title: sci-Plex-SHP2-preliminary

city: New York

first: Ross

middle: M

last: Giglio

state: NY

institute: Columbia University

description:
Library name: Sample 1
sci-Plex transcriptomic profiling of diverse SHP2 variants in HEK 293 cells

data_processing:
Expression matrices, cell annotations and gene annotations were generated according to the protocol described in our manuscript as well as in Cao et al. 2019 Nature 566(7745) p. 496-502 (three level sci-RNA-seq). Nuclear barcodes "hash" sequences were extracted from fastq files if the first 10 bp of read 2 match a hash from the appropriate hashSampleSheet.txt (2nd column) within a hamming distance of 1, the last column of the hashSampleSheet.txt file pertains to whether 1 or 2 hashes were used to identify a condition (only single hashes were used in these experiments). Reads were then deduplicated by cell barcode and UMI to create a file of hash UMI counts (hashTable.out.txt files) for each nuclear transcriptome in the experiment. Tab-delimited columns of hashTable.out.txt files correspond to a sample id, the cell barcode identified for that hash, a "_" delimited string with condition metadata, an axis id for each hash (not used in these experiments), and umi counts for each hash. The first tab-delimited column of the appropriate hashSampleSheet.txt files contains metadata for the experiment divided by underscores. The first "_" delimited string corresponds to the SHP2 variant, the second corresponds to the EGF concentration, and the third corresponds to the combination of hash plate (e.g. 01, 02) and hash well e.g. (A01, B01). The hash well also corresponds to the orientation of the cells position for drugging. The associated CellLine.RT.Plate.csv file contains information for timepoint of harvesting post-EGF stimulation.
Assembly: GrCh38
Supplementary files format and content: Expression matrices are output by our pipeline in matrix market exchange format and the cell and gene annotation files that accompany these files are in tsv file format.

source_name: kindey, embryo

growth_protocol: Cells were cultured in a 37 °C tissue culture incubator with 5% CO2. Cells were discarded by passage 25 and tested for mycoplasma every 3 months. HEK 293 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. HEK 293 SHP2 knock-out cells were grown in DMEM with 10% FBS.

extract_protocol:
24 hours hours after drug exposure, cells were harvested following the sci-Plex protocols (Srivatsan, McFaline-Figueroa, Ramani et al. 2020 Science) as described in the methods section of our manuscript. Nuclei were isolated in-well and nuclei barcoded by fixation of well-specific barcode containing oligonucleotides. After fixation wells were pooled and nuclei pellets flash frozen until sci-RNA-seq library preparation.
sci-RNA-seq3: Nuclei were subjected to a modified version of the three-level sci-RNA-seq described in Cao et al. 2019 Nature 566(7745) p. 496-502 that incorporates random hexamer priming as in Sziraki et al. 2023 Nature Genetics and Giglio et al. 2024 bioRxiv, see methods.

treatment_protocol: 10E6 HEK 293 SHP2KO cells were seeded in a 6-well plate, and transfected 24 hours later with 2 μg DNA in 200 μL empty DMEM using 6 μL of polyethylenimine (PEI). Early the next morning, each well was trypsinized and reseeded into a 96-well plate to a final density of 10,000 cells per well. 12 hours after re-seeding, cells were checked for adherence and culture media was aspirated. Cells were serum- starved overnight in DMEM + 0.2%FBS. After 12 hours of serum-starvation, EGF was added to the cells in DMEM + 0.2% FBS to a final concentration of: 1000 ng/mL, 500 ng/mL, 250 ng/mL, 100 ng/mL, 50 ng/mL, 25 ng/mL, 12.5 ng/mL, 0 ng/mL (unstimulated).

value: kindey, embryo

value: HEK 293

value: epithelial

value: SHP2 KO

value: EGF stimulation


title: UBQLN2(P497H)_2

status: Public on Jul 01 2025

type: SRA

city: baltimore

first: Yang

last: Liu

state: MD

address: 615 N wolfe street

department: BMB

country: USA

institute: Johns Hopkins

library_source: transcriptomic

data_processing:
Raw reads were processed with TrimGalore v0.6.7 and controlled for quality with FastQC v.0.11.9. The processed reads were mapped to the human genome (hg38) and GENCODE v19 annotated transcripts using Hisat2 v2.2.1 and quantified with featureCounts v2.0.1. Raw gene counts were loaded into R to perform differential expression analysis with edgeR.
Assembly: human genome (hg38)
Supplementary files format and content: excel contain the normalized reads

molecule: total RNA

organism: Homo sapiens

source_name: motor neurons

extract_protocol:
Total RNAs were isolated using an RNeasy Plus mini kit (Qiagen, 74136)
RNA libraries for sequencing were constructed with a commercial kit (Invitrogen, A39005096)

tag: cell type

value: motor neurons

tag: genotype

tag: treatment

value: glucose starvation for 28 hours


title: Isogenic control_3

description: Isogenic CTRL-3

value: wild-type

value: glucose starvation for 26 hours


title: Isogenic control_2

description: Isogenic CTRL-2

value: glucose starvation for 25 hours


title: Isogenic control_1

description: Isogenic CTRL-1

value: glucose starvation for 24 hours


title: EC038-xeno3

type: RNA

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent). For comparison among multiple arrays, probe set data were median-normalized per chip.

source_name: A xenograft from EC038 cell derived tumor

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: Total RNA from each xenograft was isolated by RNeasy Mini Kit (QIAGEN) in combination with DNase treatment (RNase-Free DNase Set, QIAGEN)

tag: tumor or non-tumor

value: tumor


title: CTL_1_Unsorted Bone Marrow Cells mERRBS

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt
Reads were aligned against a bisulfite-converted human genome using Bismark with Bowtie2
Downstream analysis  was performed on MethylSig using beta-binomial regression (FDR less than 0.1) with a minimum cutoff of 25% methylation difference to identify Differential Methylated Cytosines (DMCs). Differentially Methylated Regions (DMRs) were identified by first summarizing the methylation status of the genomic regions into 25-bp tiles and then identifying regions with an absolute methylation difference more than 25% and an FDR less than 0.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files with CpGs for each sample. mERRBS gives us base pair resolution info of the sequenced DNA (chr position of the detected base,  first column), the chromosome of the detected base (second column), the position of the detected base on the specific chromosome (third column),sequencing info was assessed from which strand (forward, reverse, fourth column), read coverage (fifth column), frequency of methylated cytosine (sixth column), frequency of unmethylated cytosine (last column).

molecule: genomic DNA

source_name: Unsorted Bone Marrow Cells

extract_protocol:
DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). 100ng of high quality genomic DNA were digested with 200U of methylation-insensitive endonuclease enzyme MspI (New England Biolabs, NEB),end repaired, A-tailed and ligated to RNA TruSeq Illumina indexed adapters (Illumina, RS-122-2001). Library fragments were gel isolated from a 1.8% agarose gel (Low range Ultra aga-rose, Biorad) using Qiaquick Gel Extraction kit and bisulfite converted using EZ DNA Methylation kit (Zymo Research). Products were amplified by PCR and final libraries were purified using AMPure XP beads (Agencort).
mERRBS libraries were prepared for sequencing using manufacturer’s recommended protocol for 50bp stranded single-end read runs (Illumina San Diego, CA)

tag: tissue

value: Unsorted Bone Marrow Cells

tag: cytogenetics

tag: mutations

value: Not Found

tag: age


title: CTL_2_Unsorted Bone Marrow Cells mERRBS


title: UPN662_T3_mERRBS

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln)


title: CTL_3_Unsorted Bone Marrow Cells mERRBS


title: EC038-xeno1


title: EC029_in vitro

source_name: esophageal cancer cell line derived from cancer tissue before chemotherapy

extract_protocol: Total RNA from each cell line was isolated by RNeasy Mini Kit (QIAGEN) in combination with DNase treatment (RNase-Free DNase Set, QIAGEN)


title: EC038_in vitro

source_name: esophageal cancer cell line derived from cancer tissue after chemotherapy


title: UPN662_T1_mERRBS

value: SRSF2 p.(Pro95_Arg102del)


title: EC029-xeno1

source_name: A xenograft from EC029 cell derived tumor


title: EC029-xeno2


title: UPN661_T3_mERRBS

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), ASXL1 p.(Arg1068*), KRAS p.(Ala18Asp), RUNX1 p.(Arg166Gln)


title: EC038-xeno2


title: UBQLN2(P497H)_4

value: glucose starvation for 30 hours


title: UPN661_T2_mERRBS

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), ASXL1 p.(Arg1068*), KRAS p.(Ala18Asp)


title: UBQLN2(P497H)_3

value: glucose starvation for 29 hours


title: UPN660_T3_mERRBS

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), RUNX1 p.(Ala187Pro)


title: UPN660_T1_mERRBS


title: UPN660_T2_mERRBS


title: EC029-xeno3


title: CAF8

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

country: China

institute: Southern Medical University

data_processing:
Hisat2 v2.0.5
Clean reads were generated by removing low quality reads and then aligned to the Human Genome Assembly GRCh38/hg38 using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads mapped to each gene, and then the FPKM (Fragments Per Kilobase of sequence per Millions base pairs) of each gene were calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Colorectal cancer tissue

extract_protocol:
Total RNA was first purified using TRIzol Reagent t and then assessed by 1% agarose gel electrophoresis and the Bioanalyzer 2100 system.
Sequencing libraries were constructed using the NEBNext UltraTM RNA Library Prep Kit for Illumina.

value: Colorectal cancer tissue

value: fibroblast

value: WT


title: UPN661_T1_mERRBS

value: SRSF2 p.(Pro95_Arg102del),  IDH2 p.(Arg140Gln), ASXL1 p.(Arg1068*)


title: CAF9


title: CAF10


title: CAF11


title: CAF12


title: UPN662_T2_mERRBS


title: CAF6


title: CAF5


title: NF12

source_name: para-carcinoma tissue

value: para-carcinoma tissue


title: CAF4


title: CAF2


title: CAF1


title: NF11


title: NF9


title: NF6


title: NF10


title: NF8


title: NF5


title: NF3


title: NF7


title: NF1


title: NF2


title: H441_input Rep 2

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore (version 0.4.2) with "-q 20 --stringency 3 --length 20".
Reads were then aligned to hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
Peaks were called for each biological replicate using MACS v2.1.0 with the following parameters: “-g hs -B --SPMR --keep-dup all -p 0.01 --nomodel --shift 0 --extsize ${FRAGLEN}”, where “FRAGLEN” was 241 and 161 for the replicate 1 and 2, respectively.
ENCODE blacklist regions (accession number ENCFF356LFX) were filtered using bedtools intersect.
Bedgraph files representing fold enrichment in treatment over input control were generated using MACS2 bdgcmp with "-m FE".  Bedgraph files were converted to bigwig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: H441 human lung papillary adenocarcinoma cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
ChIP-seq was conducted using SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) #9003 (Cell Signaling Technology).
ChIP-seq libraries were prepared by Cincinnati Children's Hospital Medical Center (CCHMC) DNA Sequencing and Genotyping Core.

tag: cell line

value: lung papillary adenocarcinoma cells

tag: chip antibody


title: H441_input Rep 1

institute: Cincinnati Children's Hospital Medical Center


title: H441_FOXA2 Rep1

value: FOXA2 (R&D Systems, #AF2400)


title: BEAS-2B_input for KRAS.G12V;Foxa2 Rep 2

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore (version 0.4.2) with "-q 20 --stringency 1 --length 20".
Reads were then aligned to hg38 genome using bowtie2 (version 2.4.2) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
Broad peaks were called for each biological replicate uing MACS v2.1.0 with the following parameters: “-g hs --SPMR --broad --broad-cutoff=0.1 --keep-dup 1 --bdg --qvalue 0.05".
ENCODE blacklist regions (accession number ENCFF356LFX) were filtered using bedtools intersect.
Bedgraph files representing fold enrichment in treatment over input control were generated using MACS2 bdgcmp with "-m FE".  Bedgraph files were converted to bigwig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

growth_protocol: BEAS-2B transformed human bronchial epithelial cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

value: Transformed human bronchial epithelial cells


title: BEAS-2B_KRAS.G12V;Foxa2 Rep 2

value: H3K27ac (Abcam, #ab4729)


title: BEAS-2B_KRAS.G12V;Foxa2 Rep 1


title: BEAS-2B_input for KRAS.G12V;Foxa2 Rep 1


title: H441_FOXA2 Rep2


title: BEAS-2B_Foxa2 Rep 2


title: CAF7


title: BEAS-2B_input for Foxa2 Rep 2


title: CAF3


title: BEAS-2B_Foxa2 Rep 1


title: BEAS-2B_input for Foxa2 Rep 1


title: BEAS-2B_input for KRAS.G12V Rep 1


title: BEAS-2B_KRAS.G12V Rep 2


title: BEAS-2B_KRAS.G12V Rep 1


title: NF4


title: BEAS-2B_Control Rep 2


title: BEAS-2B_input for Control Rep 2


title: BEAS-2B_input for KRAS.G12V Rep 2


title: BEAS-2B_Control Rep 1


title: P-R, E2, Rep 3

city: Rochester

first: Xiyin

last: Wang

state: Minnesota

address: 200 First St SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description: Library name: P-R_E2_3

data_processing:
Sequencing quality was checked using FastQC (version 0.11.8). Reads were aligned to the GRCh38 (hg38) genome using STAR (version 2.7.3a) with soft-clipping enabled for adapter sequences. featureCounts (version 2.8.2) was used to assign mapped reads. Lowly expressed genes (RPKM ≤ 1 in all samples) were removed prior to analysis. Dif-ferential expression analysis was performed using edgeR (version 3.36.0) and signifi-cance was defined as |fold change| ≥ 1.5, p < 0.05 and FDR < 0.1.
Assembly: hg38
Supplementary files format and content: excel file including raw counts and RPKM values for each sample

source_name: cell line

growth_protocol: Cells were maintained in phenol red-free DMEM/F12 medium supplemented with 10% FBS, 5 mg/L blasticidin S, 500 mg/L zeocin, and 1% antibiotic-antimycotic. To induce ERb ex-pression, cells were continuously treated with 100 ng/mL doxycycline, with the treat-ment duration specified for each experiment.

extract_protocol:
total RNA was isolated using the Qiagen miRNeasy mini kit (Qiagen, Hilden, Germa-ny) following the manufacturers protocol.
Library preparation was conducted using the TruSeq Stranded mRNA Library Prep Kit with TruSeq RNA Single Index Set B (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were plated in triplicate in charcoal-stripped FBS containing medium plus 100 ng/mL doxycycline to induce ERb expression. After 24 h, a medium change was performed containing either ethanol vehicle or 1nM E2 for 24h treatment.

value: cell line

value: MDA-MB-231-ERb-P-R cell

value: triple negative breast cancer cell

value: Paclitaxel resistant

value: 100 ng/mL doxycycline + 1nM E2


title: P-R, E2, Rep 1

description: Library name: P-R_E2_1


title: BEAS-2B_input for Control Rep 1


title: P-R, veh, Rep 2

description: Library name: P-R_veh_2

value: 100 ng/mL doxycycline + Vehicle


title: P-R, veh, Rep 3

description: Library name: P-R_veh_3


title: P-R, E2, Rep 2

description: Library name: P-R_E2_2


title: D-R, E2, Rep 3

description: Library name: D-R_E2_3

value: MDA-MB-231-ERb-D-R cell

value: Doxorubicin resistant


title: P-R, veh, Rep 1

description: Library name: P-R_veh_1


title: D-R, E2, Rep 2

description: Library name: D-R_E2_2


title: D-R, veh, Rep 3

description: Library name: D-R_veh_3


title: Par, E2, Rep 1

description: Library name: Par_E2_1

value: MDA-MB-231-ERb-Par cell

value: Parental


title: Par, E2, Rep 3

description: Library name: Par_E2_3


title: Par, E2, Rep 2

description: Library name: Par_E2_2


title: D-R, veh, Rep 2

description: Library name: D-R_veh_2


title: D-R, veh, Rep 1

description: Library name: D-R_veh_1


title: Par, veh, Rep 3

description: Library name: Par_veh_3


title: D-R, E2, Rep 1

description: Library name: D-R_E2_1


title: Par, veh, Rep 2

description: Library name: Par_veh_2


title: SMARCA3 KO 293T, rep2

first: Yael

last: David

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample 5 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA2

data_processing:
Raw reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), and then aligned to human assembly hg38 with STAR v2.4 using default parameters. Post-alignment quality and transcript coverage were assessed using the Picard tool CollectRNASeqMetrics (http://broadinstitute.github.io/picard/). Raw read count tables were created using HTSeq v0.9.1. Normalization and expression dynamics were evaluated with DESeq2 using the default parameters including library size factor normalization. Gene set enrichment analysis (GSEA, http://software.broadinstitute.org/gsea) was run against MSigDB v6 using ‘pre-ranked’ mode and log2 fold change for pairwise comparisons.
Assembly: hg38
Supplementary files format and content: txt file of raw reads

source_name: epithelial-like

growth_protocol: HEK293T were cultured in DMEM with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Frozen cells were lysed in TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA with RIN values of 9.7-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50/50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 47 million paired reads was generated per sample. Ribosomal reads represented 0-3.8% of the total reads generated and the percent of mRNA bases averaged 72%.

value: epithelial-like

value: human embryonic kidney


title: SMARCA3 KO 293T, rep3

description:
Library name: Sample 6 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA3


title: Par, veh, Rep 1

description: Library name: Par_veh_1


title: WT 293T, rep2

description:
Library name: Sample 2 WT 293T
Column name in raw counts: WT293RNA2


title: SMARCA3 KO 293T, rep1

description:
Library name: Sample 4 SMARCA3 KO 293T
Column name in raw counts: HLTFKORNA1


title: WT 293T, rep3

description:
Library name: Sample 3 WT 293T
Column name in raw counts: WT293RNA3


title: WT 293T, rep1

description:
Library name: Sample 1 WT 293T
Column name in raw counts: WT293RNA1


title: ee,temperature,29℃，rep2

city: kunming

first: yayi

last: zhao

state: yunnan province

address: 吴家营

department: School of Ecology and Environment

institute: Yunnan University

data_processing:
Illumina NovaSeq X Plus platform for computer sequencing
Start with the raw sequencing data Filter to obtain high quality sequencing data.1) The joint sequence in reads was removed, and the reads without inserted fragments were removed due to the joint self-connection and other reasons; 2) The bases with low quality (mass value less than 20) at the end of the sequence (3 'end) are pruned away. If there is still a mass value less than 10 in the remaining sequence, the whole sequence will be eliminated, otherwise retained; 3) reads containing more than 10% N were removed; 4) Discard the sequence whose length is less than 20bp after the adapter is removed and the quality is trimmed.
cleandata (reads), the original data after quality control, was compared with the reference genome to obtain mappeddata (reads), which is used for subsequent transcriptome assembly and expression calculation, etc. At the same time, the quality of the transcriptome sequencing comparison results was evaluated. The analysis mainly included sequencing saturation, gene coverage, distribution of Reads in different regions of the reference genome and distribution of Reads in different chromosomes.
Assembly: Arabidopsis thaliana
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
Arabidopsis elf3 mutant ELF3-16 and elf3 T-DNA insertion mutant ELF3-101 were selected by natural genetic variation in the context of Columbia wild type. RNA-seq was sampled at ZT8, ZT16, and ZT24 at 16, 22, and 29 Degree Celsius, respectively.
Eukaryotic mRNA sequencing based on Illumina platform of eukaryotes specific tissues or cells in a certain period all transcription of mRNA sequencing, experimental library establishment IlluminaNovaSeqReagentKit method for sequencing

value: seedling

value: ELF3 T-insert


title: ee,temperature,29℃，rep3


title: Ctrl

city: nanjing

first: Ling

last: wang

address: Chunhua Avenue, Jiangning District, Jiangsu Province, China

institute: Nanjing Medical University

data_processing:
CLC Genomics Workbenchv11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SH-SY5Y cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: SH-SY5Y cells were exposed to a mixture of TDCPP and TiO2 NPs for 24 hours and then collected.

value: neuroblastoma cell lines

value: Ctrl

value: Cytotoxicity


title: TDCPP and TiO2 NPs

value: TDCPP and TiO2 NPs


title: SP,temperature,29℃，rep3


title: SP,temperature,29℃，rep1


title: ee,temperature,29℃，rep1


title: WT,temperature,29℃，rep1

value: WT


title: WT,temperature,29℃，rep3


title: ee,temperature,22℃，rep3


title: SP,temperature,29℃，rep2


title: ee,temperature,22℃，rep2


title: ee,temperature,22℃，rep1


title: SP,temperature,22℃，rep1


title: SP,temperature,22℃，rep2


title: WT,temperature,29℃，rep2


title: WT,temperature,22℃，rep3


title: WT,temperature,22℃，rep2


title: WT,temperature,22℃，rep1


title: SP,temperature,22℃，rep3


title: ee,temperature,16℃，rep3


title: ee,temperature,16℃，rep2


title: SP,temperature,16℃，rep2


title: ee,temperature,16℃，rep1


title: SP,temperature,16℃，rep3


title: WT,temperature,16℃，rep2


title: WT,temperature,16℃，rep1


title: WT,temperature,16℃，rep3


title: WT

city: Paris

first: Yazan

last: Salloum

address: 11-13 Rue Pierre et Marie Curie

country: France

institute: Institut Curie

description: Library name: D1748T04

library_source: transcriptomic single cell

data_processing:
CellRanger pipeline
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Gut

extract_protocol:
10 guts from 5 dpf larvae were dissected and placed in 200 μL of a dissociation cocktail (1 mg/mL fresh collagenase A, 40 μg/mL proteinase K, and 0.25% trypsin in PBS) at 37°C for 30 minutes. 50 guts were dissected per condition for a total of 5 replicate tubes per condition. Cells were centrifuged at 300 RCF for 15 minutes at 4°C. The pellet was resuspended in 200 μL PBS with 0.04% non-acetylated BSA. Replicates were pooled and filtered through a 40 μm cell strainer (Fisherbrand, #22363547). Samples were centrifuged at 300 RCF for 15 minutes at 4°C and resuspended with in 50 ul of PBS with 0.04% non-acetylated BSA. To isolate live cells, an OptiPrep™ Density Gradient Medium (Sigma, #D1556-250ML) was used. A 40% (w/v) iodixanol working solution was prepared by mixing 2 volumes of OptiPrep™ with 1 volume of 0.04% BSA in 1X PBS/DEPC-treated water. This working solution was used to create a 22% (w/v) iodixanol solution in the same buffer. The cell suspension was mixed with one volume of the working solution and 0.45 volume of the cell suspension via gentle inversion, transferred to a 15 mL conical tube, and topped up to 6 mL with the working solution. This solution was overlaid with 3 mL of the 22% iodixanol, and then with 0.5 mL of PBS with 0.04% BSA. Samples were centrifuged at 800 RCF for 20 minutes at 20°C. Viable cells were collected from the top interface, diluted in PBS with 0.04% BSA, and centrifuged at 300 RCF for 10 minutes at 4°C. The supernatant was discarded, and the cells were resuspended in PBS with 0.04% non-acetylated BSA to reach the desired concentration. Data analysis was performed using the Seurat package in R (Hao et al, 2024).
Cells were loaded onto a 10× Chromium instrument (10× Genomics) and libraries were prepared using the Single Cell 3′ Reagent Kit (V2 chemistry) (10× Genomics) according to the manufacturer's instructions. The sequencing coverage was approximately 100,000 reads per cell

value: Gut


title: rzIl26_biol_rep_3

description: Library name: D832T029

data_processing:
Institut Curie - Nextflow raw-qc analysis pipeline
Institut Curie - Nextflow rna-seq analysis pipeline
Assembly: danRer11
Supplementary files format and content: A csv file containing raw read counts, with each column representing a sample

extract_protocol:
10-15 guts per replicate were dissected and RNA was extracted using the Single Cell RNA Purification Kit (Norgen, #51800) following the manufacturer’s instructions. RNA integrity and concentration were analyzed on the Agilent 4200 Tapestation system using the High Sensitivity RNA ScreenTape Analysis kit (Agilent, #5067-5579). cDNA quality was checked on the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626). After quality control, libraries were sequenced with 100-bp paired-end (PE100) reads on the NovaSeq 6000 (Illumina) sequencer. Raw data were checked for quality using FastQC (v0.11.8) and aligned to the reference genome for Danio rerio danRer11 from the Genome Reference Consortium.
RNA sequencing libraries were prepared from 500 ng to 1 μg of total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit


title: rzIl26_biol_rep_1

description: Library name: D832T027


title: rzIl26_biol_rep_2

description: Library name: D832T028


title: BSA_biol_rep_1

description: Library name: D832T024


title: il26KO_GF_biol_rep_1

description: Library name: D1221T010


title: BSA_biol_rep_3

description: Library name: D832T026


title: il26KO_GF_biol_rep_3

description: Library name: D1221T012


title: WT_GF_biol_rep_3

description: Library name: D1221T009


title: il26KO_GF_biol_rep_2

description: Library name: D1221T011


title: WT_GF_biol_rep_2

description: Library name: D1221T008


title: WT_GF_biol_rep_1

description: Library name: D1221T007


title: il26KO_biol_rep_2

description: Library name: D1151T021

value: IL-26 knockout


title: il26KO_biol_rep_3

description: Library name: D1151T022


title: WT_biol_rep_2

description: Library name: D1151T018


title: Control male ileum-2

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St, Biomed Center

department: Molecular Microbiology and Immunology

institute: Brown University

data_processing:
The quality of RNA-seq data was determined using BWA (v0.7.17).
STAR (2.7.10b) was employed to align the reads onto the mouse genome.
SAMtools (v1.16.1) was employed to sort the alignments
HTSeq Python package was employed to count reads per gene
DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed (DE) genes.
The enriched pathways were identified using GSEA software (v4.3.3).
Assembly: mm39
Supplementary files format and content: .csv files with normalized counts and lists of upregulated and downregulated genes

organism: Mus musculus

source_name: Germ-free male non-colonized control

growth_protocol: Distal ileum and colon tissues were stoed in RNAlater solution in -80∘ C freezer until RNA extraction.

extract_protocol:
Total RNA was extracted using PureLink RNA Isolation kit from Invitrogen as per manufacturer's instructions.
Libraries were prepared using a 3'End Quant seq kit from Lexogen.

value: Distal ileum

value: Wild type

value: Gastrointestinally colonized with Candida albicans


title: il26KO_biol_rep_1

description: Library name: D1151T020


title: Control male colon-2

value: Distal colon


title: WT_biol_rep_3

description: Library name: D1151T019


title: SP,temperature,16℃，rep1


title: Control male ileum-1


title: Control male colon-1


title: WT_biol_rep_1

description: Library name: D1151T017


title: il26KO

description: Library name: D1748T05


title: Control female colon-3

source_name: Germ-free female non-colonized control


title: Control female ileum-3


title: Control female ileum-2


title: Control female colon-2


title: BSA_biol_rep_2

description: Library name: D832T025


title: 21 days Ca colonized male ileum-2

source_name: Germ-free male colonized with C. albicans for 21 days


title: 21 days Ca colonized male ileum-1


title: 21 days Ca colonized male colon-2


title: 21 days Ca colonized male colon-1


title: 21 days Ca colonized female colon-3

source_name: Germ-free female colonized with C. albicans for 21 days


title: 21 days Ca colonized female ileum-1


title: 21 days Ca colonized female ileum-2


title: 21 days Ca colonized female colon-2


title: 21 days Ca colonized female ileum-3


title: 21 days Ca colonized female colon-1


title: 7 days Ca colonized male ileum-2

source_name: Germ-free male colonized with C. albicans for 7 days


title: 7 days Ca colonized male ileum-1


title: 7 days Ca colonized male colon-1


title: 7 days Ca colonized female colon-2

source_name: Germ-free female colonized with C. albicans for 7 days


title: 7 days Ca colonized female colon-3


title: 7 days Ca colonized female ileum-3


title: 7 days Ca colonized female ileum-1


title: 7 days Ca colonized female ileum-2


title: 7 days Ca colonized female colon-1


title: Control female ileum-1


title: Control female colon-1


title: RNA-seq_pEPSC_WT-2

city: Wuhan

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

institute: Huazhong Agricultural University

description: Library name: pEPSC_WT_RNA-seq-2

data_processing:
For NGS,mapped read counts were used as input for the MAGeCK (version 0.5) analysis software package.
The raw RNA-seq reads were trimmed using Trim Galore (v0.6.6) and aligned to the Sscrofa11.1 reference genome using STAR (v2.7.3). Gene expression levels were quantified in TPM (fragments per kilobase of exon per million mapped reads) using StringTie (v2.1.4). Differential gene expression analysis was performed using DESeq2 based on the read counts generated by featureCounts (v2.0.0).
Raw data from ChIP-seq and ATAC-seq were processed using TrimGalore (v0.6.6) to remove adapters and low-quality reads. Processed reads were aligned to the Sscrofa11.1 reference genome using Bowtie2 (v2.4.4) with the options "--no-mixed" and "--no-discordant." Low-quality reads (MAPQ < 30) were removed using SAMtools (v1.9), and PCR duplicates were eliminated using Picard (v2.23.9). Peak calling was performed using MACS2 with a q value threshold of 0.05, and the following parameters: '-f BAMPE -g $GENOME_SIZE –nomodel –shift 37 –extsize 73' for ATAC-seq and '-f BAMPE -g $GENOME_SIZE' for ChIP-seq. Pairwise comparisons were conducted using DiffBind to identify differentially accessible regions for ATAC-seq. Motif enrichment was performed by HOMER (version 4.11) based on Homer and Jaspar databases that exclude fly and yeast backgrounds. Transcription factor motifs showing high variability across developmental stages were identified using chromVAR. RPKM bigwig files were generated using the bamCoverage subcommand in deepTools (v3.5.0), and tracks were visualized with Integrative Genomics Viewer (IGV, v2.8.9).
Assembly: Sscrofa11.1
Supplementary files format and content: xlsx files include TPM values for Crispr_screen and RNA-seq as well as bigWig files for ATAC-seq and ChIP-seq.

molecule: polyA RNA

organism: Sus scrofa

source_name: Embryonic

extract_protocol:
For NGS, genomic DNA was extracted from each sample using a Blood & Cell Culture DNA Midi Kit (QIAGEN). The sgRNA-encoding regions were amplified by PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB) in a reaction volume of 50 µL. The PCR products were mixed and purified using the MinElute PCR purification Kit (QIAGEN). The purified PCR products were amplified by PCR using different barcoded primers.
For RNA-seq, total RNA was extracted from cells using TRIzol reagent (Invitrogen, 15596-018). A total of 2 μg of RNA was then reverse transcribed into cDNA using the cDNA Synthesis Kit (Vazyme, R212-01), following the manufacturer’s protocol. RNA-seq libraries of porcine 4-cell embryos and FACS-sorted cells were prepared using a modified Smart-seq2 protocol (Picelli et al., 2014). Either 10 zona-free embryos or 500-1000 sorted cells were transferred into 4 µL of lysis buffer containing 0.1% Triton X-100 (Sigma, 93443), 5 × 10⁻⁷ M oligo-dT primer (5′-AAGCAGTGGTATCAACGCAGAGTACT₃₀VN-3′), 1 × 10⁻³ M dNTPs (NEB, N0447S), and 4 U RNase inhibitor (Takara, 2313A). The samples were incubated at 72°C for 3 minutes for RNA denaturation. Subsequently, 5.7 µL of reverse transcription mixture was added, comprising 100 U SuperScript II reverse transcriptase (Invitrogen, 18064014), 1× Superscript II first-strand buffer, 5 × 10⁻³ M DTT, 1 M betaine (Sigma, 61962), 6 × 10⁻³ M MgCl₂ (Sigma, M1028), 1 × 10⁻⁶ M TSO (5′-AAGCAGTGGTATCAACGCAGAGT-3′), and 10 U RNase inhibitor. Reverse transcription was carried out at 42°C for 90 minutes to synthesize cDNA. Single-cell libraries were prepared using a modified STRT-seq method as previously described (Dong et al., 2018). Following digestion, single pEPSC cells were randomly selected using a mouth pipette and transferred into lysis buffer containing an 8-bp barcode. First-strand cDNA synthesis and amplification were conducted in a reverse transcription (RT) mixture comprising 4 U RNase inhibitor, 100 U SuperScript II reverse transcriptase (Invitrogen, 18064071), 1 mM dNTPs (TAKARA, 4019), 60 mM MgCl2, and 3 μM RT primer along with 10 μM TSO primer. The amplified product underwent purification twice with 0.8× AMPure XP beads (Beckman, A63882). Subsequently, biotin-based PCR enrichment was performed.
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and the reaction was quenched by adding glycine to a final concentration of 125 mM. Chromatin was then sonicated to an average size of 150–300 bp using a Bioruptor (Diagenode). A total of 1 µg antibody was pre-incubated with magnetic beads and subsequently introduced to the sonicated chromatin. This mixture was incubated overnight at 4°C. After incubation, the magnetic beads were subjected to a series of washes, and the chromatin was eluted. Crosslinks were then reversed, followed by the purification of the DNA.
For ATAC-seq, approximately 50,000 cells were collected, washed with cold PBS, and resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂; and 0.1% IGEPAL CA-630). Nuclei were isolated by centrifugation at 4°C, followed by transposition using the kit. The transposition reaction was incubated at 55°C for 10 minutes, and DNA was then amplified for 9 cycles. DNA was isolated using the Qiagen MinElute Kit and further purified with the Qiagen PCR Cleanup Kit.
For NGS, all PCR products were pooled and purified with a MinElute PCR purification Kit (QIAGEN), followed by Illumina Next-generation sequencing.
The RNA-seq libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530L) according to the manufacturer's instructions. The Smart-seq2 libraries were were constructed using the TruePrep DNA Library Prep Kit (Vazyme, TD502) following the manufacturer's protocol. The scRNA-seq library was constructed using the KAPA Hyper Prep Kit (KAPA, KK8054) following the manufacturer’s protocol for PCR Library Amplification/Illumina platforms.
ChIP-seq library preparation was conducted utilizing the KAPA Hyper Prep Kit (KK8500) in accordance with the manufacturer's guidelines..
ATAC-seq libraries from FACS-sorted pEPSCs were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).

value: Embryonic

value: EPSC


title: RNA-seq_pEPSC_WT-1

description: Library name: pEPSC_WT_RNA-seq-1


title: IAV (Flu)

city: Urbana

first: Andrew

last: Steelman

state: IL

address: 1201 West Gregory

institute: University of Illinois

description: 10x Genomics

data_processing:
Fastq files were generated and demultiplexed with the mkfastq option from Cell Ranger 2.1.1 using bcltofastq 2.20
Cell Ranger 6.0.1's mkref command was used to make a custom reference to both NCBI's Mus musculus GRCm39 genome, Annotation Release 109 and NCBI's Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Genome assembly ViralMultiSegProj15521 (RefSeq GCF_000865725.1). Then cellranger count was used to align to the custom reference, reduce reads to UMIs, count UMIs per gene per cell and call cells vs empty GEMs.
Assembly: NCBI GRCm39 and Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Supplementary files format and content: Gzipped tab-separated values files (barcodes and features) and matrix files (counts)

source_name: brain

growth_protocol: C57BL/6J mice were obtained from Jackson Laboratories (No. 000664). Animals were group-housed under constant 12-h light/dark cycles and constant temperature.

extract_protocol:
At day 8 post-infection, mice were euthanized by CO2 asphyxiation, perfused intracardially with 20 ml of ice cold artificial cerebrospinal fluid (0.087M NaCl, 0.0025M KCl, 0.00125M NaH2PO4, 0.026M NaHCO3, 0.075M sucrose, 0.02M glucose, 0.001M CaCl2, 0.002M MgSO4), and then the brain extracted. The whole brain was dissociated and viable single cell suspensions prepared with a MACS dissociator (Miltenyi Biotec) using neural dissociation, debris/myelin removal and dead cell removal kits according to the manufacturer's instructions (Miltenyi Biotec).
The libraries were constructed with the Chromium Single Cell 3′ Library & Gel Bead Kit v2. The libraries were pooled and sequenced on two 2x150nt lanes in a HiSeq 4000. Reads are 26nt (read1) and 150nt (read2) nt in length.

treatment_protocol: At 8 weeks of age, mice were anesthetized with 3% isoflurane and then intranasally inoculated with either sterile phosphate buffered saline (PBS) or 1 HAU of mouse-adapted human influenza A virus (strain A/Puerto Rico/8/1934) diluted in PBS.  Mice were maintained on standard rodent chow (Teklad #2918).

value: brain

value: brain cells

tag: Sex

value: female

value: Influenza virus inoculated (A/PR8/34; 1.0 HAU)

tag: time

value: 8 days post-inoculation


title: RNA-seq_pEPSC_WT-3

description: Library name: pEPSC_WT_RNA-seq-3


title: PBS (Saline)

description: 10x Genomics

value: PBS inoculated


title: ChIP-seq_pEPSC_WT_H3K4me1-2

description: Library name: pEPSC_WT_H3K4me1-2


title: ChIP-seq_pEPSC_WT_H3K4me1-1

description: Library name: pEPSC_WT_H3K4me1-1


title: ChIP-seq_pEPSC_WT_H3K27me3-2

description: Library name: pEPSC_WT_H3K27me3-2


title: ChIP-seq_pEPSC_WT_H3K27me3-1

description: Library name: pEPSC_WT_H3K27me3-1


title: ChIP-seq_pEPSC_WT_H3K27ac-2

description: Library name: pEPSC_WT_H3K27ac-2


title: ChIP-seq_pEPSC_WT_H3K27ac-1

description: Library name: pEPSC_WT_H3K27ac-1


title: ATAC-seq_pEPSC_WT-2

description: Library name: pEPSC_WT_ATAC-seq-2


title: ATAC-seq_pEPSC_WT-1

description: Library name: pEPSC_WT_ATAC-seq-1


title: ChIP-seq_pEPSC_POU5F1-2

description: Library name: pEPSC_POU5F1-2


title: 7 days Ca colonized male colon-2


title: ChIP-seq_pEPSC_Input

description: Library name: pEPSC_Input


title: RNA-seq_pEPSC_FOXH1_KO-2

description: Library name: pEPSC_FOXH1_KO_RNA-seq-2


title: RNA-seq_pEPSC_FOXH1_KO-1

description: Library name: pEPSC_FOXH1_KO_RNA-seq-1


title: ChIP-seq_pEPSC_FOXH1_KO_H3K27me3-1

description: Library name: pEPSC_FOXH1_KO_H3K27me3-1


title: ChIP-seq_pEPSC_FOXH1_KO_H3K4me3-1

description: Library name: pEPSC_FOXH1_KO_H3K4me3-1


title: ChIP-seq_pEPSC_FOXH1_flag-1

description: Library name: pEPSC_FOXH1_flag-1


title: ChIP-seq_pEPSC_FOXH1_KO_H3K27ac-2

description: Library name: pEPSC_FOXH1_KO_H3K27ac-2


title: ChIP-seq_pEPSC_WT_H3K4me3-1

description: Library name: pEPSC_WT_H3K4me3-1


title: ATAC-seq_pEPSC_FOXH1_KO-2

description: Library name: pEPSC_FOXH1_KO_ATAC-seq-2


title: ChIP-seq_pEPSC_WT_H3K4me3-2

description: Library name: pEPSC_WT_H3K4me3-2


title: ChIP-seq_pEPSC_FOXH1_KO_H3K27ac-1

description: Library name: pEPSC_FOXH1_KO_H3K27ac-1


title: ChIP-seq_pEPSC_FOXH1_KO_H3K27me3-2

description: Library name: pEPSC_FOXH1_KO_H3K27me3-2


title: NGS_P5-2

description: Library name: P5-2


title: NGS_OCT4_tdTomato_control

description: Library name: OCT4_tdTomato_control


title: ATAC-seq_pEPSC_FOXH1_KO-1

description: Library name: pEPSC_FOXH1_KO_ATAC-seq-1


title: ChIP-seq_pEPSC_FOXH1_flag-2

description: Library name: pEPSC_FOXH1_flag-2


title: NGS_OCT4_tdTomato_negative

description: Library name: OCT4_tdTomato_negative


title: NGS_P4-2

description: Library name: P4-2


title: NGS_P4-1

description: Library name: P4-1


title: NGS_P3-2

description: Library name: P3-2


title: NGS_P5-1

description: Library name: P5-1


title: ChIP-seq_pEPSC_POU5F1-1

description: Library name: pEPSC_POU5F1-1


title: NGS_P10-2

description: Library name: P10-2


title: NGS_P2-2

description: Library name: P2-2


title: NGS_P3-1

description: Library name: P3-1


title: NGS_P10-1

description: Library name: P10-1


title: NGS_P0-2

description: Library name: P0-2


title: NGS_P0-1

description: Library name: P0-1


title: RNA-seq_pEPSC_FOXH1_KO-3

description: Library name: pEPSC_FOXH1_KO_RNA-seq-3


title: ChIP-seq_pEPSC_FOXH1_KO_H3K4me3-2

description: Library name: pEPSC_FOXH1_KO_H3K4me3-2


title: NGS_NANOG_tdTomato_negative

description: Library name: NANOG_tdTomato_negative


title: NGS_NANOG_tdTomato_control

description: Library name: NANOG_tdTomato_control


title: NGS_Library-2

description: Library name: Library-2

value: not applicable


title: pEPSC_single_cell-2

description: Library name: STRT-seq_pEPSC_single_cell-2

data_processing:
The raw RNA-seq reads were trimmed using Trim Galore (v0.6.6) and aligned to the Sscrofa11.1 reference genome using STAR (v2.7.3). Gene expression levels were quantified in TPM (fragments per kilobase of exon per million mapped reads) using StringTie (v2.1.4). Differential gene expression analysis was performed using DESeq2 based on the read counts generated by featureCounts (v2.0.0).
For single-cell RNA-seq data processing, raw reads were first segregated based on cell-specific barcodes in read 2 of the paired-end reads. The TSO sequence and polyA tail in read 1 were trimmed using custom scripts. Sequences in read 1 with low-quality bases (N > 10%) or adapter contamination were discarded. The remaining sequences were aligned to the reference genome (NCBI Sscrofa11.1) using TopHat (version 2.0.12). Unique read counts were obtained using htseq-count from the HTSeq package, and the reads were grouped based on cell-specific barcodes. Duplicate transcripts with identical UMIs were removed. For each gene in each cell, transcript abundance was quantified based on the number of distinct UMIs. Downstream analysis was performed using Seurat, unless otherwise specified. Cells with fewer than 4000 detected genes were excluded, leaving 341 cells for analysis from an initial 381. The expression matrix was log-normalized and scaled using default Seurat parameters. Dimension reduction was performed via PCA, incorporating OSN-associated genes and variable genes. Batch effects were corrected using Harmony. The number of principal components (PCs) and Harmony dimensions for cell clustering and UMAP embedding were determined by the Elbowplot method. Pseudotime trajectory analysis was performed with Slingshot, and the cell pluripotency score was assessed using the AddModuleScore function in Seurat.
Raw data from ChIP-seq and ATAC-seq were processed using TrimGalore (v0.6.6) to remove adapters and low-quality reads. Processed reads were aligned to the Sscrofa11.1 reference genome using Bowtie2 (v2.4.4) with the options "--no-mixed" and "--no-discordant." Low-quality reads (MAPQ < 30) were removed using SAMtools (v1.9), and PCR duplicates were eliminated using Picard (v2.23.9). Peak calling was performed using MACS2 with a q value threshold of 0.05, and the following parameters: '-f BAMPE -g $GENOME_SIZE –nomodel –shift 37 –extsize 73' for ATAC-seq and '-f BAMPE -g $GENOME_SIZE' for ChIP-seq. Pairwise comparisons were conducted using DiffBind to identify differentially accessible regions for ATAC-seq. Motif enrichment was performed by HOMER (version 4.11) based on Homer and Jaspar databases that exclude fly and yeast backgrounds. Transcription factor motifs showing high variability across developmental stages were identified using chromVAR. RPKM bigwig files were generated using the bamCoverage subcommand in deepTools (v3.5.0), and tracks were visualized with Integrative Genomics Viewer (IGV, v2.8.9).
Assembly: Sscrofa11.1
Supplementary files format and content: xlsx files include TPM values for RNA-seq and bigWig files for ATAC-seq and ChIP-seq

extract_protocol:
For bulk RNA-seq, total RNA was extracted from cells using TRIzol reagent (Invitrogen, 15596-018). A total of 2 μg of RNA was then reverse transcribed into cDNA using the cDNA Synthesis Kit (Vazyme, R212-01), following the manufacturer’s protocol. RNA-seq libraries of porcine 4-cell embryos and FACS-sorted cells were prepared using a modified Smart-seq2 protocol (Picelli et al., 2014). Either 10 zona-free embryos or 500-1000 sorted cells were transferred into 4 µL of lysis buffer containing 0.1% Triton X-100 (Sigma, 93443), 5 × 10⁻⁷ M oligo-dT primer (5′-AAGCAGTGGTATCAACGCAGAGTACT₃₀VN-3′), 1 × 10⁻³ M dNTPs (NEB, N0447S), and 4 U RNase inhibitor (Takara, 2313A). The samples were incubated at 72°C for 3 minutes for RNA denaturation. Subsequently, 5.7 µL of reverse transcription mixture was added, comprising 100 U SuperScript II reverse transcriptase (Invitrogen, 18064014), 1× Superscript II first-strand buffer, 5 × 10⁻³ M DTT, 1 M betaine (Sigma, 61962), 6 × 10⁻³ M MgCl₂ (Sigma, M1028), 1 × 10⁻⁶ M TSO (5′-AAGCAGTGGTATCAACGCAGAGT-3′), and 10 U RNase inhibitor. Reverse transcription was carried out at 42°C for 90 minutes to synthesize cDNA. Single-cell libraries were prepared using a modified STRT-seq method as previously described (Dong et al., 2018). Following digestion, single pEPSC cells were randomly selected using a mouth pipette and transferred into lysis buffer containing an 8-bp barcode. First-strand cDNA synthesis and amplification were conducted in a reverse transcription (RT) mixture comprising 4 U RNase inhibitor, 100 U SuperScript II reverse transcriptase (Invitrogen, 18064071), 1 mM dNTPs (TAKARA, 4019), 60 mM MgCl2, and 3 μM RT primer along with 10 μM TSO primer. The amplified product underwent purification twice with 0.8× AMPure XP beads (Beckman, A63882). Subsequently, biotin-based PCR enrichment was performed.
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and the reaction was quenched by adding glycine to a final concentration of 125 mM. Chromatin was then sonicated to an average size of 150–300 bp using a Bioruptor (Diagenode). A total of 1 µg antibody was pre-incubated with magnetic beads and subsequently introduced to the sonicated chromatin. This mixture was incubated overnight at 4°C. After incubation, the magnetic beads were subjected to a series of washes, and the chromatin was eluted. Crosslinks were then reversed, followed by the purification of the DNA.
For ATAC-seq, approximately 50,000 cells were collected, washed with cold PBS, and resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl₂; and 0.1% IGEPAL CA-630). Nuclei were isolated by centrifugation at 4°C, followed by transposition using the kit. The transposition reaction was incubated at 55°C for 10 minutes, and DNA was then amplified for 9 cycles. DNA was isolated using the Qiagen MinElute Kit and further purified with the Qiagen PCR Cleanup Kit.
The bulk RNA-seq libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530L) according to the manufacturer's instructions. The Smart-seq2 libraries were were constructed using the TruePrep DNA Library Prep Kit (Vazyme, TD502) following the manufacturer's protocol. The scRNA-seq library was constructed using the KAPA Hyper Prep Kit (KAPA, KK8054) following the manufacturer’s protocol for PCR Library Amplification/Illumina platforms.
ChIP-seq library preparation was conducted utilizing the KAPA Hyper Prep Kit (KK8500) in accordance with the manufacturer's guidelines..
ATAC-seq libraries from FACS-sorted pEPSCs were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).


title: NGS_Library-1

description: Library name: Library-1


title: pEPSC_OTX2_OE-3

description: Library name: RNA-seq_pEPSC_OTX2_OE-3


title: pEPSC_single_cell-3

description: Library name: STRT-seq_pEPSC_single_cell-3


title: pEPSC_OTX2_OE-2

description: Library name: RNA-seq_pEPSC_OTX2_OE-2


title: pEPSC_single_cell-4

description: Library name: STRT-seq_pEPSC_single_cell-4


title: pEPSC_single_cell-1

description: Library name: STRT-seq_pEPSC_single_cell-1


title: pEPSC_OTX2_OE-1

description: Library name: RNA-seq_pEPSC_OTX2_OE-1


title: pEPSC_OTX2_KO-1

description: Library name: RNA-seq_pEPSC_OTX2_KO-1


title: pEPSC_OTX2_KO-3

description: Library name: RNA-seq_pEPSC_OTX2_KO-3


title: pEPSC_LEUTX_OE-1

description: Library name: RNA-seq_pEPSC_LEUTX_OE-1


title: NGS_P2-1

description: Library name: P2-1


title: pEPSC_LEUTX_OE-2

description: Library name: RNA-seq_pEPSC_LEUTX_OE-2


title: pEPSC_OTX2_KO-2

description: Library name: RNA-seq_pEPSC_OTX2_KO-2


title: pEPSC_WT-2

description: Library name: RNA-seq_pEPSC_WT-2


title: pEPSC_WT-1

description: Library name: RNA-seq_pEPSC_WT-1


title: pEm_4C_WT-3

description: Library name: Smart-seq2_pEm_4C_WT-3


title: pEPSC_LEUTX_OE-3

description: Library name: RNA-seq_pEPSC_LEUTX_OE-3


title: pEPSC_WT-3

description: Library name: RNA-seq_pEPSC_WT-3


title: pEm_4C_OTX2_OE-3

description: Library name: Smart-seq2_pEm_4C_OTX2_OE-3


title: pEm_4C_OTX2_OE-1

description: Library name: Smart-seq2_pEm_4C_OTX2_OE-1


title: ChIPseq_pEPSC_SOX2-2

description: Library name: ChIP-seq_pEPSC_SOX2-2


title: ChIPseq_pEPSC_SOX2-1

description: Library name: ChIP-seq_pEPSC_SOX2-1


title: pEm_4C_WT-1

description: Library name: Smart-seq2_pEm_4C_WT-1


title: ChIPseq_pEPSC_OTX2-2

description: Library name: ChIP-seq_pEPSC_OTX2-2


title: ChIPseq_pEPSC_OTX2-1

description: Library name: ChIP-seq_pEPSC_OTX2-1


title: ChIPseq_pEPSC_NANOG-2

description: Library name: ChIP-seq_pEPSC_NANOG-2


title: ChIPseq_pEPSC_Input

description: Library name: ChIP-seq_pEPSC_Input


title: ChIPseq_pEPSC_LEUTX_flag-2

description: Library name: ChIP-seq_pEPSC_LEUTX_flag-2


title: ChIPseq_pEPSC_NANOG-1

description: Library name: ChIP-seq_pEPSC_NANOG-1


title: ATACseq_pEPSC_C3-1

description: Library name: ATAC-seq_pEPSC_C3-1


title: ChIPseq_pEPSC_LEUTX_flag-1

description: Library name: ChIP-seq_pEPSC_LEUTX_flag-1


title: ATACseq_pEPSC_C1-2

description: Library name: ATAC-seq_pEPSC_C1-2


title: pEm_4C_WT-2

description: Library name: Smart-seq2_pEm_4C_WT-2


title: ATACseq_pEPSC_C1-1

description: Library name: ATAC-seq_pEPSC_C1-1


title: pEm_4C_OTX2_OE-2

description: Library name: Smart-seq2_pEm_4C_OTX2_OE-2


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 473

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_473
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

molecule: nuclear RNA

organism: Oryza sativa

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

value: seedling


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 468

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_468
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 472

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_472
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 474

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_474
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 475

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_475
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 477

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_477
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 469

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_469
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 476

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_476
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 471

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_471
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 479

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_479
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 465

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_465
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 466

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_466
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 470

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_470
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 478

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_478
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 463

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_463
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 462

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_462
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 467

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_467
sci-RNA-seq3
L1_rice_combined.RData


title: ATACseq_pEPSC_C3-2

description: Library name: ATAC-seq_pEPSC_C3-2


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 480

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_480
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 461

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_461
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 458

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_458
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 460

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_460
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 459

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_459
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 455

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_455
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 456

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_456
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 453

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_453
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 454

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_454
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 457

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_457
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 452

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_452
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 464

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_464
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 443

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_443
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 449

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_449
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 447

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_447
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 444

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_444
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 441

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_441
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 451

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_451
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 440

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_440
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 442

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_442
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 448

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_448
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 439

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_439
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 437

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_437
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 435

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_435
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 433

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_433
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 434

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_434
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 431

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_431
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 427

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_427
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 426

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_426
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 430

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_430
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 429

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_429
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 428

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_428
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 424

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_424
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 450

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_450
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 425

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_425
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 445

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_445
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 438

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_438
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 446

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_446
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 423

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_423
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 422

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_422
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 420

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_420
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 419

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_419
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 421

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_421
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 436

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_436
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 413

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_413
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 416

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_416
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 417

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_417
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 414

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_414
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 412

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_412
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 411

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_411
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 410

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_410
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 432

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_432
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 418

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_418
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 408

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_408
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 409

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_409
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 407

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_407
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 404

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_404
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 405

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_405
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 403

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_403
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 402

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_402
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 415

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_415
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 398

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_398
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 400

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_400
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 395

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_395
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 393

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_393
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 399

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_399
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 397

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_397
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 391

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_391
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 392

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_392
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 396

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_396
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 390

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_390
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 394

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_394
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 389

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_389
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 388

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_388
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 387

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_387
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 386

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_386
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 384

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_384
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 382

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_382
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 383

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_383
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 381

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_381
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 380

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_380
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 406

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_406
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 379

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_379
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 401

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_401
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 378

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_378
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 377

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_377
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 375

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_375
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 371

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_371
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 372

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_372
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 373

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_373
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 369

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_369
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 370

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_370
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 368

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_368
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 367

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_367
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 364

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_364
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 376

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_376
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 363

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_363
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 362

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_362
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 385

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_385
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 366

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_366
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 287

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_287
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 285

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_285
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 361

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_361
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 283

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_283
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 281

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_281
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 280

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_280
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 284

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_284
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 278

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_278
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 282

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_282
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 277

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_277
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 279

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_279
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 374

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_374
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 275

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_275
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 274

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_274
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 276

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_276
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 365

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_365
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 273

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_273
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 272

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_272
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 288

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_288
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 271

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_271
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 267

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_267
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 269

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_269
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 270

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_270
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 268

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_268
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 265

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_265
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 266

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_266
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 262

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_262
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 263

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_263
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 261

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_261
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 264

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_264
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 259

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_259
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 258

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_258
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 260

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_260
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 257

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_257
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 256

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_256
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 255

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_255
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 254

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_254
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 250

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_250
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 252

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_252
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 253

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_253
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 249

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_249
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 251

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_251
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 246

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_246
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 248

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_248
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 247

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_247
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 245

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_245
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 244

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_244
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 241

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_241
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 240

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_240
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 237

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_237
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 238

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_238
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 239

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_239
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 243

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_243
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 236

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_236
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 234

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_234
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 242

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_242
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 232

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_232
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 233

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_233
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 231

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_231
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 230

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_230
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 229

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_229
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 228

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_228
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 227

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_227
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 235

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_235
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 225

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_225
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 226

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_226
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 224

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_224
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 219

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_219
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 222

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_222
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 221

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_221
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 223

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_223
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 220

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_220
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 217

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_217
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 216

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_216
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 214

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_214
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 215

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_215
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 213

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_213
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 211

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_211
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 207

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_207
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 206

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_206
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 204

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_204
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 197

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_197
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 198

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_198
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 203

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_203
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 208

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_208
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 209

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_209
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 212

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_212
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 199

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_199
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 205

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_205
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 202

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_202
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 201

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_201
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 191

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_191
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 190

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_190
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 196

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_196
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 195

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_195
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 194

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_194
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old rice seedlings undergoing deetiolation for 48h - technical replicate 189

description:
Library name: 8_26_22_JS_Rice_vegetative_shoot_Light_48h_189
sci-RNA-seq3
L1_rice_combined.RData