title: abm2

city: Guangzhou

first: Mengyan

last: Hu

address: guangzhou,china

institute: SYSU

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 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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values

source_name: brain

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

value: brain

value: primary cultured

value: brain blood vessel endothelial cells

value: WT

value: ABeta40 induced migrasome


title: FO_0h1

status: Public on May 25 2023

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
RSEM (Li and Dewey 2011) was used to align RNA-Seq reads to the human genome and to quantify transcript abundance
EBSeq (Leng, Dawson et al. 2013) was used to compare the aligned reads from multiple conditions to find differentially expressed genes in wild type using a cutoff of FDR <0.05.
Comparisons between Fo and MZ activated samples were carried out DESeq2 (Love, Huber et al. 2014).
Differentially expressed genes were identified using DESeq2
Two filtering steps were followed to define differentially expressed genes in cells with modified NF-kB expression.
First, all differentially changed genes were selected based on an FDR <0.05 after DESeq2 analysis; Second, only those genes were selected that were more than 2-fold up or down-regulated in wild samples after anti-IgM treatment.
All samples were normalized to 1 million aligned reads for visualization.
Marginal zone (MZ), Follicular (FO) splenic B sample sequences were aligned to mouse genome assembly mm10
Assembly: mm10
Supplementary files format and content: .txt are matrix files containing raw counts

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol for 30 minutes

extract_protocol:
Total RNA was isolated using the RNeasy micro Kit (74004, QIAGEN)
RNA libraries were prepared for sequencing by processing 10ng total RNA with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634412, Takara Bio)

treatment_protocol: Two replicates were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0 hours (unstimulated), 1 hour, 4 hours or 18 hours, dead cell removal was performed on 18hr samples

tag: cell type

value: B cell

tag: strain


title: abm1

country: China

tag: tissue

tag: cell line

tag: genotype

tag: treatment


title: INPUT, rep3

first: Alex

last: Bortvin

state: MD

address: 3520 San Martin drive

department: Embryology

institute: Carnegie Institution for Science

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
INPUT_3

data_processing:
For genomic repeats analysis, reads were mapped to mouse mm10 reference genome using STAR v2.6.0c, option --outFilterMultimapNmax 100. The obtained .bam file was used as input for Telescope v1.0.3. The updated counts were collapsed to single repeat subfamilies using a custom Perl script and normalized using EBSeq v1.26.0. Normalized genomic repeat counts for all samples are provided in the table "repName_collapsed_counts_upper_quantile_norm.txt".
For coding genes analysis, reads were mapped to mouse mm10 using STAR v2.6.0c. Counts were normalized using DESeq2 v1.24.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files, including normalized collapsed counts for genomic repeats and DESeq2 output files for coding genes

source_name: Testis

extract_protocol:
Freshly dissected testes were collected in ice-cold PBS and homogenized in Lysis buffer containing 100 mM KCl, 20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 0.3% NP-40, Halt protease and phosphatase inhibitors (Thermo Fisher), RNasin Ribonuclease Inhibitor (Promega) in nuclease-free water. Lysates were clarified by centrifugation, supernatants were recovered and EDTA was added at a final concentration of 10 mM. Extracts (TOTAL) were further fractionated by 10-50% sucrose gradient ultracentrifugation; fractions 5, 6, 7 and 8 were pooled and used as INPUT for either anti-L1 ORF1p co-immunoprecipitations (IP) or incubations with Beads Only (BO). RNA from TOTAL, INPUT, IP and BO samples was purified using TRIzol reagent and treated with TURBO DNase (Invitrogen).
Libraries were generated using the TruSeq Stranded Total RNA kit (Illumina), with Ribo-Zero rRNA depletion.

tag: time

value: 3 months

value: Testis

tag: antibody

value: Mael-/-


title: TOTAL, rep2

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
TOTAL_2


title: hBMECs CRISPR library A Round 3

city: Nanjing

first: Zhe

last: Ma

state: JS

address: Tonwei Road No.1

institute: nanjing agricultural university

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_A_Round_3.sgrna_summa

library_source: genomic

data_processing:
Reads were trimmed with Cutadapt 4.1
MAGeCK was used for data analysis
Supplementary files format and content: The output file was Table S3.XLSX
Library strategy: Amplicon-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: hBMECs

extract_protocol:
Genomic DNA was obtained from the input library and after each of the three rounds of screening with the Blood and Cell Culture DNA Maxi Kit.
The sequenced samples was genereted by PCR with primers containing P7 or P5 adaptor

value: hBMECs

value: Endothelial cells

value: CRISPR muntant library

value: Treated with SzM protein from streptococcus equi ssp. zooepidemicus


title: hBMECs CRISPR library C Round 2

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_C_Round_2.sgrna_summa


title: hBMECs CRISPR library B Round 3

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_B_Round_3.sgrna_summa


title: anti-ORF1p IP, rep2

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
IP_2

value: LINE-1 ORF1p (Abcam, #ab216324)


title: INPUT, rep1

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
INPUT_1


title: hBMECs CRISPR library B Round 2

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_B_Round_2.sgrna_summa


title: pbsm2

value: PBS induced migrasome


title: anti-ORF1p IP, rep1

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
IP_1


title: pbsm1


title: hBMECs CRISPR library A Round 2

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_A_Round_2.sgrna_summa


title: Beads Only, rep3

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
BO_3


title: anti-ORF1p IP, rep3

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
IP_3


title: normal arterial intima 3 (miRNA-seq)

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trim_galore 0.6.6.
The filtered reads were mapped to the hg38 genome using bowtie
The counted and normalized expression of miRNA are based on miRBase database
Assembly: hg38
Supplementary files format and content: txt and xlsx files include quantification of miRNA

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: normal arterial intima

tag: Sex

value: male

tag: age

tag: lesion stage

value: normal


title: Beads Only, rep2

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
BO_2


title: hBMECs CRISPR library B Round 1

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_B_Round_1.sgrna_summa


title: normal arterial intima 1 (miRNA-seq)


title: hBMECs CRISPR library Input

description:
PCR amplicon
Control data


title: AML12 cells, 72h siUhrf2, rep2

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment of reads was performed using Kallisto software, version 0.44.0 using the following parameters: quant -t 8 --bias --bootstrap-samples 10 --seed 42 --single --rf-stranded --fragment-length 150 --sd 70, and reference genome version GRCm38.p6 from GENCODE project with gene model annotation version M23
For differential expression analysis, the edgeR software, version v3.28.0 was used with the following parameters: Normalization  method - TMM (trimmed mean of m-values), data modelling -  glm (generalised linear model), statistical test - QL (quasi likelihood), Benjamini Hochberg (BH) multiple testing correction. Prior to differential expression analysis, data were filtered by estimated counts with the threshold of 20 to avoid inclusion of genes that are expressed at extremely low levels.
Assembly: GRCm38.p6 Release_M23_2019-11-05
Supplementary files format and content: normailzed counts and FPKM

source_name: Liver

extract_protocol:
Total cellular RNA was isolated from AML12 cells using a Total RNA Mini Kit (IBI Scientific, Dubuque, IO; IB47303) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocol.

value: Liver

value: Hepatocyte

value: Uhrf2 knock-down

value: siRNA (Lipofectamine RNAiMAX)


title: AML12 cells, 72h siCtrl, rep3

value: WT (siCtrl)


title: advanced atherosclerotic plaque 3 (miRNA-seq)

value: advanced atherosclerotic plaque

value: V


title: hBMECs CRISPR library C Round 1

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_C_Round_1.sgrna_summa


title: hBMECs CRISPR library A Round 1

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_A_Round_1.sgrna_summa


title: AML12 cells, 72h siUhrf2, rep3


title: AML12 cells, 72h siCtrl, rep2


title: advanced atherosclerotic plaque 2 (miRNA-seq)


title: Mael-/- ribofootprint, rep3

description:
geneCount_ribo_mael_3
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

data_processing:
Ribofootprint reads were preprocessed with FASTX-Toolkit v0.0.14 to clip the linker sequence (ATCGAGATCGGAAGAGCACACGTCTGAACTC) and trim the UMI (5N) from the 3’ end; clipped reads were aligned to mouse ribosomal DNA (Genbank: BK000964.1) using Bowtie v1.2.2 to collect unaligned reads.
Non-rRNA ribofootprint reads and corresponding total RNA reads were mapped to mouse mm10 reference genome using STAR v2.6.0c.
Mapped reads were counted using featureCounts (Subread package v1.6.4); reads were counted on the entire mRNA length for total RNA datasets, or only on CDS for ribofootprint datasets.
Counts were normalized and translation efficiency (TE) was calculated using DESeq2 v1.24.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files, including raw counts for each sample ("counts_rna_ribo_annotated.txt") and DESeq2 output files
Library strategy: Ribo-Seq

extract_protocol:
Freshly dissected testes were collected in ice-cold PBS supplemented with 200 µg/ml cycloheximide and homogenized in Lysis buffer (McGlincy and Ingolia, 2017). Lysates were clarified by centrifugation, supernatants were recovered and the RNA concentration was determined using a Qubit Fluorometer (Thermo Fisher Scientific).
For total RNA libraries, aliquots of testicular extracts containing 2.5 µg of RNA were processed for RNA purification and libraries were generated using the TruSeq Stranded Total RNA kit (Illumina), with Ribo-Zero rRNA depletion. For ribofootprint libraries, aliquots of testicular extracts containing 20 µg of RNA were incubated with 5U MNase (Takara Bio) to generate monosomes. Ribosomes were then processed for footprints purification and libraries generation as described in McGlincy and Ingolia, 2017, with the following modifications: our linker sequence is: /5rApp/NNN NNA TCG AGA TCG GAA GAG CAC ACG TCT GAA CTC/3ddC/ (Santos et al., 2019); footprints were reverse transcribed using the following RT primer: /5Phos/AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG/iSp18/CTG GAG TTC AGA CGT GTG (Santos et al., 2019).

value: Testis

value: Mael-/-


title: Mael-/- ribofootprint, rep2

description:
geneCount_ribo_mael_2
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: E. coli rS1-His, uninfected, R1, non-RNAylated spike-in [LB_R2_no-spike-in]

city: Marburg

first: Katharina

last: Höfer

address: Karl-von-Frisch-Str. 14

country: Germany

institute: Max-Planck-Institute for terrestrial Microbiology

description: total RNA from E. coli cell lysate

data_processing:
NGS data were demultiplexed using bcl2fastq (version 2.20.0, Illumina). Fastq files were assessed using FastQC (version 0.11.9) and Illumina sequencing adapters were trimmed from reads using cutadapt (version 1.18). Reads were aligned to a reference genomes composed of an E. coli K12 (U00096.3), bacteriophage T4 (NC000866.4) and RNAI (self-designed) with hisat2 (version 2.2.1). Primary alignments were selected using samtools (version 1.7) and reads per genomic feature were counted with featureCounts (version 2.0.1 from Subread package). The resulting counts table was subjected to further analysis and data visualisation in R (version 4.1.2). Read counts were normalized to the overall amount of mapped reads per sample and to the respective read counts for the RNAI spike-in.
Data visualisation was performed in R and alignments were manually inspected in Integrative Genomics Viewer (IGV, version 2.4.9).
Assembly: reference genomes composed of an E. coli K12 (U00096.3), bacteriophage T4 (NC000866.4) and RNAI (self-designed)
Supplementary files format and content: raw count data for all samples

organism: Escherichia coli B

source_name: Escherichia coli strain B with endogenously His-tagged rS1

growth_protocol: 100 ml cultures of E. coli B strain with endogenously His-tagged rS1 in LB supplied with 1 mM CaCl2, 1 mM MgCl2 and 30 µg/ml Kanamycin were grown at 37 °C in 250 ml baffled Erlenmeyer flasks to an OD600 ~ 0.8.

extract_protocol:
Pellets from 100 ml culture infected with either T4 phage WT, T4 phage ModB R73A,G74A (R73A) or the uninfected control (LB) were resuspended in 2 ml Ni-NTA wash buffer (10 mM imidazole, 50 mM Tris-HCl pH 7.5, 1 M NaCl, 1 M urea, 5 mM MgSO4, 5 mM β-mercaptoethanol, 5 % glycerol, pH 8.0, EDTA-free protease inhibitor) on ice and lysed by sonication (6 min, 50 % amplitude, 0.5 s pulse). The lysate was cleared from cell debris by centrifugation at 21,000 x g, 4 °C, 30 min. 1.9 ml supernatant, 50 µl Ni-NTA agarose beads (Jena Bioscience, equilibrated in Ni-NTA wash buffer), 80 U murine RNase inhibitor and 4.72 µg of rS1 D2 RNAylated with NAD-capped RNAI were combined and incubated at 4 °C in a Rotary Mixer for 30 min. Entire samples were transferred to Mobicol mini spin columns. Beads were washed four times with 200 µl Ni-NTA wash buffer and subsequently eight times with 200 µl Strep wash buffer (50 mM Tris-HCl pH 7.5, 8 M urea). Beads were equilibrated in standard ligation buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.4) and blocked with BSA prior to 3’-RNA-adapter ligation at 4 °C overnight in the presence of standard ligation buffer, 50 mM β-mercaptoethanol, 0.05 µg/µl BSA, 15 % (v/v) DMSO, 5 µM adenylated RNA-3’-adapter, 0.5 U/µl T4 RNL1 (NEB) and 10 U/µl T4 RNL2, tr. K227Q (NEB). Protein was rebound by addition of NaCl to 1.5 M and incubation at 20 °C, 400 rpm for 20 min. Beads were subsequently washed six times with strep wash buffer and equilibrated in first strand buffer (50 mM Tris-HCl pH 8.3, 3 mM MgCl2, 75 mM KCl) and blocked with BSA. Reverse transcription of protein-bound RNA was performed in a 30 µl scale for 1 h at 40 °C using 10 U/µl Superscript IV Reverse Transcriptase (Invitrogen) in the presence of 5 µM RT primer, first strand buffer, 25 mM β-mercaptoethanol, 0.05 µg/µl BSA and 0.5 mM dNTPs. After incubation, NaCl was added to 1.5 M and incubated at 20 °C, 400 rpm for 1 h in order to rebind RNA-cDNA hybrids. Beads were subsequently washed five times with 0.25 x strep wash buffer (2 M urea, 50 mM Tris-HCl pH 7.5) and equilibrated in aExoI buffer (10 mM Tris-HCl pH 7.9, 5 mM β-mercaptoethanol, 10 mM MgCl2, 50 mM NaCl) and blocked with BSA. Residual RT primer was removed by ExoI digest with 1 U/µl E. coli ExoI (NEB) in ExoI buffer at 37 °C for at least 30 min. Beads were finally washed with 200 µl 0.25 x strep wash buffer five times and 200 µl immobilization buffer (10 mM Na-HEPES pH 7.2, 1 M NaCl) three times. cDNA was eluted by incubation of beads in 100 µl 150 mM NaOH at 55 °C for 25 min and by washing with 100 µl MQ water. Eluate pH was neutralized by addition of 0.05 volumes 3 M NaOAc pH 5.5. cDNA was removed from residual protein by phenol-chloroform extraction and precipitated with 2.5 volumes ethanol in the presence of 0.3 M NaOAc pH 5.5 overnight. Precipitated cDNA was C-tailed using 1 U/µl TdT (Thermo Fisher) in the presence of 1.25 mM CTP and 1 x TdT buffer at 37 °C for 30 min and subsequently inactivated at 70 °C for 10 min. 5 µM cDNA anchor (hybridization of fwd and rev anchor) were ligated to C-tailed cDNA in standard ligation buffer in the presence of 10 µM ATP and 1.5 U/µl T4 DNA Ligase (Thermo Fisher Scienttific) at 4 °C overnight. Ligation reactions were inactivated at 70 °C for 10 min and cDNA was ethanol-precipitated.
For the preparation of the Illumina RNAylome Seq library, cDNA was amplified by PCR using 2 U Phusion Polymerase (Thermo Fisher Scientific) in the presence of 5 % (v/v) DMSO, 200 µM dNTPs and 2500 nM NEBNext Universal and Index Primer each (Primer Set 1, NEB). PCR products were purified by native PAGE purification and ethanol-precipitated. dsDNA concentration was determined via Quantus fluorometer (Promega) and library size was determined with the Bioanalyzer (Agilent). Equimolar amounts of each library were sequenced on a MiniSeq system (Illumina) using the MiniSeq High-Output Kit (150 cycles, Illumina) generating 20 million 151 bp single-end reads.

treatment_protocol: T4 phage WT or T4 phage ModB R73A,G74A were added to an MOI of 5.0. For the uninfected negative control, same volumes of LB medium were added to the cultures. Cultures were then incubated at 37 °C for 8 min and E. coli harvested in by centrifugation at 3,000 x g for 13 min.

tag: medium

value: LB

tag: growth stage

value: exponential

value: uninfected, LB added

tag: spike-in

value: rS1-His not RNAylated with RNAI

tag: phage moi

value: no phage added

tag: bacterial strain

value: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (DSM 613, ATCC 11303) modified with endogenously His-tagged rS1


title: Mael-/- ribofootprint, rep1

description:
geneCount_ribo_mael_1
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: Cervix__HPV18_rep2

type: RNA

first: Xu

last: Xin

address: Jingxi road

institute: southen medical university

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 8

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: All samples were  treated following RNAiso Plus (Ruizhen Biotechnology Company, Guangzhou ) manufacturer's recommendations.

treatment_protocol: the cervix tissues were rapidly and carefully frozen in liquid nitrogen

value: female

value: Cervix

tag: hpv status


title: Cervix__HPV18_rep1

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 7


title: advanced atherosclerotic plaque 1 (miRNA-seq)

value: male


title: normal arterial intima 2 (miRNA-seq)

value: normal arterial intima

value: normal


title: Cervix__HPV negative_rep3

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 3

source_name: Cervix__HPV negative_rep3

value: negative


title: Beads Only, rep1

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_BO_comb_DESeq2.txt
BO_1

value: 3 months


title: Cervix__HPV16_rep3

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 6


title: AML12 cells, 72h siUhrf2, rep1

value: Liver

tag: cell type

value: Hepatocyte

value: Uhrf2 knock-down

value: siRNA (Lipofectamine RNAiMAX)


title: Cervix__HPV18_rep3

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 9


title: Cervix__HPV16_rep2

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 5


title: AML12 cells, 72h siCtrl, rep1

value: WT (siCtrl)


title: E. coli rS1-His, uninfected, R1, non-RNAylated spike-in [LB_R1_no-spike-in]

description: total RNA from E. coli cell lysate

tag: strain

value: Escherichia coli strain B with endogenously His-tagged rS1

value: LB

value: exponential


title: normal arterial intima 3 (RNA-seq)

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trim_galore 0.6.6.
The filtered reads were mapped to the hg38 genome using STAR.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by featureCounts.
Assembly: hg38
Supplementary files format and content: txt,csv and xlsx files include quantification of mRNA,lncRNA and circRNA

tag: tissue


title: E. coli rS1-His, uninfected, R3 [LB_R3]

description: total RNA from E. coli cell lysate

value: uninfected, LB added

value: rS1-His RNAylated with RNAI

value: no phage added


title: Mael+/- ribofootprint, rep2

description:
geneCount_ribo_het_2
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

value: Testis

value: Mael+/-


title: normal arterial intima 2 (RNA-seq)

value: normal arterial intima

value: male


title: normal arterial intima 1 (RNA-seq)

value: normal


title: E. coli rS1-His, uninfected, R2 [LB_R2]

description: total RNA from E. coli cell lysate

value: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (DSM 613, ATCC 11303) modified with endogenously His-tagged rS1


title: E. coli rS1-His, uninfected, R1 [LB_R1]

description: total RNA from E. coli cell lysate


title: Mael+/- ribofootprint, rep1

description:
geneCount_ribo_het_1
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: Mael-/- RNA, rep2

description:
geneCount_mrna_mael_2
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

data_processing:
Ribofootprint reads were preprocessed with FASTX-Toolkit v0.0.14 to clip the linker sequence (ATCGAGATCGGAAGAGCACACGTCTGAACTC) and trim the UMI (5N) from the 3’ end; clipped reads were aligned to mouse ribosomal DNA (Genbank: BK000964.1) using Bowtie v1.2.2 to collect unaligned reads.
Non-rRNA ribofootprint reads and corresponding total RNA reads were mapped to mouse mm10 reference genome using STAR v2.6.0c.
Mapped reads were counted using featureCounts (Subread package v1.6.4); reads were counted on the entire mRNA length for total RNA datasets, or only on CDS for ribofootprint datasets.
Counts were normalized and translation efficiency (TE) was calculated using DESeq2 v1.24.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files, including raw counts for each sample ("counts_rna_ribo_annotated.txt") and DESeq2 output files

value: Mael-/-


title: Mael-/- RNA, rep3

description:
geneCount_mrna_mael_3
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: E. coli rS1-His, T4 ModB R73A,G74A infected, R2 [MUT_R2]

description: total RNA from E. coli cell lysate

source_name: Escherichia coli strain B with endogenously His-tagged rS1, Bacteriophage T4 ModB R73A,G74A

value: infected with T4 phage ModB R73A,G74A

tag: bacteriophage

value: Escherichia phage T4 mutant with inactive ModB R73A,G74A


title: E. coli rS1-His, T4 ModB R73A,G74A infected, R3 [MUT_R3]

description: total RNA from E. coli cell lysate

value: Escherichia coli strain B with endogenously His-tagged rS1, Bacteriophage T4 ModB R73A,G74A


title: advanced atherosclerotic plaque 2 (RNA-seq)

value: advanced atherosclerotic plaque

value: V


title: advanced atherosclerotic plaque 1 (RNA-seq)


title: E. coli rS1-His, T4 ModB R73A,G74A infected, R1 [MUT_R1]

description: total RNA from E. coli cell lysate

value: LB


title: Mael+/- RNA, rep3

description:
geneCount_mrna_het_3
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

tag: genotype


title: Mael+/- ribofootprint, rep3

description:
geneCount_ribo_het_3
counts_rna_ribo_annotated.txt
ribo_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: E. coli rS1-His, T4 WT infected, R3 [WT_R3]

description: total RNA from E. coli cell lysate

source_name: Escherichia coli strain B with endogenously His-tagged rS1, Bacteriophage T4 WT

value: exponential

tag: treatment

value: infected with T4 phage WT

value: Escherichia phage T4 (DSMZ, Braunschweig, Germany, DSM 4505)


title: Cervix__HPV negative_rep1

description:
lncRNAs and mRNAs  expression  in cervical tissue
SAMPLE 1

source_name: Cervix__HPV negative_rep1

value: female

value: Cervix

value: negative


title: Mael+/- RNA, rep2

description:
geneCount_mrna_het_2
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

tag: time

value: Testis

value: Mael+/-


title: Cervix__HPV16_rep1

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 4


title: Dam-Dpn, larval NSCs, rep2

status: Public on May 24 2023

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

data_processing:
All FASTQ files were processed with damidseq_pipeline v1.5.3, using default options and aligned to DmR6.
Peak calls were made using find_peaks v1.0.3, default options.
Assembly: DmR6
Supplementary files format and content: Score column in bedgraph files represents scaled, normalised log2 enrichment of Dam-fusion over control.
Supplementary files format and content: peaks.gff
Library strategy: DamID-seq

organism: Drosophila melanogaster

source_name: 3rd instar larval brains

extract_protocol:
Following sample collection, genomic DNA was extracted, cut with DpnI and cut fragments isolated. DamID adaptors were ligated to the isolated DNA, fragments were digested with DpnII, and amplified via PCR before next-generation sequencing library preparation.
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina TruSeq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).

value: 3rd instar larval brains

tag: gal4 driver

value: neuroblasts (neural stem cells, NSCs)


title: advanced atherosclerotic plaque 3 (RNA-seq)

tag: Sex

value: male


title: E. coli rS1-His, T4 WT infected, R1 [WT_R1]

description: total RNA from E. coli cell lysate

value: Escherichia coli strain B with endogenously His-tagged rS1, Bacteriophage T4 WT

value: rS1-His RNAylated with RNAI

value: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (DSM 613, ATCC 11303) modified with endogenously His-tagged rS1


title: Dam-only control, larval NSCs, rep2


title: Dam-only control, larval NSCs, rep1


title: Mael-/- RNA, rep1

description:
geneCount_mrna_mael_1
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt

value: Mael-/-


title: HG00362

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

library_source: transcriptomic single cell

data_processing:
A pipeline optimized for simultaneously measuring viral and human transcripts with scRNA-seq  was modified for the analysis of EBV and HHV-6
Cell Ranger (10X Genomics) demultiplexed reads and aligned sequences to a custom reference containing the genomes of human GRCh38, EBV B95-8 (GenBank accession number NC_007605.1), and either HHV-6A U1102 (GenBank accession number NC_001664.4) or HHV-6B Z29 (GenBank accession number NC_000898.1)
Supplementary files format and content: Filtered feature barcode matrix h5

molecule: polyA RNA

organism:
Homo sapiens
human gammaherpesvirus 4
Human betaherpesvirus 6B

growth_protocol: The EBV-immortalized cell lines HG00362 and HG01277 (Coriell Institute for Medical Research, Camden, NJ), which contain iciHHV-6B and iciHHV-6A, respectively, were cultured in standard conditions for LCLs

extract_protocol:
Gel bead in EMulsion microfluidic technology
Chromium Single Cell Library & Gel Bead Kit v3

tag: cell line

value: lymphoblastoid


title: Dam-Dpn, larval NSCs, rep1


title: HG01277

organism:
Homo sapiens
human gammaherpesvirus 4
Human betaherpesvirus 6A


title: Mael+/- RNA, rep1

description:
geneCount_mrna_het_1
counts_rna_ribo_annotated.txt
rna_mael_vs_het_DESeq2.txt
TE_mael_vs_het_DESeq2.txt


title: E. coli rS1-His, T4 WT infected, R2 [WT_R2]

description: total RNA from E. coli cell lysate

value: LB


title: set1Dmst2D_minusTet_rep3

city: Waltham

first: Ajay

last: Larkin

state: MA

address: 415 South St

department: MCB

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, then aligned and quantified by STAR
downstream diff. expression quantification was performed with USEQ DRDS
Assembly: ASM294v2.29
Supplementary files format and content: Excel xlsx files contain raw transcript count matricies

organism: Schizosaccharomyces pombe

source_name: cultures

growth_protocol: YEA, grown to log phase at 32C

extract_protocol:
Hot phenol extraction followed by DNAse I treatment and Qiagen RNeasy Column Cleanup
RNAseq libraries were prepared by Novogene Corporation Inc.

treatment_protocol: +Tet cultures were supplemented with tetracycline

value: cultures


title: swi6Dset1Dmst2D_plusTet_rep2

value: +Tet


title: set1Dmst2D_minusTet_rep1


title: set1Dmst2D_minusTet_rep2


title: swi6Dset1Dmst2D_plusTet_rep3


title: set1Dmst2D_plusTet_rep1


title: swi6Dset1Dmst2D_plusTet_rep1


title: swi6Dmst2D_minusTet_rep1


title: swi6Dset1Dmst2D_minusTet_rep4


title: swi6Dmst2D_minusTet_rep3


title: no template control_1

city: New Haven

first: Thazin

middle: N

last: Aung

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

library_source: other

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx®-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses

molecule: other

organism: unidentified

source_name: control

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx®-DSP protocol (MAN-10150-01).Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5/666 nm, excitation 645/19 nm, emission 683/30 nm), CD45 for lymphocyte compartment (Texas Red/615 nm, excitation 588/19 nm, emission 623/30 nm), S100B (Cy3/568 nm, excitation 538/19 nm, emission 564/15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx®-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx®-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: control

tag: roilabel

value: no template control


title: swi6Dmst2D_minusTet_rep2


title: no template control_2


title: swi6Dset1Dmst2D_minusTet_rep2


title: swi6Dset1Dmst2D_minusTet_rep3


title: swi6Dset1Dmst2D_minusTet_rep1


title: swi6Dset1D_minusTet_rep3


title: swi6Dset1D_minusTet_rep2


title: swi6Dset1D_minusTet_rep1


title: swi6D_minusTet_rep3


title: set1Dmst2D_plusTet_rep3


title: swi6D_minusTet_rep2


title: set1Dmst2D_plusTet_rep2


title: Cervix__HPV negative_rep2

description:
lncRNAs and mRNAs  expression  in cervical cancer
SAMPLE 2

source_name: Cervix__HPV negative_rep2

value: female

value: Cervix


title: swi6D_minusTet_rep1


title: clr4D_minusTet_rep4


title: clr4D_minusTet_rep1


title: HUVEC_NAIVE_1

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

data_processing:
Sequencing reads were aligned using Tophat
Htseq count was used for reads-counting
Deseq2 was used for differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: normalised gene counts using Deseq2

growth_protocol: HD HUVECs were grown to confluency, serum-starved for 16 hrs and stimulated for 6 hrs using purified total IgG (1mg/ml) in combination with human native β2GPI (20 μg/ml) (Fitzgerald 30-AB23). HD HUVECs cultured in EBM, without growth factors and serum, were used as negative controls.

extract_protocol:
RNA extraction was performed by standard trizol based method
Libraries for RNA-seq were constructed using the Truseq RNA-seq protocol (illumina)

treatment_protocol: HUVECs were treated with total IgG derived from APS patients plus β2GPI for 6 hrs

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: none (naïve)


title: WT_minusTet_rep4

value: WT


title: clr4D_minusTet_rep2


title: WT_minusTet_rep1


title: HUVEC_TREATED_1

value: total IgG derived from APS patients plus β2GPI for 6 hrs


title: WT_minusTet_rep2


title: HUVEC_TREATED_2


title: miRNA 128 WT, 26HPF, HWT2

first: Stefania

last: Nicoli

address: 300 George st

department: Genetics/Internal Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDUK
Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR
Read count extraction was performed using HTSEQ
Differential gene expression was performed using Deseq2
Assembly: GRCz10 /GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Danio rerio

source_name: head

extract_protocol:
RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and ~10ng were used to prepare libraries.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3′ mRNA-Seq kit following manufacturer's protocols.

value: endothelial cells

value: head


title: miRNA 128 WT, 26HPF, HWT1


title: clr4D_minusTet_rep3


title: HUVEC_NAIVE_2


title: swi6D_minusTet_rep4


title: gRNA_csnk1, 26HPF, scRNAseq

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software Version 5.0.0
Downstream analysis were performed on R studio using Seurat
Assembly: Lawson Annotation V4.3.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: trunk tissue containing the AGM

extract_protocol:
Wild-type, miR-128Δ/Δ, csnk1a1 and jag1b g3’UTR mutants Tg(kdrl:GFP) zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues  were dissociated into single cell suspensions and subjected to FACS. GFP+ cells, which had 85% cell viability, were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10,000 cells per sample
10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 (CG000204) was used to generate libraires according to manufacturer intructions

value: Endothelial Cells

value: trunk tissue containing the AGM

value: Tg(kdrl:GFP) zn1

tag: age


title: miRNA 128 mutant, 26HPF, HMT2

value: miRNA 128 mutant


title: MT, 26HPF, scRNAseq

description: 10x Genomics


title: gRNA_jag1, 26HPF, scRNAseq

description: 10x Genomics


title: WT, 26HPF, scRNAseq

description: 10x Genomics


title: miRNA 128 WT, 26HPF, WT2

source_name: trunk

value: trunk


title: miRNA 128 mutant, 26HPF, HMT3


title: miRNA 128 mutant, 26HPF, HMT4


title: miRNA 128 mutant, 26HPF, HMT1


title: miRNA 128 mutant, 26HPF, MT4


title: WT_minusTet_rep3

value: cultures


title: miRNA 128 WT, 26HPF, WT1


title: miRNA 128 mutant, 26HPF, MT3


title: BXPC-3_48h_Glc- [T1]

city: WuHan

first: ZHUO

last: WENFENG

address: 湖北省武汉市硚口区航空路13号

institute: The Huazhong University of Science and Technology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: BXPC-3 cells_48h_Glc-

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Microarray analysis for lncRNAs was conducted with BxPC-3 cells cultured with saturating nutrient medium, Glc- medium and Gln- medium for 48 h.

tag: treatment/timt point

value: after 48hr in BXPC-3 cultured in Glc- medium

tag: molecule subtype

value: Long non-coding RNA


title: miRNA 128 WT, 26HPF, WT3


title: BXPC-3_48h_Gln- [T2]

address: 湖北省武汉市硚口区航空路13号

source_name: BXPC-3 cells_48h_Gln-

value: after 48hr in BXPC-3 cultured in Gln- medium


title: miRNA 128 mutant, 26HPF, MT1


title: miRNA 128 mutant, 26HPF, MT2


title: NDV-infetion HD11 cells rep2

city: Changchun

first: li

middle: jin

last: dou

state: China

address: Changchun, 130062, China

department: College of Veterinary Medicine

institute: Jilin University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (GCF_000002315.6_GRCg6a )  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: The EXCELL table includes  the coordinates of the differentially methylated RNA sites in bed format, the length of the methylated RNA sites，the transcript id and gene symbol of differentially methylated RNA，the comparison information calculated by diffreps，and the annotation of the differentially methylated gene for each sample.
Supplementary files format and content: The EXCELL table includes the FPKM value,  fold change , p_value, FDR for each sample.

organism: Gallus gallus

source_name: HD11 cells

growth_protocol: Chicken-origin macrophage HD11, a permanent chicken bone marrow macrophages cell line was stored in our laboratory and cultured in Dulbecco’s modified essential medium (DMEM) (Solarbio, Beijing, China) containing 10% fetal bovine serum (FBS) (Biological Industries, CT, USA) at 37℃ with 5% CO2.

extract_protocol:
Total RNA from HD11 cells was extracted at 24 hpi using TRIzol reagent (Invitrogen Corporation, CA, USA) according to the manufacturer’s instruction. RNA concentration and quality of each sample were determined to measure the OD260/OD230 value and OD260/OD280 value by NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity and gnomic DNA contamination were tested by denatured agarose gel electrophoresis.
MeRIP‑Seq service was performed by Cloudseq Biotech Inc (Shanghai, China). Briefly, RNA from each sample was separately chemically fragmented into fragments with a length of approximately 100 nucleotides using fragmentation buffer (Illumina Inc.). Immunoprecipitation of fragmented RNA was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) according to the the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A immunoprecipitation samples were used for RNA-seq library construction with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) following the manufacturer’s instruction. The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was subjected to 150 bp paired-end sequencing on an Illumina NovaSeq 6000 instrument.

value: HD11 cells

value: Macrophages

value: NDV infection


title: NDV-infetion HD11 cells rep3


title: Control HD11 cells rep3

value: control


title: NDV-infetion HD11 cells rep1


title: Control HD11 cells rep2


title: BXPC-3_48h_saturating nutrient

address: 湖北省武汉市硚口区航空路13号

source_name: BXPC-3 cells_48h_saturating nutrient

value: after 48hr in BXPC-3 cultured in saturating nutrient medium


title: 14B_M_2099

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 14B_M_2104


title: 14B_M_2101


title: 14B_M_2106


title: 14B_M_2096


title: 14B_M_2102


title: 14B_M_2092


title: 14B_M_2105


title: 14B_M_2094


title: 14B_M_2097


title: 14B_M_2093


title: 14B_M_2107


title: 14B_M_2108


title: 14B_M_2100


title: 14B_M_2103


title: 14B_M_2095


title: 14B_M_2098


title: Control HD11 cells rep1


title: 14B_M_2091


title: 14B_M_2090


title: 14B_M_2089


title: 14B_M_2088


title: 14B_M_2086


title: 14B_M_2087


title: 14B_M_2085


title: 14B_M_2084


title: 14B_M_2080


title: 14B_M_2082


title: 14B_M_2083


title: 14B_M_2078


title: 14B_M_2079


title: 14B_M_2069


title: 14B_M_2067


title: 14B_M_2074


title: 14B_M_2072


title: 14B_M_2073


title: 14B_M_2070


title: 14B_M_2061


title: 14B_M_2068


title: 14B_M_2075


title: 14B_M_2063


title: 14B_M_2077


title: 14B_M_2062


title: 14B_M_2076


title: 14B_M_2064


title: 14B_M_2081


title: 14B_M_2059


title: 14B_M_2060


title: 14B_M_2057


title: 14B_M_2058


title: 14B_M_2055


title: 14B_M_2054


title: 14B_M_2071


title: 14B_M_2065


title: 14B_M_2066


title: 14B_M_2050


title: 14B_M_2052


title: 14B_M_2053


title: 14B_M_2049


title: 14B_M_2048


title: 14B_M_2056


title: 14B_M_2046


title: 14B_M_2045


title: 14B_M_1977


title: 14B_M_1980


title: 14B_M_1978


title: 14B_M_1975


title: 14B_M_1976


title: 14B_M_1970


title: 14B_M_1973


title: 14B_M_1979


title: 14B_M_2047


title: 14B_M_1969


title: 14B_M_1974


title: 14B_M_1971


title: 14B_M_1972


title: 14B_M_1968


title: 14B_M_1965


title: 14B_M_1967


title: 14B_M_1966


title: 14B_M_1963


title: 14B_M_1964


title: 14B_M_1961


title: 14B_M_1962


title: 14B_M_1960


title: 14B_M_1959


title: 14B_M_1958


title: 14B_M_1957


title: 14B_M_1956


title: 14B_M_1955


title: 14B_M_1954


title: 14B_M_1951


title: 14B_M_1949


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