title: larvae, exposed to TWP, leached in solar-simulator, rep 26

city: East Lansing

first: Karilyn

middle: E

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

description:
TWP_LIGHTvsDARK; Light_CTLvsTWP
TWP_Light_26

data_processing:
Imported into Galaxy, FastQC used for read quality assessment. Paired-end reads with 2 raw files per sample.
Cutadapt used for trimming: settings for paired-end reads, a minimum filter length of 20 and a quality cutoff of 20
Alignment and annotation using Spliced Transcripts Alignment to a Reference (STAR) software, Read counts from the featureCounts software
Limma Voom used to assess differential expression for pairwise analyses.
Assembly: Genome build and transcription annotation files were the danRer11 build (GRCz11), from 2017.
Supplementary files format and content: Processed data files (featureCounts outputs) are provided for each sample
Supplementary files format and content: Four processed data files are included with the limma voom outputs (pairwise comparisons for exposure and light).

organism: Danio rerio

source_name: Pooled whole eleutherolarvae

extract_protocol:
RNA was isolated using the Thermo GeneJet RNA Extraction kit, following manufacturer instructions. RNA was stored at -80°C until library preparation and sequencing.
Library preparation and sequencing were performed at the UCSD Institute for Genomic Medicine Genomics Center. Stranded libraries were prepared using the Illumina Stranded Total RNA Prep  kit per manufacturer instructions. RINs were measured using a TapeStation, with scores averaging 9.0 (range: 7.6-10.0).
bulk RNA-sequencing, PE100, 25M reads per sample, Illumina NovaSeq 6000 platform

treatment_protocol:
RNA was isolated from 96 hpf embryos exposed to one of four treatments: 1) control [egg water only] "leached" in dark conditions, 2) control [egg water only] "leached" in solar-simulator conditions, 3) particle-filtered TWP leachates generated in dark conditions, or 4) particle-filtered TWP leachates generated in solar-simulator conditions
Leachates were produced at concentrations of 10 g/L, filtered through a 0.22 micron filter to remove TWP particles, and diluted to 25% using egg water

value: Pooled whole eleutherolarvae

tag: strain

value: AB (wild-type)

tag: developmental stage

value: 96 hours post fertilization (96 hpf)

tag: exposure

value: particle-filtered TWP leachates (approximately 2.5 g/L), prepared in egg water

tag: conditions during_leaching

value: leachates produced in a solar simulator, mimicking southern California conditions


title: UTR-seq, THP1, LPS 3 hours and OTS964 2 hours, rep2

status: Public on Aug 25 2025

type: SRA

city: Melbourne

first: Jennifer

middle: Rose

last: Devlin

state: Victoria

address: Peter MacCallum Cancer Centre, 300 Grattan Street

department: The Sir Peter MacCallum Department of Oncology at Peter MacCallum Cancer Centre

country: Australia

institute: University of Melbourne

library_source: transcriptomic

data_processing:
SLAM-seq files were processed using the slamdunk package (v.0.2.4)
SLAM-seq files were mapped to a combined hg38/dm6 genome using NextGenMap as part of the slamdunk package
SLAM-seq files were filtered and counted using slamdunk package
3'UTR-seq files were mapped to a hg19 genome using hisat2 (v.2.1.0), bam files were generared using samtools (v.1.9) and counted using Subread (v.2.0.0) featureCounts package
Assembly: hg19, hg38, dm6
Supplementary files format and content: tab separated values files for total and nascent counts for each SLAM-seq sample
Supplementary files format and content: tab delimited text files for 3'UTR-seq counts for all 3'UTR samples

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: THP1 and THP1 FLAG-CDK11-mAID cells were maintained in RPMI-16410 supplemented with 10% FBS, 2mM GlutaMax, 100U/mL penicillin and 100ug/mL streptomycin at 37C and 5% CO2

extract_protocol:
For SLAM-seq total RNA was isolated by phenol-chloroform extraction and isopropanol precipitation - total RNA was incubated with 10mM iodoacetamide for 4sU conversion prior to recovery by ethanol precipitation.
For 3'UTR-seq total RNA was isolated using the Zymo Research Direct-zol RNA isolation kit
Libraries were prepared using the Lexogen QuantSeq 3'mRNA-Seq kit as per manufacturer's instructions

treatment_protocol:
For SLAM-seq THP1 FLAG-CDK11-mAID cells were treated with 0.5mM 3-IAA (Auxin) or equivalent concentration of 100% ethanol for 4 hours, and pulse labelled with 100uM 4sU for the final 1 hour.
For 3'UTR-seq AML cells were treated with OTS964 (156nM) for 2 hours, LPS (1ug/mL) for 3 hours, or both

tag: cell line

tag: cell type

value: Acute myeloid leukeamia

tag: treatment

value: LPS 1ug/mL, OTS964 156nM


title: Cervical lymph node-scaup-PBSNP_m-6dpi-rep-1

city: Daejeon

first: Woohyun

last: Kwon

address: expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: C_LN-6d-PBSNP_m_S4
10x Genomics

library_source: transcriptomic single cell

data_processing:
10x genomics Cell Ranger (version 8.0.1)
Assembly: ASM1176430v1.1 combined with H5N1 influenza KR/W811 isolate and H5N1 influenza GA/W22-145E isolate
Supplementary files format and content: matrix files

molecule: total RNA

organism: Mustela putorius furo

source_name: Cervical lymph node

extract_protocol:
In the initial study, 16-18 weeks old male ferrets were intranasally inoculated under anesthesia with 105.5 TCID50/mL of GA/W22-145E/22 or KR/W811/21 virus (n = 24 per group).For, scRNA-seq, one ferret per group was euthanized at 3 dpi and two ferrets per group at 5 dpi to collect brain, lungs, and cervical lymph node samples. In the second study, 16-18 weeks old male ferrets were intranasally inoculated with 105.5 TCID50/mL of GA/W22-145E/22-PB2478V, GA/W22-145E/22-NP450S, and GA/W22-145E/22-PB2478V/NP450S. At 4 and 6 dpi three per group were euthanized for tissue collection, above them one cervical lymph nodes per group were used for scRNA-seq.
10x Genomics Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3.1 (PN-1000121; 10X Genomics)

tag: tissue

value: Cervical lymph node


title: Dirty_TN_rep3

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

country: USA

institute: Cornell University

data_processing:
Mapper.pl in miRDeep2 was used for preprocessing and adapter removal (-d -e -h -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -v). Quantifier.pl in miRDeep2 was used to map sequencing reads to miRNAs (-t mmu -d -e 0 -W). Sequences of precursors and mature miRNAs in mouse were downloaded from miRbase v22.
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

organism: Mus musculus

source_name: spleen

extract_protocol:
Splenic CD8+ T cells were isolated and purified using positive selection with CD8a microbeads (Miltenyi). Purified CD8+ T cells were stained using antibodies against CD4 (Gk1.5), CD44 (IM7), CD122 (TM-B1), CD49d (R1-2), and CD8a (53-6.7). ‘Stamped VMs’ populations were sorted for CD4-CD8+CD49dloGFP+CD44hi, and ‘stamped TN’ populations were sorted for CD4- CD8+CD49dloGFP+CD44lo. Samples were sorted using a BD FACS Aria Fusion II equipped with four lasers. Samples were sorted to >95% cell purity as determined by a post-sort check. 10,000 FACS sorted cells were placed in Trizol and RNA was extracted according to manufacturer’s instructions, with the addition of a chloroform extraction, Glycoblue (ThermoFisher) carrier prior to precipitation (1 hour at 4°C), and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer (AATI).
Libraries were prepared with NEBNext Small RNA Library Prep Kit (New England Biolabs) using 60-100ng total RNA as input, size selected for insert sizes ~18-35bp.
small RNA-seq

value: spleen

value: CD8+ T cells


title: UTR-seq, THP1, DMSO only 2 hours, rep2

value: DMSO


title: Cervical lymph node-scaup-NP_m-6dpi-rep-1

description:
Library name: C_LN-6d-NP_m_S5
10x Genomics


title: larvae, exposed to TWP, leached in solar-simulator, rep 25

description:
TWP_LIGHTvsDARK; Light_CTLvsTWP
TWP_Light_25


title: Cervical lymph node-scaup-PB2_m-6dpi-rep-1

description:
Library name: C_LN-6d-PB2_m_S1
10x Genomics


title: UTR-seq, THP1, LPS 3 hours and OTS964 2 hours, rep1


title: Dirty_TN_rep2


title: Cervical lymph node-scaup-PBSNP_m-4dpi-rep-1

description:
Library name: C_LN-4d-PBSNP_m_S1
10x Genomics


title: larvae, exposed to TWP, leached in solar-simulator, rep 17

description:
TWP_LIGHTvsDARK; Light_CTLvsTWP
TWP_Light_17


title: larvae, exposed to TWP, leached in dark, rep 24

description:
TWP_LIGHTvsDARK; Dark_CTLvsTWP
TWP_Dark_24

value: leachates produced in dark conditions


title: Sample 1245 leukemic blasts

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

description: Library name: 1245

data_processing:
FASTQ files were aligned to hg19 using STAR Align version 2.7.8a
Genes were counted using HTSeq-Count version 2.0.3
Assembly: hg19
Supplementary files format and content: Raw sequencing counts are provided as a txt file.

source_name: leukemic blast

extract_protocol:
Patient samples were thawed and washed with PBS supplemented with 5% FBS (Corning) supplemented with DNase I (Sigma) at 50mg/mL. Cells were incubated with a fixable viability stain 510 (FVS510, BD Biosciences) for 15 min at room temperature, washed, and then stained with antibodies against human CD45 (BD Horizon BV786), CD33 (BD Horizon BV421), CD3 (BD Horizon APCR700), and CD19 (BD Horizon BB515) for 20 min at room temperature. Cells were then washed and resuspended in PBS supplemented with 2% FBS and flow sorted to isolate viable (FVS510−) CD3−/CD19−/CD45+ / CD33+ cells using a BD FACSAria III cell sorter. Following flow sorting, primary samples were washed in PBS and then extraction was performed using the Qiagen AllPrep DNA/RNA kit. The purity and concentration of the extracted DNA and RNA were assessed using a Nanodrop before downstream applications.
RNA was sent to a commercial provider, Tempus, for library preparation and sequencing on an Illumina HiSeq. RNA libraries were prepared from PolyA selected mRNA species

value: leukemic blast

tag: stratification group

value: Bad

tag: genotype

value: WILDTYPE

tag: disease type

value: Primary Refractory, Under 2 Year Survival

tag: batch


title: UTR-seq, THP1, OTS964 2 hours, rep1


title: larvae, exposed to TWP, leached in dark, rep 23

description:
TWP_LIGHTvsDARK; Dark_CTLvsTWP
TWP_Dark 23


title: Dirty_TN_rep1


title: Clean_VM_rep3


title: UTR-seq, THP1, LPS 3 hours, rep1

value: LPS 1ug/mL


title: UTR-seq, THP1, LPS 3 hours, rep2


title: Clean_VM_rep2


title: larvae, exposed to TWP, leached in solar-simulator, rep 18

description:
TWP_LIGHTvsDARK; Light_CTLvsTWP
TWP_Light_18

value: Pooled whole eleutherolarvae


title: larvae, exposed to TWP, leached in dark, rep 16

description:
TWP_LIGHTvsDARK; Dark_CTLvsTWP
TWP_Dark_16

value: AB (wild-type)


title: UTR-seq, THP1, DMSO only 2 hours, rep1


title: Clean_VM_rep1


title: larvae, exposed to TWP, leached in dark, rep 15

description:
TWP_LIGHTvsDARK; Dark_CTLvsTWP
TWP_Dark_15

value: 96 hours post fertilization (96 hpf)


title: larvae, control, leached in solar-simulator, rep 22

description:
CTL_LIGHTvsDARK; Light_CTLvsTWP
CTL_Light_22

value: egg water only (60 mg/L "Instant Ocean" sea salts)


title: Clean_TN_rep3


title: Clean_TN_rep2


title: Cervical lymph node-W811-5dpi-rep-2

description:
Library name: C_LN-78_S2
10x Genomics


title: UTR-seq, MV4;11, OTS964 156nM 2 hours, rep2


title: UTR-seq, MV4;11, OTS964 156nM 2 hours, rep1


title: Cervical lymph node-scaup-PB2_m-4dpi-rep-1

description:
Library name: C_LN-4d-PB2_m_S1
10x Genomics


title: larvae, control, leached in solar-simulator, rep 21

description:
CTL_LIGHTvsDARK; Light_CTLvsTWP
CTL_Light_21

value: leachates produced in a solar simulator, mimicking southern California conditions


title: Cervical lymph node-W811-5dpi-rep-1

description:
Library name: C_LN-73_S1
10x Genomics


title: ChIP_KDM2B_KO_ESC_TY1-SKP1A_lot2

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

country: Japan

institute: RIKEN

description: Library name: Sample 73

library_source: genomic

data_processing:
Reads were aligned to UCSC mm9 or UCSC mm10 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM).
Assembly: mm9
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Embryonic stem cells were cultured in DMEM supplemented with 20% fetal bovine serum, GlutaMax, MEM nonessential amino acids, 2-mercaptoethanol, GlutaMax and LIF on MEF feeder layers at 37°C in a 5% CO2 incubator.

extract_protocol:
For mESCs, 10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode).  On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 2 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further  ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

treatment_protocol: For induction of conditional KO ESCs, 800 nM (final concentration) 4-OH Tamoxifen (SIGMA) dissolved in ethanol was added into the culture medium.  To inhibit the proteasome activity, 10 µM MG132 was added to ES medium for 3 hours.

value: mouse embryonic stem cells

value: Tamoxifen+

value: KDM2B KO

tag: chip antibody

value: anti-TY1 (Thermo,BB2)


title: larvae, control, leached in solar-simulator, rep 13

description:
CTL_LIGHTvsDARK; Light_CTLvsTWP
CTL_Light_13


title: UTR-seq, MV4;11, DMSO 2 hours, rep3

value: Acute myeloid leukeamia


title: Cervical lymph node-scaup-3dpi-rep-1

description:
Library name: C_LN-68_S4
10x Genomics

value: Cervical lymph node


title: Cervical lymph node-scaup-NP_m-4dpi-rep-1

description:
Library name: C_LN-4d-NP_m_S2
10x Genomics


title: ChIP_KDM2B_KO_ESC_TY1-SKP1A_lot1

description: Library name: Sample 72


title: Untreated control 1 min pre-treatment; BR 1

city: Trondheim

first: Amanda

middle: Holstad

last: Singleton

address: Erling Skjalgsons gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

description: Time-series experiment

data_processing:
FASTQ files were generated using bcl2fastq2 Conversion Software v 2.20.0.422. Processing of the sequence data was done with the ProkSeq v 2.0 program using Docker, with the  E. coli K-12 substr. MG1655 reference genome ASM584v2 (RefSeq: GCF_000005845.2) and corresponding reference transcriptome. ProkSeq is a docker based, full RNA-Seq pipeline for prokaryotes, which includes quality assessment, alignment, gene counting, and analysis. The count tables countFile.csv, countFileNucleotideAvgCount.csv and countFile_TPM_CPM.tsv were exported from ProkSeq and used for further analysis.
The sample counts were were analyzed in R using the quasi-likelihood test in EdgeR v 3.36.0 from Bioconductor. Poorly expressed genes were filtered out, and library size was normalized using trimmed mean of M-value (TMM). Differentially expressed genes were defined with FDR < 0.05 and presented as LFC compared to the control.
Assembly: ASM584v2 (RefSeq: GCF_000005845.2)
Supplementary files format and content: The processed data file (countFile.csv) contains the count for each sample of each identified gene.

organism: Escherichia coli

growth_protocol: The E. coli pre-culture was diluted to OD600 = 0.0125. E. coli was grown in cation-adjusted Mueller-Hinton broth in 1 1L Applikon bioreactors as batch culitvation. Stirring was adjusted between 200 and 600 rpm to maintain a dissolved oxygen concentration above 40%. The aeration rate was kept at 500 mL min-1. pH 7 was maintained by automatic titration of 3 M HCl and 4 M NaOH.

extract_protocol:
Transcriptomics was sampled according to the protocol provided with RNeasy Mini kit (Qiagen). The sample volume was based on OD600 at each sampling timepoint to ensure 3.35 x 10^8 cells per sample. The sample was immediately added to 2 volumes of RNA protect and vortexed. After minimum 5 min, the samples were centrifuged (10 min, max rcf). The supernatant was discarded, and the pellet was frozen in N2 (l). RNA was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer's protocol 4 (Enzymatic lysis and Proteinase K digestion of bacteria) and protocol 7 (Purification of total RNA) with on-column Dnase (Qiagen) digestion. The RNA concentration in each sample was measured using NanoDrop-1000 spectrophotometer. Isolated RNA was sent to the Genomics Core Facility at NTNU for further processing and sequencing.
RNA sequencing libraries were prepared using the QIAseq FastSelect 5S/16S/23S kit (Qiagen) for rRNA removal and the QIAseq stranded RNA Lib kit (Qiagen) for library construction, according to the manufacturer's instructions.  Briefly, 500 ng total RNA was used as starting material. Removal of ribosomal RNA (rRNA) was conducted by a combined heat fragmentation (89°C for 7 min) and FastSelect hybridization protocol (75-4°C ramping process) where the FastSelect reagent inhibited reverse transcription of bacterial rRNA. Next, purification was conducted using QIAseq Beads followed by a first-strand synthesis using a RNase H- Reverse Transcriptase (RT) in combination with random primers, a second-strand synthesis, end-repair, A-addition, and adapter ligation. The second-strand synthesis was performed using 5’phosphorylated random primers which enable subsequent strand-specific ligation. DNA fragments were further enriched by CleanStart library amplification (15 cycles of PCR reaction). Finally, the libraries were purified using the QIAseq Beads, quantitated by qPCR using Collibri Library Quantification Kit (Thermo Fisher Scientific), and validated using Perkin Elmer DNA 1K/12K/Hi Sensitivity Assay LabChip on a Labchip GX instrument (Perkin Elmer, USA). The size range of the DNA fragments were measured to be in the range of 270 to 570 bp and peaked around 355 bp. Prior to sequencing, libraries were normalized and pooled to 2.3 pM and subjected to clustering on three NextSeq 500 HO flowcells (Illumina, USA).

treatment_protocol: At OD600 = 0.2, E. coli was treated with either BTP-001 (1µM), BTP-001 (3 µM), or R11 (1 µM)

value: Wild type


title: larvae, control, leached in solar-simulator, rep 14

description:
CTL_LIGHTvsDARK; Light_CTLvsTWP
CTL_Light_14


title: ChIP_WT_ESC_TY1-SKP1A_lot2

description: Library name: Sample 71

value: Tamoxifen-

value: WT


title: Cervical lymph node-W811-3dpi-rep-1

description:
Library name: C_LN-63_S3
10x Genomics


title: larvae, control, leached in dark, rep 20

description:
CTL_LIGHTvsDARK; Dark_CTLvsTWP
CTL_Dark_20

value: leachates produced in dark conditions


title: UTR-seq, MV4;11, DMSO 2 hours, rep2

value: DMSO


title: UTR-seq, MV4;11, OTS964 156nM 2 hours, rep3


title: Cervical lymph node-scaup-5dpi-rep-2

description:
Library name: C_LN-88_S4
10x Genomics


title: UTR-seq, MV4;11, DMSO 2 hours, rep1


title: Cervical lymph node-scaup-5dpi-rep-1

description:
Library name: C_LN-83_S3
10x Genomics


title: ChIP_WT_ESC_TY1-SKP1A_lot1

description: Library name: Sample 70


title: larvae, control, leached in dark, rep 19

description:
CTL_LIGHTvsDARK; Dark_CTLvsTWP
CTL_Dark_19


title: Cervical lymph node-Control-rep-2

description:
Library name: C_LN-53_S4
10x Genomics


title: larvae, control, leached in dark, rep 12

description:
CTL_LIGHTvsDARK; Dark_CTLvsTWP
CTL_Dark_12


title: UTR-seq, THP1, OTS964 156nM 2 hours, rep2


title: Cervical lymph node-Control-rep-1

description:
Library name: C_LN-52_S3
10x Genomics


title: ChIP_WT ESC_PCGF1_lot1

description: Library name: Sample 61

value: anti-PCGF1 (in-house)


title: Cervical lymph node-Control-rep-3

description:
Library name: C_LN-58_S3
10x Genomics


title: Brain-scaup-5dpi-rep-2

description:
Library name: BR-90_S2
10x Genomics

source_name: Brain

value: Brain


title: UTR-seq, THP1, OTS964 156nM  2 hours, rep1


title: Hypothalamus male low-protein [10-12-4-16]

city: Ciudad de Buenos Aires

first: Octavio

last: Gianatiempo

state: Buenos Aires

address: Ciudad Universitaria Pabellon II piso 4

department: Quimica Biológica

country: Argentina

institute: Universidad de Buenos Aires

data_processing:
Reads were filtered to remove those with low base call quality using Illumina’s default chastity criteria. The results were then demultiplexed and converted to fastq format files by Casava.
Sequenced reads were trimmed for adaptor sequence and read quality was checked for each sample using FastQC v0.10.1.
Reads were then imported into STAR v2.5.0a for alignment with mm10 whole genome using RNA-Seq Alignment (BaseSpace Workflow) v1.0.0.
Gene expression was estimated by counting the number of reads aligning on a feature using the summarizeOverlaps function from the GenomicAlignments R package v1.8.4.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: male_Perinatal low-protein diet (LP)

extract_protocol:
Brains were removed and regions of interests were sectioned, flash frozen on liquid nitrogen, and RNA was isoleted using mirVana™ miRNA Isolation Kit (AM1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Female and male mice (F0) were fed with standard laboratory chow diet (SC) until five days prior to mating when they were fed with normal protein diet (NP). For mating one male was housed with two nulliparous females for five consecutive days, after which every male mouse was separated from females. Parents were assigned randomly (computer-based method) to either NP or low-preotein diet (LP) groups. Female and male mice (F0) were fed with the NP or the LP diet during the mating period, after which dams were kept on the same diet during pregnancy and lactation. Pups were weaned at PD21 and housed under NP conditions for five weeks, i.e., until PD56.

tag: age

value: post natal day 56

tag: Sex

value: male

value: Perinatal low-protein diet (LP)

value: Brain - Hypothalamus


title: Hypothalamus male normal-protein [9-04-04-16]

source_name: male_Perinatal normal-protein diet (NP)

value: Perinatal normal-protein diet (NP)


title: UTR-seq, THP1, DMSO 2 hours, rep3


title: K504E-white biological replicate 3

city: Bloomington

first: Hengyao

last: Niu

state: IN

address: Simon Hall MSB1, Room 415 212 S. Hawthorne Drive

department: Molecular and Cellular Biochemistry

institute: Indiana University

description: Library name: K504E-white_rep3

data_processing:
Raw reads were processed by Novogene: adapter trimming, quality filtering, and alignment to Saccharomyces cerevisiae W303 reference genome. Aligned reads provided as BAM files.
BAM files containing aligned RNA-seq reads for each sample
Assembly: Saccharomyces cerevisiae W303 reference genome
Supplementary files format and content: Raw reads quality-checked, trimmed, mapped to S. cerevisiae W303 genome; counts and FPKM calculated by Novogene pipeline.

organism: Saccharomyces cerevisiae

growth_protocol: WT and cdc13-K504E strains were grown in YPD to stationary phase for 15 days without dilution.

extract_protocol:
Total RNA was extracted by Novogene from submitted yeast cells according to their standard protocols.
mRNA libraries (poly-A enrichment) were prepared by Novogene according to their standard protocols.

value: budding yeast

value: chronic growth (15 days stationary phase)


title: K504E-white biological replicate 2

description: Library name: K504E-white_rep2


title: UTR-seq, THP1, DMSO 2 hours, rep2


title: Hippocampus female low-protein [8-4-4-16]

source_name: female_Perinatal low-protein diet (LP)

value: female

value: Brain - Hippocamppus


title: UTR-seq, THP1, DMSO 2 hours, rep1

value: Acute myeloid leukeamia


title: UTR-seq, THP1, OTS964 156nM 2 hours, rep3


title: Hippocampus female normal-protein [7-4-4-16]

source_name: female_Perinatal normal-protein diet (NP)


title: Brain-W811-5dpi-rep-2

description:
Library name: BR-80_S4
10x Genomics


title: Brain-W811-5dpi-rep-1

description:
Library name: BR-75_S3
10x Genomics


title: K504E-red biological replicate 3

description: Library name: K504E-red_rep3


title: Prefrontal cortex female low-protein [6-04-04-16]

value: Brain - Prefrontal cortex


title: K504E-white biological replicate 1

description: Library name: K504E-white_rep1


title: SLAM-seq, THP1 FLAG-CDK11-AID, no 4sU

description: EtOH-Control

value: untreated


title: SLAM-seq, THP1 FLAG-CDK11-AID, Ethanol 4 hours, 4sU, rep2

value: Ethanol, 4sU


title: Brain-W811-3dpi-rep-1

description:
Library name: BR-65_S1
10x Genomics


title: K504E-red biological replicate 2

description: Library name: K504E-red_rep2


title: larvae, control, leached in dark, rep 11

description:
CTL_LIGHTvsDARK; Dark_CTLvsTWP
CTL_Dark_11

value: Pooled whole eleutherolarvae

value: AB (wild-type)

value: 96 hours post fertilization (96 hpf)

value: egg water only (60 mg/L "Instant Ocean" sea salts)

value: leachates produced in dark conditions


title: Prefrontal cortex female normal-protein [5-04-04-16]

value: post natal day 56


title: WT-red biological replicate 3

description: Library name: WT-red_rep3

value: WT


title: K504E-red biological replicate 1

description: Library name: K504E-red_rep1


title: Brain-Control-rep-4

description:
Library name: BR-A2_S2
10x Genomics

value: Brain

value: Control sample


title: SLAM-seq, THP1 FLAG-CDK11-AID, Auxin 0.5mM 4 hours, 4sU, rep2

value: Auxin, 4sU


title: Hippocampus male low-protein [4-4-4-16]

value: male

value: Perinatal low-protein diet (LP)


title: Brain-scaup-5dpi-rep-1

description:
Library name: BR-85_S1
10x Genomics


title: SLAM-seq, THP1 FLAG-CDK11-AID, Ethanol 4 hours, 4sU, rep1


title: Hippocampus male normal-protein [3-4-4-16]

value: Perinatal normal-protein diet (NP)

value: Brain - Hippocamppus


title: Brain-Control-rep-2

description:
Library name: BR-Y2_S7
10x Genomics


title: WT-red biological replicate 2

description: Library name: WT-red_rep2

value: budding yeast

value: chronic growth (15 days stationary phase)


title: WT-red biological replicate 1

description: Library name: WT-red_rep1


title: SLAM-seq, THP1 FLAG-CDK11-AID, Auxin 0.5mM 4 hours, 4sU, rep1

value: Acute myeloid leukeamia


title: Prefrontal cortex male normal-protein [1-04-04-16]

value: Brain - Prefrontal cortex


title: Brain-Control-rep-1

description:
Library name: BR-Y1_S8
10x Genomics


title: Brain-scaup-3dpi-rep-1

description:
Library name: BR-70_S2
10x Genomics


title: B7_3_ND

status: Public on Aug 24 2025

city: Jilin

first: wang

last: yang

address: Xin-Min Street NO. 1

country: China

institute: Orthopaedic Center, The First Hospital of Jilin University

description: Library name: Sample 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Rnor_6.0
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Sciatic nerve

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Sciatic nerve

tag: model

value: sciatic nerve crush injury model

value: magnetic force stimulation


title: R_C_3

description: Library name: Sample6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

tag: group

value: control


title: B7_1_ND

description: Library name: Sample 1


title: B7_2_ND

description: Library name: Sample 2


title: R_C_2

description: Library name: Sample5


title: C7_1_ND

description: Library name: Sample 4


title: C7_2_ND

description: Library name: Sample 5


title: C7_3_ND

description: Library name: Sample 6


title: R_N_1

description: Library name: Sample1


title: R_C_1

description: Library name: Sample4


title: R_N_2

description: Library name: Sample2


title: Prefrontal cortex male low-protein [2-4-4-16]

tag: strain

value: post natal day 56


title: ID:D0136_Subject:44_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

data_processing:
The paired-end raw sequence reads were preprocessed using the Kallisto bustools package (kbpython:0.26.0). Count matrices were generated using Lamanno workflow with the GRCh38, release-105, reference genome. Downstream analysis, including quality control, integration, cell type annotations, and differential gene expression, was performed using the unspliced transcript counts.
Assembly: GRCh38, release-105
Supplementary files format and content: H5AD
Supplementary files format and content: Raw counts, normalized counts, metadata, dimensionality reduction, integration and clustering, cell-type annotations

source_name: brain

extract_protocol:
Fresh frozen brain tissue samples were thawed and micro-dissected, removing most white matter, and finely chopped using a blade. Tissue homogenization was performed in buffer containing 250mM sucrose and 0.1% TritonX100, using a glass Dounce with 0.02-0.055 mm clearance until no big clumps were visible (~30 strokes). The cellular nuclei fraction was purified using density gradient centrifugation, with the sample diluted in a 25% Iodixanol solution and layered on top of a 29% Iodixanol solution, then centrifuged at 13500g. Debris was carefully removed from the top layer and the nuclei pellet resuspended in PBS buffer containing 0.05~0.5% BSA and 2U/ml of DNAse I.  Immunostaining followed by FACS was used to remove nuclei aggregates using DAPI staining, and enrich for neuronal cells using NeuN.
We used either a modified Drop-seq method or the standard 10x Genomics Chromium Single Cell 3’ v2 or v3 assays. For Drop-seq, single nuclei were diluted to 200,000 cells/ml. To encapsulate individual nuclei and barcoded beads (Chemgenes, cat# Makosko-2011-10), we employed a microfluidic system (FlowJEM) and adjusted the flow parameters to generate ~100 µl (~0.5 nl) droplets (200 nuclei/µl; 165 beads/µl; flow rate: 3 ml/h). Lysis buffer contained 1% sarkosyl. Droplet-encapsulated nuclei were heated for 5 min at 72°C. Reverse transcription and PCR amplification followed previously described protocols (doi.org/10.1016/j.cell.2015.05.002). For 10x Genomics, ~12,500 nuclei were loaded to capture around 5,000 nuclei per sample. cDNA amplification and library construction followed the manufacturer’s instructions.

tag: assay

value: DropSeq

tag: subject

tag: apoe class

value: Frontal Cx (BA9)

tag: sort

value: NeuN

value: AD

value: III

value: int

tag: amyloid

value: DP (C0)

value: brain


title: ID:D0146_Subject:30_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)


title: ID:D0133_Subject:92_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)

value: All Nuclei

value: IV


title: ID:D0143_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0131_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0145_Subject:30_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0134_Subject:92_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0132_Subject:92_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0130_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0140_Subject:68_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: VI

value: high


title: ID:D0129_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0147_Subject:46_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0123_Subject:45_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: II

value: low


title: ID:D0122_Subject:45_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0144_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0121_Subject:44_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0107_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0106_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0120_Subject:44_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0119_Subject:32_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0105_Subject:14_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: R_N_3

description: Library name: Sample3

tag: cell line

value: magnetic force stimulation


title: ID:D0118_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: DropSeq

tag: tissue


title: ID:D0108_Subject:68_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: ID:D0138_Subject:46_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0104_Subject:14_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0103_Subject:45_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0101_Subject:44_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0098_Subject:24_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: NeuN


title: ID:D0093_Subject:35_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: AD


title: ID:D0096_Subject:74_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0089_Subject:49_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: No


title: ID:D0091_Subject:35_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0095_Subject:46_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: int


title: ID:D0099_Subject:42_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: brain


title: ID:D0090_Subject:35_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0094_Subject:45_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: DP (C0)


title: ID:D0100_Subject:42_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0109_Subject:76_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: FaDu, BRG1

city: beijing

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

description: Library name: FaDu_BRG1

data_processing:
Upload fq.gz data to Galaxy version 23.2 rc1, Using FastQC to evaluate the quality of data, using cutadapt to de concatenate raw data
Reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.0.
To create coverage plots, the locations of the mapped reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS2 callpeak v3.5.4 with the significance cut-off p-value <=0.00001
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: FaDu

growth_protocol: FaDu were cultured in MEM medium supplemented with 10 % fetal bovine serum, 100 U mL-1 penicillin, and 100 U mL-1 streptomycin (Gibco)

extract_protocol:
1 × 105 FaDu cells were collected,for the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme)
For the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme). Briefly, 1 × 105 FaDu cells were collected, resuspended in 100 μL wash buffer, transferred to an 8-tube strip containing activated ConA beads, and incubated for 10 min. Subsequently, 50 μL prechilled antibody buffer containing BACH1 or BRG1 antibodies was added to cells and incubated at 4 °C overnight, followed by the addition of diluted secondary antibodies and incubation for 60 min. After washing thrice with DIG wash buffer, samples were incubated with diluted pA/G-Tnp transposase for 1 h. Next, 50 μL diluted TTBL was added, and samples were incubated at 37 °C in a PCR instrument for 60 min for fragmentation. Subsequently, DNA extraction was performed by adding 5 μL proteinase K, 100 μL buffer L/B, and 20 μL DNA extract beads on the fragmented samples and incubating at 55 °C for 10 min. Following washes with WA and WB buffers, samples were eluted using sterile ultrapure water. The extracted DNA underwent library amplification using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme). PCR products were treated with VAHTS DNA clean beads (N411, Vazyme) for 5 min, the supernatant then was discarded, samples were washed with 80% ethanol, eluted using sterile ultrapure water, and the library was sequenced on the Illumina NovaSeq platform.

value: FaDu

tag: cell type

value: Head and neck squamous carcinoma

value: anti-BRG1 (Abcam #110641)


title: FaDu, BACH1

description: Library name: FaDu_BACH1

tag: genotype

value: BACH1(Proteintech #14018-1-AP)


title: shCatenin_RNA_1

city: Hangzhou

first: Yu

last: Qian

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

institute: Zhejiang University

description: Library name: shCatenin_RNA_1

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
The sequencing data were processed using Easy_Ribo for trimming for adaptor sequences, masking low-complexity or low-quality reads, and mapping to the GRCh38 whole genome.
RPKM were calculated to quantify gene expression levels, and differential expression analysis was performed using DESeq2.
Assembly: GRCh38 (Homo sapiens), GRCm39 (Mus musculus)
Supplementary files format and content: Comma-Separated Values file include the RPKM representing gene expression levels for each transcript.
Supplementary files format and content: Column headers are: GeneSymbol, ENSG, ENST, Start, End, TranscriptLength, RPKM

source_name: Colon

growth_protocol: All HCT116 WT, ALKBH8 KO, OE, and CTNNB1 KD cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 6cm dishes. ApcMin/+ mice were maintained under SPF conditions with free access to food and water

extract_protocol:
Cells were lysed in TRIzol, followed by chloroform extraction and isopropanol precipitation, with 1/5 of the RNA used for RNA-seq and 4/5 for ribosome profiling (Ribo-seq).
The library was constructed using Small RNA Library Prep Set for Illumina (E7330S, NEB).

treatment_protocol: Cycloheximide for 3 mins (100 ug/ml) at 37℃. Mice were sacrificed at 24 weeks of age without any treatment.

value: Colon

value: Epithelial cells

value: CTNNB1 KD


title: shCon_RNA_2

description: Library name: shCon_RNA_2

value: WT


title: ID:D0086_Subject:44_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq

value: Frontal Cx (BA9)

value: III


title: ID:D0084_Subject:92_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: All Nuclei

value: AD

value: IV


title: ID:D0085_Subject:92_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: NeuN

value: int

value: brain


title: ID:D0088_Subject:45_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: II

value: low

value: DP (C0)


title: ID:D0087_Subject:45_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0102_Subject:44_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0083_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: VI

value: high


title: ID:D0092_Subject:35_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: shCatenin_RNA

description: Library name: shCatenin_RNA

value: Colon

value: Epithelial cells

value: CTNNB1 KD


title: ID:D0082_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq

value: Frontal Cx (BA9)


title: shCon_RNA

description: Library name: shCon_RNA

value: WT


title: A8OE_RNA

description: Library name: 116_A8OE_RNA

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
The sequencing data were processed using Easy_Ribo for trimming for adaptor sequences, masking low-complexity or low-quality reads, and mapping to the GRCh38 whole genome.
RPKM were calculated to quantify gene expression levels, and differential expression analysis was performed using DESeq2.
Assembly: GRCh38 (Homo sapiens), GRCm39 (Mus musculus)
Supplementary files format and content: Comma-Separated Values file include the RPKM representing gene expression levels for each transcript.

growth_protocol: All HCT116 WT, ALKBH8 KO, and OE cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 6cm dishes.ApcMin/+ mice were maintained under SPF conditions with free access to food and water

value: ALKBH8 OE

tag: treatment

value: cycloheximide for 3 mins (100 ug/ml)


title: A8OE_Ribo

description: Library name: 116_A8OE_Ribo


title: ID:D0081_Subject:49_Brain-Region:Precuneous (BA7)_Diagnosis:PART

value: Precuneous (BA7)

value: All Nuclei

value: PART

value: No


title: ID:D0097_Subject:24_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: AD

value: brain


title: ID:D0079_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int

value: DP (C0)


title: ID:D0080_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN


title: Ctrl_RNA_2

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
The sequencing data were processed using Easy_Ribo for trimming for adaptor sequences, masking low-complexity or low-quality reads, and mapping to the GRCh38 whole genome.
RPKM were calculated to quantify gene expression levels, and differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Comma-Separated Values file include the RPKM representing gene expression levels for each transcript.

growth_protocol: All HCT116 WT and ALKBH8 KO cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 6cm dishes.

treatment_protocol: Cycloheximide for 3 mins (100 ug/ml) at 37℃

value: Colon

value: Epithelial cells


title: A8KO_RNA_2

value: ALKBH8 KO


title: ID:D0078_Subject:71_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: DropSeq

value: Control

value: low


title: A8KO_RNA_1

value: cycloheximide for 3 mins (100 ug/ml)


title: ID:D0076_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: Ctrl_RNA_1

value: WT


title: Ctrl_Ribo_2


title: ID:D0075_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei


title: A8KO_Ribo_1


title: A8KO_Ribo_2


title: ID:D0074_Subject:49_Brain-Region:Precuneous (BA7)_Diagnosis:PART

value: Precuneous (BA7)

value: PART

value: II

value: No


title: ID:D0206_Subject:94_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: III

value: brain


title: ID:D0205_Subject:74_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: NeuN

value: AD

value: VI

value: high


title: ID:D0070_Subject:73_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: DropSeq


title: ID:D0071_Subject:73_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0207_Subject:94_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART


title: ID:D0072_Subject:30_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: int

value: DP (C0)


title: ID:D0068_Subject:42_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0069_Subject:42_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0203_Subject:116_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: I

value: low


title: ID:D0201_Subject:76_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0202_Subject:116_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: Frontal Cx (BA9)

value: All Nuclei


title: ID:D0066_Subject:32_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0067_Subject:32_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0065_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0200_Subject:73_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)


title: ID:D0064_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0198_Subject:24_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0063_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0199_Subject:35_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0197_Subject:123_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART


title: ID:D0062_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: Ctrl_Ribo_1

value: Colon

value: Epithelial cells

value: WT

value: cycloheximide for 3 mins (100 ug/ml)


title: ID:D0061_Subject:24_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: NeuN

value: AD

value: brain


title: ID:D0204_Subject:74_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: DropSeq

value: VI

value: high


title: ID:D0060_Subject:24_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0194_Subject:42_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0077_Subject:71_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: Control

value: No


title: ID:D0196_Subject:117_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: I

value: low

value: DP (C0)


title: ID:D0059_Subject:76_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: ID:D0192_Subject:114_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei

value: IV

value: int


title: ID:D0193_Subject:114_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0057_Subject:74_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0191_Subject:110_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: II


title: ID:D0073_Subject:30_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)

value: NeuN

value: III


title: ID:D0190_Subject:110_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: DropSeq

value: brain


title: ID:D0056_Subject:74_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: AD

value: VI

value: high


title: ID:D0055_Subject:68_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0187_Subject:35_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0054_Subject:68_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0186_Subject:32_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0053_Subject:52_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0184_Subject:12_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0051_Subject:18_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0058_Subject:76_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0182_Subject:95_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART

value: low

value: No


title: ID:D0195_Subject:42_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0050_Subject:18_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: ID:D0181_Subject:74_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei


title: ID:D0048_Subject:12_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0180_Subject:73_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0179_Subject:126_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: I

value: DP (C0)


title: ID:D0046_Subject:92_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int


title: ID:D0177_Subject:35_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)


title: ID:D0045_Subject:73_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN


title: ID:D0044_Subject:73_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0175_Subject:115_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Control


title: ID:D0042_Subject:14_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq


title: ID:D0173_Subject:103_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:Control

value: brain


title: ID:D0174_Subject:115_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control


title: ID:D0041_Subject:69_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: AD


title: ID:D0040_Subject:69_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: VI


title: ID:D0043_Subject:14_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: high


title: ID:D0039_Subject:68_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0171_Subject:76_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0176_Subject:35_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0169_Subject:44_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: III


title: ID:D0168_Subject:44_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:D0047_Subject:92_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0038_Subject:68_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0036_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: II

value: low

value: No


title: ID:D0037_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: Frontal Cx (BA9)


title: ID:D0166_Subject:18_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei


title: ID:D0167_Subject:42_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0035_Subject:46_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int


title: ID:D0034_Subject:46_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0164_Subject:69_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: NeuN


title: ID:D0032_Subject:24_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0163_Subject:69_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0161_Subject:124_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DP (C0)


title: ID:D0029_Subject:59_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq


title: ID:D0160_Subject:124_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: brain


title: ID:D0162_Subject:24_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: AD


title: ID:D0159_Subject:94_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART


title: ID:D0028_Subject:33_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: VI


title: ID:D0027_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0170_Subject:46_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0026_Subject:30_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0031_Subject:69_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: high


title: ID:D0025_Subject:24_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)


title: ID:D0024_Subject:42_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0157_Subject:50_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART


title: ID:D0023_Subject:42_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0183_Subject:95_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART


title: ID:D0165_Subject:92_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0155_Subject:59_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0152_Subject:59_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0153_Subject:59_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0021_Subject:32_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0019_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: III


title: ID:D0020_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0158_Subject:94_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART

value: PART


title: ID:D0018_Subject:24_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0016_Subject:68_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:C0116_Subject:91_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Control


title: ID:C0115_Subject:145_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)

value: V


title: ID:D0017_Subject:24_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: ID:D0150_Subject:49_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART

value: All Nuclei

value: II

value: low

value: No


title: ID:D0156_Subject:50_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART


title: ID:C0114_Subject:145_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: NeuN


title: ID:D0011_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: DropSeq


title: ID:D0148_Subject:18_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: brain


title: ID:D0013_Subject:57_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: AD

value: IV

value: int


title: ID:D0149_Subject:18_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)

value: VI

value: high


title: ID:D0012_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART


title: ID:D0015_Subject:68_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0052_Subject:52_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0014_Subject:57_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0009_Subject:46_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0185_Subject:32_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)


title: ID:C0113_Subject:146_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: V


title: ID:C0111_Subject:145_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0151_Subject:49_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART


title: ID:C0117_Subject:91_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Frontal Cx (BA9)

value: Control


title: ID:C0110_Subject:145_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD


title: ID:D0007_Subject:71_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: All Nuclei


title: ID:D0006_Subject:71_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:Control

value: low


title: ID:D0008_Subject:71_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: No


title: ID:C0107_Subject:140_Brain-Region:Precuneous (BA7)_Diagnosis:AD


title: ID:C0106_Subject:140_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: NeuN


title: ID:D0005_Subject:71_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:Control

value: DropSeq


title: ID:C0108_Subject:146_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: brain


title: ID:D0002_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: AD


title: ID:D0003_Subject:68_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:D0004_Subject:71_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control


title: ID:C0103_Subject:137_Brain-Region:Precuneous (BA7)_Diagnosis:PART

value: II


title: ID:D0022_Subject:32_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: ID:C0104_Subject:137_Brain-Region:Precuneous (BA7)_Diagnosis:PART


title: ID:D0010_Subject:46_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int


title: ID:D0001_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD


title: YFP_rep5 (among 5 cell-types)

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
The quality of the sequencing data was assessed using FastQC
bases with fluctuating GC content were trimmed off with cutadapt
Genome mapping was performed using TopHat
A gene expression count table was generated from the aligned dataset using HTSeq
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Shoot Apical meristem (SAM)

growth_protocol: Plants were grown on soil in short day conditions for 4-5 weeks before harvesting

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all cell-types were prepared using ‘NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: About 50 SAMs of 4-5 week old plants were quickly harvested and placed in cell-wall dissolving enzyme solution in 70um cell-strainer in a small petridish. Protoplasts samples were sorted by the EMBL flow cytometry core facility using a special setup MoFlo XDP cell sorter from Beckman Coulter equipped with a Coherent Sabr Argon gas laser emitting at 514.5nm (400mW), a Coherent Innova gas laser emitting at 488nm (300mW), and a Coherent Obis 405nm solid state laser (240mW).

value: Shoot Apical meristem (SAM)

value: YFP

value: 4-5 week old plant


title: ID:C0112_Subject:146_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)

value: high


title: YFP_rep3 (among 5 cell-types)


title: ID:C0101_Subject:137_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: Frontal Cx (BA9)

value: PART


title: YFP_rep2 (among 5 cell-types)


title: YFP_rep1 (among 5 cell-types)


title: ID:C0109_Subject:146_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)

value: All Nuclei

value: V


title: monoallelic_Trp53_mut_only_replicate_4

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

description: Library name: monoallelic_GFP_pos_ctr_4

data_processing:
Quality control, mapping and differential gene expression analysis was performed using the SUSHI bioinformatics pipeline. Gene set enrichment analysis was performed using the GSEA software developed jointly by UC San Diego and the Broad Institute.
Assembly: NCBI
Supplementary files format and content: excel, normalized counts

source_name: ER-Hoxb8 cell line

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Illumina Stranded mRNA Prep, Ligation

value: ER-Hoxb8 cell line

value: Trp53-R245W/+; SFFV-tRFP

value: etoposide


title: GFP_rep4 (among 5 cell-types)

value: GFP


title: GFP_rep5 (among 5 cell-types)


title: ID:C0099_Subject:50_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART

value: NeuN

value: II

value: low

value: No

value: brain


title: monoallelic_Trp53_mut_only_replicate_3

description: Library name: monoallelic_GFP_pos_ctr_3


title: monoallelic_Trp53_mut_only_replicate_2

description: Library name: monoallelic_GFP_pos_ctr_2


title: BFPYFP_rep4 (among 5 cell-types)

value: Shoot Apical meristem (SAM)

value: BFPYFP

value: 4-5 week old plant


title: GFP_rep2 (among 5 cell-types)


title: BFPYFP_rep5 (among 5 cell-types)


title: BFPYFP_rep3 (among 5 cell-types)


title: ID:D0178_Subject:126_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq

value: Frontal Cx (BA9)

value: AD

value: I

value: DP (C0)


title: ID:C0102_Subject:137_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: All Nuclei

value: PART


title: monoallelic_Trp53_mut_Mdm2_OE_replicate_4

description: Library name: monoallelic_GFP_pos_MDM2_4

value: ER-Hoxb8 cell line

value: Trp53-R245W/+; SFFV-Mdm2-IRES-tRFP

value: etoposide


title: monoallelic_Trp53_mut_only_replicate_1

description: Library name: monoallelic_GFP_pos_ctr_1

value: Trp53-R245W/+; SFFV-tRFP


title: ID:C0096_Subject:32_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: Precuneous (BA7)

value: VI

value: high


title: ID:C0097_Subject:76_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: Primary Visual Cx (BA17)

value: NeuN

value: brain


title: BFPGFP_rep5 (among 5 cell-types)

value: Shoot Apical meristem (SAM)

value: BFPGFP

value: 4-5 week old plant


title: BFPYFP_rep1 (among 5 cell-types)

value: BFPYFP


title: BFPGFP_rep4 (among 5 cell-types)


title: BFPYFP_rep2 (among 5 cell-types)


title: ID:C0095_Subject:32_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: AD


title: BFPGFP_rep2 (among 5 cell-types)


title: monoallelic_Trp53_mut_Mdm2_OE_replicate_2

description: Library name: monoallelic_GFP_pos_MDM2_2


title: ID:C0098_Subject:76_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: All Nuclei


title: ID:C0092_Subject:103_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: Control

value: low

value: No


title: BFPGFP_rep1 (among 5 cell-types)


title: ID:C0100_Subject:50_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:PART

value: PART

value: II


title: BFP_rep5 (among 5 cell-types)

value: BFP


title: monoallelic_Trp53_mut_Mdm2_OE_replicate_1

description: Library name: monoallelic_GFP_pos_MDM2_1

value: ER-Hoxb8 cell line

value: Trp53-R245W/+; SFFV-Mdm2-IRES-tRFP

value: etoposide


title: BFP_rep3 (among 5 cell-types)


title: biallelic_Trp53_mut_only_replicate_4

description: Library name: biallelic_GFP_pos_ctrl_4

value: Trp53-R245W/R245W; SFFV-tRFP


title: BFP_rep1 (among 5 cell-types)


title: ID:C0091_Subject:103_Brain-Region:Precuneous (BA7)_Diagnosis:Control

value: Precuneous (BA7)

value: NeuN

value: brain


title: ID:C0089_Subject:44_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: III

value: int

value: DP (C0)


title: biallelic_Trp53_mut_only_replicate_3

description: Library name: biallelic_GFP_pos_ctrl_3


title: 7d_LPS_M_T_S47

city: Jerusalem

first: Nimrod

last: Madrer

address: The Edmond J. Safra Campus, Guvat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: S47

data_processing:
FASTQ files were quality-checked using FastQC (v0.11.9) following adaptor removal using FLEXBAR (v3.5.0) according to the pipeline manual. Adaptor-less output FASTQ files were aligned to miRs using miRdeep (v2.0.1.2), and to tRFs using MINTmap (v1.0).
Assembly: GRCm39
Supplementary files format and content: csv counts of miRs
Supplementary files format and content: csv counts of tRFs
Supplementary files format and content: csv file with tRFs metadata

source_name: Trigeminal ganglion

growth_protocol: Forty-eight Balb/c mice, 24 male and 24 female, aged 2.5 months, were included in the experiment.

extract_protocol:
The two trigeminal ganglia and two superior cervical ganglia were removed surgically from each mouse. Ganglia were homogenized in 700 µL QIAzol using a pellet pestle motor and RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004) according to the manufacturer's protocol, followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific). Average trigeminal ganglia yield was 193 ng/µL and average superior cervical ganglia yield was 64 ng/µL.
RIN was determined for all samples (Bioanalyzer 6000, Agilent), with an average of 8.1 (range 5.3-9.3). Half of the samples (48 out of 96, see Table 1) were selected for short RNA-seq, 2 out of the 4 in each subgroup above. Average RIN for these 48 samples was 8.3 (range 6.4-9.3). Libraries were constructed from 140 ng total RNA of each sample, using the NEBNext Multiplex Small RNA library prep kit for Illumina (New England Biolabs, NEB-E7560S) and the small RNA fraction was sequenced on the NextSeq 500 System (Illumina) at the Center for Genomic Technologies Facility, the Hebrew University of Jerusalem.

treatment_protocol: Animals received an intraperitoneal (i.p) injection containing LPS from E. coli O55:B5 (Merck, L2880), 2.5 mg/kg in 0.2 mL saline, or 0.2 mL saline alone as control. Mice were euthanized by CO2 inhalation at 4 hours, 24 hours, and 7 days after injection.

value: Trigeminal ganglion

value: Balb/c

tag: time

value: 168 hours (week)

value: LPS

value: Male


title: 7d_LPS_M_T_S48

description: Library name: S48


title: 7d_CNT_M_T_S46

description: Library name: S46

value: Saline


title: ID:C0090_Subject:44_Brain-Region:Precuneous (BA7)_Diagnosis:AD

value: All Nuclei

value: AD


title: monoallelic_Trp53_mut_Mdm2_OE_replicate_3

description: Library name: monoallelic_GFP_pos_MDM2_3

value: ER-Hoxb8 cell line

value: Trp53-R245W/+; SFFV-Mdm2-IRES-tRFP


title: ID:C0088_Subject:117_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: I

value: low


title: biallelic_Trp53_mut_only_replicate_2

description: Library name: biallelic_GFP_pos_ctrl_2

value: Trp53-R245W/R245W; SFFV-tRFP

value: etoposide


title: 24h_LPS_M_T_S43

description: Library name: S43

value: 24 hours (day)


title: 24h_CNT_M_T_S42

description: Library name: S42


title: ID:C0087_Subject:112_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: No

value: brain


title: BFP_rep4 (among 5 cell-types)

value: Shoot Apical meristem (SAM)

value: BFP

value: 4-5 week old plant


title: biallelic_Trp53_mut_Mdm2_OE_replicate_4

description: Library name: biallelic_GFP_pos_MDM2_4

value: Trp53-R245W/R245W; SFFV-Mdm2-IRES-tRFP


title: ID:C0086_Subject:112_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: NeuN


title: 24h_CNT_M_T_S41

description: Library name: S41

value: Trigeminal ganglion

value: Balb/c

value: Saline

value: Male


title: 4h_LPS_M_T_S40

description: Library name: S40

value: 4 hours

value: LPS


title: biallelic_Trp53_mut_Mdm2_OE_replicate_3

description: Library name: biallelic_GFP_pos_MDM2_3

value: ER-Hoxb8 cell line


title: 4h_LPS_M_T_S39

description: Library name: S39


title: 4h_CNT_M_T_S38

description: Library name: S38


title: ID:C0085_Subject:108_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Frontal Cx (BA9)

value: Control

value: low


title: ID:C0084_Subject:111_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: I

value: No


title: biallelic_Trp53_mut_Mdm2_OE_replicate_2

description: Library name: biallelic_GFP_pos_MDM2_2

value: etoposide


title: 7d_LPS_F_T_S36

description: Library name: S36

value: 168 hours (week)

value: Female


title: biallelic_Trp53_mut_Mdm2_OE_replicate_1

description: Library name: biallelic_GFP_pos_MDM2_1

value: Trp53-R245W/R245W; SFFV-Mdm2-IRES-tRFP


title: 24h_LPS_M_T_S44

description: Library name: S44

value: Trigeminal ganglion

value: 24 hours (day)


title: 7d_CNT_F_T_S34

description: Library name: S34

value: Balb/c

value: Saline


title: ID:C0083_Subject:14_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: AD

value: VI

value: high

value: brain


title: 7d_LPS_F_T_S35

description: Library name: S35

value: LPS


title: Control B3

city: Guangzhou

first: Dongming

last: Lv

state: None Selected

address: No.58 Zhongshan 2nd Road, Guangzhou, Guangdong Province, China,

institute: Sun Yat-sen University

description: Library name: Samlpe 6

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Back skin

extract_protocol:
Mice skin wound cells were purified. Single cell cDNA library was performed according to the manufacter's instructions.
Cellular suspensions were loaded on a GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). The scRNA-seq libraries were generated using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent kits. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Then the full-length and barcoded cDNAs were amplified by PCR to generate sufficient mass for library construction. The final libraries quantified used in Illumina bridge amplification. All the libraries were sequenced with a 150-bp paired-end run based the Illumina sequencer.

value: Back skin

value: total RNA

value: paired-end

tag: batch

value: Illumina NovaSeq X Plus


title: 7d_CNT_F_T_S33

description: Library name: S33

value: 168 hours (week)


title: biallelic_Trp53_mut_only_replicate_1

description: Library name: biallelic_GFP_pos_ctrl_1

value: ER-Hoxb8 cell line

value: Trp53-R245W/R245W; SFFV-tRFP

value: etoposide


title: ID:C0082_Subject:75_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: All Nuclei

value: V


title: 24h_PS_F_T_S32

description: Library name: S32

value: Trigeminal ganglion

value: Balb/c

value: 24 hours (day)

value: Female


title: 24h_LPS_F_T_S31

description: Library name: S31


title: Control B2

description: Library name: Samlpe 5


title: ID:C0081_Subject:75_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: AD

value: high

value: brain


title: 24h_CNT_F_T_S30

description: Library name: S30

value: Saline


title: 24h_CNT_F_T_S29

description: Library name: S29


title: ID:C0072_Subject:124_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int

value: DP (C0)


title: Control B1

description: Library name: Samlpe 4

value: Back skin

value: total RNA

value: paired-end

value: Illumina NovaSeq X Plus


title: 4h_CNT_M_T_S37

description: Library name: S37

value: 4 hours

value: Male


title: Mat2a LOF_A3

description: Library name: Samlpe 3


title: ID:C0071_Subject:124_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)


title: 4h_LPS_F_T_S27

description: Library name: S27

value: Trigeminal ganglion

value: Balb/c

value: LPS


title: ID:C0105_Subject:140_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: AD


title: Mat2a LOF_A2

description: Library name: Samlpe 2


title: 4h_CNT_F_T_S25

description: Library name: S25

value: Female


title: 4h_CNT_F_T_S26

description: Library name: S26

value: Saline


title: ID:C0070_Subject:114_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei

value: IV

value: brain


title: 7d_LPS_M_S_S24

description: Library name: S24

source_name: Super cervical ganglion

value: Super cervical ganglion

value: 168 hours (week)


title: Mat2a LOF_A1

description: Library name: Samlpe 1

value: Back skin

value: total RNA

value: paired-end


title: ID:C0069_Subject:114_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: int

value: DP (C0)


title: 7d_CNT_M_S_S21

description: Library name: S21

value: Male


title: 7d_LPS_M_S_S23

description: Library name: S23

value: Balb/c


title: ID:C0066_Subject:35_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: VI

value: high


title: 7d_CNT_M_S_S22

description: Library name: S22


title: COVID5

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

data_processing:
Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned.
CircRNAs were detected and identified by using find_circ and CIRI2 programs with default parameters.
The raw counts were first normalized using TPM.
Differential expression analysis was performed using the DEGseq (2010) R package.
Assembly: hg38
Supplementary files format and content: Excel file "Processed data 20230628.xlsx" includes TPM values for each Sample

source_name: peripheral blood

extract_protocol:
Total RNAs were extracted using Trizol Reagent. Ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit (Epicentre, USA).
RNA-Seq libraries preparation with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to the manufacturer's instructions.

value: peripheral blood

value: neutrophils

tag: disease state


title: ID:C0065_Subject:35_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: AD


title: 4h_LPS_F_T_S28

description: Library name: S28

value: Trigeminal ganglion

value: 4 hours

value: LPS

tag: Sex

value: Female


title: 24h_CNT_M_S_S18

description: Library name: S18

value: Super cervical ganglion

value: 24 hours (day)

value: Saline


title: ID:C0060_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei

value: IV

value: int

value: DP (C0)

value: brain


title: COVID4


title: 24h_LPS_M_S_S19

description: Library name: S19

value: Balb/c

value: Male


title: COVID3

value: peripheral blood

value: neutrophils


title: ID:C0059_Subject:19_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: NeuN

value: AD


title: Mouse E7.5 gastrulation ATAC rep2

city: Rehovot

first: Amos

last: Tanay

address: Herzl

institute: Weizmann Institute of Science

description: Library name: WT_lg_ATAC

data_processing:
Raw sequencing data processed using 10x Genomics Cell Ranger ARC pipeline 2.0.0
Assembly: mm10
Supplementary files format and content: CellRanger output files: For RNA samples: mRNA_barcodes.tsv/.tsv.gz, mRNA_features.tsv/.tsv.gz, mRNA_matrix.mtx/.mtx.gz, per_barcode_metrics.csv, summary.csv For ATAC samples: ATAC_fragments.tsv.gz, per_barcode_metrics.csv, summary.csv

source_name: Full embryo

growth_protocol: Timed pregnant immune competent Hsd:ICR (CD-1) female mice were maintained with ad libitum access to water and standard mouse chow under 12 h light/dark cycles. Mouse embryos were harvested at E6.5-E7.5 developmental stages and dissected in ice-cold 1×PBS.

extract_protocol:
Nuclei isolation was performed using a modified 10x Genomics low cell input protocol. 45-70K cells per embryo were washed in cold PBS/0.04% BSA, then lysed in chilled lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonident P40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, 1U/µl RNase inhibitor) for 3 min on ice. Nuclei were washed in wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1mM DTT, 1U/µl RNase inhibitor), pelleted, and resuspended in diluted nuclei buffer. >95% nuclei viability was confirmed by trypan blue staining.
Single nuclei were loaded on Chromium Next GEM Chip J (10x Genomics) for GEM generation. ATAC and gene expression libraries were constructed separately following 10x Genomics Multiome manufacturer's instructions. Library quality was assessed using Agilent D1000/D5000 ScreenTape and quantified with Qubit 4 Fluorometer. Sequencing was performed on Illumina NovaSeq 6000 in paired-end mode with the following settings: ATAC library (read1: 50bp, index1: 8bp, index2: 24bp, read2: 49bp); RNA library (read1: 28bp, index1: 10bp, index2: 10bp, read2: 90bp).

value: Full embryo

value: Hsd:ICR (CD-1)

tag: developmental stage

value: E7.5 gastrulation


title: Mouse E7.5 gastrulation GEX rep3

description: Library name: WT_sm_RNA


title: Mouse E7.5 gastrulation GEX rep2

description: Library name: WT_lg_RNA


title: COVID2


title: 24h_CNT_M_S_S17

description: Library name: S17

value: Super cervical ganglion

value: 24 hours (day)


title: ID:C0057_Subject:18_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: VI

value: high


title: Mouse E7.5 gastrulation GEX rep1

description: Library name: WT_E75_RNA


title: 24h_LPS_M_S_S20

description: Library name: S20

value: LPS


title: Mouse E7.5 gastrulation ATAC rep3

description: Library name: WT_sm_ATAC


title: ID:C0058_Subject:18_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei


title: ID:C0040_Subject:57_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: IV

value: int

value: brain


title: 4h_LPS_M_S_S15

description: Library name: S15

value: Balb/c

value: 4 hours

value: Male


title: 4h_LPS_M_S_S16

description: Library name: S16


title: ID:D0033_Subject:24_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq

value: Frontal Cx (BA9)

value: NeuN


title: Mouse E7.0 gastrulation ATAC

description: Library name: WT_E70_ATAC

value: Full embryo

value: Hsd:ICR (CD-1)

value: E7.0 gastrulation


title: S10

value: peripheral blood

value: neutrophils

value: sepsis


title: 4h_CNT_M_S_S14

description: Library name: S14

value: Super cervical ganglion

value: Saline


title: S9


title: Mouse E7.0 gastrulation GEX

description: Library name: WT_E70_RNA


title: 4h_CNT_M_S_S13

description: Library name: S13


title: ID:C0037_Subject:92_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: All Nuclei

value: AD

value: IV


title: Mouse E6.5 gastrulation ATAC

description: Library name: WT_E65_ATAC

value: E6.5 gastrulation


title: S8


title: ID:C0032_Subject:103_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Control

value: low

value: No

value: brain


title: Mouse E7.5 gastrulation ATAC rep1

description: Library name: WT_E75_ATAC

value: E7.5 gastrulation


title: APC_A8KO_Ribo

description: Library name: A8KO_APC_Ribo

source_name: small intestine tumor

value: small intestine tumor

value: Alknh8 KO


title: S6

data_processing:
Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned.
CircRNAs were detected and identified by using find_circ and CIRI2 programs with default parameters.
The raw counts were first normalized using TPM.
Differential expression analysis was performed using the DEGseq (2010) R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNAs were extracted using Trizol Reagent. Ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit (Epicentre, USA).
RNA-Seq libraries preparation with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®  according to the manufacturer's instructions.


title: Mouse E6.5 gastrulation GEX

description: Library name: WT_E65_RNA

value: Full embryo

value: Hsd:ICR (CD-1)


title: 7d_LPS_F_S_S11

description: Library name: S11

value: Balb/c

value: 168 hours (week)

value: LPS

value: Female


title: S7

value: peripheral blood

value: neutrophils

value: sepsis


title: ID:C0029_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: NeuN

value: AD

value: III

value: int

value: DP (C0)


title: 7d_CNT_F_S_S10

description: Library name: S10

value: Super cervical ganglion

value: Saline


title: 7d_CNT_F_S_S9

description: Library name: S9


title: APC_A8KO_RNA

description: Library name: A8KO_APC_RNA

value: small intestine tumor

value: Alknh8 KO


title: APC_WT_Ribo

description: Library name: WT_APC_Ribo

value: WT


title: COVID1


title: ID:C0031_Subject:103_Brain-Region:Frontal Cx (BA9)_Diagnosis:Control

value: Control

value: low

value: No

value: brain


title: S4

value: peripheral blood

value: neutrophils


title: 24h_LPS_F_S_S8

description: Library name: S8

value: Balb/c

value: 24 hours (day)

value: LPS

value: Female


title: ID:C0026_Subject:49_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: Frontal Cx (BA9)

value: All Nuclei

value: PART

value: II


title: S5

value: sepsis


title: ID:C0030_Subject:30_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: AD

value: III

value: int

value: DP (C0)


title: 7d_LPS_F_S_S12

description: Library name: S12

value: Super cervical ganglion

value: 168 hours (week)


title: ID:C0025_Subject:49_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: NeuN

value: low

value: No

value: brain


title: S3

value: peripheral blood

value: neutrophils


title: APC_WT_RNA

description: Library name: WT_APC_RNA

value: small intestine tumor

value: WT


title: 24h_LPS_F_S_S7

description: Library name: S7

value: Balb/c

value: 24 hours (day)

value: LPS

value: Female


title: Cd248_WT_3

city: Xi'an

first: Chao

last: Xu

address: 127 Changle West Road

institute: Air Force Medical University

description: Control

data_processing:
Reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
We aligned reads of all samples to the  house mouse  reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: kidney

growth_protocol: All experiment animals were in conventional barrier unit facilities with conventional bedding, 12:12h light:dark cycle, ambient temperature control and access to food and water ad libitum

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
A cDNA library constructed by technology from the pooled RNA from fibrotic kidney samples of mice was sequenced run with Illumina NovaseqTM 6000 sequence platform.

treatment_protocol: unilateral ureteral obstruction

value: kidney

value: Wild type

value: unilateral ureteral obstruction


title: ID:C0024_Subject:45_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: All Nuclei

value: AD

value: II

value: DP (C0)


title: S2

value: sepsis


title: Cd248_WT_2

description: Control


title: 24h_CNT_F_S_S6

description: Library name: S6

value: Super cervical ganglion

value: Saline


title: S1

value: peripheral blood

value: neutrophils


title: ID:C0023_Subject:45_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: low

value: brain


title: ID:D0049_Subject:1161_Brain-Region:Primary Visual Cx (BA17)_Diagnosis:AD

value: DropSeq

value: Primary Visual Cx (BA17)

value: VI

value: high


title: Cd248_WT_1

description: Control

value: kidney

value: Wild type

value: unilateral ureteral obstruction


title: HC4

value: healthy control


title: 24h_CNT_F_S_S5

description: Library name: S5

value: Balb/c

value: 24 hours (day)

value: Female


title: 4h_LPS_F_S_S4

description: Library name: S4

value: Super cervical ganglion

value: 4 hours

value: LPS


title: Cd248_KO_3

description: Knockout

value: Cd248 KO


title: ID:C0020_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: Frontal Cx (BA9)

value: All Nuclei

value: AD


title: ID:D0154_Subject:59_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: DropSeq

value: brain


title: ID:C0019_Subject:60_Brain-Region:Frontal Cx (BA9)_Diagnosis:AD

value: NeuN

value: VI

value: high


title: HC3

value: peripheral blood

value: neutrophils


title: 4h_LPS_F_S_S3

description: Library name: S3

value: Balb/c


title: HC2

value: healthy control


title: Cd248_KO_2

description: Knockout

value: kidney

value: unilateral ureteral obstruction


title: Cd248_KO_1

description: Knockout


title: ID:C0018_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: PART

value: II

value: low

value: No


title: HC1


title: ID:C0017_Subject:50_Brain-Region:Frontal Cx (BA9)_Diagnosis:PART

value: Frontal Cx (BA9)


title: 4h_CNT_F_S_S1

description: Library name: S1

value: Super cervical ganglion

value: 4 hours

value: Saline

value: Female


title: 7d_CNT_M_T_S45

description: Library name: S45

value: Trigeminal ganglion

value: 168 hours (week)

value: Male


title: Graft_PTH

status: Public on Aug 23 2025

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

description: Library name: 8-Graft_PTH

data_processing:
Barcoded samples were demultiplexed, aligned to the mouse genome, and UMI-collapsed with the Cellranger toolkit with standard settings  (version 7.1.0, 10X Genomics Inc)
Assembly: GRCm39.104
Supplementary files format and content: .h5 feature matrix
Supplementary files format and content: .h5 feature matrix

source_name: Graft tissue

growth_protocol: None. Freshly purified primary cells were used.

extract_protocol:
Target tissue was mechanically and enzymatically digested, stained for flow cytometric isolation and purified via FACS.
According to 10X Genomics manufacturer instructions

treatment_protocol: There were four treatment groups of mice receiving subcutaneous release pellets of: (1) Placebo (Control), (2) Methylprednisolone (GC), (3) Methylprednisolone removal (GC removal), (4) Methylprednisolone (GC) + hPTH 1-34 (GC+PTH). For grafting experiments the four groups investigated were: (1) Placebo (Control), (2) Methylprednisolone (GC), (3) hPTH 1-34 treatment, (4) Methylprednisolone (GC) + hPTH 1-34 (GC+PTH).

value: Graft tissue

value: tissue

value: PTH


title: soleus muscle, HFD 12w, rep4

city: Toyama

first: Makito

last: Oku

address: 2630 Sugitani

department: Research Center for Pre-Disease Science

institute: University of Toyama

description: Library name: sol_12w_4

data_processing:
FastQC version 0.11.7 was used for quality checking of the sequenced reads.
Trimmomatic version 0.38 was used to trim low-quality sequences and adapter sequences.
HISAT2 version 2.1.0 was used to map the trimmed reads to the reference genome mm10.
Samtools version 1.9 was used to convert Sequence Alignment Map (SAM) format to Binary Alignment Map (BAM) format.
featureCounts version 1.6.3 was used to count the mapped reads using BAM files.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

source_name: soleus muscle

growth_protocol: The mice were housed in groups of up to six per cage at 23 ± 3 °C on a 12-hour light (starting at 7:00 a.m.) and 12-hour dark cycle.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Total RNA was then subjected to polyadenylated mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat No. E7490, New England Biolabs, Ipswich, Massachusetts, USA). Strand-specific RNA-seq libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Cat No. E7760, New England Biolabs).

treatment_protocol: The mice were fed HFD (60 kcal% fat, D12492, Research Diets Inc., New Brunswick, New Jersey, USA) from eight weeks of age until the time of dissection.

value: soleus muscle

value: wild type

value: male

value: HFD 12w


title: soleus muscle, HFD 12w, rep5

description: Library name: sol_12w_5


title: soleus muscle, HFD 12w, rep1

description: Library name: sol_12w_1


title: soleus muscle, HFD 10w, rep5

description: Library name: sol_10w_5

value: HFD 10w


title: soleus muscle, HFD 12w, rep6

description: Library name: sol_12w_6


title: soleus muscle, HFD 12w, rep3

description: Library name: sol_12w_3


title: soleus muscle, HFD 10w, rep6

description: Library name: sol_10w_6


title: soleus muscle, HFD 10w, rep4

description: Library name: sol_10w_4


title: soleus muscle, HFD 12w, rep2

description: Library name: sol_12w_2


title: soleus muscle, HFD 10w, rep3

description: Library name: sol_10w_3


title: soleus muscle, HFD 8w, rep6

description: Library name: sol_8w_6

value: HFD 8w


title: soleus muscle, HFD 8w, rep5

description: Library name: sol_8w_5


title: soleus muscle, HFD 8w, rep3

description: Library name: sol_8w_3


title: soleus muscle, HFD 8w, rep1

description: Library name: sol_8w_1


title: soleus muscle, HFD 7w, rep6

description: Library name: sol_7w_6

value: HFD 7w


title: soleus muscle, HFD 10w, rep2

description: Library name: sol_10w_2


title: soleus muscle, HFD 8w, rep2

description: Library name: sol_8w_2


title: 4h_CNT_F_S_S2

description: Library name: S2

value: Super cervical ganglion

value: Balb/c


title: soleus muscle, HFD 7w, rep5

description: Library name: sol_7w_5


title: soleus muscle, HFD 7w, rep3

description: Library name: sol_7w_3


title: soleus muscle, HFD 8w, rep4

description: Library name: sol_8w_4


title: soleus muscle, HFD 10w, rep1

description: Library name: sol_10w_1


title: soleus muscle, HFD 7w, rep4

description: Library name: sol_7w_4


title: soleus muscle, HFD 6w, rep5

description: Library name: sol_6w_5

value: HFD 6w


title: soleus muscle, HFD 7w, rep2

description: Library name: sol_7w_2


title: soleus muscle, HFD 6w, rep6

description: Library name: sol_6w_6


title: soleus muscle, HFD 6w, rep4

description: Library name: sol_6w_4


title: soleus muscle, HFD 6w, rep3

description: Library name: sol_6w_3


title: soleus muscle, HFD 6w, rep2

description: Library name: sol_6w_2


title: soleus muscle, HFD 5w, rep6

description: Library name: sol_5w_6

value: HFD 5w


title: soleus muscle, HFD 5w, rep4

description: Library name: sol_5w_4


title: soleus muscle, HFD 5w, rep3

description: Library name: sol_5w_3


title: soleus muscle, HFD 5w, rep5

description: Library name: sol_5w_5


title: soleus muscle, HFD 6w, rep1

description: Library name: sol_6w_1


title: soleus muscle, HFD 5w, rep2

description: Library name: sol_5w_2


title: soleus muscle, HFD 4w, rep4

description: Library name: sol_4w_4

value: HFD 4w


title: soleus muscle, HFD 4w, rep5

description: Library name: sol_4w_5


title: soleus muscle, HFD 4w, rep3

description: Library name: sol_4w_3


title: soleus muscle, HFD 4w, rep1

description: Library name: sol_4w_1


title: soleus muscle, HFD 4w, rep2

description: Library name: sol_4w_2


title: soleus muscle, HFD 3w, rep6

description: Library name: sol_3w_6

value: HFD 3w


title: soleus muscle, HFD 3w, rep4

description: Library name: sol_3w_4


title: soleus muscle, HFD 3w, rep1

description: Library name: sol_3w_1


title: soleus muscle, HFD 7w, rep1

description: Library name: sol_7w_1


title: soleus muscle, HFD 2w, rep5

description: Library name: sol_2w_5

value: HFD 2w


title: soleus muscle, HFD 2w, rep4

description: Library name: sol_2w_4


title: soleus muscle, HFD 2w, rep3

description: Library name: sol_2w_3


title: soleus muscle, HFD 3w, rep5

description: Library name: sol_3w_5


title: soleus muscle, HFD 3w, rep2

description: Library name: sol_3w_2


title: soleus muscle, HFD 2w, rep6

description: Library name: sol_2w_6


title: soleus muscle, HFD 2w, rep2

description: Library name: sol_2w_2


title: soleus muscle, HFD 10d, rep6

description: Library name: sol_10d_6

value: HFD 10d


title: soleus muscle, HFD 10d, rep5

description: Library name: sol_10d_5


title: soleus muscle, HFD 4w, rep6

description: Library name: sol_4w_6


title: soleus muscle, HFD 5w, rep1

description: Library name: sol_5w_1


title: soleus muscle, HFD 10d, rep3

description: Library name: sol_10d_3


title: soleus muscle, HFD 10d, rep4

description: Library name: sol_10d_4


title: soleus muscle, HFD 1w, rep4

description: Library name: sol_1w_4

value: HFD 1w


title: soleus muscle, HFD 10d, rep2

description: Library name: sol_10d_2


title: soleus muscle, HFD 1w, rep5

description: Library name: sol_1w_5


title: soleus muscle, HFD 1w, rep3

description: Library name: sol_1w_3


title: soleus muscle, HFD 1w, rep6

description: Library name: sol_1w_6


title: soleus muscle, HFD 1w, rep1

description: Library name: sol_1w_1


title: soleus muscle, HFD 3w, rep3

description: Library name: sol_3w_3


title: soleus muscle, HFD 3d, rep5

description: Library name: sol_3d_5

value: HFD 3d


title: soleus muscle, HFD 3d, rep3

description: Library name: sol_3d_3

value: soleus muscle


title: soleus muscle, HFD 10d, rep1

description: Library name: sol_10d_1

value: wild type


title: soleus muscle, HFD 3d, rep4

description: Library name: sol_3d_4

value: male


title: soleus muscle, HFD 3d, rep1

description: Library name: sol_3d_1


title: soleus muscle, HFD 3d, rep2

description: Library name: sol_3d_2


title: soleus muscle, HFD 1d, rep6

description: Library name: sol_1d_6

value: HFD 1d


title: soleus muscle, HFD 2w, rep1

description: Library name: sol_2w_1


title: soleus muscle, HFD 1d, rep5

description: Library name: sol_1d_5


title: soleus muscle, HFD 1d, rep1

description: Library name: sol_1d_1


title: soleus muscle, HFD 1d, rep2

description: Library name: sol_1d_2


title: soleus muscle, HFD 0d, rep4

description: Library name: sol_0d_4

value: HFD 0d


title: soleus muscle, HFD 0d, rep5

description: Library name: sol_0d_5


title: soleus muscle, HFD 0d, rep3

description: Library name: sol_0d_3


title: soleus muscle, HFD 0d, rep2

description: Library name: sol_0d_2


title: soleus muscle, HFD 1w, rep2

description: Library name: sol_1w_2


title: soleus muscle, HFD 0d, rep1

description: Library name: sol_0d_1


title: soleus muscle, HFD 3d, rep6

description: Library name: sol_3d_6


title: pituitary gland, HFD 10w, rep6

description: Library name: pit_10w_6

source_name: pituitary gland

value: pituitary gland

value: HFD 10w


title: pituitary gland, HFD 12w, rep4

description: Library name: pit_12w_4

value: HFD 12w