, T3, and doxycycline to induce transcription factors (Sox10, Olig2, Nkx6.2). Medium was changed twice weekly and cells were cultured for up to two weeks to allow oligodendrocyte maturation.

extract_protocol:
Total RNA was extracted from cultured cells using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions. RNA quality was assessed using an Agilent TapeStation prior to library preparation.
cDNA libraries were constructed using the SMART-Seq mRNA kit (TAKARA), followed by purification with AMPure XP beads (Beckman Coulter). Subsequently, fragmentation and tagging were performed using the Nextera XT DNA Library Prep Kit and DNA/RNA UD Indexes (Illumina) via transposon-based tagmentation. Sequencing was conducted on an Illumina NovaSeq X Plus system using the NovaSeq X Series 25B Reagent Kit in a 150-bp paired-end configuration.

treatment_protocol: For RNA-seq analysis, oligodendrocytes were cultured under two conditions: conventional 2D culture and nanofiber culture. Cells were maintained under identical differentiation conditions except for the culture substrate. Each condition included three biological replicates (n = 3 /condition). No additional compound treatment was applied for RNA-seq experiments.

value: 201B7 iPSC

value: iPSC-derived oligodendrocytes


title: GBM43shp300 [RNA-seq]

city: Austin

first: Gaspar

last: Kitange

address: 16th Avenue NE

institute: University of Minnesota

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR (https://github.com/alexdobin/STAR)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: glioblastoma cells

extract_protocol:
Total RNA was extracted following the RNeasy kit protocol supplied by the vendor (Qiagen, Valencia, CA) and RNA quality was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The Illumina TrueSeq RNA Sample preparation Kit v.4.1 (Illumina Inc., San Diego, CA) was used to prepare cDNA libraries from 2 µg of total RNA for sequencing. Individual technologies barcoded libraries were analyzed using Agilent 2100 Bioanalyzer (Agilent).

tag: cell line/genotype

tag: cell types

value: Primary culture

tag: source type

value: Patient derived Xenograft


title: K1 cell, Control3

description: Library name: L1EHH1601576-ctrl3


title: sample_12

description: PGCd

value: challenge


title: iPSC-derived oligodendrocytes nanofiber_rep2

description: Library name: Sample5


title: sample_11

description: GFDd


title: K1 cell, Control2

description: Library name: L1EHH1601575-ctrl2


title: iPSC-derived oligodendrocytes nanofiber_rep1

description: Library name: Sample4


title: GBM43shNT [RNA-seq]


title: GBM43shRBBP4 [RNA-seq]


title: K1 cell, Control1

description: Library name: L1EHH1601574-ctrl1


title: sample_10

description: PGCd


title: iPSC-derived oligodendrocytes 2D_rep3

description: Library name: Sample3


title: post5

city: Seoul

first: Joohee

last: Lim

address: Yonseiro 50-1

country: South Korea

institute: Yonsei University

description: Library name: tx1053g

data_processing:
Raw reads were preprocessed using FastQC and Trimmomatic for quality control and adapter trimming.
Clean reads were aligned to the mouse reference genome (mm10) using HISAT2.
The expression levels were quantified and transcripts were assembled using StringTie.
Gene expression levels were quantified as raw read counts using StringTie.
Assembly: mm10 (or GRCm38)
Supplementary files format and content: An Excel (.xlsx) file containing a matrix of raw read counts for each gene across all 15 samples.

source_name: brain (ipsilateral hemisphere)

growth_protocol: ICR mice were maintained under a 12h light/dark cycle and postnatal day 7 (P7) pups were used for HI induction.

extract_protocol:
The ipsilateral  brains were dissected and homogenized using Precellys Lysing kits (Bertin Technologies, Cat # CK14) and a Precellys 24 tissue homogenizer (Bertin Technologies) in Tri Reagent (Molecular Research Center) to extract total RNA.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Dexamethasone (0.5 mg/kg, IP) was administered 6h before or after HI brain injury. HI was induced by right carotid artery ligation followed by 70min of 8% oxygen.

value: brain (ipsilateral hemisphere)

value: wild type

value: Dexamethasone (0.5 mg/kg, IP, 6h after HI)


title: Ctrl 4

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Library name: Ctrl_4
Ctrl 4

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Amygdala, Brain (BLA)

growth_protocol: Adult male and female Ift88 f/f mice were housed under standard conditions (12-hour light/dark cycle, 22°C, 50% humidity) and provided standard chow and water ad libitum. Homozygous Ift88 f/f mice received intracranial micro-injections in the BLA of AAVs carrying either GfaABC1D-tdT or GfaABC1D-Cre. Two months later, mice were deeply anesthetized with isoflurane, then decapitated and the amygdala was quickly microdissected.

extract_protocol:
The cells were separated and astrocytes were isolated using ACSA-2 beads in a MACS protocol.RNA from the isolated astrocytes was extracted using an RNA extraction kit (Qiagen, 74034).
Library constructed with SMARTSeq library prep RNA kit from Illumina

treatment_protocol: The mice did not receive any treatment.

value: Amygdala, Brain (BLA)

value: Ift88 f/f

value: astrocyte-tdT


title: iPSC-derived oligodendrocytes 2D_rep2

description: Library name: Sample2


title: post4

description: Library name: tx1053e


title: muscle-HA3

city: Changsha

first: Chen

last: Xiao

address: Lushan Road, Juzizhou Street, Yuelu District

institute: Hunan Normal University

description:
Library name: sample 9
HC3

data_processing:
Raw data in fastq format were processed to remove reads containing adapters, poly-N, and low-quality reads.
Clean reads were aligned to the reference genome
Differential expression analysis between groups was performed using the DESeq2 R package.
Assembly: GCF_003368295.1_ASM336829v1_genomic.fna
Supplementary files format and content: Expression.xlsx

organism: Carassius auratus

source_name: muscle

extract_protocol:
Total RNA was extracted from the tissue samples. RNA concentration and purity were then evaluated. RNA integrity was rigorously assessed using RNA-specific agarose gel electrophoresis and the Agilent 2100 Bioanalyzer.
Poly(A) mRNA was enriched from total RNA using Oligo(dT) magnetic beads and subsequently fragmented into approximately 300 bp pieces using ion fragmentation. First-strand cDNA was synthesized using 6-base random primers and reverse transcriptase, followed by second-strand cDNA synthesis. After initial library construction, PCR amplification was performed to enrich the fragments, and size selection was conducted to yield a final library size of approximately 450 bp. Library quality, including total and effective concentrations, was rigorously assessed using an Agilent 2100 Bioanalyzer. Libraries containing different index sequences were then pooled proportionally based on their effective concentration and target data volume. The pooled libraries were diluted to 2 nM and denatured into single-stranded DNA via alkaline treatment. Finally, Next-Generation Sequencing (NGS) was performed on an Illumina platform to generate paired-end (PE) reads.

value: muscle


title: Ctrl 3

description:
Library name: Ctrl_3
Ctrl 3


title: sample_9

description: GFDd

value: Whole blood

value: baseline


title: iPSC-derived oligodendrocytes 2D_rep1

description: Library name: Sample1


title: post3

description: Library name: tx1053d


title: Ctrl 2

description:
Library name: Ctrl_2
Ctrl 2


title: muscle-HA2

description:
Library name: sample 8
HC2


title: siXRN1 + siSMG6, Akron-seq, rep3

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

description:
Library name: Sample 12
Akron-seq from HEK-293 cells, siXRN1 + siSMG6 transfected

data_processing:
Sequencing reads were quality-trimmed using fastp with automatic adapter detection and poly-G tail removal. Trimmed reads were mapped to Repbase using STAR (v2.7.6a) with up to 30 allowed multimapping locations. Unmapped reads were subsequently aligned to the hg38 reference genome using STAR with parameters optimized for accurate splice junction detection and paired-end overlap resolution. Uniquely mapping reads were extracted using samtools (q=255) and deduplicated based on unique molecular identifiers (UMIs) with UMI-tools. Only properly paired, non-chimeric alignments were retained. To quantify putative SMG6 cleavage sites, 5' end read alignments were extracted from deduplicated BAM files using samtools and converted into BigWig tracks with CAGEfightR.
Assembly: hg38
Supplementary files format and content: BigWig files of read1 5' ends separated by  strandedness (plus/minus).

growth_protocol: DMEM, 5% FBS, 1% L-glutamine, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using Trizol Reagent and treated with shrimp dsDNase (Thermo Scientific).
150 µg total RNA was used for two rounds of poly-A RNA selection were performed using the NEB Magentic mRNA Isolation Kit, followed by Akron5-seq library preparation (Ibrahim and Mourelatos, 2019).

treatment_protocol: Reverse transfection with with non-targeting (siNT), SMG6, XRN1, or XRN1+SMG6 siRNAs using Lipofectamine RNAiMAX (Life Technologies) for 72 hours.

value: human embryonic kidney

value: siXRN1 + siSMG6


title: post2

description: Library name: tx1053c


title: Ctrl 1

description:
Library name: Ctrl_1
Ctrl 1


title: muscle-HA1

description:
Library name: sample 7
HC1


title: post1

description: Library name: tx1053b


title: siSMG6, Akron-seq, rep3

description:
Library name: Sample 11
Akron-seq from HEK-293 cells, siSMG6 transfected


title: siXRN1, Akron-seq, rep3

description:
Library name: Sample 10
Akron-seq from HEK-293 cells, siXRN1 transfected


title: muscle-MA3

description:
Library name: sample 6
HB3


title: pre5

description: Library name: tx1052g

value: Dexamethasone (0.5 mg/kg, IP, 6h before HI)


title: cKO 4

description:
Library name: cKO_4
cKO 4

value: astrocyte-Cre


title: muscle-MA2

description:
Library name: sample 5
HB2


title: cKO 2

description:
Library name: cKO_2
cKO 2


title: siNT, Akron-seq, rep3

description:
Library name: Sample 9
Akron-seq from HEK-293 cells, siNT transfected

value: siNT


title: cKO 1

description:
Library name: cKO_1
cKO 1


title: pre4

description: Library name: tx1052d


title: muscle-MA1

description:
Library name: sample 4
HB1


title: pre3

description: Library name: tx1052c


title: siXRN1 + siSMG6, Akron-seq, rep2

description:
Library name: Sample 8
Akron-seq from HEK-293 cells, siXRN1 + siSMG6 transfected


title: muscle-LA3

description:
Library name: sample 3
HA3


title: Cre_Input_4

description:
Library name: Cre_Input_4
Cre_Input_4

treatment_protocol: The mice received either GfaABC1D-tdT (astrocyte-tdT) or GfaABC1D-Cre (astrocyte-Cre) AAVs into the amygdala by micro-injecton surgery.


title: siSMG6, Akron-seq, rep2

description:
Library name: Sample 7
Akron-seq from HEK-293 cells, siSMG6 transfected


title: pre2

description: Library name: tx1052b


title: Cre_Input_3

description:
Library name: Cre_Input_3
Cre_Input_3


title: muscle-LA2

description:
Library name: sample 2
HA2


title: pre1

description: Library name: tx1052a


title: siXRN1, Akron-seq, rep2

description:
Library name: Sample 6
Akron-seq from HEK-293 cells, siXRN1 transfected


title: Cre_Input_2

description:
Library name: Cre_Input_2
Cre_Input_2


title: muscle-LA1

description:
Library name: sample 1
HA1


title: siNT, Akron-seq, rep2

description:
Library name: Sample 5
Akron-seq from HEK-293 cells, siNT transfected


title: control5

description: Library name: tx1051f

value: PBS control


title: Cre_Input_1

description:
Library name: Cre_Input_1
Cre_Input_1


title: elav[null]_rep2

city: New York

first: David

middle: W. J.

last: McQuarrie

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medicine, Cornell University

description: Library name: Sample5

data_processing:
Sequencing quality was assessed using a standard quality-control pipeline. Adapter sequences were removed with Trim Galore (v0.6.7), and reads were aligned to the D. melanogaster dm6 reference genome using STAR (v2.7.11a). Gene-level counts were generated with FeatureCounts (v2.0.8) and used for differential gene expression analysis with DESeq2 (v1.40.2) under default parameters.
Assembly: dm6
Supplementary files format and content: tab-delimited text file with counts for each sample replicate

organism: Drosophila melanogaster

source_name: Embryo

extract_protocol:
RNA was extracted with Trizol followed by phenol chloroform extraction.
mRNA was enriched from total RNA by poly(A) selection. Sequencing libraries were constructed by Novogene (UK) Company Limited using their standard Illumina-compatible mRNA library preparation protocol (Plant and Animal Eukaryotic mRNA, WOBI) and sequenced on an Illumina NovaSeq X Plus system.

value: Embryo

value: elav[null] rep2


title: SMSCs from Zhedong White goose leg muscle , embryonic days 13 (E23), scRNA-seq

city: shanghai

first: zuoyin

last: zhu

address: number 1239 siping road

institute: tongji university

description:
Library name: E23
SMSCs  were isolated from the leg muscle of three female Zhedong White geese at E23. SMSCs from three individuals were pooled to generate a single-cell suspension, which was processed for single-cell RNA sequencing using the 10x Genomics Chromium platform.

library_source: transcriptomic single cell

data_processing:
Raw FASTQ data were processed with Cell Ranger (v7.1.0) and aligned to the goose reference genome (GCF_002166845.1) using STAR. The gene-barcode matrix was analyzed with Seurat (v5.3.1). Quality filtering removed cells with <300 or >6,500 genes, <1,000 or >50,000 UMIs, or >20% mitochondrial reads (mitochondrial genes an-notated from Bean goose genome). Doublets were excluded using scDblFinder. Data were normalized and scaled, regressing out mitochondrial content. Integration across samples was performed with FindIntegrationAnchors and Inte-grateData, with further batch correction using Harmony [19]. Principal compo-nent analysis (PCA, top 30 PCs) was followed by graph-based clustering (resolution 0.5–1.2), and visualization by UMAP and t-SNE. Differential expression was assessed using the Wilcoxon rank-sum test (adjusted P < 0.05).
Assembly: Anser cygnoides genome assembly GCF_040182565.1
Supplementary files format and content: Filtered gene–cell expression matrices generated by Cell Ranger.
Supplementary files format and content: The processed data consist of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files representing cell barcodes, gene features, and UMI count matrices, respectively.

organism: Anser cygnoides

source_name: leg muscle

growth_protocol: Fertilized Zhedong White goose eggs were obtained from Wenjie Goose Breeding Department of Xiangshan Co., Ltd. (China) and incubated at 37.5°C with 60% relative humidity. Leg muscle tissues were collected from female embryos at embryonic days 13, 15, 18, and 23 (E13, E15, E18, E23).

extract_protocol:
Satellite cells were isolated and purified according to our established protocol [9]. Briefly, muscle tissues were minced and digested in high-glucose DMEM with 2 mg/mL Dispase II and 4 mg/mL Collagenase II (Roche, Gibco) at 37°C for 50 minutes. Digestion was stopped using DMEM with 10% FBS. The cell suspension was filtered through a 70 μm strainer, centrifuged at 350× g for 8 minutes, and red blood cells lysed with ACK buffer. Differential plating was performed twice to enrich SMSCs, exploiting fibroblast attachment for one hour each time. Purity was confirmed by Pax7 immunofluorescence staining [9]. Enriched SMSCs were cryopreserved in liquid nitrogen for subsequent scRNA-seq.
Thawed SMSCs were filtered through a 40 μm strainer, centrifuged at 300× g for 5 minutes at 4°C, and resuspended in PBS with 0.04% BSA. Only samples with >85% via-bility (trypan blue exclusion) and 400–1,200 cells/μL were processed for single-cell cap-ture. Chromium Single Cell 3′ Library Kit (10× Genomics) was used for cell capture, barcoding, and cDNA synthesis following manufacturer's protocols . Libraries were quantified using a Bioanalyzer 2100 and Qubit, then sequenced on Illumina NovaSeq platforms (PE 150 bp). Library preparation and sequencing were conducted at Shanghai Personal Biotechnology Co., Ltd. and Shanghai Majorbio Bio-pharm Technology Co., Ltd..

value: leg muscle

value: SMSCs

value: embryos at embryonic days 23 (E23)

value: female


title: siXRN1 + siSMG6, Akron-seq, rep1

description:
Library name: Sample 4
Akron-seq from HEK-293 cells, siXRN1 + siSMG6 transfected


title: control4

description: Library name: tx1051e

value: brain (ipsilateral hemisphere)

value: wild type


title: tdT_Input_4

description:
Library name: tdT_Input_4
tdT_Input_4

value: Amygdala, Brain (BLA)

value: Ift88 f/f

value: astrocyte-tdT


title: SMSCs from Zhedong White goose leg muscle , embryonic days 13 (E18), scRNA-seq

description:
Library name: E18
SMSCs  were isolated from the leg muscle of three female Zhedong White geese at E18. SMSCs from three individuals were pooled to generate a single-cell suspension, which was processed for single-cell RNA sequencing using the 10x Genomics Chromium platform.

value: embryos at embryonic days 18 (E18)


title: siSMG6, Akron-seq, rep1

description:
Library name: Sample 3
Akron-seq from HEK-293 cells, siSMG6 transfected

value: human embryonic kidney


title: control3

description: Library name: tx1051c


title: SMSCs from Zhedong White goose leg muscle , embryonic days 13 (E15), scRNA-seq

description:
Library name: E15
SMSCs  were isolated from the leg muscle of three female Zhedong White geese at E15. SMSCs from three individuals were pooled to generate a single-cell suspension, which was processed for single-cell RNA sequencing using the 10x Genomics Chromium platform.

value: embryos at embryonic days 15 (E15)


title: tdT_Input_3

description:
Library name: tdT_Input_3
tdT_Input_3


title: siXRN1, Akron-seq, rep1

description:
Library name: Sample 2
Akron-seq from HEK-293 cells, siXRN1 transfected


title: control2

description: Library name: tx1051b


title: tdT_Input_2

description:
Library name: tdT_Input_2
tdT_Input_2


title: SMSCs from Zhedong White goose leg muscle , embryonic days 13 (E13), scRNA-seq

description:
Library name: E13
SMSCs  were isolated from the leg muscle of three female Zhedong White geese at E13. SMSCs from three individuals were pooled to generate a single-cell suspension, which was processed for single-cell RNA sequencing using the 10x Genomics Chromium platform.

value: embryos at embryonic days 13 (E13)


title: control1

description: Library name: tx1051a


title: siNT, Akron-seq, rep1

description:
Library name: Sample 1
Akron-seq from HEK-293 cells, siNT transfected

value: siNT


title: tdT_Input_1

description:
Library name: tdT_Input_1
tdT_Input_1


title: Male mouse endothelial cells, vehicle control, biol rep 3

status: Public on Jun 17 2026

city: Cleveland

first: Iuliia

last: Molokotina

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: M3_Control
Male WT mouse endothelial cell biological replicate 3; vehicle/starvation media control for 8 h.

data_processing:
Raw paired-end FASTQ files were generated by Novogene after sequencing, base calling, and demultiplexing
Raw paired-end FASTQ files were generated by Novogene after sequencing, base calling, and demultiplexing.
Raw reads were processed by Novogene to remove adapter sequences,  reads containing undetermined bases, and low-quality reads.
Clean reads were mapped to the Mus musculus reference genome using HISAT2
Gene-level read counts and normalized expression values were generated from mapped reads using Novogene’s standard RNA-seq quantification workflow
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts generated by Novogene; rows represent genes and columns represent RNA-seq samples.

source_name: aorta

extract_protocol:
Total RNA was isolated in-house using a TRIzol-based extraction method. Cells were lysed directly in TRIzol reagent, and RNA was purified by chloroform extraction and isopropanol precipitation. RNA pellets were washed with 75% ethanol, resuspended in nuclease-free water, and quantified using NanoDrop. RNA was stored at -80°C until RNA-seq library preparation.
RNA-seq libraries were sequenced by Novogene, and raw paired-end FASTQ files were generated after base calling and demultiplexing.

value: aorta

value: endothelial cell

value: Vehicle

value: M3; male endothelial cell isolation 3


title: Male mouse endothelial cells, LPS 500 ng/mL 8 h, biol rep 3

description:
Library name: M3_LPS_500ngmL_8h
Male WT mouse endothelial cell biological replicate 3; stimulated with LPS at 500 ng/mL for 8 h.

value: LPS


title: Male mouse endothelial cells, LPS 500 ng/mL 8 h, biol rep 2

description:
Library name: M2_LPS_500ngmL_8h
Male WT mouse endothelial cell biological replicate 2; stimulated with LPS at 500 ng/mL for 8 h.

value: M2; male endothelial cell isolation 2


title: Male mouse endothelial cells, vehicle control, biol rep 2

description:
Library name: M2_Control
Male WT mouse endothelial cell biological replicate 2; vehicle/starvation media control for 8 h.


title: Male mouse endothelial cells, LPS 500 ng/mL 8 h, biol rep 1

description:
Library name: M1_LPS_500ngmL_8h
Male WT mouse endothelial cell biological replicate 1; stimulated with LPS at 500 ng/mL for 8 h.

value: M1; male endothelial cell isolation 1


title: Male mouse endothelial cells, vehicle control, biol rep 1

description:
Library name: M1_Control
Male WT mouse endothelial cell biological replicate 1; vehicle/starvation media control for 8 h.


title: MC38 tumor, SIRPαD1-αPCSK9

first: Kaicheng

last: Zhou

address: No.826 Zhangheng Road

institute: Fudan University School of Pharmacy

description:
Library name: LC_5
10x Genomics

data_processing:
scRNA-seq data generated on the 10x Genomics platform were processed using Cell Ranger(v9.0.0)
Assembly: Mouse,mm10(refdata-gex-mm10-2020-A from 10x Genomics)
Supplementary files format and content: cellranger output file:barcodes.tsv.gz;matrix.mtx.gz;features.tsv.gz

source_name: colon cancer tissue

growth_protocol: C57BL/6 mice were subcutaneously inoculated with 5×10^6 MC38 cells per mouse to establish MC38 tumor-bearing mouse models.

extract_protocol:
Due to the limited size of individual tumors, three tumors per group were pooled to obtain sufficient viable cells for downstream single-cell RNA sequencing. To retain both immune and tumor cell populations, tumors were enzymatically dissociated into single-cell suspensions and subsequently sorted by flow cytometry into CD45⁺ (immune) and CD45⁻ (non-immune) fractions. CD45+ cells were recombined with unsorted cells in a 2:1 ratio.
The resulting cell mixtures were subjected to scRNA-seq using the 10x Genomics Single Cell 3’ Protocol. Briefly, a cell suspension was loaded with barcoded gel beads and oil onto Chromium Chip B to generate Gel Bead-In-Emulsions (GEMs) using a microfluidic “double-cross” system. Each GEM encapsulated a single cell and a gel bead coated with primers containing Illumina Read 1 sequence, a 16-bp 10x Barcode, a 12-bp UMI, and a poly-dT sequence. After cell lysis and reverse transcription, barcoded cDNA was synthesized and purified. Silane magnetic beads were used for cleanup, followed by PCR amplification of full-length cDNA. Sequencing libraries were prepared via end repair, A-tailing, adaptor ligation, and indexing, and included Illumina P5/P7 adaptors. The final library was sequenced on an Illumina platform with paired-end reads: Read 1 captured cell barcode and UMI, while Read 2 covered transcript sequences. The flow cytometry cell sorting and scRNA-seq experiments were performed by LC-Bio Technology Co., Ltd. (Hangzhou, China).

treatment_protocol: Three days after tumor cell inoculation, the mice were initiated with drug treatment for 14 days before tumor collection. All therapeutic agents were administered via intraperitoneal injection twice a week with equimolar doses among different experimental groups, and the specific dosage of each group was as follows: isotype control group (equimolar control dose), αPCSK9 monotherapy group (7.2 mg/kg), mSIRPαD1-Fc monotherapy group (4 mg/kg), combination group (4 mg/kg mSIRPαD1-Fc plus 7.2 mg/kg αPCSK9), and bispecific fusion protein mSIRPαD1-αPCSK9 monotherapy group (11.0 mg/kg). Mice were euthanized 14 days after the first treatment for tumor tissue collection. Due to the limited size of individual tumors, three tumors per group were pooled to obtain sufficient viable cells for downstream single-cell RNA sequencing. To retain both immune and tumor cell populations, tumors were enzymatically dissociated into single-cell suspensions and subsequently sorted by flow cytometry into CD45⁺ (immune) and CD45⁻ (non-immune) fractions. CD45+ cells were recombined with unsorted cells in a 2:1 ratio. The resulting cell mixtures were subjected to scRNA-seq.

value: colon cancer tissue

value: cancer cell

value: WT


title: MC38 tumor, SIRPαD1-Fc+αPCSK9

description:
Library name: LC_4
10x Genomics

value: SIRPαD1-Fc + αPCSK9


title: MC38 tumor, αPCSK9

description:
Library name: LC_3
10x Genomics

value: αPCSK9 (anti-PCSK9 antibody)


title: MC38 tumor, SIRPαD1-Fc

description:
Library name: LC_2
10x Genomics


title: MC38 tumor, Control

description:
Library name: LC_1
10x Genomics

value: IgG1 control