title: HealthyControl_blood_sample4,control

description: Ribosomes removed RNA


title: Bone marrow, mRNA vaccine, scRNA-seq, Biol rep 1

status: Public on Jul 31 2025

type: SRA

city: Seoul

first: Jae-Hun

last: Ahn

address: Daehak-ro 101, Jongro-gu

department: Biomedical Research Institute

country: South Korea

institute: Seoul National Universty Hospital

description: Library name: 84TIF031

library_source: transcriptomic single cell

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v8.0.1 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Briefly, raw BCL files from Illumina NovaSeq were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’.
Then, these raw FASTQ files were analyzed using ‘cellranger count’.
The ‘cellranger count’ step includes mapping to the mouse reference genome (GRCm39), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: The reference genome sequence is Mus musculus (GRCm39) from the NCBI Genome assembly
Supplementary files format and content: ZIP file. Filtered UMI count matrix (barcode, features, matrix) from Cell Ranger

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow (Femur)

growth_protocol: Six-week-old CrlOri:CD1(ICR) female mice (Specific Pathogen Free condition) were used for this expermient.

extract_protocol:
bone marrow in the left femur of the mice was immediately harvested through cold PBS flushing followed by centrifuging at 300 RCF, 4 °C for 5 mins. The supernatant was discarded and the bone marrow pellet was dissolved with RBC lysis buffer (Cat#: 00-4333-57, Invitrogen). Five minutes after the RBC lysis reaction, cells were washed twice and suspended with cell freezing medium (Cat#: 12648010, Gibco, Waltham, MA, USA). Cells were gradually frozen using a controlled-rate freezing container before being stored in liquid nitrogen until use. Prior to sequencing, frozen cells were thawed and counted using the LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems). Cell preparation followed the recommendations provided in the 10x Genomics Single Cell Protocols Cell Preparation Guide (Document CG00053) and Guidelines for Optimal Sample Preparation (Document CG000126).
Single-cell libraries were prepared using the Chromium X platform with the Chromium GEM-X Single Cell 3' Reagent Kit v4 (10x Genomics, Document CG000731) according to the manufacturer’s protocol. Briefly, cell suspensions were diluted in PBS to achieve a target recovery of 10,000 cells. Cells were mixed with the master mix and loaded onto a Chromium GEM-X Single Cell 3’ Chip v4, along with gel beads and partitioning oil. Within the generated droplets, RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed. The resulting cDNA molecules were pooled and subjected to end repair, A-tailing, adaptor ligation, and PCR amplification to construct the final cDNA libraries. Purified libraries were quantified using qPCR following the KAPA qPCR Quantification Protocol Guide, and the quality was assessed using the Agilent 4200 TapeStation. Libraries were sequenced on an Illumina NovaSeq platform according to the read length parameters specified in the user guide.

treatment_protocol: A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, bone marrow tissue was harvested from the left side femur followed by RBC lysed and kept in Cell freezing media at liquid nitrogen

tag: tissue

value: Bone marrow (Femur)

tag: strain

tag: Sex

value: female

tag: treatment

value: mRNA vaccine


title: CHI 50 mg/mL

city: Suzhou

first: Mengyao

last: Wu

state: Jiangsu

address: No.899 Pinghai Road

country: China

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample 4

data_processing:
The raw sequencing data was processed by Fastp to trim primer sequence and low quality bases. And then cellranger was used to process sequence data and aligned to human GRCh38 in order to obtain gene expression matrix. We used Seurat (version 4.0.0) to filter low quality cells, cells with number of detected genes <200 or >5000 were omitted, and use MAD variance normal to remove cells affected by mitochondrial genes. After quality control and filtering, library-size normalization to each cell was performed by NormalizeData of Seurat. The variable genes were calculated by FindVariableGenes. Then, all libraries were combined together using FindIntegrationAnchors and IntegrateData with default parameters, and using ScaleData to regress out the variability of the numbers of UMIs. Then the RunPCA and RunUMAP was used to reduce dimensions. FindClusters was used to cluster cells using the 20 dims at a resolution of 0.8.
Assembly: mouse mm10
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output H5 file

source_name: subcutaneous cholangiocarcinoma

extract_protocol:
The tissue is washed with preconfigured PBS solution, sterilized mechanically spliced, and digested with preconfigured digestion solution for 30-60 minutes (depending on the type of tissue). After digestion is terminated, centrifugation, supernatant removal, and resuspension are performed. The suspension is collected by centrifugation through a 70 nm sieve and subjected to cell lysis red (depending on the type of tissue, lysis red treatment is selected). After lysis red is completed, centrifugation and resuspension are performed through a 40 nm sieve. Finally, counting cell number and viability to observe and judge whether the cell suspension was qualified. After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1x PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg.30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer). Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
After cell counts and viability were determined, cell suspensions were adjusted to a concentration of 1,000 cells/ml in PBS supplemented with 0.04% BSA. The 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 was used according to the manufacturer's instructions. Agilent 4200 TapeStation was used to detect the fragment length distribution of the library. Also, Qubit HS DNA Kit was used to accurately quantify the effective concentration of the library ( > 10nmol/L).The qualified library was sequenced on the DNBSEQ T7 platform at the illumina NovaSeq 6000 with PE150 read length.

value: subcutaneous cholangiocarcinoma


title: NC,WT,0-3

city: Kunming, Yunnan

first: fei

last: li

address: Dongwaihuan South Road, University Town, Chenggong District, Kunming City, Yunnan Province

institute: Yunnan university

description:
Library name: sample3
slam-WT-0-3
featurecounts_nc.txt

library_source: transcriptomic

data_processing:
SLAM-Seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) data were processed using a custom computational pipeline. First, adapter trimming was performed using Trim Galore (v0.6.10) to remove sequencing adapters and low-quality bases. Cleaned reads were then aligned to the reference genome of either Homo sapiens (GRCh38) or the Neurospora crassa using STAR (v2.7.10a) with default parameters, allowing detection of mismatches such as T>C conversions.
Following alignment, SAMtools (v1.15.1) was used to convert, sort, and index the aligned SAM files into BAM format. A custom Python script was then employed to extract reads containing T>C mutations, which are indicative of 4-thiouridine incorporation and subsequent alkylation. This step produced a mutation-specific BAM file consisting only of T>C conversion-containing reads.
To quantify gene-level expression and mutation levels, featureCounts (Subread v2.0.3) was used to separately count:
(1) the number of T>C mutation reads, and
(2) the total reads (mutation-inclusive and -exclusive),
mapped to each gene based on the corresponding genome annotation (GTF file).
Finally, for each gene, a T>C mutation ratio (termed remaining reads percentage) was calculated by dividing the number of T>C mutation reads by the total number of reads, providing a quantitative measure of RNA stability and labeling retention.
Ribosome profiling data for Neurospora crassa (assembly NC12), Mus musculus(GRCm38), and Homo sapiens(GRCh38) were processed according to established pipelines. Raw sequencing reads underwent adapter trimming and size selection (retaining 25-40 nt fragments), followed by rRNA depletion. Filtered reads were aligned using Bowtie to custom genomic references containing the longest transcript per gene plus 100-nt flanking regions at both ends.  Ribosome-protected footprints (RPFs) were stratified by length, with A-site codon assignment to nucleotides 16-18 from the 5' end. Subsequently, the groups of RPFs with a high ratio of in-frame codons (e.g., >70% for N. crassa, >70% for H. sapiens, >80% for M. musculus) are selected for further analysis. These groups include RPFs in the 0 frame, as well as the +1 and -1 frames
Assembly: hg38?nc10
Supplementary files format and content: feature counts for each sample

organism: Neurospora crassa

source_name: fungal cell

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1×penicillin-streptomycin and incubated at 37℃ with 5% concentration of CO2. Neurospora crassa strains were grown in minimal mediu at 25℃ with constant light.

extract_protocol:
total RNA was extracted with Trizol reagent.
1.For SLAM-seq :After alkylation modification with iodoacetamide, 1ug total RNA (HCT116 cell) or 50 ng mRNA (N. crassa) was prepared for library. and library preperation was following the manufacturers protocal of VAHTS Universal V8 RNA-seq Library Prep Kit
2.For Ribo-seq in human cell : 2×10? HCT116 cells were lysed in 300 µL ice-cold lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl?, 1 mM DTT, 100 ?g/mL cycloheximide, 0.5% Triton X-100, 2 U/mL DNase I, 1× protease inhibitor cocktail). Lysates were centrifuged at 10,000 × g for 10 min at 4°C. Supernatants were treated with RNase I (1 U per OD??? unit) for 45 min at 25°C. Total RNA was extracted using TRIzol reagent, precipitated with glycogen, and washed with 80% ethanol. Ribosome-protected fragments (28-34 nt) were resolved on 16% TBE-urea PAGE, excised, and eluted in RNA Gel Extraction Buffer (300 mM NaOAc, 1mM EDTA, 0.25% SDS). RNA was precipitated with 1× volume isopropanol at -20°C overnight. For library preparation, 100-200 ng RNA fragments were adenylated using poly(A) polymerase and PNK (37°C, 30 min). Preadenylated 5' adapter were ligated to ribosome-protected fragments with T4 RNA Ligase 2, truncated KQ (25°C, 2 h). Then purifying the ligation product with Streptavidin magnetic bead. And template-switching primer was used in reverse transcription with SuperScript III reverse (50°C, 30 min), following the library amplification.

treatment_protocol: 100 nM 4sU was added to medium for 2 hours (N. crassa) or 24 hours (K562 cells) labeling. Then cultures were supplied with 10uM uridine to stop further labeling.

tag: cell type

value: fungal cell

tag: genotype

value: WT


title: HealthyControl_blood_sample8,control

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

description: Ribosomes removed RNA

library_source: other

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, PCR duplicates were removed using seqkit v2.4.0. The 8-bp UMIs the 6-mer following the UMI were excised from the deduplication reads using UMI_tools v1.1.4. To enhance the accuracy of the mapping results, we trimmed the 6-mer sequence to minimize such errors.
All fastq files were aligned to the human reference genome hg38, using HISAT2 v2.2.1.
The following data analysis procedures for site identification are mainly referred to PRAISE
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

molecule: other

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
Five hundred nanogram fragmented total RNA was subjected to bisulfite treatment as previous references (PMID: 36997645; 36302989; 37968414). The BS treated RNA was labeled as ‘treat’ sample, while the BS untreated RNA was labeled as ‘Input’ sample. Ten nanogram ‘treated’ RNA sample and 10 ng ‘Input’ RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v3—Pico Input Mammalian (Takara Bio, 634485) according to the manufacturer’s protocol with several modifications as previous reference. All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).
PRAISE (PMID: 36997645), BID-seq (PMID: 36302989; PMID: 37968414)

tag: cell line

value: Peripheral blood

value: untreated


title: HealthyControl_blood_sample3,control

description: Ribosomes removed RNA


title: E14-W1-23-IVP: IVP Conceptus_Mono-culture_Rep 2

city: Knoxville

first: Daniel

last: Mathew

state: TN

address: 2506 River Drive

department: Animal Science

country: USA

institute: University of Tennessee

description: Library name: Sample59

data_processing:
The RNA-Seg raw sequences (fastq) underwent adaptor removal and quality trimming using Trimmomatic and quality reads were aligned to the bovine reference genome (ARS-UCD1.2.103) using the STAR aligner program for the endometrial sequences and Hisat2 mapper program for conceptus sequences (Dobin et al., 2013; Kim et al., 2015). The sorted binary alignment maps and the NCBI gene annotation assembly were subjected to FeatureCounts to quantify read counts of genes for each sample (Liao et al., 2014).
Assembly: ARS-UCD1.2.103
Supplementary files format and content: Gene FeatureCounts in Excel

molecule: polyA RNA

organism: Bos taurus

source_name: Conceptus

extract_protocol:
Briefly, endometrial and conceptus total RNA was extracted using bead homogenization (Beadmill 4; FisherScientific) and Trizol following kit on-column isolation (endometrium) or simply the latter (conceptus) with a DNase I digestion step (RNeasy; Qiagen). Eluted RNA was assessed for quantity and quality using a NanoDrop 1000 (ThermoFisher) and the 2100 Bioanalyzer (Agilent Technologies), respectively. Total RNA was extracted from endometrial tissue from the following cultures: Endo (n=13), Endo-IVD Conc (Endo-IVD Conc; n=15), and Endo-IVP Conc (Endo-IVP Conc; n=12) and total RNA was extracted from conceptus tissue from the following cultures: IVD Conc (n=7), IVP Conc (n=7), Endo-IVD Conc (Endo-IVD Conc; n=9), and Endo-IVP Conc (Endo-IVP Conc; n=7). Endometrial and conceptus tissue RNA integrity numbers (RIN) ranged from 5.2 to 9.3 and 6.5 to 10, respectively
Library preparation including poly (A) enrichment and RNA-Seq of the explant and conceptus total RNA was performed by the University of Missouri DNA Core facility (Columbia, MO). The cDNA libraries were prepared using the Stranded RNA Prep Ligation Kit (Illumina) as described by the manufacturer. The final amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads (Corning) and the final construct of each purified library was evaluated using a Fragment Analyzer automated electrophoresis system (Agilent), quantified using the Invitrogen Qubit HS dsDNA assay kit and Qubit fluorometer, and diluted according to Illumina’s standard protocol for sequencing on the NovaSeq 6000 (Illumina).

value: Conceptus

value: RPMI Medium

tag: batch


title: Bone marrow, D-PBS, scRNA-seq, Biol rep 3

description: Library name: 84CF024

value: D-PBS


title: NC,WT,0-2

description:
Library name: sample2
slam-WT-0-2
featurecounts_nc.txt


title: HealthyControl_blood_sample1,control

description: Ribosomes removed RNA


title: E14-U1-24-IVP: IVP Conceptus_Mono-culture_Rep 1

description: Library name: Sample58


title: NC,WT,0-1

description:
Library name: sample1
slam-WT-0-1
featurecounts_nc.txt


title: R128_r_Wm50Hil80T

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline for demultiplexing and adapter removal
Sequenced reads were aligned to 88,647 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Assembly: Glycine max cv. Williams 82 Wm82.a2 at https://phytozome-next.jgi.doe.gov/
Supplementary files format and content: Excel file of the RPKM (reads per million per kilobase) of RNA-seq hits to each soybean Glyma transcript model for each library.

organism: Glycine max

source_name: immature seed coat hilum (black)

growth_protocol: Plants were grown under optimal greenhouse conditions. The developing seed were harvested at the stated mg fresh weight ranges. Whole seeds were dissected by hand into cotyledons and seed coats. The seed coat was further dissected into the hilum region or the seed coat proper.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform, lithium chloride precipitation, and ethanol precipitation.
Libraries were constructed with Illumina Tru Seq kits by the University of Illinois DNA Services Laboratory and sequenced using Illumina machines.

treatment_protocol: Standard greenhouse conditions

value: immature seed coat hilum (black)

tag: stage or_seed_fresh_weight

tag: cultivar

value: Williams

tag: lab name

tag: phenotype

value: yellow seed coat, black hilum

tag: i locu_genotype

value: i-i RT w1

tag: other genotype

tag: grin l_number

tag: grin pi_number


title: E70-S1-62b-IVP: Endometrium_IVP Conceptus Co-culture_Rep 11

description: Library name: Sample56

source_name: Intercaruncular Endometrium

value: Intercaruncular Endometrium

value: RPMI Medium + IVP Conceptus


title: HealthyControl_blood_sample13,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: HealthyControl_blood_sample12,PRAISE

description: Ribosomes removed RNA


title: E38-Q1-37-IVP: Endometrium_IVP Conceptus Co-culture_Rep 12

description: Library name: Sample57


title: Bone marrow, mRNA vaccine, scRNA-seq, Biol rep 2

description: Library name: 84TIF033

value: Bone marrow (Femur)

value: female


title: Bone marrow, D-PBS, scRNA-seq, Biol rep 1

description: Library name: 84CF021


title: E69-U1-62a-IVP: IVP Conceptus_Mono-culture_Rep 3

description: Library name: Sample60


title: C57BL/6N mice, miR-29ab1Vilin-KO4

city: China

first: Yu qi

last: Wang

address: 17 Haidian District, Beijing

institute: China agricultural univercity

description: Library name: Sample 8

data_processing:
Reads were mapped to reference genome with Hisat2
Differential expression analysis was conducted using DESeq2 R
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon tumor

extract_protocol:
RNA was harvested using TRIzol method.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

value: colon tumor


title: R51_rwm43h2


title: HealthyControl_blood_sample2,control

description: Ribosomes removed RNA


title: E70-Q1-62a-IVP: Endometrium_IVP Conceptus Co-culture Rep 10

description: Library name: Sample55


title: RNA-seq of HSPA1A-3

city: Guangzhou

first: Wenjie

last: Zhang

address: Guangzhou Medical University, No.1 Xinzao Road, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

description: Library name: Sample 3

data_processing:
Raw data (FASTQ format) underwent base calling and quality control. Differentially expressed genes (DEGs) were identified (threshold: |log₂FC| > 0.58, adjusted P value < 0.05). DEG heatmaps were generated using the pheatmap package, and volcano plots were created with ggplot2. Downregulated DEGs were analyzed for GO enrichment using Metascape (Fisher’s exact test，P < 0.05).
Assembly: macrophages
Supplementary files format and content: .xlsx

source_name: plantar

extract_protocol:
Total RNA was isolated, treated with DNase, and purified using columns. RNA concentration was measured and adjusted. RNA quality was confirmed using a fragment analyzer.
Qualified samples were used for library preparation: mRNA was enriched with oligo-dT beads, fragmented, and cDNA was synthesized. Adapters were ligated and PCR-amplified. Libraries were sequenced (paired-end) on an Illumina platform.

value: plantar


title: E69-S1-62b-IVP: Endometrium_IVP Conceptus Co-culgure Rep 9

description: Library name: Sample54


title: C57BL/6N mice, miR-29ab1Vilin-KO2

description: Library name: Sample 6


title: R126_r_Wm25Hil78T


title: HealthyControl_blood_sample9,PRAISE

description: Ribosomes removed RNA


title: E69-Q1-62a-IVP: Endometrium_IVP Conceptus Co-culture Rep 8

description: Library name: Sample53


title: HealthyControl_blood_sample11,PRAISE

description: Ribosomes removed RNA


title: R129_r_Wm50BY81T

source_name: immature seed coat w/o hilum (yellow)

value: immature seed coat w/o hilum (yellow)


title: C57BL/6N mice, miR-29ab1Vilin-KO1

description: Library name: Sample 5


title: HealthyControl_blood_sample8,PRAISE

description: Ribosomes removed RNA

value: Peripheral blood


title: HealthyControl_blood_sample10,PRAISE

description: Ribosomes removed RNA


title: C57BL/6N mice, miR-29ab1Vilin-KO3

description: Library name: Sample 7


title: HealthyControl_blood_sample7,PRAISE

description: Ribosomes removed RNA


title: Bone marrow, D-PBS, scRNA-seq, Biol rep 2

description: Library name: 84CF022


title: E39-S1-23-IVP: Endometrium_IVP Conceptus Co-culture_Rep 7

description: Library name: Sample52


title: C57BL/6N mice, Wildtype3

description: Library name: Sample 3


title: R127_r_Wm25BY79T


title: C57BL/6N mice, Wildtype2

description: Library name: Sample 2


title: E39-Q1-24-IVP: Endometrium_IVP Conceptus Co-culture_Rep 6

description: Library name: Sample51


title: E14-S1-23-IVP: Endometrium_IVP Conceptus Co-culture_Rep 5

description: Library name: Sample50


title: HealthyControl_blood_sample5,PRAISE

description: Ribosomes removed RNA


title: HealthyControl_blood_sample6,PRAISE

description: Ribosomes removed RNA


title: R52_rwm43b


title: E14-Q1-24-IVP: Endometrium_IVP Conceptus Co-culture_Rep 4

description: Library name: Sample49


title: C57BL/6N mice, Wildtype1

description: Library name: Sample 1


title: R71_GZ7FL.R1

data_processing:
Illumina pipeline for demultiplexing and adaptor removal
Sequenced reads were aligned to 88,647 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Assembly: Glycine max cv. Williams 82 Wm82.a2 at https://phytozome-next.jgi.doe.gov/
Supplementary files format and content: Excel file of the RPKM (reads per million per kilobase) of RNA-seq hits to each soybean Glyma transcript model for each library.

source_name: flowers

growth_protocol: Plants were grown under optimal greenhouse conditions. The developing seed were harvested at the stated mg fresh weight ranges. Whole seeds were dissected by hand into cotyledons and seed coats. Other tissues as seedling cotyledons, vegetative buds, or shoots tips, were extracted from germinating seedlings or 1 month-old plants.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform, lithium chloride precipitation, and ethanol precipitation.
Libraries were constructed with Illumina Tru Seq or Stranded Tru Seq kits by the University of Illinois DNA Services Laboratory and sequenced using Illumina machines.

treatment_protocol: Standard greenhouse conditions unless otherwise noted in each sample.

value: flowers

tag: stage or_seed_fresh_wt

value: adult plant

value: Williams W1 purple flower isoline

tag: lab names

tag: phenotype descriptors

value: purple flower

tag: other

tag: grin l_number_(or_other_designation)


title: C57BL/6N mice, Wildtype4

description: Library name: Sample 4

tag: tissue

tag: strain


title: E17-S2-18-IVP: Endometrium_IVP Conceptus Co-culture_Rep 3

description: Library name: Sample48

tag: treatment


title: pIR_E65_PBAT_3

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description:
Library name: pIR_E65_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g82 for maternal) are results merged from all replicates of the indicated genotypes

library_source: genomic

data_processing:
For data processing, mm10 reference genome were masked to N-masked genome by genome preparation function of SNPsplit (v0.5.0) based on the SNPs between C57BL/6J and 129S1/SvImJ. The clean data were mapped to N-masked mm10 genome using bismark (v0.23.1) in paired-end mode with parameters --pbat --unmapped. The unmapped reads were then mapped again in single-end mode with parameter --pbat and default settings for unmapped reads 1 and 2, respectively. After being deduplicated, the three bam files above were split into paternal and maternal alignments based on SNPs with SNPsplit. Finally, according to the origin of the read segments, PE and SE alignments were merged for further downstream steps. The methylation levels of CpG sites were quantified with bismark_methylation_extractor. The DMRs were identified by CGmapTools (v0.1.2) and filtered by the DMR length (more than 100 bp), CpG number (at least 5 CpG sites in a DMR), and the methylation level difference (more than 20% absolute methylation level difference). Bigwig files were generated using bedGraphToBigWig (v4) and visualized in Integrative Genomics Viewer (IGV). The annotation files of genes and repetitive elements (RepeatMasker) were downloaded from the UCSC Genome Browser. The methylation levels of different genomic elements were calculated with bedtools (v2.30.0).
Assembly: mm10
Supplementary files format and content: tab-separated  file, methylation level for every CpG site. Bed file column headers: chr, start, end, methylation_level

molecule: genomic DNA

source_name: E6.5 embryo

extract_protocol:
Cell lysis, BS conversion and DNA purification were performed with the EZ DNA Methylation-Direct Kit (Zymo Research, D5021) following the manufacturer's instructions.
Cell lysis, BS conversion and DNA purification were performed with the EZ DNA Methylation-Direct Kit (Zymo Research, D5021) following the manufacturer's instructions. The eluted DNA were mixed with 0.4 mM dNTPs (Takara, 4019), 0.4 μM oligo 1 (5’-Biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 1x Blue Buffer (TIANGEN, NG202) (24 μl final) before incubation at 65 ℃ for 3 min followed by 4 ℃ pause. Then the samples were combined with 50 U of Klenow exo- (TIANGEN, NG202) and incubated at 4 ℃ for 5 min, + 1 ℃/15 s to 37 ℃, 37 ℃ for 1 h. Samples were incubated at 95 ℃ for 1 min and transferred to ice immediately before addition of fresh oligo 1 (10 pmol), Klenow exo- (25 U), and dNTPs (1 nmol) in 2.5 µl total. The samples were incubated at 4 ℃ for 5 min, + 1 ℃/15 s to 37 ℃, 37 ℃ for 1 h again. This random priming and extension step repeated 7 times in total. Samples were then incubated with 40 U exonuclease I (NEB) for 1 h at 37 ℃ and purified with 0.8x VAHTS DNA Clean Beads. Samples were eluted in 50 µl Elution Buffer (QIAGEN) and mixed with 50 µl washed M-280 Streptavidin Beads (ThermoFisher, 11205D) before incubation at room temperature for 30 min. Beads were washed twice with 0.1 M NaOH, twice with Wash Buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2 M NaCl) and resuspended in 48 µl of 0.4 mM dNTPs, 0.4 µM oligo 2 (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and 1x Blue Buffer. Samples were incubated at 95 ℃ for 45 s and transferred to ice immediately before addition of 100 U of Klenow exo- and incubated at 4 ℃ for 5 min, + 1 ℃/15 s to 37 ℃, 37 ℃ for 1.5 h. Then beads were washed twice with 50 µl Elution Buffer and resuspended in 50 µl Amplification mix including 25 µl 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 23 µl Nuclease-Free Water (ThermoFisher, AM9932), 1 µl Universal PCR Primer and 1 µl Index PCR Primer (NEBNext Multiplex Oligos for Illumina (NEB, E7335S)). Libraries were then amplified by PCR as follows: 95 ℃ for 3 min, 12-15 repeats of (98 ℃ for 20 s, 60 ℃ for 30 s, 72 ℃ for 1 min), 72 ℃ for 5 min and 4 ℃ hold. Amplified libraries were purified using VAHTS DNA Clean Beads (Vazyme, N411) following the manufacturer’s guidelines and sequenced on the Illumina NovaSeq 6000.

value: E6.5 embryo

tag: genotype

value: pIR


title: R58_WM43B2

tag: stage or_seed_fresh_weight

value: Williams

value: yellow seed coat, black hilum


title: HealthyControl_blood_sample4,PRAISE

description: Ribosomes removed RNA

tag: cell line

tag: cell type


title: R47_W43RT12.R1

source_name: roots 5 day, 12 hr flooding

value: roots 5 day, 12 hr flooding

value: 5 day greenhouse seedlings

tag: cultivar

value: i-i RT w1


title: pIR_E65_PBAT_2

description:
Library name: pIR_E65_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g81 for maternal) are results merged from all replicates of the indicated genotypes


title: HealthyControl_blood_sample3,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: R48_W43RT24.R1

source_name: roots 5 day, 24 hr flooding

value: roots 5 day, 24 hr flooding


title: HealthyControl_blood_sample2,PRAISE

description: Ribosomes removed RNA


title: E17-Q2-28-IVP: Endometrium_IVP Concetpus Co-culture_Rep 2

description: Library name: Sample47

value: Intercaruncular Endometrium

value: RPMI Medium + IVP Conceptus

tag: batch


title: E15-Q2-28-IVP: Endometrium_IVP Conceptus Co-culture_Rep 1

description: Library name: Sample46


title: pIR_E65_PBAT_1

description:
Library name: pIR_E65_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g80 for maternal) are results merged from all replicates of the indicated genotypes


title: R183_UC508SC5.R1

source_name: immature seed coat

value: immature seed coat

value: Harosoy isoline with defective seed coats

value: Harsoy isoline with defective seed coats

value: I r T W1

value: Def, net

value: F4 of Harosoy (6) x PI 196166


title: pIR_E55_PBAT_2

description:
Library name: pIR_E55_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g79 for maternal) are results merged from all replicates of the indicated genotypes

source_name: E5.5 embryo

value: E5.5 embryo


title: R182_UC501SC5.R1

value: Harosoy

value: Harsoy with yellow seed coat


title: E54-T1-47-AI: IVD Conceptus_Endometrium Co-culture_Rep 8

description: Library name: Sample44

value: Conceptus

value: RPMI Medium + Endometrium


title: pIR_E55_PBAT_1

description:
Library name: pIR_E55_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g78 for maternal) are results merged from all replicates of the indicated genotypes

value: pIR


title: CRC_blood_sample10,control

description: Ribosomes removed RNA

value: Peripheral blood

value: untreated


title: CRC_blood_sample9,control

description: Ribosomes removed RNA


title: R149_T157GZ400.R1

value: T157, i mutation

value: imperfect black seed coat

value: i R t


title: E39-T1-26-AI: IVD Conceptus_Endometrium Co-culture_Rep 7

description: Library name: Sample43


title: pIR_B_PBAT_6

description:
Library name: pIR_B_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g77 for maternal) are results merged from all replicates of the indicated genotypes

source_name: blastocyst

value: blastocyst


title: R148_T157GZ300.R1

value: immature seed coat


title: E38-T1-66-AI: IVD Conceptus_Endometrium Co-culture_Rep 6

description: Library name: Sample42


title: R45_T157SC.R1


title: CRC_blood_sample8,control

description: Ribosomes removed RNA


title: CRC_blood_sample7,control

description: Ribosomes removed RNA


title: E38-R1-50-AI: IVD Conceptus_Endometrium Co-culture_Rep 5

description: Library name: Sample41


title: pIR_B_PBAT_4

description:
Library name: pIR_B_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g75 for maternal) are results merged from all replicates of the indicated genotypes


title: HealthyControl_blood_sample1,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: E70-R1-71-AI: IVD Conceptus_Endometrium Co-culture_Rep 9

description: Library name: Sample45


title: E19-T1-47-AI: IVD Conceptus_Endometrium Co-culture_Rep 4

description: Library name: Sample40


title: pIR_B_PBAT_5

description:
Library name: pIR_B_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g76 for maternal) are results merged from all replicates of the indicated genotypes


title: pIR_B_PBAT_3

description:
Library name: pIR_B_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g74 for maternal) are results merged from all replicates of the indicated genotypes


title: CRC_blood_sample6,control

description: Ribosomes removed RNA


title: pIR_B_PBAT_2

description:
Library name: pIR_B_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g73 for maternal) are results merged from all replicates of the indicated genotypes


title: R139_T6WS5D_R1

source_name: immature whole seed

value: immature whole seed

value: 5 DAF


title: E14-T1-26-AI: IVD Conceptus_Endometrium Co-culture_Rep 3

description: Library name: Sample39


title: CRC_blood_sample5,control

description: Ribosomes removed RNA


title: R138_T3SC10mg_R1

value: 10-25 mg seed


title: E19-R1-22-AI: IVD Conceptus_Endometrium Co-culture_Rep 2

description: Library name: Sample38


title: CRC_blood_sample4,control

description: Ribosomes removed RNA


title: R146_RichGZ300.R1

value: Richland

value: Rich

value: yellow seed coat

value: I R t


title: CRC_blood_sample3,control

description: Ribosomes removed RNA


title: pIR_M_PBAT_4

description:
Library name: pIR_M_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g71 for maternal) are results merged from all replicates of the indicated genotypes

source_name: morula

value: morula


title: CRC_blood_sample2,control

description: Ribosomes removed RNA


title: E69-V1-71-AI: IVD Conceptus_Mono-culture_Rep 8

description: Library name: Sample36

value: Conceptus

value: RPMI Medium


title: pIR_M_PBAT_3

description:
Library name: pIR_M_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g70 for maternal) are results merged from all replicates of the indicated genotypes

value: pIR


title: R136_R1SC10mg_R1


title: CRC_blood_sample1,control

description: Ribosomes removed RNA

value: Peripheral blood

value: untreated


title: pIR_M_PBAT_2

description:
Library name: pIR_M_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g69 for maternal) are results merged from all replicates of the indicated genotypes


title: E38-X1-66-AI: IVD Conceptus_Mono-culture_Rep 7

description: Library name: Sample35


title: R137_R5WS5D_R1


title: E38-V1-50-AI: IVD Conceptus_Mono-culture_Rep 6

description: Library name: Sample34


title: CRC_blood_sample10,PRAISE

description: Ribosomes removed RNA


title: pIR_B_PBAT_1

description:
Library name: pIR_B_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g72 for maternal) are results merged from all replicates of the indicated genotypes


title: R181_UC9SC5.R1

value: Clark, i mutation

value: black seed coat

value: i  R T    W1

value: 138 kb i deletion


title: pIR_8C_PBAT_3

description:
Library name: pIR_8C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g67 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 8C embryo

value: 8C embryo


title: CRC_blood_sample9,PRAISE

description: Ribosomes removed RNA

source_name: Peripheral blood

value: PRAISE


title: R165_r55WS2.R1

value: immature whole seed

value: 5 DAF

value: Williams 55, i mutation

value: i R w1


title: pIR_M_PBAT_1

description:
Library name: pIR_M_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g68 for maternal) are results merged from all replicates of the indicated genotypes


title: E19-X1-47-AI: IVD Conceptus_Mono-culture_Rep 5

description: Library name: Sample33

source_name: Conceptus


title: E14-R1-8-AI: IVD Conceptus_Endometrium Co-culture_Rep 1

description: Library name: Sample37

value: RPMI Medium + Endometrium


title: E14-X1-26-AI: IVD Conceptus_Mono-culture_Rep 4

description: Library name: Sample32


title: pIR_8C_PBAT_2

description:
Library name: pIR_8C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g66 for maternal) are results merged from all replicates of the indicated genotypes


title: R164_r55WS1.R1


title: CRC_blood_sample8,PRAISE

description: Ribosomes removed RNA


title: R44_RichSC.R1

value: immature seed coat

value: Richland

value: Rich

value: yellow seed coat

value: I R t


title: E19-V1-22-AI: IVD Conceptus_Mono-culture_Rep 3

description: Library name: Sample31

value: Conceptus

value: RPMI Medium


title: pIR_8C_PBAT_1

description:
Library name: pIR_8C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g65 for maternal) are results merged from all replicates of the indicated genotypes

value: pIR


title: CRC_blood_sample7,PRAISE

description: Ribosomes removed RNA

value: Peripheral blood


title: pIR_4C_PBAT_4

description:
Library name: pIR_4C_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g64 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 4C embryo

value: 4C embryo


title: R153_UC55GZ400.R1

value: black seed coat

value: i-i RT w1

value: 138 kb i deletion


title: E14-V1-8-AI: IVD Conceptus_Mono-culture_Rep 2

description: Library name: Sample30


title: CRC_blood_sample6,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: R152_UC55GZ300.R1

value: Williams 55, i mutation


title: E56-V1-5-AI: IVD Conceptus_Mono-culture_Rep 1

description: Library name: Sample29


title: pIR_4C_PBAT_3

description:
Library name: pIR_4C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g63 for maternal) are results merged from all replicates of the indicated genotypes


title: R163_r55SC2.R1

value: i R w1


title: pIR_4C_PBAT_2

description:
Library name: pIR_4C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g62 for maternal) are results merged from all replicates of the indicated genotypes


title: 19 hours after  training, naive, rep 3, WH

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

data_processing:
Raw sequence reads were trimmed using Trimmomatic (version 0.39), removing low quality leading and tailing bases (below quality 3) and reads below 30 bases.
Trimmed reads were aligned to D. melanogaster genome (dm6) using STAR (version 2.7.5a). Reads were also aligned to C. elegans unc-84 gene (NC_003284.9).
Reads that aligned to multiple loci, or to one loci with >4 mismatches, and genes that mapped to Drosophila rRNA were removed.
Gene counts were obtained using using FeatureCounts from the Rsubread R package (version 2.4.2).
Assembly: dm6
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Whole head

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head (WH) homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from MB and WH fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Tecan Universal Plus Total RNA-Seq library preparation kit (Tecan: 3061-A01) according to manufacturer instructions.

value: Whole head


title: CRC_blood_sample4,PRAISE

description: Ribosomes removed RNA


title: R162_r55SC1.R1

value: immature seed coat


title: 19 hours after training, naive, rep 3, MB

source_name: Mushroom body

value: Mushroom body


title: CRC_blood_sample3,PRAISE

description: Ribosomes removed RNA


title: pIR_4C_PBAT_1

description:
Library name: pIR_4C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g61 for maternal) are results merged from all replicates of the indicated genotypes


title: R151_WM43GZ400.R1

value: Williams, W43

value: yellow seed coat, black hilum


title: pIR_2C_PBAT_7

description:
Library name: pIR_2C_PBAT_7
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g60 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 2C embryo

value: 2C embryo


title: 19 hours after training, naive, rep 2, WH


title: R150_WM43GZ300.R1


title: CRC_blood_sample2,PRAISE

description: Ribosomes removed RNA


title: D069_CGbip3, Small RNA-Seq

description:
Raw _smRNA_total_and_unique_counts_by_strand.xlsx
CHS_RPMs.xlsx

data_processing:
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and then removing it from the read.
Alignments of raw sequences were performed using the Bowtie v.1 program (Langmead et al., 2009) allowing 2 mismatches.
Assembly: Williams 82 Wm82a.4 soybean reference genome
Supplementary files format and content: Excel file of the total number or unique number of hits of small RNA sequences to each soybean Glyma transcript model by strand
Supplementary files format and content: Excel file of total and normalized CHS7 and CHS8 reads per million (RPM) for each library.

source_name: shoot tips of Clark glabrous

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and ethanol precipitation.
Libraries were constructed with Illumina True-Seq Small RNA kit or Perkin Elmer NextFlex Small RNA sample kit v. 2 by the University of Illinois DNA Services Laboratory using an Illumina HiSeq 2000, or HiSeq 2500 sequencing.

value: shoot tips of Clark glabrous

value: 1 month plant

tag: lab name

value: CG

tag: phenotype

tag: i locu_genotype

value: i-i R T, P1

tag: other genotype


title: 19 hours after training, naive, rep 2, MB


title: pIR_2C_PBAT_6

description:
Library name: pIR_2C_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g59 for maternal) are results merged from all replicates of the indicated genotypes

value: pIR


title: patient21,tumor_control

description: Ribosomes removed RNA

source_name: tumor

value: tumor

value: colorectum

value: untreated


title: D068_2C5bip2, Small RNA-Seq

source_name: shoot tips from Clark five foliate

value: shoot tips from Clark five foliate

value: CF

value: i-i R T, Lf1

tag: grin l_number

tag: grin pi_number


title: 19 hours after training, naive, rep 1, WH

value: Whole head


title: pIR_2C_PBAT_5

description:
Library name: pIR_2C_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g58 for maternal) are results merged from all replicates of the indicated genotypes


title: 19 hours after training, naive, rep 1, MB


title: pIR_2C_PBAT_4

description:
Library name: pIR_2C_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g57 for maternal) are results merged from all replicates of the indicated genotypes


title: patient19,tumor_control

description: Ribosomes removed RNA


title: patient18,tumor_control

description: Ribosomes removed RNA


title: D090_WM43Leaf130, Small RNA-Seq

source_name: leaf

value: leaf

value: 10 day seedling

value: Williams

value: W43 orUC43

value: i-i R T


title: 13 hours after  training, naive, rep 3, WH


title: pIR_2C_PBAT_3

description:
Library name: pIR_2C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g56 for maternal) are results merged from all replicates of the indicated genotypes

value: 2C embryo


title: R53_rwm43h

source_name: immature seed coat hilum (black)

value: immature seed coat hilum (black)

value: yellow seed coat, black hilum

value: i-i RT w1


title: CRC_blood_sample1,PRAISE

description: Ribosomes removed RNA

value: Peripheral blood

value: PRAISE


title: D085_SHCOT7, Small RNA-Seq

source_name: seedling cotyledon

value: seedling cotyledon

value: Stage 7:cotyledon above ground; fully green; 7-8 cm plantlets; unifoliated developed


title: patient17,tumor_control

description: Ribosomes removed RNA

value: tumor

value: colorectum

value: untreated


title: pIR_2C_PBAT_2

description:
Library name: pIR_2C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g55 for maternal) are results merged from all replicates of the indicated genotypes

value: pIR


title: 13 hours after training, naive, rep 3, MB

value: Mushroom body


title: D084_SHCOT6, Small RNA-Seq

value: Stage 6:cotyledon mostly green and straight


title: 13 hours after training, naive, rep 2, WH

value: Whole head


title: patient16,tumor_control

description: Ribosomes removed RNA


title: patient15,tumor_control

description: Ribosomes removed RNA


title: D082_SHCOT4, Small RNA-Seq

value: Stage 4:cotyledon pushing from ground;mostly yellow with green edges; hypocotyls 40-50 mm long

value: Williams

value: W43 orUC43


title: D083_SHCOT5, Small RNA-Seq

value: Stage 5:cotyledon above ground; beginning to straighten; yellow and green; primary root development initiated

value: i-i R T


title: pWT_E65_PBAT_3

description:
Library name: pWT_E65_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g53 for maternal) are results merged from all replicates of the indicated genotypes

source_name: E6.5 embryo

value: E6.5 embryo

value: pWT


title: pWT_E65_PBAT_2

description:
Library name: pWT_E65_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g52 for maternal) are results merged from all replicates of the indicated genotypes


title: patient13,tumor_control

description: Ribosomes removed RNA


title: patient14,tumor_control

description: Ribosomes removed RNA


title: D081_SHCOT3, Small RNA-Seq

value: Stage 3:yellow cotyledon underground, radicle size 16-25 mm long

value: yellow seed coat, black hilum


title: patient11,tumor_control

description: Ribosomes removed RNA


title: pWT_E65_PBAT_1

description:
Library name: pWT_E65_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g51 for maternal) are results merged from all replicates of the indicated genotypes


title: 13 hours after training, naive, rep 1, WH


title: 13 hours after training, naive, rep 1, MB


title: D080_SHCOT2, Small RNA-Seq

value: seedling cotyledon

value: Stage 2:yellow cotyledon underground and seed radicle size 10-15 mm long


title: 7 hours after  training, naive, rep 3, WH


title: pWT_E55_PBAT_3

description:
Library name: pWT_E55_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g50 for maternal) are results merged from all replicates of the indicated genotypes

source_name: E5.5 embryo

value: E5.5 embryo


title: pWT_E55_PBAT_2

description:
Library name: pWT_E55_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g49 for maternal) are results merged from all replicates of the indicated genotypes


title: D079_SHCOT1, Small RNA-Seq

value: Stage 1:yellow seed, imbibed and 48 hr underground


title: 7 hours after training, naive, rep 3, MB


title: patient10,tumor_control

description: Ribosomes removed RNA

value: tumor

value: colorectum

value: untreated


title: 13 hours after training, naive, rep 2, MB

value: Mushroom body


title: D113_200_300YAxis, Small RNA-Seq

source_name: immature embryo axis only

value: immature embryo axis only

value: 200-300 mg yellow


title: patient9,tumor_control

description: Ribosomes removed RNA


title: 7 hours after training, naive, rep 2, MB


title: pIR_2C_PBAT_1

description:
Library name: pIR_2C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g54 for maternal) are results merged from all replicates of the indicated genotypes

value: 2C embryo

value: pIR


title: 7 hours after training, naive, rep 2, WH

value: Whole head


title: D116_400YAxis, Small RNA-Seq

value: 300-400mg yellow

value: Williams

value: W43 orUC43

value: i-i R T


title: patient8,tumor_control

description: Ribosomes removed RNA


title: pWT_E55_PBAT_1

description:
Library name: pWT_E55_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g48 for maternal) are results merged from all replicates of the indicated genotypes

value: pWT


title: D114_300YCot, Small RNA-Seq

source_name: immature cotyledon no embryo axis

value: immature cotyledon no embryo axis

value: yellow seed coat, black hilum


title: patient7,tumor_control

description: Ribosomes removed RNA


title: pWT_B_PBAT_4

description:
Library name: pWT_B_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g47 for maternal) are results merged from all replicates of the indicated genotypes

source_name: blastocyst

value: blastocyst


title: 7 hours after training, naive, rep 1, WH


title: pWT_B_PBAT_3

description:
Library name: pWT_B_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g46 for maternal) are results merged from all replicates of the indicated genotypes


title: 7 hours after training, naive, rep 1, MB


title: patient6,tumor_control

description: Ribosomes removed RNA

value: tumor


title: D145_T3SC10mg, Small RNA-Seq

source_name: immature seed coat

value: immature seed coat

value: imperfect black seed coat

value: i R t


title: pWT_B_PBAT_2

description:
Library name: pWT_B_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g45 for maternal) are results merged from all replicates of the indicated genotypes


title: 1 hour after  training, naive, rep 3, WH


title: pWT_B_PBAT_1

description:
Library name: pWT_B_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g44 for maternal) are results merged from all replicates of the indicated genotypes


title: D141_T3SC5mg, Small RNA-Seq

description:
Raw _smRNA_total_and_unique_counts_by_strand.xlsx
CHS_RPMs.xlsx


title: 1 hour after training, naive, rep 3, MB

value: Mushroom body


title: D139_T2SC5mg, Small RNA-Seq


title: pWT_M_PBAT_10

description:
Library name: pWT_M_PBAT_10
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g43 for maternal) are results merged from all replicates of the indicated genotypes

source_name: morula

value: morula


title: patient2,tumor_control

description: Ribosomes removed RNA

value: colorectum

value: untreated


title: 1 hour after training, naive, rep 2, WH

value: Whole head


title: pWT_M_PBAT_9

description:
Library name: pWT_M_PBAT_9
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g42 for maternal) are results merged from all replicates of the indicated genotypes


title: D137_T1SC5mg, Small RNA-Seq


title: R147_RichGZ400.R1

tag: stage or_seed_fresh_wt

value: Richland

tag: lab names

value: Rich

tag: phenotype descriptors

value: yellow seed coat

value: I R t

tag: other


title: D143_R1SC10mg, Small RNA-Seq

tag: tissue


title: pWT_M_PBAT_8

description:
Library name: pWT_M_PBAT_8
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g41 for maternal) are results merged from all replicates of the indicated genotypes

tag: genotype

value: pWT


title: D117_DryCot, Small RNA-Seq

source_name: cotyledon, mature dry

value: cotyledon, mature dry

tag: stage or_seed_fresh_weight

value: 100-200 mg dry seed

value: Williams

value: W43 orUC43

value: i-i R T


title: 1 hour after training, naive, rep 2, MB


title: patient19,tumor,PRAISE

description: Ribosomes removed RNA

value: tumor

tag: cell line

tag: treatment

value: PRAISE


title: D135_R3SC5mg, Small RNA-Seq

value: immature seed coat

tag: cultivar


title: patient5,tumor_control

description: Ribosomes removed RNA

tag: cell type


title: pWT_M_PBAT_6

description:
Library name: pWT_M_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g39 for maternal) are results merged from all replicates of the indicated genotypes

value: morula


title: 1 hour after training, naive, rep 1, WH

source_name: Whole head


title: patient21,tumor,PRAISE

description: Ribosomes removed RNA

value: colorectum


title: 1 hour after training, naive, rep 1, MB

source_name: Mushroom body

value: Mushroom body


title: patient18,tumor,PRAISE

description: Ribosomes removed RNA


title: 1 hour during training, naive, rep 3, WH

value: Whole head


title: pWT_M_PBAT_5

description:
Library name: pWT_M_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g38 for maternal) are results merged from all replicates of the indicated genotypes


title: patient4,tumor_control

description: Ribosomes removed RNA

value: untreated


title: patient1,tumor_control

description: Ribosomes removed RNA


title: pWT_M_PBAT_7

description:
Library name: pWT_M_PBAT_7
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g40 for maternal) are results merged from all replicates of the indicated genotypes


title: D131_R1SC5mg, Small RNA-Seq

value: Richland

tag: lab name

value: Rich


title: 1 hour during training, naive, rep 3, MB


title: pWT_M_PBAT_4

description:
Library name: pWT_M_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g37 for maternal) are results merged from all replicates of the indicated genotypes


title: 1 hour during training, naive, rep 2, WH


title: pWT_M_PBAT_3

description:
Library name: pWT_M_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g36 for maternal) are results merged from all replicates of the indicated genotypes


title: D149_UC7WS50, Small RNA-Seq

source_name: immature seed coat (whole seed coat)

value: immature seed coat (whole seed coat)

value: Clark 63, UC7

tag: phenotype

value: yellow seed coat, black hilum


title: D152_UC413WS50, Small RNA-Seq

value: Clark isoline with minute hilum, defective seed coat and t

tag: i locu_genotype

value: i-i R t, miG

value: mi G


title: CRC_blood_sample5,PRAISE

description: Ribosomes removed RNA

source_name: Peripheral blood

value: Peripheral blood


title: patient15,tumor,PRAISE

description: Ribosomes removed RNA

source_name: tumor

value: tumor


title: 1 hour during training, naive, rep 2, MB


title: patient14,tumor,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: D133_R2SC5mg, Small RNA-Seq

value: immature seed coat

value: yellow seed coat

value: I R t

tag: other genotype


title: 1 hour during training, naive, rep 1, WH


title: D110_DrySC, Small RNA-Seq

source_name: seed coat, dry mature

value: seed coat, dry mature

value: 100-200 mg dry seed

value: Williams

value: W43 orUC43

value: i-i R T

tag: grin l_number


title: D035_WM44SC, Small RNA-Seq

value: Williams 44 mutation

value: W44, i mutation

value: black seed coat

value: i R T

tag: grin pi_number


title: patient13,tumor,PRAISE

description: Ribosomes removed RNA

value: colorectum


title: D115_300YSC, Small RNA-Seq

value: 200-300 mg yellow

value: yellow seed coat, black hilum


title: pWT_M_PBAT_1

description:
Library name: pWT_M_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g34 for maternal) are results merged from all replicates of the indicated genotypes

value: morula

value: pWT


title: 1 hour during training, naive, rep 1, MB

value: Mushroom body


title: pWT_8C_PBAT_5

description:
Library name: pWT_8C_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g33 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 8C embryo

value: 8C embryo


title: pWT_8C_PBAT_4

description:
Library name: pWT_8C_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g32 for maternal) are results merged from all replicates of the indicated genotypes


title: patient17,tumor,PRAISE

description: Ribosomes removed RNA

value: tumor

value: PRAISE


title: patient11,tumor,PRAISE

description: Ribosomes removed RNA


title: patient10,tumor,PRAISE

description: Ribosomes removed RNA


title: patient9,tumor,PRAISE

description: Ribosomes removed RNA


title: pWT_8C_PBAT_3

description:
Library name: pWT_8C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g31 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_M_PBAT_2

description:
Library name: pWT_M_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g35 for maternal) are results merged from all replicates of the indicated genotypes


title: patient16,tumor,PRAISE

description: Ribosomes removed RNA


title: D104_400_500SC, Small RNA-Seq

value: immature seed coat


title: D102_100_200SC, Small RNA-Seq

value: Williams


title: pWT_8C_PBAT_1

description:
Library name: pWT_8C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g29 for maternal) are results merged from all replicates of the indicated genotypes


title: patient7,tumor,PRAISE

description: Ribosomes removed RNA


title: patient6,tumor,PRAISE

description: Ribosomes removed RNA


title: pWT_4C_PBAT_6

description:
Library name: pWT_4C_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g27 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 4C embryo

value: 4C embryo


title: patient4,tumor,PRAISE

description: Ribosomes removed RNA


title: patient8,tumor,PRAISE

description: Ribosomes removed RNA


title: pWT_4C_PBAT_4

description:
Library name: pWT_4C_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g25 for maternal) are results merged from all replicates of the indicated genotypes


title: patient2,tumor,PRAISE

description: Ribosomes removed RNA


title: pWT_4C_PBAT_3

description:
Library name: pWT_4C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g24 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_8C_PBAT_2

description:
Library name: pWT_8C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g30 for maternal) are results merged from all replicates of the indicated genotypes


title: patient1,tumor,PRAISE

description: Ribosomes removed RNA


title: pWT_4C_PBAT_5

description:
Library name: pWT_4C_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g26 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_4C_PBAT_2

description:
Library name: pWT_4C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g23 for maternal) are results merged from all replicates of the indicated genotypes


title: patient5,tumor,PRAISE

description: Ribosomes removed RNA


title: patient21,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA

source_name: adjacent normal

value: adjacent normal

value: untreated


title: pWT_4C_PBAT_1

description:
Library name: pWT_4C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g22 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_2C_PBAT_6

description:
Library name: pWT_2C_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g21 for maternal) are results merged from all replicates of the indicated genotypes

source_name: 2C embryo

value: 2C embryo


title: patient20,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: pWT_2C_PBAT_5

description:
Library name: pWT_2C_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g20 for maternal) are results merged from all replicates of the indicated genotypes


title: pine1 2 IP

city: Milano

first: Vittoria

last: Brambilla

state: Milano

address: Via Celoria, 26

department: Agricoltural and environmental sciences

country: Italy

institute: University of MIlan

data_processing:
cutadapt 1.8.3 was used to trim daapter contaminations. Bowtie2 2.2.4  was used to align reads to the reference genome. Macs2 2.1.1 was used for peak calling and ChIPseeker 1.2.6 for peak annotation. DESeq2 1.30.1 and edgeR were used to find differential peak.  MEME-ChIP 4.11.2 was used to identify and annotate motifs.
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: BigWig data of each sample

organism: Oryza sativa

source_name: Shoot apical meristem

growth_protocol: Plants were grown in long day conditions (16h light/ 8h dark) in a controlled greenhouse for 20 days after sowing. A basal portion corresponding to the SAM and  a portion of the stem were sampled.

extract_protocol: 60 SAM were taken by hand using a surgical blade for each sample. Crosslinking was performed with a 3% formaldehyde solution and interrupted with a 5M glycin solution. Chromatine was extracted and fragmented through sonication. A part of it was conserved and sequenced as input chromatin, the other part was Immunoprecipiitated using a primary antibody for H3K9/14ac (Diagenode) and Dynabeads protein A (ThermoFischer), and then sequenced.

value: Shoot apical meristem

value: pine1 knockout mutant

tag: antibody

value: H3K9/14ac Antibody


title: patient19,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA

value: colorectum


title: patient18,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: pWT_2C_PBAT_4

description:
Library name: pWT_2C_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g19 for maternal) are results merged from all replicates of the indicated genotypes


title: pine1 2 input


title: patient17,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: pine1 1 IP


title: patient16,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: pine1 1 input


title: pWT_2C_PBAT_2

description:
Library name: pWT_2C_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g17 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_2C_PBAT_3

description:
Library name: pWT_2C_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g18 for maternal) are results merged from all replicates of the indicated genotypes


title: pWT_4C_PBAT_7

description:
Library name: pWT_4C_PBAT_7
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g28 for maternal) are results merged from all replicates of the indicated genotypes


title: WT 2 IP

value: Nipponbare WT


title: pWT_2C_PBAT_1

description:
Library name: pWT_2C_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g16 for maternal) are results merged from all replicates of the indicated genotypes


title: patient15,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: WT 2 input


title: patient14,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: oocyte_PBAT_8

description:
Library name: oocyte_PBAT_8
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g15 for maternal) are results merged from all replicates of the indicated genotypes

source_name: oocyte

value: oocyte

value: WT


title: sample 27 con_mil

type: RNA

city: Krakow

first: Grzegorz

last: Kreiner

address: Smetna 12

department: Dept. Brain Biochemistry

country: Poland

institute: Institute of Pharmacology

description:
con_mil
Gene expression data from C57Bl6/J mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: C57Bl6/J w/t mouse treated with milnacipran

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: We used commercial QiaGen RNAeasy kit for RNA extraction

treatment_protocol: Mice were treated with milnacipran - 3 weeks, consecutive days, dose 20mg/kg, 1x daily

tag: strain

value: hippocampus

value: w/t

tag: age

value: 16 weeks


title: sample 15 DKO_mil

description:
Adra1d mut_mil
Gene expression data from C57Bl6/J mice

source_name: C57Bl6/J Adra1d KO mouse treated with milnacipran

value: Adra1d KO


title: sample 35 BKO_mil

description:
Adra1b mut_mil
Gene expression data from C57Bl6/J mice

source_name: C57Bl6/J Adra1b KO mouse treated with milnacipran

value: Adra1b KO


title: sample_11 AKO_mil

description:
Adra1a mut_mil
Gene expression data from C57Bl6/J mice

source_name: C57Bl6/J Adra1a KO mouse treated with milnacipran

value: Adra1a KO


title: sample 28 BKO_mil


title: sample_23 AKO_mil


title: sample 31 DKO_mil


title: sample 33 con_mil


title: sample 18 DKO_mil


title: sample 7 DKO_mil


title: sample_34 AKO_mil


title: sample 21 con_veh

description:
con_veh
Gene expression data from C57Bl6/J mice

source_name: C57Bl6/J w/t mouse non-treated


title: sample_28 AKO_mil


title: sample 25 con_veh


title: sample 36 BKO_mil


title: sample 34 con_mil


title: oocyte_PBAT_7

description:
Library name: oocyte_PBAT_7
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g14 for maternal) are results merged from all replicates of the indicated genotypes


title: WT 1 IP


title: patient13,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: oocyte_PBAT_6

description:
Library name: oocyte_PBAT_6
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g13 for maternal) are results merged from all replicates of the indicated genotypes


title: WT 1 input


title: patient11,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: Ribo,hct116,erf1,3

description:
Library name: sample46
eRF1-IAA-3
featureCounts_hct116_ribo.txt

source_name: colon

value: colon

value: Cancer cell

value: eRF1 KD


title: LINC01929_MCF7_KD_rep1

first: Marie-Claire

last: Wasson

address: Rm 11-C1, 5850 College Street

description: Gene expression from MCF7 cells with LINC01929 ASO treatment

hyb_protocol: The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner#4).

data_processing: Raw CEL files were processed using the Transcriptome Analysis Console (Affymetrix).

source_name: MCF7 cells

label_protocol: Sample were prepared with the Affymetrix WT PLUS Kit and labeled with Biotin Allonamide Triphosphate.

growth_protocol: Cells were cultured in a humidified incubator at 37C, with 5% CO2 in culture media, supplemented with 10% FBS.

extract_protocol: Cells were collected in TRIzol and RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions.

treatment_protocol: Cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

value: LINC01929 ASO


title: LINC01929_MDAMB231_control_rep2

description: Gene expression from MDA-MB-231 cells with control ASO treatment

source_name: MDA-MB-231 cells

value: Control ASO


title: LINC01929_MDAMB231_KD_rep1

description: Gene expression from MDA-MB-231 cells with LINC01929 ASO treatment


title: LINC01929_MDAMB231_KD_rep2


title: LINC01929_MDAMB231_control_rep1


title: oocyte_PBAT_5

description:
Library name: oocyte_PBAT_5
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g12 for maternal) are results merged from all replicates of the indicated genotypes


title: LINC01929_MCF7_control_rep1

description: Gene expression from MCF7 cells with control ASO treatment


title: LINC01929_MCF7_KD_rep2


title: LINC01929_MCF7_KD_rep3


title: LINC01929_MDAMB231_control_rep3


title: LINC01929_MDAMB231_KD_rep3


title: DDX5 K144N mutant Replicate #1

city: West Lafayette

first: Matt

last: Olson

address: 201 St University St

institute: Purdue University

description: Library name: IP3

data_processing:
Quality trimming (quality_score=30, min_length=30) was performed using fastp tool (version 0.23.2).
Trimmed reads were mapped to human (GRCh38) reference genome with STAR aligner (version 2.7.11b).
Mapped reads were converted from BAM to BigWig format with deeptools (version 3.5.5).
Duplicate reads marking was performed with picard tools (version 3.3.0).
Peak calling was performed using MACS3 (version 3.0.0a6).
Assembly: GRCh38
Supplementary files format and content: BigWig files for each sample.

source_name: HepaRG

extract_protocol:
Enhanced CrossLinking and ImmunoPrecipitation (eCLIP) was performed by Eclipse BioInnovations following the published protocol (PMID: 27018577) without modifications. HepaRG cells expressing doxycycline-inducible FLAG-tagged DDX5 (wild-type or ATPase/RNA-binding deficient K144N mutant) were UV crosslinked, and protein-RNA complexes were immunoprecipitated using anti-FLAG antibodies. Following SDS-PAGE and transfer to PVDF membranes, regions corresponding to 69–144 kDa were excised to isolate crosslinked RNA. Size-matched input (SMInput) controls were processed in parallel. RNA was visualized via chemiluminescence, and libraries were constructed from immunoprecipitated and input RNA using reverse transcription and PCR amplification (8–11 cycles). Final libraries ranged from 225–252 nt in average size, with yields of 966–2763 fmol, and quality was assessed via Agilent TapeStation. Four immunoprecipitation and four input libraries were prepared for downstream sequencing and analysis.
Enhanced CrossLinking and ImmunoPrecipitation (eCLIP) was performed by Eclipse BioInnovations following the published protocol (PMID: 27018577) without modifications. HepaRG cells expressing doxycycline-inducible FLAG-tagged DDX5 (wild-type or ATPase/RNA-binding deficient K144N mutant) were UV crosslinked, and protein-RNA complexes were immunoprecipitated using anti-FLAG antibodies. Following SDS-PAGE and transfer to PVDF membranes, regions corresponding to 69–144 kDa were excised to isolate crosslinked RNA. Size-matched input (SMInput) controls were processed in parallel. RNA was visualized via chemiluminescence, and libraries were constructed from immunoprecipitated and input RNA using reverse transcription and PCR amplification (8–11 cycles). Final libraries ranged from 225–252 nt in average size, with yields of 966–2763 fmol, and quality was assessed via Agilent TapeStation. Four immunoprecipitation and four input libraries were prepared for downstream sequencing and analysis.

value: HepaRG


title: LINC01929_MCF7_control_rep2


title: Ribo,hct116,erf1,2

description:
Library name: sample45
eRF1-IAA-2
featureCounts_hct116_ribo.txt


title: sample 19 con_veh


title: LINC01929_MCF7_control_rep3


title: patient9,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA

value: adjacent normal

value: untreated


title: DDX5 WT Replicate #2

description: Library name: IP2


title: patient12,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA

value: colorectum


title: DDX5 K144N mutant Replicate #2

description: Library name: IP4


title: oocyte_PBAT_4

description:
Library name: oocyte_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g11 for maternal) are results merged from all replicates of the indicated genotypes

value: oocyte


title: Ribo,hct116,erf1,1

description:
Library name: sample44
eRF1-IAA-1
featureCounts_hct116_ribo.txt


title: oocyte_PBAT_3

description:
Library name: oocyte_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g10 for maternal) are results merged from all replicates of the indicated genotypes

value: WT


title: DDX5 WT Replicate #1

description: Library name: IP1


title: patient10,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: patient8,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: oocyte_PBAT_2

description:
Library name: oocyte_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g9 for maternal) are results merged from all replicates of the indicated genotypes


title: Ribo,hct116,wt,3

description:
Library name: sample43
eRF1-WT-3
featureCounts_hct116_ribo.txt


title: Input for DDX5 K144N mutant Replicate #2

description: Library name: Input4


title: oocyte_PBAT_1

description:
Library name: oocyte_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g8 for maternal) are results merged from all replicates of the indicated genotypes


title: patient6,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: STOP_AGhaESC_PBAT_2

description:
Library name: STOP_AGhaESC_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g7 for maternal) are results merged from all replicates of the indicated genotypes

source_name: AG-haESC

value: AG-haESC

value: Dnmt STOP


title: Input for DDX5 K144N mutant Replicate #1

description: Library name: Input3


title: Ribo,hct116,wt,1

description:
Library name: sample41
eRF1-WT-1
featureCounts_hct116_ribo.txt


title: Ribo,hct116,wt,2

description:
Library name: sample42
eRF1-WT-2
featureCounts_hct116_ribo.txt


title: patient5,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: Input for DDX5 WT Replicate #2

description: Library name: Input2


title: STOP_AGhaESC_PBAT_1

description:
Library name: STOP_AGhaESC_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g6 for maternal) are results merged from all replicates of the indicated genotypes


title: WT_AGhaESC_PBAT_4

description:
Library name: WT_AGhaESC_PBAT_4
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g5 for maternal) are results merged from all replicates of the indicated genotypes

value: Dnmt WT


title: patient3,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: WT_AGhaESC_PBAT_3

description:
Library name: WT_AGhaESC_PBAT_3
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g4 for maternal) are results merged from all replicates of the indicated genotypes


title: HCT116,WT,4-3

description:
Library name: sample38
eRF1-4sU-4-3
featurecounts_human.txt


title: patient2,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: WT_AGhaESC_PBAT_2

description:
Library name: WT_AGhaESC_PBAT_2
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g3 for maternal) are results merged from all replicates of the indicated genotypes


title: col098_rep1

city: Amsterdam

first: Kristiaan

middle: J

last: Lenos

address: Van der Boechorststraat 6B

department: Laboratory for Experimental Oncology and Radiobiology (LEXOR)

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample 10

data_processing:
Sequence reads were preprocessed for adaptor sequence/low-quality sequence using fastp with default parameyers.
Preprocessed reads were mapped to the UCSC human reference genome (GRCh38) using STAR (version 2.7.3a) with default parameters.
Gene expression was quantified using RNA-seq by expectation maximization (RSEM).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: primary tumor resection

extract_protocol:
Total RNAs were isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, catalog number: 80224) except for two samples (col051_rep2, col098_rep2), whose total RNAs were extracted with the RNeasy FFPE Kit (Qiagen, catalog number: 73504) according to manufacturer’s protocols.
RNA libraries for RNA-seq were prepared using TruSeq RNA Exome (Illumina) according to manufacturer’s protocol.

value: primary tumor resection


title: patient7,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: col100

description: Library name: Sample 12


title: patient1,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: HCT116,WT,6-1

description:
Library name: sample39
eRF1-4sU-6-1
featurecounts_human.txt


title: col098_rep2

description: Library name: Sample 11


title: HCT116,WT,4-1

description:
Library name: sample36
eRF1-4sU-4-1
featurecounts_human.txt


title: patient21,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: WT_AGhaESC_PBAT_1

description:
Library name: WT_AGhaESC_PBAT_1
supplementary bed files (g1g2 for overall methylation profile obtained without distinguishing parental origin; g1 for paternal; g2 for maternal) are results merged from all replicates of the indicated genotypes


title: col092

description: Library name: Sample 9


title: HCT116,WT,2-2

description:
Library name: sample35
eRF1-4sU-2-2
featurecounts_human.txt


title: HCT116,WT,6-2

description:
Library name: sample40
eRF1-4sU-6-2
featurecounts_human.txt


title: patient4,adjacent_normal_tissue_contorl

description: Ribosomes removed RNA


title: pIR_E185_liver_rep4

description: Library name: pIR_E185_liver_rep4

data_processing:
For data processing, raw data were trimmed by Trim Galore (v0.6.6) with default settings. Then, the clean data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters. Only uniquely mapped reads were kept for downstream analysis. Gene count matrices were calculated by featureCounts (v1.6.4) with the parameters -p -M -O. Differentially expressed gene (DEG) analysis was performed using DESeq2 package. Only genes with adjusted P value (for cell lines) or P value (for organs) < 0.05, fold change > 2 and basemean > 12.5 were considered to be differentially expressed. DEGs were submitted to DAVID (2021 Update) (https://david.ncifcrf.gov/) for gene ontology (GO) and KEGG pathway enrichment analyses. To evaluate the transcription level of transposons, the clean data were mapped to mm10 using Hisat2 with the parameters -k 100 -no-unal -no-mixed -no-discordant. Then the TEcount function of TE transcritps (v2.2.1) was used to count reads from TE with the parameters -mode multi. Differentially expressed TE analysis was performed using DESeq2 package. Only TEs with a P value < 0.05 and fold change > 2 were considered to be differentially expressed.
Assembly: mm10
Supplementary files format and content: comma or tab separated values file, raw counts for gene expression.

source_name: liver

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
1 μg total RNA was used for following library preparation. RNA-Seq libraries were prepared with VAHTS mRNA-Seq V3 Library Prep Kit for Illumina (Vazyme, NR611). The poly(A) mRNA isolation was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Then first strand cDNA and the second-strand cDNA were synthesized. Once the double-stranded cDNA was purified, adaptors were added to both ends after end repair and dA-tailing. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Libraries were finally subjected to 150 bp paired-end sequencing using the Illumina NovaSeq 6000 instrument. For Smart-Seq2 library preparation, the cDNA was synthesized and amplified using the Single Cell Full-Length mRNA-Amplification Kit (Vazyme, N712). The full-length cDNA was assessed for quality and quantity using QIAxcel Advanced (QIAGEN) and Qubit 3.0 (ThermoFisher). Then RNA-Seq libraries were constructed from 1 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503). Amplified libraries were purified with VAHTS DNA Clean Beads (Vazyme, N411) and sequenced on the Illumina NovaSeq 6000.

value: liver

value: pIR

tag: batch


title: Input for DDX5 WT Replicate #1

description: Library name: Input1


title: pIR_E185_liver_rep3

description: Library name: pIR_E185_liver_rep3

tag: tissue


title: col084

description: Library name: Sample 7


title: HCT116,WT,2-1

description:
Library name: sample34
eRF1-4sU-2-1
featurecounts_human.txt

value: colon

value: Cancer cell

tag: genotype


title: patient20,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: pIR_E185_liver_rep2

description: Library name: pIR_E185_liver_rep2


title: patient19,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: HCT116,WT,0-3

description:
Library name: sample33
eRF1-4sU-0-3
featurecounts_human.txt


title: HCT116,WT,4-2

description:
Library name: sample37
eRF1-4sU-4-2
featurecounts_human.txt


title: patient18,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: col051_rep2

description: Library name: Sample 6


title: pIR_E185_liver_rep1

description: Library name: pIR_E185_liver_rep1


title: pWT_E185_liver_rep3

description: Library name: pWT_E185_liver_rep3

value: pWT


title: col051_rep1

description: Library name: Sample 5


title: HCT116,WT,0-2

description:
Library name: sample32
eRF1-4sU-0-2
featurecounts_human.txt


title: HCT116,WT,0-1

description:
Library name: sample31
eRF1-4sU-0-1
featurecounts_human.txt


title: patient17,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: col047

description: Library name: Sample 4


title: pWT_E185_liver_rep4

description: Library name: pWT_E185_liver_rep4


title: col020

description: Library name: Sample 3


title: T6

first: yu

last: chao

address: 106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description:
Library name: Sample 6
T6

data_processing:
Disembarkation data quality control
Matching genome
Modification site recognition
Differential site recognition
Functional enrichment analysis
Assembly: HG19
Supplementary files format and content: The table contains the miRNA information identified by each sample

source_name: PDAC tissue

extract_protocol:
total RNA was extracted from tissue samples and RNA samples were detected in three main ways: (1) Nanodrop performs preliminary concentration and purity detection of RNA (2) Qubit accurately quantified RNA concentration (3) Agilent 2100 accurately detects RNA integrity (RIN value)
ncRNA-Seq

value: PDAC tissue


title: col014

description: Library name: Sample 2


title: col090

description: Library name: Sample 8


title: T5

description:
Library name: Sample 5
T5


title: patient16,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

source_name: adjacent normal


title: patient15,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: patient14,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: pWT_E185_liver_rep1

description: Library name: pWT_E185_liver_rep1


title: col011

description: Library name: Sample 1


title: pIR_E185_heart_rep4

description: Library name: pIR_E185_heart_rep4

source_name: heart

value: heart


title: T3

description:
Library name: Sample 3
T3


title: T4

description:
Library name: Sample 4
T4


title: patient13,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

value: adjacent normal


title: T2

description:
Library name: Sample 2
T2


title: pIR_E185_heart_rep3

description: Library name: pIR_E185_heart_rep3


title: patient12,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: MAGOHWT RIPiT, Rep1

city: Columbu

first: Manu

last: Sanjeev

state: OH

address: 484 W 12th Ave

institute: The Ohio State University

description:
Library name: MagohwtCASC3_NT_1.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-WT-CASC3-NT-1

data_processing:
Total RNA-seq:12nt UMIs at the start of Read 1 extracted using UMItools. Adapter trimming carried out with Cutadapt for the sequences AGATCGGAAGAGCACAC-GTCTGAACTCCAGTCAC and N{12}AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
RIP-seq:5nt random sequence, 5nt identifier & CC removed from 5' end and miRCat22 sequence trimmed from 3' end using Cutadapt
Trimmed reads aligned to genome using STAR
Total RNA-seq: Mapped Bam files indexed with samtools and PCR deduplicated using UMItools. Deduplicated bam files converted to fastq for transcript quantification by Kallisto.
Bam files counted using FeatureCounts for all samples.
Assembly: GRCh38, Ensembl release 100
Supplementary files format and content: Text file including raw counts calculated by Featurecounts.

source_name: Kidney

growth_protocol: Cells grown in DMEM with 10% FBS, 1% Pen-Strep antibiotic at 37C with 5% CO2

extract_protocol:
RNA extracted with Trizol for all samples. Total RNA samples Ribodepleted with Lexogen RiboCoprRNA depletion kit
Total RNA Libraries constructed with Lexogen CORALL RNA-Seq V2 library prep kit with UDIs. RIP-seq RNA libraries constructed as described in Mabin et al., 2018.

treatment_protocol: Cells transfected with siRNA/expression plasmid for 3 days for RNA seq.

value: Kidney

value: Flp-In FLAG-MAGOHWT

value: FLAG-MAGOHWT


title: pWT_E185_liver_rep2

description: Library name: pWT_E185_liver_rep2


title: pIR_E185_heart_rep2

description: Library name: pIR_E185_heart_rep2


title: T1

description:
Library name: Sample 1
T1


title: patient11,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

data_processing:
The Illumina sequencing reads were initially processed with cutadapt v4.3 to remove adapters and perform quality-based trimming.
After adapter trimming and filtering out low-quality reads, PCR duplicates were removed using seqkit v2.4.0. The 8-bp UMIs the 6-mer following the UMI were excised from the deduplication reads using UMI_tools v1.1.4. To enhance the accuracy of the mapping results, we trimmed the 6-mer sequence to minimize such errors.
All fastq files were aligned to the human reference genome hg38, using HISAT2 v2.2.1.
The following data analysis procedures for site identification are mainly referred to PRAISE
Bigwig files were generated using deeptools Python package. Score represents the Counts Per Million mapped reads of RNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: Bigwig include CPM values for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions
Five hundred nanogram fragmented total RNA was subjected to bisulfite treatment as previous references (PMID: 36997645; 36302989; 37968414). The BS treated RNA was labeled as ‘treat’ sample, while the BS untreated RNA was labeled as ‘Input’ sample. Ten nanogram ‘treated’ RNA sample and 10 ng ‘Input’ RNA sample were subjected to library construction using SMARTer Stranded Total RNA-Seq Kit v3—Pico Input Mammalian (Takara Bio, 634485) according to the manufacturer’s protocol with several modifications as previous reference. All of the quality-ensured libraries were sequenced on the Illumina Nova seq 6000 platform in 150 bp paired-end mode (sequenced by Genewiz).
PRAISE (PMID: 36997645), BID-seq (PMID: 36302989; PMID: 37968414)

value: colorectum


title: patient10,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: MAGOHWT RIPiT with CHX, Rep2

description:
Library name: MagohwtCASC3_CHX_2.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-WT-CASC3-CHX-2

value: Cycloheximide


title: patient9,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: MAGOHWT RIPiT with CHX, Rep1

description:
Library name: MagohwtCASC3_CHX_1.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-WT-CASC3-CHX-1


title: pWT_E185_heart_rep4

description: Library name: pWT_E185_heart_rep4


title: MAGOHE117R RIPiT, Rep2

description:
Library name: MagohE117RCASC3_NT_2.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-E117R-CASC3-NT-2

value: Flp-In FLAG-MAGOHE117R


title: pIR_E185_heart_rep1

description: Library name: pIR_E185_heart_rep1


title: X14

city: Guangxi

first: Jun

last: Meng

address: ShuangYong Road

institute: Guangxi Medical University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Library strategy: Spatial Transcriptomics

source_name: X14-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

growth_protocol: A maximum of five adult mice weighing up 17 to 20 g were homed in a SPF single cage, maintaining the ambient temperature at 20–27 °C, the humidity at 40%-70% and a 12-h light/12-h dark cycle.

extract_protocol:
After the mice were euthanized, their brain tissue was collected and rinsed with PBS, water was removed with absorbent paper, and their intestinal contents were collected. Frozen in liquid nitrogen for 15 minutes at -80°C.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

treatment_protocol: Lentivirus was used to induce a mouse glioblastoma model, and then the mice were subjected to intermittent fasting treatment and different experimental interventions on the basis of this treatment.

value: brain

value: wild-type

value: GBM+IF


title: patient8,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA

value: PRAISE


title: MAGOHWT RIPiT, Rep2

description:
Library name: MagohwtCASC3_NT_2.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-WT-CASC3-NT-2


title: X13

source_name: X13-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification


title: patient7,adjacent_normal_tissue,PRAISE

description: Ribosomes removed RNA


title: MAGOHE117R RIPiT, Rep1

description:
Library name: MagohE117RCASC3_NT_1.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-E117R-CASC3-NT-1


title: MAGOHE117R RIPiT with CHX, Rep2

description:
Library name: MagohE117RCASC3_CHX_2.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-E117R-CASC3-CHX-2


title: pWT_E185_heart_rep2

description: Library name: pWT_E185_heart_rep2


title: X5

source_name: X5-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

value: GBM


title: pWT_E185_heart_rep3

description: Library name: pWT_E185_heart_rep3


title: pWT_E185_heart_rep1

description: Library name: pWT_E185_heart_rep1


title: MAGOHE117R RIPiT with CHX, Rep1

description:
Library name: MagohE117RCASC3_CHX_1.fastq
1st IP : anti-FLAG M2-agarose beads (Sigma), 2nd IP: anti-CASC3 (Bethyl A302-472A)
MAGOH-E117R-CASC3-CHX-1