title: H9C2, Hypoxia, Trim 3 3

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

description:
Hy_T3vsHy_MC_deg
Hy_125bvsHy_T3_deg
Hy_T3_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, 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. All the downstream analyses were based on the clean data with high quality
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. We use HISAT2 to accomplish the mapping. If only the differential expression significant genes are needed, we map reads to the transcriptome directly.
Mapping information from all samples is combined and placed as input into the regular StringTie assembler. The assembled transfrags are then compared to the reference transcripts to determine if they are sufficiently different to be considered novel.
The abundance of transcript reflects the gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the   abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length   and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)   is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene   length on counting of fragments.
The input data for differential gene expression analysis is read counts from gene expression level analysis.
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: xls files include differential gene expression with read counts normalization, model dependent -pvalue estimation and FDR value estimation based on multiple hypothesis testing

growth_protocol: H9C2 cells (a rat cardiac myoblast cell line) were purchased from American Type Culture Collection (Manassas, Virginia) and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (vol/vol) fetal bovine serum, 2mM glutamine, 100 units/ml penicillin, and 100 g/ml streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA from H9C2 was extracted using TRIzol reagent (Invitrogen, Thermo Fisher Scientific Inc, Singapore) followed by DNase I treatment. RNA quality was determined by Nanodrop and Bioanalyzer.
The RNA-sequencing was performed by the non-stranded poly-A library method. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. This was followed library construction. The library was checked with Qubit and real-time PCR for quantification and Bioanalyzer for size distribution detection. Quantified libraries would be sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: At 70% confluence, 25 nmol/L Mimic control (MC), miR-125b mimic (miR-125b) or isomiRs including addition of A (Plus A), deletion of A (Trim A), deletion of AG (Trim AG), and deletion of AGU (Trim AGU) were transfected according to the manufacturer’s instructions.

value: Cardiac myoblast

value: miR-125b Trim 3 mimic


title: Stem apex from untreated plants at d.a.t. 1 replicate 2

status: Public on Nov 22 2023

type: SRA

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

country: USA

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic

data_processing:
FastQC (Version 0.10.1) for raw read quality evaluation
Trimmomatic-0.36 (Version 3, 29 June 2007) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 HEADCROP:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with Samtools (Tools for alignments in the SAM format) Version: 1.2 (using htslib 1.2.1)
Aligned reads were counted using featureCounts (Version 1.6.0) and summarized per gene ID
Assembly: Acomosus_321_v3.fa.gz
Supplementary files format and content: Processed data files (Text documents) contain raw read counts (not normalized) for each "Geneid" for each of the samples. Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (see Acomosus_321_v3.transcript.fa.gz).

molecule: total RNA

organism: Ananas comosus

source_name: Stem apex

growth_protocol: Plants growing on a commercial pineapple field (Ananas comosus, cultivar 'MD2', PRI 73-50) at Dole Plantation, Wahiawa, Hawaii were selected for the experiment one month before commercial forcing.

extract_protocol:
TRIzol Reagent (Ambion USA)
2 µg of total RNA were used for RNA-Seqlibrarypreparation. Low Sample Protocol with TruSeq® Stranded mRNA LT kit (Illumina USA) was follow to build the libraries.

treatment_protocol: 10 ml of either water (untreated or "control") or ethephon (50 mg) was applied into the center of the plants.

tag: tissue

value: Stem apex

tag: replicate

value: biol rep 2

tag: days after_treatment

tag: genotype

value: Cultivar 'MD1', PRI 73-50

tag: treatment

value: Water


title: VSMCs  Pi-2

city: Guangzhou

first: Junping

last: Li

address: 107 Yanjiang West Road, Yuexiu District, Guangzhou, Guangdong Province, China

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

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, reads containing ploy-N and low quality reads from raw data.
Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene annotation files were downloaded from genome website. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. W
Supplementary files format and content: RSEM was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package, include Genes with an adjusted P-value <0.05 for each sample.

organism: Rattus norvegicus

source_name: thoracic aorta

growth_protocol: VSMCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen, Waltham, MA) and 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq prepared using NEBNext® UltraTM RNA Library Prep Kit ( E7530L, NEB, USA)  following manufacturer's protocols.

treatment_protocol: Osteogenic differentiation was induced by treatment with osteogenic media (OM) (10mM β-GP plus 3.5mM CaCl2) with or without empagliflozin (1uM) for 5days.

value: thoracic aorta

tag: cell type

value: Primary thoracic aortic smooth muscle cells

value: WT

value: Osteogenic differentiation


title: VSMCs  Pi+E-1

value: Osteogenic differentiation with empagliflozin


title: WT4

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

description: Female, Wild-Type rat, rodent chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript (RGSC 6.0/rn6) set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15[2]. TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program[3].
Assembly: rn6
Supplementary files format and content: rsem_count.txt => Expected read count produced by RSEM for each gene in each sample.
Supplementary files format and content: TMM_normalized_reads_count_per_million.txt => Normalized gene expression data by TMM method

source_name: Left Hippocampus Brain

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
Kapa Stranded mRNA Kit (Roche, cat. KK8421) to generate strand-specific RNA-seq libraries

value: Left Hippocampus Brain

value: Wild Type

value: No Treatment


title: RB170 cells, Cef2mM-2

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

data_processing:
Prune and trim poor quality reads using Trimmomatic tool
Quantify gene expression data using Kallisto on Ensembl V82
Assembly: HG38
Supplementary files format and content: Tab delimited file of transcript abundance as generated by Kallisto

organism: Homo sapiens

growth_protocol: RB170 cells were culture in Neurobasal™-A Medium supplemented with 2.5% fetal bovine serum (FBS), 2.5% knock out bovine serum (KSR), 20pg/ml epidermal growth factor (EGF), 10pg/ml basic fibroblast growth factor (bFGF), 2mM of glutamax, 1mM of sodium pyruvate, 0.25ng/ml of fungizone, and antibiotics (complete media) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by TriPure Isolation reagent (Roche Applied Science, Penzberg, Germany).
RNA Libraries were constructed by using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc.)

treatment_protocol: RB170 was treated with ceftriaxone for 2 day in complete Neurobasal-A media

tag: cell line

value: Retinoblastomas

value: MYCN amplified

value: Ceftriaxone (2mM)


title: Stem apex from untreated plants at d.a.t. 1 replicate 1

value: biol rep 1


title: ΔUBR4, sgTIMM8A, Sodium arsenite 5uM 16h, biol rep2

city: Berkeley

first: Diane

middle: L

last: Haakonsen

state: CA

address: 1951 Oxford St

department: MCB

institute: UC Berkeley

description:
D4T8ASA2
All_samples_TPM_counts.csv

data_processing:
To obtain transcript abundance counts, RNA-seq reads were mapped to the human reference transcriptome (GRch38, Ensembl Release 96) using Kallisto 0.48.0
Gene-level count estimates were obtained by summing counts or TPMs across all transcripts from a given gene
Assembly: GRCh38.96
Supplementary files format and content: CSV file containing TPM and estimated counts for each sample

growth_protocol: HEK29T WT and ΔUBR4  cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA kit (Macherey-Nagel)
mRNA was purified from total RNA using polyT oliog attached magnetic beads. mRNA was fragmented and first strand synthesis was performed with random hexamers followed by second strand cDNA synthesis. This was followed by end repair, A-tailling, adapter ligation, size selection, amplification and purification.

treatment_protocol: Cells were either untreated or treated with sodium arsenite 5uM or isrib 200nM for 16 hours

value: Human embryonic kidney cells

value: {delta}UBR4 sgTIMM8A

value: Sodium arsenite 5uM, 16 hours


title: VSMCs  Pi-3


title: VSMCs  Pi+E-3


title: Single cell VEFGaIgG_2

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

library_source: transcriptomic single cell

data_processing:
Bulk RNA-seq: Pseudoalignment of RNAseq reads was performed to a kallisto index created from transcriptome Ensembl v96, Mouse:GRCm38.p6 using kallisto (0.44.0).
Single-cell RNA-seq: Raw fastq (sequencing files) were processed using the Cellranger v3.0 analysis pipeline to align reads to the GRCm38.p6 mouse genome and generate feature-barcode matrices.
Assembly: GRCm38.p6
Supplementary files format and content: bulk_r84_est_counts_gene_kallisto
Supplementary files format and content: h5

organism: Mus musculus

source_name: Spinal cord

extract_protocol:
The neural dissociation kit (P) was used to dissociate the spinal cords into a single cell suspension. Following myelin removal using Miltenyi Biotec Myelin Removal Beads II, the samples were stained with CD31-APC and PI, and live endothelial cells were FACS sorted for single cell RNA sequencing
Bulk RNA-seq: mRNA was enriched from total RNA samples after sorting cells (see extract protocol) using poly-A pull down and cDNA libraries were prepared using Illumina Truseq chemistry, followed by sequencing using Illumina NovaSeq 6000. Single cell RNA-seq: Single cells were processed on the 10x Genomics Chromium platform (v3 chemistry), and cDNA libraries were sequenced on the Illumina NovaSeq6000

value: Spinal cord

tag: strain

value: Endothelial cell

value: Complete Freund's adjuvant + Pertussis Toxin + IgG


title: VSMCs  Pi-1

value: thoracic aorta

value: Primary thoracic aortic smooth muscle cells


title: H9C2, Hypoxia, Trim 3 1

description:
Hy_T3vsHy_MC_deg
Hy_125bvsHy_T3_deg
Hy_T3_1

value: Cardiac myoblast

value: miR-125b Trim 3 mimic


title: H9C2, Normoxia, Trim 3 3

description:
Nor_T3vsNor_MC_deg
Nor_125bvsNor_T3_deg
Nor_T3_3


title: VSMCs  Pi+E-2

value: WT

value: Osteogenic differentiation with empagliflozin


title: ΔUBR4, sgTIMM8A, biol rep2

description:
D4T8A2
All_samples_TPM_counts.csv


title: Single cell VEFGaIgG_1


title: WT1

description: Female, Wild-Type rat, rodent chow

value: Left Hippocampus Brain

value: Wild Type

value: No Treatment


title: ΔUBR4,  sgTIMM8A, isrib 200nM 16h, biol rep1

description:
D4T8AISR1
All_samples_TPM_counts.csv

value: Isrib 200nM, 16 hours


title: RB170 cells, Cef0mM-1

value: Retinoblastomas

value: MYCN amplified

value: Sterile water


title: Single cell VEGFaR84_1

value: Complete Freund's adjuvant + Pertussis Toxin + 5 mg/kg r84


title: Single cell VEFGaIgG_3

value: Spinal cord


title: Bulk VEGFaR84_1

value: Endothelial cell


title: ΔUBR4, sgCNTL, Sodium arsenite 5uM 16h, biol rep2

description:
D4CTLSA2
All_samples_TPM_counts.csv

value: Human embryonic kidney cells

value: {delta}UBR4 sgCNTL

value: Sodium arsenite 5uM, 16 hours


title: H9C2, Hypoxia, Trim 3 2

description:
Hy_T3vsHy_MC_deg
Hy_125bvsHy_T3_deg
Hy_T3_2

value: Cardiac myoblast


title: Tg1

description: Female, TgF-344AD transgenic rat, rodent chow

value: Tg-AD


title: H9C2, Hypoxia, Trim 2 3

description:
Hy_T2vsHy_MC_deg
Hy_125bvsHy_T2_deg
Hy_T2_3

value: miR-125b Trim 2 mimic


title: ΔUBR4 sgTIMM8A, Sodium arsenite 5uM 16h, biol rep1

description:
D4T8ASA1
All_samples_TPM_counts.csv

value: {delta}UBR4 sgTIMM8A


title: Bulk VEGFalgG_2

value: Complete Freund's adjuvant + Pertussis Toxin + IgG


title: Bulk VEGFalgG_1


title: Bulk VEGFalgG_3


title: ΔUBR4, sgTIMM8A, biol rep3

description:
D4T8A3
All_samples_TPM_counts.csv


title: Bulk VEGFaR84_3


title: Bulk VEGFaR84_2


title: ΔUBR4, sgTIMM8A, biol rep1

description:
D4T8A1
All_samples_TPM_counts.csv


title: H9C2, Normoxia, Trim 3 2

description:
Nor_T3vsNor_MC_deg
Nor_125bvsNor_T3_deg
Nor_T3_2

value: miR-125b Trim 3 mimic


title: ΔUBR4, sgCNTL, Sodium arsenite 5uM 16h, biol rep3

description:
D4CTLSA3
All_samples_TPM_counts.csv


title: ΔUBR4,  sgCNTL, biol rep1

description:
D4CTL1
All_samples_TPM_counts.csv


title: H9C2, Hypoxia, Trim 2 2

description:
Hy_T2vsHy_MC_deg
Hy_125bvsHy_T2_deg
Hy_T2_2


title: ΔUBR4, sgCNTL, Sodium arsenite 5uM 16h, biol rep1

description:
D4CTLSA1
All_samples_TPM_counts.csv


title: Bulk RNA-seq Control_1

value: Complete Freund's adjuvant + Pertussis Toxin


title: H9C2, Normoxia, Trim 2 1

description:
Nor_T2vsNor_MC_deg
Nor_125bvsNor_T2_deg
Nor_T2_1


title: WT,  sgTIMM8A, isrib 200nM 16h, biol rep3

description:
WTT8AISR3
All_samples_TPM_counts.csv

value: WT sgTIMM8A

value: Isrib 200nM, 16 hours


title: H9C2, Hypoxia, Trim 1 3

description:
Hy_T1vsHy_MC_deg
Hy_125bvsHy_T1_deg
Hy_T1_3

value: miR-125b Trim 1 mimic


title: H9C2, Hypoxia, Trim 1 2

description:
Hy_T1vsHy_MC_deg
Hy_125bvsHy_T1_deg
Hy_T1_2


title: H9C2, Hypoxia, Trim 2 1

description:
Hy_T2vsHy_MC_deg
Hy_125bvsHy_T2_deg
Hy_T2_1


title: ΔUBR4, sgCNTL, biol rep1

description:
D4CTL3
All_samples_TPM_counts.csv


title: ΔUBR4, sgCNTL, biol rep2

description:
D4CTL2
All_samples_TPM_counts.csv


title: H9C2, Normoxia, Trim 2 2

description:
Nor_T2vsNor_MC_deg
Nor_125bvsNor_T2_deg
Nor_T2_2


title: H9C2, Normoxia, Trim 2 3

description:
Nor_T2vsNor_MC_deg
Nor_125bvsNor_T2_deg
Nor_T2_3


title: Bulk RNA-seq Control_2


title: H9C2, Hypoxia, Trim 1 1

description:
Hy_T1vsHy_MC_deg
Hy_125bvsHy_T1_deg
Hy_T1_1


title: H9C2, Normoxia, Trim 3 1

description:
Nor_T3vsNor_MC_deg
Nor_125bvsNor_T3_deg
Nor_T3_1


title: WT,ZNArip

city: Hangzhou

first: Songang

last: Wu

state: Zhejiang

address: West Wenyi Road

institute: Zhejiang University School of Medicine

data_processing:
FASTQ files was filtered using the Trim_Galore (v.0.6.5)
Filtered Sequences were aligned with STAR (v.2.5.3a) to the mm39 assembly
Gene expression and TE expression were quantified from uniquely aligned reads using Featurecounts (v.2.0.4) with -f parameters and their annotations from the UCSC
For repeat analysis, alignment positions were mapped with repeats annotated in UCSC with RepeatMasker (rmsk table from mm39)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Hippocampus

growth_protocol: All mice were on a C57BL/6 genetic background and housed in a constant temperature of 23℃ in a 12-h light/dark cycle at the Laboratory Animal Center of Zhejiang University and Xiamen University.

extract_protocol:
The immunoprecipitated RNA was extracted with the TRIzol method and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

value: Hippocampus

tag: age

value: WT


title: Bulk RNA-seq Control_3

value: Spinal cord


title: WT,  sgTIMM8A, isrib 200nM 16h, biol rep1

description:
WTT8AISR1
All_samples_TPM_counts.csv


title: WT,  sgTIMM8A, Sodium arsenite 5uM 16h, biol rep3

description:
WTT8ASA3
All_samples_TPM_counts.csv


title: WT,  sgTIMM8A, Sodium arsenite 5uM 16h, biol rep1

description:
WTT8ASA1
All_samples_TPM_counts.csv


title: H9C2, Normoxia, Trim 1 3

description:
Nor_T1vsNor_MC_deg
Nor_125bvsNor_T1_deg
Nor_T1_3


title: H9C2, Normoxia, Trim 1 1

description:
Nor_T1vsNor_MC_deg
Nor_125bvsNor_T1_deg
Nor_T1_1


title: H9C2, Hypoxia, miR-125b 3

description:
Hy_125bvsHy_MC_deg
Hy_125bvsHy_A_deg
Hy_125b_3

value: miR-125b mimic


title: WT,  sgTIMM8A, Sodium arsenite 5uM 16h, biol rep2

description:
WTT8ASA2
All_samples_TPM_counts.csv

value: Human embryonic kidney cells


title: WT_3, 9month

extract_protocol:
Total RNA was extracted with the TRIzol method, and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.


title: WT,  sgTIMM8A, biol rep3

description:
WTT8A3
All_samples_TPM_counts.csv


title: PS19_1, 9month


title: WT,  sgTIMM8A, biol rep2

description:
WTT8A2
All_samples_TPM_counts.csv


title: WT,  sgTIMM8A, isrib 200nM 16h, biol rep2

description:
WTT8AISR2
All_samples_TPM_counts.csv


title: WT_2, 9month


title: PS19,ZNArip


title: H9C2, Hypoxia, miR-125b 1

description:
Hy_125bvsHy_MC_deg
Hy_125bvsHy_A_deg
Hy_125b_1


title: WT,  sgCNTL, Sodium arsenite 5uM 16h, biol rep3

description:
WTCTLSA3
All_samples_TPM_counts.csv

value: WT sgCNTL


title: WT_1, 9month


title: PS19,ZBP1rip


title: WT,  sgTIMM8A, biol rep1

description:
WTT8A1
All_samples_TPM_counts.csv


title: WT,  sgCNTL, Sodium arsenite 5uM 16h, biol rep2

description:
WTCTLSA2
All_samples_TPM_counts.csv

value: Sodium arsenite 5uM, 16 hours


title: PS19, Zbp1+-,10month

extract_protocol:
RNA was extracted with the TRIzol method, and used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra RNA Library Prep Kit following manufacturer's protocols.


title: PS19_3, 9month


title: H9C2, Normoxia, miR-125b 2

description:
Nor_125bvsNor_MC_deg
Nor_125bvsNor_A_deg
Nor_125b_2

value: Cardiac myoblast


title: H9C2, Normoxia, miR-125b 1

description:
Nor_125bvsNor_MC_deg
Nor_125bvsNor_A_deg
Nor_125b_1


title: WT,10month

description: WT


title: WT , sgCNTL, biol rep3

description:
WTCTL3
All_samples_TPM_counts.csv


title: H9C2, Hypoxia, miR-125b A 3

description:
Hy_AvsHy_MC_deg
Hy_A_3

value: miR-125b A mimic


title: H9C2, Normoxia, Trim 1 2

description:
Nor_T1vsNor_MC_deg
Nor_125bvsNor_T1_deg
Nor_T1_2


title: PS19,10month


title: PS19_2, 9month


title: WT,  sgCNTL, biol rep2

description:
WTCTL2
All_samples_TPM_counts.csv


title: H9C2, Hypoxia, miR-125b 2

description:
Hy_125bvsHy_MC_deg
Hy_125bvsHy_A_deg
Hy_125b_2


title: H9C2, Hypoxia, miR-125b A 2

description:
Hy_AvsHy_MC_deg
Hy_A_2


title: H9C2, Normoxia, miR-125b A 3

description:
Nor_AvsNor_MC_deg
Nor_A_3


title: H9C2, Hypoxia, miR-125b A 1

description:
Hy_AvsHy_MC_deg
Hy_A_1


title: H9C2, Normoxia, miR-125b 3

description:
Nor_125bvsNor_MC_deg
Nor_125bvsNor_A_deg
Nor_125b_3


title: WT,  sgCNTL, biol rep1

description:
WTCTL1
All_samples_TPM_counts.csv


title: mouse #1 3D cultured adipose stem cells

city: Busan

first: Tae Gen

last: Son

address: 40 Jwadong-gil, Jang-an eup, Gijang-gun

country: South Korea

institute: Dongnam Institute of Radiological and Medical Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: adipose

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: adipose

value: primary culture

value: mesenchymal stem cells

tag: strain background

value: BALB/c

tag: group

value: 3D cultured


title: mouse #4 3D cultured adipose stem cells


title: WT,  sgCNTL, Sodium arsenite 5uM 16h, biol rep1

description:
WTCTLSA1
All_samples_TPM_counts.csv


title: H9C2, Normoxia, miR-125b A 2

description:
Nor_AvsNor_MC_deg
Nor_A_2


title: mouse #5 3D cultured adipose stem cells


title: Untreated-Inputs_2

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

library_source: genomic

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp.
Adapter-removed reads were aligned  to human genome hg19 using Bowtie2 with the “–very-sensitive” option.  Non-unique alignments were removed by filtering out reads with mapping quality (MAPQ) score less than 10. PCR duplicates were removed using samtools.
Regions of genomic enrichment were detected using MACS2 with the default options for pair-ended alignment and narrow peak p-value cutoff 0.001.
bigWig files were converted from the MACS2 output bedGraph files using bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

source_name: Liver

growth_protocol: HepG2 cells (from ATCC, Catalogue number HB-8065) were grown and maintained in Eagle's minimum essential medium (EMEM) medium containing 10% heat inactivated fetal bovine serum (FBS) in a 5 % CO2 environment at 37 °C in a humidified incubator. On the day of experiment, culture medium was removed, and cells were placed in serum-free media (EMEM+0.1% BSA) for 16h.

extract_protocol:
DNA extraction was performed according to the protocol described by Dafne et al (Cardamone MD, Orofino J, Labadorf A, Perissi V. Chromatin Immunoprecipitation of Murine Brown Adipose Tissue. J Vis Exp. 2018 Nov 21;(141):10.3791/58682. doi: 10.3791/58682. PMID: 30531713; PMCID: PMC6684207).
The sequencing library was prepared using Swift 2S Accel reagents on a Beckman Coulter Biomek i7 liquid handling system.

treatment_protocol: Cells were then either untreated (basal) or stimulated with 100 nM insulin for 20 min and harvested. Chromatin immunoprecipitation (ChIP) was performed by adding formaldehyde directly to the culture medium to a final concentration of 1% and incubated for 10 min at room temperature (RT) to cross-link proteins to DNA. Cell culture media was aspirated, and the cells were washed with ice-cold PBS and cells were scrapped, and performed ChIP using FoxK1 antibody as described by Dafne et al (Cardamone MD, Orofino J, Labadorf A, Perissi V. Chromatin Immunoprecipitation of Murine Brown Adipose Tissue. J Vis Exp. 2018 Nov 21;(141):10.3791/58682. doi: 10.3791/58682. PMID: 30531713; PMCID: PMC6684207).

value: Liver

value: hepatocellular carcinoma

value: Untreated

tag: type

value: Input


title: H9C2, Normoxia, miR-125b A 1

description:
Nor_AvsNor_MC_deg
Nor_A_1


title: Untreated-Inputs_3


title: mouse #4 2D cultured adipose stem cells

value: WT

value: 2D cultured


title: Untreated-FoxK1_2

value: IP


title: mouse #3 2D cultured adipose stem cells


title: Untreated-Inputs_1


title: H9C2, Hypoxia, Mimic Control 2

description:
Hy_125bvsHy_MC_deg
Hy_MC_2

value: Mimic control


title: mouse #7 3D cultured adipose stem cells


title: mouse #2 2D cultured adipose stem cells


title: Untreated-FoxK1_3


title: Untreated-FoxK1_1


title: H9C2, Hypoxia, Mimic Control 1

description:
Hy_125bvsHy_MC_deg
Hy_MC_1


title: H9C2, Normoxia, Mimic Control 3

description:
Nor_125bvsNor_MC_deg
Nor_MC_3


title: Insulin-Inputs_3

value: Insulin


title: Insulin-Inputs_2


title: H9C2, Normoxia, Mimic Control 2

description:
Nor_125bvsNor_MC_deg
Nor_MC_2


title: mouse #5 2D cultured adipose stem cells


title: KO_Veh_TRAP1

city: New York City

first: Mauricio

middle: Martins

last: Oliveira

address: 4 Washington Place, room 621

institute: New York University

description:
Creplus-Veh-2-TRAP
GADD34 knockou neurons - Vehicle - TRAP-seq 1

data_processing:
Trimming - CutAdapt
Alignment - STAR Align
Assembly: mm10
Supplementary files format and content: Processed files contain a matrix. Each sample is allocated in one column, and each gene is allocated per row. The values correspond to feature count values per gene per sample.

molecule: polyA RNA

source_name: Hippocampus/cortex

growth_protocol: Primary neurons were maintained for 14 days in Neurobasal plus supplemented with GlutaMax and B27 plus. 30% of the media was replaced every 3 days.

extract_protocol:
Ribosomes were frozen with 10 ug/ml cycloheximide for 1 minute. Neurons were lifted on PBS and centrifugated at 300 g/5min/4oC. Supernatant was removed and neurons were lyzed on TRAP lysis buffer. Cells were further lyzed using an automatic piston and lysates were cleared by centrifugation (2000 g/10 min/4oC). Lysates were incubated with 200 mM DHPC for 5 minutes on ice and centrifugated again (20.000 g/10 min/4oC). Lysates were incubated overnight in the cold room with magnetic beads coated with anti-GFP antibody. Beads were washed with high salt buffer and total RNA was extracted using RNEasy Plus kit (Qiagen).
Quality control of both total RNA and purified RNA was measured using Agilent HS TapeStation. cDNA then was synthesized with Takara SMART-Seq HT kit with 1 ng of RNA input that had RIN of 5 and greater via Agilent HS TapeStation. Libraries were constructed with 0.25 ng of cDNA input via Nextera XT DNA library kit. cDNA and libraries amplification had both 12 cycles. Quality control of libraries were analyzed via Agilent HS TapeStation and Invitrogen Quant-it.

treatment_protocol: Neurons were exposed to either vehicle (0.1% BSA) or BDNF (50 ng/ml) for 1h prior to sample collection

value: Hippocampus/cortex

value: Primary neurons

value: Excitatory neurons

value: GADD34 knockout

value: Vehicle


title: KO_Veh_TRAP3

description:
Creplus-Veh-4-TRAP
GADD34 knockou neurons - Vehicle - TRAP-seq 3


title: KO_Veh_TRAP2

description:
Creplus-Veh-3-TRAP
GADD34 knockou neurons - Vehicle - TRAP-seq 2


title: Insulin-Inputs_1


title: FABP7 KO mice 3

city: Sendai

first: Jun

last: Suzuki

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Otorhinolaryngology-Head and Neck Surgery

country: Japan

institute: Tohoku University School of Medicine

data_processing:
NextSeq500/550 version 2.5 and the NextSeq 500 System (Illumina)
Sequencing was performed using paired-end reads of 36 bases.
The basic information of the next-generation sequencing run data was checked using the CLC Genomics Workbench software (version 22.0; QIAGEN, Hilden, Germany).
During the quality assessment of the reads, a PHRED score >20 was confirmed for 99.7% of all reads, indicating the success of the run.
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample, FDR p-value, and  Fold change.

source_name: Inner ear

extract_protocol:
RNA extraction was performed using RNAiso Plus (Cat# 9180; Takara Bio, Kusatsu, Shiga, Japan), according to the manufacturer’s instructions. 500 ng of RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina and the NEBNext rRNA Depletion Kit v2 (Cat# E7770S and E7400L; New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s instructions.

treatment_protocol: Inner ears were harvested 24 h after noise exposure (8–16 kHz octave-band noise at 100 dB SPL for 2 h)

value: Inner ear

value: FABP7 KO


title: H9C2, Hypoxia, Mimic Control 3

description:
Hy_125bvsHy_MC_deg
Hy_MC_3

value: Cardiac myoblast


title: H9C2, Normoxia, Mimic Control 1

description:
Nor_125bvsNor_MC_deg
Nor_MC_1


title: FABP7 KO mice 2


title: KO_BDNF_TRAP3

description:
Creplus-BDNF-4-TRAP
GADD34 knockou neurons - BDNF - TRAP-seq 3

value: BDNF


title: Model3

first: Li

last: Xinhui

address: Guangzhou

institute: Sun Yat-sen university

data_processing:
The data from RNA-Seq were first filtered (Cutadapt and Fqtrim) and assessed for quality (FastQC), and then compared to the reference genome (miRDeep and HISAT2).
The data source for the reference genome is Ensembl database (http://asia.ensembl.org)
Supplementary files format and content: excel;gene count

source_name: lens capsules

extract_protocol: RNA was extracted using TRIzol reagent (ThermoFisher, USA)

value: lens capsules

value: Na2SeO3 is injected subcutaneously


title: Insulin-FoxK1_3

value: Liver

value: hepatocellular carcinoma


title: mice 1


title: KO_BDNF_TRAP2

description:
Creplus-BDNF-3-TRAP
GADD34 knockou neurons - BDNF - TRAP-seq 2


title: Model1


title: Wild-type mice 2

value: wild type


title: Insulin-FoxK1_2

value: IP


title: Insulin-FoxK1_1


title: WT_Veh_TRAP3

description:
Cre-Veh-4-TRAP
Wild type neurons - Vehicle - TRAP-seq 3

value: Wild Type


title: Wild-type mice 3


title: iPSC-derived spMNs (Day 12), nHOTAIRM1 KO 2

city: Napoli

first: Francesco

last: Migliaccio

address: Via Pietro Castellino 111

department: DIETI / IAC

country: Italy

institute: Federico II / IAC

data_processing:
Trimming with trimgalore-0.6.4_dev
Alignment with STAR 2.7.9a with options:  --outFilterMultimapNmax 20 --outMultimapperOrder Random --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate
RSEM to Quantify transcripts
Assembly: GRCh38.p13, Gencode Release 38, GRCh38.primary_assembly.genome.fa
Supplementary files format and content: tab-delimited text files include rounded row counts values for each Sample

source_name: iPSC-NIL, nHOTAIRM1 KO

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Stranded mRNA Library

value: iPSC-NIL, nHOTAIRM1 KO

value: spMNs (Day 12)

value: nHOTAIRM1 KO

value: spMN differentiation (12 days)


title: iPSC-derived spMNs (Day 12), nHOTAIRM1 KO 3


title: Wild-type mice 1


title: WT3

value: saline is injected subcutaneously


title: WT_Veh_TRAP1

description:
Cre-Veh-2-TRAP
Wild type neurons - Vehicle - TRAP-seq 1

value: Hippocampus/cortex

value: Primary neurons

value: Excitatory neurons

value: Vehicle


title: WT1


title: SMC3_asyn_with_auxin_rep2

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

data_processing:
In-situ Hi-C data from each individual clone or biological replicates were aligned to mouse reference genome mm9 using bowite2 (global parameters: --very-sensitive -L 30 --score-min L, -0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder). Reads were paired up and PCR duplicates were removed through the Hi-C Pro software (v3.0.0) to generate a valid interaction pair file. The output pair files were then converted to “.hic” files using the hicpro2juicebox utility. HiC files were also converted to “.cool” files using the Hicexplorer (v3.7). For replicate or clone-merged samples, similar steps were taken on reads merged from each clone or biological replicates.
Assembly: mm9
Supplementary files format and content: cool and hic files of each individual biological replicate of hic data are provided.

source_name: G1E-ER4 cells

growth_protocol: G1E-ER4 is a subline of the GATA1-null proerythroblast cell line G1E (Weiss et al, Mol. Cell. Biol. 17, 1642–51 (1997).). Cells were cultered in IMDM medium, supplemented with 15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
cells were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water.
DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacture’s protocol. To eluted DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform.

treatment_protocol: G1E-ER4:SMC3-mAID-mCherry cells were treated with or without auxin (1mM) for 4 hours.

value: G1E-ER4 cells

value: erythroid

value: with auxin


title: SMC3_asyn_with_auxin_rep1


title: WT_BDNF_TRAP3

description:
Cre-BDNF-4-TRAP
Wild type neurons - BDNF - TRAP-seq 3

value: BDNF


title: iPSC-derived spMNs (Day 12), WT 3

source_name: iPSC-NIL WT

value: iPSC-NIL WT

value: WT


title: iPSC-derived spMNs (Day 12), nHOTAIRM1 KO 1


title: SMC3_asyn_no_auxin_rep2

value: no auxin


title: Model3 miRNA-seq

value: lens capsules

value: Na2SeO3 is injected subcutaneously


title: WT_BDNF_TRAP2

description:
Cre-BDNF-3-TRAP
Wild type neurons - BDNF - TRAP-seq 2

value: Wild Type


title: iPSC-derived spMNs (Day 12), WT 2

value: spMNs (Day 12)


title: KO_BDNF_TRAP1

description:
Creplus-BDNF-2-TRAP
GADD34 knockout neurons - BDNF - TRAP-seq 1

value: GADD34 knockout


title: Model2 miRNA-seq


title: iPSC-derived spMNs (Day 12), WT 1

value: spMN differentiation (12 days)


title: WT_Veh_TRAP2

description:
Cre-Veh-3-TRAP
Wild type neurons - Vehicle - TRAP-seq 2

value: Hippocampus/cortex


title: Model2


title: WT_BDNF_TRAP1

description:
Cre-BDNF-2-TRAP
Wild type neurons - BDNF - TRAP-seq 1

value: Primary neurons


title: Model1 miRNA-seq


title: SMC3_asyn_no_auxin_rep1


title: KO_Veh_TotLys2

description:
Creplus-Veh-3-Tot-Lys
GADD34 knockou neurons - Vehicle - RNA-seq 2

value: Total neurons


title: LNCaP Cells, DMSO, Rep 3

city: West Lafayette

first: Emily

last: Dykhuizen

address: 201 S University Street

institute: Purdue University

data_processing:
Data quality control, trimming and filtering were performed with Partek Flow Software Tools
FASTQ reads were mapped to the human (hg38) genome with STAR
Partek E/M model was used to assemble gene level expression data from filtered alignments
differential gene expression analysis was conducted using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file include count matrix for each Sample

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PureLink™ Genomic RNA Mini Kit . 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep kit (20040534) following manufacturer's protocols.

treatment_protocol: Cells were treated with 1µM 2-77, 10 µM ENZA, 0.2 µM ACBI, 2 µM BD98, 10 µM PB16 or vehicle control (DMSO) for 72 hours

value: LNCaP

value: Prostate adenocarcinoma

value: DMSO

tag: sample type

value: Vehicle

tag: time

value: 72 hour


title: KO_Veh_TotLys3

description:
Creplus-Veh-4-Tot-Lys
GADD34 knockou neurons - Vehicle - RNA-seq 3


title: WT3 miRNA-seq

value: saline is injected subcutaneously


title: SMC2_Noc_auxin_4h_rep2

description: hic

extract_protocol:
FACS purified cells (0.1 million) were lysed in 1ml cold Cell Lysis Buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40/Igepal) for 10min on ice. Nuclei were pelleted at 4℃ and washed once with cold 1.4 × NEB buffer 3.1 (NEB Cat#B7203S). Nuclei were then re-suspended in 25ul of 1.4 × NEB buffer 3.1 and treated with 0.1% SDS for 10min at 65℃. Nuclei were then treated with 1% Triton X-100 to quench SDS for 1h at 37℃. Chromatin was digested with 25U DpnII restriction enzyme (NEB, Cat#R0543M) at 37℃ overnight with shaking (950rpm on a thermal mixer). After overnight digestion, an additional stroke of 25U DpnII was added into the system to further digest the genome for 4 hours at 37℃. After the 2nd stroke of digestion, nuclei were incubated at 65℃ for 20min to inactivate DpnII. Digested chromatin fragments were then cooled down to room temperature and blunted with dCTP, dGTP, dTTP (Diamond Cat#B110049, B110050, B110051) and Biotin-14-dATP (active motif, Catalog No: 14138) using 6.6U DNA Polymerase I, Large (Klenow) fragment (NEB, Cat#M0210). Chromatin was then ligated in-situ with 2000U T4 DNA ligase (NEB, Cat#M0202M) for 4 hours at 16℃ followed by further incubation for 2 hours at room temperature. Chromatin was then reverse-crosslinked overnight at 65℃ in the presence of 1% SDS and proteinase K (G-clone Cat#EZ0970). After reverse-crosslinking, DNase-free RNase A (Vazyme Cat#DE111-01) was added to the system for 30min at 37℃ to remove RNA. DNA was then extracted by phenol-chloroform extraction, precipitated, and dissolved in 130ul of nuclease free water.
DNA was sonicated to 200-300bp fragments with a QSonica Q800R3 sonicator (40% amplitude, 15s ON and 15s OFF, 13min sonication) and purified with VAHTS DNA Clean Beads (Vazyme Cat#N411). Biotin-labeled DNA fragments was enriched by incubation with 100μl Dynabeads MyOne Streptavidin C1 beads (Thermal Fisher Scientific, Cat#65002) at room temperature for 15min. Streptavidin C1 beads were then washed twice with 1 × B&W buffer (5mM Tris-HCl, pH 7.5; 0.5mM EDTA; 1M NaCl). Beads were re-suspended in 30ul of 1 × NEB Buffer2 (NEB Cat#7002S) containing 9U of T4 DNA polymerase (NEB, Cat#M0203S) and 40uM dATG/dGTP and incubated at 20℃ for 4 hours to remove unligated fragments. Beads were then washed twice with 1 × B&W buffer and subject to library construction. DNA end repair, dA-tailing and adaptor ligation were constructed on beads, using the AHTS Universal DNA Library Prep Kit for Illumina or MGI (Vazyme, Cat# ND627-01, NDM607-02) based on the manufacture’s protocol. To eluted DNA from streptavidin beads, the library mixture was treated with 0.1% SDS and incubated at 98℃ for 10min. Released DNA was collected from the supernatant and purified with VAHTS DNA Clean Beads. Finally, the library was amplified for 9 cycles on a thermal cycler, using the VAHTS® HiFi Amplification Mix. PCR products were then purified with VAHTS DNA Clean Beads and sequenced on an Illumina NextSeq500 or MGI DNBSEQ-T7 sequencing platform.

treatment_protocol: G1E-ER4:SMC2-mAID-mCherry cells were first arrested to prometaphase with nocodazole (200ng/ml) for 12 hours or 15 hours (for 8h release condition). Toward the end of mitotic arrest, cells were treated with auxin (1mM) for 0h (SMC2+), 0.5 hours, 1 hour, 4 hours or 8 hours respectively.

value: G1E-ER4 cells

value: erythroid

value: nocodazole 12h + auxin 4h


title: SMC2_Noc_auxin_4h_rep1

description: hic


title: SMC2_Noc_auxin_1h_rep2

description: hic

value: nocodazole 12h + auxin 1h


title: WT2 miRNA-seq

value: lens capsules


title: LNCaP Cells, DMSO, Rep 1


title: LNCaP Cells, DMSO, Rep 2


title: SMC2_Noc_auxin_1h_rep1

description: hic


title: KO_BDNF_TotLys3

description:
Creplus-BDNF-4-Tot-Lys
GADD34 knockou neurons - BDNF - RNA-seq 3

value: BDNF


title: WT1 miRNA-seq


title: KO_Veh_TotLys1

description:
Creplus-Veh-2-Tot-Lys
GADD34 knockou neurons - Vehicle - RNA-seq 1

value: GADD34 knockout


title: WT2


title: LNCaP Cells, P-16, Rep 1

value: Drug


title: LNCaP Cells, P-16, Rep 3


title: KO_BDNF_TotLys1

description:
Creplus-BDNF-2-Tot-Lys
GADD34 knockout neurons - BDNF - RNA-seq 1

value: Hippocampus/cortex


title: KO_BDNF_TotLys2

description:
Creplus-BDNF-3-Tot-Lys
GADD34 knockou neurons - BDNF - RNA-seq 2

value: Primary neurons


title: SMC2_Noc_auxin_0h_rep1

description: hic

value: nocodazole 12h


title: SMC2_Noc_auxin_0h_rep2

description: hic


title: R2112

city: Macau

first: Yaling

last: Zeng

address: Avenida Wai Long, Taipa, Macau, China Avenida Wai Long, Taipa, Macau, China

institute: Macau university of science and technology

data_processing:
Illumina Casava1.7 software used for basecalling.
To get high quality clean reads, reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
we aligned reads of all samples to the Rattus norvegicus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: knee joint

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

value: knee joint

value: P53r211* overexpression

tag: model

value: AIA


title: R2113


title: WT_Veh_TotLys3

description:
Cre-Veh-4-Tot-Lys
Wild type neurons - Vehicle - RNA-seq 3

value: Total neurons

value: Wild Type

value: Vehicle


title: R2111


title: AIA3

value: wt


title: SMC2_asyn_rep2

description: hic

value: G1E-ER4 cells

value: erythroid


title: LNCaP Cells, BD98, Rep 3

value: LNCaP

value: Prostate adenocarcinoma

value: 72 hour


title: WT_Veh_TotLys2

description:
Cre-Veh-3-Tot-Lys
Wild type neurons - Vehicle - RNA-seq 2


title: LNCaP Cells, BD98, Rep 2


title: WT_Veh_TotLys1

description:
Cre-Veh-2-Tot-Lys
Wild type neurons - Vehicle - RNA-seq 1


title: LNCaP Cells, BD98, Rep 1


title: WT_BDNF_TotLys3

description:
Cre-BDNF-4-Tot-Lys
Wild type neurons - BDNF - RNA-seq 3

value: BDNF


title: 67_007_posCD45

city: Trondheim

first: Miriam

middle: Soledad

last: Giambelluca

state: Sør-Trøndelag

address: NTNU, Kunnskapssenteret, Olav Kyrres gate 17, 7030 Trondheim

country: Norway

institute: NTNU

data_processing:
bcl2fastq v 2.2.20 used to demultiplex into fastq files
Transcript counts were generated using quasi alignment (Salmon v1.3.0)
Transcript counts were imported into the R statistical software and aggregated to gene counts using the tximport (v1.14.0) bioconductor package
Assembly: Ensembl genome release-104 GRCh38
Supplementary files format and content: gene_counts.tsv is a tab separated file of gene counts across all samples

source_name: Tumor 67NR

growth_protocol: 67NR and 66cl4 cell lines of the immunocompetent 4T1 mouse breast cancer model were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 2mM L-Glutamine at 37°C with 5%CO2. After 75% confluency was reached; 1,000,000 cells were injected in mammary fat pad of female BALB/cJ mice.

extract_protocol:
Total RNA of sorted cells was extracted using RNA MicroPrep Kit (Quick-RNA™ MicroPrep Kit  w/Zymo-Spin™ IC Columns, Nordic Biosite, Cat #43844) according to manufacturer’s instructions. RNA quantity, quality/integrity and purity were evaluated using Qubit (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent, CA, USA) and NanoDrop (Thermo Fisher Scientific, MA, USA).  RNA sequencing was performed on RNA extracted from the sorted populations: 67NR CD45- (n=5), 67NR CD45+ (n=5), 66cl4 CD45- (n=5), 66cl4 CD45+ (n=5).
Sequencing libraries were generated using SENSE mRNA-Seq library prep kit V2, according to the manufacturer’s instructions (Lexogen GmbH, Vienna, Austria).

value: BALB/cJ

value: Tumor 67NR

value: Immune cells


title: 67_007_negCD45

value: Non-immune cells


title: SMC2_asyn_rep1

description: hic


title: LNCaP Cells, P-16, Rep 2

value: Drug


title: LNCaP Cells, Enza, Rep 3

value: ENZA


title: AIA1

value: knee joint

value: AIA


title: WT_BDNF_TotLys2

description:
Cre-BDNF-3-Tot-Lys
Wild type neurons - BDNF - RNA-seq 2

value: Hippocampus/cortex

value: Primary neurons

value: Total neurons

value: Wild Type


title: 67_006_posCD45


title: stl746_3

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
reads were trimmed by cutadapt first, the trimmed reads were aligned against Danio Rerio genome GRCz11 using STAR with default parameters
gene counts were derived from the number of uniquely aligned unambiguous reads by featureCount
all gene level transcript counts were imported into DESeq2, and normalization method was used to adjust for differences in library size
Assembly: GRCz11
Supplementary files format and content: fastq
Supplementary files format and content: read counts

organism: Danio rerio

source_name: 8dpf whole tissue

extract_protocol:
total RNA from 7 of 8dpf zebrfish larve were purified by Qiagen RNeasy micro kit
mRNA-Seq, Ribo-depletion
~30M 2X150 reads from NovaSeq S4

value: 8dpf whole tissue

value: fam177a1a/ stl700;stl746 double homozygote


title: LNCaP Cells, Enza, Rep 2

value: LNCaP

value: Prostate adenocarcinoma


title: 67_006_negCD45


title: AIA2

value: wt


title: stl746_2


title: stl746_1


title: stl700_3

value: fam177a1a stl700 homozygote


title: 67_005_posCD45

value: BALB/cJ

value: Tumor 67NR


title: LNCaP Cells, 2-77, Rep 3

value: 72 hour


title: p38i tumor

city: Miami

first: Nipun

middle: B

last: Merchant

state: Florida

address: 1550 Northwest 10th Avenue, Fox 140

department: Surgery

institute: University of Miami/Jackson Memorial Hospital - Miami, FL

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline(version 3.1.0,10x Genomics) was used to demultiplex cellular barcodes, map reads in FASTQ files to a  reference transcriptome by using a aligner called STAR and generates a feature-barcode matrix.
Assembly: mm10
Supplementary files format and content: outs from CellRanger and matrix table with raw gene counts for every gene and every cell

source_name: Pancreatic tumor

growth_protocol: Mice were housed under pathogen-free conditions with controlled light cycles and room temperature housing. Mice were weaned at 3 weeks of age and fed a standard rodent-chow diet.

extract_protocol:
The extraction protocol from 10x Genomics was used to isolate nuclei for single-cell RNA sequencing. Nuclei were isolated from single cell suspensions, washed and then counted based on the 10X Genomics protocol.
RNA libraries were prepared with chromium Single cell 3' Reagent V3 Kits according to the manufacturer's protocol.

treatment_protocol: Mice were treated daily starting at the age of 4 weeks for 2.5 weeks and sacrified at 6.5weeks of age

value: Pancreatic tumor

value: 6.5 weeks

value: dissociated tissue


title: LNCaP Cells, 2-77, Rep 1

value: Drug


title: stl700_1

last: Li


title: WT3

value: wild type


title: Control tumor

description: 10x Genomics

value: Vehicle (10% DMSO, 40% PEG-300, 5% Tween80, 45% saline)


title: 67_005_negCD45

value: Non-immune cells


title: WT_BDNF_TotLys1

description:
Cre-BDNF-2-Tot-Lys
Wild type neurons - BDNF - RNA-seq 1

value: Hippocampus/cortex

value: Primary neurons

value: Total neurons

value: Wild Type

value: BDNF


title: LNCaP Cells, ACBI, Rep 2

value: LNCaP

value: Prostate adenocarcinoma

value: ACBI


title: stl700_2

value: 8dpf whole tissue

value: fam177a1a stl700 homozygote


title: 67_004_posCD45

value: BALB/cJ

value: Tumor 67NR

value: Immune cells


title: PDGFRα+ cells, Mutant, biol rep5

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

data_processing:
Cell barcode and UMI information from Read1 were extracted using UMI-tools (v1.1.2) with the following command: “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC”.
Adaptor sequences and low-quality sequences were removed, and reads with a length below 20bp were discarded using TrimGalore (v0.6.7)
The processed reads were then mapped to the GRCm38 reference genome using HISAT2 (v2.2.1).
Read counts for each gene were obtained using featureCounts (v2.0.1) and UMI duplications were removed using UMI-tools. Four cell barcodes, namely "ATGCAATGC," "GACACGACA," "CGATGCGAT," and "TCTGGTCTG," were assigned to each sample.
Differentially expressed genes were identified using DESeq2 (v1.36.0) with a threshold of |log2FC| > 1 and padj < 0.1.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values file includes raw counts for each Sample

source_name: Perineal LA/BC muscles

extract_protocol:
For isolation of RNA from mesenchymal progenitors of LA/BC muscles, three hundred PDGFRα+ cells were sorted to wells of 96-well plate containing 10 µL of the lysis buffer at 4˚C. The lysis buffer was prepared by mixing 1 µL of RNase Inhibitor (TaKaRa, Cat# 2313A) and 19 µL of 10X lysis buffer (TaKaRa, Cat# 635013) and diluted to 1X with nuclease free water.
The 3'UTR RNA-Seq was conducted using the CEL-Seq2 protocol, with the exception of employing the Second Strand Synthesis Module (NEB) for double-stranded cDNA synthesis. The library was then amplified through 10 cycles of PCR without any sample pooling.

value: Perineal LA/BC muscles

value: mesenchymal progenitors


title: PDGFRα+ cells, Mutant, biol rep4


title: LNCaP Cells, ACBI, Rep 3

value: Drug

value: 72 hour


title: WT1

value: wild type


title: PDGFRα+ cells, Mutant, biol rep3


title: 66_007_posCD45

source_name: Tumor 66cl4

value: Tumor 66cl4


title: 67_001_negCD45

value: Non-immune cells


title: 67_001_posCD45


title: PDGFRα+ cells, Mutant, biol rep2


title: LNCaP Cells, Enza, Rep 1

value: ENZA


title: LNCaP Cells, ACBI, Rep 1


title: LNCaP Cells, 2-77, Rep 2


title: PDGFRα+ cells, Mutant, biol rep1


title: 66_007_negCD45


title: PDGFRα+ cells, Control, biol rep5

value: PDGFRalpha-CreER;AR+/Y


title: Control Larvae from 3 dpf replica 3

city: Elche

first: Alicia

last: Martinez Lopez

state: Alicante

address: Avenida Candalix 42, 5A

country: Spain

institute: IMIB

data_processing: none provided

source_name: Whole larvae

extract_protocol: Total RNA was extracted from a pool of 25 zebrafish larvae (3 dpf) with TRIzol reagent (Invitrogen) and Invitroge RNA Mini Kit (12183018A)

value: Whole larvae


title: HCASMC, EGF, CA10

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

description:
Counts_HCASMC.csv
CA38

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 101
Assembly: hg38
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

source_name: Human aortic smooth muscle

growth_protocol: HAoSMC and HCASMC were obtained from PromoCell (C-12533) and ATCC (PCS-100-021), respectively. were cultivated with “Smooth Muscle Cell Growth Medium 2” (low-serum cell culture media from PromoCell, Germany) supplemented with “Growth Medium 2 SupplementMix” (PromoCell, Germany) (Final supplementation concentrations after addition to the medium: 5% FCS, 0.5 ng/L EGF, 2 ng/mL FBF, 5 µg/mL Insulin)

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h in media without supplementation (“Smooth Muscle Cell Growth Medium 2") and then incubated for 48h -/+ 10µg/L EGF.

value: Human aortic smooth muscle

value: HCASMC

tag: gender

value: female

tag: donor

value: EGF


title: HCASMC, Control, CA10

description:
Counts_HCASMC.csv
CA37

tag: tissue

value: Control


title: Control Larvae from 3 dpf replica 2


title: WT2

value: 8dpf whole tissue


title: 67_004_negCD45

value: BALB/cJ

value: Tumor 67NR


title: PDGFRα+ cells, Control, biol rep4

value: Perineal LA/BC muscles

value: mesenchymal progenitors


title: Control Larvae from 3 dpf replica 1


title: PDGFRα+ cells, Control, biol rep3


title: 66_006_posCD45


title: 66_006_negCD45

value: Immune cells


title: HCASMC, EGF, CA09

description:
Counts_HCASMC.csv
CA34

tag: replicate


title: HCASMC, Control, CA09

description:
Counts_HCASMC.csv
CA33


title: Tg(ifih1_mut) Larvae from 3 dpf  replica 5


title: 66_005_negCD46


title: PDGFRα+ cells, Control, biol rep2


title: HCASMC, Control, CA08

description:
Counts_HCASMC.csv
CA29


title: Tg(ifih1_mut) Larvae from 3 dpf  replica 4


title: PDGFRα+ cells, Control, biol rep1


title: 66_005_posCD45


title: HCASMC, EGF, CA08

description:
Counts_HCASMC.csv
CA30


title: HCASMC, EGF, CA07

description:
Counts_HCASMC.csv
CA26


title: Colon,Penk+/+,rep4

city: Toulouse

first: Eric

last: Espinosa

state: France

address: IRSD  INSERM U1220 105 Avenue de Casselardit

department: IMMUNOLOGY

country: France

institute: INSERM

data_processing:
The quality control of reads was performed with FastQC and all samples pass classical quality control.
Reads were then aligned and quantified with STAR (Version 2.7.8a) on the Mus musculus genome GRCm39.107 from EBI databases.
Differential analyses of RNA-Seq data at the gene level were performed using the DESeq2 R package (v1.30.0) with the recommended workflow
Assembly: Mus musculus genome GRCm39.107
Supplementary files format and content: normalized count matrix (.csv) file of normalized counts using Deseq2

source_name: colon

extract_protocol:
Frozen colon biopsies were crushed in 500 µL TRIzol™ Reagent (Molecular Research Center, Euromedex, Souffelweyersheim, France) in Precellys lysing kit D-tubes (Bertin Technologies, Montigny le Bretonneux, France) placed in a Precellys (6000 rpm, 30 seconds twice; Bertin Technologies). Total RNA was then isolated by using GenElute™ mammalian total RNA miniprep kit (Sigma-Aldrich) following the manufacturer recommendations a
RNA-seq paired-end libraries were prepared according to Illumina’s 18 protocol with some adjustments, using the TruSeq Stranded mRNA library prep Kit (Illumina, San Diego, USA). Briefly, mRNAs were first selected from 10 µg total RNA using poly-T beads. Then, RNAs were fragmented during 2 minutes and retrotranscribed to generate double stranded cDNA. Compatible adaptors were ligated, allowing the barcoding of the samples with unique dual indices. Twelve cycles of PCR were applied to amplify libraries, and a final purification step allowed to obtain 280-1000 pb fragments. Libraries quality was assessed using the HS NGS kit on the Fragment Analyzer (Agilent Technologies, Santa Clara, USA). Libraries quantification and sequencing were performed at the GeT-PlaGe core facility (INRAe, Toulouse, France). Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche, Basel, Switzerland) to obtain an accurate quantification.

value: colon

value: Penk+/+

value: male


title: Tg(ifih1_mut) Larvae from 3 dpf  replica 3


title: Colon,Penk+/+,rep3


title: Colon,Penk+/+,rep2


title: 66_004_negCD45

value: Tumor 66cl4

value: Non-immune cells


title: Control Larvae from 3 dpf stimulated with Poly I:C replica 3

value: Whole larvae


title: HCASMC, Control, CA07

description:
Counts_HCASMC.csv
CA25

value: Human aortic smooth muscle


title: HCASMC, EGF, CA06

description:
Counts_HCASMC.csv
CA22

value: HCASMC


title: Control Larvae from 3 dpf stimulated with Poly I:C replica 2


title: 66_003_posCD45


title: Control Larvae from 3 dpf stimulated with Poly I:C replica 1


title: Colon,Penk+/+,rep1


title: 66_003_negCD45


title: HCASMC, Control, CA06

description:
Counts_HCASMC.csv
CA21

value: female


title: Tg(ifih1_mut) Larvae from 3 dpf stimulated with Poly I:C replica 3


title: 66_004_posCD45


title: Tg(ifih1_mut) Larvae from 3 dpf stimulated with Poly I:C replica 2


title: HCASMC, EGF, CA05

description:
Counts_HCASMC.csv
CA18

value: EGF


title: Colon,Penk-/-,rep3

value: Penk-/-


title: Colon,Penk-/-,rep4


title: HCASMC, Control, CA05

description:
Counts_HCASMC.csv
CA17

value: Control


title: Tg(ifih1_mut) Larvae from 3 dpf stimulated with Poly I:C replica 1


title: Wilding_5 sample from cross K4

city: Liverpool

first: Naomi

middle: Anne

last: Dyer

state: Merseyside

address: Pembroke Place

department: Department of Vector Biology

country: United Kingdom

institute: Liverpool School of Tropical Medicine

data_processing:
ASEReadCounter* was used for data analysis (https://github.com/gimelbrantlab/ASEReadCounter_star, Mendelevich, A., et al., Replicate sequencing libraries are important for quantification of allelic imbalance. Nat Commun, 2021. 12(1): p. 3370.)
Maternal and paternal pseudoreference genomes were generated from the AgamP4 reference and the genome sequence of the parent or siblings of each cross. If parental genomes were available (Wilding 3, Wilding 4, Wilding 5), prepare_reference.py was run with options --HETVCF=TRUE, and supplying the parental genome sequences as –vcf_mat, -vcf_pat. If parental genomes were not available (Wilding1, Wilding2, Wilding6) then a VCF file was generated using the genome data from whole genome sequenced male siblings of the RNA sequenced fenales, using the following criteria: SNPs must be heterozygous and biallelic in all siblings where data was available.  To eliminate potential low quality SNPs, if 5 or more siblings had missing data at a SNP it was excluded. This VCF file was supplied to prepare_reference.py as -vcf-joind.
Raw fastq reads were aligned to the parental pseudoreference genomes using STAR v2.5.4, with option --outFilterMultimapNmax 1 to only consider uniquely mapped reads
Resulting sam files were sorted by read names and merged using alleleseq_merge_stream_v2.py to produce a sam file with maternal and paternal read groups
this sam file was converted to sorted bam (samtools sort), then the count table of SNP coverage depths was produced using allelecounter.py with minimim coverage 0, minimum base quality to count reads of 2, and minimum map quality of 10
Assembly: Anopheles gambiae PEST reference, assembly AgamP4 (INSDC Assembly GCA_000005575.1, Feb 2006)
Supplementary files format and content: text formatted table of  SNP coverage depths  (allelic read counts) with headers
Supplementary files format and content: ID: SNP ID which is the chromosome and position
Supplementary files format and content: ref_rep1: RNAseq read counts matching the reference allele at this position in this sample
Supplementary files format and content: alt_rep1:L RNAseq read counts matching the alternative allele at this position in this sample
Supplementary files format and content: groupID: the geneID that this SNP is found in
Supplementary files format and content: contig: chromosome
Supplementary files format and content: position: position on that chromosome
Supplementary files format and content: refAllele: which base is at this position on the ref allele
Supplementary files format and content: altAllele: which base is at this position on the alternative allele

organism: Anopheles gambiae

source_name: whole adult females pool of 10

growth_protocol: All mosquitoes were raised in an insectary with temparature 26˚C and 70% relative humidity with 12 hours light 12 hours dark cycle. Larvae were fed on ground fishfood. Adults were fed on sugar water.

extract_protocol:
RNA was extracted from pools of ten female F1 progeny 3-5 days after eclosion using RNAqueousTM-4PCR Total RNA Isolation Kit (Invitrogen) and standard protocol. RNA was quantified using Qubit® 2.0 Fluorometer.
The total RNA libraries were prepared in accordance with the Illumina TruSeq RNA sample preparation v2 guide (Part # 15026495, rev.D, September 2012) for Illumina Paired-End Indexed Sequencing.

treatment_protocol: All mosquitoes received the same treatment (raised to 3 days post exlosion, sugar fed)  because the aim was to compare allele specific expression within each sample.

tag: mother from

value: Kisumu strain

value: whole adult females pool of 10

value: all female adult cell types

value: Kisumu x Nagongera F1 females

value: 3 days post eclosion sugar fed adults


title: Colon,Penk-/-,rep2

value: colon

tag: genotype


title: HCASMC, EGF, CA04

description:
Counts_HCASMC.csv
CA14

tag: treatment


title: Wilding_3 sample from cross B5

value: Nagongera strain

tag: cell type


title: Wilding_6 sample from cross K6


title: HM, Shp-1 f/f + chemo, scRNA-seq

city: Guangzhou

first: Guo

last: Qiu

state: Guangdong

address: Guangzhou Avenue

institute: Nanfang Hospital, Southern Medical University

description: 10X Genomics

data_processing:
The scRNA-Seq data were demultiplexed and aligned to the mouse genome, version mm10, and UMI-collapsed using the CellRanger toolkit (version 3.0.2, 10X Genomics).
Cells that expressed fewer than 300 genes were excluded, as were genes expressed in fewer than three cells per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
We isolated single cells from the bone marrow of leukemic mice, which were generated by transfecting MLL-AF9 or Hoxa9-Meis1 fusion gene into mouse embryonic stem cells. We used 2% EDTA-PBS to flush out the bone marrow cells and lysed the red blood cells. We counted and assessed the cell viability by flow cytometry and adjusted the cell concentration to 1000 cells/ul.
scRNA-seq libraries were constructed using a Chromium Single Cell 30 v2 Reagent Kit, according to the manufacturer’s protocol.

value: bone marrow

value: Hoxa9-Meis1 AML model

value: Hoxa9-Meis1 + chemo

value: Arac+Dox


title: Wilding_2 sample from cross B3


title: Colon,Penk-/-,rep1

value: male


title: Wilding_1 sample from cross B1


title: HCASMC, EGF, CA03

description:
Counts_HCASMC.csv
CA10

value: Human aortic smooth muscle

value: HCASMC


title: HCASMC, Control, CA03

description:
Counts_HCASMC.csv
CA09

value: female


title: HCASMC, Control, CA04

description:
Counts_HCASMC.csv
CA13


title: HM, Shp-1 f/f, scRNA-seq

description: 10X Genomics

value: PBS


title: HCASMC, EGF, CA02

description:
Counts_HCASMC.csv
CA06

value: EGF


title: Granulosa cells, CTX, 6h, rep3

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. The library preparations were sequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd. (Beijing, China) and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using fastp[2] (version 0.20.0). In this step, 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 of the clean data were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA[3] (v0.7.12) and clean reads were aligned to the reference genome using BWA mem  -k 32 -T 30 -t 4 -M. These reads were then filtered for high quality (MAPQ＞＝13), we also removed reads that were not properly paired and with PCR duplicates. Only uniquely mapped(MAPQ＞＝13) and de-duplicated reads were used for further analysis.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER( v4.9.1) software with ‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’. The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker. Peaks of different groups were merged using ‘bedtools merge’.We caltulated the mean RPM of each group in the merge peak. Only peaks with fold change of RPM more than 2 were considered as differential peaks. Genes associated with different peaks were identified using ChIPseeker.
Assembly: mm10
Supplementary files format and content: bigWig,  narrowPeak
Library strategy: CUT&Tag

source_name: ovarian granulosa cells

extract_protocol:
Cells were centrifuged for 5 min at 600×g at 4 ℃. Cell activity was detected with LUNA-FL and counted.
The cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targeted tagmentation. DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system. (Hyperactive Universal CUT&Tag Assay Kit for Illumina, vazyme).

value: ovarian granulosa cells

value: CTX

tag: antibody


title: Mouse L1 Bone Marrow

city: Paris

first: Laurence

last: Guyonneau-Harmand

address: 27 rue Chaligny

institute: Etablissement Français du Sang

description:
10x Genomics
L1_Bone_Marrow

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Matrix (.mtx), features (.tsv) and barcodes (.tsv) output files from CellRanger
Supplementary files format and content: Metadata files (.tsv) with UMAP coordinates and cell identities

organism:
Homo sapiens
Mus musculus

source_name: Bone Marrow

extract_protocol:
EBs were dissociated in 0.1% collagenase B (Roche Diagnostics, Laval, QC, Canada) for 1 hour at 37°C. They were then treated with 0.25% trypsin for 3 minutes and digested by gentle mechanical shaking.
Mice were killed at week 20, and the femurs and tibias were removed. Bone marrow was flushed, single-cell suspensions were prepared by gently pipeting up and down several times followed by  rinsing and filtration on 40 μm cell strainers (Nylon mesh).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone Marrow

tag: cell line

value: PCI-CAU

value: 20 weeks after engraftment

tag: assembly

value: grch38 and mm10

tag: cellranger software_version

tag: chromium 10x_technology


title: Mouse L5 Bone Marrow

description:
10x Genomics
L5_Bone_Marrow


title: Granulosa cells, CTX, 6h, rep2


title: Wilding_4 sample from cross K2

value: Kisumu strain

value: whole adult females pool of 10

value: all female adult cell types

value: Kisumu x Nagongera F1 females

value: 3 days post eclosion sugar fed adults


title: HCASMC, Control, CA02

description:
Counts_HCASMC.csv
CA05

value: Control


title: Granulosa cells, CTX, 6h, rep1


title: HCASMC, EGF, CA01

description:
Counts_HCASMC.csv
CA02

value: Human aortic smooth muscle


title: Granulosa cells, PBS, 6h, rep3


title: NK latent TGF 6

city: Hefei

first: Dongyao

last: Wang

state: Anhui

address: Department of Hematology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NK cells

extract_protocol:
PBMC were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: disease state

value: Healthy

tag: culture

value: latent TGF-beta

tag: Sex

value: Female

tag: age


title: HCASMC, Control, CA01

description:
Counts_HCASMC.csv
CA01

value: HCASMC

tag: gender

value: female


title: NK latent TGF 5

institute: University of Science and Technology of China


title: HAoSMC, Control, Ao12

description:
Counts_HAoSMC.csv
u830

value: HAoSMC

tag: donor


title: HAoSMC, EGF, Ao12

description:
Counts_HAoSMC.csv
u831

tag: tissue

value: EGF


title: MSC and MEF-loaded Nanovials pooled scRNAseq

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
Data was demultiplexed and output as FASTQ in Basespace using library indexes
FASTQs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Oligo barcodes (SEC-seq or nanovial hashing tags) were also mapped to cells using Cellranger multiconfig setup.
Gene by cell matrixes were processed and filtered in R using Seurat and basic utilities
For the mixed species experiment, the data was mapped to a joined human-mouse contig genome using Cellranger. Cells were assigned to each species based on the ratio of human to mouse reads
Assembly: GRCh38 (human), GRCm38 (mouse)
Supplementary files format and content: Data was filtered and normalized in Seurat. Nanovial barcodes and VEGFA barcodes are provided in metadata as raw unnormalized reads, while the cell-gene matrix is log transformed and normalized to cell depth.
Supplementary files format and content: For the purpose of filtering based on Nanovial barcodes, cell were removed from processed data which did not satisfy either barcode to barcode ratio cutoffs ("Mixed") or which had insufficient barcode impying separation from the nanovial

source_name: adipose/mesenchyme

growth_protocol: Immortalized human adipose-derived MSCs (ATCC SCRC-4000) were cultured in MSC Basal Medium supplemented with Low Serum MSC Growth Kit for adipose MSCs.

extract_protocol:
Nanovials were loaded directly into the cell mix at a concentration of 500 nanovials per ul for use in the 10x Chromium workflow.
Libraries were constructed as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein and Cell Multiplexing)
scRNAseq libraries were constructed as typically described in the guide above.
SEC-seq libraries proceeded via normal workflow, with inclusion of construction of a library to detect the oligo-barcoded antibody using the Feature Barcode library workflow in the Single Cell User guide above

treatment_protocol: MSCs were cultured and loaded onto gelatin coated nanovials for 2 hours before straining excess cells. Cells were bound and allowed to secrete for a 12 hour incubation. Nanovials are then collected and incubated with anti human VEGF-A antibody for 30 minutes. Nanovials containing single cells were isolated by FACS using calcein stain. Cell-loaded nanovials were then diluted and added directly to the single cell RNA-seq workflow.

value: adipose/mesenchyme

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell/ Mouse Embryonic Fibroblast


title: NK latent TGF 3


title: HAoSMC, EGF, Ao11

description:
Counts_HAoSMC.csv
u827

tag: replicate


title: NK latent TGF 4

value: Male


title: Granulosa cells, PBS, 6h, rep2

value: ovarian granulosa cells

value: PBS


title: Granulosa cells, PBS, 6h, rep1


title: NK latent TGF 2


title: NK latent TGF 1


title: HAoSMC, Control, Ao11

description:
Counts_HAoSMC.csv
u826


title: Granulosa cells, CTX, 6h, 2

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, 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. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: Xls files include FPKM values and gene count for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: CTX


title: NK Active TGF 6

value: active TGF-beta


title: Granulosa cells, PBS, 6h, 3


title: HAoSMC, Control, Ao10

description:
Counts_HAoSMC.csv
u778

value: Human aortic smooth muscle

value: Control


title: Granulosa cells, CTX, 6h, 1


title: Granulosa cells, PBS, 6h, 1


title: NK Active TGF 5

value: bone marrow

value: Healthy


title: HAoSMC, Control, Ao09

description:
Counts_HAoSMC.csv
u770


title: HAoSMC, EGF, Ao09

description:
Counts_HAoSMC.csv
u771


title: Granulosa cells, CTX, 6h, 3


title: NK Active TGF 4


title: HAoSMC, EGF, Ao08

description:
Counts_HAoSMC.csv
u741


title: B cells,Mb1Cre,Day3,1

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

institute: tsinghua university

data_processing:
Clean reads were mapped to GRCm38/mm10 using Bowtie2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 50 μM β-mercaptoethanol, GlutaMax and nonessential amino acids.

extract_protocol:
Total RNA was extracted from B cells by using TRNzol reagent (Tiangen, China) and reverse-transcribed by PrimeScript RT reagent kit (Takara)
Library data were assembled and analyzed by the BGISEQ institute.

treatment_protocol: B cells were stimulated for 3 days using 10 μg/mL LPS and 50 ng/mL IL-4 to induce B cells CSR in vitro.

value: spleen

value: primary

value: B cell

value: WT

value: LPS and IL4 for 3 days


title: B cells,Mb1Cre,Day3,2


title: NK Active TGF 3

value: Female


title: DSS_CS_rep4

city: Jinan

first: Yanan

last: Xia

state: Shandong Province

address: Wen Hua Xi Road

institute: Qilu Hospital of Shandong University

data_processing:
Reads generated with Illumina NovaSeq 6000 Sequencing System were further filtered by Cutadapt. The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.
Then sequence quality was verified using FastQC, including the Q20, Q30, and GC-content of the clean data.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was used according to the RNA-seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

tag: strain

value: ICR

value: cesarean section; 3% DSS in drinking water for 8 days


title: DSS_CS_rep3

tag: genotype


title: NK Active TGF 2

value: Male


title: HAoSMC, EGF, Ao10

description:
Counts_HAoSMC.csv
u779

value: HAoSMC

value: female

tag: treatment

value: EGF


title: NK Active TGF 1

value: active TGF-beta


title: Bcells,Mctf/fMb1Cre,Day3,3

tag: cell type

value: cKO


title: Bcells,Mctf/fMb1Cre,Day3,2


title: HAoSMC, EGF, Ao07

description:
Counts_HAoSMC.csv
u733

value: Human aortic smooth muscle


title: NK control 6

value: bone marrow

value: Healthy

value: control


title: DSS_CS_rep1


title: Granulosa cells, PBS, 6h, 2

value: ovarian granulosa cells

value: PBS


title: DSS_VD_rep4

value: WT

value: vaginal delivery; 3% DSS in drinking water for 8 days


title: Bcells,Mctf/fMb1Cre,Day3,1

value: spleen

value: primary

value: B cell

value: LPS and IL4 for 3 days


title: NK control 5

value: Female


title: B cells,Mb1Cre,Day0,2


title: DSS_VD_rep3

value: colon

value: ICR


title: HAoSMC, Control, Ao07

description:
Counts_HAoSMC.csv
u732

value: HAoSMC

value: female

value: Control


title: HAoSMC, EGF, Ao06

description:
Counts_HAoSMC.csv
a823

value: Human aortic smooth muscle

value: EGF


title: NK control 4

value: bone marrow

value: Healthy

value: control

value: Male


title: HAoSMC, Control, Ao06

description:
Counts_HAoSMC.csv
a822


title: NK control 3


title: B cells,Mb1Cre,Day0,1

value: WT


title: DSS_VD_rep2

value: vaginal delivery; 3% DSS in drinking water for 8 days


title: HAoSMC, Control, Ao08

description:
Counts_HAoSMC.csv
u740


title: HAoSMC, EGF, Ao05

description:
Counts_HAoSMC.csv
a819


title: NK control 2


title: Bcells,Mctf/fMb1Cre,Day0,2

value: spleen

value: primary

value: cKO


title: DSS_VD_rep1


title: CON_CS_rep4

value: cesarean section; normal drinking water


title: Bcells,Mctf/fMb1Cre,Day0,1

value: B cell


title: HAoSMC, Control, Ao05

description:
Counts_HAoSMC.csv
a818


title: DSS_CS_rep2

value: colon

value: ICR

value: cesarean section; 3% DSS in drinking water for 8 days


title: NK control 1


title: CON_CS_rep3


title: HAoSMC, EGF, Ao04

description:
Counts_HAoSMC.csv
a797

value: HAoSMC

value: female


title: HAoSMC, Control, Ao04

description:
Counts_HAoSMC.csv
a796

value: Human aortic smooth muscle

value: Control


title: CON_CS_rep2


title: SMC2_with_DMSO_PMPM2_k27ac_rep2

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

data_processing:
For ChIP experiments against histone modification marks H3K27ac, H3K36me3, H3K27me3 and H3K9me3, spike-in samples were included to control for global change of histone marks during mitosis, especially for those with large-scale broad range peaks (such as H3K9me3). ChIP-seq reads were first aligned to human genome assembly hg19 with default parameters. Unmapped reads were then aligned to mouse genome assembly mm9. Human and mouse alignments were then both filtered for low-quality reads (MAPC <30), PCR duplicates and reads that aligned to mitochondria random contigs and ENCODE blacklisted regions were removed. The final read counts aligned to human hg19 genome was determined by SAMtools (v1.9) and scaling factor was calculated as: 10e6/hg19_counts. Valid reads that aligned to mouse genome was then normalized using the above scaling factor through Deeptools (v3.1.3).
Assembly: mm9
Supplementary files format and content: bigWig

source_name: G1E-ER4 cells

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
FACS purified cells were re-suspended in 1ml pre-cooled Cell Lysis Buffer supplemented with 1:500 protease inhibitor and 1:100 PMSF for 20min on ice. To control for global change of histone modification that cannot be detected by ChIP-seq, HEK293T cells were used as spike-in controls and added into FACS purified mitotic and asynchronous cells so that both samples contain comparable level of human genome (~10%). Nuclei were then re-suspended in 1ml Nuclear Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS, fresh supplemented with PI and PMSF) for 20min on ice. Chromatin was then fragmented to 200-300bp by sonication (Qsonica Q800R3, 80% amplitude, 20s ON, 40s OFF) for 17min. Samples were centrifuged at 15000g for 10min at 4℃ to remove cell debris. Chromatin in the supernatant was collected and diluted with 4 volumes of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS) and then supplemented with protease inhibitor, PMSF and 50ul of A/G agarose beads (Santa Cruz Cat#sc-2003). Preclear of chromatin was performed at 4℃ for 8h with rotation. Precleared chromatin was then incubated with 35μl A/G agarose beads (A:G = 1:1) pre-bound with ChIP antibody at 4℃ overnight. Beads were washed once with IP wash buffer I (20mM Tris pH 8, 2mM EDTA, 50mMNaCl, 1% Triton X-100, 0.1% SDS), twice with high salt buffer (20mMTris pH 8, 2mM EDTA, 500mMNaCl, 1% Triton X-100, 0.01% SDS), once with IP wash buffer II (10mMTris pH 8, 1mM EDTA, 0.25 M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate) and twice with TE buffer (10mM Tris pH 8, 1mM EDTA pH 8). All washing steps were performed on ice. Beads were moved to room temperature and DNA was eluted in 200μl fresh Elution Buffer (100mM NaHCO3, 1%SDS). ChIP and input chromatin were reverse crosslinked at 65℃ overnight in the prescence of proteinase K.  IP and input samples were supplemented with 10ul of 3M sodium acetate (pH 5.2), and DNA was purified with QIAquick PCR purification kit (QIAGEN Cat#28106).
ChIP-seq libraries were constructed using the AHTS Universal DNA Library Prep Kit for MGI (Vazyme, Cat#NDM607-02) according to the manufacture’s protocol.For cut and tag library: we performed CUT&TAG on asynchronously growing G1E-ER4 cells using lamin B1 antibody (ab16048) according to the manufacture’s protocol (Vazyme Hyperactive® Universal CUT&Tag Assay Kit for Illumina).

value: G1E-ER4 cells

value: erythroid


title: CON_CS_rep1


title: HAoSMC, EGF, Ao03

description:
Counts_HAoSMC.csv
a775

value: EGF


title: Adjacent normal LOCC_17

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_17_N

data_processing:
FASTQ ﬁles using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ ﬁles were analyzed with HTG EdgeSeq Parser software version v5.1.724.4793 to generate raw counts for a total of 1,410 genes.
Assembly: GRCh38.p13
Supplementary files format and content: HTG-EdgeSeq raw data counts and annotation data file as xlsx format

source_name: Colon cancer

extract_protocol:
Thirteen EOCC tumors, 13 LOCC tumors, and the respective 26 paired-adjacent normal colon tissues were processed. Normal tissues were defined as normal epithelial areas at least 2 cm away from the tumor margin. Using 5 µm unstained FFPE sections, the tumor areas were marked by referring to the H&E staining of the consecutive slide, with the accordance of a certificated pathologist. The estimated tissue areas were measured using Image J software. Then, the optimal amounts of tissue for each HTG EdgeSeq PIP assay were scraped and placed into microfuge tubes. The calculated volume of Lysis Buffer for the each collected sample was added, and the samples were then overlaid with 500 µl of HTG denaturation oil. After centrifugation, the samples were incubated at 95°C for 15-20 minutes to denature protein structures and remove paraffin wax from the FFPE tissue sections. Samples were cooled down for 10 minutes at room temperature (RT), and HTG-provided Proteinase K was pipetted into the aqueous (lysis, non-oil) phase of the samples at a volume 1/20th of the total lysis buﬀer. Finally, the samples were incubated at 50°C for three hours, with the aqueous phase being mixed by pipetting every 30 minutes. Subsequently, 25 µL of the sample lysate was loaded onto the HTG EdgeSeq instrument for probe-capture for 20 hours.
Probe-captured FFPE samples for EdgeSeq PIP assay were ampliﬁed and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buﬀer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers. The PCR reaction conditions were as follows: (1) 95°C for 4 min, (2) 95°C for 15 s, (3) 56°C for 45 s, (4) 68°C for 45 s, (5) repeating steps 2-4 for a total of 19 cycles, (6) 68°C for 10 min, and (7) holding at 4°C. Following PCR, library cleanup was performed with a mixture of Clean Up buﬀer (39% of 5M NaCl, 31.25% of 40% PEG 8000, 29.75% of molecular-grade water) and AMPure XP beads, by combining it with the PCR-ampliﬁed sample at 5:2 ratio, respectively. After 5 minutes of incubation, the samples were placed on the magnetic stand, then washed twice with 80% ethanol, followed by a 5-minute air drying period. The elution was performed using 40 µL of Trizma Hydrochloride, formulated at 10 mM Tris-HCl, pH 8.0.
Targeted mRNA Sequencing using HTG-EdgeSeq PIP assay

value: Colon cancer

tag: tissue type

value: LOCC

tag: tissue site

value: Adjacent normal

tag: age of_patients


title: HAoSMC, Control, Ao03

description:
Counts_HAoSMC.csv
a774


title: Adjacent normal LOCC_16

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_16_N


title: Adjacent normal LOCC_15

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_15_N


title: CON_VD_rep4

value: WT

value: vaginal delivery; normal drinking water


title: SMC2_with_A485_PMPM2_k27ac_rep1

tag: cell line


title: SMC2_noc_with_auxin_rep3_hp1b


title: Adjacent normal LOCC_13

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_13_N


title: CON_VD_rep3


title: HAoSMC, EGF, Ao02

description:
Counts_HAoSMC.csv
a737


title: HAoSMC, Control, Ao02

description:
Counts_HAoSMC.csv
a736


title: Adjacent normal LOCC_12

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_12_N


title: SMC2_noc_with_auxin_rep2_polii


title: CON_VD_rep2


title: CON_VD_rep1


title: SMC2_with_DMSO_PMPM2_k27ac_rep1


title: SMC2_noc_with_auxin_rep2_k36me3


title: SMC2_with_A485_PMPM2_k27ac_rep2


title: HAoSMC, Control, Ao01

description:
Counts_HAoSMC.csv
a662


title: Adjacent normal LOCC_08

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_08_N


title: HCPEpiC-Tryptase-3

city: Guangdong

first: Di

last: Can

address: Guangzhou

institute: Sun Yat-Sen university

description: RNA-seq

data_processing:
1. sn-seq: Raw BCL files obtained from the 10x GENOMICS Single-nucleus RNA-seq platform were convert to FASTQ files. The resulting FASTQ files were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x GENOMICS). For quality control, nuclei were excluded from further analysis if they were outliers in terms of number of the genes, UMIs, and the percentage of mitochondrial genes using the R (v4.1.0) software package Seurat (v4.0.6) (http://satijalab.org/seurat). After filtering, a total of 20,198 nuclei (10,444 from normal, 9,754 from EO771-VM) remained for downstream analysis. 2. ST: Raw ST sequencing data were processed using the open source ST Pipeline v1.7.2 with the genome reference mm10 transcriptome. The ST pipeline was executed with two-pass mode enabled for alignment and discarding reads in which the UMI had at least 6 low quality bases. The count matrices (spots by genes) were filtered to keep only protein-coding, long non-coding, and antisense genes, and Ensembl IDs were replaced by gene names. The matrix of counts underwent another filtering step, where only spots inside the tissue were kept using the file generated in the previous step (image alignment).  3. RNA-seq: Raw sequencing reads were quality-filtered and adapter removal was performed by fastp (v.0.18.0). Paired-end clean reads were mapped to the human reference genome Ensembl_release106 using HISAT2 (v.2.4). Gene level quantification and normalization was using RSEM (v.1.3.3) software. Fragment per kilobase of transcript per million mapped reads (FPKM) was used as an index of gene quantification.
Assembly: mm10;human reference genome Ensembl_release106
Supplementary files format and content: 1.sn-seq: Tab-separated values files and matrix files. 2. ST: Tab-delimited text files containing genes by barcode counts matrices. Tissue_positions_list.csv includes cell barcode for X,Y coordinates. 3.RNA-seq: tab-delimited text files include RPKM values for each Sample

source_name: cell line

extract_protocol:
1. sn-seq: The lateral ventricles including the choroid plexus and an about 2 mm thin layer of tissue surrounding the ventricles were carefully micro-dissected and homogenized using scissors. The resulting homogenates were filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min to pellet nuclei. To purify nuclei, the pellet was resuspended and centrifuged at 25,000 rpm at 4 ℃ for 2 hr using an ultra-centrifuge equipped with swinging bucket rotor. The supernatant was carefully removed via aspiration. 1 ml of stain buffer was added to resuspend the nuclear pellet. The nuclei were pelleted at 500 g for 10 min at 4 ℃. Stain buffer with mouse anti-NeuN conjugated to Alexa-Fluor-488 was added. The samples were incubated for 30 min at 4 ℃ and then centrifuged for 5 min at 500 g to pellet nuclei. The pallets were resuspended in stain buffer that contained 0.1 µg/ml DAPI. Single nucleus sorting was carried out on FACSAria III. Nuclei were gated on their morphology and DAPI signal. Nuclei negative for NeuN were sorted. 2. ST: EO771-VM bearing mouse brains were embedded in Tissue-Tek O.C.T. Compound and frozen in isopentane on liquid nitrogen. The embedded mouse brains were cryosectioned coronally to a thickness of 10 mm (at -0.6 mm from the bregma) slice on a cryostat. Sections were placed respectively on Visium Spatial Tissue Optimization Slide and Visium Spatial slide within the capture area. 3. RNA-seq: The different mRNA profiles of HCPEpiC cells treated with or without 500 ng/mL recombinant human tryptase  were compared by RNA-seq. Total RNA was extractedusing the TRIzol  reagent according to the manufacturer’s instructions. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
1. sn-seq:Single nucleus was loaded on a 10x GENOMICS GemCode Single-nucleus instrument that generated single-nucleus Gel Bead-In-EMlusion (GEMs). Reverse transcription and libraries preparation were performed using the Chromium Next GEM Single nucleus 3’ Reagent Kits v3.1 (10x GENOMICS, CG000204) according to the manufacturer’s protocol. Libraries were sequenced on an lllumina NovaSeq 6000 system.  2.ST: After permeabilization, tissues were degraded and removed from the slides. Reverse transcription mix containing SuperScript III reverse transcriptase  was added to each section and incubated overnight at 42 ℃ to generated cDNA with spatial barcode information. The spatially barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. The libraries were sequenced on the lllumina NovaSeq 6000 system using paired-end sequencing. 28 bases were sequenced on read 1 to determine the spatial barcode and UMIs, and 120 bases were sequenced on read 2 to cover the genetic region. 3. RNA-seq: Libraries of RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina. RNA-seq was performed using the Novaseq6000  with paired-end reads.

value: cell line

value: choriod plexus epithelial cells

value: cells were treated with tryptase


title: SMC2_noc_with_auxin_rep2_k27me3


title: Adjacent normal LOCC_09

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_09_N


title: Adjacent normal LOCC_05

description:
HTG_EdgeSeq_PIP_NGS
RNA (amplified oligo nucleotide probes)
LOCC_05_N


title: HCPEpiC-Tryptase-2

description: RNA-seq