title: GCs, Rbp4-Cre, SS2, DG_P10_C7

description:
Library name: 20210417_Blanca_Plate3_C7
Smart-seq2


title: F+6W_pulp_mRNAseq_rep1

status: Public on Sep 21 2025

type: SRA

city: Shenzhen

first: Yu

last: Ma

address: 1088 Xueyuan Bivd, Nanshan District

country: China

institute: Southern University of Science and Technology

library_source: transcriptomic

data_processing:
RNA-Seq reads were trimmed using Trimmomatic before alignment. The trimmed reads were aligned to the grape genome using STAR.
Assembly: V4
Supplementary files format and content: bigwig

molecule: polyA RNA

organism: Vitis vinifera

source_name: mRNA-seq of grape pulp in F+6W stage

extract_protocol:
TRIzol reagent (Ambion)
Total RNA was extracted with TRIzol reagent (Ambion) from pericarps of fruits. For reverse transcription, 1 μg of RNA and oligo dT primers were used to synthesize cDNA in a 20-μL reaction using the qScript cDNA SuperMix kit (Quanta). Real-time PCR was then carried out on a CFX96 Real-Time PCR Detection System (Bio-Rad) with PerfeCTa SYBR Green FastMix (Quanta). For RNA-seq, the libraries were constructed and sequenced at the Genomics Core Facility of the Shanghai Centre for Plant Stress Biology, Chinese Academy of Sciences, with an Illumina HiSeq2500.

tag: tissue

value: fruit pulp

tag: genotype

value: Cabernet Sauvignon


title: GCs, Rbp4-Cre, SS2, DG_P10_C6

city: leuven

first: Danie

last: Daaboul

address: Herestraat 49

department: Department of Neuroscience

country: Belgium

institute: KU Leuven

description:
Library name: 20210417_Blanca_Plate3_C6
Smart-seq2

library_source: transcriptomic single cell

data_processing:
Adapter trimming was performed using the fastp tool. Reads were mapped to a custom Mus musculus mm10 reference genome, which included the tdTomato gene, using the STAR tool. Quality control was applied to remove low-quality cells, filtering out cells with low mapping percentages or those lacking tdTomato gene detection.
Data from different samples were merged and subjected to quality control and filtering. Specifically, cells with fewer than 500 genes, more than 8,000 genes, or more than 5% mitochondrial gene content were filtered out. Additionally, genes expressed in fewer than 6 cells were removed, and all mitochondrial genes, along with a list of sex-related genes, were excluded from the resulting count matrix.
Assembly: custom mouse mm10 reference genome with the tdTomato gene
Supplementary files format and content: counts_SS2_unfiltered_raw.csv, csv counts matrix, merged samples raw gene expression counts
Supplementary files format and content: sample_data_SS2_unfiltered.csv, csv, sample metadata, unfiltered data
Supplementary files format and content: counts_SS2_filtered_raw.csv, csv counts matrix, merged samples raw gene expression counts, filtered genes and high-quality cells
Supplementary files format and content: sample_data_SS2_filtered.csv, csv sample metadata, filtered high-quality cells
Supplementary files format and content: SS2_filtered_raw.loom, loom file, merged cells from all samples, filtered data based on quality

molecule: total RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Brain slices from Rbp4-Cre:Ai9 mice were made using a 500 μm brain matrix, and the dentate gyrus (DG) was dissected. Next, the DG was chopped in smaller pieces and digested using Pronase. Following the digestion, the tissue pieces were homogenized using two-size Pasteur pipettes and the mix was loaded in a 20% Percoll solution to remove debris. Following centrifugation, the pellet was resuspended in OptiMEMtrehalose, and DAPI was added. Fluorescence Activated Cell Sorting (FACS) was done based on DAPI and tdTomato signal, into 96-well plates containing lysis buffer (see Methods for details).
For the first strand synthesis, the Smart-Seq2 plates were thawed to room temperature for 1 min and subsequently spun down at 2000 xg for 1 min. The RNA denaturation was carried out at 72 °C for 10 min and flash-cooled on ice for 5 min. First strand synthesis mix (1X SuperScript II first strand synthesis buffer, Thermo Fisher; 5 mM DTT, Thermo Fisher; 100 U Oligo SuperScript II reverse transcriptase enzyme, Thermo Fisher; 10 U RNAse OUT, Thermo Fisher; 1M Betaine, Sigma Aldrich; 6 mM MgCl2, Thermo Fisher; and 1 μM TSO, IDT Technologies) is added to the cell lysis mix to a total volume of 10 μM. First strand synthesis reaction was carried out with following program: 42 °C for 90 min; 10 cycles of {50 °C for 2 min; 42 °C for 2 min}; 72 °C for 15 min; 4 °C indefinite hold. PCR amplification of the first strand product was performed by adding 15 µl of the PCR mix to the first strand product (1X KAPA HiFi HotStart Ready Mix, Roche; and 0.1 µM of IS PCR primer, IDT Technologies). The 22 cycles of the following PCR program was used to amplify the first strand product: 98 °C for 3 min; 22 cycles of {98 °C for 20 s; 67 °C for 15 s; 72 °C for 6 min}; 72 °C for 5 min; 4 °C indefinite hold. Using Hamilton STAR liquid handler (Hamilton), 20 µl of Ampure XP was added to each well and mixed. Standard Ampure XP purification was carried out as per the manufacturer’s recommendation and the cDNA library was eluted in 22.5 µl of Elution buffer. 22 µl of the eluted library was transferred to fresh Echo Mass Spectrometry (MS) Qualified 384-well Polypropylene (PP) Microplate (Beckman Coulter). Labcyte Echo 550 acoustic dispenser (Beckman Coulter) was used for the next steps. 1 µl of Tn5 tagmentation mix (1X Tagment DNA buffer, Illumina; ATM mix, Illumina and cDNA library 1 ng) for cDNA fragmentation. Tn5 tagmentation was performed with the following program: 55 °C for 10 min; 4 °C indefinite hold. Tagmentation reaction was stopped by quenching the reaction with 500 nl of NT buffer for 5 min (Illumina). 750 nl of the i5 and i7 Illumina indexes were added to the plates. Finally, 2 µl of NPM master mix was added to the plate and mixed well and place for index PCR amplification: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of {95 °C for 10 s; 55 °C for 30 s; 72 °C for 30 s}; 72 °C for 5 min, and 4 °C indefinite hold. The indexed PCR products are pooled in a single tube and 0.8X Ampure XP purification (Beckman Coulter) was carried out as per manufacturer’s recommendation and finally the sequencing library was eluted in 35.5 µl of Elution buffer (Qiagen). Smart-Seq2 libraries were sequenced on NextSeq 500 (Illumina) sequencing platforms. Sequencing was done as per the protocol recommendations: paired end read of 61 bps (read 1), 61 bps (read 2), 8 bps (index 1) and 8 bps (index 2). Sequencing was performed at a depth of 500,000 reads per cell.

value: hippocampus

tag: cell type

value: granule cells


title: GCs, Rbp4-Cre, SS2, DG_P10_C5

description:
Library name: 20210417_Blanca_Plate3_C5
Smart-seq2


title: V+3W_skin_mRNAseq_rep2

source_name: mRNA-seq of grape skin in V+3W stage

value: fruit skin


title: V+3W_skin_mRNAseq_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_C4

description:
Library name: 20210417_Blanca_Plate3_C4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_C2

description:
Library name: 20210417_Blanca_Plate3_C2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_C12

description:
Library name: 20210417_Blanca_Plate3_C12
Smart-seq2


title: F+6W_skin_mRNAseq_rep1

source_name: mRNA-seq of grape skin in F+6W stage


title: GCs, Rbp4-Cre, SS2, DG_P10_C3

description:
Library name: 20210417_Blanca_Plate3_C3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_C11

description:
Library name: 20210417_Blanca_Plate3_C11
Smart-seq2


title: V+3W_pulp_BSseq_rep1

library_source: genomic

data_processing:
clean reads were mapped to grape v4 genome using bismark version 0.22.3 with parameters set to “-N 1 -I 0 -X 1000”
Assembly: V4
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: BS-seq of grape pulp in V+3W stage

extract_protocol:
Dneasy®  Plant  Maxi Kit (Qiagen)
Genomic DNA was extracted from grape fruits using a DNeasy Plant Maxi Kit (Qiagen) and then was used for library construction using Illumina’s standard DNA methylation analysis protocol and the NEB Ultra II DNA Library Prep Kit. For berry tissues, Genomic DNA was isolated with the Qiagen DNeasy plant mini kit 250 (Cat:69106) according to the manufacturer’s instructions.


title: GCs, Rbp4-Cre, SS2, DG_P10_C1

description:
Library name: 20210417_Blanca_Plate3_C1
Smart-seq2


title: F+6W_skin_mRNAseq_rep3


title: F+6W_pulp_BSseq_rep2

source_name: BS-seq of grape pulp in F+6W stage


title: GCs, Rbp4-Cre, SS2, DG_P10_B9

description:
Library name: 20210417_Blanca_Plate3_B9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_C10

description:
Library name: 20210417_Blanca_Plate3_C10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B8

description:
Library name: 20210417_Blanca_Plate3_B8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B7

description:
Library name: 20210417_Blanca_Plate3_B7
Smart-seq2


title: V+3W_skin_BSseq_rep1

source_name: BS-seq of grape skin in V+3W stage


title: V+3W_skin_BSseq_rep2


title: V+3W_pulp_BSseq_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_B6

description:
Library name: 20210417_Blanca_Plate3_B6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B5

description:
Library name: 20210417_Blanca_Plate3_B5
Smart-seq2


title: V+4W_berry_BSseq_rep2

source_name: BS-seq of grape berry in V+4W stage

value: whole berry

value: Wink


title: F+6W_skin_BSseq_rep1

source_name: BS-seq of grape skin in F+6W stage


title: GCs, Rbp4-Cre, SS2, DG_P10_B4

description:
Library name: 20210417_Blanca_Plate3_B4
Smart-seq2


title: V+4W_berry_BSseq_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_B3

description:
Library name: 20210417_Blanca_Plate3_B3
Smart-seq2


title: F+6W_skin_BSseq_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_B2

description:
Library name: 20210417_Blanca_Plate3_B2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B1

description:
Library name: 20210417_Blanca_Plate3_B1
Smart-seq2


title: Ver_berry_BSseq_rep1

source_name: BS-seq of grape berry in veraison stage


title: Ver_berry_BSseq_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_B12

description:
Library name: 20210417_Blanca_Plate3_B12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B11

description:
Library name: 20210417_Blanca_Plate3_B11
Smart-seq2


title: F+6W_skin_mRNAseq_rep2


title: F+6W_pulp_BSseq_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_A9

description:
Library name: 20210417_Blanca_Plate3_A9
Smart-seq2


title: CC_7

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Library name: Sample14

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen) was used for adaptor trimming and mapping to the miRbase 21 database allowing two base mismatches. Then, the data was normalized using reads per million mapped reads.
Assembly: miRBase 21
Supplementary files format and content: a tab-spaced txt file includes RPM counts of each sample

organism: Homo sapiens

source_name: Trophblast

extract_protocol:
FFPE samples were sectioned using rotary microtome to obtain 10-μm tissue sections placed on the coating slide and stained with hematoxylin-eosin (HE). Trophoblast regions were then microdissected using LMD7000 (Leica Microsystems). Total RNA was extracted using the miRNeasy Mini Kit (QIAGEN).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturers' protocol.

value: Trophblast

tag: age

tag: antecedent pregnancy

value: CHM

tag: organ

value: Lung

tag: figo score

tag: gestational age

tag: pre-treatment hcg

tag: outcome

value: NED


title: CC_8

description: Library name: Sample15

value: Uterus


title: GCs, Rbp4-Cre, SS2, DG_P10_A8

description:
Library name: 20210417_Blanca_Plate3_A8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A7

description:
Library name: 20210417_Blanca_Plate3_A7
Smart-seq2


title: CC_9

description: Library name: Sample16


title: CC_4-2

description: Library name: Sample13

value: Term

value: Spleen

value: DOD


title: CC_5

description: Library name: Sample12


title: snMO, hippocampus, P28, ATAC

description:
Library name: P28_snMO_ATAC
10x genomics

library_source: genomic single cell

data_processing:
The generated raw fastq files were mapped to the Mus musculus (mm10) reference genome using the Cellranger Arc (v2.02) count function with intronic reads included by default.
Genes expressed in at least three cells were retained as well as cells expressing a minimum of 200 genes and with mitochondrial DNA content below 5%.  Mitochondrial genes and a list of sex-related genes were removed
Cells belonging to the granule cell (GC) lineage—including neural progenitor cells (NPCs), type 1 and 2 neuroblasts, immature GCs (iGCs), and mature GCs (mGCs) —were identified and extracted based on GC lineage marker gene expression.
Assembly: Mouse mm10
Supplementary files format and content: combined_GCsAll_snMO_GEX_ATAC.rds, Seurat/Signac object containing GCs lineage snMO data (ATAC+GEX), merged timepoints

extract_protocol:
Nuclei preparation from mouse hippocampal tissue was done using sucrose gradient protocol. Briefly, up to 50 mg of hippocampal tissue was homogenized using 1 ml of Homogenization Lysis Buffer (HLB) (1X salt-Tris buffer: 146 mM NaCl, 10 mM Tris 7.5, 1 mM CaCl2, 21 mM MgCl2; 0.03 % v/v Tween-20, Sigma Aldrich; 0.01% v/v NP40, Sigma Aldrich; 1% BSA, Thermo Fisher; 25 mM KCl, Thermo Fisher; 250 mM Sucrose, Sigma Aldrich; 1mM DTT, Thermo Fisher; 1X Protease Inhibitor, Sigma Aldrich; 1 U/ul RNAse Inhibitor, Promega). The tissue was homogenized with 10X strokes with pestle A and 10X strokes with pestle B. The homogenized mixture was incubated in HLB for 5 min. During the incubation, the homogenized sample was passed through 70 µm nylon mesh. The nuclei were pelleted by centrifugation at 500xg for 5 min. The nuclei pellet was washed and resuspended with 520 µl of Wash Buffer 1 (1X salt-Tris buffer; 1% BSA, Thermo Fisher; 25 mM KCl, Thermo Fisher; 250 mM Sucrose, Sigma Aldrich; 1mM DTT, Thermo Fisher; 1X Protease Inhibitor, Sigma Aldrich; 1 U/µl RNAse Inhibitor, Promega). The nuclei suspension was then mixed with equal volume of Gradient Medium (1 mM CaCl2, Thermo Fisher; Optiprep 50% v/v, Sigma Aldrich; 5 mM MgCl2, Thermo Fisher; 10 mM Tris 7.5, ThermoFisher; 75 mM Sucrose, Sigma Aldrich; 1mM DTT, Thermo Fisher; 1X Protease Inhibitor, Sigma Aldrich; 0.5 U/µl RNAse Inhibitor, Promega). This was thoroughly mixed, and the mix was layered upon 948 µl of 29% density cushion (Optiprep 29% v/v, Sigma Aldrich; 72.5 mM KCl, Thermo Fisher; 14.5 mM MgCl2, Thermo Fisher; 29 mM Tris 8, Thermo Fisher; 121 mM Sucrose, Sigma Aldrich; 0.25 U/µl RNAse Inhibitor, Promega). The layered nuclei suspension was subjected to centrifugation at 9000xg for 20 min at 4 °C. After the centrifugation, the debris was removed from the top of the suspension and if excess debris was present, this could be scooped out with a 1000 µl pipette tip. The supernatant was aspirated out gradually using a glass Pasteur pipette until about 75 µl of the supernatant was left. Equal volume of 0.2X Lysis Buffer (20 mM Tris 7.5, ThermoFisher; 20 mM NaCl, ThermoFisher; 6mM MgCl2, ThermoFisher; 0.02% Tween 20, Sigma Aldrich; 0.02% NP40, Sigma Aldrich; 0.002% Digitonin, Promega; 2% BSA, Thermo Fisher; 2mM DTT, ThermoFisher; 2U/µl Protector RNAse Inhibitor, Sigma Aldrich) was added and the nuclei were resuspended and incubated for 2 min on wet ice. After the incubation the lysis was quenched by adding 1 ml of Wash Buffer 2 (10 mM Tris 7.5, ThermoFisher; 10 mM NaCl, ThermoFisher; 3 mM MgCl2, ThermoFisher; 0.01% Tween 20, Sigma Aldrich; 1% BSA, Thermo Fisher; 1 mM DTT, ThermoFisher; 1 U/µl Protector RNAse Inhibitor, Sigma Aldrich) and the nuclei suspension was resuspended. The nuclei were pelleted by centrifugation at 500xg for 5 min. The supernatant was discarded until about 20 µl of the supernatant was left in the Eppendorf. Removal was done carefully without disturbing the nuclei pellet. Nuclei pellet was resuspended with 20 µl of 2X Nuclei Buffer (2X Nuclei buffer, 10X Genomics, PN-2000153; 1 mM DTT, ThermoFisher; 1U/µl Protector RNAse Inhibitor, Sigma Aldrich).
The nuclei count and the viability of the samples were accessed using LUNA dual florescence cell counter (Logos Biosystems) and a targeted cell recovery of 10000 cells was aimed for each of the samples. Library preparations for 10X Genomics single cell Multiome were performed using 10X Genomics Chromium NextGEM Single cell Multiome ATAC+Gene Expression chemistry (10X Genomics, Pleasanton, CA, USA). Transposition of nuclei and the rest of the 10X Genomics Multiome library preparation was performed as per the protocol recommendations (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide; CG000338 Rev G). At the different check points the library quality was accessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). 10X libraries were sequenced either on Illumina platform or on MGISEQ-2000 sequencing platform (MGI Hong Kong SAR sequencing facility). Before being able to sequence on the MGI platforms, the 10X libraries need to undergo a conversion step using MGIEasy Universal DNA Library Prep kit. Briefly, the final 10X sequencing libraires were circularized using the splint-ligation step and the circularized libraries were converted to single-stranded DNA copies. DNA nanoballs were prepared from the circularized ssDNA using Rolling Circle Amplification (RCA). DNB libraries generated were then flown through the patterned flow cell of the MGISEQ-2000RS High-Throughput Sequencing kit. For a targeted sequencing saturation of 50-60%, sequencing was performed at a depth of 30,000 - 60,000 reads per cell for the RNA and ATAC libraries. For RNA libraries sequencing recipe of paired end read of 28 bps (read 1), 100 bps (read 2) and 10 bps (index 1) and 10 bps (index 2) was used for sequencing. For ATAC libraries sequencing recipe of paired end read of 50 bps (read 1), 49 bps (read 2) and 24 bps (index i5) and 8 bps (index i7) were used for sequencing.

tag: library type

value: ATAC


title: GCs, Rbp4-Cre, SS2, DG_P10_A6

description:
Library name: 20210417_Blanca_Plate3_A6
Smart-seq2


title: snMO, hippocampus, P15, ATAC

description:
Library name: P15_snMO_ATAC
10x genomics


title: CC_4-1

description: Library name: Sample11


title: GCs, Rbp4-Cre, SS2, DG_P10_A2

description:
Library name: 20210417_Blanca_Plate3_A2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A4

description:
Library name: 20210417_Blanca_Plate3_A4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A3

description:
Library name: 20210417_Blanca_Plate3_A3
Smart-seq2


title: CC_2

description: Library name: Sample9


title: GCs, Rbp4-Cre, SS2, DG_P10_A12

description:
Library name: 20210417_Blanca_Plate3_A12
Smart-seq2


title: snMO, hippocampus, P5, ATAC

description:
Library name: P5_snMO_ATAC
10x genomics


title: CC_3

description: Library name: Sample10


title: GCs, Rbp4-Cre, SS2, DG_P10_A11

description:
Library name: 20210417_Blanca_Plate3_A11
Smart-seq2


title: F+5W_berry_BSseq_rep2

source_name: BS-seq of grape berry in F+5W stage


title: snMO, hippocampus, P28, GEX

description:
Library name: P28_snMO_GEX
10x genomics

molecule: nuclear RNA

value: mRNA


title: GCs, Rbp4-Cre, SS2, DG_P5_H9

description:
Library name: 20210412_Blanca_Plate1_H9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A10

description:
Library name: 20210417_Blanca_Plate3_A10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_B10

description:
Library name: 20210417_Blanca_Plate3_B10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A1

description:
Library name: 20210417_Blanca_Plate3_A1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_A5

description:
Library name: 20210417_Blanca_Plate3_A5
Smart-seq2


title: snMO, hippocampus, P15, GEX

description:
Library name: P15_snMO_GEX
10x genomics


title: F+5W_berry_BSseq_rep1


title: CHM_5

description: Library name: Sample5


title: GCs, Rbp4-Cre, SS2, DG_P5_H8

description:
Library name: 20210412_Blanca_Plate1_H8
Smart-seq2


title: snMO, hippocampus, P5, GEX

description:
Library name: P5_snMO_GEX
10x genomics


title: CC_1-1

description: Library name: Sample7

value: Spontaneous Abortion


title: CC_1-2

description: Library name: Sample6


title: GCs, Rbp4-Cre, SS2, DG_P5_H3

description:
Library name: 20210412_Blanca_Plate1_H3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_H6

description:
Library name: 20210412_Blanca_Plate1_H6
Smart-seq2


title: Hippocampal tissue, wild type, KA+NBP1

city: Wenzhou

first: Shihao

last: Chen

address: Shangcai Village, Nanbaixiang Street

department: Department of Neurology

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Data filtering
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: process data.xls

source_name: Hippocampal tissue

extract_protocol:
1. Introduction
This procedure is suitable for Total RNA extraction of animal tissues, cells and other samples to provide high quality RNA for library preparation.
2. Experimental Procedures
2.1 Tissue Sample Fragmentation and Lysis
2.1.1 Grinding Machine
2.1.1.1 Transfer appropriate sample to corresponding grinding tube,
2.1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min
2.1.2 Liquid Nitrogen Grinding and Crushing
2.1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube.
2.1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.
Stand flat for 5 min for the fully lysis of tissue cells.
2.1.3 Cell Sample Lysis
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells)
2.2 Sample Purification
2.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃.
2.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；
2.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity).
2.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h.
2.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting.
2.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。
2.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min.
2.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1. Introduction
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.
Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly.
2.Experimental Procedure
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Hippocampal tissue

value: wild type

tag: treatment

value: 30 days after KA+NBP treatment


title: GCs, Rbp4-Cre, SS2, DG_P5_H4

description:
Library name: 20210412_Blanca_Plate1_H4
Smart-seq2

value: hippocampus

value: granule cells


title: GCs, Rbp4-Cre, SS2, DG_P5_H2

description:
Library name: 20210412_Blanca_Plate1_H2
Smart-seq2


title: CHM_4

description: Library name: Sample4


title: Hippocampal tissue, wild type, KA+NBP2


title: GCs, Rbp4-Cre, SS2, DG_P5_H10

description:
Library name: 20210412_Blanca_Plate1_H10
Smart-seq2


title: CHM_2

description: Library name: Sample2


title: CHM_3

description: Library name: Sample3


title: GCs, Rbp4-Cre, SS2, DG_P5_H11

description:
Library name: 20210412_Blanca_Plate1_H11
Smart-seq2


title: CC_6

description: Library name: Sample8


title: GCs, Rbp4-Cre, SS2, DG_P5_H12

description:
Library name: 20210412_Blanca_Plate1_H12
Smart-seq2


title: Hippocampal tissue, wild type, KA1

value: 30 days after KA injection


title: Hippocampal tissue, wild type, KA3


title: Hippocampal tissue, wild type, sham3

value: 30 days after control treament


title: GCs, Rbp4-Cre, SS2, DG_P5_G9

description:
Library name: 20210412_Blanca_Plate1_G9
Smart-seq2


title: Healthy colon cells, Patient AF

city: Jerusalem

first: Keren

last: Zohar

address: Safra Campus, Givat Ram

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: AF_H_RV539_S10

data_processing:
Standard Illumina RNA-seq data processing pipeline including quality control, alignment to reference genome, and normalization.
Assembly: Reference genome GRCh38 (human genome build 38) was used for alignment
Supplementary files format and content: Processed data files include normalized counts (TMM/TPM)

source_name: Colon

extract_protocol:
Total RNA was extracted and purified from tissue samples using Qiagen RNeasy Kit according to standard instructions.
RNA was processed and libraries were prepared following the standard Illumina TruSeq protocol for mRNA.

value: Colon


title: Hippocampal tissue, wild type, KA2


title: CHM_1

description: Library name: Sample1

value: Trophblast


title: Hippocampal tissue, wild type, sham2


title: GCs, Rbp4-Cre, SS2, DG_P5_H7

description:
Library name: 20210412_Blanca_Plate1_H7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G3

description:
Library name: 20210412_Blanca_Plate1_G3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_H5

description:
Library name: 20210412_Blanca_Plate1_H5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G6

description:
Library name: 20210412_Blanca_Plate1_G6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G7

description:
Library name: 20210412_Blanca_Plate1_G7
Smart-seq2


title: Hippocampal tissue, wild type, KA+NBP3


title: GCs, Rbp4-Cre, SS2, DG_P5_G8

description:
Library name: 20210412_Blanca_Plate1_G8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_H1

description:
Library name: 20210412_Blanca_Plate1_H1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G5

description:
Library name: 20210412_Blanca_Plate1_G5
Smart-seq2


title: Tumor colon cells, Patient AF

description: Library name: AF_T_RV530_S9


title: GCs, Rbp4-Cre, SS2, DG_P5_G4

description:
Library name: 20210412_Blanca_Plate1_G4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G11

description:
Library name: 20210412_Blanca_Plate1_G11
Smart-seq2


title: Healthy colon cells, Patient AE

description: Library name: AE_H_RV324_S32


title: GCs, Rbp4-Cre, SS2, DG_P5_G2

description:
Library name: 20210412_Blanca_Plate1_G2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G10

description:
Library name: 20210412_Blanca_Plate1_G10
Smart-seq2


title: Hippocampal tissue, wild type, sham1


title: GCs, Rbp4-Cre, SS2, DG_P5_G1

description:
Library name: 20210412_Blanca_Plate1_G1
Smart-seq2


title: snMO, hippocampus, P10, GEX

description:
Library name: P10_snMO_GEX
10x genomics


title: Tumor colon cells, Patient AD

description: Library name: AD_T_RV262_S7


title: Healthy colon cells, Patient AD

description: Library name: AD_H_RV477_S9


title: RiboTag, Rbp4-Cre, GCs, P28_r3

description:
Library name: P28_r3
bulk-RNAseq

data_processing:
The generated raw fastq files were mapped to the Mus musculus (mm10) reference genome using STAR v2.7.5b. Gene counts were then obtained using featureCounts function from SAMtools v1.10.
Genes with extreme or low expression values were filtered out. We required each gene to have an expression count greater than 50 in at least 3 samples, and no gene could have an expression value exceeding 500,000. Additionally, mitochondrial genes, sex-related genes, and genes associated with the GO term 'central nervous system myelination' (GO:0022010) were removed.
To estimate factors of unwanted variation, the RUVs function from the RUVSeq package v1.32.0 was applied with k=2.
Assembly: Mouse mm10
Supplementary files format and content: counts_matrix_RiboTag_raw_unfiltered.csv, csv file, gene expression count matrix, raw unfiltered, merged samples
Supplementary files format and content: sample_table_RiboTag.csv, csv file, sample metadata, unfiltered
Supplementary files format and content: dds_RiboTag_merged_k2.rds, DESeqDataSet, filtered gene expression data, merged samples
Supplementary files format and content: SeqSet_RiboTag_merged_k2.rds, SeqExpressionSet, filtered gene expression data, merged samples, RUVseq output

extract_protocol:
RiboTag sample preparation protocol was adapted from Sanz et al, 2019. Briefly, hippocampi were thawed in pre-chilled homogenization buffer containing 50 mM TrisCl pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% NP40, 1 mM DTT, 200 U/ml RiboLock RNase Inhibitor (Thermofisher, EO0382), 1 mg/ml Heparin (Sigma, H3393), 0.1 mg/ml cycloheximide (Sigma, C4859), 1X EDTA-free protease inhibitors. Next, samples were placed in a Dounce homogenizer where they were dissociated using 2 sizes glass pestles. Lysate was centrifuged at 10000g, 4 °C for 10 min and supernatant (named hereafter as input) was kept for further processing. 40 μl Pierce™ Anti-HA Magnetic Beads (ThermoFisher, 13464229) were added to the input and incubated overnight at 4 °C on a microtube rotator with gentle mixing. Next, samples were placed on magnetic stand for at least 1 min to remove supernatant (named hereafter as unbound), and washed 4x using high salt buffer (50 mM TrisCl pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% NP40, 0.5 mM DTT, 0.1 mg/ml cycloheximide). After the last wash, 350 μl RLT buffer (Qiagen RNeasy mini kit, 74104) supplemented with β-mercaptoethanol was used to elute RNA from the ribosomes. The mix was vortexed 30s and tubes were placed back in magnetic stand to collect the clear RLT buffer containing the RNA. Next, RNA was isolated using Qiagen RNeasy mini kit with DNase treatment and following manufacturer instructions.
Library preparation from total RNA extraction and sequencing was performed at the VIB Nucleomics Core. Per sample, an amount of 25-100 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: #1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (v1.5, SE100 (100-8-8-0), 1% PhiX).

tag: batch


title: snMO, hippocampus, P10, ATAC

description:
Library name: P10_snMO_ATAC
10x genomics


title: Healthy colon cells, Patient AC

description: Library name: AC_H_RV280_S45


title: GCs, Rbp4-Cre, SS2, DG_P5_F7

description:
Library name: 20210412_Blanca_Plate1_F7
Smart-seq2


title: Tumor colon cells, Patient AE

description: Library name: AE_T_RV325_S33


title: GCs, Rbp4-Cre, SS2, DG_P5_F9

description:
Library name: 20210412_Blanca_Plate1_F9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_F5

description:
Library name: 20210412_Blanca_Plate1_F5
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P28_r2

description:
Library name: P28_r2
bulk-RNAseq


title: Tumor colon cells, Patient AC

description: Library name: AC_T_RV281_S46


title: RiboTag, Rbp4-Cre, GCs, P21_r3

description:
Library name: P21_r3
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_F8

description:
Library name: 20210412_Blanca_Plate1_F8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_F1

description:
Library name: 20210412_Blanca_Plate1_F1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_F4

description:
Library name: 20210412_Blanca_Plate1_F4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_F3

description:
Library name: 20210412_Blanca_Plate1_F3
Smart-seq2


title: Healthy colon cells, Patient AB

description: Library name: AB_H_RV276_S41


title: GCs, Rbp4-Cre, SS2, DG_P5_F2

description:
Library name: 20210412_Blanca_Plate1_F2
Smart-seq2


title: Tumor colon cells, Patient AB

description: Library name: AB_T_RV277_S42


title: GCs, Rbp4-Cre, SS2, DG_P5_F11

description:
Library name: 20210412_Blanca_Plate1_F11
Smart-seq2


title: Healthy colon cells, Patient AA sample 2

description: Library name: AA2_H_RV475_S8


title: RiboTag, Rbp4-Cre, GCs, P21_r2

description:
Library name: P21_r2
bulk-RNAseq


title: RiboTag, Rbp4-Cre, GCs, P21_r1

description:
Library name: P21_r1
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_F10

description:
Library name: 20210412_Blanca_Plate1_F10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_G12

description:
Library name: 20210412_Blanca_Plate1_G12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E9

description:
Library name: 20210412_Blanca_Plate1_E9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E8

description:
Library name: 20210412_Blanca_Plate1_E8
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P15_r3

description:
Library name: P15_3
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_E6

description:
Library name: 20210412_Blanca_Plate1_E6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_F6

description:
Library name: 20210412_Blanca_Plate1_F6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E7

description:
Library name: 20210412_Blanca_Plate1_E7
Smart-seq2


title: Healthy colon cells, Patient AA sample 1

description: Library name: AA1_H_RV290_S23


title: RiboTag, Rbp4-Cre, GCs, P28_r1

description:
Library name: P28_r1
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_E3

description:
Library name: 20210412_Blanca_Plate1_E3
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P15_r1

description:
Library name: P15_1
bulk-RNAseq


title: RiboTag, Rbp4-Cre, GCs, P15_r2

description:
Library name: P15_2
bulk-RNAseq


title: RiboTag, Rbp4-Cre, GCs, P10_r3

description:
Library name: P10_3
bulk-RNAseq


title: Healthy colon cells, Patient Z

description: Library name: Z_H_RV185_R1


title: GCs, Rbp4-Cre, SS2, DG_P5_F12

description:
Library name: 20210412_Blanca_Plate1_F12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E4

description:
Library name: 20210412_Blanca_Plate1_E4
Smart-seq2


title: Tumor colon cells, Patient Z

description: Library name: Z_T_RV187_R1


title: GCs, Rbp4-Cre, SS2, DG_P5_E1

description:
Library name: 20210412_Blanca_Plate1_E1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E12

description:
Library name: 20210412_Blanca_Plate1_E12
Smart-seq2


title: Healthy colon cells, Patient Y

description: Library name: Y_H_RV164_S15_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_E11

description:
Library name: 20210412_Blanca_Plate1_E11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_E5

description:
Library name: 20210412_Blanca_Plate1_E5
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P10_r2

description:
Library name: P10_2
bulk-RNAseq


title: Tumor colon cells, Patient AA

description: Library name: AA1_T_RV267_S40


title: BS-seq mESC Tet2KO rep2

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

country: USA

institute: UPENN

data_processing:
Raw sequencing data were first processed by using trimmomatic.
Clean reads were mapped to the mouse genome GRCm38/mm10 using the meRanGh from meRanTK.
Unambiguously aligned reads were then used to call candidate m5Cs using meRanCall from meRanTK with a base-call quality score of Q ≥ 30, candidate cytosine sites covered by at least 10 reads and a methylation rate ≥ 0.1.
The m5C candidates were subjected to a secondary structure filter to remove false positive sites using R package “rBS2ndStructure”.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: m5C sites table files

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured in Dulbecco’s Modified Eagle Medium (GIBCO) media supplemented with 10% FBS (GIBCO), 1 % Pen/Strep (GIBCO), 1× NEAA (GIBCO), 1× L-glutamine (GIBCO), 50 μM 2-mercaptoethanol (Bio-Rad) and 1000 μ/mL mouse LIF (Gemini) in a humidified cell culture incubator with 5% CO2 at 37°C. MEF feeder cells (Sigma) were spread in the dishes one day before passaging the cells.

extract_protocol:
Total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen).
Poly(A)-RNA extracted from wild-type and Tet2 KO mESCs were subjected to fragmentation using Bioruptor Pico (Diagenode) with 30 seconds on and 30 seconds off for 40 cycles. After clean-up using RNA Clean & Concentrator (RCC) Kit (Zymo Research), 500 ng mRNA fragments were used to perform the bisulfite treatment using EZ RNA Methylation Kit (Zymo Research). After conversion, the library was constructed with TruSeq mRNA sample preparation kit (Illumina).

value: embryonic stem cells

value: Tet2 KO


title: GCs, Rbp4-Cre, SS2, DG_P5_D9

description:
Library name: 20210412_Blanca_Plate1_D9
Smart-seq2


title: Tumor colon cells, Patient Y

description: Library name: Y_T_RV165_S16_R1_001


title: RiboTag, Rbp4-Cre, GCs, P10_r1

description:
Library name: P10_1
bulk-RNAseq


title: RiboTag, Rbp4-Cre, GCs, P7_r3

description:
Library name: P7_3
bulk-RNAseq


title: Healthy colon cells, Patient X

description: Library name: X_H_RV132_S4_R1_001


title: RiboTag, Rbp4-Cre, GCs, P7_r2

description:
Library name: P7_2
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_D8

description:
Library name: 20210412_Blanca_Plate1_D8
Smart-seq2


title: BS-seq mESC Tet2KO rep1


title: Tumor colon cells, Patient X

description: Library name: X_T_RV133_S5_R1_001


title: BS-seq mESC WT rep2

value: wild-type


title: GCs, Rbp4-Cre, SS2, DG_P5_D7

description:
Library name: 20210412_Blanca_Plate1_D7
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P7_r1

description:
Library name: P7_1
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_E2

description:
Library name: 20210412_Blanca_Plate1_E2
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P5_r3_e2

description:
Library name: P5_r3_e2
bulk-RNAseq


title: RNA-seq Tet2KO 6h

description: lifetimeseq.RPKM.xlsx

data_processing:
m5CIP and input reads were aligned to UCSC canonical transcripts with Bowtie2 in local alignment mode
MACS2 was used to call peak with --nomodel, --nolambda and using the total transcript bases as the genome size
bdgdiff command in MACS2 was used to call differential peaks
Gene expression levels were normalized using DEseq2
Cufflinks was used to calculated RPKM for lifetime-seq
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using MACS2; Scores represent the peaks height

extract_protocol:
Total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen). mRNA was fragmented by sonication, and applied to antibody (Active Motif 39649) immunoprecipitation.
The library was constructed using TruSeq stranded mRNA samples preparation kit from Illumina.

treatment_protocol: For lifetime-seq, mESCs were seeded into 6-well plates. After overnight culture, cells were treated with 5 μg/ml of actinomycin D at 6 h, 3 h and 0 h before collection.

tag: genotype/variation

value: 5 ug/ml of actinomycin D at 6h before collection


title: Tumor colon cells, Patient W

description: Library name: W_T_RV81_S23_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_D5

description:
Library name: 20210412_Blanca_Plate1_D5
Smart-seq2


title: Healthy colon cells, Patient V sample 3

description: Library name: V3_H_RV197_R1_clip


title: RiboTag, Rbp4-Cre, GCs, P5_r1_e2

description:
Library name: P5_r1_e2
bulk-RNAseq


title: RNA-seq Tet2KO 3h

description: lifetimeseq.RPKM.xlsx

value: 5 ug/ml of actinomycin D at 3h before collection


title: GCs, Rbp4-Cre, SS2, DG_P5_D4

description:
Library name: 20210412_Blanca_Plate1_D4
Smart-seq2


title: RiboTag, Rbp4-Cre, GCs, P5_r3_e1

description:
Library name: P5_r3_e1
bulk-RNAseq


title: Healthy colon cells, Patient V sample 2

description: Library name: V2_H_RV24_S30_L005_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_E10

description:
Library name: 20210412_Blanca_Plate1_E10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_D3

description:
Library name: 20210412_Blanca_Plate1_D3
Smart-seq2


title: Healthy colon cells, Patient V sample 1

description: Library name: V1_H_RV23_S29_L005_R1_001


title: RiboTag, Rbp4-Cre, GCs, P5_r2_e1

description:
Library name: P5_r2_e1
bulk-RNAseq


title: Tumor colon cells, Patient V sample 3

description: Library name: V3_T_RV198_R1_clip


title: RNA-seq WT 6h

description: lifetimeseq.RPKM.xlsx


title: RiboTag, Rbp4-Cre, GCs, P5_r1_e1

description:
Library name: P5_r1_e1
bulk-RNAseq


title: GCs, Rbp4-Cre, SS2, DG_P5_D2

description:
Library name: 20210412_Blanca_Plate1_D2
Smart-seq2


title: Healthy colon cells, Patient W

description: Library name: W_H_RV80_S22_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_D1

description:
Library name: 20210412_Blanca_Plate1_D1
Smart-seq2


title: Tumor colon cells, Patient V sample 2

description: Library name: V2_T_RV22_S27_L004_R1_001


title: BS-seq mESC WT rep1


title: RNA-seq WT 3h

description: lifetimeseq.RPKM.xlsx


title: GCs, Rbp4-Cre, SS2, DG_P5_D6

description:
Library name: 20210412_Blanca_Plate1_D6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_D12

description:
Library name: 20210412_Blanca_Plate1_D12
Smart-seq2


title: mpra_F9_ds_mock_rep2

city: Cambridge

first: Matthew

middle: Harry

last: Hall

state: MA

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

description:
Library name: mpra_F9_ds_mock_rep2
Transfected with MPRA library only (mock transfected wrt miRNA); rep 2

library_source: other

data_processing:
RBNS: Reads were filtered to remove those with uncertain (N) base calls and for which the last 3-4nt did not match the library 3ʹ constant region, then reads were assigned to different miRNA site types, or a no-site background.  MPRA:  For single-site (ss) MPRA experiments from HeLa cells, 150nt single-end reads were filtered to those with no uncertain (N) base cells, and further quality filtered to those with an average Q-score of 20 across 90% of the bases.  Reads were assigned to library variants if the entire variable region sequence of that library variant was present in the read.  For single-site (ss) MPRA experiments from F9 cells, R1 and R2 paired end reads were paired using fastq-joiner, then the joined reads were identically quality filtered and reads assigned to library variants.  For dual-site (ds) MPRA experiments, paired-end sequencing was conducted but only R1 reads were used to assign reads to variants. R1 reads were filtered equivalently to joined reads from ss MPRA experiments, and reads were assigned to library variants if all 150nt of read 1 perfectly matched the variable region sequence of that library variant.
Assembly: N/A - no aligning of reads to genome, working with synthetic libraries
Supplementary files format and content: RBNS: sample_sitecounts.txt files for each sample show the number of reads assigned to each miRNA site type in table format MPRA: sample.txt files for each sample show the number of reads assigned to each library variant in table format

molecule: other

growth_protocol: MPRA: HeLa cells were grown in 1X DMEM + 10% FBS at 37°C and 5% CO2; F9 cells were grown in equivalent conditions on plates pre-coated with 0.1% gelatin; RBNS: N/A

extract_protocol:
MPRA: cells were lysed by addition of lysis buffer (10mM Tris-HCl pH7.5, 5mM MgCl2, 100mM KCl, 1% Triton X-100, 2mM DTT, 0.02U/uL SuperaseIn, 1 tab/10mL cOmplete mini EDTA-free protease inhibitor) then total RNA was extracted using Trizol-LS according to manufacturer instructions RBNS: AGO-miR-bound RNA was released from nitrocellulose membranes by proteinase K digestion according to manufacturer instructions, followed by phenol:chloroform extraction and ethanol precipitation
MPRA and RBNS: extracted RNA was reverse-transcribed using SuperScript III reverse transcriptase according to manufacturer instructions using RT primers complementary to the 3ʹ constant region of the relevant RNA libraries Resultant library cDNA was then PCR-amplified using barcoded primers complementary to the 5ʹ and 3ʹ constant regions that also contained Illumina P5 and P7 constant region sequences for sequencing on an Illumina HiSeq 2500 (RBNS) or an Illumina NovaSeq 6000 (MPRA)

treatment_protocol: MPRA: 10cm plates of cells were co-transfected with 5.8ug MPRA library, 28.9ug pUC19 carrier DNA, and pre-annealed miRNA guide:passenger duplex using Lipofectamine 2000 according to manufacturer instructions; RBNS: N/A

tag: cell line

value: wt


title: Tumor colon cells, Patient V sample 1

description: Library name: V1_T_RV21_S26_L004_R1_001


title: mpra_F9_ds_mock_rep1

description:
Library name: mpra_F9_ds_mock_rep1
Transfected with MPRA library only (mock transfected wrt miRNA); rep 1


title: 5-8F R2

city: guangzhou

first: Lizhen

address: 106 ZhongShan Er Road

institute: 1.	Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R were used for visualization
Assembly: GRCh37
Supplementary files format and content: TXT file contain counts for  each sample of RNA-seq

growth_protocol: Cells were grow in 1640 medium  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: cells were cultured for 48h, no other treatment was done

value: Nasopharyngeal carcinoma


title: mpra_F9_ds_mir1_rep2

description:
Library name: mpra_F9_ds_mir1_rep2
Co-transfected with miR-1 and MPRA library; rep 2


title: GCs, Rbp4-Cre, SS2, DG_P5_D11

description:
Library name: 20210412_Blanca_Plate1_D11
Smart-seq2


title: RNA-seq Tet2KO 0h

description: lifetimeseq.RPKM.xlsx


title: Healthy colon cells, Patient U sample 2

description: Library name: U2_H_RV4_S20_L003_R1_001


title: 5-8F R1


title: GCs, Rbp4-Cre, SS2, DG_P5_C9

description:
Library name: 20210412_Blanca_Plate1_C9
Smart-seq2


title: mpra_F9_ds_mir1_rep1

description:
Library name: mpra_F9_ds_mir1_rep1
Co-transfected with miR-1 and MPRA library; rep 1


title: GCs, Rbp4-Cre, SS2, DG_P5_D10

description:
Library name: 20210412_Blanca_Plate1_D10
Smart-seq2


title: Healthy colon cells, Patient U sample 1

description: Library name: U1_H_RV3_S19_L003_R1_001


title: Tumor colon cells, Patient U sample 2

description: Library name: U2_T_RV2_S18_L003_R1_001


title: Tumor colon cells, Patient U sample 1

description: Library name: U1_T_RV1_S17_L003_R1_001


title: RNA-seq WT 0h

description: lifetimeseq.RPKM.xlsx


title: GCs, Rbp4-Cre, SS2, DG_P5_C8

description:
Library name: 20210412_Blanca_Plate1_C8
Smart-seq2


title: 5-8F R H3K27Ac

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Assembly: GRCh38
Supplementary files format and content: bigWig

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

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated  using Bioruptor (Diagenode)
ChIP-seq libraries were prepared  using NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina® kit. 10 ng of DNA was used as starting material for input and ip samples

treatment_protocol: cells were cultured for 72 h

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: 5-8F P1


title: GCs, Rbp4-Cre, SS2, DG_P5_C7

description:
Library name: 20210412_Blanca_Plate1_C7
Smart-seq2


title: mpra_F9_ds_mir124_rep2

description:
Library name: mpra_F9_ds_mir124_rep2
Co-transfected with miR-124 and MPRA library; rep 2


title: 5-8F R H3K4me3

value: H3K4me3 (Mililpore 07-473)


title: Tumor colon cells, Patient T

description: Library name: T_T_RV572_S14


title: mpra_F9_ds_mir124_rep1

description:
Library name: mpra_F9_ds_mir124_rep1
Co-transfected with miR-124 and MPRA library; rep 1


title: GCs, Rbp4-Cre, SS2, DG_P5_C6

description:
Library name: 20210412_Blanca_Plate1_C6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_C5

description:
Library name: 20210412_Blanca_Plate1_C5
Smart-seq2


title: mpra_F9_ss_mock_rep2

description:
Library name: mpra_F9_ss_mock_rep2
Transfected with MPRA library only (mock transfected wrt miRNA); rep 2


title: 5-8F P2


title: Tumor colon cells, Patient S

description: Library name: S_T_RV486_S13


title: GCs, Rbp4-Cre, SS2, DG_P5_C4

description:
Library name: 20210412_Blanca_Plate1_C4
Smart-seq2


title: Healthy colon cells, Patient S

description: Library name: S_H_RV485_S12


title: 5-8F P H3K27Ac


title: mpra_F9_ss_mock_rep1

description:
Library name: mpra_F9_ss_mock_rep1
Transfected with MPRA library only (mock transfected wrt miRNA); rep 1


title: 5-8F P H3K4me3


title: mpra_F9_ss_mir1_rep2

description:
Library name: mpra_F9_ss_mir1_rep2
Co-transfected with miR-1 and MPRA library; rep 2


title: GCs, Rbp4-Cre, SS2, DG_P5_C3

description:
Library name: 20210412_Blanca_Plate1_C3
Smart-seq2


title: Tumor colon cells, Patient R

description: Library name: R_T_RV378_S31


title: 5-8F P  input


title: Healthy colon cells, Patient R

description: Library name: R_H_RV377_S30


title: Healthy colon cells, Patient T

description: Library name: T_H_RV523_S7


title: mpra_F9_ds_mir155_rep2

description:
Library name: mpra_F9_ds_mir155_rep2
Co-transfected with miR-155 and MPRA library; rep 2


title: mpra_F9_ss_mir1_rep1

description:
Library name: mpra_F9_ss_mir1_rep1
Co-transfected with miR-1 and MPRA library; rep 1


title: Healthy colon cells, Patient Q

description: Library name: Q_H_RV300_S25


title: rbns_mir155_input

description:
Library name: rbns_mir155_input
AGO-miR-155 input (no AGO-miR added)

organism: synthetic construct


title: GCs, Rbp4-Cre, SS2, DG_P5_C2

description:
Library name: 20210412_Blanca_Plate1_C2
Smart-seq2


title: mpra_F9_ds_mir155_rep1

description:
Library name: mpra_F9_ds_mir155_rep1
Co-transfected with miR-155 and MPRA library; rep 1


title: mpra_F9_ss_mir155_rep2

description:
Library name: mpra_F9_ss_mir155_rep2
Co-transfected with miR-155 and MPRA library; rep 2


title: GCs, Rbp4-Cre, SS2, DG_P5_C1

description:
Library name: 20210412_Blanca_Plate1_C1
Smart-seq2


title: rbns_mir155_40.00

description:
Library name: rbns_mir155_40.00
AGO-miR-155 40% relative dilution


title: GCs, Rbp4-Cre, SS2, DG_P5_C12

description:
Library name: 20210412_Blanca_Plate1_C12
Smart-seq2


title: mpra_F9_ss_mir155_rep1

description:
Library name: mpra_F9_ss_mir155_rep1
Co-transfected with miR-155 and MPRA library; rep 1


title: rbns_mir155_4.01

description:
Library name: rbns_mir155_4.01
AGO-miR-155 4.01% relative dilution


title: 5-8F R  input


title: Healthy colon cells, Patient P

description: Library name: P_H_RV288_S51


title: rbns_mir155_12.66

description:
Library name: rbns_mir155_12.66
AGO-miR-155 12.66% relative dilution


title: Healthy colon cells, Patient O

description: Library name: O_H_RV286_S49


title: Tumor colon cells, Patient O

description: Library name: O_T_RV287_S50


title: rbns_mir155_1.27

description:
Library name: rbns_mir155_1.27
AGO-miR-155 1.27% relative dilution


title: GCs, Rbp4-Cre, SS2, DG_P5_B9

description:
Library name: 20210412_Blanca_Plate1_B9
Smart-seq2


title: Tumor colon cells, Patient P

description: Library name: P_T_RV259_S6


title: mpra_F9_ss_mir124_rep2

description:
Library name: mpra_F9_ss_mir124_rep2
Co-transfected with miR-124 and MPRA library; rep 2


title: GCs, Rbp4-Cre, SS2, DG_P5_C10

description:
Library name: 20210412_Blanca_Plate1_C10
Smart-seq2


title: rbns_mir124_input

description:
Library name: rbns_mir124_input
AGO-miR-124 input (no AGO-miR added)


title: GCs, Rbp4-Cre, SS2, DG_P5_C11

description:
Library name: 20210412_Blanca_Plate1_C11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_B7

description:
Library name: 20210412_Blanca_Plate1_B7
Smart-seq2


title: Tumor colon cells, Patient Q

description: Library name: Q_T_RV301_S26


title: rbns_mir124_40.00

description:
Library name: rbns_mir124_40.00
AGO-miR-124 40% relative dilution


title: Healthy colon cells, Patient N

description: Library name: N_H_RV282_S47


title: GCs, Rbp4-Cre, SS2, DG_P5_B8

description:
Library name: 20210412_Blanca_Plate1_B8
Smart-seq2


title: W20 lactate

city: Nanjing

first: Songtao

last: Yuan

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Ophthalmology

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
The scRNA-seq library was constructed following a modified Smart-seq2 protocol. In detail, 4ul lysed sample was incubated at 72C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides. The synthesized first-strand cDNAs were amplified by 20 cycles. After purification, 0.1 ng of cDNA was used for Nextera tagmentation (Illumina) and library construction. Sequencing was then performed on Illumina HiSeq 4000.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: abdominal cavity

extract_protocol:
Primary peritoneal macrophages were isolated from 6-month-old male mice C57BL/6. The mice were euthanized, and the peritoneal cavity was injected with 7mL precooled PBS supplemented with 3% fetal bovine serum (FBS, SenBeiJia). The isolation media was drawn back 30 minutes after injection through a 10 mL syringe equipped with a 25 g needle. The isolation media was centrifuged, and erythrocytes were lysed by the addition of RBC lysis buffer (Beyotime). The erythrocyte-free peritoneal cells were resuspended in DMEM media (Gibco) supplemented with 20% FBS, 1mM L-glutamine (Gibco), 1% penicillin-streptomycin (Gibco) and incubated at 37 °C and 5% CO2 for 24 h. After 24 h incubation, non-adherent cells were removed by repeated flushing of the flasks with culture medium to obtain pure peritoneal macrophages. For in vitro treatment, primary mouse macrophages were treatments with 10mM lactate (Sigma-Aldrich),300nM AZD3965 (MedChemExpress), 100uM glycerophosphoinositol (EchelonBioscience), 100uM phosphorylcholine (MedChemExpress), or 80mM Taurine (MedChemExpress) for 72 hours. To evaluate the effects of hypoxia, cells were incubated in normoxic conditions (21% O2) or 3% O2.
The scRNA-seq library was constructed following a modified Smart-seq2 protocol(21). In detail, 4ul lysed sample was incubated at 72C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides. The synthesized first-strand cDNAs were amplified by 20 cycles. After purification, 0.1 ng of cDNA was used for Nextera tagmentation (Illumina) and library construction. Sequencing was then performed on Illumina HiSeq 4000.

value: abdominal cavity

value: primary macrophage

value: macrophages


title: rbns_mir155_0.13

description:
Library name: rbns_mir155_0.13
AGO-miR-155 0.13% relative dilution


title: rbns_mir124_4.01

description:
Library name: rbns_mir124_4.01
AGO-miR-124 4.01% relative dilution


title: F9 lactate+AZD


title: Tumor colon cells, Patient N

description: Library name: N_T_RV283_S48


title: GCs, Rbp4-Cre, SS2, DG_P5_B6

description:
Library name: 20210412_Blanca_Plate1_B6
Smart-seq2

value: hippocampus

value: granule cells


title: Healthy colon cells, Patient M

description: Library name: M_H_RV278_S43


title: GCs, Rbp4-Cre, SS2, DG_P5_B5

description:
Library name: 20210412_Blanca_Plate1_B5
Smart-seq2


title: W14 lactate+AZD


title: rbns_mir124_12.66

description:
Library name: rbns_mir124_12.66
AGO-miR-124 12.66% relative dilution


title: Tumor colon cells, Patient M

description: Library name: M_T_RV279_S44


title: mpra_F9_ss_mir124_rep1

description:
Library name: mpra_F9_ss_mir124_rep1
Co-transfected with miR-124 and MPRA library; rep 1


title: GCs, Rbp4-Cre, SS2, DG_P5_B4

description:
Library name: 20210412_Blanca_Plate1_B4
Smart-seq2


title: F18 lactate


title: Healthy colon cells, Patient L

description: Library name: L_H_RV237_S12


title: rbns_mir124_1.27

description:
Library name: rbns_mir124_1.27
AGO-miR-124 1.27% relative dilution


title: Tumor colon cells, Patient L

description: Library name: L_T_RV239_S3


title: GCs, Rbp4-Cre, SS2, DG_P5_B2

description:
Library name: 20210412_Blanca_Plate1_B2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_B3

description:
Library name: 20210412_Blanca_Plate1_B3
Smart-seq2


title: W5 lactate


title: W10 lactate+AZD


title: rbns_mir124_0.40

description:
Library name: rbns_mir124_0.40
AGO-miR-124 0.4% relative dilution


title: F8 lactate+AZD


title: T13 lactate


title: T11 lactate


title: Tumor colon cells, Patient K

description: Library name: K_T_RV224_R1_clip


title: GCs, Rbp4-Cre, SS2, DG_P5_B12

description:
Library name: 20210412_Blanca_Plate1_B12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_B1

description:
Library name: 20210412_Blanca_Plate1_B1
Smart-seq2


title: T10 lactate+AZD


title: Healthy colon cells, Patient J

description: Library name: J_H_RV217_R1_clip


title: dentate gyrus, sham, single nuclei RNAseq, rep1

city: Cincinnati

first: Anthony

middle: Joseph

last: DeSana

state: Ohio

address: 231 Albert Sabin Way

department: Neurosurgery

institute: University of Cincinnati

description:
Library name: LBN414
10X Genomics

data_processing:
Bulk: ExpressAnalyst.ca, Filtering, Low abundance filtering, Variance filtering, DESeq2, Enrichr Pathway Analysis
Single Nuclei: CellRanger, Standard Seurat Workflow in R, Enrichr Pathway Analysis
Assembly: GCF_000001895; Rnor 6.0
Supplementary files format and content: Excel File: Differentially expressed genes
Supplementary files format and content: Excel File: Pathway Analysis

organism: Rattus norvegicus

source_name: Brain, Ipsilateral Hippocampal Dentate Gyrus

extract_protocol:
Bulk: Dissection of Hippocampus, RNAlater-ICE, homogenization, extraction
Single Nuclei: Dissection of Hippocampus, Nuclei EZ prep kit
Bulk: NEBNext Ultra II Directional RNA Library Prep Kit
Single Nuclei: Chromium Single Cell 3’ Library & Gel Bead Kit v3

value: male

tag: strain

value: sprague dawley

value: sham


title: dentate gyrus, naïve, single nuclei RNAseq, rep1

description:
Library name: LBN422
10X Genomics

tag: tissue

value: Brain, Ipsilateral Hippocampal Dentate Gyrus

value: naïve


title: dentate gyrus, tbi, single nuclei RNAseq,  rep2

description:
Library name: LBN393
10X Genomics

value: tbi


title: Tumor colon cells, Patient J

description: Library name: J_T_RV219_R1_clip

value: Colon


title: Lactic17 scMeT-seq

description:
SMART2_scMeT_barcodes.tsv
SMART2_scMeT_features.tsv
SMART2_scMeT_matrix.mtx


title: dentate gyrus, tbi, single nuclei RNAseq, rep1

description:
Library name: LBN366
10X Genomics


title: Lactic16 scMeT-seq


title: GCs, Rbp4-Cre, SS2, DG_P5_B10

description:
Library name: 20210412_Blanca_Plate1_B10
Smart-seq2

tag: genotype


title: GCs, Rbp4-Cre, SS2, DG_P5_B11

description:
Library name: 20210412_Blanca_Plate1_B11
Smart-seq2

tag: cell type


title: Lactic14 scMeT-seq


title: Healthy colon cells, Patient I

description: Library name: I_H_RV214_R1_clip


title: GCs, Rbp4-Cre, SS2, DG_P5_A9

description:
Library name: 20210412_Blanca_Plate1_A9
Smart-seq2


title: SCI-7d-3, replicate 3, sNuc-Seq

city: Nantong

first: Xinghui

last: Wang

address: 19 Qixiu Road

institute: Nantong University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral cortex

extract_protocol:
The cortical motor area was determined and marked on the skull, and a circular sampling area with a diameter of about 5 mm was delineated. After the meninges were removed with toothed forceps, the cortex was dug out with a sampling curette and immediately placed in a RNase free cryopreservation tube filled with liquid nitrogen and transferred to -80℃ for preservation.Nuclei were isolated using a “Frankenstein” nuclei isolation protocol developed by Martelotto et al. for frozen tissues. Briefly, ~40 mg of frozen cortex tissue was homogenized in chilled Nuclei EZ Lysis Buffer (MilliporeSigma) using a glass dounce with ~15 strokes per pestle. Homogenate was filtered using a 70 μm-strainer mesh and centrifuged at 500× g for 5 minutes at 4°C in a benchtop centrifuge. Nuclei were resuspended in the EZ lysis buffer, centrifuged again, and equilibrated to nuclei wash/resuspension buffer (1× PBS, 1% BSA, 0.2 U/μL RNase Inhibitor). Nuclei were washed and centrifuged in this nuclei wash/resuspension buffer three times. Trypan blue staining was used to evaluate the lysis effect. The concentration was adjusted to carry out cDNA amplification and library construction.
Single nuclei of motor cortex cells were directly into reverse transcription reagents from the 10× Genomics Single Cell 3’ Reagents kit (without enzyme). Libraries were prepared according to manufacturer’s instructions (10× Genomics) and sequenced on the Illumina NovaSeq platform.

value: Cerebral cortex

value: Sprague-Dawley

tag: time point

value: 7 day

tag: age

value: 8-10 weeks old


title: SCI-7d-2, replicate 2, sNuc-Seq

description: 10X Genomics


title: Tumor colon cells, Patient I

description: Library name: I_T_RV215_R1_clip


title: Healthy colon cells, Patient H

description: Library name: H_H_RV210_R1_clip


title: GCs, Rbp4-Cre, SS2, DG_P5_A8

description:
Library name: 20210412_Blanca_Plate1_A8
Smart-seq2

source_name: hippocampus


title: SCI-7d-1, replicate 1, sNuc-Seq

description: 10X Genomics


title: Healthy colon cells, Patient K

description: Library name: K_H_RV221_R1_clip


title: Lactic13 scMeT-seq


title: Lactic7 SMART2-seq


title: GCs, Rbp4-Cre, SS2, DG_P5_A7

description:
Library name: 20210412_Blanca_Plate1_A7
Smart-seq2


title: SCI-3d-3, replicate 3, sNuc-Seq

description: 10X Genomics

value: 3 day


title: Tumor colon cells, Patient H

description: Library name: H_T_RV211_R1_clip


title: Healthy colon cells, Patient G

description: Library name: G_H_RV206_R1_clip


title: Lactic6 SMART2-seq

value: abdominal cavity


title: Lactic5 SMART2-seq

value: primary macrophage


title: Tumor colon cells, Patient G

description: Library name: G_T_RV207_R1_clip


title: GCs, Rbp4-Cre, SS2, DG_P5_A4

description:
Library name: 20210412_Blanca_Plate1_A4
Smart-seq2


title: Healthy colon cells, Patient F

description: Library name: F_H_RV199_R1_clip


title: SCI-3d-1, replicate 1, sNuc-Seq

description: 10X Genomics


title: SCI-3d-2, replicate 2, sNuc-Seq

description: 10X Genomics


title: GCs, Rbp4-Cre, SS2, DG_P5_A3

description:
Library name: 20210412_Blanca_Plate1_A3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P5_A5

description:
Library name: 20210412_Blanca_Plate1_A5
Smart-seq2


title: SCI-1d-3, replicate 3, sNuc-Seq

description: 10X Genomics

value: 1 day


title: GCs, Rbp4-Cre, SS2, DG_P5_A2

description:
Library name: 20210412_Blanca_Plate1_A2
Smart-seq2

value: hippocampus


title: CTL4 SMART2-seq

value: macrophages


title: Tumor colon cells, Patient F

description: Library name: F_T_RV200_R1_clip


title: GCs, Rbp4-Cre, SS2, DG_P5_A6

description:
Library name: 20210412_Blanca_Plate1_A6
Smart-seq2

value: granule cells


title: Lactic34

description:
CTL_Lactic_barcodes.tsv
CTL_Lactic_features.tsv
CTL_Lactic_matrix.mtx


title: SCI-1d-1, replicate 1, sNuc-Seq

description: 10X Genomics


title: SCI-1d-2, replicate 2, sNuc-Seq

description: 10X Genomics


title: Healthy colon cells, Patient E

description: Library name: E_H_RV178_S19_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_A1

description:
Library name: 20210412_Blanca_Plate1_A1
Smart-seq2


title: Tumor colon cells, Patient E

description: Library name: E_T_RV179_S20_R1_001


title: GCs, Rbp4-Cre, SS2, DG_P5_A12

description:
Library name: 20210412_Blanca_Plate1_A12
Smart-seq2


title: Lactic32


title: SCI-12h-2, replicate 2, sNuc-Seq

description: 10X Genomics

value: 12 hr


title: Healthy colon cells, Patient D

description: Library name: D_H_RV173_S17_R1_001


title: Lactic31


title: Lactic33


title: SCI-12h-3, replicate 3, sNuc-Seq

description: 10X Genomics


title: GCs, Rbp4-Cre, SS2, DG_P5_A11

description:
Library name: 20210412_Blanca_Plate1_A11
Smart-seq2


title: SCI-12h-1, replicate 1, sNuc-Seq

description: 10X Genomics


title: CTL8 SMART2-seq


title: GCs, Rbp4-Cre, SS2, DG_P5_A10

description:
Library name: 20210412_Blanca_Plate1_A10
Smart-seq2


title: Lactic30


title: Tumor colon cells, Patient D

description: Library name: D_T_RV175_S18_R1_001


title: Healthy colon cells, Patient C

description: Library name: C_H_RV156_S13_R1_001


title: ND-WT5

city: Odense M

first: Morgane

middle: Anita

last: Philippe

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

description: Library name: Sample 12

data_processing:
Fastq files were aligned using STAR algorithm (version 2.7.6a), on the Ensembl release 101 reference. Reads were then count using RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: tab-delimited results files indicate gene and transcript ID(s), length, effective length, expected count, TPM and FPKM.

source_name: epididymal white adipose tissue

extract_protocol:
Adipose progenitors defined as CD45-CD31-PDGFRb+ were flow sorted and frozen following RNeasy RNA Plus micro Kit (Qiagen) instructions to extract RNA. Quality of the RNA was measured using a Bioanalyzer 2100 (Agilent) as per the manufacturer’s instructions using pico chip kit, RIN > 6,5 were kept for sequencing.
Non-strand-oriented libraries were prepared following the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England BioLabs)

treatment_protocol: At 10 weeks of age, male mice were either fed with the standard chow diet or high fat diet (60 kJ% fat, SSNIFF  813 ref# E15742-347) during 12 weeks.

value: epididymal white adipose tissue

tag: Sex

value: male

value: WT

value: ND


title: SCI-3h-3, replicate 3, sNuc-Seq

description: 10X Genomics

value: 3 hr


title: SCI-3h-2, replicate 2, sNuc-Seq

description: 10X Genomics

value: Cerebral cortex


title: Lactic29


title: Tumor colon cells, Patient C

description: Library name: C_T_RV157_S14_R1_001

value: Colon


title: Lactic28


title: ND-WT2

description: Library name: Sample 11


title: Tumor colon cells, Patient B

description: Library name: B_T_RV129_S10_R1


title: SCI-3h-1, replicate 1, sNuc-Seq

description: 10X Genomics

value: Sprague-Dawley


title: Lactic27


title: ND-WT1

description: Library name: Sample 10


title: SCI-sham-3, replicate 3, sNuc-Seq

description: 10X Genomics

value: sham

value: 8-10 weeks old


title: ND-KO5

description: Library name: Sample 9


title: Tumor colon cells, Patient A sample 2

description: Library name: A2_T_RV93_S21_R1_001


title: CTL35

value: abdominal cavity


title: CTL34

value: primary macrophage


title: Tumor colon cells, Patient A sample 1

description: Library name: A1_T_RV61_S57_L006_R1_001


title: SCI-sham-1, replicate 1, sNuc-Seq

description: 10X Genomics


title: ND-KO1

description: Library name: Sample 7


title: Ctrl3_WGBS

city: Jinan

first: kang

last: ai

address: 44 Wenhua West Road

institute: Shandong University

data_processing:
WGBS and RNA-seq raw sequencing reads were first trimmed for adapter and low quality sequences.Then mapped to GRCz11 using BS-Seeker2(v2.1.8) and hisat2(v2.2.1) with parameters ""-t Y -m 0.04 --bt2--end-to-end"" and ""--known-splicesite-infile -p 30 -k 10 --dta -t"" separately.
Student's T-test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeq(v0.12.4) and differentially expressed genes(DEGs) were determined by DESeq2(v1.30.1)" "Student's T-test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeq(v0.12.4) and differentially expressed genes(DEGs) were determined by DESeq2(v1.30.1)
Assembly: GRCz11
Supplementary files format and content: xls flies include RPKM values for each sample

organism: Danio rerio

source_name: trunk region

extract_protocol: The HECs (mCherry+GFP+, 5000 cells) from the trunk region of 36 hpf Tg(kdrl:mCherry/runx1:en-GFP) control or dnmt3ba mo injected group were FAC-sorted and collected into TRIzol reagent (Invitrogen) or  DNA lysate.

value: trunk region

value: hemogenic endothelium


title: CTL32

value: macrophages


title: HFD2-WT7

description: Library name: Sample 6

value: 12w HFD


title: CTL33


title: Healthy colon cells, Patient A sample 2

description: Library name: A2_H_RV64_S59_L006_R1_001


title: Healthy colon cells, Patient A sample 1

description: Library name: A1_H_RV63_S58_L006_R1_001


title: Ctrl2_WGBS


title: mpra_HeLa_ss_mock_rep2

description:
Library name: mpra_HeLa_ss_mock_rep2
Transfected with MPRA library only (mock transfected wrt miRNA); rep 2

source_name: HeLa

value: HeLa

value: wt


title: CTL31


title: HFD2-WT6

description: Library name: Sample 5

value: epididymal white adipose tissue

value: male


title: CF3_WGBS

value: dnmt3ba knockdown


title: mpra_HeLa_ss_mock_rep1

description:
Library name: mpra_HeLa_ss_mock_rep1
Transfected with MPRA library only (mock transfected wrt miRNA); rep 1


title: CTL30


title: CTL28


title: HFD1-KO5

description: Library name: Sample 3


title: Healthy colon cells, Patient B

description: Library name: B_H_RV127_S9_R1_001


title: SCI-sham-2, replicate 2, sNuc-Seq

description: 10X Genomics


title: dentate gyrus, tbi, rep3

description:
Library name: LBN945
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz

value: Brain, Ipsilateral Hippocampal Dentate Gyrus

value: sprague dawley

value: tbi

value: PE406_Project 7809


title: K7 (CUT&Tag)

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
Raw reads were filtered and trimmed by Trimmomatic
The clean reads were then aligned to reference genome sequences using the bwa program
callpeak with cutoff qvalue<0.05 was performed with macs2 software
reads distributions across gene were analyzed by deeptools, and bedtools were employed to annotate peaks
Differential peak analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a FDR < 0.01 and foldchange ≥ 2 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts and normalized values for each Sample
Supplementary files format and content: merged bigwig file for WT and KO respectively
Library strategy: CUT&Tag

source_name: skeletal muscle

extract_protocol:
Instantly frozen muscle from mice and anti-H3K9me3 antibody were used. The samples were then purified using a Qiagen MinElute PCR Purification Kit (Qiagen)
Purified DNA were amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA) for library construction, which were again purified using the Qiagen MinElute PCR Purification Kit (Qiagen)

value: skeletal muscle

value: quadriceps femoris

tag: antibody


title: mpra_HeLa_ss_mir1_rep2

description:
Library name: mpra_HeLa_ss_mir1_rep2
Co-transfected with miR-1 and MPRA library; rep 2


title: Ctrl1_WGBS

value: WT


title: mpra_HeLa_ss_mir155_rep2

description:
Library name: mpra_HeLa_ss_mir155_rep2
Co-transfected with miR-155 and MPRA library; rep 2


title: mpra_HeLa_ss_mir155_rep1

description:
Library name: mpra_HeLa_ss_mir155_rep1
Co-transfected with miR-155 and MPRA library; rep 1


title: dentate gyrus, tbi, rep2

description:
Library name: LBN943
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz


title: LP04010

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

description:
Library name: Sample12
Column name in raw_counts_All_THP1 Samples.tsv: LP04010

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 5 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: raw_counts_All_U937 Samples.tsv and raw_counts_All_THP1 Samples.tsv contain a matrix with raw gene counts, gene symbols and gene types for each sample, respectively.

source_name: human acute monocytic leukemia

growth_protocol: The human cell lines THP-1 and U937 were maintained in RPMI 1640 medium (Gibco Life Technologies, CA, USA)

extract_protocol:
Total RNA was isolated with the GeneMATRIX Universal RNA purification kit with DNase digestion (EURX, Gdańsk, Poland).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). Fifteen PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: The human cell lines THP-1 and U937 were seeded into 24-well plates and exposed to 10 ng/mL phorbol-12-myristate-13-acetate (PMA, Sigma Aldrich, St. Louis, MO) for 48 hours to provoke their differentiation into macrophages. Differentiated U937 and THP1 cells were then exposed to a 30% PRF lysate or serum-free medium alone at 37°C, 5% CO2, and 95% humidity for 24 hours before RNA extraction.

value: human acute monocytic leukemia

value: monocytes

value: Treat with PRF lysate


title: mpra_HeLa_ss_mir1_rep1

description:
Library name: mpra_HeLa_ss_mir1_rep1
Co-transfected with miR-1 and MPRA library; rep 1


title: dentate gyrus, sham, rep3

description:
Library name: LBN944
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz

value: sham


title: CF1_WGBS

value: trunk region

value: hemogenic endothelium


title: HFD1-KO4

description: Library name: Sample 2

value: 12w HFD


title: CF2_WGBS


title: ND-KO3

description: Library name: Sample 8

value: epididymal white adipose tissue

value: ND


title: LP04006

description:
Library name: Sample11
Column name in raw_counts_All_THP1 Samples.tsv: LP04006


title: mpra_HeLa_ss_mir124_rep2

description:
Library name: mpra_HeLa_ss_mir124_rep2
Co-transfected with miR-124 and MPRA library; rep 2

value: HeLa

value: wt


title: LP04002

description:
Library name: Sample10
Column name in raw_counts_All_THP1 Samples.tsv: LP04002


title: CTL27

description:
CTL_Lactic_barcodes.tsv
CTL_Lactic_features.tsv
CTL_Lactic_matrix.mtx

value: abdominal cavity

value: primary macrophage

value: macrophages


title: HFD1-WT6

description: Library name: Sample 4

value: male


title: mpra_HeLa_ss_mir124_rep1

description:
Library name: mpra_HeLa_ss_mir124_rep1
Co-transfected with miR-124 and MPRA library; rep 1


title: W8 (CUT&Tag)

value: skeletal muscle

value: quadriceps femoris


title: dentate gyrus, tbi, rep1

description:
Library name: LBN872
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz

value: Brain, Ipsilateral Hippocampal Dentate Gyrus

value: sprague dawley

value: tbi

value: PE406_Project 7809


title: K5 (CUT&Tag)


title: dentate gyrus, sham, rep2

description:
Library name: LBN874
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz

value: sham


title: HFD1-KO2

description: Library name: Sample 1


title: JEG3_miR-517a-3p_rep2

description: Library name: Sample8

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a tsv file includes TPM counts of each sample

growth_protocol: Cells were maintained in RPMI 1640 (Nacalai tesque) supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Total RNA was extracted using miRNeasy mini kit.
The library construction and paired-end sequencing were conducted by Azenta.

treatment_protocol: mirVana miRNA mimics (Thermo Fisher Scientific) were used to induce miRNA overexpression in the present study. The assay IDs were as follows: miR-517a-3p (MC12660) and Negative Control #1 (4464058). Cells were transfected with miRNA mimics using Lipofectamine RNAiMax (Thermo Fisher Scientific) for 24 hours.


title: W4 (CUT&Tag)


title: K4 (CUT&Tag)


title: LP04005

description:
Library name: Sample8
Column name in raw_counts_All_THP1 Samples.tsv: LP04005

value: human acute monocytic leukemia

value: monocytes

value: untreated


title: LP04009

description:
Library name: Sample9
Column name in raw_counts_All_THP1 Samples.tsv: LP04009


title: JEG3_miR-517a-3p_rep1

description: Library name: Sample7


title: LP04001

description:
Library name: Sample7
Column name in raw_counts_All_THP1 Samples.tsv: LP04001


title: lung, STAT3Y705F/+, 24 h [KI7]

city: Fuzhou

first: Shasha

address: Shangxia Dian Road 15#

institute: Fujian Agriculture and Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly.
Stringtie- 1.3.3bwas used to count the read numbers mapped to each gene. And then FPKM was calculated,which  expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
(For edgeR with/without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized facto
Assembly: http://ftp.ensembl.org/pub/current_gtf/mus_musculus_balbcj/Mus_musculus_balbcj.BALB_cJ_v1.107.gtf.gz
Supplementary files format and content: tab-delimited text files include readcount values for each Sample …

source_name: lung

growth_protocol: Virus infection of mice was carried out under enhanced BSL-2 (BSL-2+) conditions.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries for RNA-seq were prepared using NEBNext® Ultra RNA Library Prep Kit for Illumina

treatment_protocol: For IAV infection, the mice were anaesthetized and inoculated intranasally with 5 × 104 plaque-forming units (PFU).

value: lung

value: bablc

value: infected with WSN for 24 h


title: W3 (CUT&Tag)


title: dentate gyrus, sham, rep1

description:
Library name: LBN871
Bulk Sequencing
LBN_bulkRNAseq_readcounts_kallisto.txt.gz
LBN_bulkRNAseq_readcounts_normalized.csv.gz


title: JEG3_control_rep2

description: Library name: Sample6

value: control


title: lung, STAT3Y705F/+, 24 h [KI6]


title: JEG3_control_rep1

description: Library name: Sample5


title: siOTUD4_r2

city: Shenyang

first: Shuaike

last: Qu

address: Liaoning Province,Shenyang city,Shenbei New District,79 Puhe Road

institute: China Medical University

description: Library name: Sample6

data_processing:
Using MGISEQ-2000RS sequencing platform.
The sequencing data was filtered with SOAPnuke (v.1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5 ) is more than 20%; (3) Removing reads whose unknown base ('N base') ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Transcripts per million (TPM) were calculated.
Assembly: GCF_00001405.39_GRCh38.p13
Supplementary files format and content: tpms for each Sample

source_name: pancreatic cancer

extract_protocol:
Lysis of cells with Trizol Reagent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using MGISEQ-2000RS protocols.

value: pancreatic cancer

value: pancreatic cancer cells


title: lung, STAT3Y705F/+, 24 h [KI5]


title: siOTUD4_1

description: Library name: Sample4


title: siOTUD4_r1

description: Library name: Sample5


title: LP05006

description:
Library name: Sample5
Column name in raw_counts_All_U937 Samples.tsv: LP05006

source_name: human histiocytic lymphoma

value: human histiocytic lymphoma

value: Treat with PRF lysate


title: LP05010

description:
Library name: Sample6
Column name in raw_counts_All_U937 Samples.tsv: LP05010


title: BeWo_miR-517a-3p_rep2

description: Library name: Sample4

source_name: BeWo

value: BeWo


title: LP05002

description:
Library name: Sample4
Column name in raw_counts_All_U937 Samples.tsv: LP05002


title: lung, WT, 24 h [WT10]

value: WT


title: siControl_r2

description: Library name: Sample3


title: LP05009

description:
Library name: Sample3
Column name in raw_counts_All_U937 Samples.tsv: LP05009


title: BeWo_miR-517a-3p_rep1

description: Library name: Sample3


title: lung, WT, 24 h [WT5]


title: lung, WT, 24 h [WT1]


title: BeWo_control_rep2

description: Library name: Sample2


title: siControl_r1

description: Library name: Sample2


title: BeWo_control_rep1

description: Library name: Sample1


title: siControl_1

description: Library name: Sample1


title: LP05001

description:
Library name: Sample1
Column name in raw_counts_All_U937 Samples.tsv: LP05001


title: LP05005

description:
Library name: Sample2
Column name in raw_counts_All_U937 Samples.tsv: LP05005


title: C.ZnO.PMR.0.6h.gs109

status: Public on Sep 20 2025

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: GCF_000003025.6_Sscrofa11.1_genomic
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

organism: Sus scrofa domesticus

source_name: colon

growth_protocol: To be published in various papers

extract_protocol:
Total RNA was isolated from approximately 50 mg of porcine intestinal tissue with RNAqueous™ Total RNA Isolation Kit (Invitrogen). RNA concentrations were determined using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-40 million read counts per sample.
Illumina NovaSeq6000 v1.5
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: To be published in various papers

value: colon

value: C

value: ZnO

value: PMR


title: C.ZnOi.PMRi.HeaP.6h.gs106

value: ZnOi

value: PMRi

value: HeaP


title: C.ZnOi.PMRi.DysP.6h.gs113

value: DysP


title: C.ZnOi.PMRi.DysP.6h.gs107


title: C.ZnOi.PMRi.HeaP.6h.gs100


title: C.ZnOi.PMRi.HeaP.6h.gs155


title: C.ZnOi.PMRi.HeaP.6h.gs112


title: C.ZnO.PMR.0.6h.gs096


title: C.ZnO.0.0.6h.gs030


title: C.ZnO.0.0.6h.gs093


title: C.ZnO.0.0.6h.gs022


title: C.ZnO.PMR.0.6h.gs103


title: C.ZnO.0.0.6h.gs014


title: C.ZnO.PMR.0.6h.gs097


title: C.ZnO.0.0.6h.gs006


title: C.ZnO.PMR.0.6h.gs088


title: C.0.0.SIEM.6h.gs070

value: SIEM


title: C.0.0.SIEM.6h.gs062


title: C.0.0.SIEM.6h.gs046


title: C.0.0.SIEM.6h.gs054


title: C.0.0.SIEM.6h.gs038


title: C.LGG.IFM.0.6h.gs079

value: LGG

value: IFM


title: C.LGG.IFM.0.6h.gs071


title: C.LGG.IFM.0.6h.gs087


title: C.LGG.IFM.0.6h.gs095


title: C.LGG.0.0.6h.gs037


title: C.LGG.IFM.0.6h.gs063


title: C.LGG.0.0.6h.gs045


title: C.ZnOi.PMRi.DysP.6h.gs156


title: C.ZnOi.PMRi.DysP.6h.gs101


title: C.LGG.0.0.6h.gs029


title: C.LGGi.IFMi.FFH.6h.gs154

value: LGGi

value: IFMi

value: FFH


title: C.LGGi.IFMi.FFH.6h.gs099


title: C.LGGi.IFMi.FFH.6h.gs111


title: C.LGGi.IFMi.FFH.6h.gs105


title: C.LGG.0.0.6h.gs013


title: C.LGG.0.0.6h.gs021


title: C.0.IFMi.FFH.6h.gs129


title: C.0.IFMi.FFH.6h.gs124


title: C.2FLi.IFMi.FFH.6h.gs149


title: C.2FLi.IFMi.FFH.6h.gs144


title: C.0.IFMi.FFH.6h.gs119


title: C.LGGi.IFMi.BfH.6h.gs153

value: BfH


title: C.0.IFMi.FFH.6h.gs114


title: C.LGGi.IFMi.BfH.6h.gs110


title: C.LGGi.IFMi.BfH.6h.gs098


title: C.LGGi.IFMi.BfH.6h.gs104


title: C.0.IFMi.BfH.6h.gs128


title: C.2FLi.IFMi.BfH.6h.gs148


title: C.2FLi.IFMi.BfH.6h.gs143


title: C.0.IFMi.BfH.6h.gs118


title: C.2FLi.IFMi.BfH.6h.gs138


title: C.2FLi.IFMi.BfH.6h.gs133


title: C.GOSi.PMRi.HeaP.6h.gs150

value: GOSi


title: C.GOSi.PMRi.HeaP.6h.gs145


title: C.GOSi.PMRi.HeaP.6h.gs140


title: C.GOSi.PMRi.DysP.6h.gs151


title: C.GOSi.PMRi.DysP.6h.gs141


title: C.GOSi.PMRi.DysP.6h.gs136


title: C.GOS.PMR.0.6h.gs072

value: GOS


title: C.GOS.PMR.0.6h.gs080

value: colon


title: C.GOS.PMR.0.6h.gs064

value: C


title: C.2FLi.IFMi.FFH.6h.gs134


title: C.2FLi.IFMi.FFH.6h.gs139


title: C.GOS.PMR.0.6h.gs048


title: C.GOS.0.0.6h.gs069


title: C.GOS.0.0.6h.gs061


title: C.0.IFMi.BfH.6h.gs123


title: C.0.IFMi.BfH.6h.gs108


title: C.0.PMRi.HeaP.6h.gs125


title: C.GOS.0.0.6h.gs053


title: C.0.PMRi.HeaP.6h.gs130


title: C.0.PMRi.HeaP.6h.gs120


title: C.GOS.0.0.6h.gs085


title: C.0.PMRi.DysP.6h.gs116


title: C.0.PMRi.DysP.6h.gs121


title: C.0.PMRi.DysP.6h.gs126


title: C.0.PMRi.HeaP.6h.gs115


title: C.0.PMRi.DysP.6h.gs131


title: C.0.PMR.0.6h.gs040


title: C.GOS.0.0.6h.gs077


title: C.0.PMR.0.6h.gs032


title: C.GOSi.PMRi.HeaP.6h.gs135


title: C.0.PMR.0.6h.gs024


title: C.GOSi.PMRi.DysP.6h.gs146


title: C.0.PMR.0.6h.gs008


title: C.2FL.IFM.0.6h.gs055


title: C.GOS.PMR.0.6h.gs056


title: C.2FL.IFM.0.6h.gs031


title: C.2FL.0.0.6h.gs092


title: C.2FL.IFM.0.6h.gs023


title: C.2FL.0.0.6h.gs084


title: C.2FL.0.0.6h.gs076


title: C.2FL.0.0.6h.gs068


title: C.2FL.0.0.6h.gs005


title: C.0.IFM.0.6h.gs094


title: C.0.IFM.0.6h.gs086


title: C.0.0.0.6h.gs044


title: C.0.IFM.0.6h.gs015


title: C.0.0.0.6h.gs052


title: C.0.0.0.6h.gs060


title: C.0.0.0.6h.gs036


title: C.0.0.0.0h.gs137


title: C.0.0.0.6h.gs028


title: C.0.0.0.0h.gs127


title: J.2FL.IFM.0.6h.gs042

source_name: jejunum

value: jejunum

value: J


title: C.0.0.0.0h.gs122


title: J.2FL.IFM.0.6h.gs058


title: C.0.0.0.0h.gs132


title: C.2FL.IFM.0.6h.gs047


title: C.0.0.0.0h.gs117


title: C.2FL.IFM.0.6h.gs039


title: J.2FL.IFM.0.6h.gs034


title: J.2FL.IFM.0.6h.gs026


title: J.2FL.IFM.0.4h.gs091


title: J.2FL.IFM.0.4h.gs083


title: J.2FL.IFM.0.4h.gs020


title: J.2FL.IFM.0.4h.gs004


title: J.2FL.IFM.0.2h.gs067


title: J.2FL.IFM.0.4h.gs012


title: J.2FL.IFM.0.2h.gs075


title: C.0.IFM.0.6h.gs078


title: C.0.IFM.0.6h.gs007


title: J.2FL.IFM.0.2h.gs043


title: C.0.PMR.0.6h.gs016

value: PMR


title: J.2FL.IFM.0.2h.gs051


title: J.2FL.IFM.0.2h.gs059


title: J.0.IFM.0.6h.gs073


title: J.2FL.0.0.6h.gs081


title: J.2FL.0.0.6h.gs018


title: J.0.IFM.0.6h.gs065


title: J.0.IFM.0.6h.gs057


title: J.0.IFM.0.4h.gs035


title: J.0.IFM.0.6h.gs041


title: J.0.IFM.0.4h.gs011


title: J.0.IFM.0.4h.gs019


title: J.0.IFM.0.4h.gs003


title: J.0.IFM.0.6h.gs049


title: J.0.IFM.0.4h.gs027


title: J.0.IFM.0.2h.gs090


title: J.0.IFM.0.2h.gs066


title: J.0.IFM.0.2h.gs050


title: J.0.IFM.0.2h.gs082


title: J.0.0.0.6h.gs033


title: J.0.0.0.6h.gs017


title: J.0.0.0.0h.gs157


title: J.2FL.0.0.6h.gs089


title: J.0.0.0.6h.gs009


title: J.0.0.0.6h.gs001


title: J.2FL.0.0.6h.gs002


title: J.0.0.0.0h.gs152


title: J.0.0.0.0h.gs142


title: J.2FL.0.0.6h.gs010


title: 1α,25(OH)2D3 treated γδ T cells, rep3

city: Guangzhou

first: Peng

last: Li

address: The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University

institute: Jinan University

description:
T3
fpkm_T3
γδ T cells
1α,25(OH)2D3

data_processing:
The transcriptome sequencing and analysis were conducted by BGI tech. Sequencing raw reads were preprocessed by filtering out rRNA reads, short-fragment reads, sequencing adapters and other low-quality reads to obtain the clean reads. The clean reads were next mapped to the reference genome (hg38) using HISAT.
Differentially expressed genes (DEGs) were identified using the DESeq functions estimate size factors and nbinom test. The p value was calculated, and then the p value was corrected by false discovery rate (FDR) to obtain the Qvalue. Fold changes were also estimated according to the FPKM or TPM of each sample. Usually, Qvalue≤0.05 was regarded as a significant enrichment. KEGG pathway enrichment analysis of DEGs was performed using phyper function in the R software, and Rich Ratio=Term Candidate Gene Number/Term Gene Number.
Software information, SOAPnuke: Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05; Official website: https://github.com/BGI-flexlab/SOAPnuke
HISAT2: Version: v2.0.4; Parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8; Official website: http://www.ccb.jhu.edu/software/hisat
Assembly: Reference genome hg38.
Supplementary files format and content: expression_allsamples.txt: Tab-delimited text file includes FPKM, TPM, and read counts for each Sample (named as V1, V2, V3; T1, T2, T3).

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from their whole blood, following the standard Ficoll-Paque-based (GE Healthcare) density gradient centrifugation protocol. Vγ9Vδ2 (γδ) T cell culture in vitro. PBMCs (3.0×10^6/mL) were stimulated at the indicated concentrations with 50 μM Zoledronic acid monohydrate (ZOL) and 100 IU/mL recombinant human IL-2 (Peprotech) in 24-well round-bottom microculture plates.

extract_protocol:
Total RNA was isolated using RNA simple Total RNA Kit.
Total RNA was processed by mRNA enrichment method, mRNA enrichment: mRNA with polyA tail was enriched with magnetic beads with Oligo dT. The obtained RNA was fragmented by interrupting buffer, reverse transcribed with random N6 primers, and cDNA double-stranded was synthesized to form double-stranded DNA. The end of the synthesized double-stranded DNA is blunted and phosphorylated at the 5' end, forming a sticky end with an "A" protruding from the 3' end, and then ligated with a bubbling linker with a protruding "T" at the 3' end. The ligated products are amplified by PCR with specific primers. The PCR product was heat-denatured into single-stranded DNA, and then a single-stranded circular DNA library was obtained by circularizing the single-stranded DNA with a bridge primer. The constructed library is checked for quality and sequenced after it is qualified.

treatment_protocol: γδ T cells used in all the experiments were pretreated with 100 nM 1α,25(OH)2D3 or vehicle for three times at 1-day intervals.

value: blood

value: gamma-delta T cells

tag: diagnosis

value: healthy donor


title: 1α,25(OH)2D3 treated γδ T cells, rep2

description:
T2
fpkm_T2
γδ T cells
1α,25(OH)2D3


title: Vehicle treated γδ T cells, rep2

description:
V2
fpkm_V2
γδ T cells

value: Vehicle


title: Vehicle treated γδ T cells, rep1

description:
V1
fpkm_V1
γδ T cells


title: Vehicle treated γδ T cells, rep3

description:
V3
fpkm_V3
γδ T cells


title: J.0.0.0.0h.gs102


title: 1α,25(OH)2D3 treated γδ T cells, rep1

description:
T1
fpkm_T1
γδ T cells
1α,25(OH)2D3


title: J.0.IFM.0.2h.gs074