title: WGS_pooled_ES1M5S10328-like_mutants_from_F2

city: La Jolla

first: Julie

last: Law

address: 10010 North Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
For each line, the fastq files were trimmed to remove low quality reads using trim_galore (v0.6.0) with default parameters and then mapped to the Arabidopsis TAIR10 genome using BWA (v0.7.17) with the following functions (aln and samse) and default options. The resulting SAM files were converted to BAM files using samtools (v1.6) and redundant reads were removed using the rmdup function of samtools (v1.6). SNP calling was performed using samtools (v1.6) with the following options: mpileup -Q 30 -C50 -P Illumina -t DP,DV,INFO/DPR,DP4,SP,DV and -Buf. VCF files were generated from the SNP calls using bcftools (v1.9). The SNPs were first filtered to keep only those induced by EMS (G-to-A and C-to-T) and then annotated using snpEff (v5.0e) based on the Arabidopsis TAIR10 annotation. SNPs present in the EMS mutants but not in the Col-0 parental line were considered as potential causal SNPs.
For the ES1M5S10328 (rim22-3) mapping-by-sequencing library, the read depth and SNP mutation frequency at the final set of SNPs were extracted from the DP and DP4 columns of the VCF file and the mutation frequency was plotted against the SNP positions using R (https://cran.r-project.org/) resulting in the identification of a QTL region on chromosome 3. To fine-map the causative gene, a larger F2 population containing 612 plants was grown in the greenhouse and methyl-cutting assays were used to identify homozygous mutants.
Assembly: TAIR10
Supplementary files format and content: vcf file. The header contains Chromosome, Position, SNP ID, Reference allele, Alternative allele, Quality, FILTER, INFO, and FORMAT
Library strategy: DNA-seq

growth_protocol: For HEM EMS lines and wild-type plants (Col-0 ecotype), seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. 20-day old shoot or stage 12 and younger flower buds were collected and frozen in liquid nitrogen.

extract_protocol:
Genomic DNA were extracted from flower buds or shoot tissues using CTAB method or using the DNeasy Plant Mini Kit (QIAGEN, Cat# 69014).
2 μg of genomic DNA was fragmented using a Covaris S2 sonicator. Library preparation was conducted using the NEBNext Ultra II DNA Library prep kit (NEB, Cat# E7645L) for Whole Genome Sequencing (WGS).

value: stage 12 and younger flower buds

tag: cultivar

value: Columbia


title: CF20_eTRF_Visit4

status: Public on Sep 22 2025

type: SRA

city: Nuthetal

first: Michail

last: Lazaratos

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung Potsdam-Rehbrücke

description:
Library name: CF-20-V4
CF-20-V4

library_source: transcriptomic

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.11a
Read count extraction via STRINGTIE v2.2.1 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCh38.110
Supplementary files format and content: excel file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Subcutaneous adipose tissue

extract_protocol:
RNA was isolated using the RNeasy Lipid Tissue Mini Kit (Qiagen). 1 µg of total RNA was used for the consruction of sequencing libraries.
done by BGI (Yantian District, Shenzhen, China)

tag: tissue

value: Subcutaneous adipose tissue

tag: Sex

value: female

tag: treatment

value: eTRF

tag: timepoint


title: WGS_ES1M5S10051

middle: A

state: CA

department: Plant Molecular and Cellular Biology

country: USA

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 20 day old shoot

value: 20 day old shoot

tag: genotype


title: TSC1_TSC2_control_Rep4

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

description:
10x Genomics 3' V3
This sample is named TSC1_TSC2_control_Rep3 in the publication.

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using alevin with GENCODE vM25 transcript annotations to generate cells x genes matrices85. Data were then imported into R v3.6 and Seurat objects were created for each individual sample before being merged
Cells were filtered such that there were at least 1000 UMIs and 500 genes detected, and fewer than 10% of the transcripts were mitochondrially contributed. Data were then scaled and normalized using scTransform and integrated using Seurat
Clusters were identified using Louvain-Jaccard clustering with multilevel refinement (resolution=1.5) performed on the top 100 PCs. Marker genes of each cluster were identified using Presto (https://github.com/immunogenomics/presto), and differential expression analysis was performed using distinct with log2 CPMs in R v4.188. Differential abundance testing comparing cellular proportions for each genotype was performed using the propeller test in the speckle package
Assembly: mm10
Supplementary files format and content: Tab separated values and binary matrix created by Alevin
Supplementary files format and content: Tab separated metadata for each high-quality barcode, including cluster assignment, cluster annotation, tSNE coordinates, UMIs and genes detected per cell, and percent mitochondrial contribution

organism: Mus musculus

source_name: Cerebral cortical neurons

extract_protocol:
Single-cell RNA-seq was performed as described previously in Loo et al., 201949 and  Li et al, 201884. Briefly, P0 cerebral cortical neurons from control and TSC1/2 cKO mice were dissociated and stored in 80% methanol at -80°C. Cells were then lysed in TRI-reagent and RNA was extracted using a Direct-zol kit (Zymo Research Cat#R2051) with on-column DNase treatment, following the manufacturer’s instructions.
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the 10xG 3Prime v3 single-cell RNA kit (10X Genomics) according to the manufacturer’s protocol. Libraries were sequenced single-end for a minimum of 76 bp for each index to a depth of approximately 40 million host genome reads on an Illumina NextSeq 500 instrument at the Yale Center for Genomic Analysis.

value: Cerebral cortical neurons

tag: age


title: CD8+, WT, Ctr179

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
RNA-seq reads were processed by CirComPara2 (v. 0.1.2.1):
the raw reads were pre-processed by Trimmomatic, the reads are aligned collinearly to the reference genome using HISAT2 and transcript expression analysis is performed with StringTie
Assembly: hg38
Supplementary files format and content: gene_expression_FPKM_table.csv reports the linear gene expression measured in FPKM for each sample, with samples represented as columns and ENSEMBL ID genes as rows.

source_name: peripheral blood

extract_protocol:
Purified T-LGL were obtained from PBMC with magnetic micro-beads (Miltenyi Biotec) coated with monoclonal anti-human CD57 or CD56 mAbs, for T-LGLL patients, or CD8 for CTR.
Purity and viability of purified cell populations were assessed by flow cytometry. A threshold of at least 98% T-LGLs on all the acquired events, coupled with a contamination lower than 0.1% of monocytes, was accepted.
Total RNA was extracted from purified T-LGL with the RNeasy Mini Kit (Qiagen) in combination with on-column DNase I digestion (RNase-Free DNase set, Qiagen), according to manufacturer’s instructions.
RNA quality was assessed using the RNA 6000 Nano and RNA 6000 PICO assays on a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using a TruSeq Stranded Total RNA Kit adapted for long fragments (±550 bp) with the Ribo-Zero Gold rRNA Removal Kit (Illumina) according to the manufacturer’s instructions.
Prepared libraries were run on a HiSeq3000 high-throughput sequencing system (Illumina) and paired-end reads were generated (315 million reads per sample, on average).

value: peripheral blood

tag: cell type

value: CD8+/CD57+ T-lymphocytes

value: WT

tag: disease

value: healthy


title: CD8+, WT, Ctr178


title: 1 Avg- control cell, rep1

type: RNA

city: Buenos Aires

first: Marina

last: Perona

address: Avenida General Paz 1499

department: Radiobiología

country: Argentina

institute: Comisión Nacional de Energía Atómica

description: miRNA expression data from control cells

hyb_protocol: For each sample, 21.5 µL biotin-labeled sample was loaded prior to hybridization on GeneChipTM miRNA. A Hybridization Cocktail was prepared, injected into the array and  incubated at 48°C and 60 rpm for 16 to 18 hours in the hybridization oven.

scan_protocol: GeneChips were scanned with a GCS 3000 7G scanner (GeneChip Scanner 3000 7G).

data_processing: The analysis was performed using the Transcriptome Analysis Console (TAC) Software (Applied Biosystems, Thermo Fisher Scientific), the R programming language, and different tools of Bioconductor. Data background correction and normalization were done using Robust Multi-array Average (rma). Differential miR expression was evaluated by Limma package (Linear Models for Microarray Data) [17]. The filter criteria was fold change > 2 or < -2 and p value < 0.05.

label: biotin

source_name: Anaplastic thyroid cancer cells (8505c) without treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (FlashTag™ Biotin HSR RNA Labeling Kit).

growth_protocol: Anaplastic thyroid cancer cells (8505c) were grown in a humidified 5% CO2 atmosphere in RPMI 1640 medium (GibcoTM, USA) supplemented with 10% fetal bovine serum (Natocor, Argentina).

extract_protocol: Total RNA was isolated 4 hours after irradiation using the commercially available GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).

treatment_protocol: Cells were treated with 1 mM VA for 24 hours before irradiation. Irradiation was done with a Cesium 137 (137Cs) of 189 TBq gamma source (IBL- 437C Irradiator; CIS Bio-International, CEBIRSA, Argentina) at a dose rate of 7.7 Gy/min. Cells were divided in the following experimental groups: Control, VA pretreatment (VA), irradiated (IR), and irradiated after VA pretreatment (IR+VA). Controls were sham irradiated.

tag: cell line

value: Anaplastic thyroid cancer cells

tag: growth phase

value: exponentially growing cell line

value: control


title: 1 Avg-control cell, rep2


title: TSC1_TSC2_control_Rep3

description:
10x Genomics 3' V3
This sample is named TSC1_TSC2_control_Rep2 in the publication.


title: WGS_ES1M5S10229


title: TSC1_TSC2_control_Rep1

description: 10x Genomics 3' V3


title: WGS_ES1M5S10336


title: CD8+, WT, Ctr176


title: CF20_lTRF_Visit2

description:
Library name: CF-20-V2
CF-20-V2

value: lTRF


title: CD8+, WT, Ctr164


title: CF18_lTRF_Visit2

description:
Library name: CF-18-V2
CF-18-V2


title: CF18_eTRF_Visit4

description:
Library name: CF-18-V4
CF-18-V4


title: CF17_lTRF_Visit4

description:
Library name: CF-17-V4
CF-17-V4


title: CD8+, WT, Ctr168


title: WGS_WTCol-0


title: CD4+, STAT5B mutated, LGL132

value: T-Large Granular Lymphocytes

value: STAT5B mutated

value: T-LGLL


title: Human Lung Mesenchymal Stem Cell Colony G 4th passage

city: Los Angeles

first: Brendan

middle: H

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

description:
Library name: G4
G4_counts

data_processing:
quality assessment, FastQC, v0.11.9
adapter removal, cutadapt, version 5.0
read quality trimming, Trimmomatic, version 0.38
alignment to Gencode h45, STAR with GeneCounts, version 2.10a
generation of RPKM and TMM, edgeR, version 4.0
Assembly: gencode human version 45, GRCh38.p14
Supplementary files format and content: excel spreadsheet containing: counts, RPKM, TMM, differential gene expression, and annotation
Supplementary files format and content: 16Apr24_WS_RUV_UQ_edgeR_annotated_RPKM_TMM.xlsx

source_name: Lung

growth_protocol: Enzymatically dissociated (2mg/ml dispase II, 1mg/ml collagenase, and 200U/ml DNAse) and cultured in MSC medium (alpha MEM with 20% FBS, 100U Pen/Strep, 2mM Glu, 55 micromolar beta-mercaptoethanol)

extract_protocol:
Buffered phenol extraction followed by column based isolation
Unstranded library production by Novogene (Abclonal)

value: Lung

value: Primary

value: mesenchymal stem cells

tag: batch

value: 4th passage


title: HKSM R3

first: Zeba

last: Wunderlich

state: Massachusetts

address: 610 Commonwealth Ave

department: Biology

institute: Boston University

description: Library name: Sample 6 -ATAC-seq

data_processing:
RNA-seq: Reads were aligned to the dm6 geneome with Bowtie2 and counts were generated with featureCount. Transcripts per million (TPM) were then calculated
STARR-seq:STARR-seq reads were aligned to genome with Bowtie2 and samtools. STARRPeaker was then used to compare the output STARR-seq files for each sample to the input DNA library. Based on a p-value threshold <0.05, STARRPeaker calls enhancer peaks for each replicate. We built consensus peaks that overlapped between replicates of the same treatment group. If a peak was in at least two out of three replicates (with at least 1 bp of overlap), a consensus enhancer was defined using the union of any of the enhancers from individual replicates that occur at that location. Consensus enhancers were assigned the average of the activity scores of the replicate peaks that contribute to them We defined non-overlapping enhancers or activity classes by categorizing them into one of seven groups. When comparing enhancers across treatment conditions, enhancers were considered active in two or more conditions if at least 60% of either enhancer was in the overlapping region. Coordinates for enhancers in overlapping groups were defined as the union of the treatment defined enhancers.
ATAC-seq: Reads with trimmed with CutAdapt and aligned with Bowtie2. Data was filtered for duplicate reads using the Picard MarkDuplicates tool and adjusted for Tn5 offset using bamtools Peaks were called using MACS2, using narrow peak calling and a p-value of 0.01 Consensus ATAC-seq peaks were built from the widest margins of open regions present in at least 2 replicates
Assembly: dm6
Supplementary files format and content: RNA-seq: raw counts are provided for each sample and the calcualted TPM's are provided in the combined file Allsamples_tpm.csv.
Supplementary files format and content: STARR-seq: The enhancer peak calls from STARRPeaker are provides for each sample. The columns are 1. Chromosome 2. Start position 3. end position 4. Name/rank 1 is highest  5. Score 6. strand 7. "Log2 Fold change (normalized output/input ratio, in log2 space)" 8. Input fragment coverage output fragment coverage  9. -log10 of P-value  10. -log10 of Q-value. The *consensus.merge.bed files are the consensus files for enhancers found in each condition. The Activity_class_all.bed file has the coordinates and activity class for all enhancers
Supplementary files format and content: ATAC-seq: Narrowpeak files for each sample are provided. The list the accessible regions and follow stardarrd UCSC narrowpeak format. Columns: 1. chrom 2. chromStart 3.chromEnd  4.name 5. score 6. strand 7.signalValue 8. pValue 9. qValue 10. peak

organism: Drosophila melanogaster

source_name: Hemocytes

growth_protocol:
RNA-seq: S2* cells were grown in Complete Schneider’s media, with 10% FBS, 2nM L-gulutamine, with antibiotics at 28°C.
STARR-seq: S2* cells were grown in Complete Schneider’s media, with 10% FBS, 2nM L-gulutamine, with antibiotics at 28°C.
ATAC-seq: Flies were maintained in typical conditions at 25°C

extract_protocol:
RNA-seq: Total RNA was extracted with the Zymo Direct-zol RNA miniprep kit
STARR-seq: Total RNA was extracted with RNeasy Maxi kit (Qiagen)
ATAC-seq: Hemocytes were collected by placing 20-25 anesthetized flies in 0.5 mL tubes with 3 20G needle holes at the bottom. Flies were spun at 6,000xg at 4°C for 1 min into ATAC-seq lysis buffer (Grandi et al. 2022).
RNA-seq: Library prep with polyA selection was completed by Azenta (Genewiz)
STARR-seq: Library construction followed the protocol from Neumayr et al. 2019. mRNA was isolated with oligo dT beads, Reverse transcription was done with SuperScript® III reverse transcriptase, before junction PCR to isolated STARR-seq specific transcripts
ATAC-seq: Lysate was treated with Tn5 for tagmentation, before clean up with Monarch PCR clean up kit (NEB). Barcoding PCR was completed with Illumina primers and qPCR quantification with NEBNext Library Quant Kit (New England Biolabs)

treatment_protocol:
RNA-seq: Cells were treated with 40 nM 20E or water, 24 hours before treatment with PBS or HKSM. Samples were then collected 24hrs later.
STARR-seq:  Cells electroprotated with a library of pSTARR-seq plasmids comtaining 500-750 bp genomic freagments. Cells were treated with 40 nM 20E or water, 24 hours before treatment with PBS or HKSM. Samples were then collected 24hrs later.
ATAC-seq: Flies were either left uninjected or injected with  ~50 nL of heat-killed Serratia marcescens at OD=0.5 in PBS and then incubated at  25°C for 24 hrs

value: Hemocytes

value: OregonR

value: injected with HKSM


title: CF17_eTRF_Visit2

description:
Library name: CF-17-V2
CF-17-V2

value: Subcutaneous adipose tissue

value: female

value: eTRF


title: Human Lung Mesenchymal Stem Cell Colony I 4th passage

description:
Library name: I4
I4_counts

value: WT


title: Human Lung Mesenchymal Stem Cell Colony T 4th passage

description:
Library name: T4
T4_counts


title: CD4+, STAT5B mutated, LGL379

value: peripheral blood


title: Human Lung Mesenchymal Stem Cell Colony K 4th passage

description:
Library name: K4
K4_counts


title: CF16_eTRF_Visit2

description:
Library name: CF-16-V2
CF-16-V2


title: WGS_EH1S1B549

value: 20 day old shoot

value: Columbia


title: Control R3

description: Library name: Sample 5 -ATAC-seq

value: no injection


title: CD4+, STAT5B mutated, LGL2

value: T-Large Granular Lymphocytes

value: STAT5B mutated


title: HKSM R2

description: Library name: Sample 4 -ATAC-seq


title: CD4+, STAT5B mutated, LGL196

value: T-LGLL


title: CF15_eTRF_Visit4

description:
Library name: CF-15-V4
CF-15-V4


title: Control R2

description: Library name: Sample 3  -ATAC-seq


title: CD4+, STAT5B mutated, LGL49


title: Human Lung Mesenchymal Stem Cell Colony M 4th passage

description:
Library name: M4
M4_counts

value: Lung

value: Primary


title: CF15_lTRF_Visit2

description:
Library name: CF-15-V2
CF-15-V2

value: lTRF


title: Human Lung Mesenchymal Stem Cell Colony S 4th passage

description:
Library name: S4
S4_counts

value: mesenchymal stem cells

value: 4th passage


title: Human Lung Mesenchymal Stem Cell Colony P 4th passage

description:
Library name: P4
P4_counts


title: HKSM R1

description: Library name: Sample 2  -ATAC-seq

value: Hemocytes

value: OregonR

value: injected with HKSM


title: CD4+, WT, LGL20


title: Human Lung Mesenchymal Stem Cell Colony W 4th passage

description:
Library name: W4
W4_counts


title: CD4+, WT, LGL305


title: Human Lung Mesenchymal Stem Cell Colony D 4th passage

description:
Library name: D4
D4_coujnts


title: S2* cells, IMD, replicate 3

description:
Library name: S9- RNA-seq
S9_counts

value: Hemocytes-like cells


title: CF13_eTRF_Visit4

description:
Library name: CF-13-V4
CF-13-V4

value: Subcutaneous adipose tissue

value: female

value: eTRF


title: CF13_lTRF_Visit2

description:
Library name: CF-13-V2
CF-13-V2


title: NGO treated hPBMC 4, CD3/28, IL-2 activated, 48h

city: Seoul

first: Aaron

last: Yu

address: Gwanak-ro 1

country: South Korea

institute: Seoul national university

description:
Library name: NGO-4
NGO-4

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the R package clusterProfiler
GSEA v3.0
Trimmed DEGs were used for pathway analysis using QIAGEN's Ingenuity® Pathway Analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each example

growth_protocol: hPBMCs were incubated with RPMI containing 10% FBS, 1X Antibiotic-Antimycotic

extract_protocol:
Total RNA was extracted and purified from hPBMCs studied in vitro using the TRIzol reagent. 1.2ug of total RNA was used to construct sequencing library
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: To evaluate the effect of NGO, 20 μg/mL of NGO were added to hPBMCs for 48hr

value: peripheral blood

value: peripheral blood mononuclear cell

value: 20μg/mL of NGO, CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: CF16_lTRF_Visit4

description:
Library name: CF-16-V4
CF-16-V4


title: CF12_lTRF_Visit4

description:
Library name: CF-12-V4
CF-12-V4


title: S2* cells, 20E, replicate 3

description:
Library name: S8 -RNA-seq
S8_counts


title: NGO treated hPBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: NGO-3
NGO-3


title: CD4+, WT, LGL21

value: T-Large Granular Lymphocytes

value: WT


title: CD4+, WT, LGL149

value: T-LGLL


title: CF12_eTRF_Visit2

description:
Library name: CF-12-V2
CF-12-V2


title: S2* cells, Control, replicate 3

description:
Library name: S7- RNA-seq
S7_counts

value: water/PBS


title: CD8+, WT, LGL299


title: S2* cells, IMD, replicate 2

description:
Library name: S6- RNA-seq
S6_counts


title: NGO treated hPBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: NGO-1
NGO-1


title: S2* cells, 20E, replicate 2

description:
Library name: S5 -RNA-seq
S5_counts


title: CF08_eTRF_Visit2

description:
Library name: CF-08-V2
CF-08-V2


title: CD8+, WT, LGL5


title: CF05_eTRF_Visit4

description:
Library name: CF-05-V4
CF-05-V4


title: hPBMC 4, CD3/28, IL-2 activated, 48h

description:
Library name: PBMC-4
PBMC-4

value: CD3/28 dynabead, 30U/mL of IL-2 for 48h


title: S2* cells, Control, replicate 2

description:
Library name: S4 -RNA-seq
S4_counts


title: Control R1

description: Library name: Sample 1 -ATAC-seq

value: no injection


title: CD8+, WT, LGL48


title: hPBMC 3, CD3/28, IL-2 activated, 48h

description:
Library name: PBMC-3
PBMC-3


title: S2* cells, IMD, replicate 1

description:
Library name: S3- RNA-seq
S3_counts


title: CD8+, WT, LGL56


title: CF02_eTRF_Visit4

description:
Library name: CF-02-V4
CF-02-V4


title: hPBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: PBMC-2
PBMC-2


title: S2* cells, 20E, replicate 1

description:
Library name: S2 -RNA-seq
S2_counts


title: CD4+, WT, LGL258


title: hPBMC 1, CD3/28, IL-2 activated, 48h

description:
Library name: PBMC-1
PBMC-1


title: CD8+, WT, LGL179


title: CF02_lTRF_Visit2

description:
Library name: CF-02-V2
CF-02-V2

value: lTRF


title: NGO treated hPBMC 2, CD3/28, IL-2 activated, 48h

description:
Library name: NGO-2
NGO-2


title: S2* cells, Control, replicate 1

description:
Library name: S1- RNA-seq
S1_counts


title: CF01_lTRF_Visit4

description:
Library name: CF-01-V4
CF-01-V4


title: CF08_lTRF_Visit4

description:
Library name: CF-08-V4
CF-08-V4


title: CD8+, STAT3 mutated, LGL254

value: STAT3 mutated


title: CD8+, STAT3 mutated, LGL272


title: S2* cells, IMD, replicate 3, pSTARR genomic library

description: Library name: S9- STARR-seq

value: Hemocyte-like cells

value: pSTARR genomic library


title: CF01_eTRF_Visit2

description:
Library name: CF-01-V2
CF-01-V2


title: KO, TSC

city: Pokfulam

first: Yunying

last: Huang

state: Hong Kong

address: Rm503, JCBIR, 5 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Fastq files were processed using DNBC4tools (v2.0.7) (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software/tree/version2.0) developed by BGI Genomics.
This pipeline aligns reads to the hg38 human reference genome and performs barcode error correction, PCR duplicate marking, barcode counting, and unique molecular identifier counting to produce expression count matrices.
The gene expression matrices were loaded into R (v.4.3.2) and processed using Seurat (v.4.3.0) for downstream analyses. Cells were filtered to exclude cells that had the following parameters: (1) fewer than 200 genes expressed; (2) over 15% mitochondrial reads. Genes were further filtered to eliminate those expressed in fewer than 10 cells.
Assembly: hg38 human reference genome
Supplementary files format and content: rds file

source_name: TSC

extract_protocol:
20,000 live cells were freshly harvested for scRNA-seq experiments
scRNA-seq libraries were prepared using a DNBelab C Series High-throughput Single-cell RNA Library Preparation set (MGI) according to the manufacturer's protocol. through droplet encapsulation, demulsification, mRNA captured bead collection, reverse transcription, cDNA and oligo amplification and purification. Indexed sequencing libraries were prepared according to the manufacturer’s protocol by performing fragmentation and end repair, adapter ligation, purification, size selection and PCR amplification.

value: TSC

value: KO


title: CD8+, STAT3 mutated, LGL80


title: S2* cells, Control, replicate 3, pSTARR genomic library

description: Library name: S7 - STARR-seq


title: S2* cells, 20E, replicate 3, pSTARR genomic library

description: Library name: S8 - STARR-seq


title: CD8+, STAT3 mutated, LGL16


title: CF05_lTRF_Visit2

description:
Library name: CF-05-V2
CF-05-V2

value: Subcutaneous adipose tissue

value: female


title: zs11_young_leaves_ATAC_rep2

city: Wuhan

first: Jie

last: Zhou

address: 1 Lion Rock Street

country: China

institute: Huazhong Agricultural University

description: Library name: zs11_ATAC_rep2

data_processing:
Evaluated the quality of sequencing data using Fastp.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping.
Assembly: Brassica_napus_ZS11.
Supplementary files format and content: FPKM values; peak number; DNA methylation level matrix

organism: Brassica napus

source_name: young leaf

growth_protocol: For the collection of young leaves, the plants were planted in greenhouses. Germinated seeds were grown in a phytotron with a day/night cycle of 16 h/8 h and a temperature of 22°C/18°C. Young leaves were collected from 2-week-old hydroponically grown seedlings.

extract_protocol:
Total RNA from young leaves was isolated using the RNeasy Plant Mini Kit (QIAGEN, 74904). Approximately 2 μg of RNA was used for library preparation with the Illumina TruSeq RNA kit following the manufacturer’s protocol; Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq X-Ten system (paired-end 150-bp reads).
The libraries were sequenced on an Illumina HiSeq X-Ten system.

value: young leaf

value: 14d young leaves cells


title: zs11_young_leaves_ATAC_rep1

description: Library name: zs11_ATAC_rep1


title: CD8+, STAT3 mutated, LGL3

value: peripheral blood


title: zs11_young_leaves_H3K9me2_rep2

description: Library name: zs11_H3K9me2_rep2

tag: chip antibody


title: KO, differentiated, day 7

source_name: Trophoblast

value: Trophoblast


title: S2* cells, IMD, replicate 2, pSTARR genomic library

description: Library name: S6- STARR-seq


title: KO, differentiated, day 2


title: zs11_young_leaves_H3K9me2_rep1

description: Library name: zs11_H3K9me2_rep1


title: input library

description: Library name: S10- STARR-seq

library_source: other

molecule: other

source_name: plasmid DNA library

value: plasmid DNA library

value: no cells

value: untreated


title: S2* cells, 20E, replicate 2, pSTARR genomic library

description: Library name: S5- STARR-seq


title: KO, EPSC

source_name: EPSC

value: EPSC


title: zs11_young_leaves_RNA-seq_rep2

description: Library name: zs11_RNA_rep2


title: S2* cells, Control, replicate 2, pSTARR genomic library

description: Library name: S4 - STARR-seq

value: water/PBS


title: Lung MSC membrane-bound Green Fluorescent Protein #2

description:
Library name: mG_2
mG_2_counts

data_processing:
quality assessment, FastQC, v0.11.9
adapter removal, cutadapt, version 5.0
read quality trimming, Trimmomatic, version 0.38
alignment to Gencode h45, STAR with GeneCounts, version 2.10a
generation of RPKM and TMM, edgeR, version 4.0
Assembly: Ensembl version 103 corresponding to GRCmm39
Supplementary files format and content: excel spreadsheet containing: counts, RPKM, TMM, differential gene expression, and annotation
Supplementary files format and content: 21Apr25_WS_RUV_UQ_edgeR_annotated_RPKM_TMM.xlsx

growth_protocol: Enzymatically dissociated (2mg/ml dispase II, 1mg/ml collagenase, and 200U/ml DNAse) into MSC medium (alpha MEM with 20% FBS, 100U Pen/Strep, 2mM Glu, 55 micromolar beta-mercaptoethanol) prior to flow cytometry

treatment_protocol: Doxycycline induction from Embryonic day 6.5 to Posnatal day 1

value: Lung

tag: strain

value: Doxycycline induction E6.5-P1


title: zs11_young_leaves_RNA-seq_rep1

description: Library name: zs11_RNA_rep1


title: WT, TSC

value: WT


title: zs11_young_leaves_BS-seq

description: Library name: zs11_DNAmethy


title: Lung MSC membrane-bound Green Fluorescent Protein #1

description:
Library name: mG_1
mG_1_counts


title: S2* cells, IMD, replicate 1, pSTARR genomic library

description: Library name: S3 - STARR-seq

value: Hemocyte-like cells

value: pSTARR genomic library


title: S2* cells, 20E, replicate 1, pSTARR genomic library

description: Library name: S2- STARR-seq


title: WT, differentiated, day 2


title: WT, differentiated, day 7


title: Lung MSC membrane-bound TdTomato #2

description:
Library name: mT_2
mT_2_counts


title: S2* cells, Control, replicate 1, pSTARR genomic library

description: Library name: S1 -STARR-seq


title: Lung MSC membrane-bound TdTomato #1

description:
Library name: mT_1
mT_1_counts


title: J1 primed, Tri-C Enhancer pool2, rep 3

status: Public on Sep 21 2025

city: Goettingen

first: Dimitra

last: Tsouraki

state: Lower Saxony

address: Am Fassberg 11

institute: Max Planck Institute for Multidisciplinary Sciences

description:
Library name: Sample 12
viewpoint: enhancer captured with pool 2 oligos

data_processing:
Tri-C data were analyzed using the CapCruncher pipeline (Downes, D. J. et al., 2022) in capture mode.
Custom python scripts from Karpinska, A. M. & Zhu, Y. et al., 2025 were used to extract reads with two or more reporters in cis and these reads were used to calculate multi-way interaction counts for every viewpoint.
Assembly: mm10
Supplementary files format and content: txt files: the genomic cooridnates and the read counts of the restriction fragments interacting with the viewpoints.

source_name: J1 Mouse embryonic stem cell line

extract_protocol:
Tri-C experiments were performed in 3 biological replicates according to the published protocol by Downes, D. J. et al., 2022
Tri-C experiments were performed in 3 biological replicates according to the published protocol by Downes, D. J. et al., 2022. Two pools of biotinylated oligos, each targeting a distinct set of viewpoints, were used for capture.

value: J1 Mouse embryonic stem cell line

value: primed, biological replicate 3


title: J1 primed, Tri-C Enhancer pool2, rep 2

description:
Library name: Sample 11
viewpoint: enhancer captured with pool 2 oligos

value: primed, biological replicate 2


title: J1 primed, Tri-C Enhancer pool2, rep 1

description:
Library name: Sample 10
viewpoint: enhancer captured with pool 2 oligos

value: primed, biological replicate 1


title: J1 naive, Tri-C Enhancer pool2, rep 3

description:
Library name: Sample 9
viewpoint: enhancer captured with pool 2 oligos

value: naïve, biological replicate 3


title: J1 naive, Tri-C Enhancer pool2, rep 2

description:
Library name: Sample 8
viewpoint: enhancer captured with pool 2 oligos

value: naïve, biological replicate 2


title: J1 naive, Tri-C Enhancer pool2, rep 1

description:
Library name: Sample 7
viewpoint: enhancer captured with pool 2 oligos

value: naïve, biological replicate 1


title: Lung MSC membrane-bound Green Fluorescent Protein #3

description:
Library name: mG_3
mG_3_counts


title: J1 primed, Tri-C Enhancer pool1, rep 3

description:
Library name: Sample 6
viewpoint: enhancer captured with pool 1 oligos


title: J1 primed, Tri-C Enhancer pool1, rep 1

description:
Library name: Sample 4
viewpoint: enhancer captured with pool 1 oligos


title: J1 primed, Tri-C Enhancer pool1, rep 2

description:
Library name: Sample 5
viewpoint: enhancer captured with pool 1 oligos


title: J1 naive, Tri-C Enhancer pool1, rep 3

description:
Library name: Sample 3
viewpoint: enhancer captured with pool 1 oligos


title: J1 naive, Tri-C Enhancer pool1, rep 2

description:
Library name: Sample 2
viewpoint: enhancer captured with pool 1 oligos


title: J1 naive, Tri-C Enhancer pool1, rep 1

description:
Library name: Sample 1
viewpoint: enhancer captured with pool 1 oligos


title: Lung MSC membrane-bound TdTomato #3

description:
Library name: mT_3
mT_3_counts


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H11

city: leuven

first: Danie

last: Daaboul

address: Herestraat 49

department: Department of Neuroscience

country: Belgium

institute: KU Leuven

description:
Library name: 4518_S1_SMART_H11
Smart-seq2

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

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

value: granule cells


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H3

description:
Library name: 4518_S1_SMART_H3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H8

description:
Library name: 4518_S1_SMART_H8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H6

description:
Library name: 4518_S1_SMART_H6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H2

description:
Library name: 4518_S1_SMART_H2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H7

description:
Library name: 4518_S1_SMART_H7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H9

description:
Library name: 4518_S1_SMART_H9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H1

description:
Library name: 4518_S1_SMART_H1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H10

description:
Library name: 4518_S1_SMART_H10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H12

description:
Library name: 4518_S1_SMART_H12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G8

description:
Library name: 4518_S1_SMART_G8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H5

description:
Library name: 4518_S1_SMART_H5
Smart-seq2


title: WT, EPSC


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_H4

description:
Library name: 4518_S1_SMART_H4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G9

description:
Library name: 4518_S1_SMART_G9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G7

description:
Library name: 4518_S1_SMART_G7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G6

description:
Library name: 4518_S1_SMART_G6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G3

description:
Library name: 4518_S1_SMART_G3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G5

description:
Library name: 4518_S1_SMART_G5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G4

description:
Library name: 4518_S1_SMART_G4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G1

description:
Library name: 4518_S1_SMART_G1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G2

description:
Library name: 4518_S1_SMART_G2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G12

description:
Library name: 4518_S1_SMART_G12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G11

description:
Library name: 4518_S1_SMART_G11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_G10

description:
Library name: 4518_S1_SMART_G10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F8

description:
Library name: 4518_S1_SMART_F8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F9

description:
Library name: 4518_S1_SMART_F9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F7

description:
Library name: 4518_S1_SMART_F7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F6

description:
Library name: 4518_S1_SMART_F6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F5

description:
Library name: 4518_S1_SMART_F5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E9

description:
Library name: 4518_S1_SMART_E9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E3

description:
Library name: 4518_S1_SMART_E3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F11

description:
Library name: 4518_S1_SMART_F11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E2

description:
Library name: 4518_S1_SMART_E2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E6

description:
Library name: 4518_S1_SMART_E6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F3

description:
Library name: 4518_S1_SMART_F3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E12

description:
Library name: 4518_S1_SMART_E12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F1

description:
Library name: 4518_S1_SMART_F1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F2

description:
Library name: 4518_S1_SMART_F2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F12

description:
Library name: 4518_S1_SMART_F12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F10

description:
Library name: 4518_S1_SMART_F10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E4

description:
Library name: 4518_S1_SMART_E4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E10

description:
Library name: 4518_S1_SMART_E10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D9

description:
Library name: 4518_S1_SMART_D9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D7

description:
Library name: 4518_S1_SMART_D7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D6

description:
Library name: 4518_S1_SMART_D6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D4

description:
Library name: 4518_S1_SMART_D4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D8

description:
Library name: 4518_S1_SMART_D8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E11

description:
Library name: 4518_S1_SMART_E11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D2

description:
Library name: 4518_S1_SMART_D2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D3

description:
Library name: 4518_S1_SMART_D3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D5

description:
Library name: 4518_S1_SMART_D5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E1

description:
Library name: 4518_S1_SMART_E1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D12

description:
Library name: 4518_S1_SMART_D12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E5

description:
Library name: 4518_S1_SMART_E5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D1

description:
Library name: 4518_S1_SMART_D1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_F4

description:
Library name: 4518_S1_SMART_F4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D11

description:
Library name: 4518_S1_SMART_D11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E8

description:
Library name: 4518_S1_SMART_E8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_E7

description:
Library name: 4518_S1_SMART_E7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_D10

description:
Library name: 4518_S1_SMART_D10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C9

description:
Library name: 4518_S1_SMART_C9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C7

description:
Library name: 4518_S1_SMART_C7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C5

description:
Library name: 4518_S1_SMART_C5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C4

description:
Library name: 4518_S1_SMART_C4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B9

description:
Library name: 4518_S1_SMART_B9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B8

description:
Library name: 4518_S1_SMART_B8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C3

description:
Library name: 4518_S1_SMART_C3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C11

description:
Library name: 4518_S1_SMART_C11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C10

description:
Library name: 4518_S1_SMART_C10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C12

description:
Library name: 4518_S1_SMART_C12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C2

description:
Library name: 4518_S1_SMART_C2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B7

description:
Library name: 4518_S1_SMART_B7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B5

description:
Library name: 4518_S1_SMART_B5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B3

description:
Library name: 4518_S1_SMART_B3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B1

description:
Library name: 4518_S1_SMART_B1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B6

description:
Library name: 4518_S1_SMART_B6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B11

description:
Library name: 4518_S1_SMART_B11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A8

description:
Library name: 4518_S1_SMART_A8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B4

description:
Library name: 4518_S1_SMART_B4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A9

description:
Library name: 4518_S1_SMART_A9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A7

description:
Library name: 4518_S1_SMART_A7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C8

description:
Library name: 4518_S1_SMART_C8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A5

description:
Library name: 4518_S1_SMART_A5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B2

description:
Library name: 4518_S1_SMART_B2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A6

description:
Library name: 4518_S1_SMART_A6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C6

description:
Library name: 4518_S1_SMART_C6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A3

description:
Library name: 4518_S1_SMART_A3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A11

description:
Library name: 4518_S1_SMART_A11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A4

description:
Library name: 4518_S1_SMART_A4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A1

description:
Library name: 4518_S1_SMART_A1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_C1

description:
Library name: 4518_S1_SMART_C1
Smart-seq2


title: WT M AB DIF 3

city: Richardson

first: Adedamola

middle: Saidi

last: Soladogun

state: Texas

address: 800 W Campbell Rd

department: Biological Sciences

institute: University of Texas at Dallas

description:
Library name: WT M AB DIF_3
Column name in PSENvControl de_summary.csv: WT M AB DIF_3

data_processing:
Raw sequencing data quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).Adapter sequences and low-quality bases were trimmed using CUTADAPT.
Reads were aligned to the human reference genome (GRCh38) using the STAR aligner with default parameters. The average mapping rate was approximately 85–90%.
Gene expression quantification was performed using featureCounts to generate raw count matrices.
Differential gene expression analysis was conducted using DESeq2 in R. Genes with an adjusted p-value < 0.05 and log₂ fold change > 0.8 or < -0.8 were considered differentially expressed.
Gene Ontology (GO) analysis was conducted using DAVID (https://david.ncifcrf.gov/) and STRING (https://string-db.org/) to identify enriched biological pathways.
Assembly: GRCh38
Supplementary files format and content: Normalized expression values (FPKM) were provided in separate CSV files for each sample.

source_name: Brain

growth_protocol: Neural stem cells were derived from induced pluripotent stem cells (iPSCs) of EOAD, LOAD, and WT donors. Cells were cultured in 6-well plates with DMEM/F12 medium supplemented with 1% N2 supplement, 2% B27 supplement, 20 ng/mL EGF, and 20 ng/mL FGF2. Plates were maintained in a humidified atmosphere of 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted using the SPLIT Total RNA Kit (Lexogen) following the manufacturer’s protocol. RNA was quantified using a Nanodrop spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer. RNA samples with RIN > 7 were used for downstream library preparation.
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) following the manufacturer’s instructions. Approximately 40 ng of total RNA was used for library preparation, which included poly-A selection, cDNA synthesis, and library amplification using indexed primers.

treatment_protocol: Undifferentiated Samples (UD): Cells were collected after 1 day of culture in the neural stem cell medium described above.Differentiated Samples (DIF): Cells were cultured for 35 days in differentiation medium (DMEM/F12 supplemented with 1% N2, 2% B27, and 20 ng/mL BDNF).Aβ Treatment (DIF + Aβ): For WT DIF samples, oligomeric Aβ (0.5 µM) was applied for 24 hours before collection.

value: Brain

value: Neural stem cells

value: Differentiated + Abeta

value: Male

value: DIF (35 days)+ Abeta  (24 hr)


title: WT M DIF 3

description:
Library name: WT M DIF_3
Column name in PSENvControl de_summary.csv: WT M DIF_3

value: Differentiated

value: WT

value: DIF (35 days)


title: WT M AB DIF 1

description:
Library name: WT M AB DIF_1
Column name in PSENvControl de_summary.csv: WT M AB DIF_1


title: WT M DIF 2

description:
Library name: WT M DIF_2
Column name in PSENvControl de_summary.csv: WT M DIF_2


title: WT M AB DIF 2

description:
Library name: WT M AB DIF_2
Column name in PSENvControl de_summary.csv: WT M AB DIF_2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B12

description:
Library name: 4518_S1_SMART_B12
Smart-seq2


title: WT M DIF 1

description:
Library name: WT M DIF_1
Column name in PSENvControl de_summary.csv: WT M DIF_1


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_B10

description:
Library name: 4518_S1_SMART_B10
Smart-seq2


title: WT M UD Control 3

description:
Library name: WT M UD Control_3
Column name in PSENvControl de_summary.csv: WT M UD Control_3

value: Undifferentiated

value: UD (1 day)


title: WT M UD Control 2

description:
Library name: WT M UD Control_2
Column name in PSENvControl de_summary.csv: WT M UD Control_2


title: WT M UD Control 1

description:
Library name: WT M UD Control_1
Column name in PSENvControl de_summary.csv: WT M UD Control_1


title: AD UD PSEN1 3

description:
Library name: AD UD PSEN_3
Column name in PSENvControl de_summary.csv: AD UD PSEN1_3


title: AD UD PSEN1 2

description:
Library name: AD UD PSEN_2
Column name in PSENvControl de_summary.csv: AD UD PSEN1_2


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A2

description:
Library name: 4518_S1_SMART_A2
Smart-seq2


title: AD UD PSEN1 1

description:
Library name: AD UD PSEN_1
Column name in PSENvControl de_summary.csv: AD UD PSEN1_1


title: AD DIF PSEN1 2

description:
Library name: AD DIF PSEN1_2
Column name in PSENvControl de_summary.csv: AD DIF PSEN1_2


title: AD DIF PSEN1 3

description:
Library name: AD DIF PSEN1_3
Column name in PSENvControl de_summary.csv: AD DIF PSEN1_3


title: WT F AB DIF 4

description:
Library name: WT F AB DIF_4
Column name in ApoEvcontrol de_summary.csv: WT F AB DIF_4

value: Female


title: WT F AB DIF 3

description:
Library name: WT F AB DIF_3
Column name in ApoEvcontrol de_summary.csv: WT F AB DIF_3


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A12

description:
Library name: 4518_S1_SMART_A12
Smart-seq2


title: AD DIF PSEN1 1

description:
Library name: AD DIF PSEN1_1
Column name in PSENvControl de_summary.csv: AD DIF PSEN1_1


title: WT F AB DIF 2

description:
Library name: WT F AB DIF_2
Column name in ApoEvcontrol de_summary.csv: WT F AB DIF_2


title: WT F AB DIF 1

description:
Library name: WT F AB DIF_1
Column name in ApoEvcontrol de_summary.csv: WT F AB DIF_1


title: WT F DIF 3

description:
Library name: WT F DIF_3
Column name in ApoEvcontrol de_summary.csv: WT F DIF_3


title: GCs, Rbp4-Cre, SS2, DG_P28_E4_A10

description:
Library name: 4518_S1_SMART_A10
Smart-seq2


title: WT F UD Control 2

description:
Library name: WT F UD Control_2
Column name in ApoEvcontrol de_summary.csv: WT F UD Control_2


title: WT F DIF 1

description:
Library name: WT F DIF_1
Column name in ApoEvcontrol de_summary.csv: WT F DIF_1


title: WT F UD Control 3

description:
Library name: WT F UD Control_3
Column name in ApoEvcontrol de_summary.csv: WT F UD Control_3


title: AD UD APOE 1

description:
Library name: AD UD APOE_1
Column name in ApoEvcontrol de_summary.csv: AD UD APOE_1

value: APOE


title: AD UD APOE 3

description:
Library name: AD UD APOE_3
Column name in ApoEvcontrol de_summary.csv: AD UD APOE_3


title: AD DIF APOE 3

description:
Library name: AD DIF APOE_3
Column name in ApoEvcontrol de_summary.csv: AD DIF APOE_3


title: AD UD APOE 2

description:
Library name: AD UD APOE_2
Column name in ApoEvcontrol de_summary.csv: AD UD APOE_2


title: AD DIF APOE 2

description:
Library name: AD DIF APOE_2
Column name in ApoEvcontrol de_summary.csv: AD DIF APOE_2


title: AD DIF APOE 1

description:
Library name: AD DIF APOE_1
Column name in ApoEvcontrol de_summary.csv: AD DIF APOE_1


title: NC_2_RNA

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: NC_3_RNA


title: MO_3_RNA

value: dnmt3ba knockdown


title: AD UD PSEN1 4

description:
Library name: AD UD PSEN_4
Column name in PSENvControl de_summary.csv: AD UD PSEN1_4


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H9

description:
Library name: H9_4229-S1-SMART_S93
Smart-seq2

value: hippocampus


title: MO_1_RNA


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H8

description:
Library name: H8_4229-S1-SMART_S92
Smart-seq2

value: granule cells


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H6

description:
Library name: H6_4229-S1-SMART_S90
Smart-seq2


title: WT F DIF 2

description:
Library name: WT F DIF_2
Column name in ApoEvcontrol de_summary.csv: WT F DIF_2

value: Brain


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H7

description:
Library name: H7_4229-S1-SMART_S91
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H5

description:
Library name: H5_4229-S1-SMART_S89
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H3

description:
Library name: H3_4229-S1-SMART_S87
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H11

description:
Library name: H11_4229-S1-SMART_S95
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H2

description:
Library name: H2_4229-S1-SMART_S86
Smart-seq2


title: WT F UD Control 1

description:
Library name: WT F UD Control_1
Column name in ApoEvcontrol de_summary.csv: WT F UD Control_1

value: Neural stem cells


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H12

description:
Library name: H12_4229-S1-SMART_S96
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H4

description:
Library name: H4_4229-S1-SMART_S88
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H1

description:
Library name: H1_4229-S1-SMART_S85
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G9

description:
Library name: G9_4229-S1-SMART_S81
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G7

description:
Library name: G7_4229-S1-SMART_S79
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_H10

description:
Library name: H10_4229-S1-SMART_S94
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G6

description:
Library name: G6_4229-S1-SMART_S78
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G8

description:
Library name: G8_4229-S1-SMART_S80
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G4

description:
Library name: G4_4229-S1-SMART_S76
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G3

description:
Library name: G3_4229-S1-SMART_S75
Smart-seq2


title: NC_1_RNA


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G2

description:
Library name: G2_4229-S1-SMART_S74
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G5

description:
Library name: G5_4229-S1-SMART_S77
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G11

description:
Library name: G11_4229-S1-SMART_S83
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G1

description:
Library name: G1_4229-S1-SMART_S73
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G10

description:
Library name: G10_4229-S1-SMART_S82
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F9

description:
Library name: F9_4229-S1-SMART_S69
Smart-seq2


title: MO_2_RNA


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F8

description:
Library name: F8_4229-S1-SMART_S68
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F6

description:
Library name: F6_4229-S1-SMART_S66
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F7

description:
Library name: F7_4229-S1-SMART_S67
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F5

description:
Library name: F5_4229-S1-SMART_S65
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F3

description:
Library name: F3_4229-S1-SMART_S63
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F4

description:
Library name: F4_4229-S1-SMART_S64
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F1

description:
Library name: F1_4229-S1-SMART_S61
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F2

description:
Library name: F2_4229-S1-SMART_S62
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F11

description:
Library name: F11_4229-S1-SMART_S71
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E9

description:
Library name: E9_4229-S1-SMART_S57
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F12

description:
Library name: F12_4229-S1-SMART_S72
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_F10

description:
Library name: F10_4229-S1-SMART_S70
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E6

description:
Library name: E6_4229-S1-SMART_S54
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E3

description:
Library name: E3_4229-S1-SMART_S51
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E5

description:
Library name: E5_4229-S1-SMART_S53
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_G12

description:
Library name: G12_4229-S1-SMART_S84
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E11

description:
Library name: E11_4229-S1-SMART_S59
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E4

description:
Library name: E4_4229-S1-SMART_S52
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E7

description:
Library name: E7_4229-S1-SMART_S55
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E1

description:
Library name: E1_4229-S1-SMART_S49
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E12

description:
Library name: E12_4229-S1-SMART_S60
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D9

description:
Library name: D9_4229-S1-SMART_S45
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D8

description:
Library name: D8_4229-S1-SMART_S44
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E10

description:
Library name: E10_4229-S1-SMART_S58
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D4

description:
Library name: D4_4229-S1-SMART_S40
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D7

description:
Library name: D7_4229-S1-SMART_S43
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D5

description:
Library name: D5_4229-S1-SMART_S41
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D1

description:
Library name: D1_4229-S1-SMART_S37
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D2

description:
Library name: D2_4229-S1-SMART_S38
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D11

description:
Library name: D11_4229-S1-SMART_S47
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D6

description:
Library name: D6_4229-S1-SMART_S42
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D12

description:
Library name: D12_4229-S1-SMART_S48
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D10

description:
Library name: D10_4229-S1-SMART_S46
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E8

description:
Library name: E8_4229-S1-SMART_S56
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_D3

description:
Library name: D3_4229-S1-SMART_S39
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C8

description:
Library name: C8_4229-S1-SMART_S32
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C9

description:
Library name: C9_4229-S1-SMART_S33
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C7

description:
Library name: C7_4229-S1-SMART_S31
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C5

description:
Library name: C5_4229-S1-SMART_S29
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C6

description:
Library name: C6_4229-S1-SMART_S30
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_E2

description:
Library name: E2_4229-S1-SMART_S50
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C3

description:
Library name: C3_4229-S1-SMART_S27
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C2

description:
Library name: C2_4229-S1-SMART_S26
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C4

description:
Library name: C4_4229-S1-SMART_S28
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C1

description:
Library name: C1_4229-S1-SMART_S25
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C12

description:
Library name: C12_4229-S1-SMART_S36
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B8

description:
Library name: B8_4229-S1-SMART_S20
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B9

description:
Library name: B9_4229-S1-SMART_S21
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C10

description:
Library name: C10_4229-S1-SMART_S34
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B5

description:
Library name: B5_4229-S1-SMART_S17
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B6

description:
Library name: B6_4229-S1-SMART_S18
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B7

description:
Library name: B7_4229-S1-SMART_S19
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B4

description:
Library name: B4_4229-S1-SMART_S16
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_C11

description:
Library name: C11_4229-S1-SMART_S35
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B1

description:
Library name: B1_4229-S1-SMART_S13
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B2

description:
Library name: B2_4229-S1-SMART_S14
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B3

description:
Library name: B3_4229-S1-SMART_S15
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B12

description:
Library name: B12_4229-S1-SMART_S24
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B10

description:
Library name: B10_4229-S1-SMART_S22
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A7

description:
Library name: A7_4229-S1-SMART_S7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A8

description:
Library name: A8_4229-S1-SMART_S8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A9

description:
Library name: A9_4229-S1-SMART_S9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A5

description:
Library name: A5_4229-S1-SMART_S5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A6

description:
Library name: A6_4229-S1-SMART_S6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A4

description:
Library name: A4_4229-S1-SMART_S4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A3

description:
Library name: A3_4229-S1-SMART_S3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A2

description:
Library name: A2_4229-S1-SMART_S2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A1

description:
Library name: A1_4229-S1-SMART_S1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A11

description:
Library name: A11_4229-S1-SMART_S11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A12

description:
Library name: A12_4229-S1-SMART_S12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_A10

description:
Library name: A10_4229-S1-SMART_S10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H7

description:
Library name: 4032-S4-SMART_H7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H8

description:
Library name: 4032-S4-SMART_H8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H5

description:
Library name: 4032-S4-SMART_H5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H4

description:
Library name: 4032-S4-SMART_H4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H6

description:
Library name: 4032-S4-SMART_H6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H3

description:
Library name: 4032-S4-SMART_H3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H1

description:
Library name: 4032-S4-SMART_H1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H11

description:
Library name: 4032-S4-SMART_H11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H2

description:
Library name: 4032-S4-SMART_H2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G9

description:
Library name: 4032-S4-SMART_G9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H12

description:
Library name: 4032-S4-SMART_H12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H10

description:
Library name: 4032-S4-SMART_H10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G7

description:
Library name: 4032-S4-SMART_G7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G8

description:
Library name: 4032-S4-SMART_G8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P28_E3_B11

description:
Library name: B11_4229-S1-SMART_S23
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G6

description:
Library name: 4032-S4-SMART_G6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G5

description:
Library name: 4032-S4-SMART_G5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G3

description:
Library name: 4032-S4-SMART_G3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G4

description:
Library name: 4032-S4-SMART_G4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G1

description:
Library name: 4032-S4-SMART_G1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G12

description:
Library name: 4032-S4-SMART_G12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G11

description:
Library name: 4032-S4-SMART_G11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G10

description:
Library name: 4032-S4-SMART_G10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F9

description:
Library name: 4032-S4-SMART_F9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F7

description:
Library name: 4032-S4-SMART_F7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_H9

description:
Library name: 4032-S4-SMART_H9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F6

description:
Library name: 4032-S4-SMART_F6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F4

description:
Library name: 4032-S4-SMART_F4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F5

description:
Library name: 4032-S4-SMART_F5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F3

description:
Library name: 4032-S4-SMART_F3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F2

description:
Library name: 4032-S4-SMART_F2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F1

description:
Library name: 4032-S4-SMART_F1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F12

description:
Library name: 4032-S4-SMART_F12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F11

description:
Library name: 4032-S4-SMART_F11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E9

description:
Library name: 4032-S4-SMART_E9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E5

description:
Library name: 4032-S4-SMART_E5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E4

description:
Library name: 4032-S4-SMART_E4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E7

description:
Library name: 4032-S4-SMART_E7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E8

description:
Library name: 4032-S4-SMART_E8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_G2

description:
Library name: 4032-S4-SMART_G2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E2

description:
Library name: 4032-S4-SMART_E2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E3

description:
Library name: 4032-S4-SMART_E3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E12

description:
Library name: 4032-S4-SMART_E12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E10

description:
Library name: 4032-S4-SMART_E10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F8

description:
Library name: 4032-S4-SMART_F8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D9

description:
Library name: 4032-S4-SMART_D9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E1

description:
Library name: 4032-S4-SMART_E1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D8

description:
Library name: 4032-S4-SMART_D8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D7

description:
Library name: 4032-S4-SMART_D7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D5

description:
Library name: 4032-S4-SMART_D5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D3

description:
Library name: 4032-S4-SMART_D3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D2

description:
Library name: 4032-S4-SMART_D2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D4

description:
Library name: 4032-S4-SMART_D4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D6

description:
Library name: 4032-S4-SMART_D6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D12

description:
Library name: 4032-S4-SMART_D12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D11

description:
Library name: 4032-S4-SMART_D11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D10

description:
Library name: 4032-S4-SMART_D10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_F10

description:
Library name: 4032-S4-SMART_F10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C9

description:
Library name: 4032-S4-SMART_C9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C8

description:
Library name: 4032-S4-SMART_C8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E6

description:
Library name: 4032-S4-SMART_E6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C6

description:
Library name: 4032-S4-SMART_C6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C3

description:
Library name: 4032-S4-SMART_C3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C5

description:
Library name: 4032-S4-SMART_C5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C4

description:
Library name: 4032-S4-SMART_C4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C7

description:
Library name: 4032-S4-SMART_C7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C1

description:
Library name: 4032-S4-SMART_C1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_E11

description:
Library name: 4032-S4-SMART_E11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C2

description:
Library name: 4032-S4-SMART_C2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B5

description:
Library name: 4032-S4-SMART_B5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C12

description:
Library name: 4032-S4-SMART_C12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B9

description:
Library name: 4032-S4-SMART_B9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B8

description:
Library name: 4032-S4-SMART_B8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B6

description:
Library name: 4032-S4-SMART_B6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B3

description:
Library name: 4032-S4-SMART_B3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B7

description:
Library name: 4032-S4-SMART_B7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_D1

description:
Library name: 4032-S4-SMART_D1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B1

description:
Library name: 4032-S4-SMART_B1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B4

description:
Library name: 4032-S4-SMART_B4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B2

description:
Library name: 4032-S4-SMART_B2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B11

description:
Library name: 4032-S4-SMART_B11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B12

description:
Library name: 4032-S4-SMART_B12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_B10

description:
Library name: 4032-S4-SMART_B10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A7

description:
Library name: 4032-S4-SMART_A7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C11

description:
Library name: 4032-S4-SMART_C11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A9

description:
Library name: 4032-S4-SMART_A9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A4

description:
Library name: 4032-S4-SMART_A4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A5

description:
Library name: 4032-S4-SMART_A5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A3

description:
Library name: 4032-S4-SMART_A3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A6

description:
Library name: 4032-S4-SMART_A6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_C10

description:
Library name: 4032-S4-SMART_C10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A1

description:
Library name: 4032-S4-SMART_A1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A12

description:
Library name: 4032-S4-SMART_A12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A11

description:
Library name: 4032-S4-SMART_A11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A2

description:
Library name: 4032-S4-SMART_A2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A10

description:
Library name: 4032-S4-SMART_A10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H9

description:
Library name: 20210421_Blanca_Plate2_H9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H7

description:
Library name: 20210421_Blanca_Plate2_H7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H8

description:
Library name: 20210421_Blanca_Plate2_H8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H2

description:
Library name: 20210421_Blanca_Plate2_H2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H4

description:
Library name: 20210421_Blanca_Plate2_H4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H5

description:
Library name: 20210421_Blanca_Plate2_H5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H1

description:
Library name: 20210421_Blanca_Plate2_H1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H3

description:
Library name: 20210421_Blanca_Plate2_H3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H6

description:
Library name: 20210421_Blanca_Plate2_H6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H10

description:
Library name: 20210421_Blanca_Plate2_H10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P7_A8

description:
Library name: 4032-S4-SMART_A8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G9

description:
Library name: 20210421_Blanca_Plate2_G9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H11

description:
Library name: 20210421_Blanca_Plate2_H11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G8

description:
Library name: 20210421_Blanca_Plate2_G8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G7

description:
Library name: 20210421_Blanca_Plate2_G7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G6

description:
Library name: 20210421_Blanca_Plate2_G6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G1

description:
Library name: 20210421_Blanca_Plate2_G1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G5

description:
Library name: 20210421_Blanca_Plate2_G5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_H12

description:
Library name: 20210421_Blanca_Plate2_H12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G12

description:
Library name: 20210421_Blanca_Plate2_G12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G11

description:
Library name: 20210421_Blanca_Plate2_G11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G2

description:
Library name: 20210421_Blanca_Plate2_G2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G4

description:
Library name: 20210421_Blanca_Plate2_G4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G3

description:
Library name: 20210421_Blanca_Plate2_G3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_G10

description:
Library name: 20210421_Blanca_Plate2_G10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F3

description:
Library name: 20210421_Blanca_Plate2_F3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E8

description:
Library name: 20210421_Blanca_Plate2_E8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F8

description:
Library name: 20210421_Blanca_Plate2_F8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F10

description:
Library name: 20210421_Blanca_Plate2_F10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E6

description:
Library name: 20210421_Blanca_Plate2_E6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F9

description:
Library name: 20210421_Blanca_Plate2_F9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E5

description:
Library name: 20210421_Blanca_Plate2_E5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F4

description:
Library name: 20210421_Blanca_Plate2_F4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F12

description:
Library name: 20210421_Blanca_Plate2_F12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F6

description:
Library name: 20210421_Blanca_Plate2_F6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F5

description:
Library name: 20210421_Blanca_Plate2_F5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F1

description:
Library name: 20210421_Blanca_Plate2_F1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F7

description:
Library name: 20210421_Blanca_Plate2_F7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F11

description:
Library name: 20210421_Blanca_Plate2_F11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E1

description:
Library name: 20210421_Blanca_Plate2_E1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_F2

description:
Library name: 20210421_Blanca_Plate2_F2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E3

description:
Library name: 20210421_Blanca_Plate2_E3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E4

description:
Library name: 20210421_Blanca_Plate2_E4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E2

description:
Library name: 20210421_Blanca_Plate2_E2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E12

description:
Library name: 20210421_Blanca_Plate2_E12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E10

description:
Library name: 20210421_Blanca_Plate2_E10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E11

description:
Library name: 20210421_Blanca_Plate2_E11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D9

description:
Library name: 20210421_Blanca_Plate2_D9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D7

description:
Library name: 20210421_Blanca_Plate2_D7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D6

description:
Library name: 20210421_Blanca_Plate2_D6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D5

description:
Library name: 20210421_Blanca_Plate2_D5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E7

description:
Library name: 20210421_Blanca_Plate2_E7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_E9

description:
Library name: 20210421_Blanca_Plate2_E9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D4

description:
Library name: 20210421_Blanca_Plate2_D4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D11

description:
Library name: 20210421_Blanca_Plate2_D11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C8

description:
Library name: 20210421_Blanca_Plate2_C8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D2

description:
Library name: 20210421_Blanca_Plate2_D2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D10

description:
Library name: 20210421_Blanca_Plate2_D10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C6

description:
Library name: 20210421_Blanca_Plate2_C6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C3

description:
Library name: 20210421_Blanca_Plate2_C3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C9

description:
Library name: 20210421_Blanca_Plate2_C9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C7

description:
Library name: 20210421_Blanca_Plate2_C7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C12

description:
Library name: 20210421_Blanca_Plate2_C12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C5

description:
Library name: 20210421_Blanca_Plate2_C5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C2

description:
Library name: 20210421_Blanca_Plate2_C2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D1

description:
Library name: 20210421_Blanca_Plate2_D1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D3

description:
Library name: 20210421_Blanca_Plate2_D3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B9

description:
Library name: 20210421_Blanca_Plate2_B9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D12

description:
Library name: 20210421_Blanca_Plate2_D12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B8

description:
Library name: 20210421_Blanca_Plate2_B8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B7

description:
Library name: 20210421_Blanca_Plate2_B7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C11

description:
Library name: 20210421_Blanca_Plate2_C11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_D8

description:
Library name: 20210421_Blanca_Plate2_D8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B6

description:
Library name: 20210421_Blanca_Plate2_B6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B4

description:
Library name: 20210421_Blanca_Plate2_B4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B3

description:
Library name: 20210421_Blanca_Plate2_B3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B2

description:
Library name: 20210421_Blanca_Plate2_B2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B1

description:
Library name: 20210421_Blanca_Plate2_B1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B12

description:
Library name: 20210421_Blanca_Plate2_B12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B11

description:
Library name: 20210421_Blanca_Plate2_B11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C4

description:
Library name: 20210421_Blanca_Plate2_C4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C1

description:
Library name: 20210421_Blanca_Plate2_C1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_C10

description:
Library name: 20210421_Blanca_Plate2_C10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A6

description:
Library name: 20210421_Blanca_Plate2_A6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A7

description:
Library name: 20210421_Blanca_Plate2_A7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A1

description:
Library name: 20210421_Blanca_Plate2_A1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A4

description:
Library name: 20210421_Blanca_Plate2_A4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B10

description:
Library name: 20210421_Blanca_Plate2_B10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A11

description:
Library name: 20210421_Blanca_Plate2_A11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A3

description:
Library name: 20210421_Blanca_Plate2_A3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A12

description:
Library name: 20210421_Blanca_Plate2_A12
Smart-seq2


title: ChIP-seq_WT_Th2_Bhlhe40_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.
Assembly: mm10
Supplementary files format and content: BigWig files for ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided.

source_name: peripheral lymph nodes

growth_protocol: T helper subsets were cultured or sorted in complete T cell medium with 10% FBS.

extract_protocol:
All the cell subsets were harvested by cell sorting after staining.
The total RNAs were harvested and purified by using Qiagen’s miRNeasy micro kit (217084; Qiagen). Qiagen’s DNase set (79254; Qiagen) was used for on-column DNase digestion. PolyA-tailed RNAs were purified from total RNA by using Dynabeads mRNA DIR ECT kit (61012; Ambion Life Technologies). The RNA-Seq libraries were sequenced with Illumina HiSeq system, and 50 bp reads were generated by the National Heart, Lung, and Blood Institute DNA Sequencing Core.
ChIP-seq and RNA-seq

treatment_protocol: T helper subsets in vitro were cultured in indicated conditions (Th1, Th2, Th17, iTreg). AS15-specific cells from draining lymph nodes in vivo were sorted from mice which had been immunized with AS15/CFA for two weeks, and were further identified by tetramer staining.

value: peripheral lymph nodes


title: GCs, Rbp4-Cre, SS2, DG_P15_A9

description:
Library name: 20210421_Blanca_Plate2_A9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A5

description:
Library name: 20210421_Blanca_Plate2_A5
Smart-seq2


title: ChIP-seq_Bcells_WT

source_name: spleen

value: B cells

value: spleen


title: GCs, Rbp4-Cre, SS2, DG_P15_A8

description:
Library name: 20210421_Blanca_Plate2_A8
Smart-seq2


title: ChIP-seq_WT_Th17_Bhlhe40_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_H9

description:
Library name: 20210417_Blanca_Plate3_H9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H8

description:
Library name: 20210417_Blanca_Plate3_H8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_B5

description:
Library name: 20210421_Blanca_Plate2_B5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H7

description:
Library name: 20210417_Blanca_Plate3_H7
Smart-seq2


title: ChIP-seq_Bcells_Pou2af1-HA-TG


title: ChIP-seq_WT_Th17_Bhlhe40_rep1


title: ChIP-seq_WT_Th1_Bhlhe40_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_H5

description:
Library name: 20210417_Blanca_Plate3_H5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H6

description:
Library name: 20210417_Blanca_Plate3_H6
Smart-seq2


title: ChIP-seq_WT_Th1_Bhlhe40_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_H4

description:
Library name: 20210417_Blanca_Plate3_H4
Smart-seq2


title: ChIP-seq_WT_iTreg_Bhlhe40_rep2

value: iTreg


title: GCs, Rbp4-Cre, SS2, DG_P15_A2

description:
Library name: 20210421_Blanca_Plate2_A2
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H3

description:
Library name: 20210417_Blanca_Plate3_H3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P15_A10

description:
Library name: 20210421_Blanca_Plate2_A10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H2

description:
Library name: 20210417_Blanca_Plate3_H2
Smart-seq2


title: RNA-seq_Bhlhe40_KO_Th2_rep2


title: ChIP-seq_WT_Th2_Bhlhe40_rep1

value: WT


title: RNA-seq_Bhlhe40_KO_Th2_rep1


title: RNA-seq_Bhlhe40_KO_Th17_rep1


title: RNA-seq_Bhlhe40_KO_Th17_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_H1

description:
Library name: 20210417_Blanca_Plate3_H1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_G9

description:
Library name: 20210417_Blanca_Plate3_G9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_H10

description:
Library name: 20210417_Blanca_Plate3_H10
Smart-seq2


title: RNA-seq_Bhlhe40_KO_iTreg_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_H12

description:
Library name: 20210417_Blanca_Plate3_H12
Smart-seq2


title: RNA-seq_Bhlhe40_KO_Th1_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_G8

description:
Library name: 20210417_Blanca_Plate3_G8
Smart-seq2


title: RNA-seq_Bhlhe40_WT_Th2_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_G6

description:
Library name: 20210417_Blanca_Plate3_G6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_G7

description:
Library name: 20210417_Blanca_Plate3_G7
Smart-seq2


title: RNA-seq_Bhlhe40_KO_iTreg_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_G5

description:
Library name: 20210417_Blanca_Plate3_G5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_G4

description:
Library name: 20210417_Blanca_Plate3_G4
Smart-seq2


title: RNA-seq_Bhlhe40_WT_Th2_rep1


title: RNA-seq_Bhlhe40_WT_Th17_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_G3

description:
Library name: 20210417_Blanca_Plate3_G3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_G2

description:
Library name: 20210417_Blanca_Plate3_G2
Smart-seq2


title: ChIP-seq_WT_iTreg_Bhlhe40_rep1


title: RNA-seq_Bhlhe40_WT_Th1_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_G1

description:
Library name: 20210417_Blanca_Plate3_G1
Smart-seq2


title: RNA-seq_Bhlhe40_WT_Th1_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_H11

description:
Library name: 20210417_Blanca_Plate3_H11
Smart-seq2


title: RNA-seq_Bhlhe40_KO_Th1_rep2


title: RNA-seq_Bhlhe40_WT_iTreg_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_G11

description:
Library name: 20210417_Blanca_Plate3_G11
Smart-seq2


title: RNA-seq_Bhlhe40_WT_iTreg_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_F9

description:
Library name: 20210417_Blanca_Plate3_F9
Smart-seq2


title: 22_Bhlhe40_KO-1_CXCR5+PD1+_rep2

source_name: CD4+ Tfh cells

value: draining lymph node


title: 20_Bob1_KO-1_CXCR5+PD1+_rep2


title: 19_Bob1_KO-1_CXCR5+PD1+_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_F6

description:
Library name: 20210417_Blanca_Plate3_F6
Smart-seq2


title: 21_Bhlhe40_KO-1_CXCR5+PD1+_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_F8

description:
Library name: 20210417_Blanca_Plate3_F8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_F5

description:
Library name: 20210417_Blanca_Plate3_F5
Smart-seq2


title: 17_WT-1_CXCR5+PD1+_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_F7

description:
Library name: 20210417_Blanca_Plate3_F7
Smart-seq2


title: RNA-seq_Bhlhe40_WT_Th17_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_F4

description:
Library name: 20210417_Blanca_Plate3_F4
Smart-seq2


title: 14_Bhlhe40_KO-1_CXCR5-PD1+_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_F3

description:
Library name: 20210417_Blanca_Plate3_F3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_F2

description:
Library name: 20210417_Blanca_Plate3_F2
Smart-seq2


title: 13_Bhlhe40_KO-1_CXCR5-PD1+_rep1


title: 12_Bob1_KO-1_CXCR5-PD1+_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_F1

description:
Library name: 20210417_Blanca_Plate3_F1
Smart-seq2


title: 11_Bob1_KO-1_CXCR5-PD1+_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_F12

description:
Library name: 20210417_Blanca_Plate3_F12
Smart-seq2


title: 10_WT-1_CXCR5-PD1+_rep2


title: 9_WT-1_CXCR5-PD1+_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_G12

description:
Library name: 20210417_Blanca_Plate3_G12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_F11

description:
Library name: 20210417_Blanca_Plate3_F11
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_F10

description:
Library name: 20210417_Blanca_Plate3_F10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E9

description:
Library name: 20210417_Blanca_Plate3_E9
Smart-seq2


title: 5_Bhlhe40_KO-1_CXCR5-PD1-_rep1


title: 6_Bhlhe40_KO-1_CXCR5-PD1-_rep2


title: 18_WT-1_CXCR5+PD1+_rep2


title: 4_Bob1_KO-1_CXCR5-PD1-_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_G10

description:
Library name: 20210417_Blanca_Plate3_G10
Smart-seq2


title: 3_Bob1_KO-1_CXCR5-PD1-_rep1


title: 1_WT-1_CXCR5-PD1-_rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_E5

description:
Library name: 20210417_Blanca_Plate3_E5
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E7

description:
Library name: 20210417_Blanca_Plate3_E7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E6

description:
Library name: 20210417_Blanca_Plate3_E6
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E4

description:
Library name: 20210417_Blanca_Plate3_E4
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E3

description:
Library name: 20210417_Blanca_Plate3_E3
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E8

description:
Library name: 20210417_Blanca_Plate3_E8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E2

description:
Library name: 20210417_Blanca_Plate3_E2
Smart-seq2


title: Liver, HFD-PA1-1

city: Nanjing

first: Hao

last: Xie

state: Jiangsu

address: 2#, Sipailou street

institute: Southeast University

data_processing:
The clean reads were subjected to further analysis based on the RNA-seq pipeline, by Bowtie, TopHat, CuffLinks, and CummeRbund software suite. The Cuffdiff program within Cufflinks was used to test for statistically significant differences between groups. The downstream statistical analyses and plots were performed in R.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: xls file include FPKM values for all 8 Samples

source_name: Liver

extract_protocol:
Total RNA was extracted from 100mg mouse liver for each group by using Trizol total RNA isolation reagent (Invitrogen). RNA-seq data were obtained by the service provided by BGI (Shenzhen, China).
Standard RNA-Seq
Enrich mRNA by oligo dT

value: Liver

value: High Fat Food& 1%PA


title: Liver, HFD-PA025-2

value: High Fat Food& 0.25%PA


title: Liver, HFD-PA025-1


title: GCs, Rbp4-Cre, SS2, DG_P10_E12

description:
Library name: 20210417_Blanca_Plate3_E12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E1

description:
Library name: 20210417_Blanca_Plate3_E1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E11

description:
Library name: 20210417_Blanca_Plate3_E11
Smart-seq2


title: Liver, HFD-2

value: High Fat Food


title: Liver, HFD-1


title: Liver, NF-1

value: Normal Food


title: Liver, NF-2


title: GCs, Rbp4-Cre, SS2, DG_P10_D9

description:
Library name: 20210417_Blanca_Plate3_D9
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_D8

description:
Library name: 20210417_Blanca_Plate3_D8
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_E10

description:
Library name: 20210417_Blanca_Plate3_E10
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_D7

description:
Library name: 20210417_Blanca_Plate3_D7
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_D6

description:
Library name: 20210417_Blanca_Plate3_D6
Smart-seq2


title: 2_WT-1_CXCR5-PD1-_rep2


title: Liver, HFD-PA1-2


title: GCs, Rbp4-Cre, SS2, DG_P10_D5

description:
Library name: 20210417_Blanca_Plate3_D5
Smart-seq2


title: input Tet2KO rep2

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

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

molecule: polyA RNA

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). 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.

value: embryonic stem cells

tag: genotype/variation

value: Tet2 KO

tag: antibody


title: m5CIP-seq Tet2KO rep1

value: anti-5mC (Active Motif 39649)


title: input Tet2KO rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_D4

description:
Library name: 20210417_Blanca_Plate3_D4
Smart-seq2

value: hippocampus

value: granule cells


title: GCs, Rbp4-Cre, SS2, DG_P10_D3

description:
Library name: 20210417_Blanca_Plate3_D3
Smart-seq2


title: m5CIP-seq Tet2KO rep2


title: input WT rep2

value: wild type


title: input WT rep1


title: m5CIP-seq WT rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_D2

description:
Library name: 20210417_Blanca_Plate3_D2
Smart-seq2


title: m5CIP-seq WT rep1


title: GCs, Rbp4-Cre, SS2, DG_P10_D1

description:
Library name: 20210417_Blanca_Plate3_D1
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_D12

description:
Library name: 20210417_Blanca_Plate3_D12
Smart-seq2


title: GCs, Rbp4-Cre, SS2, DG_P10_D11

description:
Library name: 20210417_Blanca_Plate3_D11
Smart-seq2


title: V+3W_pulp_mRNAseq_rep3

city: Shenzhen

first: Yu

last: Ma

address: 1088 Xueyuan Bivd, Nanshan District

institute: Southern University of Science and Technology

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

organism: Vitis vinifera

source_name: mRNA-seq of grape pulp in V+3W 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.

value: fruit pulp

value: Cabernet Sauvignon


title: GCs, Rbp4-Cre, SS2, DG_P10_D10

description:
Library name: 20210417_Blanca_Plate3_D10
Smart-seq2


title: V+3W_pulp_mRNAseq_rep2


title: GCs, Rbp4-Cre, SS2, DG_P10_C9

description:
Library name: 20210417_Blanca_Plate3_C9
Smart-seq2


title: F+6W_pulp_mRNAseq_rep2

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


title: F+6W_pulp_mRNAseq_rep3


title: V+3W_skin_mRNAseq_rep3

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

value: fruit skin


title: GCs, Rbp4-Cre, SS2, DG_P10_C8

description:
Library name: 20210417_Blanca_Plate3_C8
Smart-seq2