title: 18_S14

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Sinapis alba v1.1 Phytozome
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Sinapis alba

source_name: roots

growth_protocol: White mustard (Sinapis alba) seeds were germinated three days in the Petri dishes filled with filter paper moistened with 5 mL of culture media at room temperature in darkness. The pH of culture media was set at 6.1 – 6.3. Seventeen seeds were placed into one dish.

extract_protocol:
Protocol from RNeasy Plant Mini Kit (Qiagen)
KAPA HyperPrep kit

treatment_protocol: Ag NPs were used in the concentration of 1000 mg/L. Ca(NO3)2·4H2O as a source of nitrate ions was used in the concentration of 2.35  g/L. Exposure time was three days. Total RNA was extracted from the roots.

value: roots

value: Ca(NO3)2 + Ag


title: WTNaCl-rep3

status: Public on Dec 31 2024

type: SRA

city: Shanghai

first: Yuying

last: Ren

address: chenhua road,No 3888

country: China

institute: CAS center for excellence in Molecular plant Sciences

library_source: transcriptomic

data_processing:
Paired-end reads were cleaned by Trimimomatic
Clean reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using HISAT2
The mapped reads on each gene were counted by htseq-count
The differentially expressed genes (DEGs) were identified using the R package edgeR (FDR (false discovery rate) < 0.05, log2FoldChange > 1.5)
Assembly: TAIR 10
Supplementary files format and content: Tab separated values file include RPKM values for each sample and logFC (log2 fold change) and FDR (false discovery rate) of differentially expressed genes analysis in indicated sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants were grown in a growth chamber at 22 °C and under long day (16 h light/8 h dark) conditions for 8 days

extract_protocol:
Total RNAs were extracted from eight-day-old seedlings grown under the long-day condition using RNeasy Plant Mini Kit (Qiagen, Cat#74904) according to the manufacturer’s instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8-day-old seedings were transferred to 1/2 MS medium with or without NaCl for 24h, and then Cut off the root tip approximately 1 cm tissue

tag: tissue

value: root


title: WTNaCl-rep1


title: Lung, 3D-2D_2

city: Dearborn

first: Caymen

last: Novak

state: MI

address: HPEC 1296, 4901 Evergreen Rd

department: Mechanical Engineering

country: USA

institute: University of Michigan Dearborn

data_processing:
Reads were filtered using sequencying platform BGISEQ
HISAT was used to align the clean reads to the reference genome
Bowtie2 was used to align the clean reads to the reference genes
Reference species was Mus_musculus from NCBI, Reference genome version GCF_000001635.26_GRCm38.p6
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: excel file including raw counts for each sample

organism: Mus musculus

source_name: Lung

growth_protocol: Collagenase digestion of lung tissue followed by 2D or 3D culture in collagen hydrogels for 4 days followed by 2 days of culture in the same or opposite conditions.

extract_protocol:
TRIzol and Direct-zol RNA miniprep Plus Kit
HISAT was used to align clean reads to the reference genome

treatment_protocol: No chemical treatment was used

value: Lung

tag: disease state

value: Normal

tag: Sex

value: Male

tag: strain

tag: treatment

value: 3D culture 4 days, 2D culture 2 Days


title: WTNaCl-rep2


title: Lung, 3D-2D_3


title: 6-6MS-rep1


title: 17_S13

department: Lab. of hormonal regulations in plants

country: Czech Republic


title: WTMS-rep2


title: WTMS-rep3


title: Lung, 2D-3D_4

value: 2D culture 4 days, 3D culture 2 Days


title: 16_S12


title: 13_S11


title: Lung, 2D-3D_3


title: Lung, 3D-2D_1


title: Lung, 2D-3D_2


title: 9_S8

value: H2O + Ag


title: Lung, 2D-3D_1


title: 11_S9


title: WTMS-rep1


title: 7_S7


title: Lung, 2D-2D_4

value: 2D culture 4 days, 2D culture 2 Days


title: 12_S10


title: Lung, 2D-2D_2


title: 4_S5


title: 6_S6


title: 2_S4


title: Lung, 2D-2D_3


title: Lung, 2D-2D_1


title: 1_S3


title: TUMOR3

city: Guangzhou

first: HUI

last: CHEN

state: Guangdong

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

data_processing:
The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Uterus

growth_protocol: MBA-MD-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen) .25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).

value: Uterus

tag: cell line

tag: cell type

value: breast cancer

tag: genotype

value: Tumor

value: Inject breast cancer cells


title: T1D_6306 [IG70_Ivan_Gerling]

type: RNA

city: Gainesville

first: Alexandra

middle: E.

last: Cuaycal

state: FL

address: 1275 Center Drive

department: Infectious Diseases and Immunology/Biomedical Engineering

institute: University of Florida

hyb_protocol: Amplified RNA samples were hybridized according to Nugen protocols on the Affymetrix Fluidics Station 450.

scan_protocol: Samples were scanned on a GCS3000 7G (Affymetrix).

data_processing: Raw signal intensity values from all arrays were Robust Multichip Average (RMA)  background corrected, quantile normalized, median polish summarized, and log2transformed. Processing was carried out using Partek Genomics Suite, version 6.5.

label: Biotin

organism: Homo sapiens

source_name: Laser capture-microdissected islet from nPOD donor 6306

label_protocol: The RNA was amplified using Nugen Pico WTA amplification kit, fragmented and labeled using the Nugen Encore Biotin Module according to Nugen protocols.

extract_protocol: Total islet RNA was extracted using the PicoPure RNA kit (ThermoFisher). DNAse treatment was performed using recombinant DNase I (RNase-free DNAse kit, Worthington Biochemical Corporation).

treatment_protocol: 10 um thick OCT pancreas sections were used to laser-microdissect single islets from dehydrated slides with a Leica 7000 LMD microscope.

value: Fresh frozen pancreas section


title: TUMOR2


title: T1D_6113 [IG65_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6113


title: T1D_6070 [IG76_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6070


title: T1D_6342 [IG69_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6342


title: T1D_6113 [IG53_Ivan_Gerling]


title: T1D_6052 [IG54_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6052


title: T1D_6113 [IG67_Ivan_Gerling]


title: T1D_6209 [IG75_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6209


title: T1D_6070 [IG64_Ivan_Gerling]


title: T1D_6243 [IG57_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6243


title: T1D_6209 [IG56_Ivan_Gerling]


title: T1D_6342 [IG55_Ivan_Gerling]


title: T1D_6195 [6195-06_16_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6195


title: T1D_6052 [IG66_Ivan_Gerling]


title: T1D_6212 [IG68_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6212


title: Hep_6_1;8hr

city: Fullerton

first: Nikolas

last: Nikolaidis

state: CA

address: 800 N. State College Blvd

department: Biological Science

institute: California State Univeristy Fullerton

description:
Library name: Hep6_8R_1_B2
column: Hep6_8R

data_processing:
BBDuk was employed to perform adapter trimming, PhiX filtering, and quality filtering based on Phred scores.
STAR was employed to map high-quality reads to the human reference genome to identify the features in the dataset. It accepted the reads cleaned by BBDuk and outputting binary sequence alignment map files (.BAM).
Samtools was used to sort an input .BAM file and create a corresponding index file (.BAI).
HTSeq was utilized to create a raw gene count matrix by determining the number of reads mapped to each feature.
MultiQC was utilize to summarize and evaluate the files produced by BBDuk, STAR, Samtools, and HTSeq.
Assembly: hg38
Supplementary files format and content: csv files contain raw counts for each condition, cell, and batch number.

source_name: hepatocellular carcinoma cells

growth_protocol: HEK293 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM), while HeLa and HepG2 cells were grown in Minimum Essential Medium (MEM). Media for both cell lines were supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and penicillin-streptomycin. HeLa and HepG2 media were supplemented with 0.1 mM non-essential amino acids (NEAA) and 1 mM sodium pyruvate. All cultures were maintained in a humidified atmosphere containing 5% CO₂ at 37°C.

extract_protocol:
Cells from the control, 0R, and 8R conditions were sent to Novogene (Sacramento, CA) for RNA isolation, library preparation, and sequencing. Total RNA was isolated using the Qiagen RNeasy series kit, and quality control (QC) was meticulously performed at each step to ensure reliable data.
For transcriptome sequencing, 1 μg of total RNA per sample was used to generate sequencing libraries with the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's protocol. Libraries were purified with the AMPure XP system and validated on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were either maintained at 37°C or subjected to heat stress at 42°C for 60 minutes in a humidified CO₂ incubator. Following heat shock, cells were allowed to recover at 37°C for 8 hours. For each experimental condition, three flasks were used: one remained at 37°C as a control, while two others were exposed to 42°C for one hour to induce heat shock. Of the heat-shocked flasks, one was processed immediately after heat shock (0 hours recovery, 0R), and the other was allowed to recover at 37°C for 8 hours (8 hours recovery, 8R).

value: hepatocellular carcinoma cells

value: HepG2 cells

value: wild type

value: heatshock

tag: batch


title: T1D_6243 [IG63_Ivan_Gerling]


title: T1D_6212 [IG58_Ivan_Gerling]


title: Hep_6_1;control

description:
Library name: Hep6_cnt_1_B2
column: Hep6cnt

value: no heatshock


title: Hep_6_1;0hr

description:
Library name: Hep6_0R_1_B2
column: Hep6_0R


title: T1D_6195 [6195-06_14_Ivan_Gerling]


title: mnn9D/D grown under hypha-inducing conditions for 180 min. Rep 3

city: Salamanca

first: Angel

last: Domínguez

state: Salamanca

address: Plaza de los Doctores de la Reina

department: Microbiology and Genetics/CIETUS/IBSAL

country: Spain

institute: University of Salamanca

description: mutant clone 2, WT pool WT. Data matrix K060H

hyb_protocol: The C. albicans oligo-microarrays (Eurogentec) were prehybridised for 45 min at 42ÂºC in 5x SSC, 1% SDS and 1% BSA. Prehybridised microarrays were washed five times with water, once with isopropanol and the washed arrays were air dried.  Before hybridization, concentrated Cy5- and Cy3-labeled cDNA from mutant and parental cells was mixed. Then 5 microl of denatured herring sperm salmon DNA (10mg/ml) was added. After DNA denaturation for 5 min at 95ÂºC, DIG easy hybridisation buffer (50% formamide, 10x SSC, 0.2% SDS, ROCHE) was incorporated up to a final volume of 60 microl. The mixture was applied on the prehybridised microarray, covered with a LifterSlip (60x24 mm, Sigma-Aldrich) and incubated overnight in a humidified chamber (Corning) in a water bath at 42ÂºC. Hybridised microarrays were washed for 15 min in 2x SSC, 1% SDS, for 8 min in the same solution and twice for 5 min in 0.2x SSC. Then microarrays were dried by centrifugation at 1100 rpm at room temperature.

scan_protocol: The microarrays were scanned with a GenePix4000B scanner and intensity data were captured using the GenePix Pro version 6.0 software package (Axon Instruments).

data_processing: Data were analysed in GeneSpring 5.0 sofware (Axon Instruments). Data were per-chip and per-spot normalized by intensity dependent (LOWESS) normalization applied to the print-tip region. Genes with differential expression were obtained by first filtering genes with a fold change ≥ 1.5 in at least one hybridisation and then applying a “statistical group comparison” (Wilconxon-Mann-Whitney test) and the multiple testing correction Benjamini and Hochberg False Discovery Rate (FDR) with p-value   0.02. The second filter was introduced to control the stringency of the FDR correction, which is directly influenced by the number of genes analysed. Among genes selected by the test we considered only genes as being significantly regulated, if they were differentially expressed by at least a mean factor of 1.5 considering the three replicates.

organism: Candida albicans

source_name: cDNA, mutant 37ºC, 180 min

label_protocol: 15 micrograms of total RNA was labelled using the CyScribe First-Strand cDNA labeling kit (RPN 6200, Amersham, GE Healthcare) following manufacturer’ s instructions, with 1 micrograms anchored oligo-dT-primer (Amersham Biosciences) and 0.1 pmol C. albicans-specific primer mix (provided by Eurogentec).  Labelled cDNA was purified using “CyScribe GFX Purification Kit (GE Healthcare)”. cDNA was checked for proper labelling measuring the amount of probe and incorporated dye using a NanoDrop 1000 device and calculating the frequency of incorporation. Then it was stored at -20ºC until further use.

growth_protocol: For transcriptional profile analysis of cells grown in yeast form, strains were grown to mid exponential phase in Lee’ s medium (pH 6.8, 1.25% glucose) (Lee et al., 1975) at 28ºC. recovered and frozen in liquid nitrogen. To induce the yeast-to-hypha transition, first, cells were incubated in Lee medium at 28ºC until the OD600 reached 0.5, collected, washed and resuspended in distilled water at a final concentration of 2x 107 cells/ml. In order to synchronize the cells in G1, they were incubated with shaking at 200 rpm for 2 hours at 28ºC and next maintained without shaking for 24 hours at 4ºC. Finally, they were collected and inoculated at 1x 107 cells/ml into pre-warmed Lee’s pH 6.8 and incubated at 37ºC. Samples of cells were extracted after 15, 60 and 180 min and then centrifuged and the resulting pellet was immediately frozen in liquid nitrogen and stored at -80ºC until further use.

extract_protocol: The isolation of total RNA were performed according to Galar Fungail standard operating procedures (www.pasteur.fr/recherche/unites/Galar_Fungail/)


title: Hep_5_1;8hr

description:
Library name: Hep5_8R_1_B2
column: Hep5_8R


title: TUMOR1


title: CON2

value: Control


title: T1D_6052 [IG46_Ivan_Gerling]


title: Hep_5_1;0hr

description:
Library name: Hep5_0R_1_B2
column: Hep5_0R


title: Hep_5_1;control

description:
Library name: Hep5_cnt_1_B2
column: Hep5cnt


title: CDs3

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)   was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Text Document  include Raw read counts for each Sample

source_name: Erythroblast

growth_protocol: TER119-negative fetal liver erythroblasts were purified and cultured in Epo containing medium

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ  platform.

treatment_protocol: Treated with or without CDs (1 ug/ml) for 30 h

value: Fetal liver

value: treated with CDs for 30 hours


title: Hep_4_1;8hr

description:
Library name: Hep4_8R_1_B2
column: Hep4_8R


title: CDs2


title: CON3


title: mnn9D/D grown under hypha-inducing conditions for 180 min. Rep 1

description: mutant clone 1, WT pool WT. Data matrix K060H

source_name: cDNA, WT 37ºC, 180 min

source_name: cDNA, mutantT 37ºC, 180 min


title: T1D_6228 [IG52_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6228


title: T1D_6243 [IG45_Ivan_Gerling]


title: T1D_6306 [IG47_Ivan_Gerling]


title: Hep_4_1;0hr

description:
Library name: Hep4_0R_1_B2
column: Hep4_0R


title: mnn9D/D grown under hypha-inducing conditions for 180 min. Rep 2

description: mutant clone1, WT pool WT. Data matrix K060H


title: T1D_6209 [IG43_Ivan_Gerling]


title: T1D_6247 [IG42_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6247


title: T1D_6228 [IG44_Ivan_Gerling]


title: T1D_6342 [IG4_Ivan_Gerling]


title: T1D_6212 [IG41_Ivan_Gerling]


title: Hep_4_1;control

description:
Library name: Hep4_cnt_1_B2
column: Hep4cnt


title: CON1

source_name: Uterus


title: Hep_3_1_B2;8hr

description:
Library name: Hep3_8R_1_B2
column: Hep3_8R


title: Ctrl2

value: untreated


title: CDs1


title: mnn9D/D grown under hypha-inducing conditions for 60 min. Rep 1

source_name: cDNA, WT 37ºC, 60 min

source_name: cDNA, mutant 37ºC, 60 min


title: Hep_3_1_B2;0hr

description:
Library name: Hep3_0R_1_B2
column: Hep3_0R


title: Ctrl1


title: Ctrl3


title: F, OA

city: Hamadan

first: Fahimeh

last: Piryaei

state: Hamadan

address: Shahid Fahmideh

department: Molecular Medicine and Genetics

country: Iran

institute: Hamadan University of Medical Sciences

data_processing:
R version 3.6.0
Using Bowtie2 and cmsearch, the filtered reads were mapped to the reference genome and sRNA databases.
The differential expression of identified piRNAs was analyzed using the DEseq2 algorithm with a cut-off of Log2foldchange of > 1.
proTRAC version 2.4.3 was used for cluster prediction.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Testis

extract_protocol:
Total RNA extraction was performed using RiboEx reagent (GeneAll, Korea), according to the manufacturer's recommendations.
Equal amounts of RNA samples were pooled to make 3 NOA (4:3:3 samples pooled in each) and 2 OA (4 samples pooled in each) groups. Small RNA (sRNA) libraries were prepared using BGISEQ-500 sRNA sample preparation kit.

value: Testis

tag: disease

value: obstructive azoospermia


title: Hep_3_1;8hr

description:
Library name: Hep3_8R_1_B1
column: Hep9_8R


title: mnn9D/D grown under hypha-inducing conditions for 60 min. Rep 3


title: T1D_6268 [IG37_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6268


title: D, OA


title: T1D_6306 [IG77_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6306


title: Hep_3_1;0hr

description:
Library name: Hep3_0R_1_B1
column: Hep9_0R


title: C, NOA, SCOS

value: non-obstructive azoospermia


title: Hep_3_1;control

description:
Library name: Hep3_cnt_1_B1
column: Hep9cnt


title: mnn9D/D grown under hypha-inducing conditions for 15 min. Rep 3

source_name: cDNA, mutant 37ºC, 15 min


title: mnn9D/D grown under hypha-inducing conditions for 15 min. Rep 2

source_name: cDNA, WT 37ºC, 15 min


title: mnn9D/D grown under hypha-inducing conditions for 15 min. Rep 1


title: T1D_6342 [IG36_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6342


title: mnn9D/D grown under hypha-inducing conditions for 60 min. Rep 2


title: Hep_3_1_B2;control

description:
Library name: Hep3_cnt_1_B2
column: Hep3cnt


title: T1D_6209 [IG35_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6209


title: A, NOA, SCOS


title: Hep_2_1_B2;8hr

description:
Library name: Hep2_8R_1_B2
column: Hep2_8R

source_name: hepatocellular carcinoma cells


title: B, NOA, SCOS


title: mnn9D/D  grown in yeast form at 28ºC Rep 3

source_name: cDNA, WT 28ºC

source_name: cDNA, mutant 28ºC


title: T1D_6052 [IG34_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6052


title: T1D_6195 [6195-06_13_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6195


title: Hep_2_1_B2;0hr

description:
Library name: Hep2_0R_1_B2
column: Hep2_0R


title: T1D_6342 [IG32_Ivan_Gerling]


title: T1D_6228 [IG33_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6228


title: WT_DOX

city: SHATIN

first: XUN

last: MA

state: NT

address: Rm105, Area 39, CUHK

country: Hong Kong

institute: CUHK

data_processing:
Sequencing on DNBSEQ platform
Sequencing data is called raw reads or raw data, and quality control (QC) is then performed on the raw reads.
After quality control, the filtered clean reads were aligned to the reference sequence, GCF_000001405.38_GRCh38.p12.
Sequencing data filtering using filtering software SOAPnuke developed by BGI
Assembly: GCF_000001405.38_GRCh38.p12.
Supplementary files format and content: tab-delimited text files include FPKM,TPM and read count values for each Sample

growth_protocol: H1 human ESCs (WiCell Research Institute) were cultured as previously described (He et al., 2016), on Matrigel (BD Biosciences) coated plates under feeder-free conditions in mTeSR1 medium.

extract_protocol:
Total RNA from cell samples was extracted using TRIzol reagent. 1000 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGISEQ-2000 RNASeq (Quantification) following manufacturer's protocols.

treatment_protocol: DE differentiation was induced by adopting previous previously described methods (D'Amour et al., 2006; Hay et al., 2008; Kunisada et al., 2012). Briefly, wt hESC (H1) were seeded one day before to reach about 25% confluency., The mTeSR1 medium was then replaced by RPMI 1640 supplemented with 1x B27 supplement (Gibco) and 100 ng/ml Activin A (R&D Systems, Minneapolis, MN), and refreshed every day. For wt hESC (H1), 3 μM CHIR99021 (CHIR) (Cayman) was added for the first day of the DE induction. For the CTNNB1-/- hESCs or rescue clones carrying different β-catenin mutants, 0.5 μg/ml Doxycycline (Dox) (Sigma) was added at one day before the DE induction and removed at day 2 post induction.

value: human embryonic stem cell (hESC)

value: CTNNB1 KO;CTNNB1 OE

value: Definitive endoderm differentiation

tag: time

value: Day 0


title: T1D_6070 [IG31_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6070

value: Fresh frozen pancreas section


title: T1D_6306 [IG3_Ivan_Gerling]


title: Hep_2_1_B2;control

description:
Library name: Hep2_cnt_1_B2
column: Hep2cnt

value: hepatocellular carcinoma cells


title: WT_DE_D1

value: Day 1


title: Hep_2_1;8hr

description:
Library name: Hep2_8R_1_B1
column: Hep8_8R

value: HepG2 cells

value: wild type


title: S33Y_DOX

value: CTNNB1 KO;S33Y-CTNNB1 OE


title: S33Y_DE_D1


title: NC_DOX

value: CTNNB1 KO;{delta}N148C-CTNNB1 OE


title: Hep_2_1;control

description:
Library name: Hep2_cnt_1_B1
column: Hep8cnt

value: no heatshock


title: Hep_2_1;0hr

description:
Library name: Hep2_0R_1_B1
column: Hep8_0R

value: heatshock


title: NC_DE_D1


title: N90_DOX

value: CTNNB1 KO;{delta}N90-CTNNB1 OE


title: Hep_1_1_B2;0hr

description:
Library name: Hep1_0R_1_B2
column: Hep1_0R


title: T1D_6070 [IG25_Ivan_Gerling]


title: melanoma 43, BRAF wt

city: Biella

first: Giovanna

last: Chiorino

state: Biella

address: via malta 3

country: Italy

institute: fondazione edo ed elvo tempia onlus

description: Dye-swap technical replicates are combined.

hyb_protocol: Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B.

data_processing:
Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the Agilent Human Whole Genome pattern file.  To compare class expression patterns between BRAF mutated samples and wild-type ones, t-test and  empirical Bayes statistics (LIMMA package) for two class comparison were applied. Transcripts with significant modulation (B value greater than 2 for empirical Bayes statistic) were further considered. Moreover we applied to the ratio experiment a one-way ANOVA available within the Resolver System with Multiple Test Correction method (Benjamini Hochberg FDR). Three classes were considered for the  ANOVA (wt, ++, +++). For all the transcripts with significant modulation (p-value<0.01), we looked for those with increasing or decreasing expression and with in particular an absolute log ratio difference >0.7 between the wt class and the +++ one.

GSM*.txt file: test sample is labeled with Cy5, reference sample is labeled with Cy3.
GSM*_DS.txt file: test sample is labeled with Cy3, reference sample is labeled with Cy5.

source_name: melanoma, Clark's level IV

label_protocol: RNA isolated from each fresh tissue and from the human universal reference (BD™ Human Universal Reference Total RNA, Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Two rounds of amplification were performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

extract_protocol: All of the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) with 600 ul of RNA lysis buffer plus 1% 2-mercaptoethanol, and total RNA was isolated by using RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

value: melanoma

tag: braf class

value: wt

tag: clark's level

value: IV

tag: growth phase

value: vertical

tag: gender

value: male

tag: age

source_name: commercial human universal reference

tag: sample type

value: reference


title: melanoma 45, BRAF ++

source_name: melanoma, Clark's level V

tag: tissue

value: V


title: Hep_1_1_B2;8hr

description:
Library name: Hep1_8R_1_B2
column: Hep1_8R


title: melanoma 40, BRAF +


title: Hep_1_1_B2;control

description:
Library name: Hep1_cnt_1_B2
column: Hep1cnt


title: T1D_6342 [IG23_Ivan_Gerling]

value: Fresh frozen pancreas section


title: N90_DE_D1

value: human embryonic stem cell (hESC)

value: Definitive endoderm differentiation


title: melanoma 42, BRAF ++


title: T1D_6212 [IG26_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6212


title: melanoma 46, BRAF wt


title: Hep_1_1;8hr

description:
Library name: Hep1_8R_1_B1
column: Hep7_8R

value: hepatocellular carcinoma cells

value: HepG2 cells


title: melanoma 44, BRAF wt

value: female


title: melanoma 41, BRAF ++


title: N148_DOX

value: CTNNB1 KO;{delta}N148-CTNNB1 OE

value: Day 0


title: melanoma 9b, BRAF wt


title: melanoma 39, BRAF +++


title: T1D_6113 [IG22_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6113


title: T1D_6306 [IG21_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6306


title: T1D_6195 [6195-06_12_Ivan_Gerling]


title: melanoma 38, BRAF +


title: T1D_6243 [IG24_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6243


title: Hep_1_1;0hr

description:
Library name: Hep1_0R_1_B1
column: Hep7_0R

value: wild type

value: heatshock


title: melanoma 36, BRAF +++

source_name: melanoma, Clark's level III

value: melanoma

value: III


title: Hep_1_1;control

description:
Library name: Hep1_cnt_1_B1
column: Hep7cnt

value: no heatshock


title: T1D_6247 [IG20_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6247


title: melanoma 35, BRAF +++

value: vertical


title: N148_DE_D1

value: Day 1


title: KO7_DOX

value: CTNNB1 KO


title: T1D_6228 [IG2_Ivan_Gerling]


title: KO7_DE_D1


title: HeLa_6_1;8hr

description:
Library name: HeLa6_8R_1_B2
column: HeLa6_8R

source_name: Henrietta Lacks cells

value: Henrietta Lacks cells

value: HeLa cells


title: HeLa_6_1;control

description:
Library name: HeLa6_cnt_1_B2
column: HeLa6cnt


title: H1_DOX

value: human embryonic stem cell (hESC)

value: WT


title: H1_DOX_DE_D1

value: Definitive endoderm differentiation


title: HeLa_5_1;0hr

description:
Library name: HeLa5_0R_1_B2
column: HeLa5_0R


title: HeLa_5_1;8hr

description:
Library name: HeLa5_8R_1_B2
column: HeLa5_8R


title: T1D_6212 [IG15_Ivan_Gerling]

value: Fresh frozen pancreas section


title: H1_DE_D1


title: H1


title: melanoma 33, BRAF +++

source_name: melanoma, Clark's level II

value: II

value: radial

value: female

value: reference


title: T1D_6070 [IG13_Ivan_Gerling]


title: HeLa_6_1;0hr

description:
Library name: HeLa6_0R_1_B2
column: HeLa6_0R

value: wild type

value: heatshock


title: HeLa_5_1;control

description:
Library name: HeLa5_cnt_1_B2
column: HeLa5cnt


title: C_DOX

value: CTNNB1 KO;{delta}C-CTNNB1 OE

value: Day 0


title: HeLa_4_1;8hr

description:
Library name: HeLa4_8R_1_B2
column: HeLa4_8R


title: melanoma 32, BRAF ++

value: melanoma


title: melanoma 31, BRAF +++

value: male


title: C_DE_D1

value: Day 1


title: T1D_6113 [IG12_Ivan_Gerling]


title: T1D_6209 [IG118_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6209


title: T1D_6268 [IG119_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6268


title: HeLa_4_1;0hr

description:
Library name: HeLa4_0R_1_B2
column: HeLa4_0R

value: Henrietta Lacks cells


title: melanoma 29, BRAF wt

value: wt


title: melanoma 7b, BRAF +


title: T1D_6243 [IG117_Ivan_Gerling]


title: T1D_6070 [IG116_Ivan_Gerling]


title: T1D_6113 [IG115_Ivan_Gerling]


title: HeLa_4_1;control

description:
Library name: HeLa4_cnt_1_B2
column: HeLa4cnt

value: HeLa cells

value: no heatshock


title: DKO_C14

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Quality was assessed using FastQC (v0.11.9) & Fastq-Screen (v0.15.2)
Files were mapped to GRCh38 using Hisat2 (v.2.2.1)
Reads wre counted using Rsubread (v.2.2.6) in R (v4.2.2) using the Enseml GRCh38.p13 annotation (release 103)
Differential enrichment analysis performed using edgeR (v.3.42.4) in R (v4.2.2)
Assembly: GRCh38
Supplementary files format and content: Tab-deliminated text file with raw counts for each sample

growth_protocol: Cell culture in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
RNeasy kit (Qiagen) according to manufacture's protocol with 0.1mM butylated hydroxytoluene and 0.1mM deferoxamine added to prevent oxidative damage during isolation.
Standard library preparation by BGI Tech solutions

value: near-haploid

value: MUTYH-/ X OGG1-/


title: T1D_6195 [6195_8_Ivan_Gerling]

value: Fresh frozen pancreas section


title: DKO_C4


title: OGG1_C22


title: HeLa_3_1_B2;control

description:
Library name: HeLa3_cnt_1_B2
column: HeLa3cnt


title: OGG1_C1


title: HeLa_3_1;8hr

description:
Library name: HeLa3_8R_1_B1
column: HeLa9_8R


title: T1D_6209 [IG114_Ivan_Gerling]


title: MUTYH_C8

value: MUTYH-/


title: HeLa_3_1;0hr

description:
Library name: HeLa3_0R_1_B1
column: HeLa9_0R


title: WT_C2

value: WT


title: HeLa_3_1;control

description:
Library name: HeLa3_cnt_1_B1
column: HeLa9cnt


title: dysplastic nevus_19_DS

description: technical replicate of 19_NORM

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing:
Images were analyzed using Feature Extraction software (Agilent Technologies) version 7.6. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into the Resolver SE System (Rosetta Biosoftware, Seattle, WA) together with the scan images and the Agilent Human Whole Genome pattern file. Data processing and normalization were performed using the Agilent Human Whole Genome platform-specific error model.  The Log10 (test/ref) ratios are reported in the Sample VALUE column in the data table below.

The final, processed data (those that form the basis of the conclusions of the study) are contained in the file named all_vs_average_nevi.txt which has been linked as a supplementary file on the Series GSE12391 record. Experiments (displastic nevi, melanoma, melanoma metastasis samples) were combined to form ratio experiments, by applying the ratio split with common reference option and calculating ratios over the average of non tumor samples (CMN).
More details: Replicated expression profiles were combined to form ratio experiments where each gene is associated to an expression fold-change and a p-value to assess the statistical significance of its modulation in the sample compared to the reference. New ratio experiments were also built by applying the “ratio split with common reference” option and calculating ratios over the average of non tumor samples (CMN). A “weight by error” divisive clustering algorithm available within the Rosetta Resolver system (with cosine correlation as similarity metrics) was applied to such new ratios to compare their expression profiles. At the same time, data treatment with the LIMMA (LInear Models for MicroArray data) package available within Bioconductor (http://www.bioconductor.org/) was also performed applying normexp background calculation, lowess within-array and A-quantile between-array normalization methods.

extract_protocol: All the samples were homogenized (Ultra – TurraxT8, Ika – Werke, Staufen, Germany) with 600 ul of RNA lysis buffer plus 1% 2-mercaptoethanol, and total RNA was isolated by using RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

value: Clontech human universal reference

source_name: dysplastic nevus: low atypia

value: Female


title: MUTYH_C7


title: common melanocytic nevus_14_DS

description: technical replicate of 14_NORM

source_name: common acquired melanocytic nevus

value: Male


title: T1D_6228 [IG113_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6228


title: HeLa_3_1_B2;8hr

description:
Library name: HeLa3_8R_1_B2
column: HeLa3_8R

value: wild type

value: heatshock


title: common melanocytic nevus_15_DS

description: technical replicate of 15_NORM


title: T1D_6113 [IG110_Ivan_Gerling]


title: T1D_6268 [IG105_Ivan_Gerling]


title: common melanocytic nevus_16_DS

description: technical replicate of 16_NORM


title: common melanocytic nevus_12_DS

description: technical replicate of 12_NORM


title: common melanocytic nevus_10_DS

description: technical replicate of 10_NORM


title: HeLa_2_1_B2;control

description:
Library name: HeLa2_cnt_1_B2
column: HeLa2cnt


title: T1D_6268 [IG104_Ivan_Gerling]


title: common melanocytic nevus_11_DS

description: technical replicate of 11_NORM


title: HeLa_2_1;8hr

description:
Library name: HeLa2_8R_1_B1
column: HeLa8_8R


title: common melanocytic nevus_13_DS

description: technical replicate of 13_NORM


title: WT_C11


title: common melanocytic nevus_5_DS

description: technical replicate of 5_NORM


title: TG_L, snRNA-seq

city: Beijing

first: Kaiyi

last: Zhang

state: Beijing

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the Sscrofa11.1 reference genome (Ensembl release104, http://asia.ensembl.org ) using the 10× Genomics Cell Ranger software (version 3.1.0) with default parameters.
After mapping, UMI sequences were corrected for sequencing errors, with empty droplets removed according to the EmptyDrops method. The cell by gene matrices were produced via UMI counting and cell barcodes calling. The cell by gene matrices for each sample were individually imported to Seurat (version 3.1.1) for downstream analysis.
Cells with the following criteria were filtered out: (1) unusually high number of UMIs (≥ 22000) (2) percentage of mitochondrial genes ≥ 25% (3) genes fewer than 380 or more than 4500 (4) doublet GEMs. We utilized the DoubletFinder tool (version 2.0.3) to filter doublet GEMs.
After removing unwanted cells from the dataset, we employed a global-scale normalization method "LogNormalize" to normalize the gene expression measurements of each cell to the total expression
Assembly: Sscrofa11.1 reference genome (Ensembl release104, http://asia.ensembl.org )
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Sus scrofa

source_name: liver

extract_protocol:
The frozen liver sample was minced with a blade and transferred to a Dounce homogenizer containing 500 µl of chilled lysis buffer. Samples were gently homogenized five to ten times without rotation, then incubated on ice for 5 minutes. A 700 µl lysis buffer was added to the lysate and filtered gently through a 70 µm filter into a 50 ml centrifuge tube. Then 1 ml 50% of iodixanol was added to the filtrate and mixed gently. A total of 2 ml of the nuclei suspension was transferred into a 15 ml centrifuge tube containing 3 ml of chilled iodixanol gradient solution (1 ml 33% iodixanol, 2 ml 30% iodixanol). Nuclei were recovered after centrifugation and resuspended gently in wash buffer, followed by counting on a hemocytometer.
Nuclei were processed with the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 from 10× Genomics. In brief, cellular suspensions were loaded on a 10× Genomics GemCode Single-cell instrument to generate single-cell Gel Bead-In-EMlusion (GEMs). After dissolution of the Gel Bead in a GEM, reverse transcription, barcoding, complementary DNA amplification and purification for sequencing libraries preparation was performed according to the Single Cell 3' protocol.

value: liver

value: triple-transgenic Bama pig

value: 6 months high-fat-high-sucrose diet intervention


title: T1D_6306 [IG111_Ivan_Gerling]


title: T1D_6209 [IG11_Ivan_Gerling]


title: common melanocytic nevus_6_DS

description: technical replicate of 6_NORM


title: common melanocytic nevus_7a_DS

description: technical replicate of 7a_NORM


title: HeLa_2_1;control

description:
Library name: HeLa2_cnt_1_B1
column: HeLa8cnt

value: Henrietta Lacks cells


title: HeLa_2_1_B2;0hr

description:
Library name: HeLa2_0R_1_B2
column: HeLa2_0R


title: WT_L, snRNA-seq

description: 10× Genomics

value: wild-type Bama pig


title: HeLa_2_1;0hr

description:
Library name: HeLa2_0R_1_B1
column: HeLa8_0R

value: HeLa cells


title: HeLa_1_1_B2;8hr

description:
Library name: HeLa1_8R_1_B2
column: HeLa1_8R


title: HeLa_1_1_B2;0hr

description:
Library name: HeLa1_0R_1_B2
column: HeLa1_0R


title: MC38 cells,shACSL4-3

city: NanJing

first: Yiming

last: Liu

address: The Avenue of Sleeping Dradon

institute: China Pharmaceutical University

description: Library name: Sample 6

data_processing:
Based on SequencingBySynthesis (SBS) technology, Illumina high-throughput sequencing platform sequenced cDNA libraries, and the image Data obtained by high-throughput sequencers were converted into a large amount of high-quality data through CASAVA base recognition, which was called RawData.RawData is usually provided in fastq format and mainly contains sequence information of sequenced fragments and corresponding sequencing quality information.
After raw data filtering, sequencing error rate checking and GC content distribution checking, clean reads for subsequent analysis were obtained.Using HISAT2, Clean Reads was sequentially compared with the reference genome to obtain the position information on the reference genome or gene and the specific sequence characteristics of the sequenced samples.
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was used as a measure of transcript or gene expression level
For samples with biological duplications, DESeq2 was used to conduct differential expression analysis between sample groups to obtain differential expression gene sets between the two biological conditions.Unstandardized reads count data of input genes are required, rather than standardized data such as RPKM and FPKM.After the difference analysis, the Benjamini-Hochberg method should be used to correct the hypothesis testing probability (P value) by multiple hypothesis testing to obtain the False Discovery Rate (FDR).The screening criteria for differential genes were |log2Fold Change| >= 1, and FDR < 0.05
Assembly: Mus_musculus.GRCm39.109
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol. 2 ug of total RNA was used forthe construction of sequencing libraries.
Ribosomal RNA is removed from total RNA to produce mRNA.Then the RNA was broken into short fragments by fragmentation buffer, and the first cDNA was synthesized with six-base random hexamers based on the fragment RNA template.Then the buffer, dNTPs(dTTP, dATP, dGTP and dCTP) and DNA polymerase I were added to synthesize the double-stranded cDNA, which was then purified by DNA purification magnetic beads.The purified double-stranded cDNA was then end-repaired, A tail was added and a sequencing joint was connected, and then fragment size was seleted by DNA purification magnetic beads, and finally PCR enrichment was performed to obtain the final cDNA library.

value: colorectal cancr cell

value: Acsl4 konckdown


title: P62

city: Shenyang

first: Xinyi

last: Long

state: State...

address: Shenyang

institute: China Medical university

description: circRNA expression profiles in U-937 cells

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing:
Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 2 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed.

source_name: p62-knockdown U937 cells

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: The human acute monocytic leukemia cell line, U937, was purchased from Bena Culture Collection (Beijing, China) and stored in our laboratory. U937 cells were cultured in RPMI-1640 (HyClone; GE Healthcare Life Sciences, Logan, UT, USA) with 10% fetal bovine serum (Biological Industries, Beit, HaEmek, Israel), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (Gibco/Thermo Fisher Scientific, Waltham, MA, USA). The cells were grown in a 37°C incubator with 5% CO2. A recombinant lentivirus vector–mediated SQSTM1 gene (LV-SQSTM1-RNAi) and an empty recombinant adenovirus vector (Hu6-MCS-CMV-EGFP) were constructed. U937 cells were placed in a six-well plate. Polybrene (Gene, Shanghai, China) was used for the transfection. The transfection system included 1.8 mL of RPMI-1640 with 10% fetal bovine serum, 10 μL of LV-SQSTM1-RNAi or Hu6-MCS-CMV-EGFP and 0.9 μL of polybrene. After transfection for 24 h, the cell suspension was collected and centrifuged at 800 rpm for 5 min, the supernatant with lentivirus discarded, and 2 mL of RPMI-1640 with 10% fetal bovine serum then added.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The total RNA of each sample was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA); after which, the amounts of extracted RNA were quantifed by a NanoDrop ND-1000 spectrophotometer. The structural integrity of isolated RNA was evaluated by agarose gel electrophoresis under denaturing conditions, and the RNA purity was assessed by the ratio of absorbance at 260 and 280 nm.


title: U-937

source_name: U937 cells

value: human acute monocytic leukemia cell line

value: control


title: HeLa_1_1_B2;control

description:
Library name: HeLa1_cnt_1_B2
column: HeLa1cnt

value: no heatshock


title: MC38 cells,shACSL4-2

description: Library name: Sample 5


title: T1D_6247 [IG1_Ivan_Gerling]

value: Fresh frozen pancreas section


title: common melanocytic nevus_4a_DS

description: technical replicate of 4a_NORM

source_name: commercial human universal reference

value: Clontech human universal reference


title: T1D_6195 [6195_4_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6195


title: common melanocytic nevus_1_DS

description: technical replicate of 1_NORM

value: Female


title: T1D_6268 [IG103_Ivan_Gerling]


title: T1D_6247 [IG10_Ivan_Gerling]


title: MC38 cells,shACSL4-1

description: Library name: Sample 4


title: common melanocytic nevus_16

description: technical replicate of 16_DS


title: HeLa_1_1;8hr

description:
Library name: HeLa1_8R_1_B1
column: HeLa7_8R


title: MC38 cells,shControl-3

description: Library name: Sample 3

value: WT


title: common melanocytic nevus_15

description: technical replicate of 15_DS

value: Male


title: HeLa_1_1;0hr

description:
Library name: HeLa1_0R_1_B1
column: HeLa7_0R

value: wild type

value: heatshock


title: dysplastic nevus_19

description: technical replicate of 19_DS


title: MC38 cells,shControl-1

description: Library name: Sample 1


title: T1D_6396 [6396-02_2_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6396


title: melanoma 34, BRAF wt

description: Dye-swap technical replicates are combined.

value: melanoma

value: wt

value: III

value: vertical

value: female

value: reference


title: T1D_6396 [6396-02_8_Ivan_Gerling]


title: common melanocytic nevus_14

description: technical replicate of 14_DS


title: HEK_6_1;8hr

description:
Library name: HEK6_8R_1_B2
column: HEK6_8R

source_name: human embryonic kidney cells

value: human embryonic kidney cells

value: HEK293 cells


title: T1D_6396 [6396-02_11_Ivan_Gerling]


title: T1D_6396 [6396-02_4_Ivan_Gerling]


title: common melanocytic nevus_13

description: technical replicate of 13_DS


title: T1D_6396 [6396-02_10_Ivan_Gerling]


title: T1D_6396 [6396-02_12_Ivan_Gerling]


title: common melanocytic nevus_12

description: technical replicate of 12_DS


title: MC38 cells,shControl-2

description: Library name: Sample 2

value: colorectal cancr cell


title: Mkx-CreER/flox, replicate3

city: Bunkyo-ku

first: Hiroshi

last: Asahara

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

country: Japan

institute: Institute of Science Tokyo

description: Library name: Mkx-KO3

data_processing:
Sequenced reads were trimed adaptor and filtered low-quality sequences using fastp.
Trimmed and filtered reads were aligned to mouse genome mm10 using STAR
Read count extraction and TPM calculation were peformed using feacureCounts and TPMCalculator, respectively.
Differential expression analysis was performed using iDEP 2.0 (South Dakota State University, http://bioinformatics.sdstate.edu/idep/)
Assembly: mm10
Supplementary files format and content: tab-delimited text file incudes raw counts for each samples

source_name: Achilles tendon

extract_protocol:
Tendons were crushed using Precellys Evolution Touch in TRI-reagent and purified using Direct-zol RNA MicroPrep kit
RNA-Seq libraries were construnted using the GenNext RamDA-seq Single Cell Kit (Toyobo, Osaka, Japan) according manufacturer's instruction.

treatment_protocol: 20mg/kg Tamoxifen was administrated at 6 weeks old

value: Achilles tendon

value: Mkx-CreER/flox


title: HeLa_1_1;control

description:
Library name: HeLa1_cnt_1_B1
column: HeLa7cnt

value: Henrietta Lacks cells

value: HeLa cells

value: no heatshock


title: HEK_5_1;8hr

description:
Library name: HEK5_8R_1_B2
column: HEK5_8R


title: Mkx-flox, replicate4

description: Library name: Mkx-flox4

value: Mkx flox/+


title: common melanocytic nevus_4b_DS

description: technical replicate of 4b_NORM

value: Clontech human universal reference

value: Male


title: HEK_6_1;0hr

description:
Library name: HEK6_0R_1_B2
column: HEK6_0R

value: wild type

value: heatshock


title: common melanocytic nevus_10

description: technical replicate of 10_DS


title: T1D_6396 [6396_8_Ivan_Gerling]

value: Fresh frozen pancreas section


title: HEK_5_1;control

description:
Library name: HEK5_cnt_1_B2
column: HEK5cnt


title: common melanocytic nevus_6

description: technical replicate of 6_DS

value: Female


title: Mkx-CreER/flox, replicate2

description: Library name: Mkx-KO2


title: T1D_6396 [6396-02_1_Ivan_Gerling]


title: common melanocytic nevus_11

description: technical replicate of 11_DS


title: HEK_4_1;8hr

description:
Library name: HEK4_8R_1_B2
column: HEK4_8R


title: common melanocytic nevus_7a

description: technical replicate of 7a_DS


title: HEK_6_1;control

description:
Library name: HEK6_cnt_1_B2
column: HEK6cnt


title: common melanocytic nevus_5

description: technical replicate of 5_DS


title: Mkx-CreER, replicate3

description: Library name: Mkx-Cre3

value: Mkx-CreER/+


title: Mkx-flox, replicate2

description: Library name: Mkx-flox2


title: Mkx-flox, replicate3

description: Library name: Mkx-flox3


title: T1D_6396 [6396_6_Ivan_Gerling]


title: Mkx-CreER/flox, replicate1

description: Library name: Mkx-KO1


title: HEK_5_1;0hr

description:
Library name: HEK5_0R_1_B2
column: HEK5_8R


title: Mkx-CreER, replicate2

description: Library name: Mkx-Cre2


title: HEK_4_1;control

description:
Library name: HEK4_cnt_1_B2
column: HEK4cnt


title: HEK_3_1_B2;8hr

description:
Library name: HEK3_8R_1_B2
column: HEK3_8R


title: Mkx-CreER, replicate1

description: Library name: Mkx-Cre1


title: HEK_3_1_B2;0hr

description:
Library name: HEK3_0R_1_B2
column: HEK3_0R


title: HEK_4_1;0hr

description:
Library name: HEK4_0R_1_B2
column: HEK4_0R


title: CD19 MLR 5

city: Boston

first: Urvashi

last: Bhatia

state: MA

address: 450 Brookline Avenue

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 5

hyb_protocol: Following fragmentation, fragmented cRNA were hybridized to Affymetrix hu133 plus2 microarray chip for overnight at 45C.

scan_protocol: cRNA bound by complementary oligonucleotide were excited using confocal laser scanner and emission information recorded

data_processing: Data was analyzed with Qlucore Omics Explorer and annotated using the Affymatrix file HG-U133_Plus_2-na36-annot-csv

label: biotin

source_name: CD19+ B cells from MLR 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-15ug total RNA

growth_protocol: Mixed lymphocytes reaction (MLR) cultures were maintained in vitro at 37 C, 5% CO2 incubator

extract_protocol: RNA was isolated using the SV Total RNA isolation system (Promega, WI) according to the manufacturer's instructions

treatment_protocol: MLRs using 6 responder-stimulator pairs (MLR: PBMC from one donor (responder) co-cultured with irradiated PBMC from second donor (stimulator) for 3 days)

tag: donor

value: Donor pair 5

value: CD19+ B cells


title: T1D_6371 [6371_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6371


title: T1D_6195 [6195_3_Ivan_Gerling]


title: HEK_3_1_B2;control

description:
Library name: HEK3_cnt_1_B2
column: HEK3cnt

value: human embryonic kidney cells

value: HEK293 cells


title: T1D_6396 [6396_4_Ivan_Gerling]


title: T1D_6396 [6396_12_Ivan_Gerling]


title: common melanocytic nevus_4b

description: technical replicate of 4b_DS


title: Native aging (BM) old 2

city: Barcelona

first: Michael

last: Scherer

address: C/ Dr. Aiguader 88

institute: Centre for Genomic Regulation

description: Library name: M.7 old 2

library_source: genomic

data_processing:
Custom pipeline available at https://github.com/veltenlab/scTAM-seq-scripts
Assembly: mm10
Supplementary files format and content: The processed data files are in tsv (tab-separated) tabular format and contain read counts for amplicons (CpGs) times cells.

molecule: genomic DNA

source_name: bone marrow

extract_protocol: scTAM-seq based on Mission Bio Tapestri

value: bone marrow

value: immune cells


title: common melanocytic nevus_1

description: technical replicate of 1_DS


title: CD19 MLR 6

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 6

source_name: CD19+ B cells from MLR 6

value: Donor pair 6


title: common melanocytic nevus_4a

description: technical replicate of 4a_DS


title: Mkx-flox, replicate1

description: Library name: Mkx-flox1

value: Achilles tendon


title: Native aging (BM) young 2

description: Library name: M.7 young 2


title: T1D_6371 [6371_2_Ivan_Gerling]


title: CD19 MLR 2

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 2

source_name: CD19+ B cells from MLR 2

value: Donor pair 2


title: T1D_6371 [6371_6_Ivan_Gerling]


title: T1D_6371 [6371_7_Ivan_Gerling]


title: T1D_6371 [6371_4_Ivan_Gerling]


title: Transplantation experiment (BM)

description: Library name: M.8 transplant


title: HEK_3_1;8hr

description:
Library name: HEK3_8R_1_B1
column: HEK9_8R


title: CD19 MLR 1

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 1

source_name: CD19+ B cells from MLR 1

value: Donor pair 1


title: Native aging (BM) young 1

description: Library name: M.7 young 1


title: HEK_2_1_B2;8hr

description:
Library name: HEK2_8R_1_B2
column: HEK2_8R


title: CD19 MLR 4

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 4

source_name: CD19+ B cells from MLR 4

value: Donor pair 4


title: LARRY endothelial cells (lung)

description: Library name: M.6 lung

source_name: lung

value: lung


title: Native aging (BM) old 1

description: Library name: M.7 old 1


title: T1D_6371 [6371_1_Ivan_Gerling]


title: CD19 MLR 3

description: Gene expression data from human B cells enriched from allo-stimulated MLR culture of donor pair 3

source_name: CD19+ B cells from MLR 3

value: Donor pair 3


title: rns2 enz+tRNA rep1

city: Chengdu

first: Lei

last: Zhu

state: --- Select One ---

address: No.17 People's South Road

institute: Sichuan University

library_source: other

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence. 13-40 nt reads were mapped to TAIR10 whole genome using soap v2.20 with parameters -M 0 -v 0 -p 7 -r 2
count the number of sRNA that mapped to the genome
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include sequence and raw count of 13-40 nt reads for each Sample

molecule: other

source_name: Leaf

growth_protocol: plants were grown under long-day (16h light) condition at 23°C

extract_protocol:
TRIzol reagent
The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific)

value: Leaf

value: enzyme+tRNA


title: HEK_3_1;0hr

description:
Library name: HEK3_0R_1_B1
column: HEK9_0R

value: wild type

value: heatshock


title: LARRY mature immune cells (BM+spleen)

description: Library name: M.5 BM+Spleen

source_name: bone marrow and spleen

value: bone marrow and spleen


title: WT enz+tRNA rep2

value: WT


title: rns2 enz rep2

value: enzyme


title: HEK_2_1_B2;0hr

description:
Library name: HEK2_0R_1_B2
column: HEK2_0R

value: human embryonic kidney cells

value: HEK293 cells


title: WT enz+tRNA rep1


title: LARRY mature myeloid cells (BM+PB)

description: Library name: M.4b BM+PB

source_name: bone marrow and peripheral blood

value: bone marrow and peripheral blood

value: immune cells


title: T1D_6362 [6362-1_7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6362

value: Fresh frozen pancreas section


title: HEK_2_1;8hr

description:
Library name: HEK2_8R_1_B1
column: HEK8_8R


title: HEK_2_1_B2;control

description:
Library name: HEK2_cnt_1_B2
column: HEK2cnt

value: no heatshock


title: T1D_6195 [6195_2_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6195


title: T1D_6362 [6362-1_5_Ivan_Gerling]


title: rns2 enz+tRNA rep2


title: rns2 enz rep1


title: T1D_6362 [6362-2_10_Ivan_Gerling]


title: HEK_3_1;control

description:
Library name: HEK3_cnt_1_B1
column: HEK9cnt


title: T1D_6362 [6362-1_2_Ivan_Gerling]


title: HEK_2_1;0hr

description:
Library name: HEK2_0R_1_B1
column: HEK8_0R


title: LARRY mature myeloid cells (lung)

description: Library name: M.4a lung


title: T1D_6362 [6362-1_17_Ivan_Gerling]


title: Native hematopoiesis (BM)

description: Library name: M.3 mouse 1

value: bone marrow


title: WT enz rep1


title: rns2 3h rep2

value: Wounding


title: HEK_1_1_B2;8hr

description:
Library name: HEK1_8R_1_B2
column: HEK1_8R


title: HEK_2_1;control

description:
Library name: HEK2_cnt_1_B1
column: HEK8cnt


title: HEK_1_1_B2;0hr

description:
Library name: HEK1_0R_1_B2
column: HEK1_0R


title: rns2 3h rep1


title: LARRY main experiment (BM) mouse 4

description: Library name: M.1 mouse 4


title: HEK_1_1_B2;control

description:
Library name: HEK1_cnt_1_B2
column: HEK1cnt


title: rns2 0h rep2

value: No treatment


title: T1D_6362 [6362-1_13_Ivan_Gerling]


title: LARRY replicate experiment (BM) mouse 1

description: Library name: M.2 mouse 1


title: LARRY main experiment (BM) mouse 3

description: Library name: M.1 mouse 3


title: T1D_6362 [6362-1_15_Ivan_Gerling]


title: rns2 0h rep1


title: T1D_6362 [6362-1_10_Ivan_Gerling]


title: LARRY main experiment (BM) mouse 2

description: Library name: M.1 mouse 2


title: T1D_6362 [6362-1_16_Ivan_Gerling]


title: T1D_6224 [6224_3_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6224


title: WT enz rep2


title: HEK_1_1;8hr

description:
Library name: HEK1_8R_1_B1
column: HEK7_8R

source_name: human embryonic kidney cells


title: T1D_6224 [6224_11_Ivan_Gerling]


title: LARRY replicate experiment (BM) mouse 2

description: Library name: M.2 mouse 2


title: rns1 3h rep3


title: HEK_1_1;0hr

description:
Library name: HEK1_0R_1_B1
column: HEK7_0R


title: LARRY main experiment (BM) mouse 1

description: Library name: M.1 mouse 1


title: rns1 3h rep2


title: T1D_6228 [IG99_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6228


title: rns1 3h rep1


title: HEK_1_1;control

description:
Library name: HEK1_cnt_1_B1
column: HEK7cnt


title: CRISPRko, sgRNA enrichment  scRNA-seq, rep3

city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

institute: Tianjin Medical University

description:
Library name: sgRNA_enrichment_CRISPRko (rep3)
10x Genomics + sgRNA enrichment PCRs

data_processing:
Data processing for scRNA-seq and sgRNA enrichment scRNA-seq datasets was performed using the Cell Ranger software v5.0.1, developed by 10x Genomics. The processing steps for both types of data followed similar procedures. For standard scRNA-seq data, the initial steps involved demultiplexing and barcode processing using Cell Ranger. The software assigned cell barcodes and molecular barcodes (UMIs) to individual reads and performed quality control. Gene counting and aggregation were then carried out to generate a gene-cell matrix, quantifying the expression of genes across cells. In the case of sgRNA enrichment scRNA-seq data, the enrichment reads were aligned to a reference genome using Cell Ranger v5.0.1, following the same procedure as for standard scRNA-seq data processing. Reads that failed to align to the reference genome were extracted using Samtools. These extracted reads were subsequently mapped to the sequences of the sgRNA library and its reverse complement, utilizing ACCG as the left anchor (located at the end of the U6 promoter) and GTTT as the right anchor. This mapping process allowed for the identification of sgRNA sequences and the determination of their expression levels in each cell. The resulting data, including cell barcodes and sgRNA UMI counts for each perturbed cell, were added to the dataset.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; sgRNA enrichment output files: txt.

molecule: polyA RNA

growth_protocol: HAP1 (Horizon Discovery) cells were cultured in IMDM (ThermoFisher) supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Adherent cells were digested with 0.25% trypsin and collected in a 15mL tube containing serum-containing medium, followed by centrifugation and washing of the cell pellet with serum-free basal medium to obtain a single-cell suspension.
The library construction protocol for single-cell RNA sequencing (scRNA-seq) was performed following the manufacturer's instructions using the 10x Genomics Chromium Single Cell 3' Library reagents V3. The protocol involved the generation of gel bead-in-emulsion (GEM) using cells resuspended in a master mix along with partitioning oil and gel beads. The GEMs encapsulated individual cells' poly-A RNA, which was retrotranscribed into cDNA containing an Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The barcoded cDNA was then subjected to various steps, including cleaning up with Silane DynaBeads, PCR amplification, sgRNA enrichment PCR, and fragmentation of the remaining amplified cDNA. Appropriately sized fragments were selected using SPRIselect reagent. The library was then prepared by ligating paired-end constructs with P5 and P7 sequences and a sample index. Finally, the enriched sgRNA library and fragmented cDNA were sequenced on an Illumina NovaSeq6000 PE150 platform, following the standard 10x libraries configuration.

treatment_protocol: Diploid HAP1 cells were isolated from Hoechst (MCE)-stained HAP1 cells by flow sorting. Lentivirus containing dCas9-KRAB-blast, dCas9-VP64-blast asn Cas9-Blast were separately used to construct stably-expressing HAP1 cells with diploid cells. The activation, inhibition or knock out efficiency of single clones were verified by infection with lentivirus containing sgRNA targeting the TSS of EZH2. The three most efficient clones of each cell line were selected for perturbation.

value: Cas9 stably expressed single clone

value: transduced with lentivirus


title: Mouse neocortex, single-cell gRNA expression library, batch 9

city: Chapel Hill

first: Hyejung

last: Won

state: NC

address: 116 Manning Dr #6110

department: Genetics

institute: UNC Chapel Hill

description:
Library name: gE20230516inlt1F
gRNA library enriched from 10x 3' cDNA library using custom primers

data_processing:
Single-cell gene and gRNA library sequencing files were processed using the cellranger count 6.1.2 pipeline for demultiplexing, barcoded processing, gene counting and aggregation.
Assembly: mm10
Supplementary files format and content: Tab-separated value files, matrices, comma-separated values and cloupe files.

source_name: Brain, neocortex

extract_protocol:
Briefly, minced neocortical tissue was incubated in papain/DNase solution with constant agitation for 90 min at 37ºC in a 5% CO2 incubator. After chemical digestion, the tissue was gently triturated using a serological pipet. Dissociated cells were filtered through a 70-μm cell strainer, and protease inhibitor and DNase were added before pelleting at 300g for 5 min. Cells were resuspended in Hibernate A (BrainBits, cat. no. HALF500) / B27 (ThermoFisher, cat. no. A3582801) / 10% FBS resuspension buffer. Y-27632 ROCK inhibitor (Selleck Chemicals, cat. no. S1049) was added to media in 1:1000 ratio to reduce cell death during single-cell prep. Next, live RFP-expressing cells were sorted by FACS and processed using the 10x Genomics 3' v3.1 Dual Index workflow for scRNA-seq library generation by the UNC Advanced Analytics (AA) Core. gRNA reads were separately enriched from cDNA using custom-design primers targeting the CROP-seq backbone sequence for assigning gRNAs to cells. The resulting libraries were sequenced with Illumina high-throughput sequencers (NextSeq2000 P2 or P3 for gene expression library, NovaSeq6000 SP for gRNA library). We used cycles R1 x i1 x i2 x R2 = 28 x 10 x 10 x 90, with 1% PhiX for gene library,  and cycles R1 x i1 x i2 x R2 = 28 x 10 x 10 x 42, with 20% PhiX for gRNA library.
Library preparation was done by UNC Advanced Analytics Core according to manufacturer instructions (Chromium 10x Genomics 3' v3.1 Dual Index Workflow).

value: Brain, neocortex

value: Cas9 heterozygous


title: T1D_6195 [6195-06_7_Ivan_Gerling]

city: Gainesville

first: Alexandra

last: Cuaycal

address: 1275 Center Drive

institute: University of Florida

data_processing: Raw signal intensity values from all arrays were Robust Multichip Average (RMA)  background corrected, quantile normalized, median polish summarized, and log2transformed. Processing was carried out using Partek Genomics Suite, version 6.5.

extract_protocol: Total islet RNA was extracted using the PicoPure RNA kit (ThermoFisher). DNAse treatment was performed using recombinant DNase I (RNase-free DNAse kit, Worthington Biochemical Corporation).


title: rns1 0h rep2

value: Leaf


title: T1D_6247 [IG94_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6247


title: CRISPRi, sgRNA enrichment  scRNA-seq, rep3

description:
Library name: sgRNA_enrichment_CRISPRi (rep3)
10x Genomics + sgRNA enrichment PCRs

value: dCas9-KRAB staby expressed single clone


title: CRISPRa, sgRNA enrichment  scRNA-seq, rep3

description:
Library name: sgRNA_enrichment_CRISPRa (rep3)
10x Genomics + sgRNA enrichment PCRs

value: dCas9-VP64 stably expressed single clone


title: rns1 0h rep1


title: CRISPRko, sgRNA enrichment  scRNA-seq, rep2

description:
Library name: sgRNA_enrichment_CRISPRko (rep2)
10x Genomics + sgRNA enrichment PCRs


title: Mouse neocortex, single-cell gRNA expression library, batch 6

description:
Library name: gE20230425inlt1M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: WT 3h rep3

value: WT


title: Mouse neocortex, single-cell gRNA expression library, batch 10

description:
Library name: gE20230613inlt1M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: T1D_6212 [IG9_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6212


title: CRISPRa, sgRNA enrichment  scRNA-seq, rep2

description:
Library name: sgRNA_enrichment_CRISPRa (rep2)
10x Genomics + sgRNA enrichment PCRs


title: Mouse neocortex, single-cell gRNA expression library, batch 5

description:
Library name: gE20230418inlt1F
gRNA library enriched from 10x 3' cDNA library using custom primers


title: WT 3h rep2


title: Mouse neocortex, single-cell gRNA expression library, batch 4

description:
Library name: gE20230131inlt1M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: CRISPRko, sgRNA enrichment  scRNA-seq, rep1

description:
Library name: sgRNA_enrichment_CRISPRko (rep1)
10x Genomics + sgRNA enrichment PCRs


title: WT 3h rep1


title: Mouse neocortex, single-cell gRNA expression library, batch 3

description:
Library name: gE20230130inlt2M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: rns1 0h rep3


title: WT 0h rep3


title: Mouse neocortex, single-cell gRNA expression library, batch 8

description:
Library name: gE20230502inlt2M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: Mouse neocortex, single-cell gRNA expression library, batch 7

description:
Library name: gE20230502inlt1M
gRNA library enriched from 10x 3' cDNA library using custom primers


title: T1D_6268 [IG86_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6268


title: T1D_6070 [IG88_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6070


title: Mouse neocortex, single-cell gRNA expression library, batch 2

description:
Library name: gE20230130inlt1F
gRNA library enriched from 10x 3' cDNA library using custom primers


title: T1D_6212 [IG87_Ivan_Gerling]


title: CRISPRa, sgRNA enrichment  scRNA-seq, rep1

description:
Library name: sgRNA_enrichment_CRISPRa (rep1)
10x Genomics + sgRNA enrichment PCRs


title: WT 0h rep2


title: T1D_6306 [IG89_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6306


title: T1D_6306 [IG79_Ivan_Gerling]


title: T1D_6243 [IG80_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6243


title: CRISPRi, sgRNA enrichment  scRNA-seq, rep2

description:
Library name: sgRNA_enrichment_CRISPRi (rep2)
10x Genomics + sgRNA enrichment PCRs


title: Mouse neocortex, single-cell gRNA expression library, batch 1

description:
Library name: gE20221114inlt1F
gRNA library enriched from 10x 3' cDNA library using custom primers


title: CRISPRa, transcriptomes scRNA-seq, rep3

description:
Library name: scRNA-seq_CRISPRko (rep3)
10x Genomics


title: CRISPRi, transcriptomes scRNA-seq,rep3

description:
Library name: scRNA-seq_CRISPRi (rep3)
10x Genomics

value: dCas9-KRAB stably expressed single clone


title: N2, 4C 5d, rep 1

city: Oslo

first: Eivind

last: Valen

address: Blindernveien 31

department: Department of Biosciences

institute: University of Oslo

description: Ribo-seq

data_processing:
Both RNA-seq and ribosome profiling were processed with the ribo-seq pipeline in ORFik (v1.22.2).The pipeline was run with default parameters andwraps several steps: stripping adapters using fastp (v0.23.4) using the adapter sequence “TGGAATTCTCGGGTGCCAAGG”, mapping reads with STAR (v2.7.11b) and expression (FPKM) estimates using DESeq2(v1.42.1).The code for this pipeline can be found athttps://www.bioconductor.org/packages/release/bioc/vignettes/ORFik/inst/doc/Ribo-seq_pipeline.html.
Assembly: WBcel235
Supplementary files format and content: FPKM expression values in CSV format

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: C. elegans animals were synchronized by hypochloride treatment, eggs were allowed to hatch overnight in M9 buffer. Synchronized L1 larvae were grown at 20°C on NG 2% plates seeded with OP50, until the 1-day-old adult stage.

extract_protocol:
Animals were washed off the plates with M9 buffer, followed by three washes with M9 buffer before being frozen in liquid nitrogen. Worms were lysed, monosomes purified and RNA was isolated using Trizol. The RNA from the monosomal fraction was separated using a 15% TBE-Urea Gel (Invitrogen) and the region around 28-30 nucleotides excised to isolate Ribosome protected fragments (RPFs). The gel piece was forced through a pierced small tube inside an eppendorf tube by centrifugation and RNA from the gel debris was eluted by overnight incubation in 600 µl cracking buffer (20 mM Tris-HCl (pH 7.9), 1 mM EDTA, 400 mM NH4Acetate, 0.5 % SDS). RNA was precipitated with isopropanol at -80 °C for at least 4 hours (isopropanol precipitation).
RPFs were 3’ dephosphorylated with 10 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer with 40 Units of RNasin for 1 hour at 37 °C. Following isopropanol precipitation, the RNA samples were ligated to 3’ adapters according to the Illumina® TruSeq™ Small RNA Sample Preparation protocol and using the reagents of the kit, then again precipitated with isopropanol. Ligation products were 5’ phosphorylated for 30 minutes at 37 °C with 15 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer, 1 mM ATP and 40 Units of RNasin. Following heat-inactivation of the enzyme for 10 minutes at 70 °C, the RNA was precipitated by isopropanol. Ligation to 5’ adapters, reverse transcription, PCR amplification with barcoded primers and gel-purification of the PCR products were performed using the Illumina® TruSeq™ Small RNA Sample Prep kit. Four different barcodes (RPIX 2, 4, 5, 6) were used.

treatment_protocol: Animals were either collected at the end of the growth protocol or shifted to 10°C for 2 hours and collected, or shifted to 10°C for 2 hours followed by 1, 3, or 5 days at  4°C and collected.

value: Whole animal


title: CRISPRa, transcriptomes scRNA-seq, rep2

description:
Library name: scRNA-seq_CRISPRko (rep2)
10x Genomics


title: F_9HOTrE 2

city: Clemson

first: Jazmine

last: Eccles

state: SC

address: 132 Long Hall

institute: Clemson University

data_processing:
PE150 strategy by Novogene. HISAT2 was used to map clean reads.
Assembly: GRCm39
Supplementary files format and content: Excel file containing raw counts performed by Novogene named "gene_count.xls"

source_name: Liver

extract_protocol:
RNA extractions were performed on 20 mg of liver tissue previously stored at -80C. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop (Thermo Fisher Scientific, Walkham, MA USA) to ensure both A260/280 and A260/230 values were about 2.0.
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).

value: Liver

tag: Sex

value: F

value: 20-hour fast, 9-HOTrE


title: T1D_6342 [IG85_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6342

value: Fresh frozen pancreas section


title: N2, 4C 3d, rep 2

description: Ribo-seq


title: CRISPRko, transcriptomes scRNA-seq, rep3

description:
Library name: scRNA-seq_CRISPRa (rep3)
10x Genomics

tag: strain


title: N2, 4C 5d, rep 2

description: Ribo-seq

tag: treatment


title: T1D_6268 [IG78_Ivan_Gerling]


title: T1D_6195 [6195_1_Ivan_Gerling]


title: CRISPRi, sgRNA enrichment scRNA-seq, rep1

description:
Library name: sgRNA_enrichment_CRISPRi (rep1)
10x Genomics + sgRNA enrichment PCRs

tag: cell line


title: F_9HOTrE 1


title: WT 0h rep1

source_name: Leaf


title: N2, 4C 1d, rep 2

description: Ribo-seq


title: F_Control 8

value: 20-hour fast


title: CRISPRko, transcriptomes scRNA-seq, rep2

description:
Library name: scRNA-seq_CRISPRa (rep2)
10x Genomics


title: CRISPRi, transcriptomes scRNA-seq, rep2

description:
Library name: scRNA-seq_CRISPRi (rep2)
10x Genomics


title: F_9HOTrE 4


title: sAAb_6181 [6181_6_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6181


title: F_9HOTrE 3


title: F_Control 7


title: CRISPRa, transcriptomes scRNA-seq, rep1

description:
Library name: scRNA-seq_CRISPRko (rep1)
10x Genomics


title: N2, 4C 1d, rep 1

description: Ribo-seq


title: F_Control 6


title: N2, 10C, rep 2

description: Ribo-seq


title: N2, 4C 3d, rep 1

description: Ribo-seq


title: CRISPRko, transcriptomes scRNA-seq, rep1

description:
Library name: scRNA-seq_CRISPRa (rep1)
10x Genomics


title: F_Control 5


title: CRISPRi, transcriptomes scRNA-seq, rep1

description:
Library name: scRNA-seq_CRISPRi (rep1)
10x Genomics


title: N2, 20C, rep 2

description: Ribo-seq


title: F_9HODE 4

value: 20-hour fast, 9-HODE


title: HAP1-delta17, ATAC-seq

description: Library name: ATAC-seq(HAP1-delta17)

data_processing:
The data analysis was performed using the nf-core pipeline (Ewels et al., 2020). Sequencing quality was first assessed with FastQC, and reads were subsequently trimmed using Trim Galore. The trimmed reads were then aligned to the hg19 reference genome using Bowtie2 with default settings. Following alignment, the data underwent additional quality control and further processing for analysis.
Assembly: hg19
Supplementary files format and content: ATAC-seq result files: bigwig.

extract_protocol:
Adherent cells were digested with 0.25% trypsin and collected in a 15mL tube containing serum-containing medium, followed by centrifugation and washing of the cell pellet with serum-free basal medium to obtain a single-cell suspension.
1 × 10⁵ freshly cultured cells were washed with PBS, digested, and centrifuged at 500 × g for 5 min at 4°C. The cell pellet was resuspended in 400 μL lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and incubated on ice for 5 min. Spin down at for 500 × g for 5 min at 4°C. Then the resulting pellet was performed using the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501) according to the manufacturer's instructions. Briefly, the resulting pellet were incubated with 5× TTBL, TTE Mix V50, and ddH₂O at 37°C for 30 min, followed by fragmentation. DNA fragments were purified using phenol-chloroform-isoamyl alcohol (25:24:1). Libraries were constructed by 8 cycles of PCR amplification using the TruePrep Library Prep Kit, followed by magnetic bead purification. Libraries were sequenced on a Novogene HiSeq PE150 platform. Two biological replicates were performed for each condition.

treatment_protocol: HAP1-sgURE and HAP1-sgNTC cells were  generated by  transduced KRAB-blast stably expressed HAP1 cell with sgRNA targeted rs73156934-tagged CRE or non-targeting control(NTC) . HAP1-delta64 and HAP1-delta17 cells were generated by CRISPR/Cas9 editing of the rs73156934 locus in wild-type HAP1 cells. Single clones were selected and confirmed by Sanger sequencing to contain 64bp and 17bp deletions, respectively.

value: wild-type

value: edited at rs73156934 locus with a 17bp deletion


title: N2, 10C, rep 1

description: Ribo-seq


title: sAAb_6181 [6181_2_Ivan_Gerling]


title: T1D_6195 [6195-06_4_Ivan_Gerling]


title: N2, 20C, rep 1

description: Ribo-seq


title: sAAb_6181 [6181_1_Ivan_Gerling]


title: sAAb_6181 [6181_5_Ivan_Gerling]


title: sAAb_6397 [6397_7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6397


title: F_9HODE 3


title: N2, 4C 5d, rep 2

extract_protocol:
Animals were washed off the plates with M9 buffer, followed by three washes with M9 buffer before being frozen in liquid nitrogen. Total RNA was extracted by Trizol treatment. Note that total RNA was extracted from the same lysate used for the corresponding ribosome profiling experiment.
Library preparation was performed using the ScriptSeq v2 RNA-seq library preparation kit according to the manufacturer's protocol.


title: sAAb_6397 [6397_5_Ivan_Gerling]


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, ATAC-seq

description: Library name: ATAC-seq(sgURE)

value: KRAB-blast stably expressed HAP1 cell

value: transduced with sgRNA targeted rs73156934-tagged CRE


title: F_9HODE 2


title: sAAb_6147 [6147_7_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6147


title: N2, 4C 5d, rep 1


title: sAAb_6397 [6397_4_Ivan_Gerling]


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, ATAC-seq

description: Library name: ATAC-seq(sgNTC)

value: transduced with non-targeting control (NTC) sgRNA


title: HAP1-delta64, ATAC-seq

description: Library name: ATAC-seq(HAP1-delta64)

value: edited at rs73156934 locus with a 64bp deletion


title: F_Control 4


title: sAAb_6397 [6397_3_Ivan_Gerling]


title: sAAb_6181 [6181_3_Ivan_Gerling]


title: N2, 4C 3d, rep 2


title: HAP1,wild-type,ATAC

description: Library name: ATAC-seq(wild-type)


title: F_Control 3


title: N2, 4C 3d, rep 1


title: F_Control 2


title: sAAb_6397 [6397_2_Ivan_Gerling]


title: F_9HODE 1


title: molm-13 sh-circ 3

city: Jinan

first: Daoxin

last: Ma

state: shandong

address: No.107,West of Wenhua Road

institute: Qilu Hospital of Shandong University

description: Library name: sample 16

data_processing:
Double-ended reads were harvested by Illumina NovaSeq 6000 sequencer. Q30 was used for quality control, cutadapt software (v1.9.3) was used to remove the connection, and low quality reads were removed.
circRNA: High quality reads were compared to the reference genome using STAR software (v2.5.1b), and circular RNA was detected and identified using DCC software (v0.4.4). CircBase database and Circ2Traits were used to annotate the identified circular Rnas.
LncRNA&mRNA: High quality reads were compared to the human reference genome (UCSCHG19) using hisat2 software (v2.0.4). Then, the FPKM of transcription-level LncRNA and gene-level mRNA was obtained using cuffdiff software (v2.2.1, part of the cufflinks software suite) (Fragmentsper kilobase of exon per million fragments mapped), with the guidance of the gtf gene annotation file.
AML cell RNA-seq: After using Cutadapt to filter out unqualified sequences (sequencing joints, low-quality sequences, etc.) from the original Data to obtain Clean Data, the reference genome is compared using Hisat2. According to the comparison results of Hisat2,The transcript was reconstructed using StringTie and the expression levels of all genes in each sample were calculated.
Assembly: GRCh37/hg19
Supplementary files format and content: Excel files include the circRNA expression profile for exosome Sample.
Supplementary files format and content: Excel files include the LncRNA expression profile for exosome Sample.
Supplementary files format and content: Excel files include the mRNA expression profile for exosome Sample.
Supplementary files format and content: Excel files include the mRNA expression profile for molm-13 cell Sample.

extract_protocol:
exosomal RNA were extracted with exosome RNA Purification Kit; molm-13 RNA was extracted with TRIzol.
Ribosomal RNA (rRNA) was removed from the sample using the GenSeq® rRNA Removal Kit (GenSeq, Inc.). After removal of rRNA from samples, library construction was completed using GenSeq ® Low Input RNA Library Prep Kit (GenSeq, Inc.) in accordance with the manufacturers construction.
The fragmented mRNA was reversed into cDNA and then, E. coli DNA polymerase I (NEB, cat.m0209, USA) and RNase H (NEB, cat.m0297, USA) are used for double strand synthesis, dUTP Solution (Thermo Fisher, cat. R0133, CA, USA) was added to the double-stranded DNA, The two chains were digested with UDG enzyme (NEB, cat.m0280, MA, US), to form a fragment size of 300bp±50bp library (chain specific library).

tag: cell type

value: AML cell line


title: molm-13 sh-circ 1

description: Library name: sample 14


title: N2, 4C 1d, rep 1

tag: genotype


title: N2, 4C 1d, rep 2


title: molm-13 sh-circ 2

description: Library name: sample 15


title: M_9HOTrE4

value: M


title: N2, 10C, rep 2


title: molm-13 NC-circ 3

description: Library name: sample 13


title: M_9HOTrE 3


title: sAAb_6347 [6347_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6347


title: N2, 10C, rep 1


title: molm-13 NC-circ 2

description: Library name: sample 12


title: M_9HOTrE 2


title: molm-13 NC-circ 1

description: Library name: sample 11


title: N2, 20C, rep 2


title: sAAb_6347 [6347_7_Ivan_Gerling]


title: M_9HOTrE1


title: sAAb_6347 [6347_2_Ivan_Gerling]


title: N2, 20C, rep 1


title: healthy4

description: Library name: sample 10

source_name: bone marrow exosome

value: bone marrow exosome


title: M_9HODE 4


title: EII_3

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

data_processing:
The raw sequencing data underwent a stringent filtering process to ensure high quality: 1. Reads containing adapter sequences were removed. 2. Low-quality reads, where bases with a quality score less 20 constituted more than 50% of the read length, were discarded. 3. Reads with a high percentage of unknown bases (more than 10% of the read length) were excluded.
Quality metrics such as Q20, Q30 scores, and GC content were calculated for the clean data. Clean reads were obtained after data processing and subsequently mapped to the reference genome (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000005845.2/) using Bowtie2 v2.2.6.
Assembly: ASM584v2
Supplementary files format and content: xls file includes raw counts for each sample
Supplementary files format and content: xls file includes fpkm values for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: prokaryotic cells

growth_protocol: cells were cultured in LB medium at 37 °C under 180 rpm in the dark.

extract_protocol:
The total ribonucleic acid (RNA) was extracted using the TRIzol reagent (Tiangen, Beijing, China), following the manufacturer's protocol. For each sample, 1.5 μg of RNA was used for library preparation.
The libraries were sequenced using the paired-end 150 bp read configuration on a Beijing Allwegene Technology Company Limited platform.

treatment_protocol: 1 mL overnight E. coli suspension was inoculated into 9 mL of LB medium containing 30 mg/L of AgNPs and incubated in darkness for 4 h. Then, 1 mL of the treated suspension was collected, washed and inoculated into 10 mL of fresh LB medium for a 20-h recovery period. This treatment cycle was repeated for a total of 14 consecutive cycles.

tag: substrain

value: WT

value: prokaryotic cells

value: AgNP evolution, Day14


title: healthy3

description: Library name: sample 9


title: F_Control 1

value: Liver

value: F


title: sAAb_6397 [6397_1_Ivan_Gerling]

value: Fresh frozen pancreas section


title: M_9HODE 3


title: healthy2

description: Library name: sample 8


title: sAAb_6314 [6314_8_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6314


title: EII_2


title: sAAb_6347 [6347_1_Ivan_Gerling]


title: M_9HODE 2


title: EII_1


title: sAAb_6314 [6314_6_Ivan_Gerling]


title: sAAb_6147 [6147_6_Ivan_Gerling]


title: M_9HODE 1


title: healthy1

description: Library name: sample 7


title: M_Control 4

value: 20-hour fast


title: EI_3

value: AgNP evolution, Day9


title: AML6

description: Library name: sample 6


title: EI_2


title: AML5

description: Library name: sample 5


title: sAAb_6347 [6347_5_Ivan_Gerling]


title: EI_1


title: AML4

description: Library name: sample 4


title: sAAb_6314 [6314_3_Ivan_Gerling]


title: M_Control 3


title: M_Control 2


title: Ewt_3

value: AgNP evolution, Day0


title: AML3

description: Library name: sample 3


title: sAAb_6314 [6314_2_Ivan_Gerling]


title: Ewt_2


title: M_Control 1


title: AML2

description: Library name: sample 2


title: F_CYP2B6 4


title: Ewt_1


title: AML1

description: Library name: sample 1


title: sAAb_6314 [6314_1_Ivan_Gerling]


title: F_CYP2B6 3


title: sAAb_6314 [6314_4_Ivan_Gerling]


title: sAAb_6310 [6310_9_Ivan_Gerling]

source_name: Laser capture-microdissected islet from nPOD donor 6310


title: prp43a mutant, heat stress, biological replicate #2

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

country: South Korea

institute: Hallym University

data_processing:
CLC Genomics Workbench v20.0.4
Assembly: TAIR10
Supplementary files format and content: Exel file including TPM values for each Sample

source_name: Seven-day-old seedlings

growth_protocol: Arabidopsis thaliana ecotype Columbia (Col-0) was used in this study. Arabidopsis Plants were grown under long-day conditions (16h light/8h dark) at 22°C on 1/2 MS medium with 1% sucrose and 0.6% plant agar, adjusted to pH 5.7. The T-DNA insertion lines including prp43a-1(SALKseq_42682), prp43bs-1(WiscDsLox508D09) were obtained from Arabidopsis Biological Resource Center (ABRC).

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using Quick-RNA Plant Miniprep Kit (Zymo Research).
RNA-seq libraries were constructed using TruSeq Stranded mRNA library preparation kit (Illumina) and paired-end sequencing was performed to produce 2 X 75-bp reads using the Illumina Miseq platform.

treatment_protocol: Seedlings were gown on ½ MS medium. 7 days after germination (DAG) seedlings were treated with 38°C for 16 hours.

value: Seven-day-old seedlings

value: prp43a mutant

value: Heat stress (38°C for 16 h)


title: sAAb_6310 [6310_7_Ivan_Gerling]


title: F_CYP2B6 1


title: F_CYP2B6 2


title: prp43a mutant, heat stress, biological replicate #1


title: prp43a mutant, control condition, biological replicate #1

value: No treatment


title: prp43a mutant, control condition, biological replicate #2


title: M_CYP2B6 4


title: M_CYP2B6 3


title: T84 cells,shACSL4-3

description: Library name: Sample 6

data_processing:
After qualified library check, different libraries are pooled according to the requirements of effective concentration and target data volume for Illumina sequencing.The basic principle of Sequencing is Sequencing by Synthesis.
Image data of sequencing fragments measured by high-throughput sequencers were converted into sequence data (reads) by CASAVA base recognition in fastq format, which mainly contained sequence information of sequencing fragments and corresponding sequencing quality information.
fragments are randomly interrupted mrnas, and in order to determine which genes are transcribed from these fragments, the controlled clean reads need to be matched to the reference genome.HISAT2 software was used to quickly and accurately compare Clean Reads with the reference genome to obtain the location information of Reads on the reference genome
We carried out a quantitative analysis of the gene expression level of each sample, and then combined to obtain the expression matrix of all samples. The first list was the ID of the gene, and the rest was the original read count value of each sample.Due to the influence of sequencing depth and gene length, the gene expression value of RNA-seq is generally not expressed by read count, but by FPKM. FPKM has corrected the sequencing depth and gene length successively.
After the quantitative analysis of gene expression, it is necessary to conduct statistical analysis on the expression data and screen the genes whose expression levels are significantly different in different states of the samples.First of all, the original readcount is normalized, mainly the correction of sequencing depth.Then the statistical model was used to calculate the hypothesis testing probability (pvalue).Finally, the FDR value is obtained by multiple hypothesis testing.The screening criteria for differential genes are very important, and the criterion we proposed |log2(FoldChange)| >= 1&padj <= 0.05 is the commonly used empirical value.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: T84 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol. 2 ug of total RNA was used forthe construction of sequencing libraries.
Ribosomal RNA is removed from the total RNA, resulting in mRNA.Subsequently, the obtained mRNA was randomly interrupted with divalent cations in the NEB Fragmentation Buffer.Build the library according to the NEB method.

value: colorectal cancr cell

value: Acsl4 konckdown


title: T84 cells,shACSL4-1

description: Library name: Sample 4


title: T84 cells,shControl-3

description: Library name: Sample 3


title: T84 cells,shACSL4-2

description: Library name: Sample 5


title: sAAb_6147 [6147_5_Ivan_Gerling]


title: T84 cells,shControl-2

description: Library name: Sample 2


title: Col-0 wild type, heat stress, biological replicate #1

value: Col-0 wild type


title: Col-0 wild type, heat stress, biological replicate #2


title: M_CYP2B6 2

value: M


title: sAAb_6310 [6310_5_Ivan_Gerling]


title: T84 cells,shControl-1

description: Library name: Sample 1

value: WT


title: sAAb_6310 [6310_4_Ivan_Gerling]


title: sAAb_6310 [6310_8_Ivan_Gerling]


title: M_CYP2B6 1