title: X1

source_name: X1-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification


title: X15

status: Public on Jul 31 2025

type: SRA

city: Guangxi

first: Jun

last: Meng

address: ShuangYong Road

country: China

institute: Guangxi Medical University

description: Fresh frozen Spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: X15-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

growth_protocol: A maximum of five adult mice weighing up 17 to 20 g were homed in a SPF single cage, maintaining the ambient temperature at 20–27 °C, the humidity at 40%-70% and a 12-h light/12-h dark cycle.

extract_protocol:
After the mice were euthanized, their brain tissue was collected and rinsed with PBS, water was removed with absorbent paper, and their intestinal contents were collected. Frozen in liquid nitrogen for 15 minutes at -80°C.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

treatment_protocol: Lentivirus was used to induce a mouse glioblastoma model, and then the mice were subjected to intermittent fasting treatment and different experimental interventions on the basis of this treatment.

tag: tissue

value: brain

tag: genotype

value: wild-type

tag: treatment

value: GBM+IF


title: pTKO_E185_ht_2

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Library name: pTKO_E185_ht_2

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matrices were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed using DESeq2 package. Only genes with adjusted P value (for cell lines) or P value (for organs) < 0.05, fold change > 2 and basemean > 12.5 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. To evaluate the transcription level of transposons, the clean data were mapped to mm10 using Hisat2 with the parameters -k 100 -no-unal -no-mixed -no-discordant. Then the TEcount function of TE transcritps (v2.2.1) was used to count reads from TE with the parameters -mode multi. Differentially expressed TE analysis was performed using DESeq2 package. Only TEs with a P value < 0.05 and fold change > 2 were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: comma or tab separated values file, raw counts for gene expression.

molecule: polyA RNA

source_name: heart

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for following library preparation. RNA-Seq libraries were prepared with VAHTS mRNA-Seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 instrument. For Smart-Seq2 library preparation, the cDNA was synthesized and amplified using the Single Cell Full-Length mRNA-Amplification Kit (Vazyme, N712). The full-length cDNA was assessed for quality and quantity using QIAxcel Advanced (QIAGEN) and Qubit 3.0 (ThermoFisher). Then RNA-Seq libraries were constructed from 1 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Amplified libraries were purified with VAHTS DNA Clean Beads (Vazyme, N411) and sequenced on the Illumina NovaSeq 6000.

value: heart

value: pTKO

tag: batch


title: 4 cell embryo-3, siRNA for SON

city: Chang Chun

first: Sheng

last: Zhang

address: xi an da lu 5333 hao

institute: Jilin University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to the reference mouse genome (version GRCm38) using HISAT2 (version 2.0.5)
expression levels were calculated as Fragments per Kilobase of transcript per Million reads(FPKM) using StringTie (version 1.3.3b)
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: 4 cell embryo

extract_protocol:
4 cell embryos  are put into lysis solution for library construction. Lysis solution is from  Annoroad company.
We adopted the Smart-Seq2 single-cell transcriptome sequencing strategy to construct the cDNA library required for sequencing.

value: 4 cell embryo

tag: cell type

value: early embryo

value: siRNA for SON


title: pTKO_E185_ht_1

description: Library name: pTKO_E185_ht_1


title: HEK293T cells, Ev_MeDIP

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

library_source: genomic

data_processing:
Adapter trimming and Quality filtering of paired reads using fastp version 0.23.4 at default parameters
Paired end-to-end alignment using Bowtie2 at default parameters after imposing a read length constraint of minimum 100bp and maximum 1000bp. Alignment mean read length = 192bp for Lc_MeDIP, 201bp for Ac_MeDIP, 227bp for Gg_MeDIP,282bp for Hs_MeDIP, 233bp for Ev_MeDIP, 221bp for Input (MeDIP).
Bigwigs were created using bamCoverage by deeptools version 3.5.1 at default parameters in bin size of 50bp
Assembly: hg38 unmasked
Supplementary files format and content: Bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10 % FBS and 1% antibiotic-antimycotic at 37°C and 5% CO2.

extract_protocol:
MeDIP-Seq: After 72 h of transfection, cells over-expressing Lc, Ac, Gg, Hs and Ev were harvested for genomic DNA isolation using phenol-chloroform-isoamyl alcohol extraction method. Genomic DNA was sonicated to obtain 700-1000 bp fragments. 1µg fragment DNA was end repaired using NEBNext Ultra II End Repair/dA-Tailing Module (NEB #E7546). PCR adapters from Oxford Nanopore Technologies (ONT #SQK-PSK004) were ligated to end repaired DNA using NEB Blunt/TA Ligase Master Mix (NEB #M0367). 1x MeDIP master mix (10 mM Sodium Phosphate Buffer, 0.14 M NaCl and 0.05% TritonX-100) was added to adapter ligated DNA which was then denatured at 95℃ for 5 mins followed by snap chilling on ice. An antibody cocktail against 5-methylcytosine (EMD Millipore #MABE146, Sigma #SAB2702243 and Novus Biologicals #NBP2-42813) was added to snap-chilled DNA and was incubated at 4℃ overnight. Protein G Plus/Protein A Agarose beads were added to the mix followed by incubation at room temperature for 2 h. Then beads were collected by centrifugation in a separate tube and were washed thrice with 1x MeDIP master mix buffer and were subjected to Proteinase K (Sigma #P2308) digestion at 56℃ for 2 h. The slurry was centrifuged and immunoprecipitated DNA in the supernatant was collected into new tubes. This DNA was subjected to 18 cycles of PCR using whole genome primers (ONT #SQK-PSK004) and LongAmp Hot Start Taq 2X Master Mix (NEB #M0533).
MeDIP-Seq: Library preparation was done using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB #E7645, #E7103) as per manufacturer’s instruction. DNA was quantified using Qubit and quality assessment was done using TapeStation. DNA was sequenced on Illumina HiSeq 2500 platform

treatment_protocol: HEK293T cells were transduced with the following shRNA lentiviruses: non-targeting (CT), Human CGGBP1-targeting (KD). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. CT cells were then transfected with Hs overexpression plasmid and empty pcDNA3.1(+) plasmid using Polyplus JetOptimus (cat #101000051) transfection reagent (5ug plasmid per 10cm dish). HEK293T KD cells were transfected with Lc, Ac, Gg over-expression plasmids using the same protocol as for Hs.

tag: cell line

tag: cggbp1 overexpression

value: Ev

tag: antibody


title: X3

source_name: X3-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

value: GBM


title: pTKO_E185_brain_2

description: Library name: pTKO_E185_brain_2

source_name: brain


title: patient1,adjacent_normal_tissue,PRAISE

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description: Ribosomes removed RNA

library_source: other

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, PCR duplicates were removed using seqkit v2.4.0. The 8-bp UMIs the 6-mer following the UMI were excised from the deduplication reads using UMI_tools v1.1.4. To enhance the accuracy of the mapping results, we trimmed the 6-mer sequence to minimize such errors.
All fastq files were aligned to the human reference genome hg38, using HISAT2 v2.2.1.
The following data analysis procedures for site identification are mainly referred to PRAISE
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: other

source_name: adjacent normal

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
Five hundred nanogram fragmented total RNA was subjected to bisulfite treatment as previous references (PMID: 36997645; 36302989; 37968414). The BS treated RNA was labeled as ‘treat’ sample, while the BS untreated RNA was labeled as ‘Input’ sample. Ten nanogram ‘treated’ RNA sample and 10 ng ‘Input’ RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v3—Pico Input Mammalian (Takara Bio, 634485) according to the manufacturer’s protocol with several modifications as previous reference. All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).
PRAISE (PMID: 36997645), BID-seq (PMID: 36302989; PMID: 37968414)

value: adjacent normal

value: colorectum

value: PRAISE


title: 4 cell embryo-3, control

value: control


title: 4 cell embryo-1, siRNA for SON


title: HEK293T cells, Gg_MeDIP

value: Gg

value: EMD Millipore #MABE146, Sigma #SAB2702243 and Novus Biologicals #NBP2-42813


title: pWT_E185_ht_2

description: Library name: pWT_E185_ht_2

value: pWT


title: 4 cell embryo-2, siRNA for SON


title: patient3,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: HEK293T cells, Hs_MeDIP

value: Hs


title: pWT_E185_ht_1

description: Library name: pWT_E185_ht_1


title: patient2,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: HEK293T cells, Ac_MeDIP

value: Ac


title: 4 cell embryo-2, control


title: HEK293T cells, Lc_MeDIP

value: Lc


title: KO_Stage1_4

city: Memphis

first: Asha Jacob

last: Jannu

state: TN

address: Inspiration4 Advanced Research Center

department: Developmental Neurobiology

country: USA

institute: St Jude Children's Research Hospital

data_processing:
With input of read counts for all samples, counts per million mapped reads (CPMs) were obtained by using the function cpm in the edgeR package.
Genes were removed when the corresponding CPMs for all samples were smaller than the CPM whose corresponding raw read count is 10. Then, the top 3000 most variable genes were selected by ranking the mean absolute deviation (MAD) of the log2-transformed CPMs in descending order.
Based on these most variable genes, the PCA analysis was performed on the log2-transformed CPMs by using the prcomp function available in the standard R language. The top two principal components (PCs) were used to draw the PCA figures.
Assembly: hg19
Supplementary files format and content: count and FPKM files

source_name: retinal organoid

growth_protocol: Retinal organoids derived from hESC line H9 VSX2-GFP/CRX-TdTomato were generated using an established protocol from the Laboratory of Dr David Gamm.

extract_protocol:
RNA was extracted from individual TRIzol (Life Technologies) preparations via a phenol-chloroform extraction.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).

value: retinal organoid

value: KO

tag: Stage

value: Stage 1


title: pTKO_E185_brain_1

description: Library name: pTKO_E185_brain_1

value: brain

value: pTKO


title: 4 cell embryo-1, control

value: 4 cell embryo

value: early embryo


title: R0_Stage3_2

value: Stage 3


title: XYA0516B

city: changsha

first: xi

last: zhang

state: hunan

address: xiangya road

institute: xiangya hospital, central south university

data_processing:
Reads were aligned to the human genome (hg38) using STAR. Differential expression was analyzed using DESeq2. Genome build: hg38
The raw data was processed using the bcl2fastq (v2.20).
The fastp (0.20.0) software was used for quality control, adapters trimming, filtering by quality, and read pruning to obtain clean reads.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files include FPKM values for each samples
Supplementary files format and content: tab-delimited excel files include raw counts for each samples

source_name: Temporal lobe

growth_protocol: standard growth conditions

extract_protocol:
Trizol extraction
Libraries were prepared using the RNA-seq Library Prep Kit following the standard protocol provided by the manufacturer.

value: Temporal lobe

tag: disease state


title: patient5,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

value: adjacent normal

value: colorectum

value: PRAISE


title: R3_Stage3_3


title: XYA0513A

value: control


title: pWT_E185_brain_1

description: Library name: pWT_E185_brain_1

value: pWT


title: PL_179_EV

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description:
Library name: PL_179_EV
PDAC

data_processing:
FASTX-Toolkit was used to quality-filter reads and cutadapt was used to remove adaptor sequences. Fastqc was used to ensure high quality sequencing data
Reads with identical insert and UMI were collapsed using seqcluster collapse
Filtered reads were mapped using Bowtie to human miRNAs from miRBase v22
Assembly: human miRBase v22
Supplementary files format and content: Tab delimited txt file with miRNA expression levels in reads per million (RPM) relative to total number of filtered reads in each sample. Samples as columns, miRNAs as rows

source_name: Plasma EV

growth_protocol: Peripheral fasting blood samples were drawn via a freshly inserted 18-22G peripheral cannula or 21-23G butterfly syringe into BD K2 Ethylenediaminetetraacetic acid (EDTA) lined tubes and processed within 4 h. Blood was centrifuged at 2,500 x g for 10 min at room temperature to remove cells and aliquot the resulting platelet-free supernatant (plasma). The latter was frozen at -80°C until required.

extract_protocol:
Samples obtained by SEC for RNA extraction were concentrated using Vivaspin Turbo 4 centrifugal concentrators with 10 kDa molecular weight cut-off (Sartorius). A fresh device was used for each sample, loaded with an equal volume and spun at 4,000 g for 1 hour at 4°C. Samples were transferred immediately to a 1.5 mL Eppendorf safe lock microtube and weighed using a fine weighing scale. These values were plotted against a standard curve generated using PBS and an estimated volume calculated for subsequent reactions. Total RNA from plasma samples (total and EV) were extracted using the phenol-free miRNeasy Serum/Plasma advanced kit according to manufacturer’s instructions. Stations were prepared for RNA extraction using RNaseZap RNase decontamination solution (Thermo Fisher Scientific). Lysis involved addition of proprietary Buffer RPL at a volumetric ratio of 10:3 and vortexed before incubation at RT for 3 minutes. 1 µL of Buffer RPP per 3 µL of Buffer RPL was added, vortexed for 20 seconds and incubated at RT for 3 minutes. Samples were centrifuged at 12,000 x g for 3 minutes at RT to obtain a pellet and an equal volume (Sample Volume + Buffer RPL + Buffer RPP) of isopropanol added to the supernatant. Up to 700 µL of the sample was transferred to an RNeasy UCP MinElute spin column (QIAGEN) and centrifuged at 8,000 x g for 30 seconds at RT. This was repeated using the remainder of the sample in 700 µL aliquots. Optional on-column DNase digestion was not performed. 700 µL of Buffer RWT was added to the RNeasy UCP MinElute spin column and centrifuged at 8,000 x g for 30 seconds at RT with the flow-through discarded. 500 µL of Buffer RPE was then added to the RNeasy UCP MinElute spin column and centrifuged at 8,000 x g for 30 seconds at RT with the flow-through discarded. Finally, 500 µL of 80% ethanol was added to the RNeasy UCP MinElute spin column and centrifuged at 8,000 x g for 2 minutes at RT with the flow-through discarded. RNA remaining in the spin column was transferred to a fresh 2 mL collection tube after drying the membrane by spinning the column with the lid open at 16 000 x g for 5 minutes. RNA was eluted with 14 µL of RNase-free water and used immediately, or frozen at -80°C until required.
RNA samples were prepared for small RNA sequencing using Qiagen’s QIAseq small RNA Library Prep kit according to manufacturer protocol. 5 µL of the RNA eluate was used in low input samples (i.e. EV-RNA). The finished libraries were quality controlled using an Agilent Bioanalyzer 2100 and quantified by use of qPCR. Libraries were pooled and sequenced on an NextSeq 500 system (Illumina, San Diego, USA) using the default single-end 75 base pair protocol to include integrated unique molecular indices (UMIs).

treatment_protocol: 1 mL of plasma was thawed on ice, after which size exclusion chromatography (SEC)  was performed using commercially available qEVoriginal 70nm SEC columns (iZON Science, UK ) according to the manufacturer’s protocol. Plasma samples were loaded onto the column and eluted with PBS (pH 7.4; Sterile-filtered, Sigma Aldrich). The eluate was collected in 30 sequential fractions of 0.5 mL, which were used immediately for EV characterisation and RNA extraction, or frozen at -80°C until required. For the purposes of analysis, we deemed fractions 7-10 as EV-enriched (EV).

value: Plasma EV

value: EV isolation


title: PL_161_EV

description:
Library name: PL_161_EV
PDAC


title: R3_Stage2_4

value: Stage 2


title: pWT_E185_brain_2

description: Library name: pWT_E185_brain_2


title: pTKO_E185_lung_2

description: Library name: pTKO_E185_lung_2

source_name: lung

value: lung


title: XY171229


title: pWT_E185_lung_2

description: Library name: pWT_E185_lung_2


title: patient6,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: XY180413


title: WT_Stage1_2

value: retinal organoid

value: DR

value: WT


title: R3_Stage1_5

value: Stage 1


title: PL_128_EV

description:
Library name: PL_128_EV
PDAC


title: KO_Stage1_3

value: KO


title: R0_Stage2_3


title: PL_153_EV

description:
Library name: PL_153_EV
PDAC


title: pTKO_E185_lung_1

description: Library name: pTKO_E185_lung_1

value: pTKO


title: PL_133_EV

description:
Library name: PL_133_EV
PDAC


title: R3_Stage1_6


title: pWT_E185_lung_1

description: Library name: pWT_E185_lung_1


title: XY161222

value: brain


title: TLE7_DG

value: Temporal lobe

value: Temporal lobe epilepsy


title: pTKO_E185_kid_1

description: Library name: pTKO_E185_kid_1

source_name: kidney

value: kidney


title: pTKO_E185_kid_2

description: Library name: pTKO_E185_kid_2


title: pWT_E185_kid_2

description: Library name: pWT_E185_kid_2


title: TLE6_DG


title: TLE8_DG


title: PL_115_EV

description:
Library name: PL_115_EV
Benign


title: PL_119_EV

description:
Library name: PL_119_EV
PDAC


title: TLE5_DG


title: KO_Stage2_1


title: XY171205


title: TLE3_DG


title: PL_129_EV

description:
Library name: PL_129_EV
Benign


title: pWT_E185_kid_1

description: Library name: pWT_E185_kid_1


title: pTKO_E185_liv_2

description: Library name: pTKO_E185_liv_2

source_name: liver

value: liver


title: KO_Stage2_2


title: R3_Stage2_3


title: TLE1_DG


title: PL_095_EV

description:
Library name: PL_095_EV
Benign


title: WT_Stage2_3


title: PL_106_EV

description:
Library name: PL_106_EV
Benign


title: pTKO_E185_liv_1

description: Library name: pTKO_E185_liv_1


title: WT_Stage2_2


title: LF1 cells, senescent, replicate 3

city: Providence

first: Nicola

last: Neretti

state: RI

address: 225 Dyer St.

institute: Brown University

data_processing:
The resulting fastqs were aligned to hg38 with STAR.
Features were counted with HTSeq and assessed for differential expression with EdgeR.
Replicates were checked using EdgeR’s MDS function.
Assembly: hg38
Supplementary files format and content: pro_qui_sen_ft_counts.txt: feature counts
Supplementary files format and content: *_pro_out.txt: edgeR output

growth_protocol: Cells were passaged in regular growth media (HAMS F10, 15% FBS, and 1x of Penicillin Streptomycin and Glutamine) and maintained at 37 degrees Celsius at 5% CO2 and 2.5% O2.

extract_protocol:
Total RNA for proliferating and RS samples (extracted using trizol) and cell pellets for quiescent cells were sent to Azenta. where libraries were prepared using a stranded ribosomal depletion method. The proliferating and RS cells were split across two HiSeq lanes. The quiescent cells were run on one HiSeq lane.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

treatment_protocol:
Proliferating cells were harvested at 60 - 80% confluency.
Quiescent cells were obtained by allowing cells to reach 100% confluency and subsequently incubating cells in serum free media for 1-2 days.
Replicative senescent (RS) cells were passaged in regular growth media until replicative exhaustion. These cells were maintained in the senescent state for 3-4 months.

value: lung fibroblasts

value: Replicative Exhaustion


title: pWT_E185_liv_2

description: Library name: pWT_E185_liv_2

value: pWT


title: pWT_E185_liv_1

description: Library name: pWT_E185_liv_1


title: WT_Stage2_1


title: PL_116_EV

description:
Library name: PL_116_EV
PDAC

value: Plasma EV

value: EV isolation


title: PL_107_EV

description:
Library name: PL_107_EV
PDAC


title: KO_Stage1_2


title: LF1 cells, senescent, replicate 1


title: PL_082_EV

description:
Library name: PL_082_EV
Benign


title: pIR_B_4

description: Library name: pIR_B_4

source_name: blastocyst

value: blastocyst

value: pIR


title: R0_Stage1_4

value: retinal organoid


title: PL_074_EV

description:
Library name: PL_074_EV
PDAC


title: LF1 cells, quiescent, replicate 3

value: WT

value: Contact Inhibition + Serum Starvation


title: pIR_B_3

description: Library name: pIR_B_3


title: R3_Stage1_3

value: Stage 1


title: PL_071_EV

description:
Library name: PL_071_EV
Benign


title: KO_Stage1_1


title: pIR_B_1

description: Library name: pIR_B_1


title: LF1 cells, quiescent, replicate 2


title: LF1 cells, senescent, replicate 2


title: PL_084_EV

description:
Library name: PL_084_EV
Benign


title: PL_011_EV

description:
Library name: PL_011_EV
Benign


title: R0_Stage1_3


title: pWT_B_4

description: Library name: pWT_B_4


title: pWT_B_3

description: Library name: pWT_B_3


title: WT_Stage1_1

value: DR


title: PL_008_EV

description:
Library name: PL_008_EV
Benign


title: R0_Stage2_2

value: Stage 2


title: pWT_B_2

description: Library name: pWT_B_2


title: pIR_B_2

description: Library name: pIR_B_2


title: LF1 cells, proliferating, replicate 3


title: EWS502_RNA_DMSO_REP3_250313_CTTGTA_S3

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 9

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
Raw per-gene counts were calculated with HTSeq (htseq-count, v0.6.1pl) and differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Assembly: GRCh38/hg38
Supplementary files format and content: DESeq2 differential expression summary data (Excel .xlsx format)

extract_protocol:
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
rRNA depletion and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

value: DMSO

tag: timepoint


title: R3_Stage2_2


title: EWS502_RNA_DMSO_REP2_250313_GGCTAC_S2

description: Library name: Sample 8


title: LF1 cells, proliferating, replicate 2


title: PL_055_EV

description:
Library name: PL_055_EV
Benign


title: LF1 cells, proliferating, replicate 1


title: LF1 cells, senescent, replicate 2, Hi-C

data_processing:
The fastqs were aligned against hg38 and assembled into Hi-C maps with the Juicer pipeline version 1.6.
Replicates were checked using HiCRep at 100kb and combined using juicer's mega tool.
Compartments were called using dchic v1
Subcompartments were called using calder v2
Loops were called using juicer's hiccups
Assembly: hg38
Supplementary files format and content: *_inter.hic: hic map
Supplementary files format and content: *_differential_compartments.bedGraph: differential compartment calls
Supplementary files format and content: *_full_compartments.bedGraph: all compartment calls
Supplementary files format and content: *_collapse_compartments.txt: compartments converted to start/end (not bins)
Supplementary files format and content: *_all_sub_compartments.bed: subcompartment calls
Supplementary files format and content: *_calder2.txt: subcompartment switching between conditions
Supplementary files format and content: *_collapse_subcompartments.txt: subcompartment switching converted to start/end (not bins)
Supplementary files format and content: *_merged_loops.bedpe: loop calls
Supplementary files format and content: pro_sen_30kb.txt: pro sen compared loops calls at 30kb

extract_protocol:
All conditions (proliferating, quiescent, RS) were crosslinked with 1% PFA at room temperature for 10 minutes while still attached to cell culture plates. Crosslinking was quenched with glutamine. Cells were washed with PBS three times before being scraped into a microcentrifuge tube.
To perform Hi-C the Arima Genomics Hi-C kit was used.


title: R0_Stage2_1


title: pWT_B_1

description: Library name: pWT_B_1


title: pIR_M_4

description: Library name: pIR_M_4

source_name: morula

value: morula


title: LF1 cells, senescent, replicate 1, Hi-C


title: pIR_M_3

description: Library name: pIR_M_3


title: EWS502_RNA_dCBP1_REP2_250313_GAGTGG_S8

description: Library name: Sample 5


title: EWS502_RNA_dCBP1_REP1_250313_CGTACG_S7

description: Library name: Sample 4


title: R3_Stage1_2


title: R0_Stage1_2


title: EWS502_RNA_A485_REP3_250313_GTTTCG_S6

description: Library name: Sample 3


title: pIR_M_1

description: Library name: pIR_M_1


title: LF1 cells, quiescent, replicate 2, Hi-C


title: EWS502_RNA_DMSO_REP1_250313_TAGCTT_S1

description: Library name: Sample 7


title: LF1 cells, senescent, replicate 3, Hi-C


title: LF1 cells, quiescent, replicate 1


title: R3_Stage2_1


title: R3_Stage1_1


title: LF1 cells, quiescent, replicate 1, Hi-C


title: LF1 cells, proliferating, replicate 3, Hi-C


title: pWT_M_3

description: Library name: pWT_M_3


title: pWT_M_2

description: Library name: pWT_M_2


title: pIR_M_2

description: Library name: pIR_M_2


title: CTNNB1 knock out clone 9-2 at neural precursor cell stage

city: Adelaide

first: Mark

middle: A

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

data_processing:
Real-time basecalling was performed by the Illumina NovoSeq 6000 built-in software, RTA, and binary bcl data was produced. Demultiplexing performed by bcl2fastq (v2.17; Illumina) installed on high performance cluster to output FASTQ files. During the sequencing process, chastity value of the first 25 cycles were caculated, and reads with less than 2 bases with a chastity value more than 0.6 passsed filtering.
Read counts were generated from RNA-sequencing reads by pseudo-alignment to transcripts from GENCODE using the pre-built index for Salmon v1.10.0 available from the RefGenie server.
Read counts were mapped to ENSEMBL gene and transcript IDs using the tximeta package v1.12.4; R version 4.1.2
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set RefGenie Digest 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4
Supplementary files format and content: transcript.counts.txt.gz: gzipped, tab delimited text file containing read counts for all transcripts annotated against ENSEMBL Homo sapiens release 97 transcript ID.
Supplementary files format and content: gene.counts.txt.gz: gzipped, tab delimited text file containing read counts for all transcripts collapsed to genes and annotated against ENSEMBL Homo sapiens release 97 gene ID.

source_name: embryonic stem cell

growth_protocol: Directed differentiation of hESCs into cortical neurons was performed using dual SMAD inhibition (Shi et al., 2012) with the modifications described in Homan et al. (2018). SMAD inhibitors; SB431542 (10 µM; STEMCELL Technologies, Cat#72232) and Dorsormorphin (1 µM; Sigma Aldrich, Cat#P5499) were used to promote neural lineages.

extract_protocol:
Pelleted cells were homogenized in TRIzol reagent (Invitrogen, Cat#15596026) and RNA was isolated using RNeasy kit (QIAGEN, Cat#74104). Residual genomic DNA was removed on column by incubation with DNase I (QIAGEN, Cat#79254). RNA quality was assessed by nanodrop UV spectroscopy and Agilent Tapestation electrophoresis.
Library preparation and RNA-sequencing was performed by GENEWIZ (now Azenta). Libraries were prepared from total RNA with ribosomal RNA depletion.

value: embryonic stem cell

value: Neural precursor

tag: developmental stage

value: day 23


title: CTNNB1 knock out clone 9-1 at neural precursor cell stage


title: Replicate 3, TF-1 cells expressing TPOR and CSF2RB treated with TPO

city: Oxford

first: David

last: Cruz

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine, Oxford University

description: Library name: TRNA32

data_processing:
150-bp paired-end FASQ files were processed with the NexFlow nf-core/rnaseq v3.14.0 (https://doi.org/10.5281/zenodo.1400710) pipeline
Assembly: GRCh38
Supplementary files format and content: RSEM gene-level quantification results for each sample, STAR via RSEM output file

source_name: Hematopoietic

growth_protocol: TF1 cells were cultured in RPMI basal media supplemented with 10% FBS and 1% Pen/Strep. TF1 cells were additionally supplemented with 2 ng/mL of recombinant human GM-CSF (Cat No: 300-03, Prepotech)

extract_protocol:
RNA was isolated with the RNEasy kit in triplicates 3 hrs after being treated with TPO.
RNA polyA selection, library preparation and sequencing were performed by GENEWIZ/Azenta with their Standard RNA-Seq services. cDNA from each sample was indexed and sequenced to 30E6 paired end reads

treatment_protocol: Cells were harvested by centrifugation and washed 3 times with phosphate buffer saline (PBS) to remove any trace of cytokines from the culture medium.  Cells were re-suspended in assay medium (RPMI supplemented with 10% FBS) at 50.000 cells/mL. 2.500 cells (50 uL at 5E4  cells/mL) were seeded per well in 96-wells plates pre-filled with 50 uL of assay medium or not with indicated concentrations of recombinant human TPO (Miltenyi, cat no: 130-095-745).

value: Hematopoietic

value: Transformed leukemic cell

value: TPOR and CSF2RB

value: TPO 100 ng/ml

tag: time

value: 13 hours


title: CTNNB1 knock out clone 7-1 at neural precursor cell stage


title: pWT_M_1

description: Library name: pWT_M_1

value: pWT


title: pIR_2C_4

description: Library name: pIR_2C_4

source_name: 2C embryo

value: 2C embryo

value: pIR


title: EWS502_RNA_A485_REP2_250313_AGTTCC_S5

description: Library name: Sample 2


title: Replicate 3, TF-1 cells expressing TPOR and EV no treatment

description: Library name: TRNA30

value: TPOR and Empty Vector

value: No treatment

value: 12 hours


title: HEK293T cells, Input_MeDIP

value: Input

value: not applicable


title: patient4,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

value: adjacent normal

value: colorectum

value: PRAISE


title: pIR_2C_3

description: Library name: pIR_2C_3


title: Pnx-sham, IP

city: Chengdu

first: Liyin

state: Sichuan

address: Remin nan Road

institute: Sichuan University

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Then methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: GRCm39
Supplementary files format and content: bigwig files and fastq files

source_name: right lobe of lung

extract_protocol:
For mouse m6A RNA-IP-seq, we started with ~200–300μg of total RNA of CD31+CD45- ECs isolated from lung 0 day and 7 days after PNX, using magnetic beads.
The NEBNext® Ultra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without immunoprecipitation, as well as IP RNA samples after immunoprecipitation. m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads. Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.

value: right lobe of lung

value: primary cells

value: lung endothelial cells

value: Wild type

value: Sham


title: EWS502_RNA_A485_REP1_250313_AGTCAA_S4

description: Library name: Sample 1


title: pIR_2C_2

description: Library name: pIR_2C_2


title: LF1 cells, quiescent, replicate 3, Hi-C

value: lung fibroblasts

value: WT

value: Contact Inhibition + Serum Starvation


title: CTNNB1 knock out clone 10-1 at neural precursor cell stage

value: embryonic stem cell

value: Neural precursor

value: day 23


title: LF1 cells, proliferating, replicate 2, Hi-C


title: Replicate 3, TF-1 cells expressing TPOR and EV treated with TPO

description: Library name: TRNA29

value: Hematopoietic

value: Transformed leukemic cell

value: TPOR and Empty Vector

value: TPO 100 ng/ml

value: 11 hours


title: Pnx-sham, Input


title: Pnx-7d, IP


title: Replicate 2, TF-1 cells expressing TPOR and CSF2RB no treatment

description: Library name: TRNA24

value: TPOR and CSF2RB

value: No treatment

value: 10 hours


title: Heterozygous CTNNB1 knockout line 20-2 at neural precursor cell stage


title: Heterozygous CTNNB1 knockout line 7-1 at neural precursor cell stage


title: Replicate 2, TF-1 cells expressing TPOR and CSF2RB treated with TPO

description: Library name: TRNA23

value: 9 hours


title: Heterozygous CTNNB1 knockout line 20-1 at neural precursor cell stage


title: LF1 cells, proliferating, replicate 1, Hi-C


title: Replicate 2, TF-1 cells expressing TPOR and EV no treatment

description: Library name: TRNA21

value: 8 hours


title: pWT_2C_4

description: Library name: pWT_2C_4

value: 2C embryo

value: pWT


title: Pnx-7d, Input

value: right lobe of lung

value: primary cells

value: lung endothelial cells

value: Wild type


title: pWT_2C_3

description: Library name: pWT_2C_3


title: Heterozygous CTNNB1 knockout line 107-1 at neural precursor cell stage

value: embryonic stem cell

value: Neural precursor

value: day 23


title: ER13_Aux_2

city: New York

first: Bruno

last: Guillotin

state: NY

address: 12 Waverly Place, Floor 6

department: Biology

institute: NYU-Biology-CGSB

description: 10Xgenomics 3'end V3

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data was analyzed by Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices.
Data was integrated using the R package Seurat V3 and the default VST integration
Assembly: Arabidopsis thaliana TAIR10.38
Supplementary files format and content: csv matrix files, Seurat object

organism: Arabidopsis thaliana

source_name: Root  700um from the tip

growth_protocol: For roots confocal imaging and scRNA-seq experiments, A. thaliana transgenic lines, and mutants were grown on half-strength Murashige and Skoog (MS) medium supplemented with 1% sucrose and 1% agar at 20°C long-day conditions (16 h light/8 h darkness).

extract_protocol:
Plants were grown 7 days Arabidopsis roots were cut 700 µm above the meristem and placed in an enzyme solution optimized for Arabidopsis (Mannitol 8%, 400 mM, MES 20 mM, KCl 20 mM, CaCl2 40 mM, pH 5.8 with Tris, BSA 100 µg/ml, 1.2% cellulase “Onozuka” R10, 0.4% macerozyme R‐10 (both Yakult Pharmaceutical Industry CO.). Protoplasts were then filtered through a 20-µm cell strainer and transferred to microcentrifuge tubes for centrifugation.Protoplasts were centrifuged for 3 mins at 500 x g and the pellets were washed and resuspended in washing solution twice (Mannitol 8%, MES 20 mM, KCl 20 mM, CaCl2 10 mM, pH 5.8 with Tris, and BSA 100 µg/ml) and used immediately for single-cell RNAseq.An aliquot of protoplasts was stained with trypan blue (0.2% final) and checked on a hemocytometer under the microscope to determine cell viability and concentration before loading into the 10x Chromium.
For each experiment, 16,000 cells were loaded in a Single Cell B Chip (10x Genomics). Single-cell libraries were then prepared using the Chromium Single Cell 3´ library kit V3, following manufacturer instructions. Libraries were sequenced with Novaseq 6000 chip SP V2.5 (4 libraries per chip).

treatment_protocol: treated with IAA 1 μM for 16 h or Mock

value: Root  700um from the tip

tag: line

value: All root

tag: ecotype

value: IAA 1 μM for 16 h


title: Replicate 2, TF-1 cells expressing TPOR and EV treated with TPO

description: Library name: TRNA20

value: Hematopoietic

value: Transformed leukemic cell

value: TPOR and Empty Vector

value: TPO 100 ng/ml

value: 7 hours


title: pWT_2C_2

description: Library name: pWT_2C_2

value: 2C embryo


title: Empty vector control line 3-2 at neural precursor cell stage


title: ER13_Aux_1

description: 10Xgenomics 3'end V3


title: Replicate 1, TF-1 cells expressing TPOR and CSF2RB no treatment

description: Library name: TRNA15

value: TPOR and CSF2RB

value: No treatment

value: 6 hours


title: pWT_2C_1

description: Library name: pWT_2C_1

value: pWT


title: pIR_2C_1

description: Library name: pIR_2C_1

value: pIR


title: Empty vector control line 30-1 at neural precursor cell stage

value: embryonic stem cell


title: ER13_Ctr_2

description: 10Xgenomics 3'end V3

value: Mock


title: STOP2

description: Library name: STOP2

source_name: AG-haESC

value: AG-haESC

value: Dnmt STOP


title: Empty vector control line 28-1 at neural precursor cell stage

value: Neural precursor

value: day 23


title: ER13_Ctr_1

description: 10Xgenomics 3'end V3

value: Root  700um from the tip

value: All root


title: Replicate 1, TF-1 cells expressing TPOR and CSF2RB treated with TPO

description: Library name: TRNA14

value: Hematopoietic

value: Transformed leukemic cell

value: 5 hours


title: Replicate 1, TF-1 cells expressing TPOR and EV no treatment

description: Library name: TRNA12

value: TPOR and Empty Vector

value: 4 hours


title: Parental H1 cell line at neural precursor cell stage


title: STOP1

description: Library name: STOP1


title: IR8_Ctr_1

description: 10Xgenomics 3'end V3


title: IR8_Aux_1

description: 10Xgenomics 3'end V3

value: IAA 1 μM for 16 h


title: TKO3

description: Library name: TKO3

value: Dnmt TKO


title: Replicate 1, TF-1 cells expressing TPOR and EV treated with TPO

description: Library name: TRNA11

value: TPO 100 ng/ml

value: 3 hours


title: TKO2

description: Library name: TKO2


title: CTNNB1 knock out clone 9-2 at neural rosette cell stage

value: embryonic stem cell

value: Neural rosette

value: day 13


title: SKNMC_ChIP_input_DMSO_REP1_250221_CCGTCC_S15

description: Library name: Sample 19

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers or single 75-mer reads) were aligned to the human genome (Gencode GRCh38/hg38 v33) using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 2000), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4). Final “deduped” .BAM files were indexed using SAMtools (v1.95).
MACS2 (v2.1.4) was used to call peaks with appropriate input samples as controls for peak calling. Peaks were called with q-value cut-off of 0.01 and broad peak mode.
Promoter-associated signal was determined using bedtools “coverage” (v2.28.0), using annotated gene body genomic intervals and TSS region intervals (-1kb to +3kb for each protein-coding transcript TSS, using gene orientation).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots; v3.1.3; regions around TSS/promoter intervals plotted using referencePoint or scaledRegion option and k=1).
Read counts were normalized were normalized using ratios of total read counts between treated and control sample pairs
Assembly: GRCh38/hg38
Supplementary files format and content: Broad IGV (.tdf) files for visualization

source_name: SK-N-MC

growth_protocol: All Ewing Sarcoma cell lines were grown in RPMI or DMEM in 10cm tissue culutre dishes. Cells were maintained by splitting 1/3 three times weekly.

extract_protocol:
In brief, cells were fixed in either 1% Formaldehyde (FA) for 10 minutes (histone modifications) or with 2uM DSG (30 mins) following by 1% FA (10 mins, for non histone proteins). Following fixation, cells were lysed and sonicated. Beads and antibody complexes were incubated with sonicated lysis overnight. ChIP material was washed 3x ChIP wash buffer and 1x TE+50mM NaCl. DNA-rpotein complexes were eluted from beads and de-crosslinked overnight. The following day, DNA clean up was performed using column purification.
1-10 ng of ChIP DNA was used for the library preparation using the SMARTer ThruPLEX DNA-Seq Kit (Takara)

treatment_protocol: Treatment/CRISPR time points are indicated per sample

value: SK-N-MC

value: DMSO


title: CTNNB1 knock out clone 9-1 at neural rosette cell stage


title: SKNMC_ChIP_input_vori_1000nM_REP1_250221_GTGAAA_S17

description: Library name: Sample 20

value: 1000nM vorinostat


title: TKO1

description: Library name: TKO1

value: AG-haESC


title: DR15_Aux_1

description: 10Xgenomics 3'end V3

value: Root  700um from the tip

value: All root


title: DR15_Ctr_1

description: 10Xgenomics 3'end V3

value: Mock


title: WT3

description: Library name: WT3

value: Dnmt WT


title: SKNMC_ChIP_input_dCBP1_100nM_vori_1000nM_REP1_250221_GTGGCC_S18

description: Library name: Sample 18

value: 100nM dCBP1, 1000nM vorinostat


title: CTNNB1 knock out clone 10-1 at neural rosette cell stage


title: DR5_Aux_3

description: 10Xgenomics 3'end V3


title: SKNMC_ChIP_input_dCBP1_100nM_REP1_250221_GTCCGC_S16

description: Library name: Sample 17

value: 100nM dCBP1


title: WT2

description: Library name: WT2


title: Heterozygous CTNNB1 knockout line 7-1 at neural rosette cell stage


title: DR5_Aux_2

description: 10Xgenomics 3'end V3

value: IAA 1 μM for 16 h


title: SKNMC_ChIP_H3K27ac_vori_1000nM_REP1_250221_CAGATC_S7

description: Library name: Sample 16

tag: chip target

tag: chip antibody

value: Abcam ab4729


title: WT1

description: Library name: WT1


title: pTKO_lu

description: Library name: pTKO_lu

data_processing:
For data processing, the clean data were mapped to N-masked mm10 mouse reference genome using Bowtie2 (v2.2.5). Duplicates were removed using Picard (v2.22.4). Reads were assigned to paternal or maternal genomes using SNPsplit (v0.3.4) with default parameters. Methylation levels were called using asTair (v3.2.6) and the single-C files of the replicates were merged together for downstream analysis. Bigwig files were generated using bedGraphToBigWig (v4) and visualized in Integrative Genomics Viewer (IGV). CGmapTools (v0.1.2) was used for DMR calling, for which only the CpG sites with at least 5×coverage were kept. And for the separate analysis of paternal or maternal genome, all reads were kept. DMRs were defined by a dynamic fragment strategy: the length (the maximal distance between two adjacent common cytosines is 100 bp, and the maximal DMR size is 1000 bp), methylation level difference (at least 20% absolute methylation level difference), P value (less than 0.05) and CpG number (at least 5 CpG sites) were considered. All the annotated information was downloaded from the UCSC Genome Browser (mm10). Promoters were defined as the regions from - 1.0 to + 0.5 kb of the TSS (Transcription Start Site).
Assembly: mm10
Supplementary files format and content: tab-separated  file, methylation level for every CpG site. Bedgraph file column headers: chr, start, end, methylation_level, modified_C, unmodified_C
Library strategy: TAPS

extract_protocol:
DNA was extracted using conventional phenol-chloroform method
Whole-genome TAPS libraries were constructed as previously described. In brief, 100 ng genomic DNA spiked with 1.0% of fully CpG-methylated lambda DNA was sonicated in EB buffer and purified by DNA clean beads to select for the desired DNA fragment size. DNA fragments were oxidized by recombinant human TET2CD twice and then reduced with pyridine borane. The library was amplified with KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems).

tag: tissue

value: lung


title: Heterozygous CTNNB1 knockout line 20-2 at neural rosette cell stage

tag: genotype


title: DR5_Ctr_3

description: 10Xgenomics 3'end V3

tag: treatment


title: CTNNB1 knock out clone 7-1 at neural rosette cell stage


title: Heterozygous CTNNB1 knockout line 20-1 at neural rosette cell stage


title: pWT_lu

description: Library name: pWT_lu


title: Empty vector control line 3-2 at neural rosette cell stage


title: SKNMC_ChIP_H3K27ac_dCBP1_100nM_vori_1000nM_REP1_250221_ACTTGA_S8

description: Library name: Sample 14


title: DR5_Ctr_2

description: 10Xgenomics 3'end V3


title: Heterozygous CTNNB1 knockout line 107-1 at neural rosette cell stage


title: SKNMC_ChIP_H3K27ac_dCBP1_100nM_REP1_250221_GCCAAT_S6

description: Library name: Sample 13


title: SKNMC_ChIP_H3K27ac_DMSO_REP1_250221_ACAGTG_S5

description: Library name: Sample 15


title: EWS502_ChIP_MLL4_dTAGv1_1uM_REP1_250313_ACTTGA_S8

description: Library name: Sample 12

value: Millipore ABE1867

value: 1uM dTAG-v1


title: pTKO1_ht

description:
Library name: pTKO1_ht
supplementary file is bedgraph file for merged bam of TKO1 and TKO2

source_name: heart

value: heart


title: pTKO2_ht

description:
Library name: pTKO2_ht
supplementary file is bedgraph file for merged bam of TKO1 and TKO2, available on GSM8857109


title: EWS502_ChIP_MLL4_DMSO_REP1_250313_CAGATC_S7

description: Library name: Sample 11


title: pWT2_ht

description:
Library name: pWT2_ht
supplementary file is bedgraph file for merged bam of WT1 and WT2, available on GSM8857107


title: DR5_Ctr_1

description: 10Xgenomics 3'end V3


title: Empty vector control line 30-1 at neural rosette cell stage

value: embryonic stem cell

value: Neural rosette

value: day 13


title: EWS502_ChIP_input_dTAGv1_1uM_REP1_250313_CGATGT_S2

description: Library name: Sample 10


title: Empty vector control line 28-1 at neural rosette cell stage


title: Mature leaf, H3K4me3, ChIP

city: Seoul

first: Cheljong

last: Hong

address: Gwanak-ro 1

department: Chemistry

country: South Korea

institute: Seoul National University

data_processing:
Raw paired-end ChIP-seq reads were aligned to the reference genome sequence of Arabidopsis thaliana (TAIR10) using Bowtie2 (v.2.3.4.3) with default parameters
Duplicated reads were eliminated using Samtools (v.1.11)
Peaks were identified using findPeaks script of HOMER suite (v.4.10.4) with -style histone -gsize 119667750 -norm 10000000 -fragLength 347 -o auto -size 150 -minDist 370 parameters for H3ac and -style histone -gsize 119667750 -norm 10000000 -fragLength 355 -o auto -size 150 -minDist 370 for H3K4me3, respectively
Identified peaks were merged using mergePeaks of HOMER suite (v.4.10.4) with default parameter
Differentially enriched peaks were identified using getDifferentialPeaks script of HOMER suite (v.4.10.4) with  -tagAdjust 185 -tagAdjustBg 175 -F 2 -P 0.01 -size 147 parameters for H3ac and -tagAdjust 180 -tagAdjustBg 185 -F 2 -P 0.01 -size 147 for H3K4me3, respectively
genome build/assembly: Arabidopsis thaliana (TAIR10)
processed data files format and content Merged peaks (region.txt)
processed data files format and contentDifferentially enriched peaks (txt)

source_name: rosette leaf

growth_protocol: Leaf explant excised from 2-week-old seedlings were incubated on CIM for 15 days. Parental leaves and leaf-explant-derived calli were harvested

extract_protocol:
anti-H3ac (06-599, Millipore) and anti-H3K4me3 (07-473, Milipore) antibodies were used to expract histone-DNA complex based on the phenol/chloroform/isoamyl alcohol-isopropanol DNA purification method
Sequencing libraries were prepared according to manufacturere's instructions of TruSeq ChIP sample Preparation (Illumina). 10 ng of ChIPed DNAs were end-repaired to create 5' phosphoryated, blunt-ended dsDNA molecules. Following end-repair, these DNA fragments were subjected to addition of a single 'A' base, and TruSeq DNA UD indexing adapters were ligated. The products were then purified and enriched through PCR to create the final library. The libraries were quantified using the TapeStation D1000 Screen Tape (Agilent Technologies)

value: rosette leaf


title: Leaf-explant-derived callus, H3K4me3, ChIP

source_name: leaf-explant-derived callus

value: leaf-explant-derived callus


title: Leaf-explant-derived callus, H3ac, ChIP


title: Parental H1 cell line at neural rosette cell stage


title: EWS502_ChIP_input_DMSO_REP1_250313_ATCACG_S1

description: Library name: Sample 9

value: DMSO


title: DR5_Aux_1

description: 10Xgenomics 3'end V3

value: Root  700um from the tip

value: All root


title: Mature leaf, H3ac, ChIP


title: EWS502_ChIP_input_DMSO_REP1_250221_GTTTCG_S19

description: Library name: Sample 8


title: CTNNB1 knock out clone 9-1 at neuroepithelial cell stage

value: Neuroepithelia

value: day 10


title: M694I_mouse

city: Nagasaki

first: Tomohiro

last: Koga

address: 1-7-1 Sakamoto

country: Japan

institute: Nagasaki University

description: Library name: Sample 2

data_processing:
Raw sequencing data was processed using Cell Ranger software v7.1.0 (10X Genomics). FASTQ files were generated using cellranger mkfastq. Reads were aligned to the mm10 reference genome (Ensembl 98) using cellranger count, generating feature-barcode matrices. Quality control and downstream analysis were performed using R package Seurat v5.0.3. Cells were filtered based on the following criteria: gene count between 200 and 6,000, UMI count between 500 and 40,000, and mitochondrial gene percentage less than 10%. Data normalization was performed using SCTransform. Dimension reduction was performed using principal component analysis followed by uniform manifold approximation and projection (UMAP). Cell clusters were annotated based on canonical marker genes. Differential expression analysis was performed using the Wilcoxon rank sum test. Pathway enrichment analysis was conducted using Metascape (http://metascape.org). Integration of samples was performed using Seurat's standard integration workflow with default parameters.
Assembly: Mouse mm10
Supplementary files format and content: Matrix Market format (.mtx) and tab-separated values (.tsv)

source_name: spleen

growth_protocol: Mice were maintained under specific pathogen-free conditions at 22 ± 2°C with 12h light/dark cycles.

extract_protocol:
Single cell suspensions were prepared by mechanical disruption of spleens followed by red blood cell lysis.
Single cell suspensions were prepared at a concentration targeting 10,000 cells per sample with confirmed viability >85% by trypan blue staining. Libraries were constructed using the Chromium Single Cell 3' v3.1 Library & Gel Bead Kit (10X Genomics, PN-1000121). Single cell suspensions were loaded onto a Chromium Controller to generate Gel Beads-in-Emulsion (GEMs), where reverse transcription was performed. After GEM-RT cleanup, cDNA was amplified followed by enzymatic fragmentation, end repair and A-tailing. Adaptor ligation was performed followed by post-ligation cleanup using SPRIselect beads. Sample indexing was performed by PCR amplification followed by another round of cleanup. Library quality was assessed using Bioanalyzer High Sensitivity DNA Kit (Agilent, cat. no. 5067-4626) for size distribution analysis and Qubit dsDNA HS Assay Kit (Thermo Fisher, cat. no. Q32854) for quantification.

value: spleen

value: splenocytes

value: M694I knock-in


title: EWS502_ChIP_input_A485_1000nM_REP1_250221_CGTACG_S20

description: Library name: Sample 7


title: PC-12, PCSK9,rep2

city: Urumqi

first: Mengjie

last: Wang

state: Xinjiang Uygur Autonomous Region

address: No.137,Liyushan South Road

department: Department of Neurology

institute: First Affiliated Hospital of Xinjiang Medical University

description: Library name: PCSK9_2nd

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
clean reads were aligned to the Rnor6.0 genome by tophat2 (version 2.0.4) allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
Assembly: Rnor6.0
Supplementary files format and content: raw counts, FPKM for each Sample

organism: Rattus norvegicus

source_name: Adrenal gland

extract_protocol:
Total RNA extraction using TRIZOL (15596-018, Ambion, USA). The RNA was treated with RQ1 DNase (Promega, USA) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544, Roche, Switzerland).
Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01, Vazyme, China) and Fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). After purification of ligation product and size fractioning to 300-500bps, the ligated products were amplified, purified, quantified, and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.

value: Adrenal gland

value: Rat pheochromocytoma cells

value: PCSK9 overexpression


title: pWT1_ht

description:
Library name: pWT1_ht
supplementary file is bedgraph file for merged bam of WT1 and WT2

value: heart


title: EWS502_ChIP_H3K27ac_DMSO_REP1_250221_AGTCAA_S12

description: Library name: Sample 6

value: Abcam ab4729


title: EWS502_ChIP_H3K27ac_A485_1000nM_REP1_250221_AGTTCC_S13

description: Library name: Sample 5


title: CON 1 PROX+ FOS+

first: Miklos

last: Toth

address: 525 E 68th St

department: Pharmacology

institute: Weill Cornell Medicine

description:
Library name: Sample_WT_Fos
10x genomics

data_processing:
Raw sequencing data was processed using the CellRanger v6.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
vHPC were dissected one hour after EPM and pooled 6 animals per sample group per replicate. Nuclei were isolated using the Minute™ Single Nucleus Isolation Kit for Neuronal Tissues/Cells, and stained with anti-PROX1 and anti-cFOS antibodies. PROX1+ FOS- and PROX1+ FOS+ nuclei were sorted for library preparation.
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: Brain

tag: Sex

value: male

tag: region

value: vDG

tag: strain

value: Swiss Webster

value: WT

value: CON FOS+

tag: batch


title: Heterozygous CTNNB1 knockout line 7-1 at neuroepithelial cell stage

value: embryonic stem cell

tag: cell line

tag: cell type


title: CON 2 PROX+ FOS-

description:
Library name: Sample_SW_WT_Prox
10x genomics

value: CON FOS-


title: PC-12, control,rep3

description: Library name: Ctrl_3rd

value: control


title: EWS502_ChIP_H3K18ac_DMSO_REP1_250221_GATCAG_S9

description: Library name: Sample 4

value: Abcam ab8580

value: DMSO


title: CON 1 PROX+ FOS-

description:
Library name: Sample_WT_Prox
10x genomics


title: PC-12, control,rep2

description: Library name: Ctrl_2nd


title: Heterozygous CTNNB1 knockout line 20-2 at neuroepithelial cell stage

value: Neuroepithelia

value: day 10


title: Heterozygous CTNNB1 knockout line 20-1 at neuroepithelial cell stage


title: PC-12, PCSK9,rep3

description: Library name: PCSK9_3rd

value: Adrenal gland

value: Rat pheochromocytoma cells


title: EWS502_ChIP_H3K18ac_A485_1000nM_REP1_250221_GGCTAC_S10

description: Library name: Sample 3


title: 5HT1AR MIA 2 PROX1+ FOS+

description:
Library name: Sample_SW_F1_Fos
10x genomics

value: MIA FOS+


title: WT_mouse

description: Library name: Sample 1

value: spleen

value: splenocytes

value: M694I WT


title: EWS502_ChIP_EP300_dTAGv1_1uM_REP1_250313_GCCAAT_S6

description: Library name: Sample 2

value: Bethyl A300-358A

value: 1uM dTAG-v1


title: 5HT1AR MIA 1 PROX+ FOS+

description:
Library name: Sample_F1_Fos
10x genomics

value: Brain

value: male

value: vDG

value: Swiss Webster


title: CTNNB1 knock out clone 7-1 at neuroepithelial cell stage

value: embryonic stem cell


title: CTNNB1 knock out clone 10-1 at neuroepithelial cell stage


title: EWS502_ChIP_EP300_DMSO_REP1_250313_ACAGTG_S5

description: Library name: Sample 1


title: Heterozygous CTNNB1 knockout line 107-1 at neuroepithelial cell stage


title: 5HT1AR MIA 2 PROX+ FOS-

description:
Library name: Sample_SW_F1_Prox
10x genomics

value: MIA FOS-


title: CTNNB1 knock out clone 9-2 at neuroepithelial cell stage


title: Empty vector control line 3-2 at neuroepithelial cell stage


title: CON 2 PROX+ FOS+

description:
Library name: Sample_SW_WT_Fos
10x genomics

value: WT

value: CON FOS+


title: LNCaP cells, C9 DHT

type: RNA

city: Kaga, Itabashi-ku

first: Takao

last: Susa

state: Tokyo

institute: Teikyo University, School of Mediocine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: HOXC9 stably expressed LNCaP cells, 10-7M of DHT treatment.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Prostate cancer LNCaP cells were maintained in monolayer cultures in RPMI-1640 phenol red free medium supplemented with 5% (v/v) fetal bovine serum and antibiotics (Life Technologies) in humidified 5% CO2–95% air at 37°C.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: At 24 h before hormone or chemical treatment, the culture media was replaced with serum-free media, and the cells were exposed to the indicated hormones with serum-free media for 24 h.

value: Human prostate cancer cells

value: LNCaP

value: HOXC9 stably expressed

value: DHT


title: 5HT1AR MIA 1 PROX+ FOS-

description:
Library name: Sample_F1_Prox
10x genomics


title: vDGC CON 4

description: Library name: SW_WT_4

data_processing:
Paired end 100 bp eRRBS sequencing, with a target of 100 million reads per sample, was performed on an Illumina NovaSeq6000 according to the manufacturer’s instructions. Bisulfite sequencing data was processed using an in-house BisSeq pipeline (https://pubmed.ncbi.nlm.nih.gov/25742437/)
bcl files generated from the sequencer were demultiplexed and converted to FASTQ files using the Illumina bcl2fastq software
Adapters were trimmed using cutadapt 2.6 and python 3.7.7
Trimmed files were aligned to the mm10 reference genome with methylation calling using Bowtie2 and Bismark v22.3
CpG reports of sites filtered for 10x coverage were used for differential methylation analysis using methylkit
Assembly: mm10
Supplementary files format and content: .txt files containing CpG reports of sites filtered for 10x coverage

extract_protocol:
vDG granule cell layer was dissected from flash frozen mouse brain and DNA extracted using Qiagen QIAamp DNA Micro Kit
Libraries were constructed by the Weill Cornell Epigenomics Core as previously described (https://pubmed.ncbi.nlm.nih.gov/25742437/)

value: vDG DGC

value: CON


title: Empty vector control line 30-1 at neuroepithelial cell stage

value: Neuroepithelia

value: day 10


title: subject6 day3 timepoint10

city: Yushima, Bunkyo-ku, Tokyo

first: Atsushi

last: Satomura

address: 5F ITP Hongo Office , 2-25-7

institute: Craif

description: Library name: library143

data_processing:
Raw sequencing reads were initially processed using UMI-tools. The 5′-end bases, corresponding to miRNA sequences located upstream of the 3’ adapter, were extracted. Simultaneously, 12 bp unique molecular identifiers (UMIs), positioned immediately downstream of the 3′-adapter, were appended to the read identifiers to enable deduplication and subsequent analyses. Reads longer than 19 bases were retained and aligned to the human miRNA reference database provided by miRge 3.0 using Bowtie v1.2.3. Alignment settings allowed no mismatches within a 25-base seed and disallowing reverse complement matches.
Assembly: miRge 3.0
Supplementary files format and content: comma separated file with raw miRNA counts

source_name: Urine

extract_protocol:
Approximately 3.5 mL of urine was centrifuged at 2,000 × g for 30 minutes at 4°C to remove cells and debris. From the resulting supernatant, 3 mL was mixed with an equal volume of Total Exosome Isolation Reagent for urine (Thermo Fisher Scientific, Waltham, MA) and incubated at room temperature on a shaker at 100 rpm for 1 hour. The mixture was then centrifuged at 3,000 × g for 1 hour at 4°C to precipitate the EVs. The resulting EV pellet was resuspended in 250 μL of phosphate-buffered saline and subjected to RNA extraction using the MagMAX mirVana Total RNA Isolation Kit with the KingFisher Apex automated system (Thermo Fisher Scientific), following the manufacturer’s instructions. RNA was initially eluted in 30 μL of elution buffer. The eluate was then concentrated at 60°C for 30 to 45 minutes using a centrifugal concentrator (Eppendorf, Hamburg, Germany) and finally resuspended in 5 μL of nuclease-free water. Purified RNA samples were stored at −80°C until further analysis.
Small RNA libraries were prepared using 5 μL of total RNA and the QIAseq miRNA Library Kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions. Library concentrations were quantified using the Qubit Flex Fluorometer (Thermo Fisher Scientific) with the Qubit™ dsDNA High Sensitivity Assay Kit. Prepared libraries were stored at −20°C until sequencing. Sequencing was performed on a NextSeq 550 system (Illumina, San Diego, CA) using 2 pmol of denatured libraries and single-end 75 bp reads, following the manufacturer’s protocol.

value: Urine


title: Empty vector control line 28-1 at neuroepithelial cell stage


title: Parental H1 cell line at neuroepithelial cell stage


title: vDGC CON 2

description: Library name: SW_WT_2

value: Brain


title: vDGC CON 3

description: Library name: SW_WT_3

value: male


title: subject6 day3 timepoint7

description: Library name: library140


title: subject6 day3 timepoint6

description: Library name: library139


title: CTNNB1 knock out clone 9-2 at embryonic stem cell stage

value: day 0


title: CTNNB1 knock out clone 9-1 at embryonic stem cell stage


title: LNCaP cells, C9 V

source_name: HOXC9 stably expressed LNCaP cells, vehicle treatment.

value: V


title: R0_Stage1_1

data_processing:
With input of read counts for all samples, counts per million mapped reads (CPMs) were obtained by using the function cpm in the edgeR package.
Genes were removed when the corresponding CPMs for all samples were smaller than the CPM whose corresponding raw read count is 10. Then, the top 3000 most variable genes were selected by ranking the mean absolute deviation (MAD) of the log2-transformed CPMs in descending order.
Based on these most variable genes, the PCA analysis was performed on the log2-transformed CPMs by using the prcomp function available in the standard R language. The top two principal components (PCs) were used to draw the PCA figures.
Assembly: hg19
Supplementary files format and content: count and FPKM files

source_name: retinal organoid

extract_protocol:
RNA was extracted from individual TRIzol (Life Technologies) preparations via a phenol-chloroform extraction.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).

value: retinal organoid

tag: Stage

value: Stage 1


title: vDGC CON 1

description: Library name: SW_WT_1

value: Swiss Webster

value: WT


title: vDGC 5HT1AR MIA 4

description: Library name: 5HT1AR_F1_4

value: MIA


title: subject6 day3 timepoint5

description: Library name: library138


title: LNCaP cells, WT DHT

source_name: LNCaP cells, 10-7M of DHT treatment.

value: Human prostate cancer cells

value: LNCaP


title: subject6 day3 timepoint8

description: Library name: library141


title: vDGC 5HT1AR MIA 3

description: Library name: 5HT1AR_F1_3


title: CTNNB1 knock out clone 7-1 at embryonic stem cell stage

source_name: embryonic stem cell

value: embryonic stem cell


title: CTNNB1 knock out clone 10-1 at embryonic stem cell stage


title: subject6 day3 timepoint4

description: Library name: library137


title: HEK293T cells, Ev over-expression 40°C rep 1

first: Umashankar

institute: IIT Gandhinagar

description: Gene expression after 72 hrs of transfection the truncated form

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies).

data_processing: Images were quantified using Agilent Feature Extraction Software . Feature extracted raw data was analysed using Agilent GeneSpring GX software.

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labelling Kit (Part No. 5190-0424). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic at 37°C and 5% CO2. HEK293T cells were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic at 40°C and 5% CO2 for the heat-shock experiment.

extract_protocol: RNA was extracted using Trizol precipitation and was then purified using Qiagen’s RNeasy mini kit (74106). The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100).

treatment_protocol: HEK293T cells were transduced with the following shRNA lentiviruses: non-targeting (CT), Human CGGBP1-targeting (KD) (PMIDs: 35070079; 34585631; 33081720; 32727353; 31547883 ). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 µg/ml puromycin for a week. CT cells were then transfected with Hs over-expression plasmid and empty pcDNA3.1(+) plasmid using Polyplus JetOptimus (cat #101000051) transfection reagent (5ug plasmid per 10cm dish). HEK293T KD cells were transfected with Lc, Ac, Gg over-expression plasmids using the same protocol as for Hs. In the heat-shock experiment, the procedure was consistent until the transfection of different CGGBP1 variants. Post-transfection, cells were maintained at 37°C for 24 hours. Following this incubation, the cells were exposed to continuous heat stress at 40°C for a duration of 48 hours.

tag: cggbp1 overexpression

value: Ev

tag: temperature


title: subject6 day3 timepoint3

description: Library name: library136


title: LNCaP cells, WT V

source_name: LNCaP cells, vehicle treatment.


title: vDGC 5HT1AR MIA 2

description: Library name: 5HT1AR_F1_2

value: vDG DGC


title: Heterozygous CTNNB1 knockout line 7-1 at embryonic stem cell stage

tag: developmental stage


title: vDGC 5HT1AR MIA 1

description: Library name: 5HT1AR_F1_1


title: subject6 day3 timepoint2

description: Library name: library135


title: Replicate 3, TF-1 cells expressing TPOR and CSF2RB no treatment

description: Library name: TRNA33

source_name: Hematopoietic

value: Hematopoietic

value: Transformed leukemic cell

value: TPOR and CSF2RB

value: No treatment

tag: time

value: 14 hours


title: Heterozygous CTNNB1 knockout line 20-2 at embryonic stem cell stage

value: day 0


title: HEK293T cells, Ev over-expression 40°C rep 2


title: subject6 day3 timepoint1

description: Library name: library134

value: Urine


title: dbdb_fracture

city: 杭州

first: XING

last: JI

state: State

address: 余杭塘路866号

institute: zhejiang university

description: 10x Genomics

data_processing:
Library sequencing was carried out on an Illumina NovaSeq PE150 platform
Aligned reads and gene-barcode matrices were generated from FASTQ files, which included Read 1, Read 2, and the i7 index, using the Cell Ranger software package (version 3.0) with default parameters.
Assembly: mm10/hg38
Supplementary files format and content: barcodes.tsv.gz files contain unique identifiers for each cell, which are typically used to track and identify individual cells.
Supplementary files format and content: features.tsv.gz files contain unique identifiers for genes, such as gene names or gene IDs, that correspond to the columns in the count matrix.
Supplementary files format and content: matrix.mtx.gz files contain matrixs where the rows represent genes, the columns represent cells, and the values in the cells indicate the expression level of a specific gene in a specific cell.

source_name: periosteum

extract_protocol:
murine tibias and femurs were digested in alpha Minimum Essential Media (αMEM) with 3 mg/ml collagenase and 4 mg/ml dispase
Human periosteum samples were prepared from surgical discard specimens obtained from patient with T2DM undergoing surgery
A single-cell library was created using the Chromium Single Cell 3' Library Kit v3 (10x Genomics)

value: periosteum

tag: age


title: HEK293T cells, Hs over-expression 40°C rep 2

city: Gandhinagar

last: Singh

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

value: Hs


title: HEK293T cells, Hs over-expression 40°C rep 3


title: subject6 day3 timepoint9

description: Library name: library142


title: Heterozygous CTNNB1 knockout line 20-1 at embryonic stem cell stage


title: subject6 day2 timepoint11

description: Library name: library133


title: Heterozygous CTNNB1 knockout line 107-1 at embryonic stem cell stage


title: HEK293T cells, Hs over-expression 40°C rep 1


title: HEK293T cells, Ev over-expression 40°C rep 3


title: HEK293T cells, Gg over-expression 40°C rep 3

value: Gg


title: subject6 day2 timepoint10

description: Library name: library132


title: db+_fracture

description: 10x Genomics


title: db+

description: 10x Genomics


title: HEK293T cells, Gg over-expression 40°C rep 2


title: Empty vector control line 30-1 at embryonic stem cell stage


title: subject6 day2 timepoint9

description: Library name: library131


title: Empty vector control line 3-2 at embryonic stem cell stage


title: dbdb

description: 10x Genomics


title: subject6 day2 timepoint8

description: Library name: library130


title: HEK293T cells, Ac over-expression 40°C rep 3

value: Ac


title: striatum, 6 months old, wild type,  male, replicate 3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38(mm10) as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Library was prepared using TruSeq Stranded mRNA (Poly-A)
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end, 2X100bp, Novaseq S4

value: Striatum

value: WT

value: male


title: Empty vector control line 28-1 at embryonic stem cell stage

data_processing:
Real-time basecalling was performed by the Illumina NovoSeq 6000 built-in software, RTA, and binary bcl data was produced. Demultiplexing performed by bcl2fastq (v2.17; Illumina) installed on high performance cluster to output FASTQ files. During the sequencing process, chastity value of the first 25 cycles were caculated, and reads with less than 2 bases with a chastity value more than 0.6 passsed filtering.
Read counts were generated from RNA-sequencing reads by pseudo-alignment to transcripts from GENCODE using the pre-built index for Salmon v1.10.0 available from the RefGenie server.
Read counts were mapped to ENSEMBL gene and transcript IDs using the tximeta package v1.12.4; R version 4.1.2
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set RefGenie Digest 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4
Supplementary files format and content: transcript.counts.txt.gz: gzipped, tab delimited text file containing read counts for all transcripts annotated against ENSEMBL Homo sapiens release 97 transcript ID.
Supplementary files format and content: gene.counts.txt.gz: gzipped, tab delimited text file containing read counts for all transcripts collapsed to genes and annotated against ENSEMBL Homo sapiens release 97 gene ID.

extract_protocol:
Pelleted cells were homogenized in TRIzol reagent (Invitrogen, Cat#15596026) and RNA was isolated using RNeasy kit (QIAGEN, Cat#74104). Residual genomic DNA was removed on column by incubation with DNase I (QIAGEN, Cat#79254). RNA quality was assessed by nanodrop UV spectroscopy and Agilent Tapestation electrophoresis.
Library preparation and RNA-sequencing was performed by GENEWIZ (now Azenta). Libraries were prepared from total RNA with ribosomal RNA depletion.

value: embryonic stem cell


title: striatum, 6 months old, wild type,  male, replicate 4


title: subject6 day2 timepoint7

description: Library name: library129


title: Parental H1 cell line at embryonic stem cell stage


title: HEK293T cells, Gg over-expression 40°C rep 1


title: striatum, 6 months old, wild type,  male, replicate 2


title: subject6 day2 timepoint6

description: Library name: library128


title: striatum, 6 months old, wild type,  male, replicate 1


title: Mesentery, Crohn's disease, Non-inflamed, rep 3, scTCR-seq

first: Emma

middle: Claire

last: Erlich

address: 417 E 68th St

institute: Memorial Sloan Kettering

description: 10x Genomics

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data
Library strategy: scTCR-seq

source_name: Mesentery

extract_protocol:
Two pieces of matched ileum and the associated mesentery was collected from consenting patients who were undergoing surgical resection of their ileum to treat Crohn's disease. Under a pathologist’s supervision, one piece of tissue was collected from an area of the ileum with active inflammation and the other piece was from adjoining normal region. Control ileum and mesentery was collected from gastrointestinal cancer patients from regions of the intestine upstream of their tumors. After collection, tissue was stored for under an hour in RPMI-1640 before undergoing single cell digestion. In the lab, the tissue was first rinsed in fresh HBSS before the mesentery, intestinal lamina propria, and muscularis were separated using a scalpel. To remove mucus and epithelial cells, the lamina propria was cut into thin 0.5 cm thick strips and then placed in 10 ml of HBSS with 5 mM EDTA and digested at 37° C for 20 minutes, before vortexing the tubes for 20 seconds, removing the tissue from the HBSS/ETDA, placing it in fresh HBSS and vortexing the tissue again. The lamina propria was then minced into small pieces and weighed. Mesentery was also minced into small pieces with a scalpel, before being weighed. Then tissue was digested in 1 g of tissue per 5 ml of RPMI-1640 media containing 10% FBS, 1 mg/ml Collagenase IV, 0.2 mg/ml DNase I at 37° C for 45 minutes (for mesentery) or 1 hour (for ileum) on an orbital at 100 rpm. Tissue was then vortexed, filtered through a 100m filter into a fresh tube, and washed with an equal volume of FACS buffer (2% FBS, 5mM EDTA, 0.2% sodium azide in PBS). Cells were then spun down for 10 minutes at 500 x g at 4° C, RBC lysis was performed for 5 minutes on the cells, which were washed with additional 10 ml of FACS buffer. After spinning cells down at 10 minutes at 500 x g at 4C, they were resuspended in 1 ml of FACS buffer, counted using an automatic cell counter and frozen at -80° C in 10% DMSO in 90% FBS before being moved to long-term storage in liquid nitrogen. On a later day, aliquots of cells were rapidly thawed in a 37° C water bath, stained for flow cytometry sorting and live, CD45+ immune cells were sorted for sequencing.
The 10x Genomics Chromium Single Cell 5' Library and Gel Bead Kit was used. We sequenced 5' RNA expression, TCR sequencing, and BCR sequencing as per the manufacturer's protocol.

value: Mesentery

value: TCR+ cells

tag: disease

value: Crohn's disease

tag: disease state

value: Non-inflamed

value: M


title: Mesentery, Crohn's disease, Non-inflamed, rep 3, scBCR-seq

description: 10x Genomics

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data
Library strategy: scBCR-seq

tag: tissue

value: BCR+ cells


title: subject6 day2 timepoint4

description: Library name: library126


title: HEK293T cells, Lc over-expression 40°C rep 3

value: Lc


title: subject6 day2 timepoint5

description: Library name: library127


title: HEK293T cells, Ac over-expression 40°C rep 1


title: HEK293T cells, Ac over-expression 40°C rep 2


title: subject6 day2 timepoint3

description: Library name: library125


title: Mesentery, Crohn's disease, Non-inflamed, rep 3, scRNA-seq

description: 10x Genomics

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data

value: CD45+ immune cells


title: HEK293T cells, Lc over-expression 40°C rep 2


title: striatum, 6 months old, wild type,  female, replicate 3

tag: genotype

value: female


title: Mesentery, Crohn's disease, Inflamed, rep 3, scTCR-seq

description: 10x Genomics

value: Inflamed


title: striatum, 6 months old, wild type,  female, replicate 2


title: Mesentery, Crohn's disease, Inflamed, rep 3, scBCR-seq

description: 10x Genomics


title: striatum, 6 months old, wild type,  female, replicate 1


title: subject6 day2 timepoint2

description: Library name: library124

value: Urine


title: HEK293T cells, Ev over-expression 37°C rep 3

value: Ev


title: subject6 day2 timepoint1

description: Library name: library123


title: subject6 day1 timepoint9

description: Library name: library122


title: HEK293T cells, Ev over-expression 37°C rep 2


title: Mesentery, Crohn's disease, Inflamed, rep 3, scRNA-seq

description: 10x Genomics


title: striatum, 6 months old, wild type,  female, replicate 4


title: HEK293T cells, Lc over-expression 40°C rep 1


title: striatum, 6 months old, with Alfy het,  male, replicate 4

value: Alfy OE het


title: HEK293T cells, Ev over-expression 37°C rep 1


title: Ileum, Crohn's disease, Non-inflamed, rep 3, scTCR-seq

description: 10x Genomics

source_name: Ileum

value: Ileum


title: HEK293T cells, Hs over-expression 37°C rep 3

value: Hs


title: subject6 day1 timepoint8

description: Library name: library121


title: striatum, 6 months old, with Alfy het,  male, replicate 3

value: Striatum

value: male


title: Ileum, Crohn's disease, Non-inflamed, rep 3, scBCR-seq

description: 10x Genomics


title: striatum, 6 months old, with Alfy het,  male, replicate 2


title: subject6 day1 timepoint7

description: Library name: library120


title: HEK293T cells, Hs over-expression 37°C rep 2


title: subject6 day1 timepoint6

description: Library name: library119


title: striatum, 6 months old, with Alfy het,  male, replicate 1


title: Ileum, Crohn's disease, Non-inflamed, rep 3, scRNA-seq

description: 10x Genomics


title: Ileum, Crohn's disease, Inflamed, rep 3, scTCR-seq

description: 10x Genomics


title: striatum, 6 months old, with Alfy het, female, replicate 4


title: HEK293T cells, Gg over-expression 37°C rep 3

value: Gg


title: Ileum, Crohn's disease, Inflamed, rep 3, scBCR-seq

description: 10x Genomics


title: striatum, 6 months old, with Alfy het, female, replicate 3


title: subject6 day1 timepoint4

description: Library name: library117


title: striatum, 6 months old, with Alfy het, female, replicate 2


title: subject6 day1 timepoint3

description: Library name: library116


title: striatum, 6 months old, with Alfy het, female, replicate 1


title: subject6 day1 timepoint2

description: Library name: library115


title: HEK293T cells, Hs over-expression 37°C rep 1


title: HEK293T cells, Gg over-expression 37°C rep 1


title: HEK293T cells, Ac over-expression 37°C rep 3

value: Ac


title: Mesentery, Crohn's disease, Non-inflamed, rep 2, scRNA-seq

description: 10x Genomics

value: Mesentery

value: Crohn's disease


title: subject6 day1 timepoint5

description: Library name: library118


title: striatum, 6 months old, with Q140+Alfy homo,  male, replicate 4

value: Q/Alfy OE homo


title: HEK293T cells, Ac over-expression 37°C rep 2


title: subject6 day1 timepoint1

description: Library name: library114


title: subject5 day3 timepoint4

description: Library name: library113


title: Mesentery, Crohn's disease, Inflamed, rep 2, scTCR-seq

description: 10x Genomics

value: TCR+ cells

value: M


title: subject5 day3 timepoint3

description: Library name: library112


title: Ileum, Crohn's disease, Inflamed, rep 3, scRNA-seq

description: 10x Genomics

value: CD45+ immune cells


title: Mesentery, Crohn's disease, Inflamed, rep 2, scRNA-seq

description: 10x Genomics


title: Mesentery, Crohn's disease, Non-inflamed, rep 2, scBCR-seq

description: 10x Genomics

value: BCR+ cells

value: Non-inflamed


title: Mesentery, Crohn's disease, Inflamed, rep 2, scBCR-seq

description: 10x Genomics

value: Inflamed


title: subject5 day3 timepoint2

description: Library name: library111

value: Urine


title: PC-12, control,rep1

description: Library name: Ctrl_1st

value: Adrenal gland

value: Rat pheochromocytoma cells

value: control


title: HEK293T cells, Gg over-expression 37°C rep 2


title: HEK293T cells, Lc over-expression 37°C rep 3

value: Lc


title: striatum, 6 months old, with Q140+Alfy homo,  male, replicate 2

value: Striatum

value: male


title: striatum, 6 months old, with Q140+Alfy homo,  male, replicate 1


title: Ileum, Crohn's disease, Non-inflamed, rep 2, scTCR-seq

description: 10x Genomics

value: Ileum


title: PC-12, PCSK9,rep1

description: Library name: PCSK9_1st

value: PCSK9 overexpression


title: HEK293T cells, Ac over-expression 37°C rep 1

value: Ac


title: subject5 day3 timepoint1

description: Library name: library110


title: tlr2-/-_CONVD_3, 5 dpf

city: LEIDEN

first: Li

last: Liu

address: Verbeekstraat 29D

country: Netherlands

institute: Leiden University

description:
Library name: Sample 12
150 nucleotides

data_processing:
RNAseq reads of mutants their corresponding wild type controls were aligned and mapped to the zebrafish genome GRCz11 using Salmon v1.2.1
Differential gene expression was analyzed by using DESeq2 v1.24.0. Statistical significance was determined by a padj value of ≤ 0.05 by utilizing apeglm.
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: excel files include RPKM values for each sample
Supplementary files format and content: excel files include fold change values and padj values of  mutants compared with their corresponding wild type controls

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from all groups  groups (n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: tlr2 mutant

value: whole embryos

value: 5 days post fertilization


title: HEK293T cells, Lc over-expression 37°C rep 2


title: Ileum, Crohn's disease, Non-inflamed, rep 2, scBCR-seq

description: 10x Genomics

value: Crohn's disease

value: M


title: striatum, 6 months old, with Q140+Alfy homo,  female, replicate 3

value: Q/Alfy OE homo

value: female


title: HEK293T cells, Lc over-expression 37°C rep 1


title: striatum, 6 months old, with Q140+Alfy homo,  male, replicate 3


title: tlr2-/-_CONVD_1, 5 dpf

description:
Library name: Sample 10
150 nucleotides


title: tlr2-/-_CONVD_2, 5 dpf

description:
Library name: Sample 11
150 nucleotides


title: subject5 day2 timepoint5

description: Library name: library108

value: Urine


title: striatum, 6 months old, with Q140+Alfy homo,  female, replicate 2


title: tlr2-/-_GF_3, 5 dpf

description:
Library name: Sample 9
150 nucleotides


title: Ileum, Crohn's disease, Inflamed, rep 2, scTCR-seq

description: 10x Genomics

value: TCR+ cells

value: Inflamed


title: subject5 day2 timepoint4

description: Library name: library107


title: subject5 day2 timepoint2

description: Library name: library105


title: tlr2-/-_GF_2, 5 dpf

description:
Library name: Sample 8
150 nucleotides


title: striatum, 6 months old, with Q140+Alfy homo,  female, replicate 1


title: striatum, 6 months old, with Q140+Alfy het,male, replicate 4

value: Q/Alfy OE het


title: subject5 day2 timepoint3

description: Library name: library106


title: subject5 day2 timepoint1

description: Library name: library104


title: striatum, 6 months old, with Q140+Alfy homo,  female, replicate 4


title: tlr2-/-_GF_1, 5 dpf

description:
Library name: Sample 7
150 nucleotides


title: Ileum, Crohn's disease, Non-inflamed, rep 2, scRNA-seq

description: 10x Genomics

value: CD45+ immune cells

value: Non-inflamed


title: tlr2+/+_CONVD_2, 5 dpf

description:
Library name: Sample 5
150 nucleotides

value: wild type


title: striatum, 6 months old, with Q140+Alfy het,male, replicate 2

value: Striatum

value: male


title: Ileum, Crohn's disease, Inflamed, rep 2, scBCR-seq

description: 10x Genomics

value: Ileum

value: BCR+ cells


title: Ileum, Crohn's disease, Inflamed, rep 2, scRNA-seq

description: 10x Genomics


title: Mesentery, Crohn's disease, Non-inflamed, rep 1, scBCR-seq

description: 10x Genomics

value: Mesentery

value: F


title: Mesentery, Crohn's disease, Non-inflamed, rep 1, scTCR-seq

description: 10x Genomics

value: Crohn's disease


title: tlr2+/+_CONVD_1, 5 dpf

description:
Library name: Sample 4
150 nucleotides

value: whole embryos

value: 5 days post fertilization


title: subject5 day1 timepoint7

description: Library name: library102


title: subject5 day2 timepoint6

description: Library name: library109


title: striatum, 6 months old, with Q140+Alfy het, female, replicate 4

value: female


title: subject5 day1 timepoint6

description: Library name: library101

value: Urine


title: Mesentery, Crohn's disease, Inflamed, rep 1, scTCR-seq

description: 10x Genomics

value: TCR+ cells


title: tlr2+/+_GF_3, 5 dpf

description:
Library name: Sample 3
150 nucleotides


title: Mesentery, Crohn's disease, Non-inflamed, rep 1, scRNA-seq

description: 10x Genomics


title: striatum, 6 months old, with Q140+Alfy het, female, replicate 3


title: striatum, 6 months old, with Q140+Alfy het,male, replicate 3


title: tlr2+/+_CONVD_3, 5 dpf

description:
Library name: Sample 6
150 nucleotides


title: subject5 day1 timepoint8

description: Library name: library103


title: tlr2+/+_GF_1, 5 dpf

description:
Library name: Sample 1
150 nucleotides


title: striatum, 6 months old, with Q140+Alfy het, female, replicate 2


title: Mesentery, Crohn's disease, Inflamed, rep 1, scRNA-seq

description: 10x Genomics

value: Inflamed


title: subject5 day1 timepoint5

description: Library name: library100


title: KCL_7Dpci_67

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Reads were demultiplexed using bcl2fastq (v2.20.0, Illumina)
Adapter trimming and quality control was performed with Trim Galore! (v.0.6.4_dev)
Reads from 2 lanes of sequencing were combined
Alignment and gene counting was performed using STAR (v.2.7.6a)
Assembly: GRCz11 (soft-masked, primary assembly, ftp://ftp.ensembl.org:21/pub/release-104/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz)
gene annotations: Ensembl v.104 (ftp.ensembl.org/pub/release-104/gtf/danio_rerio/Danio_rerio.GRCz11.104.gtf.gz)

source_name: cardiac ventricle

extract_protocol:
RNA was extracted from individual ventricles using the Quick-RNA MicroPrep kit (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) from Lexogen.

treatment_protocol: Cryo-injury was induced on the tip of the ventricle using a copper probe pre-chilled in liquid nitrogen.

value: cardiac ventricle

value: KCL

tag: treatment

value: cryo-injury

tag: time (days)


title: subject5 day1 timepoint4

description: Library name: library99


title: Mesentery, Control, Non-inflamed, rep 2, scTCR-seq

description: 10x Genomics

value: Control (Gastrointestinal cancer)

value: Non-inflamed

tag: Sex


title: striatum, 6 months old, with Q140+Alfy het, female, replicate 1

value: Striatum

value: Q/Alfy OE het


title: striatum, 6 months old, Q140,  male, replicate 4

value: Q

value: male


title: subject5 day1 timepoint3

description: Library name: library98


title: KCL_7Dpci_66

tag: strain


title: striatum, 6 months old, with Q140+Alfy het,male, replicate 1


title: Mesentery, Control, Non-inflamed, rep 2, scBCR-seq

description: 10x Genomics

value: Mesentery

value: BCR+ cells

value: F


title: striatum, 6 months old, Q140,  male, replicate 3


title: tlr2+/+_GF_2, 5 dpf

description:
Library name: Sample 2
150 nucleotides

value: wild type

value: whole embryos

value: 5 days post fertilization


title: subject5 day1 timepoint2

description: Library name: library97

value: Urine

tag: batch


title: striatum, 6 months old, Q140,  male, replicate 2


title: Mesentery, Control, Non-inflamed, rep 2, scRNA-seq

description: 10x Genomics

value: CD45+ immune cells


title: subject5 day1 timepoint1

description: Library name: library96


title: KCL_7Dpci_65

value: cardiac ventricle


title: striatum, 6 months old, Q140,  male, replicate 1


title: Mesentery, Crohn's disease, Inflamed, rep 1, scBCR-seq

description: 10x Genomics

value: Crohn's disease

value: Inflamed


title: KCL_1Dpci_64

value: KCL

value: cryo-injury


title: Mesentery, Control, Non-inflamed, rep 1, scTCR-seq

description: 10x Genomics

value: TCR+ cells

value: Control (Gastrointestinal cancer)

value: Non-inflamed

value: M


title: KCL_1Dpci_63


title: subject4 day3 timepoint5

description: Library name: library94


title: striatum, 6 months old, Q140, female, replicate 4

value: Striatum

value: Q

value: female