title: IV_T2_INP_C

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for -sp hg38. The libraries were analyzed using a pipeline described in Bonnal et al
Assembly: hg38
Supplementary files format and content: cRPKM files have raw read counts to each human gene annotated in vast-tools. They were generated using vast-tools align with --expr option.  TRUSTED_ASSOCIATIONS have the trusted barcode-variant associations. CORRECTED_COUNTS have PSI and different metrics for BARCODE-VARIANT association in each experimental condition. INCLUSION_TABLE have PSI and different metrics per VARIANT and experimental condition. enr_INPUT_COUNTS and enr_OUTPUT_COUNTS have CPM values.
Library strategy: amplicon-seq

source_name: HeLa nuclear extracts

growth_protocol: Described in Bonnal et al

extract_protocol:
Described in Bonnal et al
mRNA sequencing: RNA was isolated using the RNeasy Mini Qiagen kit and the RNA quality was checked using Bioanalyzer (Agilent). Libraries were prepared at the CRG Genomics Unit using the TruSeq stranded mRNA Library Prep (ref. 20020595, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA were used for polyA-mRNA selection using Oligo-dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, that was performed using reverse transcriptase (SuperScript II; ref. 18064-014, Invitrogen). Then, a second strand cDNA was synthesized, incorporating dUTP in place of dTTP and generating blunt-ended ds cDNA. A single ‘A’ nucleotide was added to the 3′ ends of the blunt fragments (A-tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref. 5067-1504 or ref. DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (ref. 07960204001, Roche). Amplicon sequencing: Amplicons were checked using Bioanalyzer (Agilent) and the final steps amplification (consisting in the addition of the Illumina adaptors) were performed at CRG Genomics Unit. Both the input and output PCR products were deep sequenced. After quantification by qubit, amplification was performed by PCR using NEBNext Q5 Hot Start HiFi PCR Master Mix (ref. M0543L) and Index 1 (i7) and Index 2 (i5) primers containing Illumina's P5 and P7 sequences. Final libraries were analyzed using Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (ref. 5067‐4626 or ref. DNF‐474) to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (Ref. 07960204001, Roche).

treatment_protocol: Described in Bonnal et al

value: HeLa nuclear extracts


title: CDXRP_1

status: Public on Jun 10 2025

type: SRA

city: Boston

first: Heng

last: Du

address: 45 Francis St

country: USA

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
clean data (clean reads) were obtained by removing reads containing adapter and poly-N. Q20, Q30 and GC content of the clean data were calculated
sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: mm10/hg38
Supplementary files format and content: tab-delimited text file including raw counts
Supplementary files format and content: tab-delimited text file including RPKM values

molecule: total RNA

organism: Mus musculus

source_name: 105K Xenograft after tumor regrowth

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and streptomycin, and incubated at 37℃ in 5% CO2.

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen, #74104).
1 μg RNA per sample was used for cDNA library preparation using the NEBNextÒ UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Cells were treated with DMSO, Rapamycin (10 nM), or RMC-6272 (3 nM) for 24h (triplicates per condition).

tag: tissue

value: 105K Xenograft after tumor regrowth

tag: cell type

value: rapamycin persistant Renal cell carcinoma xenograft

tag: genotype

value: Tsc2 null

tag: treatment

value: Rapamycin

tag: concentration

value: 3 mg/kg

tag: time

value: 4 weeks


title: IV_T2_INP_B

library_source: other

molecule: other

organism: Homo sapiens

tag: cell line


title: 969_T_input

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

library_source: genomic

data_processing:
Peaks were called from each of the aligned bam files against input reads using MACS2. ChIP input was used as the background for MACS2. MACS was used to produce normalized bedgraphs, which were subsequently converted to bigWig files
Chromatin loops were determined using the Hichipper pipeline 26 and those with an FDR value of less than 0.05 were selected as high-confidence loops for further investigation.
Generate BedGraph using macs2. then Convert BedGraph to BigWig using the bedGraphToBigWig. The scores in the BigWig file represent the normalized signal intensities or read coverage, reflecting the strength of the signal detected in the ChIP-Seq experiment
Assembly: mm10
Supplementary files format and content: bigwig, mango for loop information in HiChIP
Library strategy: Hi-ChIP

molecule: genomic DNA

source_name: Sys mouse tumor

extract_protocol:
Zymo DNA clean up and concentration kit
Approximately 5-10 million cells were crosslinked and then H3K27ac antibodies were used for DNA fragment capture.
For ChIP-seq sequencing libraries were prepared from chromatin immunoprecipitated DNA samples (1 to 10 ng) using the New England Biolabs NEBNext Ultra II DNA Library Prep kit (cat#E7634L).  PCR-amplified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583) and the molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Libraries were normalized and pooled in preparation for Illumina sequencing.
HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit.

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene

tag: chip antibody


title: CVS_K07_EVT_rep1

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

description:
Stem_State_protocol: TS cells were cultured in tissue culture treated dishes pre-coated with type IV collagen in complete TS Cell Medium (Okae et al., 2018). Cell medium was replaced every two days of culture.
EVT_protocol_1_2018: EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium and analyzed on day 8 of EVT cell differentiation (Okae et al., 2018).
EVT_protocol_2_2022: EVT cell differentiation was induced by plating human TS cells into 6 cm petri dishes at a density of 1x105 TS cells per dish and cultured for two days in Spheroid Medium. After two days spheroids collected and replated in EVT Differentiation Medium and Matrigel. Cells were analyzed on day 7 of EVT cell differentiation.
ST3D_protocol: Syncytiotrophoblast cell differentiation was induced by plating TS cells into 6 cm petri dishes at a density of 300,000 cells per dish in Three-dimensional (3D) Syncytiotrophoblast Differentiation Medium (Okae et al., 2018). Cells were analyzed on day 6 of syncytiotrophoblast cell differentiation.

data_processing:
Sequence data were converted from .bcl to FASTQ file format using bcl2fastq software and de-multiplexed.
Raw FASTQ files were trimmed using default parameters (-r 0.1 -d 0.03) in Skewer (Version 0.2.2), and reads shorter than 18 bp were discarded.
Transcripts were quantified using Kallisto (Version 0.46.2).
Differentially expressed genes at FDR of 0.05 were discovered using the Bioconductor package DESeq2 in R (Version 1.32.0)

source_name: CVS

extract_protocol:
Total RNA was isolated using TRIzol/chloroform precipitation (15596018, Thermo Fisher Scientific) as previously reported (Varberg et al., 2021).
Stranded mRNA-sequencing was performed on the Illumina NovaSeq 6000 Sequencing System in the Genomics Core at the University of Kansas Medical Center. Quality control was completed with the RNA Screen Tape Assay kit (5067-5576, Agilent Technologies) on the Agilent TapeStation 4200. Total RNA (1 μg) was processed in the following steps: i) oligo dT bead capture of mRNA, ii) fragmentation, iii) reverse transcription, iv) cDNA end repair, v) Unique Dual Index (UDI) adaptor ligation, vi) strand selection, and vii) library amplification using the Universal Plus mRNA-Seq with NuQuant library preparation kit (0520-A01, Tecan Genomics). Library validation was performed with the D1000 Screen Tape Assay kit (5067-5582, Agilent) on the Agilent Tape Station 4200. Library concentrations were determined with the NuQuant module using a Qubit 4 Fluorometer (Thermo Fisher Scientific). Libraries were pooled based on equal molar amounts and the multiplexed pool was quantified, in triplicate, using the Roche Lightcycler96 with FastStart Essential DNA Green Master (06402712001, Roche) and KAPA Library Quant (Illumina) DNA Standards 1-6 (KK4903, KAPA Biosystems). Using the qPCR results, the RNA-Seq library pool was adjusted to 2.125 nM for multiplexed sequencing. Pooled libraries were denatured with 0.2 N NaOH (0.04N final concentration), neutralized with 400 mM Tris-HCl, pH 8.0, and diluted to 425 pM. Onboard clonal clustering of the patterned flow cell was performed using the NovaSeq 6000 S1 Reagent Kit (200 cycle, 20012864, Illumina). A 2x101 cycle sequencing profile with dual index reads was completed using the following sequence profile: Read 1 – 101 cycles x Index Read 1 – 8 cycles x Index Read 2 – 8 cycles x Read 2 – 101 cycles.

value: CVS

value: human trophoblast stem cells

tag: cell state

value: EVT

tag: passage

tag: protocol

tag: days of_differentiation


title: CDX_2

source_name: 105K Xenograft

value: 105K Xenograft

value: Renal cell carcinoma xenograft

value: DMSO


title: CDX_1


title: IV_T2_INP_A


title: K05_Stem_rep2

value: Stem


title: m705RP_ATAC_Rep2

data_processing:
Raw reads were filtered and aligned to hg38 or mm10 using bowtie2.
peaks were called using MACS3 with the cut-off q < = 0.01
bw files were generated using deepTools 3.5
Assembly: hg38/mm10
Supplementary files format and content: peak files and bw files

extract_protocol:
CUT&RUN was performed using a CUTANA ChIC/CUT&RUN Kit (EpiCypher, #14-1048) per manufacture’s protocol.  ATAC-seq was performed using ATAC-Seq Kit (Active Motif, #53150) per manufacture’s protocol.
For each sample, 5 ng of the purified CUT$RUN chromatin was subjected to library preparation with a NEB Ultra II DNA Library Prep Kit, followed by sequencing

value: rapamycin persistant RCC

value: 500 nM rapamycin


title: IV_T2_CTR

value: HeLa nuclear extracts


title: K05_Stem_rep1


title: 857_T_H2AK119ub

value: H2AK119ub (Cell Signaling, # 8240T)


title: CVS_K05_ST3D_rep3


title: m705RP_ATAC_Rep1

value: Tsc2 null


title: 857_T_input


title: IV_T1_INP_C


title: CVS_K05_ST3D_rep2


title: m705_ATAC_Rep2

value: Renal cell carcinoma/RCC


title: K05_Stem_rep3


title: CVS_K05_ST3D_rep1


title: 171_T_input


title: m705_ATAC_Rep1


title: CVS_K05_EVT_prot2_rep3


title: IV_T1_INP_A


title: 969_T_H2AK119ub


title: 969_T_H3K4me3

value: H3K4me3 (Cell Signaling, # 9751S)


title: m705RP_H3K27ac_Rep2

data_processing:
Raw reads were filtered and aligned to hg38 or mm10 using bowtie2.
peaks were called using MACS3 with the cut-off q < = 0.01
bw files were generated using deepTools 3.5
Assembly: hg38/mm10
Supplementary files format and content: peak files and bw files
Library strategy: CUT&RUN


title: CVS_K05_EVT_prot2_rep2


title: 171_T_H2AK119ub


title: IV_T1_CTR


title: T4_MID

source_name: HEK 293 Flp-In T-Rex

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: CVS_K05_EVT_prot2_rep1


title: 171_T_H3K4me3

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene


title: m705RP_H3K27ac_Rep1


title: m705_H3K27ac_Rep2


title: K05_EVT_prot1_rep3

value: CVS

value: human trophoblast stem cells


title: 163_T_input


title: T4_LOW


title: T4_INP_C


title: 857_T_H3K4me3


title: 163_T_H2AK119ub


title: 163_T_H3K4me3


title: m705_H3K27ac_Rep1


title: IV_T1_INP_B


title: m705RP_H3K9Lac_Rep2


title: 128_T_input


title: K05_EVT_prot1_rep1

value: EVT


title: m705RP_H3K9Lac_Rep1


title: T4_INP_B


title: K01_Stem_rep3


title: m705_H3K9Lac_Rep2


title: 128_T_H2AK119ub


title: T4_HIGH


title: K01_Stem_rep2


title: m705_H3K9Lac_Rep1


title: K01_Stem_rep1


title: 128_T_H3K4me3


title: 128 double input


title: T4_GFP


title: m705RP_H3K4me3_Rep1


title: 171 double input


title: T3_MID


title: m705_H3K4me3_Rep1


title: T3_LOW


title: K05_EVT_prot1_rep2


title: 128 input 2


title: CVS_K01_ST3D_rep3


title: CVS_K01_ST3D_rep2


title: m705RP_H3K4me1_Rep1


title: T3_INP_C


title: CVS_K01_ST3D_rep1


title: T4_INP_A


title: 163 input


title: m705_H3K4me1_Rep1


title: T3_INP_A


title: CVS_K01_EVT_prot2_rep3


title: CVS_K01_EVT_prot2_rep2


title: T3_INP_B


title: m705RP_MYC_Rep1


title: 171 input 2


title: m705RP_MYC_Rep2


title: CVS_K01_EVT_prot2_rep1


title: T3_GFP


title: 171 double ARID1A

value: ARID1A (Cell Signaling, Cat# 12354)


title: 171 BRD9

value: BRD9 (Proteintech, 24785-1-AP)


title: T3_HIGH


title: CT29_Stem_rep3

source_name: Cytotrophoblast

value: Cytotrophoblast

value: Stem


title: Knee joint single-cell RNAseq at Postnatal day 5

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
KJP5
10x Genomics
sequencing_date: Dec, 2019

library_source: transcriptomic single cell

data_processing:
Data was aligned to mouse genome mm10 (reference v3.0.0 provided by 10X Genomics) by CellRanger (version 3.1.0).
Data was also aligned to a reference file of exogenous sequences, including tdTomato (1431bp), by CellRanger (version 3.1.0).
The resulting matrix files were integrated and further processed on Seurat (version 3).
Dimension reduction including CCA, PCA, tSNE and UMAP were performed.
Clustering were performed, and differentially expressed genes between one cluster and another (or all remaining clusters) were performed. A further filtering of abs(log2(fold-change)) > 1/2 and FDR <0.05 was applied to ensure higher specificity and correct for multiple testing.
Assembly: mm10
Supplementary files format and content: *.tar archives include files containing cell-IDs, gene names, and expression counts (barcodes.tsv, genes.tsv/features.tsv, matrix.mtx).
Supplementary files format and content: EGFPs.csv: Comma-separated file containing EGFP counts per cell.

source_name: whole knee joint

growth_protocol: The mice grew under normal condition.

extract_protocol:
RNA extraction from disassociated cells was done according to standard 10X Genomics Protocol (version 2).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No special treatment is applied.

tag: age

value: whole knee joint


title: T2_INP_C


title: CVS_K01_EVT_rep3


title: 163 BRD9


title: T2_LOW


title: Meniscus single-cell RNAseq at Postnatal day 5

description:
MCP5
10x Genomics
sequencing_date: Dec, 2019

source_name: meniscus

value: meniscus


title: CVS_K01_EVT_rep2


title: CVS_K01_EVT_rep1


title: Knee joint single-cell RNAseq at E18.5

description:
KJ185
10x Genomics
sequencing_date: July, 2019

value: Lgr5eGFP-IRES-CreERT2 (Lgr5-GFP)


title: 128 input 1


title: m705_MYC_Rep1

value: Tsc2 null


title: CT29_ST3D_rep3


title: CT29_Stem_rep1


title: 171 SS18::SSX

value: SS18::SSX (Cell Signaling, # 72364)


title: 128 double SS18::SSX


title: 171 single ARID1A


title: CT29_Stem_rep2


title: 171 input 1


title: T2_HIGH


title: m705_MYC_Rep2

value: Renal cell carcinoma/RCC


title: Knee joint single-cell RNAseq at E13.5

description:
KJ135
10x Genomics
sequencing_date: Nov, 2018


title: T2_MID

value: HEK 293 Flp-In T-Rex


title: 128 SS18::SSX


title: CT29_ST3D_rep1


title: T1_MID

value: humanembryonickidney


title: T2_INP_B


title: 969 input

value: Sys mouse tumor


title: Knee joint single-cell RNAseq at E15.5

description:
KJ155
10x Genomics
sequencing_date: June, 2019


title: 969 SS18::SSX

value: mouse  express SS18::SSX2 gene


title: T2_GFP


title: T1_INP_C


title: CT29_EVT_prot2_rep3


title: Knee joint single-cell RNAseq at E12.5

description:
KJ125
10x Genomics
sequencing_date: Feb, 2021


title: CT29_EVT_prot2_rep2


title: T2_INP_A


title: N255 input


title: D3C Diabetic Cortex

type: RNA

city: Isfahan

first: Yousof

last: Gheisari

state: Isfahan

address: Isfahan university of medical sciences, isfahan, iran

department: Genetics and Molecular Biology

country: Iran

institute: Isfahan University of Medical Sciences

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a diabetic mouse; microRNA profiling conducted using the miRCURY LNA™ microarray (Cy3 labeled) to delineate diabetes-induced changes.

hyb_protocol: The hybridation process was done by Exiqon company.

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The data processing  was done by Exiqon company.

source_name: Cortex compartment of kidney, Diabetic

label_protocol: The labels contain 3 parts. First, the first letter of Diabetic or Normal, second, the indivual number of sample, and third, the first letter of Cortex or Medulla. So, this dataset has four groups: D#C, D#M, N#C, and N#M.

extract_protocol: The lef kidneys were harvested, and the cortex and medulla were separated. Te tissues were kept in RNAlater (Qiagen, Valencia, CA, USA) and stored at −70 °C until RNA extraction. Te tissues were lysed in 1 mL QIAzol (Qiagen, Valencia, CA, USA) and homogenized with TissueLyser LT (Qiagen). Next, 250 µL chloroform (Merck, Darmstadt, Germany) was added and centrifuged at 12,000 rpm for 20 min at 4 °C afer 15 min of incubation. An equal volume of cold ethanol (Merck) was added to the upper aqueous phase in a new tube and incubated at −20 °C overnight afer which, the samples were centrifuged at 14,000 g for 45 min at 4 °C. To dislodge the pellet, 75% ethanol was added and centrifuged at 12,000 g for 15 min at 4 °C. Te dried pellet was dissolved in double-distilled water. Using a BioPhotometer (Eppendorf, Hamburg, Germany), RNA concentration was measured at 260 nm.

treatment_protocol: Male DBA/2 J mice, aged 6–10 weeks, were supplied from the Pasteur Institute of Iran (Tehran, Iran). All animal studies were performed according to the NIH guide for the care and use of laboratory animals16. In addition, the study was conducted in compliance with the ARRIVE guidelines. All protocols were approved by the Isfahan University of Medical Sciences Ethics Committee (IR.MUI.MED.REC.1399.933). For fve consecutive days, streptozotocin (STZ) was dissolved in sodium citrate bufer and intraperitoneally administered to pre-starved mice at the dose of 40 mg/kg (total amount: 200 mg/kg). Control mice received citrate bufer. Mice were supplied with 10% sucrose water during STZ injection and a few days afer to avoid sudden hypoglycemia. As the mice with a lesser extent of diabetes usually do not show renal injury, one week afer the fnal STZ injection, their non-fasting blood glucose was evaluated and those with blood glucose levels below 280 mg/dL were excluded from the study. Tree months afer the last dose of STZ, mice with the blood glucose range of 300–600 mg/dL were transferred to metabolic cages to collect 24-h urine. Urine albumin concentration was measured with an ELISA test (Exocell, Philadelphia, PA), and urine volume was used to calculate total albumin excretion. Urine-specifc gravity, kidney weight, serum glucose, HbA1C, serum creatinine, and urea were also measured. Moreover, kidney tissues were sampled. Histopathologic parameters such as glomerular basement membrane thickening, mesangial matrix, increased mesangial cell proliferation, and difuse mesangial sclerosis were assessed afer Hematoxylin and Eosin (H&E) and Periodic Acid–Schif (PAS) staining. For each pathology feld, 20 serial glomeruli were evaluated, and the percentages of afected glomeruli were calculated. The Mann–Whitney U test was applied for statistical analysis.

tag: gender

value: Male

tag: strain

value: 6-8 weeks

tag: condition

value: Diabetic

tag: kidneycompartment

value: Cortex


title: D3M Diabetic Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a diabetic mouse; microRNA expression analyzed via the miRCURY LNA™ microarray (Cy3 labeled) to determine diabetes-associated alterations.

source_name: Medulla compartment of kidney, Diabetic

value: Medulla


title: T1_INP_B


title: CT29_ST3D_rep2

tag: tissue

value: Cytotrophoblast

value: human trophoblast stem cells


title: CT29_EVT_prot2_rep1

tag: cell type

value: EVT


title: N255 180

tag: genotype

value: PBRM1(Cell Signaling, Cat# 89123)


title: N8M Normal Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a normal control; microRNA expression measured on the miRCURY LNA™ microarray (Cy3 labeled).

source_name: Medulla compartment of kidney, Normal

value: Normal


title: N255 DPF2


title: CT29_EVT_prot1_rep3


title: T1_INP_A


title: 969 BRD9

value: BRD9 (Proteintech, 24785-1-AP)


title: T1_LOW


title: T1_HIGH


title: CT29_EVT_prot1_rep2


title: CT29_EVT_prot1_rep1


title: N5M Normal Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a normal control; microRNA profiling carried out using the miRCURY LNA™ microarray (Cy3 labeled).


title: N302 180


title: D9C Diabetic Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a diabetic mouse; microRNA expression analyzed via the miRCURY LNA™ microarray (Cy3 labeled) to identify diabetes-associated changes.


title: T1_GFP


title: N302 DPF2


title: CT27_Stem_rep3

value: Stem


title: Hs578T_siEPIC1_2#

city: Pittsburgh

first: Min

last: Zhang

state: PA

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

data_processing:
Sequenced reads were mapped to whole genome using STAR
Read counts were calculated using RSEM
Assembly: GRCh38
Supplementary files format and content: csv file include counts values for the samples

source_name: Mammary gland/breast

growth_protocol: A2780 cells were maintained in RPMI 1640 medium (Hyclone) supplemented with 10% fetal bovine serum (FBS), and A2780cis cells were maintained in RPMI 1640 supplemented with 10% FBS and 1µM cisplatin, and Hs578T cells were maintained in high-glucose Dulbecco's modified Eagle's medium (DMEM, Hyclone) supplemented with 10% FBS and 0.01mg / ml insulin (Sigma), and MCF-7 cells were maintained in DMEM supplemented with 10% FBS, and cells were cultured at 37 degree Centigrade and 5% CO2.

extract_protocol:
After transfection for 72 hours, total RNA was isolated using Rneasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 40 nM siRNAs targeting EPIC1 or a control gene luciferase using the Lipofectamine RNAiMAX (Life Technologies).

value: Mammary gland/breast

tag: treatment

value: EPIC1 siRNA_2#


title: A2780cis_siEPIC1_2#

source_name: Ovary

value: Ovary

value: A2780cis, cisplatin-resistant


title: D11C Diabetic Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a diabetic mouse; microRNA profiling performed using the miRCURY LNA™ microarray (Cy3 labeled) for evaluation of diabetic effects.


title: D11M Diabetic Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a diabetic mouse; microRNA expression profiled on the miRCURY LNA™ microarray (Cy3 labeled) to examine diabetic alterations.


title: CT27_Stem_rep2


title: D5M Diabetic Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a diabetic mouse; microRNA profiling performed using the miRCURY LNA™ microarray (Cy3 labeled) for diabetes-related changes.


title: D1M Diabetic Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a diabetic mouse; microRNA expression analyzed on the miRCURY LNA™ microarray (Cy3 labeled) to assess diabetic impact.


title: N339 input

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene


title: N339 180


title: CT27_ST3D_rep3


title: N302 input


title: D9M Diabetic Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a diabetic mouse; microRNA profiling performed using the miRCURY LNA™ microarray (Cy3 labeled) to capture diabetic-related alterations.

value: Male

value: 6-8 weeks


title: N339 DPF2


title: D5C Diabetic Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a diabetic mouse; microRNA profiling conducted with the miRCURY LNA™ microarray (Cy3 labeled) to evaluate diabetes effects.

value: Diabetic

value: Cortex


title: Hs578T_siEPIC1_1#

value: EPIC1 siRNA_1#


title: CT27_ST3D_rep2

description:
Stem_State_protocol: TS cells were cultured in tissue culture treated dishes pre-coated with type IV collagen in complete TS Cell Medium (Okae et al., 2018). Cell medium was replaced every two days of culture.
EVT_protocol_1_2018: EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium and analyzed on day 8 of EVT cell differentiation (Okae et al., 2018).
EVT_protocol_2_2022: EVT cell differentiation was induced by plating human TS cells into 6 cm petri dishes at a density of 1x105 TS cells per dish and cultured for two days in Spheroid Medium. After two days spheroids collected and replated in EVT Differentiation Medium and Matrigel. Cells were analyzed on day 7 of EVT cell differentiation.
ST3D_protocol: Syncytiotrophoblast cell differentiation was induced by plating TS cells into 6 cm petri dishes at a density of 300,000 cells per dish in Three-dimensional (3D) Syncytiotrophoblast Differentiation Medium (Okae et al., 2018). Cells were analyzed on day 6 of syncytiotrophoblast cell differentiation.

value: Cytotrophoblast

value: human trophoblast stem cells


title: N269 imput


title: A2780_siEPIC1_1#


title: N8C Normal Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a normal control; microRNA expression measured on the miRCURY LNA™ microarray (Cy3 labeled).

source_name: Cortex compartment of kidney, Normal


title: N5C Normal Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a normal control; microRNA expression determined using the miRCURY LNA™ microarray (Cy3 labeled).


title: CT27_ST3D_rep1


title: Hs578T_siLuc

value: Control siRNA


title: N269 DPF2


title: A2780_siEPIC1_2#


title: CT27_EVT_prot2_rep3

value: EVT


title: D1C Diabetic Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a diabetic mouse; microRNA profiling conducted using the miRCURY LNA™ microarray (Cy3 labeled) to assess diabetes-associated changes.


title: CT27_Stem_rep1


title: CT27_EVT_prot2_rep2


title: CT27_EVT_prot2_rep1


title: A2780_siLuc


title: N7C Normal Cortex

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney cortex sample from a normal control; microRNA expression analyzed via the miRCURY LNA™ microarray (Cy3 labeled).

value: Normal


title: Hybrid poplar stem under severe drought condition replicate 1 snRNA-seq

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

description: Library name: Drought 1 snRNA-seq

data_processing:
When using the Singleron snRNA-seq technology, sequencing data are initially preprocessed by the  CeleScopeV3.0.1 pipeline. CeleScope integrates a series of bioinformatic tools that align sequencing reads, generate feature-barcode matrices, and the output files for further clustering and gene expression analysis. For the bulk RNA-seq, reads were mapped to the reference genome of Populus tremula x alba HAP2 v5.1 with HISAT2.
Assembly: P. tremula × alba INRA clone 717-1B4 genome (HAP2 v5.1) and annotation files were used in these analyses.
Supplementary files format and content: For each snRNA-seq library, the processed data files correspond with the 3 outputs of the CeleScope: barcodes.tsv, features.tsv and matrix.mtx. For the bulk RNA-seq, processed data is the csv file containing the raw counts of each gene after mapping, in each sample.

molecule: nuclear RNA

organism: Populus tremula x Populus alba

source_name: Internode 15th of the stem

growth_protocol: Shoot tips and stem cuttings from in vitro-grown hybrid poplar (Populus tremula×alba INRA clone 717 1B4) were used as explants for plant multiplication. The explants were cut into small segments (10-15 mm long) and placed aseptically in Murashige and Skoog (MS) medium 1B (pH 5.7) supplemented with 2% sucrose and with indole acetic and indole butyric acids (0.5 mg/L) containing 0.7% (w/v) plant. Explants were grown under long-day (LD) 16-h light/8-h dark and 22°C conditions, 65% relative humidity, and 100 μmol m−2 s−1 photosynthetic photon flux. For the severe drought treatments, in vitro-cultivated hybrid poplars of WT, were transferred to pots containing peat, and grown under LD and 22°C conditions for 6 weeks. Then well-watering and severe drought treatment started.

extract_protocol:
To perform nuclei isolation for each library, internode 15 from one plant were placed on a glass plate with 400 μl of the Nuclei Extraction Buffer of the CyStain UV Precise P kit (Sysmex) supplemented with 2mM DTT, 0.8 U/μl of SUPERase-IN (Invitrogen), and 1:100 Protease Inhibitor (Sigma-Aldrich). Next, samples were chopped with a sterile razor blade for 2 min. This step was repeated with a 30-second interval. The homogenate was washed with 5 ml of the Staining Buffer of the CyStain UV Precise P kit from the glass plate and filtered through a pre-wetted (using the Staining Buffer) 40 μm strainer laid on top of a 50 ml conical tube placed on ice. To minimize the contamination of organelles such as chloroplast and remove the debris, the final solution, with around 5 ml of volume, was used to sort the nuclei using fluorescence-activated nuclei sorting. 80,000 nuclei were sorted with a total recovery volume of 100-120 μl in 1.5 ml RNase-free non-stick Eppendorf low binding tubes containing 10 μl of supplemented Nuclei Extraction Buffer as described above. Total RNA was extracted from hybrid poplar stem following a previosly described procedure (10.1371/journal.pone.0003567).
Nuclei were loaded to the GEXSCOPE Single Nucleis RNA chip of Singleron following their procedure targetting transcriptomic data from 10,000 nuclei per library. Bulk RNA-seq libraries and sequencing was performed with the company Macrogen. Libraries were performed using the TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: Six weeks after potting, the plants were divided into two groups: control and severe drought treatment. Irrigation was carefully controlled during the two weeks of treatment. Soil moisture in the pot of each plant was measured daily with a TEROS 10 soil moisture probe attached to a ZL6 recording station (METER Group, USA). The weight of each pot was calculated at the FC before treatments. Control plants were well-watered, keeping the solid moisture around FC (0.46 m3/m3) during the treatment. The weight of each pot was calculated at the FC before treatments. Severe drought treatment was achieved by stopping irrigation until the soil reached 15 % of its FC for 14 days. The wilting threshold was reached when soil moisture decreased to 0.10 m3/m3. Then, a small amount of water was added per pot daily to keep the 15 % of FC by weighing the pots daily.

value: Internode 15th of the stem

value: Wild type

value: Drought


title: CT27_EVT_prot1_rep3


title: VpP2326 treatment_rep3

city: 扬州市

first: Mengxian

last: Wang

state: 江苏省

address: 扬州市邗江区扬州大学文汇路校区7号楼313

country: China

institute: Yangzhou University

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Gene expression was calculated using Htseq software (V0.6.1), which calculated gene expression using FPKM (Fragments Per Kilo bases Per Million reads) (Mortazavi, 2008). FPKM is the expected number of fragments per kilobase per million base pairs of a transcriptional sequence. It also considers the impact of sequencing depth and gene length on fragments count, and is currently the most commonly used estimate of gene expression level method
Assembly: Vibrio parahaemolyticus RIMD2210633, complete genome (NC_004603.1; NC_004605.1)
Supplementary files format and content: gene expression (read counts and fpkm for each stra).

organism: Vibrio parahaemolyticus RIMD 2210633

growth_protocol: Vibrio parahaemolyticus was cultured in Tryptic Soy Broth (TSB) medium at 37℃ overnight. The strain was diluted 1:100 in fresh medium and grew to the middle of the index (OD600 = 0.6).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
Subsequent library preparation was performed using 1ug total RNA. Libraries with different indexes are then multiplexed and loaded onto the Illumina X Ten instrument according to the manufacturer's instructions (Illumina, San Diego, CA, USA) or according to the manufacturer's instructions (MGI, Shenzhen, China).

treatment_protocol: The culture medium was divided into 2 parts and 100ul H2O and 100ul phage VpP2326 were added, respectively. After 15 minutes of treatment, bacterial cells were collected for RNA extraction.

tag: phase

value: mid-exponential phase

value: VpP2326 treatment


title: ChIP-Seq of H3K27me3, EPIC1 overexpression, IP

data_processing:
Reads were aligned using bowtie2 and duplicates were removed using samtools.
MACS2 was used to do peak calling with '--broad -q 0.01'
Assembly: hg38
Supplementary files format and content: broadpeak and gappedpeak are MACS2 output.

source_name: Mammary gland/Breast

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Cells at exponential phase were treated with GFP vector or overexpressing EPIC1.

value: Mammary gland/Breast

tag: disease

value: Adenocarcinoma

value: Human epithelial cell

value: WT

value: EPIC1 overexpression


title: Hybrid poplar stem under severe drought condition replicate 2 snRNA-seq

description: Library name: Drought 2 snRNAseq


title: Hybrid poplar stem under well-watering condition replicate 2 snRNA-seq

description: Library name: Control 2 snRNA-seq

value: Control


title: A2780cis_siEPIC1_1#

value: Ovary

tag: cell line

value: A2780cis, cisplatin-resistant

value: EPIC1 siRNA_1#


title: N7M Normal Medulla

description: Mus musculus (male, DBA/2J, 6–8 weeks) kidney medulla sample from a normal control; microRNA profiling performed using the miRCURY LNA™ microarray (Cy3 labeled).

value: Male

value: 6-8 weeks

value: Medulla


title: VpP2326 treatment_rep2

address: 扬州市邗江区扬州大学文汇路校区7号楼313


title: ChIP-Seq of H3K27me3, EPIC1 overexpression, Input

tag: chip antibody

value: none (input)


title: CT27_EVT_D6_rep3

value: Cytotrophoblast

value: human trophoblast stem cells

tag: cell state

value: EVT


title: VpP2326 treatment_rep1

address: 扬州市邗江区扬州大学文汇路校区7号楼313

value: mid-exponential phase

value: VpP2326 treatment


title: Hybrid poplar stem under well-watering condition replicate 1 snRNA-seq

description: Library name: Control 1 snRNA-seq

value: Internode 15th of the stem

value: Wild type


title: ChIP-Seq of H3K27me3, Control, IP

value: Mammary gland/Breast

value: Adenocarcinoma

value: Human epithelial cell

value: WT

value: GFP vector


title: CT27_EVT_D6_rep2

tag: passage


title: water treatment_rep3

address: 扬州市邗江区扬州大学文汇路校区7号楼313

value: water treatment


title: N269 180

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene

value: PBRM1(Cell Signaling, Cat# 89123)


title: rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 4, sequencing batch 19)

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
Library name: SHR_4
SHR_4_batch19

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.4.5) to rRNA
genome Alignment Hisat2 (v2.2.1)
Stringtie (v2.2.1) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v2.2.1)
Run RSEM (v1.3.3) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.3) on filtered reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

organism: Rattus norvegicus

source_name: liver

extract_protocol:
RNA was collected from liver using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Tissue frozen in RNA later.

value: liver

value: SHR/OlaIpcv

tag: batch


title: CT27_EVT_D6_rep1

value: Cytotrophoblast

value: human trophoblast stem cells

tag: protocol

tag: days of_differentiation


title: A2780cis_siLuc

value: Ovary

value: A2780cis, cisplatin-resistant

value: Control siRNA


title: T0_MID_F

description:
T0_INCLUSION_TABLE_rep6.tab
T0_CORRECTED_COUNTS_rep6.tab

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: water treatment_rep2

address: 扬州市邗江区扬州大学文汇路校区7号楼313

value: mid-exponential phase


title: CT27_EVT_D3_rep3

value: EVT


title: rRNA Depleted totalRNA from liver from untreated LEXF5 rats (replicate 1, sequencing batch 19)

description:
Library name: LEXF5_1
LEXF5_1_batch19


title: water treatment_rep1

address: 扬州市邗江区扬州大学文汇路校区7号楼313


title: CT27_EVT_D3_rep2


title: rRNA Depleted totalRNA from liver from untreated LEXF10B rats (replicate 1, sequencing batch 19)

description:
Library name: LEXF10B_1
LEXF10B_1_batch19


title: rRNA Depleted totalRNA from liver from untreated BDIX rats (replicate 1, sequencing batch 19)

description:
Library name: BDIX_1
BDIX_1_batch19

value: BDIX/NemOdaMcwi


title: CT27_EVT_prot1_rep2


title: Primary NRCMs, lenti-TCF7L2 shRNA, replicate 2

city: Guangzhou

first: Ning

last: Hou

address: No.1 Xinzao Road

institute: Guangzhou Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2.Bowtie2 was applied to align the clean reads to the gene set,to detect genes
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05
Assembly: ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro

growth_protocol: Primary NRCMs were isolated from 1–2-day-old neonatal SD rats. In brief, hearts collected from anesthetized neonatal rats were digested with pancreatic enzymes and type II collagenase. The dissociated cells were cultured at a density of 5×106 cells/mL in Dulbecco’s modified Eagle medium containing 10% fetal bovine serum and 1% penicillin-streptomycin for 1820 h in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from lenti-TCF7L2-, lenti-shTCF7L2 -or lenti-NC-infected NRCMs using a Trizol reagent kit. The RNA quality was evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and confirmed with agarose gel electrophoresis. The mRNA was enriched with Oligo (dT) beads, fragmented, and reversely transcribed into cDNA using a NEBNext Ultra RNA Library Prep Kit
The double-stranded cDNA fragments were purified and used in a standard Illumina library preparation involving end-repair, A-tailing, adapter-ligation, and amplification by PCR. The resulting cDNA library was subjected to sequencing using the BGISEQ-500 sequencing platform at BGI Genomics (China).

treatment_protocol: For TCF7L2 overexpression or knockdown, the NRCMs were infected with Lenti-TCF7L2, Lenti-shTCF7L2, or Lenti-NC  for 16 h, followed by incubation in culture medium containing 10% fetal bovine serum and 1% penicillin-streptomycin for 48 h.

value: SD

value: cardiomyocytes

value: TCF7L2 knock down

value: Lenti-TCF7L2 shRNA infection


title: T0_MID_C

description:
T0_INCLUSION_TABLE_rep3.tab
T0_CORRECTED_COUNTS_rep3.tab


title: Primary NRCMs, lenti-TCF7L2 shRNA, replicate 3

value: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro


title: T0_MID_D

description:
T0_INCLUSION_TABLE_rep4.tab
T0_CORRECTED_COUNTS_rep4.tab


title: CT27_EVT_prot1_rep1


title: rRNA Depleted totalRNA from kidney from untreated BXH2 rats (replicate 1, sequencing batch 2)

description:
Library name: BXH2_1
BXH2_1_batch2

source_name: kidney

extract_protocol:
RNA was collected from kidney using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).

value: kidney


title: Primary NRCMs, lenti-TCF7L2 shRNA, replicate 1


title: T0_MID_B

description:
T0_INCLUSION_TABLE_rep2.tab
T0_CORRECTED_COUNTS_rep2.tab


title: ChIP-Seq of H3K27me3, Control, Input

value: Mammary gland/Breast

value: Adenocarcinoma

value: Human epithelial cell

value: none (input)

value: WT

value: GFP vector


title: Primary NRCMs, lenti-TCF7L2 WT, replicate 3

value: TCF7L2 overexpression

value: Lenti-TCF7L2 WT infection


title: Primary NRCMs, lenti-TCF7L2 WT, replicate 2


title: CT27_EVT_D3_rep1

value: Cytotrophoblast

value: human trophoblast stem cells


title: Whole heart, postnatal day 56, rep2

city: Luzhou city

first: Yuqing

last: Zheng

state: Sichuan province

address: Longmatan district No.1 Xianglin Road Section 1

institute: Southwest medical university

description: Library name: Sample5

data_processing:
Fastq files were produced using the MGI DNBSEQ-Tx sequencer.
Data quality control, genome alignment, and gene expression quantification of raw data were carried out using STOmics Analysis Workflow  (SAW v5.1.4) of BGI.
Seurat v4.0.0 was used to conduct matrix statistics, cell clustering, marker gene screening, and other analyses on gene expression data.
Assembly: GRCm38
Supplementary files format and content: gem.gz: raw gene expresion matrix
Supplementary files format and content: TissueCut.gem.gz: tissue raw gene expresion matrix
Supplementary files format and content: seurat.rds: cell cluster
Supplementary files format and content: tif: image of tissue
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Hearts of mice at P0, P7 and P56 stages were sacrificed, followed by direct dissection. Hearts were cleaned with cooled 1× PBS buffer and dried with Kimwipes. Subsequently, all heart tissue samples were rapidly frozen in liquid nitrogen before being embedded in Tissue-Tek OCT. Coronal cryosections with a thickness of 10 μm were then prepared using a Leica CM1950 cryostat. Finally, these tissue sections were affixed to Stereo-seq chips for subsequent experimental procedures.
The spatially designated probe located on the surface of the STOmics chip was capable of capturing the mRNA molecules that were released. Subsequently, a reverse-transcription process was carried out, and the resulting cDNA product was released. cDNA is amplified by PCR, digested by enzymes, screened, reamplified, looped, and constructed into a standard library for DNBSEQTM sequencing.

value: Heart


title: Whole heart, postnatal day 56

description: Library name: Sample4


title: rRNA Depleted totalRNA from liver from untreated LEXF8A rats (replicate 1, sequencing batch 19)

description:
Library name: LEXF8A_1
LEXF8A_1_batch19

value: liver


title: T0_MID_A

description:
T0_INCLUSION_TABLE_rep1.tab
T0_CORRECTED_COUNTS_rep1.tab

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: Whole heart, postnatal day 7, rep2

description: Library name: Sample3


title: T0_MID_E

description:
T0_INCLUSION_TABLE_rep5.tab
T0_CORRECTED_COUNTS_rep5.tab


title: Whole heart, postnatal day 7

description: Library name: Sample2


title: T0_LOW_D


title: Primary NRCMs, lenti-TCF7L2 WT, replicate 1

value: SD

value: cardiomyocytes


title: T0_LOW_E


title: T0_LOW_F


title: Whole heart, postnatal day 0

description: Library name: Sample1


title: 7DPIpPMA_rep2_m6A-IP

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
Library name: Sample 6_IP
m6A-IP sample corresponding to 7DPIpPMA-rep2_input

data_processing:
Base-calling using real time analaysis software within HiSeqX
Quality trimming using the highest scoring path algorithm (hsptrim-1.2.6)
Adapter trimming using cutadapt (version 4.8)
Remove sequencing artifacts using fastx_artifacts_filter of fastx_toolkit (version 0.0.14)
Remove reads aligned to human non-coding RNAs using Bowtie 2 (version 2.5.1)
Alignment of remaining reads to HCMV TB40/E complete genome using STAR (version 2.7.11a)
PCR duplicate filtering using markdup of SAMtools (version 1.18)
Remove fragments outside the 50 to 5000 length range using SAMtools (version 1.18)
Peak calling using fisher_exact and false_discovery_control of SciPy (version 1.13.0) package of python
Assembly: Human herpesvirus 5 strain TB40/E clone TB40-BAC4, complete sequence (GenBank: EF2999921.1)
Supplementary files format and content: *_peaks.bedgraph: bedgraph file containing the center bases of peaks with their FDR-adjusted p-values

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: THP-1 cells

growth_protocol: THP-1 (TBI-202; ATCC) was cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Hyclone) supplemented with 10% FBS (Hyclone), GlutaMAX-I (Gibco), HEPES (Gibco), and Normocin (InvivoGen). The cells were incubated at 37 °C under 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from latently infected THP-1 cells and treated with rDNase to remove genomic DNA. Poly(A)+ RNA was purified using a Poly(A) Purist Mag Kit (AM1922; Invitrogen). After fragmentation using RNA fragmentation reagents (AM8740; Invitrogen), an anti-m6A antibody (202-003; Synaptic Systems) was used for immunoprecipitation.
Both the input and IP samples were subjected to sequencing library preparation using SMARTer Stranded RNA-Seq Kits (634839; Takara)

treatment_protocol: PMA was treated in 5DPI.

value: THP-1 cells

value: human monocytic leukemia cells

tag: infection

value: HCMV TB40/E strain

tag: time

value: 7 DPI

value: PMA (at 5DPI)

tag: sample type

value: m6A-IP (RNA IP against m6A)

tag: merip antibody

value: 202-003; Synaptic Systems


title: Primary NRCMs, lenti-NC, replicate 2

tag: tissue

value: Neonatal rat cardiomyocytes (NRCMs) are isolated from the hearts of newborn rats and cultured in vitro

tag: strain

value: WT

value: Lenti-NC (Lentiviral vector control) infection


title: Primary NRCMs, lenti-NC, replicate 1

tag: cell type

tag: genotype


title: T0_LOW_C

source_name: HEK 293 Flp-In T-Rex


title: T0_LOW_A


title: Primary NRCMs, lenti-NC, replicate 3

tag: treatment


title: T0_LOW_B


title: R8-Lt-D

first: Le Na

last: Lau

address: Daehakro 101, Jongnogu

description: Library name: Sample 16

data_processing:
STAR v.2.7.1a alignment software
For whole transcriptome analysis, low-quality reads were filtered using the following criteria: average quality score < 20 and minimum read length < 50 bases
Filtering was performed using in-house scripts.
Assembly: Filtered reads were aligned to the rabbit reference genome (Ensembl release 103) using STAR v.2.7.1a alignment software. Gene expression levels were quantified using Cufflinks v2.2.1 with the Ensemble database, with multiread correction and frag-bias-correct options enabled to enhance measurement accuracy
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Oryctolagus cuniculus

source_name: Tissue from implant-bone contact area

extract_protocol:
To obtain RNA from the drilling site and implant-bone contact area, a curette was used to scrape the inside of the drilled holes in the rabbit tibiae after the implant had been removed from the bone section. The tissue scraped from the drilled site or implant-bone contact area was used for analysis of total RNA, which was isolated using TRIzol reagent. The extracted RNA was then treated with DNase I and purified using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Sequencing libraries were then prepared using the TruSeq stranded Total RNA library preparation kit, and paired-end sequencing (2 × 75 bp) was performed on the Illumina HiSeq 2500 platform (Illumina In., San Diego, CA, USA).

tag: rabbit number

value: Rabbit 4

tag: implant type

value: Sham

value: Tissue from implant-bone contact area

tag: location

value: left distal


title: 7DPIpPMA_rep1_m6A-IP

description:
Library name: Sample 5_IP
m6A-IP sample corresponding to 7DPIpPMA-rep1_input

tag: cell line


title: #8 Rat_Ethylene glycol_Vitamin D_1 week

city: Uchinada

first: Katsuhito

last: Miyazawa

country: Japan

institute: Kanazawa Medical University

description: Ethylene glycol (daily administration) _ Vitamin D (every other day) _ 1 week

hyb_protocol: After fragmentation, cDNA (5.5 µg) were hybridized for 16 hr at 45℃ on Affymetrix Rat Gene 2.0 ST Array. GeneChips were stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into the Affymetrix Expression Console™ Software and CHP files were generated.RMA summarization in GeneSpring GX14.9.1. RMA summarized raw signal value, and per gene normalized are both provided.

label: biotin

source_name: #8 Rat_Ethylene glycol_Vitamin D_1 week

label_protocol: Biotinylated sense-strand DNA targets were prepared from expressed transcripts (100 ng total RNA) using Ambion WT Expression Kit and GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: The collected rat kidney tissue was homogenized using a BHA-6 bead milling machine (As One Corp., Osaka, Japan), and the total RNA was extracted using an RNeasy Mini kit (QIAGEN N.V., Venio, Netherlands).

tag: age

value: Ten-week-old

tag: Sex

value: male

value: Wistar

value: kidney

tag: tissue region

value: medulla


title: T0_INP_B

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for -sp hg38. The libraries were analyzed using a pipeline described in Bonnal et al
Assembly: hg38
Supplementary files format and content: cRPKM files have raw read counts to each human gene annotated in vast-tools. They were generated using vast-tools align with --expr option.  TRUSTED_ASSOCIATIONS have the trusted barcode-variant associations. CORRECTED_COUNTS have PSI and different metrics for BARCODE-VARIANT association in each experimental condition. INCLUSION_TABLE have PSI and different metrics per VARIANT and experimental condition. enr_INPUT_COUNTS and enr_OUTPUT_COUNTS have CPM values.
Library strategy: amplicon-seq

extract_protocol:
Described in Bonnal et al
mRNA sequencing: RNA was isolated using the RNeasy Mini Qiagen kit and the RNA quality was checked using Bioanalyzer (Agilent). Libraries were prepared at the CRG Genomics Unit using the TruSeq stranded mRNA Library Prep (ref. 20020595, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA were used for polyA-mRNA selection using Oligo-dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, that was performed using reverse transcriptase (SuperScript II; ref. 18064-014, Invitrogen). Then, a second strand cDNA was synthesized, incorporating dUTP in place of dTTP and generating blunt-ended ds cDNA. A single ‘A’ nucleotide was added to the 3′ ends of the blunt fragments (A-tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref. 5067-1504 or ref. DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (ref. 07960204001, Roche). Amplicon sequencing: Amplicons were checked using Bioanalyzer (Agilent) and the final steps amplification (consisting in the addition of the Illumina adaptors) were performed at CRG Genomics Unit. Both the input and output PCR products were deep sequenced. After quantification by qubit, amplification was performed by PCR using NEBNext Q5 Hot Start HiFi PCR Master Mix (ref. M0543L) and Index 1 (i7) and Index 2 (i5) primers containing Illumina's P5 and P7 sequences. Final libraries were analyzed using Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (ref. 5067‐4626 or ref. DNF‐474) to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (Ref. 07960204001, Roche).

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: R8-Lt-P

description: Library name: Sample 15

value: Turned Ti

value: left proximal


title: T0_INP_C


title: R8-Rt-P

description: Library name: Sample 13

value: Turned Cu

value: right proximal


title: 7DPIpPMA_rep1_input

description:
Library name: Sample 5_input
input sample corresponding to 7DPIpPMA-rep1_m6A-IP

value: THP-1 cells

value: human monocytic leukemia cells

value: HCMV TB40/E strain

value: 7 DPI

value: PMA (at 5DPI)

value: input (no IP)


title: #3 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #3 Rat_Ethylene glycol_Vitamin D_1 week

value: Ten-week-old

value: cortex


title: #7 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #7 Rat_Ethylene glycol_Vitamin D_1 week

value: male

value: Wistar


title: R8-Rt-D

description: Library name: Sample 14

value: Rabbit 4

value: SLA Ti

value: Tissue from implant-bone contact area

value: right distal


title: #4 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #4 Rat_Ethylene glycol_Vitamin D_1 week

value: kidney


title: 7DPI_rep2_m6A-IP

description:
Library name: Sample 4_IP
m6A-IP sample corresponding to 7DPI-rep2_input

value: DMSO (at 5DPI)

value: m6A-IP (RNA IP against m6A)

value: 202-003; Synaptic Systems


title: #6 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #6 Rat_Ethylene glycol_Vitamin D_1 week

value: medulla


title: NK_CXCL10_2

city: Valhalla

first: Shiori

last: Eguchi

state: New York

address: 40 Sunshine Cottage Road

institute: New York Medical College

description:
Library name: B1_S2_group_S4_NK_CXCL10
Parse Biosciences

data_processing:
Single cell data were loaded into Seurat V5 in R and filtered to remove dead cells (percent of mitochondrial reads > 20%) and doublets using sample-specific cutoffs on nCount_RNA. Cell type assignment was performed using the rPanglaoDB R package. All samples were aligned to human & mouse mixed genome. A cutoff of > 75% of reads/UMIs (Unique Molecular Identifiers) was used to assign mouse and human cells. Separated human and mouse cells were analyzed independently.
Assembly: GRCh38.p12 assembly and GRCm38.p6 assembly
Supplementary files format and content: A csv file includes processed normalized data for human.
Supplementary files format and content: A csv file includes processed normalized data for mouse.

organism: Homo sapiens/Mus musculus xenograft

source_name: tumor

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee at New York Medical College (Protocol #20860) and conformed to all relevant regulatory standards.

extract_protocol:
Tumors were dissociated using the Tumor Dissociation Kit, mouse (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s protocol. The single-cell suspension was fixed using the Evercode Cell Fixation Kit (Parse Biosciences, Seattle, WA) and libraries were constructed using the Parse Biosciences platform according to the manufacturer’s protocol.
The Parse Biosciences Evercode WT Mini protocol, a simplified version of their scRNA-seq workflow, uses a split-pool combinatorial barcoding approach to profile single-cell transcriptomes without microfluidics. Instead of compartmentalizing cells into droplets, the protocol treats each cell as its own reaction compartment, using a series of barcoding rounds to label transcripts with unique sequences. This allows for scalable analysis of many cells and samples with standard lab equipment. Libraries were sequenced on Illumina NextSeq 2000 system (RRID:SCR_023614, Illumina, Inc., San Diego, CA).

treatment_protocol: Tumor bearing mice were divided into 2 treatment groups: 1) phosphate buffered saline (PBS) control and 2) expanded NK and NKTR-255. One day after tumor inoculation, expanded human NK cells (1.5 × 10^7) and NKTR-255 (0.3 mg/kg) were injected intraperitoneally (I.P), followed by NK cell injection once a week. Mice not injected with NK cells and NKTR-255 received I.P injections of 100 µL PBS.

value: tumor

value: osteosarcoma

value: NK + NKTR-255


title: NK_CXCL10_1

description:
Library name: A1_S1_group_S4_NK_CXCL10
Parse Biosciences


title: T0_INP_A

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: #5 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #5 Rat_Ethylene glycol_Vitamin D_1 week

value: Ten-week-old


title: 7DPI_rep1_m6A-IP

description:
Library name: Sample 3_IP
m6A-IP sample corresponding to 7DPI-rep1_input

value: THP-1 cells

value: human monocytic leukemia cells

value: HCMV TB40/E strain

value: 7 DPI


title: 7DPIpPMA_rep2_input

description:
Library name: Sample 6_input
input sample corresponding to 7DPIpPMA-rep2_m6A-IP

value: PMA (at 5DPI)

value: input (no IP)


title: R7-Lt-D

description: Library name: Sample 12

value: Rabbit 3

value: Turned Cu

value: Tissue from implant-bone contact area

value: left distal


title: T0_HIGH_E


title: 7DPI_rep2_input

description:
Library name: Sample 4_input
input sample corresponding to 7DPI-rep2_m6A-IP

value: DMSO (at 5DPI)


title: #1 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #1 Rat_Ethylene glycol_Vitamin D_1 week

value: male

value: Wistar

value: kidney

value: cortex


title: NK_WT_1

description:
Library name: A1_S1_group_S3_NK_WT
Parse Biosciences

value: tumor

value: osteosarcoma

value: WT

value: NK + NKTR-255


title: T0_HIGH_F

description:
T0_INCLUSION_TABLE_rep6.tab
T0_CORRECTED_COUNTS_rep6.tab

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: T0_HIGH_D


title: NK_WT_2

description:
Library name: B1_S2_group_S3_NK_WT
Parse Biosciences


title: R7-Rt-D

description: Library name: Sample 10

value: Turned Ti

value: right distal


title: R7-Lt-P

description: Library name: Sample 11

value: Rabbit 3

value: Sham

value: left proximal


title: 7DPI_rep1_input

description:
Library name: Sample 3_input
input sample corresponding to 7DPI-rep1_m6A-IP

value: THP-1 cells

value: human monocytic leukemia cells

value: HCMV TB40/E strain

value: 7 DPI

value: input (no IP)


title: PBS_CXCL10_2

description:
Library name: B1_S2_group_S2_PBS_CXCL10
Parse Biosciences

value: PBS


title: R7-Rt-P

description: Library name: Sample 9

value: SLA Ti

value: Tissue from implant-bone contact area

value: right proximal


title: #2 Rat_Ethylene glycol_Vitamin D_1 week

source_name: #2 Rat_Ethylene glycol_Vitamin D_1 week

value: Ten-week-old

value: male

value: Wistar

value: kidney

value: cortex


title: 1DPI_rep2_m6A-IP

description:
Library name: Sample 2_IP
m6A-IP sample corresponding to 1DPI-rep2_input

value: 1 DPI

value: m6A-IP (RNA IP against m6A)

value: 202-003; Synaptic Systems


title: PBS_CXCL10_1

description:
Library name: A1_S1_group_S2_PBS_CXCL10
Parse Biosciences

value: tumor

value: osteosarcoma


title: R6-Lt-D

description: Library name: Sample 8

value: Rabbit 2

value: left distal


title: T0_HIGH_C

description:
T0_INCLUSION_TABLE_rep3.tab
T0_CORRECTED_COUNTS_rep3.tab

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: T0_HIGH_B

description:
T0_INCLUSION_TABLE_rep2.tab
T0_CORRECTED_COUNTS_rep2.tab


title: 1DPI_rep1_m6A-IP

description:
Library name: Sample 1_IP
m6A-IP sample corresponding to 1DPI-rep1_input

value: THP-1 cells

value: human monocytic leukemia cells

value: HCMV TB40/E strain


title: PBS_WT_2

description:
Library name: B1_S2_group_S1_PBS_WT
Parse Biosciences

value: WT

value: PBS


title: 1DPI_rep2_input

description:
Library name: Sample 2_input
input sample corresponding to 1DPI-rep2_m6A-IP

value: input (no IP)


title: R6-Lt-P

description: Library name: Sample 7

value: Turned Cu

value: Tissue from implant-bone contact area

value: left proximal


title: PBS_WT_1

description:
Library name: A1_S1_group_S1_PBS_WT
Parse Biosciences


title: 1DPI_rep1_input

description:
Library name: Sample 1_input
input sample corresponding to 1DPI-rep1_m6A-IP

value: 1 DPI


title: T0_HIGH_A

description:
T0_INCLUSION_TABLE_rep1.tab
T0_CORRECTED_COUNTS_rep1.tab


title: R6-Rt-D

description: Library name: Sample 6

value: Sham

value: right distal


title: T0_GFP_F


title: T0_GFP_E

description:
T0_INCLUSION_TABLE_rep5.tab
T0_CORRECTED_COUNTS_rep5.tab


title: R6-Rt-P

description: Library name: Sample 5

value: Turned Ti

value: right proximal


title: Hybrid poplar stem under severe drought condition replicate 3 bulk RNA-seq

description: Library name: Drought 3 bulk RNA-seq

source_name: Stem

value: Stem

value: Wild type

value: Drought


title: Hybrid poplar stem under severe drought condition replicate 2 bulk RNA-seq

description: Library name: Drought 2 bulk RNA-seq


title: lon1-1 replicate C

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

description: stranded

data_processing:
The Sequencing was performed in a DNBSEQ G400 platform, BGI (Beijing Genomics Institute, Shenzhen, China).
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (GCF_000001735.4_TAIR10.1_NCBI_20230423)
RNA-seq data were analyzed using the SOAPnuke (version v1.5.6) with parameters ‘‘ -n 0.001 -l 20 -q 0.4 -A 0.25’’ and the HISAT2 pipeline (version v2.0.4) with parameters ‘ --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000 --rna-strandness RF’’
Clean reads were mapped to reference with Bowtie2 (version v2.2.5).
Gene expression level was calculated with RSEM with default parameters.
Normalization in fragments per kilobase per million mapped fragments FPKM)
Assembly: Arabidopsis genome (GCF_000001735.4_TAIR10.1_NCBI_20230423)
Supplementary files format and content: Excel file with  FPKM values of the trascripts of lon1-1 mutants and Col-0 plants as control

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Col-0 (control) and lon1-1 mutant seedlings were grown for 6 days vertically at Petri dishes in  dark

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA, USA) with an on-column DNase treatment from snap frozen powder of Col-0 and lon1-1 6-day old seedlings.
The concentration of RNA samples was tested by Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) and the purity was tested by NanoDropTM.Library Construction by BGI (Beijing Genomics Institute, Shenzhen, China). The stranded RNA-seq libraries were generated at BGI (Beijing Genomics Institute, Shenzhen, China) using the in-house rRNA Removal Library Construction Protocol.

value: seedlings


title: lon1-1 replicate B

description: stranded


title: R5-Lt-D

description: Library name: Sample 4

value: Rabbit 1

value: left distal


title: lon1-1 replicate A

description: stranded


title: T0_GFP_D

first: Manuel

last: Irimia

description:
T0_INCLUSION_TABLE_rep4.tab
T0_CORRECTED_COUNTS_rep4.tab

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney


title: Hybrid poplar stem under severe drought condition replicate 1 bulk RNA-seq

description: Library name: Drought 1 bulk RNA-seq


title: R5-Lt-P

description: Library name: Sample 3

value: SLA Ti


title: wt replicate C

description: stranded


title: T0_GFP_C


title: Hybrid poplar stem under well-watering condition replicate 3 bulk RNA-seq

description: Library name: Control 3 bulk RNA-seq

value: Control


title: R5-Rt-D

description: Library name: Sample 2

value: Turned Cu

value: Tissue from implant-bone contact area


title: Hybrid poplar stem under well-watering condition replicate 2 bulk RNA-seq

description: Library name: Control 2 bulk RNA-seq


title: T0_GFP_A


title: T0_GFP_B


title: wt replicate B

description: stranded


title: patch-seq, pcd145, replicate 24

status: Public on Jun 09 2025

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description:
Library name: 5_1H3
SMART-seq3

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

organism: Macaca mulatta

source_name: dlPFC

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

value: tissue

value: cortical cells

value: wild type

value: no treatment

tag: batch

value: patch-seq, pcd145, replicate 1


title: wt replicate A

description: stranded


title: patch-seq, pcd145, replicate 22

description:
Library name: 5_1F3
SMART-seq3


title: patch-seq, pcd145, replicate 21

description:
Library name: 5_1E3
SMART-seq3


title: patch-seq, pcd145, replicate 23

description:
Library name: 5_1G3
SMART-seq3


title: patch-seq, pcd145, replicate 20

description:
Library name: 5_1D3
SMART-seq3


title: patch-seq, pcd145, replicate 19

description:
Library name: 5_1C3
SMART-seq3


title: patch-seq, pcd145, replicate 17

description:
Library name: 5_1A3
SMART-seq3


title: R5-Rt-P

description: Library name: Sample 1

value: Sham

value: right proximal


title: Hybrid poplar stem under well-watering condition replicate 1 bulk RNA-seq

description: Library name: Control 1 bulk RNA-seq

value: Stem

value: Wild type


title: patch-seq, pcd145, replicate 16

description:
Library name: 5_1H2
SMART-seq3


title: patch-seq, pcd145, replicate 14

description:
Library name: 5_1F2
SMART-seq3


title: patch-seq, pcd145, replicate 18

description:
Library name: 5_1B3
SMART-seq3


title: patch-seq, pcd145, replicate 9

description:
Library name: 5_1A2
SMART-seq3


title: patch-seq, pcd145, replicate 10

description:
Library name: 5_1B2
SMART-seq3


title: patch-seq, pcd145, replicate 13

description:
Library name: 5_1E2
SMART-seq3


title: patch-seq, pcd145, replicate 8

description:
Library name: 5_1H1
SMART-seq3


title: patch-seq, pcd145, replicate 6

description:
Library name: 5_1F1
SMART-seq3


title: patch-seq, pcd145, replicate 15

description:
Library name: 5_1G2
SMART-seq3


title: patch-seq, pcd145, replicate 11

description:
Library name: 5_1C2
SMART-seq3


title: patch-seq, pcd145, replicate 3

description:
Library name: 5_1C1
SMART-seq3


title: patch-seq, pcd145, replicate 12

description:
Library name: 5_1D2
SMART-seq3


title: patch-seq, pcd145, replicate 5

description:
Library name: 5_1E1
SMART-seq3


title: patch-seq, pcd145, replicate 2

description:
Library name: 5_1B1
SMART-seq3


title: patch-seq, pcd145, replicate 4

description:
Library name: 5_1D1
SMART-seq3


title: patch-seq, pcd145, replicate 1

description:
Library name: 5_1A1
SMART-seq3


title: patch-seq, pcd125, replicate 22

description:
Library name: 5_1F6
SMART-seq3

value: patch-seq, pcd125, replicate 1


title: patch-seq, pcd125, replicate 23

description:
Library name: 5_1G6
SMART-seq3


title: patch-seq, pcd125, replicate 21

description:
Library name: 5_1E6
SMART-seq3


title: patch-seq, pcd125, replicate 18

description:
Library name: 5_1B6
SMART-seq3


title: patch-seq, pcd125, replicate 20

description:
Library name: 5_1D6
SMART-seq3


title: patch-seq, pcd125, replicate 17

description:
Library name: 5_1A6
SMART-seq3


title: patch-seq, pcd125, replicate 19

description:
Library name: 5_1C6
SMART-seq3


title: patch-seq, pcd125, replicate 16

description:
Library name: 5_1H5
SMART-seq3


title: patch-seq, pcd125, replicate 15

description:
Library name: 5_1G5
SMART-seq3


title: patch-seq, pcd125, replicate 13

description:
Library name: 5_1E5
SMART-seq3


title: patch-seq, pcd125, replicate 12

description:
Library name: 5_1D5
SMART-seq3


title: patch-seq, pcd125, replicate 11

description:
Library name: 5_1C5
SMART-seq3


title: patch-seq, pcd125, replicate 10

description:
Library name: 5_1B5
SMART-seq3


title: patch-seq, pcd145, replicate 7

description:
Library name: 5_1G1
SMART-seq3


title: patch-seq, pcd125, replicate 8

description:
Library name: 5_1H4
SMART-seq3


title: patch-seq, pcd125, replicate 5

description:
Library name: 5_1E4
SMART-seq3


title: patch-seq, pcd125, replicate 9

description:
Library name: 5_1A5
SMART-seq3


title: patch-seq, pcd125, replicate 1

description:
Library name: 5_1A4
SMART-seq3


title: patch-seq, pcd125, replicate 3

description:
Library name: 5_1C4
SMART-seq3


title: patch-seq, pcd125, replicate 6

description:
Library name: 5_1F4
SMART-seq3


title: patch-seq, pcd125, replicate 4

description:
Library name: 5_1D4
SMART-seq3


title: snRNA-seq, pcd125, replicate 2

description:
Library name: multiome snRNA-seq 9
10X genomics

value: snRNA-seq, pcd125, replicate 2


title: snRNA-seq, pcd145, replicate 1

description:
Library name: multiome snRNA-seq 10
10X genomics

value: snRNA-seq, pcd145, replicate 1


title: patch-seq, pcd125, replicate 7

description:
Library name: 5_1G4
SMART-seq3


title: snATAC-seq, pcd125, replicate 2

description:
Library name: multiome snATAC-seq 9
10X genomics

library_source: genomic single cell

value: snATAC-seq, pcd125, replicate 2


title: snRNA-seq, pcd125, replicate 1

description:
Library name: multiome snRNA-seq 8
10X genomics

value: snRNA-seq, pcd125, replicate 1


title: snATAC-seq, pcd145, replicate 1

description:
Library name: multiome snATAC-seq 10
10X genomics

value: snATAC-seq, pcd145, replicate 1


title: snATAC-seq, pcd125, replicate 1

description:
Library name: multiome snATAC-seq 8
10X genomics

value: snATAC-seq, pcd125, replicate 1


title: Xpr1fl/fl control macrophages 4

city: Zurich

first: Sebastian

middle: A

last: Stifter

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

data_processing:
Sample reads were quality control tested using FastQC.
Reads were quasi-mapped to mouse reference genome GRCm39 with the salmon package.
Data import, processing and analysis were performed using the DeSeq2 package.
Assembly: mm39
Supplementary files format and content: comma separated file contains normalized counts matrix for each sample

source_name: liver

extract_protocol:
RNA was isolated using Rneasy micro kit (Qiagen). 45ng of total RNA was used to prepare sequencing libraries.
RNA libraries for RNA-seq were prepared with Illumina stranded mRNA prep kit according to the manufacturer's instructions.

value: liver

tag: developmental stage

value: CD45+ F4/80hi CD11blow macrophages


title: Xpr1fl/fl control macrophages 3


title: Xpr1fl/fl control macrophages 2


title: patch-seq, pcd125, replicate 14

description:
Library name: 5_1F5
SMART-seq3

value: dlPFC

value: tissue

value: cortical cells


title: Xpr1fl/fl control macrophages 1


title: Mrc1Cre Xpr1fl/fl macrophages 5

value: Mrc1Cre Xpr1fl/fl


title: Mrc1Cre Xpr1fl/fl macrophages 3


title: Mrc1Cre Xpr1fl/fl macrophages 1


title: Mrc1Cre Xpr1fl/fl macrophages 4


title: Mrc1Cre Xpr1fl/fl macrophages 2


title: patch-seq, pcd125, replicate 2

description:
Library name: 5_1B4
SMART-seq3

value: wild type

value: no treatment


title: Testis, replicate 1, snRNA-seq

city: Shenzhen

first: juan

middle: li

last: chen

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Sus scrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa domesticus

source_name: Testis tissue

extract_protocol: One male and one female Meishan pig, aged 180 days , were obtained from a commercial pig farming company. Each tissue was minced into 5-10 pieces weighing approximately 50-100 mg each on ice with sterilized scissors, which were then snap-frozen in liquid nitrogen and stored at -80℃ until nuclear extraction was performed.Briefly, the tissue samples were homogenized using the Dounce homogenizer with 25 strokes of the loose pestle A and then 25 strokes of the tight pestle B in 1 ml of ice-cold homogenization buffer. After this, the mixture was filtered through a 40-μm cell strainer into a 1.5-ml tube. To collect dissociated single nuclei, the sample was centrifuged at 500g for 5 min at 4℃, and the supernatant was discarded. After centrifugation, the nucleus pellet was resuspended using the desired amount of 1× PBS/0.5% BSA with RNase inhibitor, filtered through a 40-μm cell strainer, and counted. A final concentration of 1,000 nuclei per µl was used for library preparation.

tag: breed

value: Meishan Pig

value: Testis tissue


title: Spleen, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Spleen tissue

value: Spleen tissue


title: Pituitary, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Pituitary tissue

value: Pituitary tissue


title: Ovary, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Ovary tissue

value: Ovary tissue


title: Pancreas, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Pancreas tissue

value: Pancreas tissue


title: Muscle, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Muscle tissue

value: Muscle tissue


title: Lymph, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Lymph tissue

value: Lymph tissue


title: TERRA_captured_Nanopore_direct_RNA-seq

city: Taipei

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

department: Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

description: TERRA captured RNA direct sequencing by Nanopore

data_processing:
For Nanopore dataset, the raw fast5 files were processed using Guppy base caller (guppy_GPUv5.0.7) with default settings to convert them into fastq files. Outputs from this step were merged and compressed by 'cat' and 'gzip' commands. For Illumina datasets, fastq files are raw data, no base calling step
For Nanopore dataset, fastq files will automatically split into 'pass' (Q>7) and 'fail' (Q<7) groups during base calling, all reads passed quality filter were merged into a single fastq file. For Illumina datasets, adapter sequence and low-quality reads were removed by Trimgalore (v0.6.3) using default options.
Reads were mapped to the Homo sapiens T2T-CHM13 reference genome by different alignment tools. For Illumina datasets, alignment was performed using STAR (v2.7.9a) with default parameters. For Nanopore dataset, alignment was performed using minimap2 (v2.22) with options: -ax splice, -uf, -k14
SAM format files were converted to BAM, sorted and indexed by samtools (v1.9)
Bigwig files were generated by deepTools (v3.1.1) bamCoverage with parameters: --normalizeUsing RPKM
Compared bigwig files were generated by deepTools (v3.1.1) bamCompare with parameters: --scaleFactorsMethod None, --normalizeUsing RPKM, --operation log2
TERRA transcription regions were defined on chromosome ends of T2T-CHM13 genome and recorded as a BED format file.
Reads mapped to TERRA regions were extracted from BAM file using samtools v1.17 according to the defined TERRA transcription region bed file. (samtools view -b -h -M -L TERRA_region.bed TERRA-captured_RNA-seq.bam -o TERRA_selected.bam) The number of extracted reads of each group were quantified.
Assembly: T2T-CHM13
Supplementary files format and content: tab-delimited text files include raw read counts that was mapped to TERRA regions. (Illumina and Nanopore datasets)
Supplementary files format and content: bigwig or bw are read coverage files (Illumina dataset)
Supplementary files format and content: bam file is alignment result (Nanopore dataset)
Supplementary files format and content: bed file contains TERRA transcription regions defined on the T2T-CHM13 genome.

growth_protocol: U2OS cells were cultured using Gibco Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum, L-glutamine, and 1% penicillin/streptomycin in a 37℃, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol.
For Illumina sequencing, the cDNA library was constructed using the NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S) according to the manufactory instruction with some modifications. The first-strand synthesis step was carried out by SuperScript IV (Thermo Fisher Scientific, Cat: 18090010). The TERRA-captured RNA sample was divided into two equal halves for the reverse transcription reaction. Half of the TERRA-captured sample was reverse transcribed using 2 μM random hexamers (Thermo Fisher Scientific, 48190011), while the other half using 1 μM of telomeric C-rich primer. These two groups are referred to as the random and specific groups, respectively. The rest steps were performed as the protocol provided by manufactor. For Nanopore sequencing, TERRA-enriched sample was polyadenylated using E. coli Poly (A) polymerase (New England Biolabs, #M0276S) at a final concentration of 0.25 U/μl in 1X Poly(A) Polymerase Reaction Buffer with 1 mM dATP and 2 Unit/μl RNaseOUT, (Thermo Fisher Scientific, Cat: 10777019) at 37°C for 30 minutes. The reaction was terminated by adding 10 mM EDTA. The RNA sample was purified by AMPureXP RNA beads (Beckman Coulter, A66514) then subjected to Nanopore direct RNA sequencing protocol (Cat#SQK-RNA002).


title: Kidney, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Kidney tissue

value: Kidney tissue


title: Uterus, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Uterus tissue

value: Uterus tissue


title: TERRA_captured_Nanopore_direct_RNA-seq 2

description:
Library name: TERRA_captured_Nanopore_direct_RNA-seq
TERRA captured RNA direct sequencing by Nanopore

data_processing:
For Nanopore dataset, the raw fast5 files were processed using Guppy base caller (guppy_GPUv5.0.7) with default settings to convert them into fastq files. Outputs from this step were merged and compressed by 'cat' and 'gzip' commands. Fastq files will automatically split into 'pass' (Q>7) and 'fail' (Q<7) groups during base calling, all reads passed quality filter were merged into a single fastq file. Alignment was performed using minimap2 (v2.22) with options: -ax splice, -uf, -k14. Then converted to bigwig format using DEEPTOOLS(v3.3.1) bamcoverage.
Assembly: T2T-CHM13
Supplementary files format and content: bigwig file

source_name: HeLa

growth_protocol: HeLa cells were cultured using Gibco Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum, L-glutamine, and 1% penicillin/streptomycin in a 37℃, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from 1 x 10^7 cells using TRIzol™ Reagent (Invitrogen™, Cat:15596018) following the manufacturer's protocol.
For Nanopore sequencing, TERRA-enriched RNA was polyadenylated using E. coli Poly(A) Polymerase (New England Biolabs, #M0276S) at a final concentration of 0.25 U/μl in 1× Poly(A) Polymerase Reaction Buffer containing 1 mM dATP and 2 U/μl RNaseOUT (Thermo Fisher Scientific, Cat: 10777019), and incubated at 37°C for 30 minutes. The reaction was terminated by adding 10 mM EDTA. The RNA sample was then purified using AMPure XP RNA beads (Beckman Coulter, A66514) and subsequently processed using the Oxford Nanopore direct RNA sequencing protocol (Cat# SQK-RNA004). Then subjected to FLO-MIN004RA flow cell for sequencing.

value: HeLa

value: epithelial cell


title: Jejunum, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Jejunum tissue

value: Jejunum tissue


title: Ileum, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Ileum tissue

value: Ileum tissue


title: T-cell_3xTg_rep3

city: Charleston

first: Mohamed Faisal

last: Kassir

state: SC

address: 86 Jonathan Lucas St HO509

institute: Medical University of South Carolina

description:
20230811_210502641124_Sample 09 Tg O3_09
SAMPLE 12

hyb_protocol: RNA samples isolated from T-cells were all adjusted to a concentration of 20 ng per µL in nuclease-free water (Fisher Bioreagents, Waltham, MA) for nCounter analysis (nCounter Pro MAX/Flex). Briefly, nCounter analysis begins with the hybridization of 100 ng of RNA to the capture and reporter CodeSet overnight. The samples are automatically processed by the Prep Station (NanoString, Seattle, WA).

scan_protocol: The cartridge containing the probes bound to the immobilized RNA is then scanned at 555 fields of view (FOV) into the Digital Analyzer (NanoString) for image acquisition and barcodes are counted and analyzed through the nCounter analysis software (nSolver 4.0).

data_processing: Data were normalized using the mean of the Positive Control counts

label: not provided

source_name: 12mo 3xTg T-cells

label_protocol: not provided

growth_protocol: T-cells were activated with plate-bound anti-CD3 (2ug/ml) and anti-CD28 (5ug/ml) in the presence of 100IU/ml IL-2 for 3 days in IMDM supplemented with 10% fetal bovine serum, antibiotics, and b-mercaptoethanol.

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen).

treatment_protocol: T-cells were treated with vehicle or fumarate (20mM) for three days during activation.

value: 12 months old

value: T-cells


title: Hypothalamus, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Hypothalamus tissue

value: Hypothalamus tissue


title: T-cell_Old+Fum_rep3

description:
20230811_210502641124_Sample 12 WT O Fu3_12
SAMPLE 9

source_name: 12mo T-cells + 20uM Fumarate


title: T-cell_3xTg_rep1

description:
20230811_210502641124_Sample 07 Tg O1_07
SAMPLE 10


title: WT_24h_A

city: Seongnam-si

first: Gae Hoon

last: Jo

address: 64 Yatap-ro

institute: CHA university

description: replicate 1

hyb_protocol: The Illumina Mouse WG-6 V2 (48 K) array (Illumina, San Diego, CA, USA) was hybridized with appropriate cRNA probes at ISTECH (Goyang, South Korea).

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were quantificated using Beadstudio and normalized using quantile normalisation in R.
<<< Submitter states that raw (non-normalized) data is unavailable for this submission due to circumstances beyond their control >>>

label: Biotin

source_name: Uterine tissue

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was extracted from mouse uteri by using a Trizol reagent (Thermo Fisher Scientific) according to manufacturer instructions.

tag: egr1 knockout status

value: WT

tag: e2-elapsed time

value: 24 hour

value: Uterine tissue


title: WT_6h_A

description: replicate 1

value: 6 hour

tag: tissue


title: WT_3h_B

description: replicate 2

value: 3 hour


title: T-cell_Old+Fum_rep2

description:
20230811_210502641124_Sample 11 WT O Fu2_11
SAMPLE 8


title: WT_24h_B

description: replicate 2


title: WT_6h_B

description: replicate 2


title: EGR1_KO_24h_B

description: replicate 2

value: KO


title: EGR1_KO_24h_A

description: replicate 1


title: WT_3h_C

description: replicate 3


title: T-cell_Old+Fum_rep1

description:
20230811_210502641124_Sample 10 WT O Fu1_10
SAMPLE 7


title: T-cell_Old_rep3

description:
20230811_210502641124_Sample 06 WT O6_06
SAMPLE 6

source_name: 12mo T-cells


title: EGR1_KO_6h_B

description: replicate 2


title: EGR1_KO_6h_A

description: replicate 1


title: Liver, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Liver tissue

value: Meishan Pig

value: Liver tissue


title: WT_0h_A

description: replicate 1

value: 0 hour


title: WT_0h_B

description: replicate 2


title: Duodenum, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Duodenum tissue

value: Duodenum tissue


title: Heart, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Heart tissue

value: Heart tissue


title: T-cell_Old_rep2

description:
20230811_210502641124_Sample 05 WT O5_05
SAMPLE 5


title: T-cell_3xTg_rep2

description:
20230811_210502641124_Sample 08 Tg O2_08
SAMPLE 11


title: WT_3h_A

description: replicate 1


title: T-cell_Old_rep1

description:
20230811_210502641124_Sample 04 WT O1_04
SAMPLE 4


title: T-cell_Young_rep3

description:
20230811_210502641124_Sample 03 WT Y3_03
SAMPLE 3

source_name: 2mo T-cells

value: 2 months old


title: Colon, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Colon tissue

value: Colon tissue


title: T-cell_Young_rep2

description:
20230811_210502641124_Sample 02 WT Y2_02
SAMPLE 2


title: EA.hy926 cells, siELMO1, poly(I:C) 24 h_rep3

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

institute: University of North Carolina at Chapel Hill

description:
Library name: Sample 18
18_24H_E3_TGTCTAAC-GCCAGCCG_S10_L001_R1_001.fastq.gz

data_processing:
Raw 101 bp paired‐end reads were obtained from a NextSeq 200 run and demultiplexed (allowing one mismatch) with bclconvert v3.8.2-12. These reads were then aligned to the GRCh38 reference genome and Gencode v44 for annotation via STAR, producing sorted BAM files. StringTie was subsequently used to quantify gene and transcript expression, yielding TPM, FPKM, and raw count values. The prepDE.py script from StringTie was run to assemble gene- and transcript-level count matrices, which were then imported into R.
After performing filtering and normalization, the voom transformation was applied to the normalized counts, and linear models incorporating experimental groups and time points were fitted using limma. Empirical Bayes moderation was applied to these fitted models, and subgroup contrasts were analyzed using the DREAM method. Finally, preranked GSEA was conducted with fgsea to identify enriched pathways
Assembly: GRCh38 reference genome and Gencode v44 for annotation
Supplementary files format and content: Gene/Transcript count matrix: CSV files with one row per ENST|TranscriptID and columns of raw counts per sample.
Supplementary files format and content: Limma subgroup analysis files: tab-delimited text containing columns for gene ID (ENSG|GeneName), log2 fold change (logFC), average expression (AveExpr, log2 CPM), moderated t-statistic (t), raw p-value (P.Value), adjusted p-value (adj.P.Val), and B-statistic (B) for each condition–timepoint contrast. GSEA result files: tab-delimited text files listing pathway names, enrichment score (ES), normalized enrichment score (NES), nominal p-value (pval), FDR (padj), number of more extreme permutations (nMoreExtreme), gene set size (size), and comma-separated leading-edge gene IDs.

source_name: human umbilical vein

growth_protocol: EA.hy926 human umbilical vein endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin/100 μg/mL streptomycin in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNAeasy mini kit (Qiagen).
RNA libraries for RNAseq were prepared using KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer's protocol.

treatment_protocol: EA.hy926 cells were transfected with 10 nM siRNA. Forty-eight hours after the transfection, cells were stimulated with 1 μg/ml poly(I:C) and incubated for 24 h. Cells before (0 h) or after (24 h) the poly(I:C) stimulation were lysed for RNA extraction.

value: human umbilical vein

value: vascular endothelial cells

value: ELMO1 siRNA

value: poly(I:C) 24 h


title: Cerebrum, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Cerebrum tissue

value: Cerebrum tissue


title: EA.hy926 cells, siELMO1, poly(I:C) 24 h_rep1

description:
Library name: Sample 16
16_24H_E1_ACCGCTAT-TGGTTGCA_S8_L001_R1_001.fastq.gz


title: Cerebellum, replicate 1, snRNA-seq

description: 10x Genomics

source_name: Cerebellum tissue

value: Cerebellum tissue


title: EGR1_KO_3h_B

description: replicate 1

value: Uterine tissue


title: T-cell_Young_rep1

description:
20230811_210502641124_Sample 01 WT Y1_01
SAMPLE 1

value: T-cells


title: EA.hy926 cells, siNT, poly(I:C) 24 h_rep2

description:
Library name: Sample 14
14_24H_C2_TTCAGAAC-TTACGCCG_S6_L001_R1_001.fastq.gz

value: non-targeting siRNA


title: MEF, 1 hour Thapsigargin, CLIP, replicate 1

city: Baton Rouge

first: Anastasios

middle: A.

last: Vourekas

state: LA

address: 202 life sciences building

institute: Louisiana State University

data_processing:
sequence reads were trimmed for adapter sequence/ low quality sequences using cutadapt version 4.1 with python 3.9.13 with the options -n 1 -e 0.15.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner version 2.7.0d and UCSC gene transfer format for annotations.
Read counts table extraction using CLIPSEQTOOLS with the option count_reads_on_genic_elements.
Normalization and other data processing for the count reads tables were performed using custom python scripts which can be found in the following GitHub page: https://github.com/Abdelmonsif/DDX3X.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing raw counts for each sample
Supplementary files format and content: Tab-delimited file containing TPM values for each sample

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts were maintained in DMEM supplemented with 10% defined FBS, 2mM L-glutamine, 100 units/mL  penicillin,   and 100 ug/mL streptomycin in humidified atmosphere with 5% CO2  at 37C.

extract_protocol:
CCells were grown to ~80% confluency and treated with control (DMSO) or Thapsigargin (400 nM) containing full medium to induce ER stress. The cells where then collected by trypsinization and kept in ice-cold HBSS during UV crosslinking (254 nm, 3x400 mJ/cm2). For the IP step our own custom rabbit polyclonal DDX3X antibody was used. The rest of the CLIP-Seq procedure was performed as previously described (Vourekas and Mourelatos, 2014).
RNA  libraries  for RNA-seq were prepared using Illumina Stranded mRNAs prep Ligation Reference Guide, Document # 1000000124518 V03 protocol without changes.

treatment_protocol: ER stress was induced  by treating cells with 400 nM Thapsigargin for 1 hour for MEFs

value: MEF

value: Mouse embryonic fibroblast

value: Wt

value: Thapsigargin


title: MEF, Rest, CLIP, replicate 2

value: DMSO


title: EGR1_KO_3h_C

description: replicate 2

value: KO

value: 3 hour


title: EA.hy926 cells, Mock, poly(I:C) 24 h_rep3

description:
Library name: Sample 12
12_24H_LF3_TAAGTACC-GTGAGCCA_S4_L001_R1_001.fastq.gz

value: Mock transfection


title: EGR1_KO_0h_A

description: replicate 1

value: 0 hour


title: EGR1_KO_0h_B

description: replicate 2


title: MEF, Rest, CLIP, replicate 1


title: EA.hy926 cells, Mock, poly(I:C) 24 h_rep2

description:
Library name: Sample 11
11_24H_LF2_CGTACGTT-AGGATTAG_S3_L001_R1_001.fastq.gz

value: human umbilical vein

value: vascular endothelial cells