title: DMSO_3

value: DMSO,24 h


title: C48_1

status: Public on Aug 01 2024

type: SRA

city: Nanjing

first: wen

middle: wen

last: xue

address: 22 Han Kou Road, Nanjing

department: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences

country: China

institute: Nanjing University

library_source: transcriptomic

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium containing 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were incubated for 24 hours in the absence or presence of 1 μM Loonamycin A.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Triple negative breast cancer

tag: genotype

value: WT

tag: treatment

value: Loonamycin A,1 μM,24 h


title: Eye-antennal disc, Eyeless-Gal4 Dam-Sd Replicate 1 (Set 1)

city: Melbourne

first: Kieran

last: Harvey

state: Victoria

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
DamIDcounts.csv
sd_peaks
sd_peaks_filtered.bed
sd_peaks_filtered.togene
Sd1

library_source: genomic

data_processing:
DamID alignment: Subread and featureCounts DamID analysis: process with EdgeR in R for differentially methylated GATC motifs DamID analysis: generate peaks from adjacent mehtylated sites, find closest gene with Bedtools
Assembly: dm6
Supplementary files format and content: sd_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: yki_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: jun_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: DamIDcounts.csv contains a list of GATC features/'tags' and the raw counts for all replicates
Library strategy: DamID-seq

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Eye-antennal disc

growth_protocol: Crosses producing larvae with the indicated genotype were allowed to lay eggs o/n at 25°C. Eggs were transferred to the non-permissive temperature (18°C) for 4 days. To restrict expression of the TaDa transgenes to a defined period, larvae were transferred to the permissive temperature (29°C) 24 hours before dissection.

extract_protocol:
Eye-antennal discs were treated with protK, RNase A followed by phenol chloroform DNA extraction. DNA was ethanol precipitated, washed and dissolved, followed by DpnI digestion, DamID adaptors ligation, DpnII digestion and PCR amplification. MePCR product was sonicated using a Covaris S2 device to generate fragments of 100-500bp, with an average of 300bp. DNA was purified using Agencourt AMPure beads purification.
Illumina sequencing libraries were prepared using KAPA Hyper prep kit (Kapa Biosystems) and 300ng starting material. Five to seven cycles of PCR were performed.

value: Eye-antennal disc

value: Eyeless-Gal4 Gal80ts UAS-Dam-Sd


title: Wild Type, time 3, replicate 1 [RNA-seq]

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

country: Spain

institute: CRG

data_processing:
Basecalling with Illumina bcl2fastq version 2.17.1.14
STAR v2.5.3a mapping to Mus musculus Gencode version M14 (mm10) with –quantMode geneCounts option to get raw counts per gene and per sample
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene obtained by STAR mapper’s –quantMode GeneCounts parameter (4th column: reverse stranded protocol)

organism: Mus musculus

source_name: Wild Type, time 3

extract_protocol:
In order to perform the RNA-sequencing, total RNA was extracted with the Maxwell 16 LEV simplyRNA Cells Kit (AS1270, Promega) according to manufacturer’s instructions from WT, Sam68-/- and QKI -/-  EBs in three biological replicates. DNA-free RNA was then quantified using the Nanodrop and quality checked with the Bioanalizer
rRNA depletion and library preparation was done with the TruSeq stranded total RNA Library prer Human/Mouse/Rat (20020596, Illumina). The sequencing was performed using 2x125bp paired-ends reads on a HiSeq 2500 sequencer with HiSeq v4 chemistry.

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out

value: Wild Type

tag: time point


title: HCC-18

city: Chengdu

first: Ling

last: Bai

state: Sichuan

address: No.37 Guoxue Alley

department: Department of Laboratory Medicine

institute: West China Hospital, Sichuan University

data_processing:
GATK 3.7 best practices workflow
After removing terminal adaptor sequences and low-quality data, sequences were mapped to the reference human genome using the Burrows-Wheel Aligner (BWA) software.
Duplicate reads were removed with Gene Analysis Toolkit. MuTect2 algorithm was utilized to call single-nucleotide variants (SNVs) and somatic insertions/deletions (InDel).
GnomAD database was applied to filter germline mutations. Afterwards, mutated variant allele frequency (VAF) ≥0.01 was filtered.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw mutations for each sample
Library strategy: DNA-seq

source_name: Liver

extract_protocol:
Genomic DNA was extracted from the fresh HCC tumor tissues of individual patients with the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the standard procedures. In brief, tissue samples (less than 10 mg) were digested overnight at 56°C with protein K and Buffer ALT. After extraction with Buffer AL and reprecipitation in ethanol (97%), nucleic acids were then rinsed with Buffer AW1 and Buffer AW2. After that, DNA was solubilized in Buffer AE and stored at -20°C.
DNA libraries for DNA-seq were prepared using The Human 1021 Gene Mutation Detection Kit (Gene+, Beijing, China) following manufacturer's protocols.

value: Liver

tag: disease state

value: Hepatocellular Carcinoma

value: surgical resection


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 3 (Set 1)

description:
DamIDcounts.csv
Dam6

value: Eyeless-Gal4 Gal80ts UAS-Dam


title: Wild Type, time 10, replicate 1 [RNA-seq]

source_name: Wild Type, time 10


title: HCC-15


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 2 (Set 1)

description:
DamIDcounts.csv
Dam5


title: Wild Type, time 0, replicate 1 [RNA-seq]

source_name: Wild Type, time 0


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 1 (Set 1)

description:
DamIDcounts.csv
Dam4


title: HCC-12


title: B cells, input

city: Milano

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

description: ChIP-seq reads were trimmed to get a final length of 35 bp

data_processing:
ChIP-seq reads were processed using the ENCODE pipeline 2.1.5, setting default peak caller and bowtie2 aligner.
Homo sapiens ChIP-seq reads were aligned to the hg38 v4 genome provided by ENCODE pipeline.
Mus musculus ChIP-seq reads were aligned to the mm10 v4 genome provided by ENCODE pipeline.
Supplementary files format and content: hg38, mm10
Supplementary files format and content: bigWig, bed narrowPeak (except for Input sample)

source_name: B cells

extract_protocol:
HeLa: material was processed for ChIP.
DNA libraries were prepared using the NEbNext ChIP-Seq Library kit and TruSeq sample prep (Illumina)

treatment_protocol: HeLa cells at 25-30% confluence were transfected with 50 nM siRNA using Lipofectamine 3000 Reagent (ThermoFisher).

value: B cells

value: Normal

tag: chip antibody


title: HCC-30


title: Quaking KO, time 3, replicate 3 [RNA-seq]

source_name: Quaking KO, time 3

value: Quaking


title: Eye-antennal disc, RNAseq scrib mutant Replicate 3

data_processing:
RNA alignment: subread and featureCounts
RNA analysis: edgeR to compute RPKM
Assembly: dm6
Supplementary files format and content: RNAseq_count.table.csv contains list of all genes with the raw counts from the replicates

growth_protocol: Flies were reared at 25°C

extract_protocol:
Cells were pelleted and resuspended in Trizol. RNA was isolated according to manufacturer’s protocol. Samples from sorts executed on different days were pooled into three different samples containing 180-330ng RNA.
Libraries prepared according to standard protocols (TruSeq RNA, Illumina).

value: eyFLP FRT82B Cell lethal / FRT82B scrib1


title: HCC-9


title: C1R, input, rep2

source_name: CCRF

value: CCRF

value: Tumor


title: Quaking KO, time 10, replicate 3 [RNA-seq]

source_name: Quaking KO, time 10


title: Eye-antennal disc, RNAseq scrib mutant Replicate 2


title: HCC-7


title: C1R, input, rep1

value: Immortalized


title: HCC-21


title: DMSO_2

value: cell line

value: Triple negative breast cancer

value: WT

value: DMSO,24 h


title: Quaking KO, time 0, replicate 3 [RNA-seq]

source_name: Quaking KO, time 0

value: mouse embryonic stem cells


title: B cells, NFYB, IP, rep2

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_B_cells_ENCODEpipeline_hg38_fc_signal.bigwig
NFYB_B_cells_ENCODEpipeline_hg38.bed

value: NFYB, IP


title: HCC-6

value: Liver


title: Eye-antennal disc, RNAseq scrib fos mutant Replicate 3

value: Eye-antennal disc

value: eyFLP FRT82B Cell lethal / FRT82B scrib1 fosKM


title: Eye-antennal disc, RNAseq scrib mutant Replicate 1


title: DMSO_1


title: B cells, NFYB, IP, rep1


title: Quaking KO, time 3, replicate 2 [RNA-seq]


title: HCC-5

value: Hepatocellular Carcinoma

value: surgical resection


title: Eye-antennal disc, RNAseq scrib fos mutant Replicate 2


title: Quaking KO, time 10, replicate 2 [RNA-seq]


title: Quaking KO, time 0, replicate 2 [RNA-seq]


title: CCRF, NFYB, IP, rep2

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_CCRF_ENCODEpipeline_hg38_fc_signal.bigwig
NFYB_CCRF_ENCODEpipeline_hg38.bed


title: HCC-4


title: Eye-antennal disc, RNAseq scrib fos mutant Replicate 1


title: HCC-2


title: CCRF, NFYB, IP, rep1


title: Quaking KO, time 3, replicate 1 [RNA-seq]


title: Eye-antennal disc, RNAseq fos mutant Replicate 3

value: eyFLP FRT82B Cell lethal / FRT82B fosKM


title: Quaking KO, time 10, replicate 1 [RNA-seq]

value: Quaking


title: MEL, NFYB, IP, rep1

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_MEL_ENCODEpipeline_mm10_fc_signal.bigwig
NFYB_MEL_ENCODEpipeline_mm10.bed

source_name: MEL

value: MEL


title: Eye-antennal disc, RNAseq fos mutant Replicate 2


title: C1R, NFYB, IP, rep1

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_C1R_ENCODEpipeline_hg38_fc_signal.bigwig
NFYB_C1R_ENCODEpipeline_hg38.bed


title: HCC-1


title: C1R, NFYB, IP, rep2


title: Eye-antennal disc, RNAseq fos mutant Replicate 1


title: biological replicate 1, saline, Xenium mouse spinal cord

type: RNA

city: Pittsburgh

first: Michael

last: Leone

address: 4315 Tesla St

country: USA

institute: Carnegie Mellon University

description:
Xenium spatial transcriptomics platform
10x Genomics

hyb_protocol: For both mice, lumbar region was quickly isolated and embedded following 10x Genomics'  Xenium in situ for Fresh Frozen Tissues Preparation Guide: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/tissue-prep-fresh-frozen/xenium-in-situ-spatial-profiling-for-fresh-frozen-%E2%80%93-tissue-preparation-guide

scan_protocol: Xenium In Situ Analyzer

data_processing:
The .tar.gz dataset provided are the direct outputs of the Xenium assay, and contain both raw and processed data. See: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs#transcript-file
The cell labels generated by our own integration analysis is also provided as top and subtype annotations. See Readme.txt
Code for integrative analysis that generated cell labels at: https://github.com/pfenninglab/dorsalhorn_conserved_rna_atac_xen
Xenium proprietary probes used to target mouse gene transcripts.
Description of Xenium assay output files is provided on the 10x website: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/understanding-xenium-outputs

label: Xenium Mouse Probe Set

source_name: spinal cord

label_protocol: Xenium Mouse Probe Set

extract_protocol:
The first mouse  was a 10-week-old C57Bl/6 male that underwent sterile saline injection. The mouse was put under anesthesia at 4% isoflurane and then maintained at 2% isoflurane for the duration of the injection. A hamilton syringe was used to inject 5uL of saline intradermally into the left calf. The mouse was left under 1.25% isoflurane for 30 minutes after the injection. The mouse was IP injected with a solution of 100mg/kg ketamine and 20mg/kg xylazine one hour after the saline injection. It was then perfused using ice-cold RNAse-free PBS. The spinal cord was dissected, approximately one hour and 15 minutes after the injection of saline. The second mouse was a 10-week-old C57Bl/6 female, and put under at 4% iso and then maintained at 1-1.5% isoflurane. The mouse's left paw had a 0.07g von Frey filament applied for 3 seconds and was brushed, alternating between the two over the course of 5 minutes. The mouse was IP injected with a solution of 100mg/kg katamine and 20mg/kg xylazine one hour after stimulus was completed. It was then perfused using ice-cold RNAse-free PBS. The spinal cord was dissected approximately one hour after stimulus.
The tissue was then stored at -80 degrees Celsius before being cryosectioned at 20um based on the Xenium guidelines. The cryosections were non-consecutive in order to capture information about distinct cells in each section. The slide was then stored again at -80 degrees Celsius until the Xenium run was completed per the protocols from 10x Genomics.

tag: strain

tag: Sex

value: male

value: spinal cord

value: all

tag: age (years)


title: Sam68 KO, time 3, replicate 3 [RNA-seq]

source_name: Sam68 KO, time 3


title: control-45_re-used

city: Guangzhou

first: guodong

last: he

address: zhongshan road No.102

institute: Guangdong Provincial People's Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 with parameters -p 12 -5 5 -3 5 --rna-strandness RF
HTseq was used to calculate the counts of the Reads mapped the genome.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene read counts for every gene and every sample

source_name: exosome from plasma

extract_protocol:
2mL of venous blood from patients were collected into Ethylene Diamine Tetraacetic Acid (EDTA) routine blood tubes. Plasma was separated by centrifugation at 3000 rpm for 10 min at 4℃ and collected into cryogenic vials and stored at −80℃. The exoRNeasy Serum Plasma kit (Qiagen) was applied to extract the exosomal total RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: exosome from plasma

tag: age

value: 51 years old

value: healthy individual


title: biological replicate 2, naive brush, Xenium mouse spinal cord

value: female


title: Eye-antennal disc, RNAseq CtBP scrib mutant Replicate 3

value: eyFLP FRT82B Cell lethal / FRT82B scrib1 CtBP87De-10


title: h0_C3_3

city: chongqing

first: Biao

last: He

state: chongqing

address: Gaotanyan street 30, Shapinba district

department: Department of Pathogen Biology

institute: Army medical university

description: Parallel sample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Mosquitoes fed on P. yoelii-infected C57BL/6 or C3-/- mice, 12h and 24h later mosquitoes were collected Mosquito fed on P. yoelii infection mice using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Anopheles stephensi
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Anopheles stephensi

source_name: Body without head

extract_protocol:
Total RNA was extracted from 18 samples using Tiangen Kit, RNAprep Pure. The integrity and quality of RNA was assessed by agarose gel (Agarose horizontal electrophoresis machine model DYCP-32C) and Agilent Agilent 2100 Bioanalyzer.
The first strand of cDNA was synthesised in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers, and the second strand of cDNA was synthesised using dNTPs as raw material. The double-stranded cDNA was purified and subjected to PCR amplification to finally obtain the library. Qubit2.0 Fluorometer was used for preliminary quantification, and the library was diluted to 1.5 ng/ul. Agilent2100 bioanalyzer was used to insertsize the library to ensure the quality of the library.

value: Body without head

value: Wild type

value: mosquito has not been blood fed


title: control-43_re-used

value: 56 years old


title: Sam68 KO, time 3, replicate 2 [RNA-seq]

value: mouse embryonic stem cells


title: h0_C3_2

description: Parallel sample 2

growth_protocol: Mosquitoes fed on P. yoelii-infected C57BL/6 or C3-/- mice, 12h and 24h later mosquitoes were collected

treatment_protocol: Mosquito fed on P. yoelii infection mice


title: Eye-antennal disc, RNAseq CtBP scrib mutant Replicate 2

value: Eye-antennal disc


title: Quaking KO, time 0, replicate 1 [RNA-seq]


title: Sam68 KO, time 3, replicate 1 [RNA-seq]


title: Eye-antennal disc, RNAseq CtBP scrib mutant Replicate 1


title: control-42_re-used

value: 66 years old


title: h0_C3_1

description: Parallel sample 1


title: control-41_re-used

value: 39 years old


title: Sam68 KO, time 10, replicate 3 [RNA-seq]

source_name: Sam68 KO, time 10


title: h0_WT_3

description: Parallel sample 3

value: mosquitoes had not blood fed


title: Sam68 KO, time 10, replicate 2 [RNA-seq]


title: Eye-antennal disc, RNAseq CtBP mutant Replicate 3

value: eyFLP FRT82B Cell lethal / FRT82B CtBP87De-10


title: Eye-antennal disc, RNAseq CtBP mutant Replicate 2


title: control-36_re-used

value: 42 years old


title: Sam68 KO, time 10, replicate 1 [RNA-seq]


title: control-34_re-used

value: 54 years old


title: h0_WT_2

description: Parallel sample 2


title: Eye-antennal disc, RNAseq CtBP mutant Replicate 1


title: C_2

city: Hongo, Bunkyo-ku

first: Chikako

last: Shibata

state: Tokyo

country: Japan

institute: The University of Tokyo

data_processing:
The quality of the raw sequence reads was assessed with FastQC (Version0.11.7).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic software Version 0.38 (parameter- ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.)
Trimmed sequence reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0)
The result files of HISAT2 (.sam) were converte into .bam files with Samtools (Version 1.9).
Read count extraction and normalization were performed using featureCounts (Version 1.6.3) and transcripts per million (TPM).

source_name: HUVEC

extract_protocol:
Total RNAs were extracted using ISOGEN 2 Reagent (Nippon Gene). 1 ug of total RNA was used for the construction of sequencing libraries.
Library construction was performed at Rhelixa Corporation (Japan) using NEBNext® Ultra TM2 Directional RNA Library Prep Kit.

value: HUVEC

value: SELE overexpression

value: PBS


title: h0_WT_1

description: Parallel sample 1


title: control-33_re-used

value: exosome from plasma

value: healthy individual


title: Eye-antennal disc, RNAseq FRT82B control Replicate 3

source_name: Eye-antennal disc

value: eyFLP FRT82B Cell lethal / FRT82B


title: Sam68 KO, time 0, replicate 3 [RNA-seq]

source_name: Sam68 KO, time 0


title: Sam68 KO, time 0, replicate 2 [RNA-seq]


title: Eye-antennal disc, RNAseq FRT82B control Replicate 2


title: h12_C3_3

description: Parallel sample 3

value: Body without head

value: Wild type

value: mosquito fed on P. yoelii-infected C3-/- C57BL/6J mice 12h later


title: control-32_re-used

value: 17 years old


title: control-31_re-used


title: Eye-antennal disc, RNAseq FRT82B control Replicate 1

value: Eye-antennal disc


title: Sam68 KO, time 0, replicate 1 [RNA-seq]

value: mouse embryonic stem cells


title: h12_C3_2

description: Parallel sample 2


title: control-30_re-used

value: 35 years old


title: h12_WT_3

description: Parallel sample 3

value: mosquito fed on P. yoelii-infected WT C57BL/6J mice 12h later


title: TSA

city: Shiyan

first: Shan

last: Li

address: Renming Road 30th

institute: Hubei University of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM and read counts value of each transcript(protein_coding) was calculated using bowtie2 and eXpress.
DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern.
Assembly: GCA_001624535.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RFKM for each sample

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd.(Shanghai, China).

value: liver

value: FVB/N

value: c-Myc hydrodynamic injections

value: TSA


title: control-44

value: 63 years old


title: h12_WT_2

description: Parallel sample 2


title: Myc


title: control-35

value: 45 years old


title: C3，treated with PBS, rep 3, scRNAseq

city: Xi’an

first: Penggao

last: Dai

state: Shaanxi Province

address: No.229, North Taibai Road

department: National Engineering Research Center for Miniaturized Detection Systems

institute: Northwest University

description: Drop-seq

library_source: transcriptomic single cell

data_processing:
The processing of raw data using Drop-seq Tool (v2.3.0) and STAR (v2.7.2b)
Assembly: mm10
Supplementary files format and content: Value files and matrix files

source_name: Breast cancer tumor

extract_protocol:
Fresh tumor tissues were collected and washed with PBS. The tissues were then cut into approximately 1 mm3 pieces and incubated with a dissociation solution containing DNase I (2 mg/mL; Sigma-Aldrich) and Liberase TL (2 mg/mL; Sigma-Aldrich) at 37°C for 1 h. The dissociated cells were subsequently incubated with 1 × Red Blood Cell Lysis buffer (RBCL; Roche) at room temperature (RT) for 10 min. The cell pellets were collected via centrifugation for 5 min and resuspended in PBS. The suspension was filtered through 40-μm strainers, and single cells were counted using a hemocytometer.
The Nextera XT DNA Sample Prep Kit (Illumina) protocol was followed to prepare the sequencing libraries.

treatment_protocol:
FVIOs were injected into the tumor site at a concentration of 0.1 mg/cm3 of tumor volume.
Then the mice were exposed to an alternating magnetic field at 365 kHz for 10 min and incubated for 24 hours.

value: Breast cancer tumor

value: murine breast cancer cells

value: PBS


title: h12_WT_1

description: Parallel sample 1

value: Body without head


title: stroke-55

value: exosome from plasma

value: 55 years old

value: ischemic stroke


title: h24_C3_3

description: Parallel sample 3

value: Wild type

value: mosquito fed on P. yoelii-infected C3-/- C57BL/6J mice 24h later


title: C2，treated with PBS, rep 2, scRNAseq

description: Drop-seq


title: stroke-54

value: 36 years old


title: stroke-53

value: 68 years old


title: SD1

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: Gene expression data from E3.5 dpc

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

label: biotin

source_name: uteri of Stat3 d/d at E3.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect intact 3.5 dpc mice

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

value: uterus

tag: gender

value: Female


title: h24_C3_2

description: Parallel sample 2


title: C1，treated with PBS, rep 1, scRNAseq

description: Drop-seq


title: SD2

description: Gene expression data from E3.5 dpc


title: MF4

description: Gene expression data from E3.5 dpc

source_name: uteri of Stat3 f/f at E3.5


title: S3，treated with FVIO-MHT, rep 3, scRNAseq

description: Drop-seq

value: FVIO-MHT


title: h24_C3_1

description: Parallel sample 1


title: stroke-51

value: 58 years old


title: Pparg2, High fat diet, ZT18 MiSeq_rep2

city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

data_processing:
Adapters and primer sequences were trimmed using Trim Galore,
files were aligned to mm9 mouse genome with bowtie2.
Assembly: mm9
Supplementary files format and content: Bam files
Library strategy: 4C-seq

extract_protocol:
4C templates were prepared from 0.5-0.7 g of mouse  liver tissues homogenized in PBS 1X pH 7.4, filtered in 70 µm cell strainer and diluted to 30 ml with PBS. Cells were pelleted and crosslinked in 25 ml of DMEM with 1% of formaldehyde at room temperature under rotation for 15 minutes and immediately quenching the reaction with glycine at 0.125 M final concentration for 5 minutes at 4°C. Nuclear isolation was performed in NI buffer (10mM Tris HCl, 10mM NaCl, 0.2% NP-40) for 1 h at 4°C. For first restriction, selected six-cutter enzymes were EcoRI for Pparγ2 bait, and HindIII for Dbp, Pparα and Srebp1c baits. Ten million nuclei per sample were resuspended in 500 µl of 1X NEBbuffer 2.1 (New England BioLabs) containing 0.3% SDS and incubated 10 min at 60°C and 50 min at 37°C. Triton X100 was added at 1.8% v/v, incubated 1 h at 37°C, and 400U of restriction enzyme were added and incubated at 37°C overnight with agitation. First ligation was performed with 100U of T4 DNA ligase (ThermoScientific Cat. No. EL0011) with 5% polyethylenglicol in 7ml final volume, during 6h at 16°C. DNA crosslinking was reversed by adding 30 µl of 10 mg/ml proteinase K (EMD Millipore Cat. No. 124568) and incubating 6h at 65°C, followed by addition of 30 µl of 10 mg/ml RNAse A (Sigma Cat. No.R5000) and incubation 45 min at 37°C. DNA was purified with phenol/chloroform extraction and sodium acetate/ethanol precipitation. The purified DNA had a second restriction with 200U of Csp6I (New England BioLabs) in 500 µl reaction volume. Finally, a second round of ligation with 200U de T4 DNA ligase with 5% PEG in a 14 ml final volume was performed. Circular DNA was resuspended in molecular grade H2O. Efficiency of each reaction was evaluated by loading DNA in 0.8% agarose gel.
Libraries were prepared with a two-step PCR procedure. For each 4C template, eight reactions of 100-200 ng were amplified by PCR using high fidelity Hot Start Phusion II DNA polymerase (ThermoFisher, F549) and long-template specific-bait primers containing the NexteraXT overhang sequences (Pparγ2_EcorI: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGATTAGTTTTATCTCTATTTAACTTGA Pparγ2_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATAGACTTGTTGAATAAATCACCT Dbp_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAACCTGTTCTGTGGTGGATAAGC Dbp_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCACTGGTTTTTGCCTGGAGGTC Pparα_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCATCTCCAGGGTCTCAGTTTTGCA Pparα_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCATTTTCCTACCCTGGCCTGTA Srebp1c_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATCTGTCCCTGTCCCTTGCTGG Srebp1c_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTGTCGGGGTAGCGTCTG), 2 min at 98°C, (15s at 98°C, 1 min at 48°C , 3 min at 72°C) x 30 cycles and a final extension of 7 min at 72°C. PCRs were pooled and for a second round of PCR using NexteraXT index kit. PCR products were size selected with 2% agarose gel to 200 bp-2kb, purified with gel purification kit (Qiagen) and fragment size distribution analyzed with bioanalyzer tapestation (Agilent).

value: liver

tag: time

tag: diet

value: High Fat

tag: gene


title: S2，treated with FVIO-MHT, rep 2, scRNAseq

description: Drop-seq

tag: tissue

value: Breast cancer tumor

tag: cell line


title: h12_C3_1

description: Parallel sample 1

tag: genotype

value: mosquito fed on P. yoelii-infected C3-/- C57BL/6J mice 12h later


title: h24_WT_3

description: Parallel sample 3

tag: treatment

value: mosquito fed on P. yoelii-infected WT C57BL/6J mice 24h later


title: Pparg2, High fat diet, ZT18 MiSeq_rep1


title: MF2

description: Gene expression data from E3.5 dpc


title: Pparg2, High fat diet, ZT6 MiSeq_rep2


title: stroke-49

value: 71 years old


title: MF1

description: Gene expression data from E3.5 dpc


title: h24_WT_1

description: Parallel sample 1

value: Body without head


title: h24_WT_2

description: Parallel sample 2


title: SD3

description: Gene expression data from E3.5 dpc


title: stroke-48

value: exosome from plasma

value: 63 years old


title: CT26-sgMEN1-3-3_S7

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR/2.4.2a with parameters --clip3pNbases 0       --clip5pNbases 0 --outFilterMultimapNmax 2    --outFilterMismatchNoverReadLmax 0.04  --outSAMmapqUnique 255 --outSAMtype BAM SortedByCoordinate  --outSAMattributes All
The number of reads falling in the exons were calculated using HTSeq/0.11.0.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CT26 tumor

growth_protocol: CT26 cells were cultured in RPMI-1640 and supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Men1 was knockout by lenti-guide virus.

tag: cell type

value: colon

tag: growth

value: in vivo

value: BALB/c


title: stroke-46

value: 64 years old

value: ischemic stroke


title: Ad-FAT10 Pema n4

city: Lille

first: Lucie

last: Bernard

state: North

address: Boulevard du Professeur Jules Leclercq

country: France

data_processing:
SOAPnuke was used on fastq data in order to filter adapter, read length, remove N, remove polyX and filter low quality data
Alignment was made using STAR version 2.7.6
DESeq2(version 2.11.40.6) was run on a local galaxy instance (v 19.09) for differential gene expression
DESeq2(version 1.36.0) was also used on a R instance (version 4.2.0) for differential gene expression
Assembly: GRCm39 version 104
Supplementary files format and content: BAM file are binary alignment format generated by STAR

source_name: Liver

extract_protocol:
Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.
Fat10 overexpression was performed on C57BL/6J wild-type mice (8 weeks of age) by injecting via the tail vein a solution containing 2.5x108 genome copies (GC) of a control adenovirus: Ad-CTRL or the overexpressing adenovirus: Ad-FAT10 both purchased from Genecust. Four days after adenovirus injections, mice were treated with 1 mpk of pemafibrate or vehicule (CMC) by oral gavage 18h and 5h before livers were taken. Mice were fasted 5h before the livers were taken.
RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).
The library construction method and sequencing process are carried out according to the following steps: 1.Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3.The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5.The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6.Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Liver

value: Ad-FAT10 Pema


title: CT26-sgMEN1-3-2_S10


title: Ad-FAT10 Pema n3


title: stroke-45

value: 50 years old


title: Ad-FAT10 Pema n2


title: stroke-50

value: 65 years old


title: Pparg2, Control diet, ZT18 MiSeq_rep1

value: liver

value: Control


title: Day22CART_Biorep3

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
*library strategy: CRISPR Screen
Paired-end read files for each sample were merged with bbmerge before using MAGeCK-VISPR to perform quality and differential expression analysis. The maximum likelihood estimation method within MAGeCK-VISPR was used to determine selection of gRNAs in the screen as normalized to the list of 1,000 non-targeting gRNAs included in the GeCKO library A.
Assembly: sgRNA sequences in the GeCKO v2 library A (supplementary file)
Supplementary files format and content: tab deliminated file containing normalized counts for each gRNA in each sample

source_name: T-cell

extract_protocol:
To prepare for sequencing, 3.5x10^7 cells from baseline (Day 8) and chronically stimulated (Day 22) timepoints were washed and pelleted before storage at -20°C. Next, genomic deoxyribonucleic acid (gDNA) was isolated from each cell pellet with the Quick-DNA Midiprep Plus Kit (cat #D4075, Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. An ethanol precipitation protocol was performed to enhance the purity of the gDNA following isolation. Next, the gDNA was prepared for sequencing through library PCR.
For the library PCR, the NEBNext® High-Fidelity 2X PCR Master Mix (cat #M0541S, New England BioLabs, Ipswich, MA, USA) was used with the primers and the cycling conditions that were developed and described in the referenced protocol paper for the GeCKO v2 library (https://doi.org/10.1038/nprot.2017.016).

treatment_protocol: T-cells from three healthy donors were isolated and stimulated with CD3/CD28 beads. 24-hours later, they were transduced with a lentivirus to generate CART19-28ζ cells. Then, the next day (Day 2), the CART cells were transduced with a lentivirus for the GeCKO v2 library A CRISPR knockout library. Then, the CART cells were expanded and treated with puromycin until Day 8 to select for cells successfully transduced with the CRISPR library. On Day 8, a sample of CART cells were kept for DNA isolation and sequencing and another sample of cells were exposed to chronic stimulation in our in vitro model of exhaustion for two weeks (until Day 22). On Day 22, a sample of CART cells were isolated and preserved for DNA isolation and sequencing.

value: T-cell

value: Day 22


title: CT26-sgMEN1-1-3_S6


title: S1，treated with FVIO-MHT, rep 1, scRNAseq

description: Drop-seq

value: Breast cancer tumor

value: murine breast cancer cells

value: FVIO-MHT


title: Day8CART_Biorep3

value: Day 8


title: CT26-sgMEN1-3-4_S1

value: colon


title: Day22CART_Biorep2


title: Ad-FAT10 CMC n4

value: Ad-FAT10 CMC


title: CT26-sgMEN1-1-1_S8

value: in vivo

value: BALB/c


title: Dbp, High fat diet, ZT18 MiSeq_rep2

value: High Fat

value: Dbp


title: CT26-sgEV-6_S5


title: Ad-FAT10 CMC n3

value: Liver


title: Day8CART_Biorep2


title: Pparg2, High fat diet, ZT6 MiSeq_rep1


title: Pparg2, Control diet, ZT6 MiSeq_rep1


title: Ad-FAT10 CMC n2


title: CT26-sgEV-4_S9


title: Pparg2, Control diet, ZT18 MiSeq_rep2


title: Day22CART_Biorep1


title: Dbp, High fat diet, ZT6 MiSeq_rep2


title: CT26-sgEV-3_S3


title: CT26-sgMEN1-1-4_S2


title: Pparg2, Control diet, ZT6 MiSeq_rep2


title: Ad-FAT10 Pema n1

value: Ad-FAT10 Pema


title: Ad-FAT10 CMC n1


title: Dbp, Control diet, ZT18 MiSeq_rep2


title: GROseq_wildtype_rep3

first: Yinxiu

last: Zhan

address: Via Adamello 16

institute: European Institute for Oncology

description:
T180xNI746_st5_rep3
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv

data_processing:
The GRO-seq data was processed as in Ibarra et al. 2021. In brief, 5’ adaptamers were trimmed using Cutadapt [Martin et al., 2011] (version 2.5) (-a “NNNNTGGAATTCTCGGGTGCCAAGG” --overlap=3 --minimum-length=12 --max-n). Afterwards, the SE library was mapped using Bowtie2 v2.3.3.1 with default parameters and bowtie2 –local alignment  [Langmead and Salzberg, 2012]. Only alignments with MAPQ3 or higher were kept. For sequence read quality control samtools v1.10.0 [Li et al., 2009], deeptools v3.3.1 [Ramirez et al., 2014], FastQC v0.11.5 [Andrews., 2010] and MultiQC v1.8 [Ewels et al., 2016] were used.
For differential gene expression analysis, featureCounts from the subread package v1.5.3 (-t gene -Q 3 -s 1) [Liao et al., 2014] followed by DESeq2 analysis 1.30.1 [Love et al., 2014] were used. For the DESeq2 run, genes with less than 10 reads were discarded and the condition was used for the design matrix. After the DESeq2 analysis, log-fold change shrinkage was applied using the DESeq2 built-in ‘normal’ mode.
For differential repeat expression, the trimmed fastq files were processed by the noncoding-RNA-seq module from snakePipes v2.5.1 [Bhardwaj et al., 2019]. In brief, the noncoding-RNA-seq module used TEtranscript [Jin et al., 2015] to estimate the abundance in repeat families followed by the snakePipes implementation of the DESeq2 analysis.
Assembly: dm6.22; ensembl96
Supplementary files format and content: tsv; counts table for genes (featureCounts) and repeats (TEcount)
Library strategy: Gro-seq

source_name: cycle 14  embryo

growth_protocol: Embryos were aged at 25C

extract_protocol:
After running the nuclear run-on reaction the RNA was extracted by TRIzol extraction and subjected to streptovidin pull-down and extracted by Phenol:Chloroform purification.
For purified RNA 3' and 5' adapters were added and purified by sptreptovidin beads. The RNA was reverse transcribed and cDNA was amplified.

value: cycle 14  embryo

value: wildtype

value: control


title: Dbp, High fat diet, ZT6 MiSeq_rep1

value: liver


title: CT26-sgEV-2_S4


title: KO-3

first: Xinghua

last: Gao

state: Jiangsu

address: #639 Longmian Dadao

institute: China Pharmaceutical University

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
Hisat2 (version:2.0.4) was used to map the cleaned reads to the human GRCh38 reference genome with two mismatches. After genome mapping, Stringtie (version:1.3.0) was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using edgeR.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) .The fold-changes were also estimated according to the FPKM in each sample. The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: mm8
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Mouse colon tissue

growth_protocol: Age-matched male TRPC-hepta knockout and TRPC-hepta control mice treated with DSS.

extract_protocol:
Colon tissue were removed, flash frozen on dry ice, and total RNA was extracted using RNeasy mini kit (Qiagen, Germany) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon tissue from DSS-treated TRPC-hepta knockout mice

tag: developmental stage

value: DSS treatment for 6 days and sacrifice


title: Day8CART_Biorep1

value: T-cell


title: Dbp, High fat diet, ZT18 MiSeq_rep1


title: Ad-CTRL Pema n3

value: Ad-CTRL Pema


title: KO-2

treatment_protocol: Age-matched male TRPC-hepta knockout and TRPC-hepta control mice treated with DSS.


title: GROseq_wildtype_rep2

description:
T180xNI746_st5_rep2
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv


title: Ad-CTRL Pema n4


title: GROseq_wildtype_rep1

description:
T180xNI746_st5_rep1
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv


title: Ad-CTRL Pema n2


title: KO-1


title: GROseq_tripleMutant_rep4

description:
NI762xNI746_st5_rep4
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv

value: triple mutant

value: H3K9 HMT removed


title: Dbp, Control diet, ZT18 MiSeq_rep1

value: Control


title: Ad-CTRL Pema n1


title: Dbp, Control diet, ZT6 MiSeq_rep1


title: Ad-CTRL CMC n4

value: Ad-CTRL CMC


title: GROseq_tripleMutant_rep3

description:
NI762xNI746_st5_rep3
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv


title: C2

value: Colon tissue from DSS-treated TRPC-hepta control mice


title: C3


title: GROseq_tripleMutant_rep2

description:
NI762xNI746_st5_rep2
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv


title: MEF_WT_bioreplicate2

city: Memphis

first: Chunliang

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

data_processing:
Library strategy: Capture-C
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: mm9

source_name: fibroblast

growth_protocol: Wildtype MEFs were prepared from mouse embryos of C57Bl/6 strain at 13.5 days post coitum (dpc) as described previously [2]. Primary MEFs were maintained in DMEM (Lonza) supplemented with 10% FBS (Hyclone), 2mM glutamine (Invitrogen), 0.1mM non-essential amino acids (Invitrogen), and 55 uM b-mercaptoethanol (Invitrogen). HCT1116 cells (ATCC, CCL-247) IMR90 cells (ATCC, CCL-186) were maintained with DMEM (Lonza) supplemented with 10% FBS (Hyclone). SEM cells (DSMZ, ACC-546) were grown in RPMI 1640 with L-glutamine (Fisher Scientific). All cells were maintained at 37 °C in a 5% CO2 atmosphere and 95% humidity.

extract_protocol:
Suspension cells (SEM) cells were collected at 1X107 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.

value: Mouse Embryonic Fibroblasts

tag: genotype/variation

value: CTCF probe

tag: variation

value: wild type


title: MEF_MYC-OE_bioreplicate2

tag: strain

value: myc knockout


title: C1

city: Nanjing


title: Ad-CTRL CMC n2

value: Liver


title: GROseq_tripleMutant_rep1

description:
NI762xNI746_st5_rep1
GRO-seq.featureCounts.mapq3.tsv
GROseq_TEcount.tsv

value: cycle 14  embryo


title: MEF_WT

data_processing:
Library strategy: Capture-C
The paired-end reads were reconstructed into single reads with FLASH1.2.11
Digested in silico with the DpnII2E.pl script
aligned to the human genome using Bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml).
Interaction frequencies were determined using CCanalyser2.pl (https://github.com/telenius/captureC/releases).
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
Suspension cells (SEM) cells were collected at 1X10^7 cells per reaction while adherent cells (IMR90, HCT116 and human iPS) were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction. Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.
NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.

tag: mouse strain

value: fibroblast


title: Dbp, Control diet, ZT6 MiSeq_rep2

value: liver

value: Dbp


title: Ad-CTRL CMC n1


title: MEF_MYC-OE


title: ND18_RNAi_A_D_4

city: Glasgow

first: Alberto

last: Sanz

address: Davidson Building

department: School of Molecular Biosciences

country: United Kingdom

institute: University of Glasgow

data_processing:
Raw reads were pre-processed through TrimGalore V.0.6.5, which combines FastQC to determine quality and Cutadapt to trim reads if necessary
Mapping of the trimmed reads was conducted in HISAT2 V.2.2.1
All reads were aligned to the pre-built Hisat2 D. Melanogaster BDGP6 index (obtained through HISAT2’s website – last accessed 14/9/22)
Sam files were sorted and converted to Bam files using Samtools V.1.10
Counts were established using StringTie V.2.1.1
Assembly: Each sample was annotated via StringTie using ‘dmel-all-r6.41.gtf’
Supplementary files format and content: gene_count_matrix_ND75.csv: a csv file containing normalized counts for all sequenced samples
Supplementary files format and content: gene_count_matrix_ND18.csv: a csv file containing normalized counts for all sequenced samples

source_name: whole flies

growth_protocol: Flies were maintained on standard media (1% agar, 1.5% sucrose, 3% glucose, 3.5% dried yeast, 1.5% maize, 1% wheat, 1% soya, 3% treacle, 0.5% propionic acid, 0.1% Nipagin) at 25°C in a controlled 12 h light: dark cycle

extract_protocol:
Total RNA was extracted in quadruplicate from male  3-5 day old adults of the indicated genotypes and experimental groups using standard Trizol (ThermoFisher) extraction
RNA samples were submitted to the University of Glasgow Polyomics facility for QC (Agilent), PolyA selection, Library preparation (TruSeq Stranded mRNA Library Prep) and sequencing using the Illumina Next Seq platform (NextSeq 2000 P3 Reagents, NextSeq 500/550 High Output Kit v2.5)

treatment_protocol: To activate tubGS from development, mating adults were flipped onto media containing titrated concentrations of RU486 (up to 0.5µM). To activate tubGS from adulthood, male progeny were collected and placed on standard media containing 500µM RU486

value: whole flies

tag: Sex

value: male


title: Replicate 3, macaque, snRNA-seq

description: 10x Genomics

data_processing:
Illumina sequencing bcl files were converted to fastq format using the cellranger mkfastq command line tool. Fastq reads were then aligned to the rheMac10 reference genome and quantified into a raw UMI count matrix using the STAR aligner with the -solo option against a custom transcriptome annotation that we previously developed was also given as input to the STAR aligner. Each biological replicate underwent a separate but standardized quality control (qc) filtering, whereby empty droplets were detected using the defaultDrops() function, which is a quantile filtering approach based on number of UMIs, with default parameters in the DropletUtils package. Doublet filtering was also performed using the cxds_bcds_hybrid() function, which uses a hybrid approach utilizing artificial generated doublets and unlikely coexpression pairs to create a doublet score in the SCDS package. Droplets with doublet scores above 1.0 were removed.  After both rounds of filtering, 12,243 cells were left across 3 replicates. Both functions were run with default parameters. The filtered digital gene expression matrices were then loaded into Scanpy to perform the pre-clustering needed for Scran normalization. Each biological replicate expression count matrix was then normalized with log counts per million (CPM), and denoised using iterative pca with 50 components. The pre-clustering was done via the Leiden community detection algorithm using Scanpy’s leiden() function. All 3 biological replicates were then co-normalized using the computeSumFactors() function in Scran and normalize() function in Scuttle with the pre-clusters as input. The size factor normalization that was used was chosen for its ability to handle sparse single cell data which may have cell types with different expression values.
Post-normalization clustering was performed again using Scanpy’s Leiden function. The clusters were classified into oligodendrocytes 1 and oligodendrocytes 2, neurons, astrocyte 1 and astrocyte 2, oligodendrocyte precursor cells, microglia, meninges, ependymal cells and Schwann cells based on the expression of established marker genes. Neuronal clusters were then manually selected using the marker gene RBFOX3, which left a total of 2,698 cells across replicates. Data integration across biological replicates and neuron filtered gene expression matrices were performed using the integrate_scanpy() function in Scanorama, which uses a panoramic stitching algorithm to integrated datasets by producing a batch corrected cell-cell distance graph. Leiden community detection was then performed with a resolution of 1.0 on the batch corrected cell-cell distance graph to get an initial integrated clustering. It is important to note that while the Scanorama batch corrected data was used for clustering and integration, the ‘un-corrected’ data was used for marker gene and differential expression analysis to reduce possible bias added during batch correction.  Our initial clustering was organized into a dendrogram using Ward hierarchical clustering. Further refinement of these clusters was performed by splitting clusters that had both excitatory and inhibitory markers (SLC17A6 and SLC32A1, respectively). We computed a mid-ventral and dorsal score for each cluster based on the average z-score scaled expression of genes that have a high discriminative ability (AUROC) between the spinal cord regions as computed by previous studies.  Two of the macaque clusters were thus grouped into a single cluster labeled midVentral. This cluster is excluded from our analysis of the dorsal horn populations as it lies outside our region of interest. The list of dorsal horn clusters was initially 11 excitatory clusters and 5 inhibitory clusters, and then extended to 7 inhibitory clusters. Inh-SORCS1/Inh-PDZD2 and Inh-MEF2C/Inh-NXPH1 were split afterwards based on discrepancies between mouse and macaque
Assembly: rheMac10
Supplementary files format and content: Processed H5 Seurat object of all neurons: macaque_integrated_neuronsv3.h5seurat
Supplementary files format and content: Processed H5 Seurat object of dorsal horn subtypes with conserved labels: macaque_rna_dh_conserved_names.h5seurat

molecule: nuclear RNA

organism: Macaca mulatta

source_name: spinal cord grey matter dorsal to central canal

extract_protocol:
Three male macaques (3-years old) were used for the single nuclear RNA-sequencing. Snap-frozen lumbar spinal cord segments were removed from -80ºC storage and placed into separate Petri dishes containing a cold slurry of dissection buffer consisting of 1x Phosphate Buffered Saline (PBS, ThermoFisher Scientific; AM9625), 10% Dithiothreitol (DTT, Sigma; 43816-50ML). From each animal, transverse sections (~50-75 mg) were made using a sterile razor blade. Three sections were selected for further dissection and the rest were discarded. The sections were cut in the coronal plane at the middle of the spinal cord to obtain dorsal and ventral halves. Any residual meningeal membranes were removed. The three dorsal halves were retained and the ventral halves discarded. Nuclei were isolated according to Martelotto with modifications73. The dorsal halves for each animal were transferred into separate Dounce homogenizers (Sigma) containing 1 mL of ice-cold homogenization buffer consisting of EZ Nuclei Lysis Buffer (Sigma; NUC101-1KT) with 0.5% RNasin Plus (Promega; N2615), 0.5% SUPERase-In (ThermoFisher; AM2696) and 1mM DTT. The samples were homogenized on ice using 20 strokes of Pestle A followed by 20 strokes of Pestle B. Any residual meningeal membrane was removed before switching pestles. The homogenate was filtered through a 50 µm filter (Sysmex; 04-004-2327) into a 2 mL microcentrifuge tube (Eppendorf; 022431048). An additional 0.5 mL of homogenization buffer was used to wash the Dounce homogenizer and filter. The sample was then placed on ice while the remaining samples were processed. The sample was centrifuged at 500g at 4ºC for 5 min to obtain a crude pellet containing spinal nuclei. The supernatant was removed and discarded, being careful to not disturb the pellet. The pellet was resuspended in 1.5 mL of Homogenization Buffer and allowed to sit on ice for 5 mins. The samples were again centrifuged at 500x g, 4ºC for 5 min. The supernatant was removed and the pellet was resuspended in 1 mL of Nuclei Resuspension Buffer (NRB) consisting of 1x PBS, 1% Bovine Serum Albumin (BSA, Sigma; 2905-5GM) and 1% SUPERas-In followed by centrifugation at 500g, 4ºC for 5 mins. This wash step was repeated twice more for a total of 3 washes. The final pellet was resuspended in 0.5 mL of NRB containing 6 µM 4′,6-diamidino-2-phenylindole, dihydrochloride (DAPI, ThermoFisher; D1306). The suspension was filtered through a 20 µm filter (Sysmex; 04-004-2325) into a polypropylene tube and kept on ice. Fluorescence Activated Nuclear Sorting (FANS) was performed to purify nuclei from debris on a FACSAria II (BD). Gates were set to isolate DAPI+ singlet nuclei based on forward scatter and side scatter as well as fluorescence intensity. The instrument was set to 40 pounds per square inch (psi) of pressure and a 70 μm nozzle was used, with sterile PBS sheath fluid. Nuclei were sorted into a 1.5 ml microcentrifuge tube containing 15 μl of NRB at 4ºC. For each sample, 18,000 events were sorted into the collection tube. The sorted nuclei and NRB total volume were approximately 45 µl, allowing for loading the entire suspension into the Chromium Single Cell 3’ v3 solution (10x Genomics) without further manipulation. The 10x libraries were processed according to the manufacturer’s instructions. Completed libraries were run on the Novaseq 6000 (Illumina).
Library construction and sequencing were done at the 10X Genomics Core at the University of Pittsburgh according to standard 10x workflow: https://www.10xgenomics.com/support/single-cell-atac/documentation/steps/library-prep

value: all

tag: age (years)


title: Replicate 2, macaque, snRNA-seq

description: 10x Genomics

value: spinal cord grey matter dorsal to central canal


title: hepatocytes, ss, rep4

city: Beijing

first: Li

last: Wang

address: No.15, Beisihuan Road

institute: Institute of Mechanics

data_processing:
DNBSEQ
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using  Bowtie2 and RSEM
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hepatocytes

extract_protocol:
Total RNA from each sample was extracted using TRIzol reagent (Sigma-Aldrich)
RNA libraries for RNA-seq were prepared using phi29 (Thermo Fisher Scientific) following manufacturer's protocols.

value: WT

tag: age

value: 6-8 week

value: hepatocytes

value: shear stress


title: hepatocytes, ss, rep3


title: ND18_RNAi_A_D_1


title: HEK293, pThr4, Input

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, pSer2 and  RPRD1B (HA-tag) ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters. pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg19, using BWA v.0.7.17.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20).
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
After alignment, MACS2 v.2.2.7.1 in Galaxy (parameters: --broad; --broad-cutoff of q < 0.1 for pThr4 and HA-RPRD1B; pSer2 -default) was used to call peaks for IP-samples against Input.
Assembly: hg19 (pThr4), hg38 (pSer2, HA-RPRD1B)
Supplementary files format and content: bigWig, broadPeak

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, for HA-tagged RPRD1B, HEK293 cells were double crosslinked with 2mM DSG for 15 min followed by secondary fixation with 1% formaldehyde for 10 min at room temperature. Single crosslinking was used for RPB1 ChIP using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of HA antibody (cat: C29F4), pThr4 antibody (Active Motif, cat: 61361), or pSer2 antibody (Sigma, SKU: MABE953) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000 or NovaSeq X Plus system.

treatment_protocol: To prepare samples for pThr4 ChIP, we treated HEK293 cell lysate with Ssu72/symplekin complex at 4°C for 30 minutes before binding to the 6D7 antibody. To generate T4A and T4WT CTD samples for pSer2 immunoprecipitation, transient transfection of 12 μg of either plasmid was performed using PEI. Following transfection, 2.5 μg of alpha amanitin was added to cells for 48 hours. Finally, to prepare HA-RPRD1B samples, HEK293 were transfected with HA-RPRD1B using PEI (1:7 plasmid to reagent ratio) to overexpress the protein of interest.

value: Human embryonic kidney

tag: chip antibody


title: HEK293, pThr4, Ssu72, rep6

value: pThr4 (ActiveMotif, #61361)


title: ND18_RNAi_A_D_2


title: ND18_RNAi_A_D_3


title: hepatocytes, ss, rep2


title: U937 (p53-R280I) treated with DMSO for 24 h

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Quality filtered reads were then mapped to hg38 using Hisat2
Read counts were calculated by using htseq count
Assembly: hg38
Supplementary files format and content: excel file generated by htseq count. GeneSymbol, FKPM

source_name: Myeloid malignant cell line

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
Total RNA was isolated using total RNA Purification Kit (B518651, Sangon Biotech). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U937 cells expressing indicated p53 were treated with or without 1 μg/mL ATO for 24 h.

value: Myeloid malignant cell line

value: monocyte

value: DMSO


title: Ad-CTRL CMC n3

value: Liver

value: Ad-CTRL CMC


title: U937 (p53-R280I) treated with 1 μg/ml ATO for 24 h

institute: Shanghai Jiao Tong University School of Medicine

value: ATO


title: Replicate 1, macaque, snRNA-seq

first: Michael

last: Leone

address: 4315 Tesla St

institute: Carnegie Mellon University

description: 10x Genomics


title: ND18_RNAi_A_4

value: EtOH


title: U937 (p53 wild-type) treated with ATO for 24 h

value: p53-wild type


title: U937 (p53-R273H) treated with 1 μg/ml ATO for 24 h

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Quality filtered reads were then mapped to hg38 using Hisat2
Read counts were calculated by using htseq count
Genome_build: hg38
Supplementary_files_format_and_content: excel file generated by htseq count. GeneSymbol, FKPM

tag: cell types

tag: p53 status

tag: agent

value: 1microg/ml ATO


title: HEK293, pThr4, Ssu72, rep5

tag: cell line


title: hepatocytes, ss, rep1

tag: genotype

value: male


title: ND18_RNAi_A_3

tag: tissue

value: whole flies

tag: treatment


title: U937 (p53-R273H) treated with DMSO for 24 h


title: HEK293, pThr4, Ssu72, rep4

tag: cell type


title: ND18_RNAi_A_2


title: hepatocytes, static, rep3

value: WT

value: static


title: hepatocytes, static, rep4

value: 6-8 week

value: hepatocytes


title: hepatocytes, static, rep2


title: ND18_RNAi_A_1


title: Control_A2_D_4

value: TubGS>UAS-empty


title: Sham-41_1

city: Hangzhou

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description:
MIR_rat_bulkRNAseq_gene_counts.csv
MIR_rat_bulkRNAseq_gene_TPM.csv

data_processing:
Paired-end 150 bp reads of bulk RNA-seq data were aligned to rn7 reference genome (ENSEMBL, version 67) using STAR alignment tool (version 2.7.3a) with default parameters.
Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1).2 Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth.
Assembly: rn7
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each Sample

organism: Rattus norvegicus

source_name: infarct zone

extract_protocol:
total RNA was purified from the infarct zone of Sham, MI and MI/R using RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA. The mRNA was purified from 2 μg of total RNA.
libraries for massive parallel sequencing were constructed with NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB). Library quality was assessed with Agilent Bioanalyzer 2100 system. Next-generation sequencing was performed on an Illumina HiSeq 4000 platform.

value: infarct zone

tag: group

value: Sham

value: Sprague Dawley


title: U937 (p53-V272A) treated with DMSO for 24 h

value: monocyte

value: DMSO


title: Control_A2_D_3


title: hepatocytes, static, rep1


title: U937 (p53-F270V) treated with 1 μg/ml ATO for 24 h


title: Control_A2_D_1


title: Control_A2_D_2


title: Sham-11_1


title: MI6h_R-31_1


title: U937 (p53-V272M) treated with DMSO for 24 h


title: Control_A2_4


title: U937 (p53-F270V) treated with DMSO for 24 h


title: MI6h_R-11_1


title: U937 (p53-M237V) treated with 1 μg/ml ATO for 24 h


title: MI6h_R-21_1


title: Control_A2_2


title: Control_A2_3


title: U937 (p53-F270I) treated with DMSO for 24 h


title: U937 (p53-V272A) treated with 1 μg/ml ATO for 24 h


title: Sham-31_1


title: U937 (p53-V272M) treated with 1 μg/ml ATO for 24 h


title: MI6h-18h-F4_1


title: MI6h-18h-F2_1


title: U937 (p53-M237V) treated with DMSO for 24 h


title: Control_A2_1


title: ND75_RNAi_A_D_4


title: U937 (p53-F270I) treated with 1 μg/ml ATO for 24 h


title: 4B

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomalized by RMA with Parteck Genomic Suit 7.1

organism: Caenorhabditis elegans

source_name: PLM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wormswere growen at room temparature and fed on E. coli (OP50 ) seeded NGM plate.  RNAi-exposed embryos were isolated by dissection on a depression slide glass and incubated in a wet chamber at room temparature before isolating total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Wild type (N2) hermaphrodite worms are injected with mex-1, lit-1 and pal-1 dsRNA (~300 ng/ml each) to their body cavity, and injected worms are incubated at room temprarture for >12 hours before correcting embryos.

tag: strain background

tag: time point

value: 4 hours post collection


title: U937 (p53-V143M) treated with 1 μg/ml ATO for 24 h


title: MI6h-18h-F1_1

tag: strain


title: ND75_RNAi_A_D_3


title: U937 (p53-V143M) treated with DMSO for 24 h


title: 3C

value: 3 hours post collection


title: MI24h-F4_1


title: MI24h-F2_1


title: U937 (p53-P142L) treated with 1 μg/ml ATO for 24 h


title: ND75_RNAi_A_D_1


title: U937 (p53-P142L) treated with DMSO for 24 h


title: 4C


title: 4A


title: MI24h-F1_1


title: ND75_RNAi_A_4

value: EtOH


title: U937 (p53-L130R) treated with 1 μg/ml ATO for 24 h


title: ND75_RNAi_A_3


title: 3A


title: MI24h-41_1


title: 3B


title: 2C

value: 2 hours post collection


title: 2B


title: MI24h-21_1


title: 2A


title: 1B

value: 2 hour post collection


title: ND75_RNAi_A_2

value: male


title: U937 (p53-L130F) treated with 1 μg/ml ATO for 24 h

value: 1microg/ml ATO


title: ND75_RNAi_A_D_2

value: whole flies


title: 1A

value: 1 hour post collection


title: U937 (p53-L130F) treated with DMSO for 24 h


title: 0C

value: 0 hour post collection


title: ND75_RNAi_A_1


title: 1C

value: 3 hour post collection


title: 0B


title: U937 (p53-L130V) treated with 1 μg/ml ATO for 24 h


title: MI1h_R-31_1


title: Control_A_D_3

value: TubGS>UAS-empty


title: WT

city: shanghai

first: Jianxuan

address: No. 180 Fenglin Road, Xuhui District, Shanghai

department: Department of Cardiology, Zhongshan Hospital

institute: Fudan University

data_processing:
Reads obtained from the sequencing machineswere further filtered by fastp  (version 0.18.0)，including removing reads containing adapters; removing reads containing more than 10% of unknown nucleotides (N) and removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4  with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1  in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
RNAs differential expression analysis was performed by DESeq2  software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: danREr11
Supplementary files format and content: all.genes.expression text file includes raw counts for each sample
Supplementary files format and content: all.genes.expression text file includes  FPKM values for each sample

organism: Danio rerio

source_name: cardiac tissue

extract_protocol: Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol

value: cardiac tissue

value: WT


title: salvianolate-treated zebrafish embryos

value: salvianolate-treated


title: U937 (p53-L130V) treated with DMSO for 24 h

value: monocyte


title: Control_A_D_2


title: 0A


title: U937 (p53 wild-type) treated with DMSO for 24 h

value: p53 wild-type

value: DMSO


title: U937 (p53-null) treated with DMSO for 24 h

description: Vec


title: Control_A_D_4


title: Control_A_4


title: MI1h_R-11_1

value: infarct zone

value: Sprague Dawley


title: Hs3st3a1;3b1 DKO female SMG-5

first: Vaishali

middle: N

last: Patel

state: Maryland

address: 9000 Rockville Pike

department: NIDCR

institute: National Institutes of Health

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25human genome using STAR v2.5.2a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: mm10
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Submandibular Gland

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a HiSeq2500 sequencer (Illumina).

value: Submandibular Gland

value: double knockout

value: female


title: Hs3st3a1;3b1 DKO female SMG-4


title: MI24h-11_1


title: MI1h-23h-F5_1


title: U937 (p53-L130R) treated with DMSO for 24 h


title: MI1h-23h-F4_1


title: Hs3st3a1;3b1 DKO female SMG-1


title: MI1h-23h-F1_1


title: Wildtype female SMG-5

value: Wildtype


title: T_vaginalis_rep3

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
ONT reads were basecalled using guppy. For Giardia lamblia we were using one replicate prepared in this study and two datasets from our previous paper (10.1261/rna.078793.121, GSE168675)
Poly(A) tail length was assesed using nanopolish and reads with poly(A) tail shorter than 15 nt (N. gruberi) or 30 nt (others) were discarded.
Alignment was performed using minimap2
Quantification was performed using featureCounts from Rsubread
Annotation of 3’UTRs, cleavage sites, poly(A) signals and auxiliary elements was done with custom scripts.
Assembly: Entamoeba_histolytica.JCVI-ESG2-1.0.dna_rm.toplevel.
Assembly: GiardiaDB-56_GintestinalisAssemblageAWB_Genome
Assembly: GiardiaDB-56_GintestinalisAssemblageBGS_Genome
Assembly: GiardiaDB-56_GmurisRobertsThomson_Genome
Assembly: Naegleria_gruberi_gca_000004985.V1.0.dna_rm.toplevel
Assembly: TrichDB-56_TvaginalisG3_Genome
Assembly: TrichDB-56_TfoetusK_Genome
Supplementary files format and content: Tab separated files with feature counts gene quantifications for every replicate in every organism together with genes coordinates.

organism: Trichomonas vaginalis

source_name: protist cells

growth_protocol: Giardia strains were grown in Keister’s modified TYI-S-33 medium, Trichomonas vaginalis and Tritrichomonas foetus were grown in trypticase-yeast extract maltose (TYM) medium, supplemented with 10% horse serum (Omega), 0.74% ammonium iron (II) sulfate hexahydrate (Sigma-Aldrich) and 1% penicillin-streptomycin (Sigma-Aldrich), and adjusted to pH 6.2. Entamoeba histolitica was grown in TYI-S-33 medium. All were grown axenically at 37ºC under anaerobic conditions. Naegleria gruberi was grown in M7 media in 26ºC.

extract_protocol:
RNA was extracted using TRIZOL reagent.
Nanopore libraries were prepared according to the direct RNA sequencing protocol from ONT (SQK-RNA002). Because the lengths of poly(A) tails were unknown when we initiated this study, total RNA was used in place of oligo(dT)-selected RNA. Libraries were sequenced on a FLO-MIN106 flow cell and minION sequencing device.
Oxford Nanopore Technology direct RNA sequencing

treatment_protocol: Giardia spp, E. histolitica, T. vaginalis and T. foetus were grown in log phase to no more than 80% confluence, detached by cooling on ice (E. histolytica and Giardia) or by vigorous shaking (others), and washed twice by centrifugation and resuspension in ice-cold PBS. The washed pellets were lysed in TRI Reagent (Zymo research) and RNA was extracted and purified using Direct-zol RNA Miniprep Kit (Zymo research) following the manufacturer’s instructions. Total RNA concentration and purity (A260/A280 ratio) were quantified using a NanoDropTM 1000 instrument (Thermo Fisher Scientific). RNA concentrations were >200 ng/µl and A260/A280 ratios >2.0 for all samples. Cell harvesting and RNA extraction were repeated for each parasite strain on three different three different days. Between 2X10^6 and 5X10^6 N. gruberi cells (on their 5th, 6th, or 7th passage after thawing liquid nitrogen stocks) were washed once in 2 mM Tris and spun down at 1500 RCF in a Beckman Coulter microfuge 20R at room temperature. The supernatant was aspirated, and the pellet was suspend in 1 ml TRIzol, vortexed, and promptly stored at -80 C until RNA extractions. The samples were lysed using FastPrep homogenizer with bead beating in TRIzol. Lysate was cleaned up using a Zymo kit with on column DNase treatment. Finally eluted in kit provided MQ water (40 ul). RNA integrity was vrified on Qubit.

value: protist cells


title: MI1h_R-41_1


title: Control_A_3

value: whole flies

value: male

value: EtOH


title: Control_A_D_1

value: TubGS>UAS-empty


title: Control_A_2


title: Wildtype female SMG-4


title: S1pr1CMKO Heart tissue_Post AR 24h_rep2

first: xiuxiang

last: liu

address: 150 Jimo Rd, Pudong New District

institute: Shanghai East Hospital, Tongji University School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) for 17 hours at 65Â°C in a rotating Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: heart apex, post AR 24hr, replicate 2

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared usingTRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.

treatment_protocol: Sham-operated and post-apical resection models were established in 3-day-old neonatal mouse of WT and S1pr1CMKO, and hearts from1-day post-AR were harvested.

value: heart apex


title: Wildtype female SMG-1


title: T_vaginalis_rep1


title: human subcutanous neck adipose tissue replicate4

status: Public on Jul 30 2024

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
Mapping was performed by cellranger
Cellbender was used to removie empty droplets and ambient RNA
scDblFinder was used to exclude potential doublets
Downstream analysis was performed by seurat
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Raw count matrices from cell ranger

source_name: nuclei

extract_protocol:
Frozen human subcutanous adipose tissue were miced and homogenized in dounce homogenizer on ice. The homogenized adipose tissue nuclei were washed with 1% BSA in PBS and filtered 35 um straners. Nuclei suspensions were uploaded 10x snRNAseq
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry)

value: adipose tissue

tag: source

value: subcutanous neck


title: human subcutanous neck adipose tissue replicate2


title: S1pr1CMKO Heart tissue_Post AR 24h_rep1

source_name: heart apex, post AR 24hr, replicate 1


title: human subcutanous neck adipose tissue replicate1


title: S1pr1CMWT Heart tissue_Post AR 24h_rep2

value: WT


title: CE4

data_processing:
Mapping was performed by cellranger
Cellbender was used to remove empty droplets and ambient RNA
scDblFinder was used to exclude potential doublets
Downstream analysis was performed by seurat
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Raw count matrices from cell ranger

extract_protocol:
mice adipose tissue were miced and homogenized in dounce homogenizer on ice. The homogenized adipose tissue nuclei were washed with 1% BSA in PBS and filtered 35 um straners. Nuclei suspensions were stained with Hoechst 33342 and loaded to FACS sorting and sorted based on RFP fluorecence
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry)

treatment_protocol: room temeperature, cold exposure 4 days and cold exposure 7 days

value: adipocyte


title: Primary AML bone marrow, ADT-derived cDNA, Pt-69_Dx (re-sequenced)

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw sequencing data for converted Element Aviti libraries were processed using Cell Ranger 8.0.1 to produce a filtered, aggreagated count matrix.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered, aggregated RNA count matrix

source_name: Element Aviti Library S2/AG2, Pt-69_Dx [AG2]

extract_protocol:
Cells were processed using the 10X Genomics Chromium platform to generate single-cell mRNA, ADT, and HTO libraries.
10X Genomics 3' end library kit (v3/v3.1), followed by processing with the Element Adept Library Compatibility Kit v1.1 for mRNA libraries

value: bone marrow

value: mononuclear cells

tag: library type

value: mRNA

tag: orginal illumina_library


title: Primary AML bone marrow, ADT-derived cDNA, Pt-69_Rl (re-sequenced)

source_name: Element Aviti Library S3/AG3, Pt-69_Rl [AG3]


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 49

status: Public on Jul 26 2024

city: Bunkyo

first: Zhiyang

last: Yu

state: Tokyo to

address: Hongo 2-1-1

department: Department of Neurology

institute: Juntendo University

data_processing:
Generated sequencing data was aligned and mapped to miRBase using the Bowtie2.
Assembly: hg19(whole genome) miRBase(miRNA)
Supplementary files format and content: xlsx file containing raw counts and RPM values for all samples

source_name: Serum exosome

extract_protocol:
Total Exosome RNA and Protein Isolation Kit (Thermo Fisher Scientific, Waltham, MA) was utilised to extract total RNA from serum exosomes, following the manufacturer's instructions.
Small RNA library construction, alignment and mapping were performed by staff at Thermo Fisher Scientific. The small RNA libraries were prepared with the Ion Total RNA-Seq Kit version 2 on the Ion PGM System (Thermo Fisher Scientific, Waltham, MA). Quality control of the generated small RNA library was carried out using the Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Serum samples were collected from participants at the outpatient department of Juntendo University Hospital. Upon collection, the serum samples were immediately stored at −80°C until use.

value: Serum exosome

tag: disease state

value: PD (Rasagiline Treatment)

value: Extracellular vesicles


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 48


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 47


title: Cells from relapse (Rl) specimen of Pt-12 (re-sequenced)

source_name: Element Aviti Library S1/AG1, Pt-12_Rl [AG1]


title: RT


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 46


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 45


title: S1pr1CMWT Heart tissue_Post AR 24h_rep1


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 50


title: Control_A_1

tag: Sex


title: CE7


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 42


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 43


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-10 (re-sequenced)

source_name: Element Aviti Library S4/AG4, AML-10 [AG4]

value: peripheral blood


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 41


title: T_vaginalis_rep2

value: protist cells


title: human subcutanous neck adipose tissue replicate3


title: Primary AML peripheral blood, mRNA-derived cDNA, AML-14 (re-sequenced)

source_name: Element Aviti Library S5/AG5, AML-14 [AG5]


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 39


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 38


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 37


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 35


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 36


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 34


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 44


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 32


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 31


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 30


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 28


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 29


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 26


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 21


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 23


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 40


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 25


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 24


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 16


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 22


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 19


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 17


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 18


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 15


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 13


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 20


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 12


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 10


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 04


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 11


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 03


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 05


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 14


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 33


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 09


title: Serum exosome miRNA, PD, Baseline, 2023, 48

value: PD (Baseline)


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 06


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 08


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 27


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 02


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 07


title: Serum exosome miRNA, PD, Baseline, 2023, 43


title: Serum exosome miRNA, PD, Baseline, 2023, 50


title: Serum exosome miRNA, PD, Baseline, 2023, 42


title: Serum exosome miRNA, PD, Baseline, 2023, 46


title: Serum exosome miRNA, PD, Baseline, 2023, 49


title: Serum exosome miRNA, PD, Baseline, 2023, 45


title: Serum exosome miRNA, PD, Baseline, 2023, 47


title: Serum exosome miRNA, PD, Baseline, 2023, 44


title: Serum exosome miRNA, PD, Baseline, 2023, 38


title: Serum exosome miRNA, PD, Rasagiline Treatment, 2023, 01


title: Serum exosome miRNA, PD, Baseline, 2023, 39


title: Serum exosome miRNA, PD, Baseline, 2023, 37


title: Serum exosome miRNA, PD, Baseline, 2023, 41


title: Serum exosome miRNA, PD, Baseline, 2023, 36


title: Serum exosome miRNA, PD, Baseline, 2023, 40


title: Serum exosome miRNA, PD, Baseline, 2023, 35


title: Serum exosome miRNA, PD, Baseline, 2023, 34


title: Serum exosome miRNA, PD, Baseline, 2023, 33


title: Serum exosome miRNA, PD, Baseline, 2023, 31


title: Serum exosome miRNA, PD, Baseline, 2023, 28


title: Serum exosome miRNA, PD, Baseline, 2023, 25


title: Serum exosome miRNA, PD, Baseline, 2023, 26


title: Serum exosome miRNA, PD, Baseline, 2023, 24


title: Serum exosome miRNA, PD, Baseline, 2023, 23


title: Serum exosome miRNA, PD, Baseline, 2023, 20


title: Serum exosome miRNA, PD, Baseline, 2023, 30


title: Serum exosome miRNA, PD, Baseline, 2023, 22


title: Serum exosome miRNA, PD, Baseline, 2023, 19


title: Serum exosome miRNA, PD, Baseline, 2023, 29


title: Serum exosome miRNA, PD, Baseline, 2023, 14


title: Serum exosome miRNA, PD, Baseline, 2023, 16


title: Serum exosome miRNA, PD, Baseline, 2023, 18


title: Serum exosome miRNA, PD, Baseline, 2023, 13


title: Serum exosome miRNA, PD, Baseline, 2023, 17


title: Serum exosome miRNA, PD, Baseline, 2023, 21


title: Serum exosome miRNA, PD, Baseline, 2023, 27


title: Serum exosome miRNA, PD, Baseline, 2023, 15


title: Serum exosome miRNA, PD, Baseline, 2023, 08


title: Serum exosome miRNA, PD, Baseline, 2023, 06


title: Serum exosome miRNA, PD, Baseline, 2023, 10


title: Serum exosome miRNA, PD, Baseline, 2023, 09


title: Serum exosome miRNA, PD, Baseline, 2023, 11


title: Serum exosome miRNA, PD, Baseline, 2023, 05


title: Serum exosome miRNA, PD, Baseline, 2023, 04


title: Serum exosome miRNA, PD, Baseline, 2023, 07


title: Serum exosome miRNA, PD, Baseline, 2023, 03


title: Serum exosome miRNA, PD, Baseline, 2023, 02


title: Serum exosome miRNA, PD, Baseline, 2023, 01


title: Non-decidualized ESF cells on physiological matrix, sample 2

status: Public on Jul 19 2024

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

data_processing:
Alignment to the human transcriptome on Hisat2
Reads counted against genes using featureCount
Differential expression and TPM values computed using DESeq2
Assembly: GRCh38
Supplementary files format and content: TPM values

source_name: Endometrial stromal fibroblast

growth_protocol: Human isolated ESFs were maintained in phenol red free DMEM/F12 50:50 containing 25 mM glucose and supplemented with 10% charcoal stripped fetal bovine serum (Thermo Fisher), 1% antibiotic/antimycotic, and ITS (insulin, transferrin, and selenium). To induce decidualization, ESFs were treated with 0.5 mM 8-bromo-cyclic 3',5'-(hydrogen phosphate)-adenosine (Cayman Chemicals) and 1uM Medroxyprogesterone acetate (Cayman Chemicals) in DMEM/F12 medium with 2% FBS for 4 days.

extract_protocol:
Cells were lysed and RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. RNA integrity was evaluated with Bioanalyzer 2100 (Agilent) and RIN ~8 was used for library preparation.
Library prep and RNA sequencing were performed by Novogene Inc. HISAT2 pipeline was used to align reads to NCBI GRCh38 genome assembly.

value: Endometrial stromal fibroblast


title: Non-decidualized ESF cells on physiological matrix, sample 3


title: Non-decidualized ESF cells on physiological matrix, sample 1


title: Decidualized ESF cells on scar mimetic matrix, sample 3

value: Decidualized ESF cells on physiological matrix


title: Serum exosome miRNA, PD, Baseline, 2023, 12


title: Decidualized ESF cells on scar mimetic matrix , sample 1


title: Decidualized ESF cells on physiological matrix, sample 1

value: Decidualized ESF cells on scar mimetic matrix


title: Decidualized ESF cells on physiological matrix, sample 2


title: TAK-2

status: Public on Jul 18 2024

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-GRCh38-3.0.0 genome assembly using cellranger v5.0.0
Counting data of reference gene expression levels were generated by cellranger v5.0.0 (automatic identification of chemistry properties)
Assembly: hg38
Supplementary files format and content: Tab separated values; MatrixMarket

source_name: T cell

extract_protocol:
MM1S-Luc cells were intravenously (i.v.) injected to 6-10-week old NSG mice via tail vein (2x106 cells/mouse). After 5 days, tumor xenografts were confirmed by bioluminescence imaging. Mice were injected intravenously with dosed 2.5 × 105BCMA-CAR T cells followed by treatment with TAK-981 (7.5 mg/kg, intraperitoneally (i.p.) twice per week, BIW) or Vehicle (Veh) for 2 weeks. Bone marrow mononuclear cells were isolated and stained with human CD45 antibody. Total human T cells were sorted by gating GFP-/DAPI-/human CD45+.
About 1000 cells were captured per sample on a 10xGenomics Chromium controller using a 10X V3.1 Single Cell 3’ Solution kit (10xGenomics, Chromium Next GEM Single Cell 3’ Regent kits V3.1, Cat. PN-1000268). All protocols were performed following the manufacture’s instruction. Final sequencing libraries were analyzed on a High Sensitivity DNA Chip (Agilent, Cat 5067-4626) to determine the library size. The library concentration was determined with a Qubit high Sensitivity DNA assay Kit (Thermo, Cat. Q32854). The libraries were sequenced with the paired end setting of 28 cycles of read1, 101 cycles of R2, 8 cycles of index i7 and 8 cycles of index i5 read on Illumina NovaSeq 6000 platform with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at TGEN with a depth of 100K - 135K reads per cell.

value: T cell

value: TAK-981 7.5mg/kg, twice per week, 2 weeks