title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_G06]


title: DU145 cells, siSLC7A5, repeat1

status: Public on Jul 30 2025

type: SRA

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

country: Germany

institute: OncoRay

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
Performed by RNAseq service provider Genewiz (Standard RNA-Seq analysis, value package)
Assembly: hg38
Supplementary files format and content: Raw counts in tab-delimeted txt format

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

growth_protocol: DMEM (for DU145) or RPMI-1640 (for LNCaP) supplemented with 10%FBS, 2mM l-glutamine, 10mM HEPES, 1mM sodium piruvate and 1x MEM-NEAA

extract_protocol:
NucleoSpin RNA Plus
Performed by RNAseq service provider Genewiz (Illumina, RNA with PolyA selection, value package)

treatment_protocol: 200 000 (for DU145) or 300 000 (for LNCaP) cells per well of 6-well plate were transfected with 40pmol of siRNA and 9ul Lipofectamine RNAiMax in 300 ul of OptiMEM.

tag: tissue

value: Prostate

tag: cell line

tag: cell type

value: Prostate carcinoma

tag: treatment


title: mRNA_FLAD5

city: Guelph

first: Sonja

last: Fonfara

state: Ontario

address: 36 College Ave W

department: Clinical Studies

country: Canada

institute: University of Guelph

data_processing:
The raw trimmed reads are aligned to the reference genome using the STAR aligner.After sequencing, the quality of the data was assessed using FastQC v.0.11.5. The adaptors were trimmed using Trim Galore v.0.4.4. After trimming, the quality of reads was re-assessed with FastQC.
Raw trimmed reads were aligned to reference genome using the STAR aligner, followed by HTSeq- count v.0.6.1p2 to obtain uniquely mapped gene counts.
The identification of differentially expressed genes between different comparison groups was performed using edgeR R package v.3.22.3
For miRNA, sequencing libraries were generated for all samples using the NEBNext small RNA Library Prep Kit from Illumina. Total RNA from each sample was ligated to 3’ and 5’ adaptors, and poly (A) tails were added using poly (A) polymerase. RNA was reverse transcribed and amplified by PCR with primers specific to the adaptor sequences. MicroRNA enrichment was completed by extracting the 15-30 nucleotide fraction of the polyacrylamide gel. Sequencing was performed on the Hiseq 2500 SR50 bp (Illumina) platform, with 150M reads total. Quality of sequencing data was assessed using fastq.gzC v.0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastq.gzc/).
Assembly: The Felis_Catus_9.0.96 (Ensembl gene models) with annotations was used as the reference genome.
Supplementary files format and content: Excel files containing counts for each gene in FPKM (Fragments per kilobase per million mapped reads)

organism: Felis catus

source_name: Left atrium

extract_protocol:
The miRNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate total RNA.RNA purity was assessed using the Nanodrop 2000 spectrophotometer. Samples with a 260/280 ratio of >1.9 and RNA integrity number of >5.7 were used for sequencing.
A stranded, paired-end poly-A mRNA library was prepared for each sample. Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA) as per manufacturer’s instructions. Briefly, mRNA was isolated, fragmented and primed from total RNA and cDNA synthesis were performed. The cDNA fragments were adapter ligated and PCR amplification was done according to Illumina instructions.  The libraries were sequenced on the NovaSeq 6000 system, SP flowcell 2 x 150 bp (Illumina).

value: Left atrium

tag: genotype

value: Hypertrophic Cardiomyopathy Female


title: DU145 cells, siSCR, repeat1

description: Library name: Sample 1

value: siSCR


title: DU145 cells, siSCR, repeat2

description: Library name: Sample 5


title: mRNA_FLVD4

source_name: Left ventricle

value: Left ventricle


title: Endo+, Clinical PID+, #2

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

country: USA

institute: UNC-CH

description: Library name: sample2

data_processing:
Sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina. Gene expression quantification used BBMap (v37.25) and samtools (v1.4.1).
Assembly: hg38
Supplementary files format and content: Comma-separated values (csv) file includes counts for each sample.

source_name: Endometrial tissue

extract_protocol:
mRNA Extraction and Profiling: Total RNA was extracted from endometrial biopsies stored at -80°C in tubes containing RNA/DNA Shield (Zymo Research, Irvine, CA). After thawing, samples were weighed, minced, and processed for simultaneous DNA and RNA extraction using the Quick DNA/RNA™ isolation kit according to the manufacturer's protocol (Zymo) with on column DNase I treatment prior to total RNA elution. Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies) and sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina.
Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies).

value: Endometrial tissue

tag: infection group

value: Endo+, Clinical PID+

tag: Sex

value: Female


title: human intestine organoids cells cultured in a presence of V#3

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description:
Library name: DNA lentiV # 3
CC-Vector3_S37

data_processing:
Reads aligned to human genome GRCh38 using STAR version=2.5.4b
Transcript abundance was quantified using RSEM version 1.3.0
Assembly: GRCh38 genome assembly
Supplementary files format and content: matrix_tpm: Matrix of Transcripts per Million (TPM)

source_name: organoids

growth_protocol: Three-dimensional intestinal organoids were generated from iPSC lines using episomal plasmid reprogramming

extract_protocol:
RNA samples were extracted by using RNeasy Micro kit (Qiagen)
Library was prepared with NEBNext Ultra II Directional RNA library prep kit (Illumina)

treatment_protocol: Cells were infected with lentiGH or lentiV, both of which contained GFP. After 1 month in culture, cells were sorted for GFP positivity using FACSAria III cells sorter (BD Biosciences). Only GFP negative cells (not expressing GH or vector) were included in testing

value: organoids

value: intestine organoid cells

value: WT


title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_G01]

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

data_processing:
Sequencing was performed in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent cartridge.
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al. 2022) was indexed with STAR v2.7.10a and concurrently had in-house gene annotations loaded. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 149.
After performing quality control on the raw FASTQ data using FastQC and MultiQC v1.12, raw reads were trimmed using Trim Galore! v0.6.6 to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp.
Trimmed reads were then mapped with STAR v2.7.10a to the indexed genome using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS.
Samtools v1.13 was used to sort (via the command: samtools view -buS [.sam_file] | samtools sort -m 1G -@ 100 -o [orted.bam_file] -O bam) and index (via the command: samtools index [sorted.bam_file]) the alignment files.
HTSeq v0.13.5 was used to assign counts to each gene with the following parameters: -f bam -r pos -s no.
FastQC and MultiQC v1.12 were used to assess quality control metrics of the processed reads.
Counts to each gene were parsed, and raw count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Quality control screening and filter steps were applied to each raw count matrix using the R statistical computing software. Samples were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out. Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Multidimensional scaling (MDS) plots were generated to look for possible outliers. Overall, quality control procedures resulted in the removal of samples 6PPD_C_D12 and 6PPD_C_H11 from the normalized count matrix for 6PPD-Q.
Assembly: RefSeq GCF_016745375.1 (EPA_FHM_2.0; NCBI Annotation Release 100)
Supplementary files format and content: tab-delimited text file providing raw counts for each Sample (both 6PPD and 6PPD-Q exposures together + controls)
Supplementary files format and content: tab-delimited text file providing log2(CPM+1) counts for each Sample for 6PPD exposure and controls
Supplementary files format and content: tab-delimited text file providing log2(CPM+1) counts for each Sample for 6PPD-Q exposure and controls

organism: Pimephales promelas

source_name: whole body fathead minnow

growth_protocol: Fathead minnows (Pimephales promelas) used for the present were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division. Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  At five-day post-fertilization  , larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use.

extract_protocol:
Exposure media was removed from each well, 100 ul of Omega Biotek MagBind Total RNA homogenization buffer was added and individual fish were homogenized using a bead mill at 30 Hz for 2 min. Whole-body homogenates were extracted using MagMAX-96 Total RNA Isolation kits (ThermoFischer Scientific AM1830) and RNA quality verified using an Agilent Tapestation (Agilent, Santa Clara, CA).
Complementary DNA libraries were prepared from 250 ng total RNA using SENSE mRNA-Seq Library Prep kits (Lexogen).

treatment_protocol: Larval (five day post hatch) fathead minnow were exposed for 24 hr in 1-mL, 96-well plate format to 600 uL of either the tire rubber antioxidant chemical 6ppd (n=30) or its quinone transformation product, 6ppd-quinone (6ppd-q; n=40). Exposures were conducted without feeding (reliant on yolk and not independently feeding at this age) in a total volume of 700 µl with 0.3% DMSO per well. Fish were exposed to either six (6ppd) or eight (6ppd-q) concentrations, with 5 replicate fish exposed per plate and triplicate plates (A, B, C). Plates were sealed and placed in a 25°C incubator under a 16:8h light routine for 24 h.

value: whole body fathead minnow

tag: developmental stage

value: larval (5-day post hatch)

tag: biological replicate

tag: dose (mg/l)


title: mRNA_FLAD4


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_F12]


title: mRNA_FLAD3


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_G05]


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_F11]


title: Endo+, Clinical PID+, #1

description: Library name: sample1


title: IBC3 cells, Non-treated, rep1

city: San Juan

first: Mariela

last: Rivera-Serrano

state: PR

address: 601 Ave Universidad

institute: University of Puerto Rico Rio Piedras

data_processing:
The library was quantified with KAPA SYBR® FAST qPCR and then sequenced using the Illumina HiSeq platform (2 × 150 bp) with a sequencing depth of approximately 100 million reads per sample. Sequence reads were trimmed to remove possible adapter sequences and nucleotides of poor quality via Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene counts were calculated via featureCounts from the Subread package (version 1.5.2, Parkville, Victoria, Australia), and initial gene expression analysis was performed using the DESeq2 (version 1.28.1) package in the R version 4.0.1 package.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: comma-delimeted excel file include raw counts for each sample

molecule: polyA RNA

extract_protocol:
RNA was extracted with the Mirvana RNA Isolation Kit (Fisher, Grand Island, NY, USA). The integrity of the RNA samples was evaluated via an Agilent Bioanalyzer 2100, and 1.0 µg of high-quality RNA was used for the sequencing protocol.
The RNA was enriched, and the library was prepared via GENEWIZ® Strand-specific RNA sequencing with rRNA depletion (GENEWIZ, Inc. South Plainfield, NJ, USA).

value: HER2+ breast cancer cells

value: Non-treated


title: mRNA_MLV5

value: Young healthy male


title: human intestine organoids cells cultured in a presence of GH#3

description:
Library name: DNA lentiGH #3
CC-GH3_S38

value: GH


title: IBC3 cells, Non-treated, rep3


title: human intestine organoids cells cultured in a presence of GH#2

description:
Library name: DNA lentiGH #2
CC-GH2_S36


title: IBC3 cells, LCN2 Knockdown siRNA, rep2

value: LCN2 knockdown

value: 100 nM LCN2 siRNA


title: mRNA_MLV4


title: human intestine organoids cells cultured in a presence of V#2

description:
Library name: DNA lentiV #2
CC-Vector2_S35


title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_F06]


title: whole body larval fathead minnow, control, biol rep8 [6PPD_C_F10]

value: control


title: IBC3 cells, Non-treated, rep2


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_F08]


title: mRNA_FLAD1

value: Left atrium

value: Hypertrophic Cardiomyopathy Female


title: human intestine organoids cells cultured in a presence of GH #1

description:
Library name: DNA lentiGH #1
CC-GH1_S34


title: IBC3 cells, LCN2 Knockdown siRNA, rep3


title: mRNA_MLV3

value: Left ventricle


title: IBC3 cells, LCN2 Knockdown siRNA, rep1


title: GiMO_scRNA-seq_Day3

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

description: Library name: GiMO Day 3

library_source: transcriptomic single cell

data_processing:
Reads were aligned to Hg38 by Cellranger v5.0.1 using standard parameters.
Assembly: Hg38
Supplementary files format and content: Raw cell barcode, gene and combined matrixes from Cellrnager output (v5.0.1)

extract_protocol:
Cells were washed with cold D-PBS 3X in 30sec increments to dissolve Geltrex overlay. Next, samples were treated with 0.25% Trypsin/EDTA for 10 mins at 37 °C and 5% CO2.  After incubation, cells were quenched with cold E8 medium and centrifuged at 1.2 rpm for 3.5 min. Cells were then resuspended with FACS buffer, D-PBS containing 0.5% Bovine Serum Albumin (BSA, Sigma-Aldrich, # A3311), as a wash step and centrifuged at 0.7 rpm for 4 min. Cells were resuspended again with FACS buffer and dissociated to single cells using a Falcon 100 mm Cell Strainer (Corning, # 352360) and manually counted. hPSCs were then further dissociated using EASYstrainer Cell Sieves 40 mm filter and centrifuged at 0.3 rpm for 3 min and resuspended in FACS buffer at a total volume of 1000 cells mL-2.
Library construction was performed using 10X Genomics Chrominium platform.

tag: time

value: Day 3


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_F04]


title: GiMO_scRNA-seq_Day2

description: Library name: GiMO Day 2

value: Day 2


title: mRNA_MLV12


title: human intestine organoids cells cultured in a presence of V#1

description:
Library name: DNA lentiV #1
CC-Vector1_S33

value: organoids


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_F05]


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_F03]


title: IBC3 cells, Negative control siRNA, rep3

value: 100 nM NC siRNA


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_F01]


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_E12]


title: GiMO_scRNA-seq_Day1

description: Library name: GiMO Day 1

value: Day 1


title: IBC3 cells, Negative control siRNA, rep2

value: WT


title: SR2, biological replicate 3

city: Nedlands

first: Peter

middle: J.

last: Leedman

state: Western Australia

address: 6 Verdun Street

department: Cancer and Cell Biology

country: Australia

institute: Harry Perkins Institute of Medical Research

description:
messenchymal-like
H9_SR2

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3
The Illumina bcl2fastq 2.18.0.12 pipeline was used to generate the sequence data
Sequence data were aligned to the Hg19 genome build. The Tophat aligner (v2.0.14) was used to map reads to the genomic sequences.
Raw Gene Counts are generated using featureCounts v1.4.6-p5 and default TMM normalization method of edgeR was used to normalize the counts.
Assembly: Hg19
Supplementary files format and content: Tab-delimited text files include counts (DGE, digital gene expression) values for each sample.

growth_protocol: Huh-7, Huh-7/SR1 and Huh-7/SR2 cells were cultured in low glucose DMEM supplemented with 10% FBS and 4 mM L-glutamine at 37 degrees and 5% CO2. Mycoplasma testing was routinely carried out to exclude contamintion.

extract_protocol:
Total RNA extraction was carried out using a mirVana miRNA isolation kit (Ambion, #AM1560) according to manufacturer’s instruction. RNA integrity was assessed using Nanodrop One (Thermofisher Scientific). For RNA-sequencing the purity of RNA was further evaluated using AGRF’s 2100 Bioanalyzer (Agilent). Samples with an RNA Integrity number (RIN) of 10/10 were used for library preparation.
RNA libraries were prepared for sequencing using Illumina's Ribo-zero Gold protocol

treatment_protocol: Huh-7/SR1 and Huh-7/SR2 cells were established by treating parental Huh-7 cells with increasing concentration of sorafenib to a mximum dose of 10 microM for 3 months. The cells were continuously  maintained with 10 microM of sorafenib.

tag: group

value: sorafenib-resistant

tag: agent

value: Maintained with sorafenib  10 microM


title: mRNA_MLA9


title: hepatocytes, obese cord plasma, 24hrs, 14

city: Milwaukee

first: T. Hang

last: Nghiem-Rao

state: WI

address: 999 N. 92 Street, Suite C410

department: Pediatrics

institute: Medical College of Wisconsin

description: Library name: Sample HNR40

data_processing:
Quantification analysis of RNA-seq data was performed by Novogene Corporation Inc. (Sacramento, CA). Briefly, FastQC software (version 0.11) was used to validate raw sequence data quality. Reads were aligned to the Human reference genome (GRCh38) using Hisat2 (version 2.0.5). FeatureCounts (version 1.5.0-p3) was used to count the read numbers mapped to each gene, and fragments per kilobase of transcript sequence per million base pairs sequenced was calculated based on the length of the gene and read count mapped to the gene. Differential expression analysis of RNA-seq data was done using DESeq2 R package (version 1.20.0) and the Benjamini-Hochberg approach to estimate false discovery rate and adjust p-values for multiple testing
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: excel file containing gene counts for all samples

source_name: HepaRG cells

growth_protocol: Cryopreserved terminally differentiated HepaRG cells (BioPredic International, Saint Grégoire, France) were cultured per manufacturer guidelines. Cells were resuspended with HepaRG Thaw, Plate, and General Purpose medium (Invitrogen; Waltham, MA) and plated on to 48 well polypropylene tissue culture plates. Cells were then cultured at 37ºC in 5% CO2 and fed with HepaRG Maintenance/Metabolism medium on days 1, 4, and 7.

extract_protocol:
Total mRNA was isolated from cord plasma-exposed cells using the RNeasy Mini Kit with on-column DNase treatment per manufacturer instructions and quantified by Qubit and quantitative real-time PCR (qRT-PCR). RNA integrity number (RIN) was determined using the Agilent Technologies 2100 Bioanalyzer and all samples with RIN > 9 underwent RNA-sequencing (RNA-seq).
Sequencing libraries of RNA from cord plasma-exposed HepaRG cells were prepared by Novogene Corporation Inc. (Sacramento, CA) using the low input pipeline and sequenced on an NovaSeq 6000 (PE150) to generate 6 Gb of raw data per sample.

treatment_protocol: Cultured terminally differentiated HepaRG cells were exposed to media supplemented with 30% cord plasma and incubated at 37ºC in 5% CO2. After 24 hours, cord plasma-exposed cells were harvested with Trizol and stored at -80ºC until use.

value: HepaRG cells

value: hepatocyte

value: obese cord plasma


title: IBC3 cells, Negative control siRNA, rep1

value: HER2+ breast cancer cells


title: mRNA_MLA6

value: Young healthy male


title: mRNA_MLA4


title: hepatocytes, normal weight cord plasma, 24hrs, 15

description: Library name: Sample HNR41

value: normal weight cord plasma


title: hepatocytes, normal weight cord plasma, 24hrs, 14

description: Library name: Sample HNR35


title: SR2, biological replicate 1

description:
messenchymal-like
H7_SR2


title: SR2, biological replicate 2

description:
messenchymal-like
H8_SR2


title: mRNA_LV9_RNA

value: Adult healthy male


title: mRNA_MLA5

value: Left atrium


title: DU145 cells, siSLC1A5, repeat1

description: Library name: Sample 2

value: Prostate

value: Prostate carcinoma


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_E10]

value: whole body fathead minnow

value: larval (5-day post hatch)


title: hepatocytes, normal weight cord plasma, 24hrs, 13

description: Library name: Sample HNR34


title: mRNA_MLA1


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_E08]


title: whole body larval fathead minnow, 6PPD-Q, biol rep4 [6PPD_C_E09]


title: SR1, biological replicate 3

description:
messenchymal-like
H6_SR1


title: hepatocytes, obese cord plasma, 24hrs, 13

description: Library name: Sample HNR33


title: hepatocytes, obese cord plasma, 24hrs, 15

description: Library name: Sample HNR42


title: mRNA_LV6

value: Left ventricle


title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_E11]


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_E07]


title: mRNA_MLV2


title: SR1, biological replicate 2

description:
messenchymal-like
H5_SR1


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_E06]


title: hepatocytes, obese cord plasma, 24hrs, 11

description: Library name: Sample HNR31


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_E03]


title: mRNA_LV23B


title: SR1, biological replicate 1

description:
messenchymal-like
H4_SR1


title: hepatocytes, normal weight cord plasma, 24hrs, 12

description: Library name: Sample HNR30


title: mRNA_LV22


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_E02]


title: mRNA_LV15


title: hepatocytes, normal weight cord plasma, 24hrs, 11

description: Library name: Sample HNR29


title: hepatocytes, normal weight cord plasma, 24hrs, 10

description: Library name: Sample HNR28


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_E01]


title: hepatocytes, obese cord plasma, 24hrs, 10

description: Library name: Sample HNR27


title: mRNA_LA23


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_D12]


title: mRNA_LA6


title: mRNA_LA22


title: whole body larval fathead minnow, 6PPD, biol rep5 [6PPD_C_D11]


title: Huh7, biological replicate 2

description:
well-differentiated, epithelial-like
H2_Huh7

value: sorafenib-sensitive

value: untreated


title: hepatocytes, obese cord plasma, 24hrs, 9

description: Library name: Sample HNR26


title: hepatocytes, obese cord plasma, 24hrs, 12

description: Library name: Sample HNR32


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_D10]


title: hepatocytes, obese cord plasma, 24hrs, 8

description: Library name: Sample HNR25


title: mRNA_LA20


title: mRNA_LA15


title: Huh7, biological replicate 3

description:
well-differentiated, epithelial-like
H3_Huh7


title: Huh7, biological replicate 1

description:
well-differentiated, epithelial-like
H1_Huh7


title: hepatocytes, normal weight cord plasma, 24hrs, 9

description: Library name: Sample HNR23


title: whole body larval fathead minnow, 6PPD-Q, biol rep3 [6PPD_C_D09]


title: mRNA_MLVD17

value: Hypertrophic Cardiomyopathy male


title: hepatocytes, obese cord plasma, 24hrs, 7

description: Library name: Sample HNR24


title: mRNA_MLVD1


title: mRNA_X0552LV


title: hepatocytes, normal weight cord plasma, 24hrs, 8

description: Library name: Sample HNR22


title: mRNA_MLVD18


title: hepatocytes, obese cord plasma, 24hrs, 5

description: Library name: Sample HNR18


title: mRNA_MLVD19


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_C12]


title: hepatocytes, normal weight cord plasma, 24hrs, 6

description: Library name: Sample HNR16


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_D06]


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_D05]


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_D04]


title: whole body larval fathead minnow, 6PPD-Q, biol rep2 [6PPD_C_D03]


title: hepatocytes, normal weight cord plasma, 24hrs, 7

description: Library name: Sample HNR21


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_C11]


title: mRNA_MLVD2


title: hepatocytes, obese cord plasma, 24hrs, 6

description: Library name: Sample HNR19


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_D01]


title: hepatocytes, obese cord plasma, 24hrs, 4

description: Library name: Sample HNR14


title: WRC100, leaf, moderate drought, Day 5, rep 3

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

description: Library name: D116

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were surface sterilized with 375 ppm of pefurazoate at 15°C for 24 h. Then the seeds were soaked in water to germinate in a dark place at 30°C for two days. The calcined clay (Profile Greens Grade, PROFILE Products LLC, http://www.profileevs.com) was used as the soil. The soil was washed with water before use, then dried, filled in the pots (24.5 cm upper outer diameter, 20 cm lower outer diameter, 30 cm height; SP2530P, Tecs Inc., http://www.tecs.ne.jp) up to a depth of 25cm, and irrigated with modified Kimura B (Yoshida et al., 1976) culture solution (273.2 µM K2SO4, 546.9 µM MgSO4.7H2O, 182.0 µM NaH2PO4.2H2O, 182.3 µM CaCl2.2H2O, 182.4 µM CaSO4.2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg L-1 FeC6H5O7.nH2O [pH 5.5]). The germinated seeds were individually planted in separate pots, and they were cultivated in a growth chamber (Nippon Medical & Chemical Instruments Co., http://www.nihonika.co.jp) under a 14 h light/ 10 h dark photoperiod, with 50% relative humidity (R.H.) at daytime and 60% R.H. at nighttime. The temperature in the growth chamber was maintained at 25°C at nighttime and varied from 25°C to 30°C at daytime.  We used iPOTs (Numajiri et al. 2021), which is a pot that incorporates auto-irrigation system to mimic soil condition similar to the drought stress in the field. The water level in the supply pot, connected in parallel with the pots through a hose, was maintained at a height of 10 cm to ensure that the upper layers of the pots were moistened during the irrigation period.

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: Plants at 14 days after sowing were subjected to severe drought treatment for 9 days, and then watered for 6 days. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf

tag: cultivar

value: moderate drought

tag: days after_treatment

tag: replicate


title: WRC16, leaf, moderate drought, Day 5, rep 3

description: Library name: D115


title: WRC04, leaf, moderate drought, Day 5, rep 3

description: Library name: D112


title: WRC44, leaf, moderate drought, Day 5, rep 3

description: Library name: D114


title: WRC32, leaf, moderate drought, Day 5, rep 3

description: Library name: D111


title: Koshihikari, leaf, moderate drought, Day 5, rep 3

description: Library name: D110

value: Koshihikari


title: IR64, leaf, moderate drought, Day 5, rep 3.

description: Library name: D113


title: KP, leaf, moderate drought, Day 5, rep 3

description: Library name: D119

value: KP


title: WRC57, leaf, moderate drought, Day 5, rep 3

description: Library name: D120


title: WRC46, leaf, moderate drought, Day 5, rep 3

description: Library name: D117


title: WRC21, leaf, moderate drought, Day 5, rep 3

description: Library name: D118


title: mRNA_MLAD6


title: WRC25, leaf, moderate drought, Day 5, rep 3

description: Library name: D109


title: whole body larval fathead minnow, control, biol rep7 [6PPD_C_C10]

value: control


title: hepatocytes, normal weight cord plasma, 24hrs, 5

description: Library name: Sample HNR12

value: HepaRG cells

value: hepatocyte


title: mRNA_X0457LV


title: mRNA_MLAD2


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_C09]


title: mRNA_MLAD 19


title: whole body larval fathead minnow, 6PPD, biol rep4 [6PPD_C_C08]


title: WRC47, leaf, moderate drought, Day 5, rep 3

description: Library name: D108


title: hepatocytes, obese cord plasma, 24hrs, 3

description: Library name: Sample HNR9

value: obese cord plasma


title: WRC33, leaf, moderate drought, Day 5, rep 3

description: Library name: D107


title: mRNA_MLAD16

value: Left atrium


title: hepatocytes, normal weight cord plasma, 24hrs, 4

description: Library name: Sample HNR10

value: normal weight cord plasma


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_C07]


title: mRNA_MLAD13


title: hepatocytes, normal weight cord plasma, 24hrs, 3

description: Library name: Sample HNR7


title: mRNA_XO552LA


title: whole body larval fathead minnow, control, biol rep6 [6PPD_C_C05]


title: mRNA_0457 LA


title: Dro1-NIL, leaf, moderate drought, Day 5, rep 3

description: Library name: D104


title: whole body larval fathead minnow, control, biol rep5 [6PPD_C_C04]


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_C03]


title: WRC27, leaf, moderate drought, Day 5, rep 3

description: Library name: D105


title: WRC13, leaf, moderate drought, Day 5, rep 3

description: Library name: D103


title: hepatocytes, normal weight cord plasma, 24hrs, 1

description: Library name: Sample HNR2


title: hepatocytes, obese cord plasma, 24hrs, 2

description: Library name: Sample HNR3


title: hepatocytes, normal weight cord plasma, 24hrs, 2

description: Library name: Sample HNR5


title: Long-read RNA-seq Mesoderm Repeat 1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

description:
bulk_longread_rnaseq_mesoderm_LR.count.tsv.gz
bulk_longread_rnaseq_combined_assembly.count.tsv.gz
transcripts_mesoderm.annotated.gtf.gz
transcriptscombined_assembly.gtf.gz

data_processing:
Transcript assembly was done using IsoSeq V3 pipeline of the PacificBiosciences (PacBio) (https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md). For each sample, the high-fidelity (HiFi) consensus reads were first generated from the raw PacBio subreads using ccs (https://github.com/PacificBiosciences/ccs). The following parameters were used: --min-rq 0.9 --min-passes 1 --min-snr 1. The full-length sequences were then generated by primer removal and demultiplexing using lima (https://github.com/lima-vm/lima). The full-length sequences were refined by isoseq3 (https://github.com/PacificBiosciences/IsoSeq) to remove the noise. The noiseless full-length sequences were then converted to the fastq format using PacBio’s bam2fastq (https://github.com/PacificBiosciences/pbtk#bam2fastx). After the processing of the PacBio raw reads, replicates of the same cell states were merged.
For the mapping of the noiseless full-length sequences to human genome, Minimap212 reference was prepared using version GRCh38 primary assembly of human genome and version 43 (GENCODEv43) of human reference GTF obtained from the GENCODE database13.  GENCODE reference GTF junctions were made using paftools in Minimap2 package. The sequence mapping was done using Minimap2. The output alignment was then sorted using SAMtools14. The transcript assembly was sone using StringTie15,16. For StringTie assembly, the following parameters were used: -s 2 -c 1 -L. The assembled transcripts were then filtered to remove transcripts with undefined strand. For expression comparison across different cell states, the assemblies from each cell state were merged together into merged human early development transcripts (hEDTs) using gffcompare17.
Assembly: hg38
Supplementary files format and content: GTF files assembled from StrinTie are provided for the merged replicate longread samples
Supplementary files format and content: TSV files contain quantified transcript abundance with either counts, or TPM estimated from the long-read abundance, abundance is provided per cell type-speciufic GTF, or for a combined_assembly. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have ant accession number.

source_name: cell line

growth_protocol: H1 human pluripotent stem cell lines were maintained on a Matrigel treatment plate, cultured in mTeSR1 (STEMCELL TECHNOLOGIES, 85850) medium and digested with Accutase (Sigma, A6964) every 5-7 days. In vitro germ layers were generated by changing the medium and adding inhibitors or cytokines when human PSC reached 60-70% confluency as previously reported1. For endoderm differentiation, cells were cultured in RPMI supplemented with 2X GlutaMax (Thermo Fisher, 35050061), 0.2x MEM Non-Essential Amino Acids Solution (Thermo Fisher,11140050), 55 µM b-mercaptoethanol (BBI, A600194), 0.5% FBS (BIOWEST, S1580), 50nM/ml WNT3A (MedChemExpress, HY-P70453A), and 100ng/ml Activin A (PEPROTECH, 120-14E-100). For mesoderm differentiation, at the first 24 hour, Activin A was introduced to the culture medium. The cells were cultured in DMEM/F12 supplemented with 2X GlutaMax, 0.2X MEM Non-Essential Amino Acids Solution, 55µM b-mercaptoethanol, 0.5% FBS, 100ng/ml VEGF (PEPROTECH,100-20-50), 100ng/ml BMP4 (PEPROTECH, 120-05ET), 10 ng/ml bFGF (PEPROTECH, 100-18B-100), and 100ng/ml Activin A. Then Activin A was removed from the culture. For ectoderm differentiation from the PSC, the cells were cultured in DMEM/F12 supplemented with 0.2X MEM Non-Essential Amino Acids Solution, and 55 µM b-mercaptoethanol 15% KOSR (Life Technologies) 2µM A83-01(Tocris, 2939), 2µM PNU-74654(Tocris, 113906), and 2uM Dorsomorphin (Tocris, 3093). Media was changed daily and the cells were collected after 5 days

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol. Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). Short-read RNA sequencing was performed on Illumina Novaseq 6000 platform.
Samples for long-read RNA sequencing were purified by the RNAeasy Mini kit. The RNA library generated with PacBio binding kit (Pacbio, 101-849-000) was sequenced on Sequel II (Pacbio).

treatment_protocol: No special treatment

value: cell line

value: Mesoderm


title: hepatocytes, obese cord plasma, 24hrs, 1

description: Library name: Sample HNR1


title: Long-read RNA-seq Mesoderm Repeat 2


title: WRC28, leaf, moderate drought, Day 5, rep 3

description: Library name: D101


title: WRC09, leaf, moderate drought, Day 5, rep 3

description: Library name: D102


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B12]

value: whole body fathead minnow

value: larval (5-day post hatch)


title: PSO 5 CD45pos#2, TCR

city: San Francisco

first: Victoire

last: Gouirand

state: CALIFORNIA

address: 513 Parnassus av

department: Dermatology

institute: UCSF

description: Library name: PSO10x5_CD45pos2_TCR

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: filtered feature bc matrices
Library strategy: TCR-Seq

source_name: skin

extract_protocol:
Cell subsets were purified from skin that was enzymatically digested overnight with collagenase IV in the presence of DNAse.
scRNASeq was performed using the 10x Single Cell 5’ Chemistry by UCSF 10x Genomics Core

value: skin


title: Long-read RNA-seq hPSCs Repeat 2

description:
bulk_longread_rnaseq_hPSC_LR.count.tsv.gz
bulk_longread_rnaseq_combined_assembly.count.tsv.gz
transcripts_hPSCs.annotated.gtf.gz
transcriptscombined_assembly.gtf.gz

value: hPSCs


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_B11]


title: Long-read RNA-seq hPSCs Repeat 1


title: PSO 5 CD45pos#1, TCR

description: Library name: PSO10x5_CD45pos1_TCR


title: WRC03, leaf, moderate drought, Day 5, rep 3

description: Library name: D100


title: WRC24, leaf, moderate drought, Day 5, rep 3

description: Library name: D99


title: WRC23, leaf, moderate drought, Day 5, rep 3

description: Library name: D106


title: PSO 4 CD45pos#2, TCR

description: Library name: PSO10x4_CD45pos2_TCR


title: Long-read RNA-seq Endoderm Repeat 2

description:
bulk_longread_rnaseq_endoderm_LR.count.tsv.gz
bulk_longread_rnaseq_combined_assembly.count.tsv.gz
transcripts_endoderm.annotated.gtf.gz
transcriptscombined_assembly.gtf.gz

value: Endoderm


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B09]


title: PSO 4 CD45pos#1, TCR

description: Library name: PSO10x4_CD45pos1_TCR


title: WRC05, leaf, moderate drought, Day 5, rep 3

description: Library name: D98

value: leaf


title: Long-read RNA-seq Ectoderm Repeat 2

description:
bulk_longread_rnaseq_ectoderm_LR.count.tsv.gz
bulk_longread_rnaseq_combined_assembly.count.tsv.gz
transcripts_ectoderm.annotated.gtf.gz
transcriptscombined_assembly.gtf.gz

value: Ectoderm


title: WRC02, leaf, moderate drought, Day 5, rep 3

description: Library name: D97

value: moderate drought


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B10]


title: PSO 3 CD45pos, TCR

description: Library name: PSO10x3_CD45pos_TCR


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B07]


title: WRC06, leaf, moderate drought, Day 5, rep 3

description: Library name: D95


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B08]


title: WRC51, leaf, moderate drought, Day 5, rep 3

description: Library name: D94


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_B06]


title: PSO 1 Treg_nonTreg, TCR

description: Library name: PSO10x1TregnonTreg_TCR


title: PSO 2 TregCD8, TCR

description: Library name: PSO10x2_nonTreg_TCR

value: nonTreg


title: WRC36, leaf, moderate drought, Day 5, rep 3

description: Library name: D93


title: WRC48, leaf, moderate drought, Day 5, rep 3

description: Library name: D92


title: WRC19, leaf, moderate drought, Day 5, rep 3

description: Library name: D96


title: PSO 5 CD45pos#2, GEX

description: Library name: PSO10x5_CD45pos2

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: filtered feature bc matrices


title: whole body larval fathead minnow, 6PPD, biol rep3 [6PPD_C_B05]


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_A12]


title: PSO 2 nonTreg, TCR

description: Library name: PSO10x2_TregCD8_TCR


title: whole body larval fathead minnow, 6PPD-Q, biol rep1 [6PPD_C_B02]


title: Long-read RNA-seq Ectoderm Repeat 1


title: PSO 5 CD45pos#1, GEX

description: Library name: PSO10x5_CD45pos1


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_B03]


title: PSO 1 CD8, TCR

description: Library name: PSO10x1CD8_TCR


title: WRC01, leaf, moderate drought, Day 5, rep 3

description: Library name: D90


title: Long-read RNA-seq Endoderm Repeat 1


title: whole body larval fathead minnow, control, biol rep4 [6PPD_C_A11]

value: control


title: whole body larval fathead minnow, control, biol rep3 [6PPD_C_A10]


title: WRC18, leaf, moderate drought, Day 5, rep 3

description: Library name: D89


title: PSO 4 CD45pos#2, GEX

description: Library name: PSO10x4_CD45pos2


title: PSO 4 CD45pos#1, GEX

description: Library name: PSO10x4_CD45pos1


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_C_A09]


title: WRC15, leaf, moderate drought, Day 5, rep 3

description: Library name: D88


title: WRC37, leaf, moderate drought, Day 5, rep 3

description: Library name: D91


title: skeletal muscle, dmd, d11

city: Pavia

first: bartolo

last: rizzo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: D11

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differental expression analysis for mRNA and lncRNA was performed using R package DESeq2
Assembly: HG19

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated from skeletal muscle biopsies using Trizol® reagent. The specifications from the manufacturer were followed.
Illumina TruSeqStranded RNA Library Prep, version 2, Protocol D,  using 500-ng total RNA. Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagnt kit. RNA processing has been carried out using Illumina NextSeq 550 Sequencing.

value: skeletal muscle

value: Duchenne phenotype


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_C_A08]


title: WRC35, leaf, moderate drought, Day 5, rep 3

description: Library name: D87


title: PSO 2 TregCD8, GEX

description: Library name: PSO10x2_TregCD8


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_C_A07]


title: WRC42, leaf, moderate drought, Day 5, rep 3

description: Library name: D86


title: skeletal muscle, dmd, d9

description: Library name: D9


title: PSO 2 nonTreg, GEX

description: Library name: PSO10x2_nonTreg


title: skeletal muscle, dmd, d12

description: Library name: D12


title: skeletal muscle, dmd, d10

description: Library name: D10


title: WRC31, leaf, moderate drought, Day 5, rep 3

description: Library name: D85


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_C_A06]


title: skeletal muscle, dmd, d8

description: Library name: D8


title: WRC34, leaf, moderate drought, Day 5, rep 3

description: Library name: D84


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_C_A05]


title: PSO 2 CD3 neg, GEX

description: Library name: PSO10x2_CD3neg


title: PSO 1 Treg_nonTreg, GEX

description: Library name: PSO10x1TregnonTreg


title: WRC55, leaf, moderate drought, Day 5, rep 3

description: Library name: D83


title: PSO 1 CD8, GEX

description: Library name: PSO10x1CD8


title: skeletal muscle, dmd, d6

description: Library name: D6


title: skeletal muscle, dmd, d7

description: Library name: D7


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_A04]


title: PSO 3 CD45pos, GEX

description: Library name: PSO10x3_CD45pos


title: WRC50, leaf, moderate drought, Day 5, rep 3

description: Library name: D82


title: whole body larval fathead minnow, control, biol rep2 [6PPD_A_F10]


title: PSO 1 CD3neg, GEX

description: Library name: PSO10x1CD3neg


title: skeletal muscle, dmd, d5

description: Library name: D5


title: whole body larval fathead minnow, 6PPD, biol rep1 [6PPD_A_C01]


title: whole body larval fathead minnow, 6PPD, biol rep2 [6PPD_C_C06]


title: whole body larval fathead minnow, control, biol rep1 [6PPD_A_A11]


title: skeletal muscle, dmd, d4

description: Library name: D4


title: Healthy  5 CD45#3, GEX

description: Library name: NST29_CD45pos_3


title: WRC22, leaf, moderate drought, Day 5, rep 3

description: Library name: D81


title: WRC16, leaf, moderate drought, Day 5, rep 2

description: Library name: D80


title: skeletal muscle, dmd, d3

description: Library name: D3


title: Healthy  5 CD45#2, GEX

description: Library name: NST29_CD45pos_2


title: WRC19, leaf, moderate drought, Day 5, rep 2

description: Library name: D79


title: ovaries, C_U_3

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

description: Library name: Sample 12

data_processing:
SOAPnuke (v1.5.2)
HISAT and  Bowtie2
Assembly: GCF_000001635.27_GRCm3
Supplementary files format and content: text file includes FPKM and counts

organism: Mus musculus

source_name: Ovary

extract_protocol:
total RNA was extracted with Tizol
the mRNA libraries were prepared using RNA-seq library Pre KIT according to the instructions.

value: Ovary

value: WT


title: Healthy  4 CD8, GEX

description: Library name: NST10_CD8


title: Mixture of HEK293T, A375, HeLa, and NIH/3T3 cell lines

city: New York

first: Junyue

last: Cao

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: cell_line_mixture

data_processing:
Low quality cells were removed using UMI cutoffs of >500 for mouse brain and >1000 for cell lines. Doublets were removed using custom pipelines, Scrublet, and manual inspection. Initial mouse brain cell type annotations were generated using the Allen Institute MapMyCells tool and validated by checking marker expression. Further oligodendrocyte subtypes were manually annotated using specific marker expression.
Assembly: mm39, hg38
Supplementary files format and content: gene count matrix, cell metadata, exon count matrix, gene metadata, exon metadata

molecule: nuclear RNA

source_name: HEK293T, A375, HeLa, NIH/3T3

extract_protocol:
hypotonic lysis buffer for nuclei extraction from cell lines and mouse brains
after HCR RNA FISH labeling of target cell type and FACS isolation, combinatorial indexing-based single-nucleus RNA-seq was performed.

value: HEK293T, A375, HeLa, NIH/3T3


title: skeletal muscle, dmd, d2

description: Library name: D2


title: skeletal muscle, dmd, d1

description: Library name: D1


title: WRC50, leaf, moderate drought, Day 5, rep 2

description: Library name: D77


title: WRC02, leaf, moderate drought, Day 5, rep 2

description: Library name: D78


title: Healthy  3 CD8, GEX

description: Library name: NST9_CD8


title: ovaries, C_U_2

description: Library name: Sample 11


title: ovaries, C_U_1

description: Library name: Sample 10


title: Healthy  5 CD45#1, GEX

description: Library name: NST29_CD45pos_1


title: skeletal muscle, bmd, b6

description: Library name: B6

value: Becker phenotype


title: Healthy  2 CD8, GEX

description: Library name: NST8_CD8skin


title: WRC46, leaf, moderate drought, Day 5, rep 2

description: Library name: D76


title: skeletal muscle, bmd, b5

description: Library name: B5


title: ovaries, Cy_3

description: Library name: Sample 9


title: WRC48, leaf, moderate drought, Day 5, rep 2

description: Library name: D75


title: ovaries, Cy_2

description: Library name: Sample 8


title: skeletal muscle, bmd, b4

description: Library name: B4


title: WRC35, leaf, moderate drought, Day 5, rep 2

description: Library name: D74


title: Healthy  1 CD8, GEX

description: Library name: NST7_CD8


title: Donor4, sgLAYN

description: Library name: V09

data_processing:
Read alignment done with kallisto (v. 0.46.2) using Ensembl reference genome GRCh38  (109)
Assembly: GRCh38
Supplementary files format and content: Abundance tsv files for individual samples

source_name: Blood

extract_protocol:
Treg cells were isolated respectively by gating on live CD45+CD4+CD25+LAYN+ or CD45+CD4+CD25+LAYN+ cells. Cells were sorted into fresh media, plate and keep in culture for 24h. After 24h cells were pellet then flash frozen on dry ice before being processed by Novogen. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis
The library was prepared at and by Novogen. Library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Then checked with Qubit and real-time PCR

value: Blood

value: primary Treg

value: Treg

value: sgLAYN


title: skeletal muscle, bmd, b3

description: Library name: B3


title: WRC47, leaf, moderate drought, Day 5, rep 2

description: Library name: D73


title: ovaries, Cy_1

description: Library name: Sample 7


title: Donor1, sgLAYN

description: Library name: V06


title: skeletal muscle, bmd, b2

description: Library name: B2


title: WRC13, leaf, moderate drought, Day 5, rep 2

description: Library name: D72


title: ovaries, UA_2

description: Library name: Sample 5


title: Donor4, sgCTRL

description: Library name: V04

value: sgCTRL


title: WRC04, leaf, moderate drought, Day 5, rep 2

description: Library name: D71


title: K562, H3K36me3, ChIP, dTAG7, rep2, 4h

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

institute: Max Planck Institute for Multidisciplinary Sciences

library_source: genomic

data_processing:
ChIP-seq reads were aligned to human hg38 genome assembly merged with D.melanogaster genome using Bowtie 2 with the following parameters: -p 24 --no-discordant --no-mixed --very-sensitive. Duplicates were removed using Picard tools.
Assembly: GRCh38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: genome edited K562

growth_protocol: K562 human cells were sourced from the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. K562 cells and genome edited cell lines were cultured in RPMI medium (Thermo Fisher Scientific), enriched with 10% fetal bovine serum and 1x GlutaMax, within a humidified incubator at 37°C and 5% CO2. These cells underwent subculturing every 2-3 days, maintaining a density of 150,000 to 700,000 cells/mL. To deplete IWS1-dTAG, the culture medium was supplemented with 500 nM of dTAG7 ligand, previously dissolved in dimethyl sulfoxide (DMSO) at a 10 mM concentration. Control cells were treated with solvent only with the same treatment time.

extract_protocol:
ChIP-seq was performed as previously described by  Zumer et al., 2024. For each replicate, 30 million cells were crosslinked using 1% formaldehyde (Thermo Fisher Scientific) and chromatin was extracted. The crosslinked chromatin was then sheared using an S220 Focused-ultrasonicator (Covaris) for 18 minutes. Subsequently, 100 µg of the sheared chromatin was combined with 600 ng of similarly processed D. melanogaster chromatin as in Caizzi et al., 2021. This mixture was then incubated with one of the antibodies pre-coupled to Dynabeads Protein G (Invitrogen): 20 µL Rpb1 NTD and 20 µL SETD2 (both from Cell Signaling Technology), or 20 µL Histone H3K36me3 (Active Motif), and 1.5 µL of a spike-in antibody (histone H2Av, Active Motif) was added to each sample.
Following IP, the DNA was purified from the complexes, and library preparation was conducted using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The prepared libraries were then sequenced paired-end using 43 cycles on the NextSeq550 (Illumina) platform.

treatment_protocol: 30 million cells per biological replicate were treated with dTAG7 or DMSO (control) for 1 h or 4 h.

value: genome edited K562

value: chronic myelogenous leukemia

value: IWS1 N-terminal dTAG

value: dTAG7 4h

tag: chip antibody

value: H3K36me3 antibody (CST, #61021)


title: ovaries, UA_1

description: Library name: Sample 4

tag: tissue


title: Dro1-NIL, leaf, moderate drought, Day 5, rep 2

description: Library name: D70

value: leaf

value: moderate drought


title: K562, H3K36me3, ChIP, DMSO, rep2, 4h

tag: cell line

value: DMSO 4h


title: ovaries, UA_3

description: Library name: Sample 6

value: Ovary


title: skeletal muscle, bmd, b1

description: Library name: B1

value: skeletal muscle


title: Donor2, sgCTRL

description: Library name: V02

tag: cell type


title: ovaries, NC_3

description: Library name: Sample 3

value: WT


title: WRC09, leaf, moderate drought, Day 5, rep 2

description: Library name: D69

tag: treatment


title: K562, H3K36me3, ChIP, dTAG7, rep1, 4h

tag: genotype


title: ovaries, NC_2

description: Library name: Sample 2


title: WRC44, leaf, moderate drought, Day 5, rep 2

description: Library name: D68


title: K562, H3K36me3, ChIP, DMSO, rep1, 4h


title: Donor1, sgCTRL

description: Library name: V01


title: WRC42, leaf, moderate drought, Day 5, rep 2

description: Library name: D66


title: ovaries, NC_1

description: Library name: Sample 1


title: Donor3, sgLAYN

description: Library name: V08


title: K562, H3K36me3, ChIP, dTAG7, rep2, 1h

value: dTAG7 1h


title: OE_RBM47_2

city: urumqi

first: tuerjun

last: tuohuti

state: xinjiang

address: People′s Hospital of Xinjiang Uygur Autonomous Region

data_processing:
Illumina bcl2fastq software used for basecalling. The raw reads were trimmed of low-quality bases using a FASTX-Toolkit (v.0.0.13;   http://hannonlab.cshl.edu/fastx_toolkit/).  Then the clean reads were evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Clean reads were aligned to the GRCh38 genome by HISAT2 (Kim, Langmead et al. 2015) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)(Trapnell, Williams et al. 2010).
The R Bioconductor package DESeq2 (Love, Huber et al. 2014) was utilized to screen out the differentially expressed genes (DEGs). The P value <0.01 and fold change>1.5 or < 3/2 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified by using the ABLas pipeline as described previously (Jin, Li et al. 2017, Xia, Chen et al. 2017). In brief, ABLas detection of ten types of ASEs was based on the splice junction reads, including exon skipping(ES), alternative 5' splice site(A5SS), alternative 3'splice site(A3SS), mutually exclusive exons(MXE), mutually exclusive 5'UTRs(5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES and A5SS&ES. To assess RBP regulated ASE, Student’s t-test was performed to evaluate the significance of the ratio alteration of AS events. Those events which were significant at P-value cutoff corresponding to a false discovery rate cutoff of 5% were considered RBP regulated ASEs.
To sort out functional categories of DEGs, Gene Ontology (GO) terms and KEGG pathways were identified using KOBAS 2.0 server (Xie, Mao et al. 2011). Hyper geometric test and Benjamini-Hochberg FDR controlling procedure were used to define the enrichment of each term.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HCT116 cells

growth_protocol: HCT116 cells line (Procell Life Science & Technology Co., Ltd.,China) were cultured at 37 ℃ with 5% CO2 in DMEM with 10% fetal bovine serum (FBS), 100 μg/mL streptomycin, 100 U/mL penicillin.

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1μg of total RNA was used for RNA-seq library preparation with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (#E7420). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted NEBNext® Adaptor. After purification, ligation products corresponding to 300-500bps were digested with Heat-labile UDG, the single strand cDNA was amplified, purified, quantified, and stored at -80 ℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: Plasmid transfection of HCT116 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR and Western blotting analysis. pcDNA3.1-3xFlag-RBM47 was purchased from Youbio Biotech (NM_019027, Changsha PRC).

value: HCT116 cells

value: RMB47 overexpression


title: Donor3, sgCTRL

description: Library name: V03

value: Blood

value: primary Treg

value: Treg


title: K562, H3K36me3, ChIP, DMSO, rep2, 1h

value: genome edited K562

value: DMSO 1h


title: WRC32, leaf, moderate drought, Day 5, rep 2

description: Library name: D65


title: K562, H3K36me3, ChIP, dTAG7, rep1, 1h

value: chronic myelogenous leukemia

value: IWS1 N-terminal dTAG


title: OE_RBM47_1

institute: People′s Hospital of Xinjiang Uygur Autonomous Region


title: CENTRINONE, rep_2

city: Benevento

first: Luca

last: Faretra

state: BN

address: Via dei Mulini

department: DST

institute: University of Sannio

description: Library name: Sample 6

data_processing:
Raw RNA-seq reads were assessed for quality using FastQC (v0.12.0). Quality metrics including per-base sequence quality, adapter content, and duplication levels were evaluated to confirm the integrity of the sequencing data prior to downstream processing.
Adapter trimming and quality filtering were performed using Trim Galore (v0.6.5) with default parameters. Low-quality bases and residual sequencing adapters were removed, retaining high-quality reads suitable for alignment and quantification.
Filtered reads were aligned to the GRCh38 primary genome assembly using STAR (v2.7.11b). The genome index was generated from the Ensembl GRCh38 reference. STAR was run in two-pass mode with default settings, allowing for accurate splice junction discovery and annotation-guided alignment.
RNA-seq reads were quantified at the transcript level using Salmon (v1.10.2) in alignment-based mode. Quantification was performed against the Homo_sapiens.GRCh38.113 transcriptome, using the corresponding Ensembl FASTA and GTF files. Bias correction flags --seqBias and --gcBias were enabled to improve quantification accuracy. The resulting transcript abundances were reported in Transcripts Per Million (TPM).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM and counts for each sample.

source_name: SK-N-SH

extract_protocol:
Total RNA was extracted by using  the Maxwell® RSC simplyRNA Cells Kit (AS1390) with the Maxwell instrument (Promega Corporation) according to manufacturer's protocol. Total RNA concentrations were determined by using NanoDrop spectrophotometer (Thermo Fisher) and their quality was assessed with the TapeStation 4150 (Agilent Technologies).
150 ng of total RNA of each sample were subjected to mRNAs capture by using polyT-coated beads followed by the indexed library preparation with the SureSelect XT HS2 mRNA Library Preparation System (Agilent Technologies), according to the manufacturer’s instructions. Finally, an equimolar amount of each DNA library was pooled together and subject to cluster generation and sequencing into the Illumina NextSeq550 System (Illumina) with a 2×75 paired-end format.

value: SK-N-SH

value: neuroblastoma cells

value: RA (10uM), CENTRINONE (100nM)


title: AR10, rep_2

description: Library name: Sample 4

value: RA (10uM)


title: AR10, rep_1

description: Library name: Sample 3


title: Control, rep_1

description: Library name: Sample 1

value: control


title: CENTRINONE, rep_1

description: Library name: Sample 5


title: WRC01, leaf, moderate drought, Day 5, rep 2

description: Library name: D64

value: leaf

value: moderate drought


title: Control, rep_2

description: Library name: Sample 2


title: NC_2

value: Control plasmid


title: WRC33, leaf, moderate drought, Day 5, rep 2

description: Library name: D63


title: K562, RNA Pol II, ChIP, dTAG7, rep2, 1h

value: dTAG7 1h

value: Rpb1 NTD antibody (CST, #14958)


title: WRC34, leaf, moderate drought, Day 5, rep 2

description: Library name: D67


title: NC_1

value: HCT116 cells


title: KP, leaf, moderate drought, Day 5, rep 2

description: Library name: D62

value: KP


title: NC_3


title: K562, RNA Pol II, ChIP, DMSO, rep2, 1h


title: WRC24, leaf, moderate drought, Day 5, rep 2

description: Library name: D61


title: K562, RNA Pol II, ChIP, dTAG7, rep1, 1h


title: H2023 Onco g2-1 2 (g2-1=Clone2-2)

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University

data_processing:
Macrogen NGS service analysis workflow
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCh38 using HISAT2
Transcript is assembled by StringTie with aligned reads.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for all Samples

source_name: H2023 cells

extract_protocol:
RNA was harvested using the ReliaPrepTM RNA  Cell Miniprep Systems (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Reference Guide Document # 1000000040498 v00

value: H2023 cells

value: ZC3H12A knockout

value: stem cell enriched culture condtion


title: WRC37, leaf, moderate drought, Day 5, rep 2

description: Library name: D60


title: H2023 Onco g2-1 1 (g2-1=Clone2-2)


title: K562, H3K36me3, ChIP, DMSO, rep1, 1h

value: genome edited K562

value: chronic myelogenous leukemia

value: DMSO 1h

value: H3K36me3 antibody (CST, #61021)


title: K562, RNA Pol II, ChIP, DMSO, rep1, 1h

value: IWS1 N-terminal dTAG


title: WRC05, leaf, moderate drought, Day 5, rep 2

description: Library name: D59


title: H2023 Onco WT 2

value: wild-type


title: WRC18, leaf, moderate drought, Day 5, rep 2

description: Library name: D58


title: mNET-Seq, K562, mNET-seq, dTAG7, rep2, 1h

data_processing:
For mNET-seq, the alignment was performed against a composite reference consisting of the human GRCh38 genome and the S. cerevisiae SacCer3 genome, using STAR version 2.6.0 (Dobin et al., 2013) with parameters: --runThreadN 24 --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.02 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 500000. For TT-seq and mNET-seq, the quantifications of reads aligning to the spike-in sequences were used to calculate normalization factors, ensuring accurate comparison of expression levels across samples as in Zumer et al., 2024. Spike-in read counts were assessed by summarizeOverlaps function (Bioconductor package “IRanges”) and normalization factors were calculated with DESeq2 (Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Following fractionation, the isolated chromatin was subjected to a 2-minute digestion at 37°C and 1,400 rpm using micrococcal nuclease (MNase, NEB). The reaction was halted by adding 25 mM EGTA. The resultant soluble chromatin fraction was then diluted 8-fold with IP buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.05% NP-40, 1% Empigen, 1x protease and phosphatase inhibitors (Sigma-Aldrich)). For immunoprecipitation (IP), 30 µg of RNA Polymerase II antibody (Diagenode) was pre-coupled overnight with Dynabeads M-280 Sheep Anti-Mouse IgG (Invitrogen) and added to each diluted sample. The mixtures were incubated for 1 hour at 4°C. Following IP, the beads were washed seven times with IP buffer and once with PNKT buffer (1x T4 PNK buffer (NEB), 0.1% Tween-20). The 5’ ends of RNA were phosphorylated using T4 Polynucleotide Kinase (PNK, NEB) for 10 minutes at 37°C and 800 rpm. After a final wash with IP buffer, the beads were resuspended in TRIzol reagent (Invitrogen), and 2.5 µg of S. cerevisiae spike-in RNA, prepared as per Caizzi et al., 2021, was added to each sample. RNA was extracted from the beads and precipitated overnight with ethanol and GlycoBlue co-precipitant (Invitrogen) at -20°C. The RNA pellets were then dissolved in buffer containing 7 M urea, and size selection was carried by size separation in a 6% polyacrylamide gel containing 7 M urea and excision of 25-110 nt long RNA fragments. The recovered RNA was precipitated again with GlycoBlue and ethanol at -20°C overnight.
For library preparation, 28.95 ng of RNA from each replicate was used with the TruSeq Small RNA Library Prep Kit (Illumina). The quality of the libraries were assessed using TapeStation (Agilent), followed by paired-end sequencing with 42 cycles on the NextSeq550 (Illumina).

treatment_protocol: mNET-seq was performed as previously described bySchlakowet al., 2017,Nojimaet al., 2015;Nojima et al., 2016; Gresselet al., 2019; andCaizziet al., 2021, utilizing two biological replicates with slight modifications. Following treatment, 100 million cells were fractionated as described previously (Conrad andØrom, 2017).


title: OE_RBM47_3

value: RMB47 overexpression


title: mNET-Seq, K562, mNET-seq, DMSO, rep2, 1h


title: WRC55, leaf, moderate drought, Day 5, rep 2

description: Library name: D57

value: leaf


title: A549 Onco g2-3 2  (g2-3=Clone2-2)

source_name: A549 cells

value: A549 cells


title: WRC28, leaf, moderate drought, Day 5, rep 2

description: Library name: D56

value: moderate drought


title: A549 Onco g2-3 1  (g2-3=Clone2-2)


title: mNET-Seq, K562, mNET-seq, DMSO, rep1, 1h


title: mNET-Seq, K562, mNET-seq, dTAG7, rep1, 1h

value: dTAG7 1h


title: WRC31, leaf, moderate drought, Day 5, rep 2

description: Library name: D55


title: A549 Onco WT 2


title: A549 Onco WT 1


title: WRC100, leaf, moderate drought, Day 5, rep 2

description: Library name: D54


title: H2023 Onco WT 1


title: H2023 Parent g2-1 2 (g2-1=Clone2-2)

value: normal culture condition


title: WRC21, leaf, moderate drought, Day 5, rep 2

description: Library name: D53


title: WRC51, leaf, moderate drought, Day 5, rep 2

description: Library name: D52


title: H2023 Parent g2-1 1 (g2-1=Clone2-2)


title: DEN30w

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

description:
Library name: Sample4
Fresh frozen Spatial trascriptome sequencing

data_processing:
Sequencing data were processed using the Space Ranger software (v1.3.1, 10x Genomics) with the spaceranger count pipeline and STAR aligner to map reads to the mouse reference genome (mm10-2020-A).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial varcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10-μm-thick frozen sections were cut with cryostat
After H&E staining to correlate morphological features with gene expression, tissue sections were permeabilized, and spatially barcoded cDNA synthesis was carried out in situ. Libraries were prepared using Visium Spatial Gene Expression Reagent Kits (10x Genomics).

value: liver


title: DEN22w

description:
Library name: Sample3
Fresh frozen Spatial trascriptome sequencing


title: PT2

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

description: Library name: sample11

data_processing:
bcl2fastq2 tools for base calling
Mobivision software for single cell identifying
PCA and UMAP/TSNE for dimensionality reduction
Seurat for finding clusters
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: metastatic nodes

extract_protocol:
The cells were then loaded onto a Chip A Single Cell Kit v2.0 (MobiDrop, cat. no. S050100201), and droplets were generated with a MobiNova-100 (MobiDrop, cat. no. A1A40001).Each droplet encapsulated a single cell along with a gel bead coated with millions of oligonucleotides containing unique cell barcodes. The en-capsulated droplets were photo-cleaved using a MobiNovaSP-100 (MobiDrop, cat. no. A2A40001), allowing mRNA to bind to the oligonucleotidcoated gel beads.
Libraries were prepared for sequencing using standard illumina protocols

value: metastatic nodes

value: cisplatin metastasis


title: C2

description: Library name: sample2

source_name: peritoneal irrigation fluid

value: peritoneal irrigation fluid

value: Control


title: CT1

description: Library name: sample4

value: Control metastasis


title: P1

description: Library name: sample7

value: cisplatin


title: CT3

description: Library name: sample6


title: WRC22, leaf, moderate drought, Day 5, rep 2

description: Library name: D51


title: C1

description: Library name: sample1


title: STAM16w

description:
Library name: Sample1
Fresh frozen Spatial trascriptome sequencing


title: CT2

description: Library name: sample5


title: P3

description: Library name: sample9


title: P2

description: Library name: sample8


title: PT3

description: Library name: sample12


title: PT1

description: Library name: sample10


title: C3

description: Library name: sample3


title: STAM20w

description:
Library name: Sample2
Fresh frozen Spatial trascriptome sequencing


title: WRC57, leaf, moderate drought, Day 5, rep 2

description: Library name: D50


title: aMHC-Cre control, replicate 2

city: Birmingham

first: Yang

last: Zhou

state: AL

address: 1825 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: Library name: MHC_Cre_2

data_processing:
The paired-end reads were mapped to the mouse genome (mm10) using STAR (v2.5.1b) with default parameters.
RNA-Seq data were analyzed using DESeq2, which calculated fold change, p- and adjusted p- (False Discovery Rate; FDR) values for genotype effects.
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text file including read counts

source_name: Heart

extract_protocol:
Total RNA was isolated from male mice hearts using TRIzol™ Reagent (#15596026, Invitrogen) according to manufacturer’s instruction.
RNA-Seq library were prepared using the NEBNext Ultra RNA library Prep Kit (New England Biolabs).

value: Heart

value: aMHC-Cre+/-


title: H2023 Parent WT 1

value: H2023 cells


title: aMHC-Cre control, replicate 1

description: Library name: MHC_Cre_1


title: 3rd instar control 2

city: Oxford

first: Alexander

middle: Dean

last: Berry

state: OH

address: 501 E HIGH ST

department: Biology

institute: Miami Unviersity

description:
JC2
mRNA

data_processing:
Basecalls performed by CASAVA version 1.6.
Transcriptome was assembled using TRINITY version 2.6.6, minKmerCov=3, min_glue=4, with redundancy removed by Corset version 4.6, -f ture, Default, -m 10.
Mapping and quantification was done in RSEM Version 1.2.28, --estimate-rspd -mismatch-rate 0.3.
DESeq2 Version 1.26.0 was used for differential expression (settings padj < 0.05 padj).
Genome_build: FASTA
Supplementary_files_format_and_content: readcount_genename.txt: Gene count data in tab-delimited text format.

organism: Pardosa milvina

source_name: whole body

extract_protocol:
mRNA was extracted using Maxwell RSC simplyRNA extraction kit following all the instructions.
mRNA library construction followed all the instructions for the NEBNext Ultra II Directional library prep kit.

treatment_protocol: Individual spiders were exposed to predator chemical cues throughout development. Whole body mRNA was extracted from 3 exposed and 3 unexposed adults and from the offspring of exposed and unexposed spiders.

value: whole body

value: maternal control

tag: age

value: 3rd instar


title: A549 Parent g2-3 2  (g2-3=Clone2-2)

value: A549 cells

value: ZC3H12A knockout


title: Koshihikari, leaf, moderate drought, Day 5, rep 2

description: Library name: D49

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

source_name: leaf

value: leaf

value: Koshihikari

value: moderate drought


title: Elmsan1 fl/fl control, replicate 2

description: Library name: ELM_homo_3

value: Elmsan1 fl/fl


title: IR64, leaf, moderate drought, Day 5, rep 2.

description: Library name: D48


title: 3rd instar control 3

description:
JC3
mRNA


title: H2023 Parent WT 2

value: wild-type

value: normal culture condition


title: 3rd instar maternal predator exposure 3

description:
JE3
mRNA

value: maternal exposure to predators


title: WRC06, leaf, moderate drought, Day 5, rep 2

description: Library name: D45


title: Elmsan1 KO, replicate 4

description: Library name: ELM_cKO_4

value: Elmsan1 fl/fl;aMHC-Cre+/-


title: Elmsan1 KO, replicate 3

description: Library name: ELM_cKO_3


title: Elmsan1 KO, replicate 2

description: Library name: ELM_cKO_2


title: WRC15, leaf, moderate drought, Day 5, rep 2

description: Library name: D47


title: Adult control 3

description:
AC3
mRNA

value: control

value: adult

tag: Sex

value: female


title: 3rd instar maternal predator exposure 2

description:
JE2
mRNA


title: Elmsan1 fl/fl control, replicate 1

description: Library name: ELM_homo_2

value: Heart


title: 3rd instar maternal predator exposure 1

description:
JE1
mRNA

value: whole body


title: 6A_control

city: Spring House

first: Dylan

middle: Jack

last: Richards

state: PA

address: 1400 McKean Rd

institute: Johnson & Johnson

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0
Cell Ranger output was immediately processed to remove ambient RNA using cellbender v0.3.0 to create ambient RNA adjusted matrix/tsv processed data
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: D2- Duodenum desending part

extract_protocol:
Cryopreserved biopsies were thawed by immersing in a 37°C water bath for ~ 2 min with periodic shaking. RPMI with 10% FCS was added to each biopsy, dropwise in a 50 ml tube. The biopsies were washed in serum free RPMI over a cell strainer. Single cell suspensions were made by placing biopsies in a mixture of Liberase TM (SIGMA – 5401127001) and DNase (SIGMA - D5025-15 KU) while slowly rotating at 37°C (Smilie et al.,). Dissocicated biopsies were washed with 0.1% BSA over a cell strainer. Dead cells were removed using EasySep™ Dead Cell Removal (Annexin V) Kit (Stemcell Technologies -  17899). Cells counts were determined using AOPI staining solution and a Nexcelom fluorescent cell counter.
scRNA libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics) according to manufacturer’s instruction on the Chromium Controller (10X Genomics). Sequence-ready libraries were validated and quantitated using the Agilent High Sensitivity D1000 ScreenTape Kit on the TapeStation 4200 System (Agilent Technologies). Individual libraries were normalized to 3nM and quantified by qPCR using the KAPA Library Quantification Kit – Illumina/ROX Low (Roche) on the QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems) according to manufacturer’s instructions. The libraries were then pooled to 3nM and quantified again by qPCR as described above. The quantified library pool was denatured and diluted according to the NovaSeq 6000 Denature and Dilute Libraries Guide and loaded onto a NovaSeq 6000 System (Illumina) for paired end sequencing. BCL conversion and demultiplexing was performed using the bcl2fastq2 script (v2.20, Illumina).

value: D2- Duodenum desending part

tag: disease state

tag: histologic severity

value: Marsh 0

tag: subject id


title: 3A_control


title: WRC03, leaf, moderate drought, Day 5, rep 2

description: Library name: D44

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.


title: WRC25, leaf, moderate drought, Day 5, rep 2

description: Library name: D46


title: A549 Parent WT 2

value: A549 cells

tag: time


title: WRC36, leaf, moderate drought, Day 5, rep 2

description: Library name: D43


title: Elmsan1 KO, replicate 1

description: Library name: ELM_cKO_1


title: A549 Parent WT 1


title: Adult control 1

description:
AC1
mRNA


title: 39A_control


title: WRC27, leaf, moderate drought, Day 5, rep 2

description: Library name: D42


title: 38A_control


title: 3rd instar control 1

description:
JC1
mRNA

value: maternal control

value: 3rd instar


title: EomesDot E16.5 WT 239.4

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

description: Library name: EomesDot16WT4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger v7.0.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral cortex

extract_protocol:
The cerebral cortex was extracted from the embryos and the cells were dissociated using the Worthington papain dissociation system and resuspended in PBS.
The library was performed according to the manufacturer's instructions (single cell 3' v3.1 single index protocol, 10x Genomics). Briefly, the dissociated brain cells resuspended in PBS were added to the master mix and loaded, together with gene expression beads and partitioning oil, into the chip and to generate the gel-bead emulsion using the Chromium machine. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, a unique molecular identifier (UMI), and 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the fragments with the appropriate sizeswere selected using SPRIselect beads for subsequent library construction. During the library construction Illumina R2 sequence, paired-end constructs with P5 and P7 sequence, and a sample (single) indexwere added.

value: Cerebral cortex

value: WT


title: Adult exposure 3

description:
AE3
mRNA

value: predator exposed


title: A549 Parent g2-3 1 (g2-3=Clone2-2)

value: ZC3H12A knockout


title: Adult control 2

description:
AC2
mRNA


title: EomesDot E16.5 WT 239.1

description: Library name: EomesDot16WT1


title: Adult exposure 2

description:
AE2
mRNA


title: 36A_control


title: WRC23, leaf, moderate drought, Day 5, rep 2

description: Library name: D41

value: leaf

value: moderate drought


title: WRC04, leaf, moderate drought, Day 5, rep 1

description: Library name: D40


title: 35 mer oligomer (100%D, 0%U), treated, SSIV RT, 1mM dGTP+10μM dNTP

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

library_source: other

data_processing:
The sequencing data were all trimmed with cutadapt tool (v4.8) to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (v.38.73), 5-mer random barcodes at reads ends were trimmed and low-quality or short reads (less than 20 nt) were removed using cutadapt tool.
For tRNAs, remaining reads were aligned to tRNA sequence obtained from GtRNAdb (https://gtrnadb.ucsc.edu/) using hisat-3n (v.2.2.1-3n-0.0.3). Mitochondria and chloroplast tRNA sequences are obtained from published papers.
Meanwhile, we have also aligned remaining reads to hg38, mm10, or TAIR10 genome using hisat3n to investigate D sites in other RNA species.
The generated table from hisat-3n were parsed and analyzed by inhouse scripts. Internal mutation ratio at each D candidate site suggested by hisat-3n, was further confirmed by direct IGV visualization (v.2.8.0).
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107), TAIR10
Supplementary files format and content: For samples with cellular RNA, the mutation ratio at D sites in treated, input samples are shown. For samples with RNA probes, mutations at D sites are shown.
Library strategy: Chemical Reduction Assisted Cytosine Incorporation sequencing (CRACI)

molecule: other

organism: synthetic construct

source_name: 35 mer oligomer (100%D

growth_protocol: Human HepG2 cell lines and mouse embryonic stem cells (mESC) used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell lines were maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). mESC cells were grown under a typical feeder-free culture condition: cells were cultured in DMEM (GIBCO, 11995), supplemented with 15% FBS, 1% Pen/Strep (GIBCO), 1X Glutamax (GIBCO), 1X non-essential amino acids (GIBCO), 1X 2-Mercaptoethanol (GIBCO), and 1000 U/ml leukemia inhibitory factor (Millipore, ESG1107), together with two inhibitors: 3 mM CHIR99021 (STEMCELL Technologies, dissolved in DMSO) and 1 mM PD0325901 (STEMCELL Technologies, dissolved in DMSO). mESC cells were distinctively cultured on gelatinized culture plates (0.2% Gelatin). The culture of mESC cells were passaged every 2 days. All cells were cultured at 37 Co under 5.0% CO2.

extract_protocol:
Generally, with harvesting cells as the first step, the media was aspirated, and the cells were washed once with proper volume of ice cold DPBS buffer for each plate. Then total RNA was isolated from cells with TRIzol reagent (Invitrogen) and then extracted following manufacturer’s protocol by isopropanol precipitation. Small RNA fraction was purified from total RNA with RNA Clean & Concentrator kit (Zymo Research) following manufacturer’s protocol. mRNA was extracted by two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion).
CRACI for D site detection Wild-type HepG2, mESC, and arabidopsis thaliana seedling cells (two replicates for each sample, one 10-cm plate per replicate); HepG2 siControl or DUS knockdown cells were prepared as described (two replicates for each sample, one 10-cm plate per replicate). After extracting the polyA+ RNA or small RNA from mammalian cells or plant cells, around 100 ng RNA was fragmented using RNA Fragmentation Reagents (catalog no. AM8740, Invitrogen) and heated at 70 °C for 14 min, followed by purification with Oligomer Clean and Concentrator (Zymo Research). 3′-End repair and 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). RNA was mixed with 3 µL 10× T4 PNK reaction buffer (catalog no. B0201S, NEB) and 3 µl T4 PNK, diluted to a final volume of 30 µl, and incubated at 37 °C for 45 min; then 1.5 µl T4 PNK and 1.5 µl 10 mM ATP were added for another incubation at 37 °C for 45 min, followed by Oligomer Clean and Concentrator (Zymo Research) purification eluting with 10 µl RNase-free water.  To perform 3′-adapter ligation, 10 µl 3′-repaired and 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNNATCACG AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 45 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 45 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 10 µl RNase-free water. The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC -3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 12 µl RNase-free water.  A 2 µl aliquot of the purified RNA was saved for ‘Input1’ library construction, 2 µl aliquot of the purified RNA was saved for ‘Input2’ library construction, and the rest 6 µl was subjected to CRACI optimized reduction treatment, as the ‘Treated’ sample. The 6 µl RNA was mixed with 40 µl freshly prepared KBH4 (1 M KBH4, prepared by dissolving 54 mg KBH4 in 1000 µl RNase-free water) and Incubated the reaction mixture at 25 °C for 3 h, followed by purification with RNA Clean and Concentrator (Zymo Research) and elute with 10 µl H2O. ‘Input1’, ‘Input2’ and purified ‘Treated’ samples were diluted to 10 µl and mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. Then for ‘Input2’ and ‘Treated’ samples, a stock with 2 µl 10x AMV RT Buffer (New England BioLabs, cat. no. B0277AVIAL), 2 µl 1 mM dNTP Solution Mix (dilute from 10 mM dNTP Solution Mix, New England BioLabs, catalog no. N0447L), 2 µl 10mM dGTP (dilute from 100 mM dNTP Solution Mix, New England BioLabs, catalog no. N0442S), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 2 µl HIV RT (Worthington Biochemical, catalog no. LS05003) was added. For ‘Input1’ sample, a stock with 2 µl RNase-free water, 2 µl 10x AMV RT Buffer, 2 µl 10 mM dNTP Solution Mix (New England BioLabs, catalog no. N0447L), 1 µl RNaseOUT Recombinant Ribonuclease Inhibitor and 2 µl HIV RT was added.  The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina NovaSeqX with single-end 100 bp read length.

value: 35 mer oligomer (100%D

tag: fraction

value: RNA probes


title: EoMltt3 E16.5 WT 333.5

description: Library name: EoMltt316WT5

source_name: Brain hemispheres

extract_protocol:
The cortex was extracted from the embryos and the cells were dissociated using the Worthington papain dissociation system and resuspended in PBS.
The library was performed according to the manufacturer's instructions (single cell 3' v3.1 single index protocol, 10x Genomics). Briefly, the dissociated brain cells resuspended in PBS were added to the master mix and loaded, together with gene expression beads and partitioning oil, into the chip and to generate the gel-bead emulsion using the Chromium machine. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, a unique molecular identifier (UMI), and 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the fragments with the appropriate sizeswere selected using SPRIselect beads for subsequent library construction. During the library construction Illumina R2 sequence, paired-end constructs with P5 and P7 sequence, and a sample (single) indexwere added.

value: Brain hemispheres


title: 35 mer oligomer (100%D, 0%U), treated, SSIV RT, 1mM dGTP+20μM dNTP


title: WRC28, leaf, moderate drought, Day 5, rep 1

city: Tsukuba

first: Taiji

last: Kawakatsu

address: 3-1-3 Kan-nondai

institute: National Agriculture and Food Research Organization

description: Library name: D39


title: 30A_control

value: control


title: WRC02, leaf, moderate drought, Day 5, rep 1

description: Library name: D38


title: WRC15, leaf, moderate drought, Day 5, rep 1

description: Library name: D37


title: Adult exposure 1

description:
AE1
mRNA

value: adult

value: female


title: EoMltt3 E14.5 WT 233.3

description: Library name: EoMltt314WT3

extract_protocol:
The dorsal telencephalon was extracted from the embryos and the cells were dissociated using the Worthington papain dissociation system and resuspended in PBS.
The library was performed according to the manufacturer's instructions (single cell 3' v3.1 single index protocol, 10x Genomics). Briefly, the dissociated brain cells resuspended in PBS were added to the master mix and loaded, together with gene expression beads and partitioning oil, into the chip and to generate the gel-bead emulsion using the Chromium machine. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, a unique molecular identifier (UMI), and 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the fragments with the appropriate sizeswere selected using SPRIselect beads for subsequent library construction. During the library construction Illumina R2 sequence, paired-end constructs with P5 and P7 sequence, and a sample (single) indexwere added.


title: 19A_control

value: D2- Duodenum desending part


title: 35 mer oligomer (100%D, 0%U), treated, SSIV RT, 1mM dGTP+50μM dNTP


title: EoMltt3 E14.5 WT 233.1

description: Library name: EoMltt314WT1


title: 25A_control

value: Marsh 0


title: 17A_control


title: Koshihikari, leaf, moderate drought, Day 5, rep 1

description: Library name: D36

value: Koshihikari


title: 35 mer oligomer (100%D, 0%U), treated, SSIV RT, 1mM dGTP+100μM dNTP


title: 13A_control


title: EomesDot E14.5 WT 243.4

description: Library name: EomesDot14WT4


title: WRC24, leaf, moderate drought, Day 5, rep 1

description: Library name: D35


title: EomesDot E14.5 WT 243.2

description: Library name: EomesDot14WT2


title: WRC19, leaf, moderate drought, Day 5, rep 1

description: Library name: D34


title: 35 mer oligomer (100%D, 0%U), treated, SSIV RT, 1mM dNTP


title: FAC-sorted cells, DNMT1 knockout, rep 3

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Biology 2

institute: RWTH Aachen University

description:
Library name: Sst_KO_3_RNA
E14.5

data_processing:
FASTQ files were generated using bcl2fastq (Illumina, U.S.A.). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/rnaseq pipeline version 3.17.0 implemented in Nextflow 24.10.2 with the minimal command. In brief, lane-level reads were trimmed using Trim Galore 0.6.10 and aligned to the mouse genome (GRCm39) using STAR 2.7.11b. Gene-level and transcript-level quantification was done by Salmon v1.10.3. All analysis was performed using custom scripts in R version 4.3.3 using the DESeq2 v.1.42.1 framework.
Assembly: GRCm39
Supplementary files format and content: Comma-separated table listing the normalized counts of detected genes per sample

source_name: Cortex

extract_protocol:
The Cortex samples were collected in cold HBSS (w/ phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose; 4 µg/µL (600 U) of DNAse I (AppliChem GmbH, Germany). After treatment with 0.04% trypsin for 17 min at 37 °C, HBSS was replaced by DMEM with additional L-glutamine and 4.5 g/L D-glucose, 10% FBS and 1% P/S to stop the trypsinization. Subsequently, the cells were pelletized, resuspended and triturated in cold HBSS (w/o phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose, before being filtered through a nylon gauze (pore size 140 µm, Merck, U.S.A.) for FACS. Respective parameters for the procedure using a BD FACS Aria Fusion (BD Biosciences, U.S.A) were defined as follows: 5-laser (FCS, SSC, PE, BV421), 18-color (3-6-2-4-3). TdTomato-positive cells were collected in 100 µL of cold TRIzol™ (Thermo Fisher Scientific, U.S.A.) for subsequent RNA sequencing. Samples were mixed by inversion and stored at -80°C until processing. RNA was isolated from 50,000 cells pooled per genotype. The samples were filled up to 1 ml with TRIzol™ and dounced 25 times in a glass homogenizer using the small-clearance pestle. Samples were incubated for 5 min at room temperature, supplemented with 200 µL chloroform and mixed by shaking vigorously until a homogenous milky solution appeared. Following another incubation at room temperature (until a visible phase separation appeared) samples were centrifuged at 13,000x g and 4°C for 15 min in a tabletop centrifuge with cooling function. For precipitation, the clear upper phase was collected and mixed with 70% ethanol. Samples were bound onto RNeasy mini columns (Qiagen, Germany) and washed according to the instructions in the manual. RNA was eluted with 30 µL nuclease-free water.
Prior to library preparation, samples were digested with HL dsDNAseI (ArcticZymes Technologies ASA, Norway) for 10 min at 37°C to remove traces of gDNA. To avoid a digestion of the newly generated cDNA during library preparation, the dsDNAseI was heat inactivated for 5 min at 58°C. Thereafter, samples were subjected to library preparation using the  SMART-Seq Total RNA Pico Input with UMIs (ZapR Mammalian) for Illumina (Takara Bio, Japan). Fragmentation was done at 94°C for 4 min. Illumina adaptors and indices were ligated to cDNA in a PCR reaction with 5 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). RRNA depletion was performed on the amplified libraries. Final libraries were subjected to an upscale PCR with 15 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). Amplified libraries were cleaned with magnetic AMPure XP beads (Beckman Coulter, U.S.A.). Library concentration was determined with a Qubit™ 4 fluorometer using the 1x dsDNA HS reagent (Thermo Fisher Scientific, U.S.A.). Library size was assessed on a Tape Station 4200 using the DNA D1000 kit (Agilent Technologies, U.S.A.). Libraries were diluted, equimolarly pooled, denatured, and loaded for clustering onto an Illumina NovaSeq 6000 SP (200 cycles) flow cell (Illumina, U.S.A.) in conjunction with 1% PhiX control library, and run on an Illumina NovaSeq machine (Illumina, U.S.A.) in 75 bp paired-end mode. The 1% PhiX control library was spiked in to improve base calling accuracy.

value: Cortex

value: Sst interneuron

value: Sst-Cre/tdTomato


title: EoMltt3 E16.5 WT 333.4

description: Library name: EoMltt316WT4

value: WT


title: WRC21, leaf, moderate drought, Day 5, rep 1

description: Library name: D33


title: FAC-sorted cells, DNMT1 knockout, rep 2

description:
Library name: Sst_KO_2_RNA
E14.5


title: 35 mer oligomer (100%D, 0%U), treated, HIV RT, 1mM dGTP+10μM dNTP


title: 9A_coeliac

value: Coeliac

value: Marsh 3c


title: 35 mer oligomer (100%D, 0%U), treated, HIV RT, 1mM dGTP+20μM dNTP


title: FAC-sorted cells, DNMT1 knockout, rep 1

description:
Library name: Sst_KO_1_RNA
E14.5


title: WRC48, leaf, moderate drought, Day 5, rep 1

description: Library name: D32

value: leaf


title: 13A_rep2_control


title: 35 mer oligomer (100%D, 0%U), treated, HIV RT, 1mM dGTP+50μM dNTP


title: FAC-sorted cells, DNMT1 control, rep 3

description:
Library name: Sst_WT_3_RNA
E14.5


title: FAC-sorted cells, DNMT1 control, rep 2

description:
Library name: Sst_WT_2_RNA
E14.5