title: RNA  enriched in the precipitates of ILF3 antibody in ARP1 cells [ILF3_IP]

data_processing:
Fastp 0.19.11 software performs basic quality statistics for raw reads
QC analysis was used by  fastqc v0.11.5
burrows Wheeler aligner(0.7.12-r1039) can  compare reads to reference genome
Peak calling was performed by MACS22.1.0
The motifs were recognized by Homer findMotifsGenome.pl(v4.9.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: ILF3_RIP_narrow_peaks_table.tsv

growth_protocol: Human multiple myeloma cell lines ARP1 were cultured in RPMI 1640 Medium  with 10% fetal bovine serum 100 U/ml penicillin and 100 mg/ml streptomycin All cells were cultured in a humidified atmosphere of 5 % CO2 at 37℃.

extract_protocol:
~5-20 × 10^6 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of ILF3 and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using a phenol-chloroform lysate to obtain a purified product.
RNA samples were fragmented into 200-300-nucleotide-long fragments by RNA fragmentation buffer.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.PCR was performed and PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: rip antibody

value: HNRNPA2B1/ILF3, Proteintech)


title: DCC07 (RNA-seq)

status: Public on Nov 30 2021

type: SRA

city: Houston

first: James

middle: Cushing

last: Bayley

state: Texas

address: One Baylor Plaza

department: Neurosurgery

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and in-house pipeline for expression count.
The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of the raw counts data for the entire cohort of 110 primary meningiomas.

molecule: total RNA

organism: Homo sapiens

source_name: meningioma

extract_protocol: FFPE fixed tumor samples were sent, along with whole blood, to Tempus (Tempus Labs | 600 West Chicago Ave, Suite 510 | Chicago, IL 60654) for whole exome RNA-sequencing according to their protocol.

tag: tissue

value: meningioma tumor


title: 18-49 (RNA-seq)


title: ARP1 cells for input RNA [ILF3_In]

city: Nan jing

first: Feng

middle: Jie

last: Jiang

state: Jiangsu

address: Xianlin Avenue 138

department: School of Medicine&Holistic Integrative Medicine

country: China

institute: Nanjing University of Chinese Medicine

tag: cell line

tag: cell type

value: Multiple Myeloma cells


title: 18-45 (RNA-seq)


title: 18-48 (RNA-seq)


title: ARP1_HNRNPA2B11_input

data_processing:
library strategy: m6A-seq
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38

source_name: HNRNPA2B1 kockdown(KD) cells for input RNA

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

tag: genotype

value: knockdown


title: RNA-seq_VC_No UV Round 1_re-analyzed

city: Saint Louis

first: Ryan

last: McCulla

state: Missouri

address: 3501 Laclede Ave

department: Chemistry

institute: Saint Louis University

description:
Control - cells treated with 1%DMSO in VC
Union_for_cluster-round1
fpkm_genename-round1
fpkm_group-round1
fpkm_sample-round1
readcount_genename-round1
readcount-round1
1-SO_NoUVvsVC_NoUV
1-SO_UVvsVC_NoUV_DEG
VC_UVvsVC_NoUV_DEG-round1
Re-analysis of GSM4680432

data_processing:
Data analysis: Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Quantification of gene expression level: HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis: Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method.
Clustering: To identify the correlation between difference, we clustered different samples using expression level FPKM to see the correlation using hierarchical clustering distance method with the function of pheatmap package in R
Genome_build: Homo_sapiens_hg19 (1-SO_NoUV and 1-SO_UV)  and Homo_sapiens_hg38 ( (Sample  1-S_UV and 1-S_NoUV)
Supplementary_files_format_and_content: xls files include FPKM count of each sample and DEG list for each comparison.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cell line was purchased from ATCC (Manassas,VA). The cells were incubated at 37°C in 95% relative humidity with 5% CO2. The cells were cultured in DMEM medium containing 10% FBS, and 1% L-glutamine. The cells were grown to 90% confluency and passaged by removing media, washing the cells with PBS buffer, and splitting the cells.

extract_protocol:
Following treatment protocol, cell media was aspirated and each well was washed with PBS. 350 µL of lysis buffer (included in Gen Elute™ Total RNA Purification Kit) was added. Wells were coated in lysis buffer for 5 minutes and transfered to seperate microcetrifuge tubes. 200 µL absolute ethanol was added and tubes were vortexed for 10 seconds. Columns were assembled with elution tubes and the lysates were applied directly onto seperately assembled columns. Tubes were centrifuged at 3,500 g for 1 minute. If lysate hasn't passed through the column. Centrifuge an additional minute at 14,000 g. Flowthrough was discarded. 400 µL of wash solution A was applied to each column and centrifuged for 1 minute at 3,500 g (or increased to 14,000 g as necessary). Flowthrough was discarded and the column was washed twice more with a 2 minute centrifuge time for the last wash. The columns were placed into fresh elution tubes and 50 µL of elution solution was added to each. The columns were centrifuged at 200 g for 2 minutes, followed by 14,000 g for 1 minute. The elution procedure was repeated to maximize yield. Samples were stored at -80 C until shipping at -20 C.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented by addition of fragmentation buffer. NEB library and strand specific libraries were then chosen. (Novogene Corporation - protocol associated with NEB library and strand specific library) Libraries were constructed using standard Illumina protocol.

treatment_protocol: MDA-MB-231 cells (600,000 cells/1.8mL/well) were plated on a six-well plates. The plates were incubated with compounds (10uM-final concentration) for 24 hours (VC - 1% DMSO). For UV experiment, one plate was placed in a Luzchem photoreactor equipped with 8 LZC-UVA bulbs  (fwhm, 325-375 nm) for 30 minutes and for the No_UV experiment, the plate was covered with an aluminum foil for 30 minutes

tag: passage

tag: agent

value: 1 percent DMSO in VC


title: 1855a_6G_PolyIC_M_6

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

data_processing:
Read Filtering and Trimming: Trimmomatic v0.39 in paired-end mode, phred33 scoring, a 4 bp sliding window, and minimum average, leading, and trailing quality scores of 15, 3, and 3 respectively. Minimum Fragment length was 36 bp.
Read QC Analysis: Performed before filtering and trimming and after filtering and trimming with FastQC v0.11.5
Transcript Quantification: Pseudo-alignment quantification was done with Salmon v0.8.2 with the GENCODE M13 reference genome.
Transcript Conversion: Conversion from ENSEMBL transcript to ENSEMBL gene abundances accomplished with Tximport v1.4.0
Genome_build: GENCODE M13
Supplementary_files_format_and_content: Processed data in quant.sf file format and contain ENSEMBL transcript abundances

organism: Mus musculus

growth_protocol: Adult female and adult male (8-12 weeks old) C57BL/6N mice from Taconic were mated overnight, then separated. Presence of a vaginal semen plug the following morning was used to indicate embryonic day 0.5.

extract_protocol:
RNA was extracted from homogenized placental tissues using phenol/cholorform (Trizol reagent).
Libraries were prepared according to manufacturer instructions with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Pregnant female mice received intraperitoneal injection of 20 mg/kg potassium polyI:C or saline at embryonic day 11.5 and 12.5.

value: placenta

tag: strain

tag: date of isolation

tag: perturbation

value: PolyIC

tag: fetal sex

value: M

tag: hours after injection

tag: fetal age at injection

tag: sequencing batch


title: OC9

city: Changchun

first: Lixin

last: Chen

address: 1266 Fujin Road

institute: Jilin University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens (GRCh38.p13) whole genome using bowtie version 2.3.5 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
generation of normalized abundance using RSEM,Version 1.3.1
Genome_build: hg18
Supplementary_files_format_and_content: processed data file is a xls file contains the gene id,gene name ,normalized abundance and gene description

source_name: ovarian tissue

extract_protocol:
Total RNA was isolated from the OC samples using the NucleoSpin RNAII kit (Macherey-Nagel, Hoerdt, France) and RNA integrity (RNA integrity NC8) was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The RNA-seq library was constructed using the VAHTS mRNA-seqV2 LibraryPrep Kit for Illumina (NR601, Vazyme) according to the manufacturer's instructions.

tag: Stage


title: 18-43 (RNA-seq)


title: 1855a_6H_PolyIC_F_6

value: F


title: OC8


title: 18-50 (RNA-seq)


title: OC7


title: 1855a_6F_Saline_F_6

value: Saline


title: H929_shHNRNPA2B1_input


title: 18-42 (RNA-seq)


title: OC6


title: 1855a_6E_Saline_M_6


title: OC5


title: 18-41 (RNA-seq)


title: OC4


title: LOC2


title: 1855_144H_PolyIC_F_144


title: 1855_144G_PolyIC_M_144


title: LOC1


title: LOC3


title: Wildtype of human multiple myeloma cells for input RNA [C-W-input]

city: Nanjing

first: Rong

middle: Fang

last: Wei

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential acetylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peaks

source_name: Multiple Myeloma cell

extract_protocol:
RNA fragments were incubated with anti-N4-acetylcytidine (ac4C) antibodies immunoprecipitation (IP) buffer for 4h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

value: Human Mutiple Myeloma cell

tag: genotype/variation

value: control/wild type


title: Wildtype of human multiple myeloma cells for ac4C-seq [C-W]

value: anti-N4-acetylcytidine (ac4C) antibody


title: 18-39 (RNA-seq)


title: 18-38 (RNA-seq)


title: 18-40 (RNA-seq)


title: RNA-seq_1-SO_No UV

description:
Sample - cells treated with 10uM of 1-SO
Union_for_cluster-round1
fpkm_genename-round1
fpkm_group-round1
fpkm_sample-round1
readcount_genename-round1
readcount-round1
1-SO_NoUVvsVC_NoUV

value: 10uM of 1-SO


title: Human multiple myeloma cells with NAT10 overexpression for input RNA [C-OE-inpt]

value: NAT10 overexpression


title: 1855_144E_Saline_M_144


title: Human multiple myeloma cells with NAT10 overexpression for ac4C-seq [C-OE]


title: 18-35 (RNA-seq)


title: 1855_144F_Saline_F_144


title: THC/SIV_IV90

city: San Antonio

first: Mahesh

last: Mohan

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

data_processing:
Raw reads were first processed through perl scripts to remove reads containing adapter or -N or with base quality score lower than 20. At the same time, the Q20, Q30 and GC contents of the clean data were calculated. The clean reads were aligned to the genome assembly of Macaca mulatta 10 (https://www.ncbi.nlm.nih.gov/genome/215?genome_assembly_id=468623) using TopHat2, and read numbers mapped to each gene were calculated using the HTSeq program. The fragments per kilobase of transcript sequence per million base pairs of each gene were determined by the length of the gene and read counts mapped to this gene. Differential expression analyses of VEH or THC-treated SIV-infected RMs and control groups were performed using the DESeq of R package. Genes with a P-value <0.05 and |log2 fold change| > 0.585 were defined as differentially expressed.
Genome_build: Macaca_mulatta.Ensembl_release_76
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Macaca mulatta

source_name: Gingiva

extract_protocol:
Total RNA was extracted from gingival tissues at necropsy using the miRNeasy kit (Qiagen Inc).
Transcriptome profiling by RNA-seq and data analysis were performed by Novogene (Sacremento, CA). cDNA library construction and sequencing were performed by Novogene Co. Ltd, Beijing, CA (http://www.novogene.cn/). For library construction, ~3 μg of total RNA from each sample was used to enrich mRNA with the poly-T oligo-attached magnetic beads. The purified mRNA was then randomly cleaved into small fragments using NEBNEXT RNA fragmentation buffer following the manufacturer’s instructions. First-strand cDNA was synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis by nick translation was subsequently performed using E coli DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. The final cDNA library was prepared after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. The cDNA fragments of preferentially 250−300 bp in length were selected using with AMPure XP system (Beckman Coulter, Beverly, U.S.A.) and PCR amplified using Phusion High-Fidelity DNA polymerase (NEB, Beijing, China), Universal PCR primers and Index (X) Primer. PCR products were then purified using AMPure XP system (Beckman Coulter, U.S.A.), and library quality was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, U.S.A.). The clustering of the index-coded samples was performed on a cBot Cluster Generation System, using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired end reads were generated.

treatment_protocol: SIV-infected rhesus macaques were treated with Vehicle or delta-9-tetrahydrocannabinol at 0.32 mg/kg for 6 months post SIV infection.

tag: treatment

value: SIV Infected with THC treatment


title: 1851_3L_PolyIC_F_3


title: THC/SIV_JT80


title: 18-34 (RNA-seq)


title: THC/SIV_JI45


title: VEH/SIV_JD66

value: SIV Infected Vehicle treatment


title: 1851_3K_PolyIC_M_3


title: 1851_3J_Saline_F_3


title: VEH/SIV_KM98


title: 18-33 (RNA-seq)


title: 18-30 (RNA-seq)


title: VEH/SIV_LF29


title: 1851_3I_Saline_M_3


title: VEH/SIV_LB49


title: 18-29 (RNA-seq)


title: 1851_144D_PolyIC_F_144


title: VEH/SIV_LB06


title: 18-28 (RNA-seq)


title: 1851_144C_PolyIC_M_144


title: Uninfected Controls_II28

value: Untreated


title: 1851_144B_Saline_F_144


title: 18-26 (RNA-seq)

value: meningioma tumor


title: VEH/SIV_IN30


title: Uninfected Controls_JT95


title: Uninfected Controls_KK15


title: 1851_144A_Saline_M_144


title: Uninfected Controls_JB61


title: 18-20 (RNA-seq)


title: 18-18 (RNA-seq)


title: 18-17 (RNA-seq)


title: 1845_48C_PolyIC_M_48


title: 1845_48B_Saline_F_48


title: 1845_48D_PolyIC_F_48


title: 18-24 (RNA-seq)


title: 1845_48A_Saline_M_48


title: 1845_3H_PolyIC_F_3


title: 1845_3G_PolyIC_M_3


title: 18-13 (RNA-seq)


title: Uninfected Controls_JB84


title: 1845_3F_Saline_F_3


title: 18-08 (RNA-seq)


title: 1808_6D_PolyIC_F_6


title: 18-05 (RNA-seq)


title: 18-03 (RNA-seq)


title: 18-07 (RNA-seq)


title: 1845_3E_Saline_M_3


title: 18-14 (RNA-seq)


title: 17-34 (RNA-seq)


title: 17-35 (RNA-seq)


title: 1808_6C_PolyIC_M_6


title: 1808_3D_PolyIC_F_3


title: 17-33 (RNA-seq)


title: 17-30 (RNA-seq)


title: 18-15 (RNA-seq)


title: 17-29 (RNA-seq)


title: 1808_6B_Saline_F_6


title: 1808_6A_Saline_M_6


title: 1808_3B_Saline_F_3


title: VEH/SIV_JH47


title: 17-28 (RNA-seq)


title: 1808_3A_Saline_M_3


title: 1808_3C_PolyIC_M_3


title: 17-25 (RNA-seq)


title: Sample t64

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description: low H3.1/H3.2 expression

data_processing:
Base calling using Illumina CASAVA software
DRAGEN RNA Pipeline 3.7.5 (Illumina)
Genome_build: Human GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text file with Ensembl ID and read counts for all the samples

source_name: Brain tumor

extract_protocol:
Total RNA from glioma tissues was extracted using TRI Reagent (Sigma-Aldrich), and the quality was determined using the Qubit RNA IQ Assay Kit in a Qubit 4 Fluorometer (Thermo Fisher) according to the manufacturers’ instructions. Only the RNA samples with integrity values > 6 were used for subsequent DNase treatment with the TURBO DNA-free Kit (Thermo Fisher) and retrotranscription into cDNA with the RevertAid First-Strand cDNA Synthesis Kit (Fermentas, Thermo Fisher).
The starting amount of total RNA was 100 ng following Illumina’s recommendations for preparing the sequencing library using the Illumina Stranded Total RNA Prep with Ri-bo-Zero Plus.

treatment_protocol: No treatment

tag: diagnosis

value: Glioblastoma grade IV

tag: age

tag: gender

value: Male


title: Sample t63

description: low H3.1/H3.2 expression

value: Female


title: 17-24 (RNA-seq)

tag: tissue


title: Sample t59

description: low H3.1/H3.2 expression


title: Sample t57

description: high H3.1/H3.2 expression


title: 17-22 (RNA-seq)


title: Sample t52

description: high H3.1/H3.2 expression


title: 17-20 (RNA-seq)


title: 17-19 (RNA-seq)


title: Sample t44

description: high H3.1/H3.2 expression


title: Sample t41

description: low H3.1/H3.2 expression


title: Sample t34

description: low H3.1/H3.2 expression

value: Oligodendroglioma grade II


title: Sample t37

description: high H3.1/H3.2 expression


title: 17-15 (RNA-seq)


title: 17-12 (RNA-seq)


title: 17-11 (RNA-seq)


title: 17-13 (RNA-seq)


title: Sample t33

description: low H3.1/H3.2 expression


title: 17-10 (RNA-seq)


title: 17-08 (RNA-seq)


title: PC-3 cell line with empty vector [EMPTY_B_S8]

city: Modena

first: Carol

last: Imbriano

address: Via Campi 213/D

department: Life Sciences

country: Italy

institute: University of Modena and Reggio Emilia

data_processing:
alignment on human transcriptome performed with bowtie2. Quantification performed with RSEM
rsem-calculate-expression -p 16 --paired-end --bowtie2 --estimate-rspd --no-bam-output --append-names ${name}_R{1,2}_001.fastq.gz $REF $RESULTS/$onlyname
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing gene or isoforms expression as counts, TPM and FPKM for each sample.

source_name: PC-3 cell line with empty vector

extract_protocol:
RNA for RNAseq was extracted by automatic extractor MaxwellRSC (simply RNA Cells kit, Promega).
RNA-seq libraries were prepared using Illumina TruSeq Stranded TotalRNA  kit , starting from 500ng of total RNA

tag: cell line

value: with empty vector


title: 17-09 (RNA-seq)


title: 3007a_repl_2_patient day 18

city: Bergamo

first: Susanna

last: Tomasoni

state: BG

address: Via Stezzano 87

department: Molecular Medicine

institute: Istituto di Ricerche Farmacologiche Mario Negri IRCCS

description:
run3_absolute_count.txt
run_3_IonXpress_011

data_processing:
reads mapped to hg19_AmpliSeq_Transcriptome_ERCC.fasta
read count obtained by ampliSeqRNA plugin on Torrent Server
Genome_build: hg19_ampliseq_transcriptome_ercc_v1.fasta
Supplementary_files_format_and_content: absolute read count per amplicon per sample per run

source_name: patient iPSC-derived podocytes

extract_protocol:
Total RNA was extracted using the PureLink RNA Micro Scale Kit (Invitrogen), according to the protocol provided by the manufacturer.
Libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (ThermoFisher), according to the protocol provided by the manufacturer.

tag: cell type

value: patient iPSC-derived podocytes

tag: group

value: patient

tag: day

tag: sequencing replicate

tag: run


title: 3007c_repl_1_patient day 18

description:
run1_absolute_count.txt
run_1_IonXpress_012


title: PC-3 cell line over-expressing NF-YAl [LONG_D_S6]

source_name: PC-3 cell line over-expressing NF-YAl

value: over-expressing NF-YAl


title: 17-23 (RNA-seq)


title: PC-3 cell line with empty vector [EMPTY_A_S7]


title: PC-3 cell line over-expressing NF-YAl [LONG_B_S5]


title: 17-03 (RNA-seq)


title: Sample t30

description: low H3.1/H3.2 expression

value: Astrocytoma grade II


title: 17-05 (RNA-seq)


title: 3006c_repl_2_patient day 13

description:
run2_absolute_count.txt
run_2_IonXpress_008


title: 3007c_repl_2_patient day 18

description:
run3_absolute_count.txt
run_3_IonXpress_012


title: 17-04 (RNA-seq)


title: 17-02 (RNA-seq)


title: 17-01 (RNA-seq)


title: 3007a_repl_1_patient day 18

description:
run1_absolute_count.txt
run_1_IonXpress_011


title: PC-3 cell line over-expressing NF-YAs [SHORT_C_S3]

source_name: PC-3 cell line over-expressing NF-YAs

value: over-expressing NF-YAs


title: 3006b_repl_2_patient day 13

description:
run2_absolute_count.txt
run_2_IonXpress_007


title: 16-51 (RNA-seq)


title: PC-3 cell line with empty vector [EMPTY_C_S9]


title: PC-3 cell line over-expressing NF-YAs [SHORT_A_S1]


title: 16-50 (RNA-seq)


title: PC-3 cell line over-expressing NF-YAl [LONG_A_S4]


title: 16-49 (RNA-seq)


title: PC-3 cell line over-expressing NF-YAs [SHORT_B_S2]


title: 3006b_repl_1_patient day 13

description:
run1_absolute_count.txt
run_1_IonXpress_007


title: Ribo_PFB_Lib5_Tyr_rep2

city: Worcester

first: Yue

last: Zhang

state: Massachusetts

address: GeneTherapyCenter, 368 Plantation st

institute: Umass medical school

description: ribosome proteced RNA fragments

data_processing:
Illumina bcl2fastq was used to convert base call (BCL) files into FASTQ files.
3′ adapter sequences were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5). Then 1 nucleotide from the 3' end of each read was trimmed using FASTX-Toolkit Trimmer.
The trimed reads that mapped to noncoding RNA sequences (rRNA, from RefSeq; Mt_rRNA, Mt_tRNA, rRNA, miRNA, scRNA, scaRNA, snoRNA, snRNA, sRNA, vaultRNA from GENCODE v30 were discarded. STAR8 was used for this alignment step with following parameters: --limitBAMsortRAM 20000000000 --outFilterMismatchNmax 1 --outFilterMultimapNmax 100 --alignIntronMax 1 --outWigType wiggle read1_5p.
The remaining reads were mapped to the hg38 human or mm10 mouse genome using annotations from GENCODE (v30) and (v25), respectively. For this step, STAR was used with following parameters to keep only uniquely mapped reads: --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterType BySJout --outFilterMultimapNmax 200 --outSAMmultNmax 1 --outMultimapperOrder Random --outWigType wiggle read1_5p.
Following alignment, reads were assigned to a custom transcriptome annotation  where single transcripts are selected for each protein-coding gene. Further data analysis was performed on the Ribosome-Profiling pipeline of the DolphinNext, available at https://dolphinnext.umassmed.edu/index.php?np=1&id=695.
Genome_build: hg38 human or mm10 mouse
Supplementary_files_format_and_content: csv files containing raw counts and FPKM values for each Sample

source_name: Patient fibroblasts (PFB)

growth_protocol: Patient and control fibroblasts were purchased from Coriell Institute and were maintained in EMEM supplemented with 15% (v/v) fetal bovine serum and antibiotics at 37 °C with 5% CO2.

extract_protocol:
PFB cells and ground  mouse livers powder were lysed on ice in the presence of cycloheximide.  Lysates were clarified by centrifugation. For ribosome profiling, monosomes were generated by RNaseI digest followed by ultracentrifugation and purified by miRNeasy mini kit.
Ribosome proteced RNA fragments ranging from 26-34 nt were gel purified. Upon dephosphorylation of sample RNA, linker was ligated and this product  was followed by reverse transcription and gel purification. Then the RT product was circularized by CircLigase ssDNA ligase followed by rRNA depletion with biotinylated subtraction oligo pool. Libraries were then PCR-amplified, and gel-purified libraries were pooled in equimolar ratios and submitted for sequencing.
Ribosome profiling

treatment_protocol: Patient fibroblasts were infected with lentiviral vectors in the presence of 8 µg/mL polybrene. G418 was added to culture media to a final concentration of 0.1 mg/mL or 0.5 mg/mL as indicated 24 hours prior to harvest. 6-week old MPS1 KI male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

tag: strain

value: Patient fibroblasts cell line

tag: genotype

tag: treat

value: Lentivirus_rAAV9.2xsup-tRNATyr, MOI200


title: 3005b_repl_1_patient day 6

description:
run2_absolute_count.txt
run_2_IonXpress_004

source_name: patient iPSC-derived renal progenitors

value: patient iPSC-derived renal progenitors


title: Ribo_PFB_Lib5_Tyr_rep1

description: ribosome proteced RNA fragments


title: 3005a_repl_2_patient day 6

description:
run3_absolute_count.txt
run_3_IonXpress_003


title: Ribo_PFB_Lib4_EGFP_rep2

description: ribosome proteced RNA fragments

value: Lentivirus_EGFP, MOI200


title: 16-44 (RNA-seq)


title: 16-47 (RNA-seq)


title: 3002b_repl_2_Control day 18

description:
run3_absolute_count.txt
run_3_IonXpress_010

source_name: control iPSC-derived podocytes

value: control iPSC-derived podocytes

value: control


title: Ribo_PFB_Lib3_05G418_rep2

description: ribosome proteced RNA fragments

value: 0.5mg/mL G418, 24 hours


title: 3006c_repl_1_patient day 13

description:
run1_absolute_count.txt
run_1_IonXpress_008


title: 16-35 (RNA-seq)

value: meningioma tumor


title: 3002b_repl_1_Control day 18

description:
run1_absolute_count.txt
run_1_IonXpress_010


title: Ribo_PFB_Lib4_EGFP_rep1

description: ribosome proteced RNA fragments


title: Ribo_PFB_Lib3_05G418_rep1

description: ribosome proteced RNA fragments


title: 3005b_repl_2_patient day 6

description:
run3_absolute_count.txt
run_3_IonXpress_004


title: 16-28 (RNA-seq)


title: 3001c_repl_2_Control day 13

description:
run2_absolute_count.txt
run_2_IonXpress_006


title: 16-14 (RNA-seq)


title: 3002a_repl_1_Control day 18

description:
run1_absolute_count.txt
run_1_IonXpress_009


title: Ribo_PFB_Lib1_NT_rep2

description: ribosome proteced RNA fragments

value: untreat


title: Ribo_PFB_Lib2_01G418_rep2

description: ribosome proteced RNA fragments

value: 0.1mg/mL G418, 24 hours


title: 16-02 (RNA-seq)


title: 16-06 (RNA-seq)


title: 3001c_repl_1_Control day 13

description:
run1_absolute_count.txt
run_1_IonXpress_006


title: Ribo_PFB_Lib2_01G418_rep1

description: ribosome proteced RNA fragments


title: 3001b_repl_1_Control day 13

description:
run1_absolute_count.txt
run_1_IonXpress_005


title: 15-35 (RNA-seq)


title: 3005a_repl_1_patient day 6

description:
run2_absolute_count.txt
run_2_IonXpress_003


title: Ribo_PFB_Lib1_NT_rep1

description: ribosome proteced RNA fragments


title: 15-32 (RNA-seq)


title: 3001b_repl_2_Control day 13

description:
run2_absolute_count.txt
run_2_IonXpress_005


title: 15-25 (RNA-seq)


title: 3000b_repl_2_Control day 6

description:
run3_absolute_count.txt
run_3_IonXpress_002

source_name: control iPSC-derived renal progenitors

value: control iPSC-derived renal progenitors


title: 15-24 (RNA-seq)


title: K562-H3K9me3-G1-K562_singlecells.K562-H3K9me3-G1-K562_singlecells

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Fastq files were demultiplexed, trimmed, mapped (BWA-0.7.16a, ENSEMBL Build 95) using the single-cell multiomics pipeline: https://github.com/BuysDB/SingleCellMultiOmics
Count tables are 50 kb regions genome-wide across individual cells, counted from bam files
Single-cell data are clustered to create pseudobulk bam files
Bam files are tagged using the single-cell multiomics pipeline (https://github.com/BuysDB/SingleCellMultiOmics). Tagged bams include information such as UMI and cell barcode information. Bam tags are explained on the github: https://github.com/BuysDB/SingleCellMultiOmics/blob/master/TAGS.MD
Genome_build: mm10
Supplementary_files_format_and_content: Cells are annotated by total number of cuts in genome, spike-in cuts, cluster name, UMAP location. Bams come from clustering single cells and generating pseudobulk of each cell type. Count tables quantify cuts in 50 kb genome wide across cells.

molecule: genomic DNA

extract_protocol:
K562 cells (ATCC CCL-243) were grown in RPMI 1640 Medium, GlutaMAX supplemented with 5%FCS, Pen-Strep and Non-essential amino acids. After harvesting cells were washed 3 times with room temperature PBS before continuing with the scChIC protocol.
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.  Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).  Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.  Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).

tag: molecule subtype


title: 15-23 (RNA-seq)


title: K562-H3K4me3-G1-K562_singlecells.K562-H3K4me3-G1-K562_singlecells


title: 3000a_repl_2_Control day 6

description:
run3_absolute_count.txt
run_3_IonXpress_001


title: 16-41 (RNA-seq)


title: 3000a_repl_1_Control day 6

description:
run2_absolute_count.txt
run_2_IonXpress_001


title: 3000b_repl_1_Control day 6

description:
run2_absolute_count.txt
run_2_IonXpress_002


title: K562-H3K4me3-37Uor75Umerged-K562_Ncells.K562-H3K4me3-37Uor75Umerged-K562_Ncells


title: K562-H3K27me3-37Uor75Umerged-K562_Ncells.K562-H3K27me3-37Uor75Umerged-K562_Ncells


title: 15-13 (RNA-seq)


title: 3002a_repl_2_Control day 18

description:
run3_absolute_count.txt
run_3_IonXpress_009


title: K562-H3K27me3-G1-K562_singlecells.K562-H3K27me3-G1-K562_singlecells


title: M306

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

description:
Control, Human Only
both rawCounts.xlsx

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence files were trimmed with TrimGalore version 0.6.2 using parameters --trim-n --trim1 --nextseq 20 --fastqc_args
Trimmed sequence reads were aligned with STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the alignment files using HTSeq-Count version 0.11.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.24.0 was used with default setting following their vignete to normalize and calculate differential expression
Genome_build: Gencode GRCh38 p13 Release 32 & Strep agalactiae strain 874391
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: Monocytes

growth_protocol: U937 monocytes (100,000/ml) were infected with Sa in wells of 6-well culture plates at a MOI of 100-200 for 6h prior to RNA extraction. Extensive optimizations were performed to validate these assay conditions to achieve sufficient yield and quality of Sa RNA from infected monocytes.

extract_protocol: Promega SV Total RNA Isolation System kit to extract RNA. Cell pellets (infected monocytes) resuspended in 100µl RNase-free TE Buffer containing 30mg/ml lysozyme. Five replicates were combined to a final volume of 500µl in 2ml tubes containing 50mg acid-washed glass beads. The suspensions were subject to bead-beating (10s), and 50µl (500U) of mutanolysin was added prior to incubation (90min at 37C). Digests were transferred 15ml tubes and lysis buffer was added at a ratio of 175µl per 5x1,000,000 viable monocytes in the initial cell pellet. The mixture was passed through a 20 gauge needle ten times to shear genomic DNA. Twice the volume of dilution buffer (to lysis buffer) was added and the mixture was inverted before aliquoting into four 2ml tubes for incubation (3min at 70C). After centrifuging (10min at 13000 x g, 4C), supernatants were combined into a 15ml tube and cold ethanol was added at a ratio of 200µl per 500µl supernatant. Ten spin columns for RNA isolation. DNA removed using Turbo DNAfree Ambion.

treatment_protocol: Media used was RPMI 1640 supplemented with 1mM sodium pyruvate, 1X non-essential amino acids, 25mM HEPES, 25μM beta-mercaptoethanol and 1% FBS to limit the growth of Sa. Gentamicin (50µg/ml) and penicillin-streptomycin (250 U/ml) were added to the infected cultures at 1h into the 6h incubation period to kill extracellular Sa (killed at efficiency >99.99%), as established in assay optimizations.

tag: sample type

value: Suspension culture

tag: culture

value: Equivalent culture conditions


title: 14-04 (RNA-seq)


title: M296

description:
Control, Human Only
both rawCounts.xlsx


title: M286

description:
Control, Human Only
both rawCounts.xlsx


title: M266

description:
Control, Human Only
both rawCounts.xlsx


title: 20-28 (RNA-seq)


title: 20-50 (RNA-seq)


title: targeted_tRNA-sup_tRNA_treat-3

data_processing:
Library strategy: amplicon NGS
Follow the MGH CCIB DNA Core CRISPR Amplicon Sequencing standard protocol
Paired-end reads (2 x 150 b) can be read from a single FASTQ file in which the entries for the first read (1) and second read (2) from each pair alternate. The first read in each pair comes before the second.
Genome_build: mm10
Supplementary_files_format_and_content: Multiple alignment text files including reads counts for each sample
Supplementary_files_format_and_content: combined reads sequences

source_name: liver

extract_protocol:
Total RNA was extracted using acid Trizol followed by oxidation and β-elimination.
Mature tRNAs were isolated by denaturing 8% TBE-Urea PAGE, and spiked in with two synthetic RNA standards with intact 3’-CCA or or a 3’-CC end. The mature tRNAs were demethylated with rtStar tRF&tiRNA Pretreatment Kit (Arraystar Inc, Cat. No. AS-FS-005) followed by end repair using T4 PNK. ). Demethylated tRNAs were ligated with the I4 3’ adapter using T4 RNA ligase 2, truncated KQ (New England Biolabs, Cat. No. M0373L). 100ng of adapter-ligated tRNAs were incubated with SuperScript™ IV Reverse Transcriptase (Invitrogen, Cat. No. 18090200) at 55˚C for 16 hours.  ).  KAPA HiFi HotStart ReadyMix (Roche, Cat. No. 7958935001) was used to amplify tRNA cDNA and amplicons were subjected to next-generation sequencing at the Massachusetts General Hospital CCIB DNA Core under standard conditions.

treatment_protocol: 6-week old MPS1 KI/KI male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

value: Idua-W401X KI/KI

tag: treatment

value: liver


title: targeted_tRNA-sup_tRNA_treat-2


title: 20-39 (RNA-seq)

source_name: meningioma


title: targeted_tRNA-sup_tRNA_treat-1


title: 20-27 (RNA-seq)


title: targeted_tRNA-No_treat-3


title: 15-18 (RNA-seq)


title: targeted_tRNA-No_treat-2


title: 20-48 (RNA-seq)


title: K562-H3K4me1-G1-K562_singlecells.K562-H3K4me1-G1-K562_singlecells


title: targeted_tRNA-No_treat-1


title: 20-22 (RNA-seq)


title: 20-11 (RNA-seq)


title: 20-26 (RNA-seq)


title: PCR_NGS-Liver-sup_tRNA_treat-3

data_processing:
Follow the MGH CCIB DNA Core CRISPR Amplicon Sequencing standard protocol
Paired-end reads (2 x 150 b) can be read from a single FASTQ file in which the entries for the first read (1) and second read (2) from each pair alternate. The first read in each pair comes before the second.
Genome_build: mm10
Supplementary_files_format_and_content: Multiple alignment text files including reads counts for each sample
Supplementary_files_format_and_content: combined reads sequences
Supplementary_files_format_and_content: alignment and read counts

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini Kit with on-column DNA digestion using the RNase-Free DNase Set.
Oligo d(T)23 VN was used to reverse-transcribe mRNA into cDNA using the High-Capacity cDNA Reverse Transcription kit. KAPA HiFi HotStart ReadyMix was used to amplify a portion of the Idua cDNA spanning the nonsense mutation (W401X in mouse and W402X in human). Amplicons were purified with DNA Clean & Concentrator Kit and subjected to next-generation sequencing by Massachusetts General Hospital CCIB DNA Core under standard conditions.
amplicon NGS

treatment_protocol: 6-week old MPS1 KI/+ male mice were injected with rAA9.2xsup-tRNATyr by IV. 10 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C.

value: Idua-W401X KI/+


title: PCR_NGS-Liver-sup_tRNA_treat-4


title: MA931: Human sigmoid mucosa - Obese/Non hungry gut patient

city: Rochester

first: Maria

middle: Laura

last: Ricardo Silgado

state: Minnesota

address: 222 3rd Ave SW

department: Gastroenterology and Hepatology

institute: Mayo Clinic

data_processing:
Base-calling was performed by 10X Genomics Cellranger Single Cell Software Suite, v3.0.0. FASTQ files, alignment to hg38 reference genome, filtering, barcode counting and UMI counting was generated.
Subsequente analysis was performed by Seurat package (v3.1)
Data from sample was excluded if: Genes that are expressed in fewer than 3 cells, cells express fewer than 200 genes, and >40% mitochondria genes
Cell clustering was performed in R, (v 3.5.2).
Pathway analysis was performed based on Gene Set Enrichment Analysis (GSEA)
Genome_build: hg38

source_name: sigmoid mucosa

extract_protocol:
Sigmoid mucosal biopsies were cryopreserved and FACS isoleted, using a BD FACSAria II cell sorter. A QC analysis was completed using a Vi-Cell XR to evaluate quality and compatibility of cells. Reverse transcription was conducted using Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics).
cDNA was recovered. Pre-amplified cDNA was further subjected to library preparation. Libraries were sequenced on an Illumina Hiseq 4000

value: Sigmoid colon

value: Mucosa


title: 20-18 (RNA-seq)


title: VS982: Human sigmoid mucosa - Obese/Non hungry gut patient


title: PCR_NGS-Liver-sup_tRNA_treat-1


title: JQ507: Human sigmoid mucosa - Obese/hungry gut patient


title: DH663: Human sigmoid mucosa - Obese/Non hungry gut patient


title: M14: mRNA_WT_liver_suptRNA_rep5

data_processing:
3′ adapter sequence were removed using Trimmomatic (with parameters ILLUMINACLIP, minlength, 10; seed mismatches, 2; palindrome clip threshold, 30; simple clip threshold, 5)
Then, reads were mapped to mm10 mouse genome or hg38 human genome using STAR。
To estimate expression levels, RSEM was used to align reads to a predefined set of transcripts from GENCODE. Finally, the RSEM quantification matrix, i.e., estimated counts for each gene and/or for each annotated isoform, was used for differential gene expression analysis. Count matrix was loaded into DEBrowser software for interactive analysis.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Matrix table with raw transcript counts for each sample
Supplementary_files_format_and_content: tab-delimited text files include differential expression analysis for each Sample

source_name: Liver

extract_protocol:
RNA from mouse liver samples was extracted RNA by RNeasy plus mini kit (Qiagen). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc.,).
Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England BioLabs Inc.,). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction).

treatment_protocol: 6-week old C57BL/6 wild type male mice were injected with  rAAV9_mCherry and rAA9.2xsup-tRNATyr by IV. 4 weeks post injection,  mice were transcardially perfused with ice-cold PBS, and tissues were immediately dissected, snap-frozen in liquid nitrogen, and stored under -80 °C. For human fibroblast, Idua +/- (GM00799, Coriell Institute) were treated with lenti-EGFP or lenti-EGFP_sup-tRNATyr.

value: wildtype

value: Liver


title: PCR_NGS-Heart-sup_tRNA_treat-4

source_name: heart


title: PCR_NGS-Liver-No_treat-2


title: NF355: Human sigmoid mucosa - Obese/hungry gut patient


title: PCR_NGS-Heart-sup_tRNA_treat-3


title: M11: mRNA_WT_liver_suptRNA_rep4


title: EK084: Human sigmoid mucosa - Lean patient


title: PCR_NGS-Liver-sup_tRNA_treat-2


title: PCR_NGS-Heart-sup_tRNA_treat-2


title: 15-17 (RNA-seq)

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and in-house pipeline for expression count.
The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: hg38
Supplementary_files_format_and_content: CSV file of the raw counts data for the entire cohort of 110 primary meningiomas.

extract_protocol: FFPE fixed tumor samples were sent, along with whole blood, to Tempus (Tempus Labs | 600 West Chicago Ave, Suite 510 | Chicago, IL 60654) for whole exome RNA-sequencing according to their protocol.


title: M5: mRNA_WT_liver_suptRNA_rep2


title: PCR_NGS-Heart-No_treat-3


title: BMSCs AOT3

city: cleveland

first: Wen-Cheng

last: Xiong

state: OH

address: 2210 circle drive, robbins building E765

institute: Case western reserve university

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)    .
Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value <=0.05.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for each Sample …
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

source_name: BMSCs

extract_protocol:
BMSCs were cultured and collected, then collect AI9+ BMSCs through FACS, and RNA was harvested using Trizol reagent. Using1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard DNBSEQ-G400 protocols

value: BMSCs


title: PCR_NGS-Liver-No_treat-3


title: BMSCs AOT2


title: BMSCs AOT1


title: M10: mRNA_WT_liver_mCherry_rep4


title: PCR_NGS-Heart-sup_tRNA_treat-1


title: PCR_NGS-Heart-No_treat-1


title: M13: mRNA_WT_liver_mCherry_rep5


title: JV576: Human sigmoid mucosa - Lean patient


title: BMSCs OT2


title: SZ687: Human sigmoid mucosa - Lean patient


title: BMSCs OT1


title: copY4

description: Test, copY mutant

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence files were trimmed with TrimGalore version 0.6.2 using parameters --trim-n --trim1 --nextseq 20 --fastqc_args
Trimmed sequence reads were aligned with STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the alignment files using HTSeq-Count version 0.11.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.24.0 was used with default setting following their vignete to normalize and calculate differential expression
Genome_build: GCF_002289205.1_ASM228920v1_genomic
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

organism: Streptococcus agalactiae

source_name: Bacteria

growth_protocol: 1mL overnight THB cultures were back-diluted 1/100 in 100mL of THB (prewarmed at 37°C in 250mL Erlenmeyer flasks) supplemented with 0.25, 0.5, 1.0 or 1.5mM Zn or Cu. Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

extract_protocol:
Total RNA SV kit (Promega) and removal of trace DNA using Turbo DNA-free (Life Technologies).
Library construction consisted of random fragmentation of the poly(A) mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired and A-tailed, and adaptors were ligated for indexing (with up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, Massachusetts) prior to cluster generation. Clusters were generated to yield approximately 725K–825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed.

treatment_protocol: RNA quality was analysed by RNA LabChip using GX Touch (Perkin Elmer). RNase-free DNase-treated RNA that passed Bioanalyzer 2100 (Agilent) analysis was used for RNA sequencing (RNA-seq) using the Illumina NextSeq 500 platform. We used TruSeq library generation kits (Illumina, San Diego, California).

value: copY mutant

value: Pure culture

tag: condition

tag: agent

value: 0.25 mM Zn


title: PCR_NGS-Liver-No_treat-1


title: M1: mRNA_WT_liver_mCherry_rep1


title: PCR_NGS-Heart-No_treat-2


title: M8: mRNA_WT_liver_suptRNA_rep3


title: AJ100: Human sigmoid mucosa - Lean patient


title: copY3

description: Test, copY mutant


title: copY2

description: Test, copY mutant


title: BMSCs OT3

tag: age


title: M2: mRNA_WT_liver_suptRNA_rep1

tag: tissue


title: mid-senescence_leaf [MS]

city: New Delhi

first: Jyothish

last: S

state: Delhi

address: Benito Juarez road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi

description: small RNA profiling

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequencing data was filtered through a pipeline of UEA small RNA workbench 3.0 with default parameters (Stocks et al. 2012). The sequences without 3’ adaptor and those trimmed sequences not lying between the specified sequence lengths were discarded and sequences with the length specified by the user (16-35 nt) were extracted. Further, low complexity sequences (sequences containing less than 3 distinct nucleotides), invalid tags with ‘N’ nucleotides, degradation products and other non-small RNAs were discarded. The fragments of rRNA, tRNA, snRNA or snoRNA were removed after being mapped on plant t/rRNAs sequences from “Rfam” (except miRNA), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95.
For identification of miRNAs and their precursors, the clean putative small RNA reads obtained after filtration through elimination pipeline were aligned to rice reference genome dataset with no mismatch by using miRCat pipeline of UEA sRNA tool kit with set parameters (Stocks et al. 2012).
Genome_build: Rice genome  MSU7.0; http://rice.plantbiology.msu.edu/
Supplementary_files_format_and_content: The .txt files report abundance measurements of small RNA reads

organism: Oryza sativa

source_name: small RNA libraries of flag leaf senescence

growth_protocol: Oryza sativa cv. Pusa Basmati 1 seeds were obtained from National Seed Centre, Indian Agricultural Research Institute (IARI), Delhi, India and were grown in the field during the rice-growing season.

extract_protocol:
Total RNA was isolated using modified guanidinium isothiocyanate (GITC) method (Chomzynski and Sacchi, 1987). Quantity and quality of RNA was assessed using a spectrophotometer (Bio-Rad, USA) followed by checking on MOPS-formaldehyde-agarose gel.
Low molecular weight RNA fraction was extracted from the total RNA by resolving on a TBE-urea-PAGE gel and excising 15-30 nt portion. The Low molecular weight RNA was ligated with 5’ and 3’ RNA adapters using T4 RNA ligase. First strand cDNA was synthesized from the adapter ligated low molecular weight fraction and cDNA library was enriched using adapter-specific primers. The enriched libraries were purified, and the quality of the same was evaluated using Bioanalyzer (Agilent Technologies, USA). High-throughput sequencing of libraries was performed using Illumina GA IIx sequencing platform.

tag: cultivar

value: Pusa Basmati 1

tag: developmental stage

value: grain filling stage

tag: senescence stage

value: mid-senescence

value: flag leaf


title: un-senesced_leaf [US]

description: small RNA profiling

value: panicle development

value: un-senesced


title: late-senescence_leaf [LS]

description: small RNA profiling

value: seed maturation stage

value: late-senescence


title: early senescence_leaf [ES]

description: small RNA profiling

value: early senescence


title: copY1

description: Test, copY mutant

value: Equivalent culture conditions


title: CD45+ immune cells-E2

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Sequencing data was de-multiplexed, trimmed, filtered, aligned, and quantified using the Cell Ranger 3.1.0
Reads were aligned to CSC mm10 transcriptome
Cells that express <200 or >2000 genes and cells that express >5% of mitochondrial genes were removed
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix

source_name: Immune cells

extract_protocol:
Tumors were dissociated and live/CD45+ immune cells were isolated by flow cytometry
Libraries were prepared using chromium single cell 3' library preparation kit (10X Genomics)

tag: cell type

value: Tumor infiltrating CD45+ cells


title: HEK293 UBE3D WT cells 2

city: Boston

first: Huiyun

last: Liu

address: 150 Harrison Avenue, Jaharis building, Room 401A

department: Development, Molecular & Chemical Biology

institute: Tufts university school of medicine

data_processing:
Reads were trimmed using cutadapt v1.8.1
Trimmed reads were aligned to the hg38 annotation of human genome using STAR v2.5.2b
DESeq2 was used to analyze differential gene expression.
The raw read counts were normalized using reads per kilobase of transcript per million mapped reads (RPKM)
The significance of differential expression was estimated for each gene using the Wald test and then corrected for multiple comparisons using the Benjamini and Hochberg procedure (Padj)
Visualization of the generated data was achieved using ggplot2 and EnhancedVolcano.
GO enrichment analyses were performed using Metascape
Downstream of Genes (DoG) transcripts were identified using DoGFinder
Differential expression analysis of normalized read counts in DoG regions was performed using DESeq2, with shrinking of log2 fold changes using ashr
Eulerr was used to generate proportional Venn diagrams for overlap analysis.
Normalized reads maps were visualized using Jbrowse
Genome_build: hg38
Supplementary_files_format_and_content: "KOvsWT.csv" contains differential gene expression analysis in UBE3D KO samples compared to UBE3D WT samples, "KO_UvsKO.csv" contains differential gene expression analysis in UBE3D addback samples compared to UBE3D KO samples, "DoGs_stats_KOvsWT.csv" contains differential expressed DoGs in UBE3D KO samples compared to UBE3D WT samples, "DoGs_stats_KO_UvsKO.csv" contains differential expressed DoGs in UBE3D addback samples compared to UBE3D KO samples,

molecule: polyA RNA

source_name: Human embryonic kidney 293

growth_protocol: The human embryonic kidney HEK293 were cultured in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (10,000 U/mL).

extract_protocol:
Total RNA from HEK293 cells was prepared using TRIzol Reagent
Poly(A) selected RNAs were reversed transcribed to cDNA

treatment_protocol: UBE3D gene was knocked out by CRISPR/Cas9

tag: cell line

value: UBE3D WT

value: Pooled


title: CD45+ immune cells-Placebo

value: Ovariectomy+ Placebo


title: G195B

description:
Control, Bacterial Only
both rawCounts.xlsx

value: Wild-type strain 874391


title: M7: mRNA_WT_liver_mCherry_rep3

value: wildtype

value: Liver


title: HEK293 UBE3D addback cells 3

value: UBE3D addback


title: HEK293 UBE3D WT cells 3


title: NOD.GW_SN_S3_10x_scRNA-seq

city: Los Angeles

first: Maureen

last: Su

state: California

address: 615 Charles E Young Dr S

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #3

data_processing:
Single cell feature counts were generated by aligning sequencing data with the mm10 mouse reference genome (version 2020-A) using 10x Cell Ranger software (5.0.1)
Filtered output matrices and barcodes were analyzed with SEURAT 4.0 on R studio (version 1.2.5033) using the Read10X function to return a unique molecular identified (UMI) count matrix for creation of a Seurat object
Cells with fewer than 200 RNA count, more than 3000 unique genes and more than 12.5% mitochondria gene counts were excluded from the analysis.
Samples were integrated and then raw counts and metadata files were generated as the processed data files.
Cells were then clustered as described.
Genome_build: mm10
Supplementary_files_format_and_content: gw_integrated_counts.csv

source_name: NOD.GW Sciatic Nerves

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
10x Genomics single cell RNA-Seq

treatment_protocol: Fresh sciatic nerves were removed after cardiac perfusion. Nerves were minced with a razor blade and digested in DPBS containing collagenase with 10% FBS. A 20-gauge needle was then used to triturate the nerve fragments to further aid in digestion. The further digested nerves were then filtered through a 40 μm mesh and washed to generate a single-cell suspension for flow cytometry analysis.

value: NOD.GW Sciatic Nerves

value: NOD.AIRE GW/+

tag: cell number

value: 15 weeks

tag: sequencing method

value: 5' sequencing


title: HEK293 UBE3D WT cells 1

tag: genotype


title: G185B

tag: strain

value: Pure culture


title: M4: mRNA_WT_liver_mCherry_rep2


title: C2H4_2_1

city: Lanzhou

first: Weibiao

last: Liao

address: 1 Yinmen Village, Anning District

institute: Gansu Agricultural University

data_processing:
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: 1639
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cucumis sativus

source_name: Explants treated with 0.5 μM ethrel

growth_protocol: The seeds, soaking in distilled water for 5-6 h, with the same size and full grains were chosen and put on a tray with wet filter paper. The seeds in the tray were moved to the incubator with illumination with a 14-h photo period (photo synthetically active radiation was 200 μmol m−2 s−1) at 25 ± 1 °C for 7 d, and the filter paper was kept wet in the tray during this period. The primary roots of explants were carefully cut off after 7 d.

extract_protocol:
After cutting the primary roots, every ten explants with the same size were selected and placed in Petri dishes containing 70 mL of with distilled water or 0.5 μM ethrel, and the solutions were changed every 24 h. At 48 h after treatment, samples (cucumber explants) were collected and stored at −80 °C until being used.Total RNA for RNA-Seq and qRT-PCR analyses was extracted from about 500 mg cucumber explants using Trizol reagent (Sangon, Shanghai, China) according to the manufacturer’s instructions. Total RNA was dissolved in 100 ml of RNase-free water and was quantified using a NanoDrop spectrophotometer (Thermo Scientific). RNA quality was evaluated using the 6000 Pico LabChip of the Agilent 2100 Bioanalyzer (Agilent, Shanghai, China). RNA samples were sent to Novogene Co.Ltd (Beijing, China) for cDNA library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The primary roots of explants were carefully cut off after 7 d.Cucumber explants were placed in Petri dishes with different treatments (distilled water or 0.5 μM ethrel) and allowed to grow for 48 h. The temperature and photoperiod conditions were same as the above conditions.

value: explant

tag: time point

value: 48 h after treatment

value: 0.5 uM ethrel


title: C2H4_3_1


title: G175A

tag: sample type

value: Equivalent culture conditions


title: HEK293 UBE3D KO cells 3

value: UBE3D KO


title: HEK293 UBE3D addback cells 1


title: C2H4_1_1


title: G185A

tag: culture


title: CK2_1

source_name: Explants treated with distilled water

tag: treatment

value: distilled water


title: CK3_1


title: HEK293 UBE3D addback cells 2

value: Pooled


title: BM-DKI-monocytes

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Subread package (PMC3664803) for mapping RNA-Seq reads to the mouse genome of mm10, featureCounts within the Rsubread R package (PMC6486549) for counting the number of reads mapped to genes, RPKM (PMID: 18516045) for gene expression level.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file, columns from left to right represent "EntrzID", "Gene Symbol", and gene expression values (log2(RPKM+1)) for each sample from this study and three samples from GSE137801.

source_name: monocytes isolated from the bone marrow following EAE induction

extract_protocol:
RNA from the purified monocytes and monocyte-derived cells was isolated using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The libraries were quantified using Qubit Fluorometer, and the quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA).

treatment_protocol: Experimental autoimmune encephalomyelitis (EAE) was induced in mice on a C57BL/6J background by subcutaneously injection of myelin oligodendrocyte glycoprotein peptide emulsified in complete Freund’s adjuvant. Pertussis toxin (250 ng) was injected intraperitoneally at 2- and 24-hours following the injection of emulsion.

value: Bone marrow

value: Monocytes

value: EAE-induced by active immunzation with MOG35-55 in CFA and pertussis toxin


title: m_l3

city: Dalian

first: Hailing

last: Cheng

address: 467 Zhongshan Road

institute: The Second Hospital of Dalian Medical University

data_processing:
Illunima Casava 1.8 software used for basecalling.
Clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using STAR and  paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).  STAR used the  method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Genome_build: GRCh38(hg38)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all Samples

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, MA, USA).RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer  (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0  Flurometer (Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer  2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: HCC1954 breast cancer cells were treated with DMSO, Melatonin (mela, 2mM), Lapatinib (lapa, 1uM) and their combination (m_l) for 24 hours

tag: source

value: breast cancer

value: epithelial cell


title: m_l2


title: SCA1+ PDGFRa- Msc [PDGF_F]

city: Cambridge

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were mapped to the GRCm38/mm10 UCSC reference genome using STAR aligner (version 2.5.0a).
Samtools was used to filter unmapped and low-quality reads (-F 1804 and -q 20).
Raw counts were generated using featureCounts from the Rsubread package (version 1.24.2)
RPKMs were generated with raw counts and gene lengths reported by featureCounts package.
TPM values were generated by normalising the RPKM values.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: TPM (csv)

source_name: FACS sorted from liver

extract_protocol:
Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
SmartSeq2 followed by NexteraXT tagmentation (according to protocols published in PMID 24385147)

tag: strain background

value: Adult (12 weeks)

tag: Sex

value: female

value: liver

value: SCA1+ Pdgfra-H2BGFP- CD11b- CD45- CD31- mesenchymal cells


title: HEK293 UBE3D KO cells 1


title: SCA1+ PDGFRa- Msc [PDGF_E]

value: male

tag: tissue


title: dsGFP-3

city: Guiyang

first: Wen-Jing

last: Zhao

state: Guizhou

address: Dongqing Road

department: School of Basic Medical Sciences

institute: Guizhou Medical University

data_processing:
Alignment：  HISAT2  2.1.0，  --dta –t –p 4，  mapping reads to genome
Transcript Assembly:  StringTie  1.3.2d,  -G ref.gtf, sequence assembly
Gene Expression Quantity ：HTSeq  0.6.0 ，-i gene_id -f bam -s no -a 10 -q ，estimating gene expression level
Differential Expression  ：DEGseq  1.18.0，  method="MARS"
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Musca domestica

source_name: 2 instar larvae of housefly

extract_protocol:
The 2nd instar larvae were used for dsRNA injection (n = 3/group). The whole larval body was collected at 24 h post injection, then, immediately frozen in liquid nitrogen, and stored at -80 °C. The total RNA was extracted  using Trizol reagent; 3 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

value: 2 instar

value: RNAi with dsGFP


title: m_l1


title: SCA1+ PDGFRa- Msc [PDGF_A]


title: dsGFP-1


title: lapa3


title: dsMdCht9-3

value: RNAi with dsMdCht9


title: Late Ecodormancy 3rd Rep

city: Montpellier

first: Gautier

last: Sarah

address: Place Pierre Viala

country: France

institute: INRAE

data_processing:
Basecalls performed using CASAVA version ???
Reads were mapped to the apple “Golden Delicious”reference genome GDDH13 v1.1 with bowtie v. 0.12.9
Read counts were obtained using Mir-Island 2.0
Mir-Island read counts were then used for differential expression analysis
Genome_build: Malus x domestica GDDH13 v1.1

organism: Malus domestica

source_name: Malus domestica buds

extract_protocol: Small RNAs were extracted using Lexogen’s TraPR Small RNA Isolation kit (Lexogen).

value: Late Ecodormancy

tag: chilling hours


title: SCA1+ PDGFRa+ Msc [Msc_Pos_F]

tag: developmental stage

value: SCA1+ Pdgfra-H2BGFP+ CD11b- CD45- CD31- mesenchymal cells


title: Late Ecodormancy 2nd Rep


title: dsGFP-2


title: lapa2


title: HEK293 UBE3D KO cells 2

value: UBE3D KO

value: Pooled


title: lapa1


title: SCA1+ PDGFRa+ Msc [Msc_Pos_A]


title: Early Ecodormancy 3rd Rep

value: Early Ecodormancy


title: mela3


title: SCA1- PDGFRa+ Msc [Msc_Neg_F]

value: SCA1- Pdgfra-H2BGFP+ CD11b- CD45- CD31- mesenchymal cells


title: CK1_1

value: explant

value: 48 h after treatment

value: distilled water


title: mela2

value: breast cancer

value: epithelial cell


title: Early Ecodormancy 2nd Rep


title: SCA1- PDGFRa+ Msc [Msc_Neg_E]

value: Adult (12 weeks)

value: liver


title: Early Ecodormancy 1st Rep


title: Late Endodormancy 3rd Rep

value: Late Endodormancy


title: ctrl3


title: Ductal cells (DC) [DC_F]

value: female

value: EpCAM+ CD11b- CD45- CD31- ductal cells


title: dsMdCht9-1

value: whole body

value: 2 instar

value: RNAi with dsMdCht9


title: Late Endodormancy 2nd Rep


title: ctrl2


title: Late Ecodormancy 1st Rep

value: Late Ecodormancy


title: Ductal cells (DC) [DC_E]

value: male


title: Early Endodormancy 3rd Rep

value: Early Endodormancy


title: Ductal cells (DC) [DC_A]


title: Early Endodormancy 2nd Rep


title: ctrl1


title: dsMdCht9-2


title: Early Endodormancy 1st Rep


title: Late Endodormancy 1st Rep


title: sPE_Plasma_exosome_case2

city: Wuhan

first: zhi

middle: rui

last: chen

state: Hubei

address: jianshe street

institute: Huazhong University of Science and Technology

data_processing:
the adaptor sequences were removed using Cutadapt
Sequences with sequence length less than 15 bp or greater than 41 bp were removed by sequence length filtering. The software FastX_Toolkit (version 0.0.13) was used to carry out Q20 quality control on the sequences, and the sequences with Q20 reaching 80% or more were retained.
MiRNAs were identified using the miRDeep2
Raw miRNA counts were anlaysed using the DESeq2 package (version 1.30.0)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
exosomal miRNAs were extracted using mirVana RNA isolation kit (Ambion-1561, Austin, TX, USA)
Libraries were constructed using Illumina TruSeq Small RNA Library Preparation Kits (Cat. No. RS-200-0012, Illumina, USA)

tag: subject status

value: preeclampsia with severe features

value: blood


title: sPE_Plasma_exosome_case3


title: normal_plasma_exosome_con2

value: control


title: OE: Human multiple myeloma cells with NAT10 overexpression for Ribo-seq

city: Nanjing

first: Rong

last: Wei

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

data_processing:
Library strategy: Ribo-seq
Adapter sequences were removed from raw sequencing data using cutadapt1 software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis.
Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to human reference genome and transcriptome (Ensembl GRCh38 Version 91) using hisat23 and bowtie2 software separately
The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz4 package. ORF identification was performed using Price5 software. Read counts were calculated using featureCounts6 software. Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package.
Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq) as previously repored8.
Different   translational efficiencies were estimated using DESeq27 package, genes with fold changes > 2 and FDR < 0.05 were regarded as significant. GO and KEGG analysis were performed using clusterProfiler9 package in R software. Heatmap was drawn using pheatmap package in R software.

source_name: CAG NAT10 OE

extract_protocol:
After the cells are treated with cycloheximide, they are treated with nuclease to degrade the unprotected nuclease and recover the ribosomes
Adapter sequences were removed from raw sequencing data using cutadapt1 software. Meanwhile, reads with length between 25 and 35 bp were kept for downstream analysis. Then reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to human reference genome and transcriptome (Ensembl GRCh38 Version 91) using hisat23 and bowtie2 software separately. The trinucleotide periodicity of ribosomes and codon usage frequency were estimated using revised riboWaltz4 package. ORF identification was performed using Price5 software. Read counts were calculated using featureCounts6 software. Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package. Translational efficiencies were determined as the ratio of (normalized abundance determined by ribosome profiling)/(normalized abundance determined by RNA-seq) as previously repored8. Different   translational efficiencies were estimated using DESeq27 package, genes with fold changes > 2 and FDR < 0.05 were regarded as significant. GO and KEGG analysis were performed using clusterProfiler9 package in R software. Heatmap was drawn using pheatmap package in R software.

tag: cell type

value: Mutiple Myeloma

tag: genotype/variation

value: NAT10 overexpression


title: normal_plasma_exosome_con1


title: sPE_Plasma_exosome_case1


title: S2-RNAPII-ChIA-PET (RNaseA + 400μg/ml)

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description:
Nuclear chromatin
Includes spike-in control (human GM12878 cells).

data_processing:
RChIA-PET raw reads were filtered by linker sequence composition and the PET reads with specific ligation linkers (R1D1 or R2D2 linkers) were kept for downstream mapping and analyses. BatMis (Tennakoon et al., 2012) was used to map the retained PET sequences to human genome build dm3. The mapping results were then filtered based on very stringent criteria: 1) both ends of the PET sequence had to be uniquely mapped (allowing a maximum of two mismatches on each end); 2) PET sequences with both ends mapped to precisely the same locations were merged and considered as one read, i.e., redundant reads were removed. With the mapped PETs, linker barcodes were used to distinguish the tag sequences that originated from the RNA molecules (RNA-tags) from the target chromatin DNA-tags.
ChIRP-Seq bioinformatics analysis was performed as previously described (Quinn, J.J. et al. 2014). Raw fastq data were mapped to dm3 reference genome by BWA mem with default parameters and minimum seed length (-k) set to 18. Duplicate reads were removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Only uniquely mapped reads (mapping score ≥ 20) were kept for further analysis. ChIRP-Seq peaks were identified by using MACS (version 2.0.10) with configuration of --nomodel and --keep-dup set to all.
ATAC-Seq raw reads in fastq format were first aligned to Drosophila dm3 genome assembly with BWA mem. PCR redundancy was removed by using the Picard toolkit (http://broadinstitute.github.io/picard/). Sequences with alignment score ≥ 20 were retained for further analysis. For each ATAC-Seq library, ATAC-Seq peaks were identified by using MACS (version 2.0.10) with default parameters.
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 or hg19 using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/). Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
Genome_build: dm3 and hg19
Supplementary_files_format_and_content: (I) *_coverage.bedgraph files are of reads pileup coverage in bedgraph format.
Supplementary_files_format_and_content: (II) *_peak.bed files are peaks called by MACS2 in bed format.
Supplementary_files_format_and_content: (III) RChIA-PET_Combined_DNA-RNA_PET.txt and pRChIA-PET_Combined_DNA-RNA_PET.txt are tab-delimited bedpe files documenting the genomic coordinates of DNA and RNA of each interaction PET with RNA strand information. "Combined" means these data are the combination of the two replicates of RChIA-PET and pRChIA-PET, respectively.
Supplementary_files_format_and_content: (IV) S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt is a tab-delimited bedpe file documenting the genomic coordinates and frequency of each interaction PET clusters from the combination of two replicated ChIA-PET libraries.
Supplementary_files_format_and_content: (V) S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph is the reads pileup coverage bedgraph file.

organism: Drosophila melanogaster

growth_protocol: S2 was cultured following manufacturer’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 500 bp by sonication. The anti-RNAPII monoclonal antibody 8WG16 (Biolegend, 920102) was used to enrich RNAPII-bound chromatin fragments, respectively.
The DNA fragments in the streptavidin beads-bound chromatin for RChIA-PET or antibody beads-bound chromatin for RNAPII RChIA-PET were end-repaired using T4 polymerase (Promega) in mixture (70 µl 10× T4 polymerase buffer, 7 µl 10mM dNTP, 3.5 µl RI, 612.3 µl Nuclease-free water, with 7.2 µl of T4 polymerase), washed with RChIA-PET Wash Buffer (10 mM Tris.HCl pH 7.0, 10 mM Tris.HCl pH 8.0, 10 mM EDTA, 50 mM NaCl) three times. The RNA fragments were linked to RNA linker for first-strand cDNA synthesis using the Superscript III First Strand Synthesis System (Thermo Fisher Scientific). In more details, 1 µg of biotinylated and barcoded RNA linker R1 (tube 1) and R2 (tube 2) containing a flanking MmeI site were added to two tubes containing cDNA synthesis mixture (20 µl RNA liker, 20 µl dNTP, 80 µl 5× RT buffer, 20 µl 0.1 M DTT, 20 µl RI, 220 µl Nuclease-free water) and incubated at 65 °C for 5 min (Alternative, incubated at 42 °C for 5 min when performing RNAPII RChIA-PET), then placed on ice for at least 1 min, and added 20 µl superScriptIII RT, and incubated for 10 min at 25 °C on Intelli-Mixer (Program F1, 10rpm), followed by 30 min at 50 °C (Alternative, 1 hour at 37 °C when performing RNAPII RChIA-PET). The RNA linker ligated chromatin was washed with Wash Buffer three times, then incubated with 1 µg of DNA linker D1 (tube 1) and D2 (tube 2) respectively in the ligation mixture (15 µl DNA linker, 140 µl 5× T4 DNA ligase buffer with PEG, 3.5 µl RI, 536.5 µl Nuclease free water) by using 5 µl of T4 DNA ligase at 16 °C for overnight. The linker-added DNA fragments were washed with Wash Buffer three times and then phosphorylated with 14 µl of T4 polynucleotide kinase (NEB) in PNK master mix buffers (70 µl 10× T4 DNA ligase buffer, 3.5 µl RI in 612.5 µl Nuclease-free water). The samples from two tubes were washed with Wash Buffer three times and then were mixed and followed by proximity ligation with 34 µl of T4 DNA ligase in reaction buffer (1,000 µl 10× T4 DNA ligase buffer, 50 µl RI, 8,916 µl Nuclease-free water) overnight at 16 °C. After washing with Wash Buffer three times, the chromatin DNA fragments with linkers were subjected to second-strand cDNA synthesis with a Superscript Double-stranded cDNA Synthesis Kit (Thermo Fisher Scientific) and chromatin mixing with second-strand cDNA mixture (333 µl Nuclease-free water, 90 µl 5× second-strand reaction buffer, 9 µl 10 mM dNTP mix, 3 µl E.coli DNA ligase, 12 µl E.coli DNA Polymerase I, 3 µl E.coli RNase H) were incubated at 16 °C for 2 hours; then 6 µl of T4 DNA polymerase were added and continued to be incubated at 16 °C for 5 min. Crosslinks in the DNA/RNA/protein complexes were then reversed by incubation at 65 °C overnight with 0.5% SDS (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific), and the cDNA-DNA fragments were purified by phenol/chloroform isopropanol precipitation. The purified cDNA-DNA was then digested by 1 µl of MmeI (NEB) in buffer (5 µl 10× NE Buffer 4, 5 µl Half linker non-Biotinylated to quench excess MmeI, 5 µl 10× SAM) for 2 hours at 37 °C to release the [cDNA tag]-[RNA linker]-[DNA linker]-[DNA tag] Paired-End-Tag structure. The biotinylated PETs were then immobilized on streptavidin-conjugated magnetic Dynabeads (Thermo Fisher Scientific, 11206D-10ml) in 50 µl of 2× B&W buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 1 M NaCl), and rotated at room temperature for 45 min. The ends of each PET structure were then ligated to a sequencing adaptor by 1 µl of T4 DNA ligase (Thermo Fisher Scientific, EL0013) in Adaptor ligation buffer (4 µl Adaptor A, 4 µl Adaptor B, 5 µl 10× T4 DNA ligase buffer, 36 µl Nuclease-free water) at 16 °C for overnight with rotation. Then the beads were washed three times with 1× B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl). Nick translation was performed by adding 4 µl of E.coli DNA polymerase I solution mixture (38.5 µl Nuclease free water, 10× NEBuffer 2, 2.5 µl 10 mM dNTP) and incubated at room temperature for 2 hours with rotation on the Intelli-Mixer (F8, 30rpm, U = 50, u = 60). Then 10-16 rounds of PCR reactions were performed to amplify the PETs, and the resultant RChIA-PET libraries were subjected for sequencing by MiSeq with paired-end reads of 36 bp.

treatment_protocol: Drosophila S2 cells were permeabilized with DPBS containing 0.015% Triton X-100 for 5 min at room temperature, then treated with or without RNaseA at a series of concentration at 100 μg/ml, 200 μg/ml, 400 μg/ml and 800 μg/ml respectively for 10min, then washing with DPBS.

tag: cell line

tag: spike-in control

value: Human GM12878 cell line

tag: factor

value: RNAPII


title: normal_plasma_exosome_con3


title: WT: Wildtype of human multiple myeloma cells for Ribo-seq

source_name: CAG WT

value: Wildtype


title: SCA1- PDGFRa+ Msc [Msc_Neg_A]

value: Adult (12 weeks)

tag: genotype

value: liver

value: SCA1- Pdgfra-H2BGFP+ CD11b- CD45- CD31- mesenchymal cells


title: SCA1+ PDGFRa+ Msc [Msc_Pos_E]

value: SCA1+ Pdgfra-H2BGFP+ CD11b- CD45- CD31- mesenchymal cells


title: mela1

value: breast cancer

value: epithelial cell


title: S2-RNAPII-ChIA-PET (RNaseA - control)


title: iPSC mutant SF3B1 proerythroblast

status: Public on Nov 29 2021

city: Seattle

first: Courtnee

last: Clough

state: Washington

address: 1959 Pacific St

department: Hematology

institute: University of Washington

data_processing:
RSEM v1.2.4 was used to map all RNA-seq reads to this transcriptome annotation.
Remaining unaligned reads were then mapped a database of all possible junctions between annotated 5' and 3' splice sites of the transcriptome annotation, as well as to the genome sequence, with TopHat v2.0.8b, and the resulting aligned reads were merged with the RSEM output
The expression levels of isoforms annotated in MISO v2.0’s annotation were estimated with MISO v2.0.
To identify events that were differentially spliced, we defined the metric deltaPSI (ΔPSI) as the isoform ratio (absolute percentage of mRNA) in SF3B1-mutant samples - isoform ratio in SF3B1-WT cells, and computed a significance statistic using Wagenmakers’s Bayesian framework  for single-sample comparisons or the Mann-Whitney U test for group comparisons. An event was classified as differentially spliced if it exhibited an absolute change of ΔPSI ≥ 10% and Bayes factor ≥ 5 or p < 0.05.
Genome_build: transcriptome annotation for the hg19/GRCh37 human genome assembly was created by merging gene annotations from Ensembl v71.1, the UCSC knownGene track, and MISO v2.0 isoform annotations.
Supplementary_files_format_and_content: tab delimited text files including splicing analysis for iPS derived cell lines including dPSI and PSI values.

source_name: iPSC line

extract_protocol:
RNA was extracted from 3e5-5e5 cells of each population using the TRIzol reagent.
500 ng of total RNA was used as input to make poly(A)-selected RNA-seq libraries with the TruSeq RNA library prep kit v2 (Illumina).

value: iPSC line

tag: erythroid stage


title: K562 SF3B1 mutant

source_name: K562 cell line

value: K562 cell line


title: iPSC isogenic WT erythroblast


title: K562 isogenic WT


title: iPSC isogenic WT proerythroblast


title: iPSC isogenic WT progenitor


title: B98

city: Harbin

first: Yingwei

last: Xue

address: 150, Haping St, Nangang District

department: Department of Gastrointestinal Oncology

institute: Harbin Medical University Cancer Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: gastric tumor

extract_protocol:
①RNA degradation and contamination was monitored on 1% agarose gels.② RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tumor stage

value: ⅢB

tag: gender

value: female

tag: tissue type

value: gastric tumor


title: B97

value: ⅠB

value: male


title: B96

value: ⅡA


title: B99


title: iPSC mutant SF3B1 progenitor


title: iPSC mutant SF3B1 erythroblast


title: Xindong20 wheat root_CP_rep3

type: RNA

city: Shihezi

first: Xiangchi

last: Zhang

address: Beisi Road, Shihezi, Xinjiang

institute: Shihezi University

description: Gene expression data fromXindong20 root under drought stress for 7 days by CP

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner with 7G upgrade.

data_processing: Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then Expression Console software (version 1.4.1, Affymetrix) offered RMA normalization. Then, a moderated t-test was performed to identify probe sets with differential expression between the different variants.

label: biotin

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The wheat plants were grown in growth cabinets (JNYQ, RXZ-300B-LED, China) with an 18 h day-length at 25°C under photosynthetically active light (250 µmole m-2 s-1) and a night temperature of 20°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The seedlings with each box contained the same capacity of Hoagland nutrient solution, which were divided into conventional phosphorus level (CP: 1.0 mmol /L) and low phosphorus level (LP: 0.05 mmol /L), respectively. KCl was used to replace part of KH2PO4 under low phosphorus condition. The nutrient solution was changed every 3 days. After 14d of culture, the Hoagland nutrient solution (both CP and LP) was configured with 15% (w/v) PEG-6000 to simulate drought stress on wheat seedlings for 7d.

value: wheat seedlings root

tag: variety

tag: stress

value: under drought stress for 7 days by CP


title: NI vs Hpy

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted dual-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and within-array normalized using method LOESS  was applied.

source_name: H.pylori infection, pooled RNA from antral 5 mice

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

extract_protocol: RNA was isolated from snap-frozen antral tissue using RNeasy Mini Kit (Qiagen)

tag: treatment

value: Helicobacter pylori infection for 2 months

value: pooled tissue from stomach antrum from 5 mice

source_name: Non-infected controls, pooled RNA from 5 mice

value: Uninfected controls


title: Xindong23 wheat root_CP_rep1

description: Gene expression data fromXindong23 root under drought stress for 7 days by CP

tag: tissue