title: Negative control sample 3

city: Guangzhou

first: Wenda

last: Guan

state: Guangdong

address: No. 151, Yan Jiang Xi Road

institute: Guangzhou Institute of Respiratory Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NC_045512.2 whole genome using STAR v2.6.1d with parameters --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --quantMode TranscriptomeSAM --twopassMode Basic
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using salmon v1.5.2
Genome Coverage were calculated using igvtools v2.5.3
Genome_build: GCF_009858895.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: wig files were generated using igvtools; Scores represent genome coverage

organism: Severe acute respiratory syndrome coronavirus 2

source_name: kidney epithelial

growth_protocol: A SARS-CoV-2 dilution series (10, 1, 0.1, and 0.01 TCID50/mL) were cultured respectively, for 24 and 48 h in African green monkey kidney epithelial (Vero E6) cells in triplicate (n = 3). The cells were cultured at 37°C and 5% CO2 in infection medium, which was Dulbecco’s modified Eagle’s medium (Gibco, USA) supplemented with 2% fetal bovine serum and 100 U/mL mycillin.

extract_protocol:
First-strand cDNA was synthesized by the HiScriptIII 1st Strand cDNA Synthesis Kit in the presence of specific reagents to ensure that only RNA was used as template. Double-stranded cDNA was synthesized using DNA Polymerase I Klenow Fragment exo (Vazyme, Nanjing, China), dNTP mix (Thermo Fisher), and random hexamer primer (Thermo Fisher) and was purified with Agencourt AMPure XP beads (Beckman, CA, USA). Next, the DNA libraries were prepared using the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To construct the RNA library for metagenomics next-generation sequencing, we cultured the 1 TCID50 titer of the virus in Vero E6 cells for 24 h. Three study groups were established: (i) negative control (NC): only Vero E6 cells; (ii) non-culture; and (iii) 24 h culture.

value: Vero E6

tag: host


title: HSP90a treated mono, biological replicate 4

status: Public on Jun 29 2022

type: RNA

city: Mannheim

first: Feyza Gul

middle: Ozbay

last: Kurt

address: Theodor-Kutzer-Ufer 1-3

department: Skin Cancer Unit

country: Germany

institute: German Cancer Research Center/ Mannheim University Medical Center

description: Gene expression data from human monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

hyb_protocol: Labeled cRNA is then randomly fragmented and then added to the array for hybridization.

scan_protocol: The entire array is scanned with Agilent Microarray Scanning system with a laser and the information is kept in a computer for quantitative analysis.

data_processing: Two experiments were performed at different times. Samples 1-3 (control) and 8-10 (HSP90α treated) are from the same experiment/array. Samples 4-7 (control) and 11-14 ( HSP90α treated) are from the same experiment/array. Affymetrix CEL files were RMA normalized and expression values log2-transformed. All arrays were normalized together and experiment effect was adjusted. Differentially expressed probesets/genes between groups were identified using the empirical Bayes approach based on moderated t-statistics as implemented in the Bioconductor package limma accounting for batch effects. Gene set enrichment analysis was performed using the camera test. KEGG, Reactome and gene ontology data bases were used in pathways analysis. An enrichment map was used to visualize results from pathway tests. All p-values were adjusted for multiple testing using the Benjamini-Hochberg correction in order to control the false discovery rate. All analyses were performed with statistical software R 4.0 using the add-on package EnhancedVolcano.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human peripheral blood monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

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

growth_protocol: Human monocytes were isolated from peripheral blood mononuclear cells (PBMC) from buffy coats of healthy donors

extract_protocol: Total RNA from 24h treated monocytes was isolated using Rneasy Kit from Qiagen (Hilden, Germany) according to manufacturer`s instructions. RNA concentration was determined by the microplate reader Tecan Infinite M200 using a Nanoquant plate. The quality of total RNA was confirmed by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Quality and concentration of all samples were checked again on Nanodrop ND-1000, Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany). Microarray experiment were performed at Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ) in Heidelberg, Germany.

treatment_protocol: HSP90a treated monocyte: Human monocytes were treated with recombinant HSP90α (2µg/mL) in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h. Control monocytes: Human monocytes were incubated in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h.

tag: tissue

value: Peripheral blood

tag: disease

value: Healthy donor


title: HSP90a treated mono, biological replicate 2


title: HSP90a treated mono, biological replicate 1

description: Gene expression data from human monocytes incubated in RPMI medium for 24h


title: Cr(VI)-transformed BEAS-2B cells-3

city: Cleveland

first: Chengfeng

last: Yang

state: OHIO

address: 2500 MetroHealth Drive

department: Medicine

country: USA

institute: Case Western Reserve University

hyb_protocol: The cRNAs were combined together and hybridized onto Arraystar Human mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 15 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to show the distinguishable m6A-methylation pattern among samples.

source_name: Cr(VI)-transformed BEAS-2B cells-3

label_protocol: Briefly, the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: BEAS-2B control cells and Cr(VI)-transformed cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 5% fetal bovine serum (FBS)

extract_protocol: Total RNAs were extracted using the TRIzol reagent. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

treatment_protocol: BEAS-2B cell transformation by chronic Cr(VI) exposure: BEAS-2B cells were continuously exposed to 0.25 uM of K2Cr2O7 for 20 weeks to induce cell transformation as described in our recent publication (Wang Z et al., Toxicol Appl Pharmacol. 2018 Mar 1; 342: 22–30.). Passage-matched Control BEAS-2B cells were used as Control cells

tag: cell type

value: Cr(VI)-transformed BEAS-2B cells

tag: fraction

value: IP

source_name: Cr(VI)-transformed BEAS-2B cells

value: supernatant


title: MHP4Y

type: SRA

city: Beijing

first: Qiang

last: Ma

address: Datun Road, #15

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to macaca mulatta (release 95) pre-mRNA genome by Cell Ranger(v3.0.2)
Genome_build: macaca mulatta release 95
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information were with tsv format

organism: Macaca mulatta

source_name: adult macaque hippocampus

extract_protocol:
macaque hippocampal formation sample was homogenized in nuclei lysis buffer, isolated nuclei were loaded on 10X Genomics system.
Chromium Single Cell 3' Reagent Kits v3

tag: age

value: 4 years old

value: hippocampus


title: Cr(VI)-transformed BEAS-2B cells-2

source_name: Cr(VI)-transformed BEAS-2B cells-2


title: FWT-18

city: Atlanta

first: Jason

last: DeBruyne

state: GA

address: 720 Westview Dr, Research Wing 315

department: Pharmacology & Toxicology

institute: Morehouse School of Medicine

description: RNA pooled from livers harvested 3 replicate animals

data_processing:
The reads were mapped to the mouse MGSCv39-mm9 genome using Tophat 2.1.0.
Expression levels were assessed using Cufflinks 2.2.1, which calculates raw counts and the number of fragments per kilobase per million (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: wild type_Female_ZT18_liver

extract_protocol:
Livers were removed, flash frozen in cold Isopentane (2-methylbutane), and RNA harvest using combined Trizol / RNEasy kit(Qiagen, cat#74104) methods. Equal amounts of RNA (determined using nanodrop)  were pooled from livers from 3 mice/time/genotype/sex for RNAseq.
These RNA pools were converted into sequencing libraries by using Illumina TruSeq stranded mRNA Library Prep kits

tag: strain

value: Liver

tag: Sex

value: Female

tag: genotype

value: wild type

tag: time point


title: FWT-15

source_name: wild type_Female_ZT15_liver


title: untreated mono, biological replicate 5

source_name: Human peripheral blood monocytes incubated  in RPMI medium for 24h


title: Negative control sample 1

tag: cell line


title: Control sample 3

description: Before sequencing, Vero E6 cells were added to this group to make the sequencing background consistent with that of the cultured group

source_name: Control sample

value: Homo Sapiens


title: Negative control sample 2


title: FWT-21

source_name: wild type_Female_ZT21_liver


title: LV_NC

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

data_processing:
Fastp v0.20.0 was used to remove adapter and low-quality reads. Both m6A-IP and input reads were aligned to the human genome (UCSC hg19) using HISAT2 v2.1.0 with parameter --rna-strandness RF --fr. m6A peak calling was performed using R package MeTDiff v 1.1.0. Pvalue < 0.05 and log2(foldChange) > 0.58 was set as the threshold for significantly m6A peak. MEME-ChIP v5.0.5 was used to search for the enriched motif in m6A peak region. m6A peak distribution on the metagene was plotted by R package Guitar v1.1.1.18. Differential analysis of m6A methylation was performed using MeTDiff, too. Peak annotation was performed using ChIPseeker v1.12.1.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq. DEGs were identified using the DESeq Rpackage functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and log2(foldChange) > 0.58 was set the threshold for significantly differential expression. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed using R package clusterProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: wig files; peak text files

source_name: HNSCC cell, LV_NC

extract_protocol:
Total RNA from cells or tissues was extracted using Trizol reagent (15596018; Thermo Fisher Scientific, Waltham, MA). Total RNA was treated with DNase I (04 716 728 001; Roche Diagnostics, Indianapolis, IN) for 20 minutes at 37 ˚C to remove genomic DNA contamination. The RNA was precipitated using glycogen (25 μg/mL final) (5 mg/mL; AM9510; Thermo Fisher Scientific) and isopropanol at −20 ˚C for 2 hours. The precipitated RNA was then washed with 70% ethanol. The final pellet was resuspended in RNase-free water. The concentration of total RNA was measured by Qubit RNA HS Assay Kit (Q32855; Thermo Fisher Scientific).
The library is constructed using the NEBNext® Ultra™ II RNA Library Prep Kit(E7775). The library was quantified using a Qubit Fluorometer (Thermo Fisher Scientific), and the size distribution was checked using TapeStation D1000 ScreenTape (Agilent Technologies). The samples were then sequenced by illumina sequencer using PE150.

tag: genotype/variation

value: HN6 overexpressed NC


title: FKO-0

source_name: Siah2 KO_Female_ZT0_liver

value: Siah2 KO


title: FKO-3

source_name: Siah2 KO_Female_ZT3_liver


title: untreated mono, biological replicate 4


title: Spn D39 wt, Rep3

city: Bloomington

first: David

last: Giedroc

state: IN

address: 800 E. Kirkwood Ave

department: Chemistry

institute: Indiana University

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.33 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the Streptococcus pneumoniae D39 genome reference, NC_008533.1 using bowtie2 (version 2.1.0) (Langmead et al. 2012).
Individual gene expression was quantified by counting the number reads mapping to each of the annotated genes from the accession NC_008533.1 using htseq-count tool (version 0.11.1) . Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s reverse)
Genome_build: Streptococcus pneumoniae D39  NC_008533.1
Supplementary_files_format_and_content: Text files with counts of reads aligned to each annotated gene

organism: Streptococcus pneumoniae D39

source_name: Spn D39 wt

growth_protocol: Overnight preculture were made in BHI from frozen cell stock and grow in 37°C 5%CO2 without shaking. 5ml fresh culture were made by innoculating at OD600 =0.005 and grwoth in degassed BHI at 37°C. Cell pellets were collected at OD600=0.2 and washed by iced PBS. The collected cell pellets were stored at -80°C.

extract_protocol:
Pellets were thawed on ice and resuspended in 1 ml of TRI Reagent (catalog no. TR-118; Molecular Research Center). Resuspended cells were placed in tubes containing 0.1-mm silica beads (Lysing matrix B tubes, catalog no. 6911-100; MP Biomedicals) and lysed in a bead beater (Bead Ruptor 24 Elite; Omni) at a rate of 6 m/s for 45 s twice, with a 5-min cooling on ice between runs. Then, 200 μl of chloroform was added, followed by vigorous mixing and centrifugation for 15 min at 13,200 rpm. The top aqueous layer was removed to a new tube, and 70% ethanol was added at a 1:1 volume ratio. RNA purification was completed using the RNeasy minikit (catalog no. 74104; Qiagen) following DNase I treatment (catalog no. 79254; Qiagen).
Integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 1ug of total RNA was used for ribosome RNA depletion with the Illumina ScriptSeq Bacterial RNA Library.  After rRNA depletion, the libraries were prepared following the rest of the Illumina ScriptSeq Bacterial RNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads. Finally, the demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline

value: Spn D39 wt


title: Control sample 2


title: untreated mono, biological replicate 3


title: FWT-9

source_name: wild type_Female_ZT9_liver


title: Spn D39 wt, Rep1


title: LV_H2AFV

source_name: HNSCC cell, LV_H2AFV

value: HN6 overexpressed lnc-H2AFV-1


title: Cr(VI)-transformed BEAS-2B cells-1

source_name: Cr(VI)-transformed BEAS-2B cells-1


title: Case sample 3

source_name: kidney epithelial


title: Control sample 1


title: LV_NC_input

source_name: HNSCC cell, LV_NC_input


title: FWT-12

source_name: wild type_Female_ZT12_liver


title: LV_H2AFV_input

source_name: HNSCC cell, LV_H2AFV_input


title: FWT-3

source_name: wild type_Female_ZT3_liver


title: Spn D39 Dspd, 1448::KanrpsL, Rep3

source_name: Spn D39 Dspd_1448::KanrpsL

value: Spn D39 Dspd_1448::KanrpsL


title: FWT-6

source_name: wild type_Female_ZT6_liver


title: RIP2-IgG-265762635

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

data_processing:
For RNA-seq analysis, data was analyzed with Illumina Basespace app suite (https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/rna-seq-alignment.html). The sequencing reads were aligned to the Homo sapiens UCSC hg19 using the STAR aligner. Salmon was used for quantification of reference genes and transcripts. The Strelka Variant caller identifies single nucleotide variants (SNVs) and small indels and generates output in a VCF file. Manta was used to detect gene fusions. GC and mean coverage information for every target was computed using Picard. The gene counts, gene FPKMs, principal component analysis and differential expression results were produced by DESeq2 RNA Seq Analysis
In EFI4A1 binding RNA analysis, there were pairwise sequence data from two RNA-seq samples (eIF4A1 and IgG). The quality check was performed on each sample. The samples were aligned against GRch38Decoy reference genome using BWA (http://bio-bwa.sourceforge.net). The peaks were identified in the alignment using MACS2 [18, 19]. The peaks were called on RIP-eIF4A1 using RIP-IgG as a control. The peaks were annotated using R package ChIPseeker [20]. The bed files were produced by the MACS2 and expanded the region to 50 bp using bed tools to create expanded bed files. These files were then used to extract the corresponding sequences from the genomes using bed tools. Finally, the motifs were found using DREME (http://meme-suite.org/doc/dreme.html).
Genome_build: Human GRCh38/hg38

source_name: DU145 cells

growth_protocol: Cells were cultured on 2 x 100 mm2 plate to reach a 70% confluency of 106 cells.

extract_protocol:
Cells were collected by scraping in cytoplasmic extract buffer, protease cocktail, and RNAse out then collected, lysed, pelleted, and the supernatant removed to fresh tubes. Lysates were incubated with pre-swollen beads to clear non-specific interactions and pelleted. Ten percent of the supernatant was collected for “input”, the remainder was split into two paired tubes for rabbit anti-eIF4A1 or control rabbit IgG IP. Antibody and beads were allowed to conjugate at 2 hours on ice, and then mixed with lysate and the paired mixtures incubated for 6 hours to O/N at 4°C with gentle rotation (antibody - bead with lysate). The lysate was pelleted and washed x 6 times and then total RNA was isolated using TRIzol RNA isolation protocol.
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol. The RNA concentration was measured with Nanodrop 2000c spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA). Integrity was assessed using Agilent 2200 Tapestation instrument (Agilent Technologies, Santa Clara, CA, USA). Briefly, 10ng-20ng of RNA was fragmented and primed for cDNA synthesis. First-strand cDNA syntheses were performed at 25°C for 10 minutes, 42°C for 15 minutes and 70°C for 15 minutes, using random hexamers and ProtoScript II Reverse Transcriptase (NEW ENGLAND BioLabs Inc.). In a second strand cDNA synthesis, the RNA templates were removed and a second replacement strand was generated by incorporation dUTP (in place of dTTP, to keep strand information) to generate ds cDNA. The blunt-ended cDNA was cleaned up from the second strand reaction mix with beads. The 3’ ends of the cDNA were then adenylated and followed by the ligation of indexing adaptors. PCR (15 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds) were used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.  The libraries were quantified and qualified using Agilent D1000 Screen Tape on an Agilent 2200 TapeStation instrument. The libraries were normalized, pooled and subjected to cluster and pair read sequencing was performed for 150 cycles on a HiSeqX10 instrument (Illumina, Inc. San Diego, CA, USA), according to the manufacturer's instructions.
RNA immunoprecipitation (RIP) assay with RNA-seq (RIP-seq)

value: DU145 cells

value: human prostate cancer cells

tag: rip antibody

value: IgG (Abcam, ab37415)


title: Passage-matched BEAS-2B control cells-2

source_name: Passage-matched BEAS-2B control cells-2

value: Passage-matched BEAS-2B control cells

source_name: Passage-matched BEAS-2B control cells


title: Case sample 2

value: Vero E6


title: FWT-0

source_name: wild type_Female_ZT0_liver


title: Spn D39 wt, Rep2


title: Case sample 1


title: RIP2-EIF-265762634

value: eIF4A1 (Abcam, ab31217)


title: Spn D39 Dspd, 1448::KanrpsL, Rep1


title: Passage-matched BEAS-2B control cells-3

source_name: Passage-matched BEAS-2B control cells-3

value: IP

value: supernatant


title: mESC-OE rep2 [OE-2]

status: Public on Jun 28 2022

city: tianjin

first: wen

last: hang

address: tianjing city

institute: nankai university

data_processing:
BGISEQ-500 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000001635.26_GRCm38.p6 genome using HISAT
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.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited xlsx files include RPKM values for each Sample ...

source_name: mESC

growth_protocol: Mouse ESCs were all cultured in high glycose DMEM (HyClone) supplemented with 15% fetal bovine serum (HyClone), 2mM L-glutamine (Gibco), 5000U/mL penicillin and streptomycin (Gibco), 0.1mM NEAA (Gibco), 0.1mM 2-Mercaptoethanol (CAS No. 60-24-2, Sigma) and 1000U/ml LIF (ESG1107, Millipore Crop) at 37℃ in 5% CO2 incubator.

extract_protocol:
Cells were removed , and RNA was harvested using Trizol reagent.BGISEQ-500  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard huada protocols

treatment_protocol: over expression Dppa3

value: Dppa3 over expression

value: mESC


title: mESC-OE rep1 [OE-1]


title: mESC-OE rep3 [OE-D7]


title: mESC-Con rep3 [Con-D7]

value: wild type


title: mESC-Con rep2 [Con-2]


title: mESC-Con rep1 [Con-1]


title: Passage-matched BEAS-2B control cells-1

source_name: Passage-matched BEAS-2B control cells-1


title: Spn D39 Dspd, 1448::KanrpsL, Rep2


title: untreated mono, biological replicate 2

source_name: Human peripheral blood monocytes incubated  in RPMI medium for 24h

value: Peripheral blood

value: Healthy donor


title: untreated mono, biological replicate 1


title: 15_Ethanol bio rep 2

city: Boston

first: Cynthia

last: Bradham

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

data_processing:
Reads were trimmed and put through quality control using fastp
Reads were aligned to the Lvar 3.0 genome using STAR
Read alignments were quantified using featureCounts
Assembly: LVAR 3.0
Supplementary files format and content: samples.csv
Supplementary files format and content: master_top_hits.csv
Supplementary files format and content: count_matrix.csv

organism: Lytechinus variegatus

source_name: sea urchin embryo

extract_protocol:
Total RNA was collected from approximately 150 embryos per sample using TRIzol, and precipitated along with glycogen carrier. After DNase treatment, samples were reverse-transcribed using the TaqMan reverse transcription kit.
libraries were prepared following sequecing company protocol.

treatment_protocol: Embryos were treated with EtOH at fertillzation and collected at specific timpoints during development

value: whole embryo

value: WT

tag: treatment

value: Ethanol Exposure

tag: time

value: 15 hours post fert.


title: 18_Control bio rep 2

value: Control

value: 18 hours post fert.


title: 18_Ethanol bio rep 2


title: 18_Control bio rep 3


title: 21_Ethanol bio rep 1

value: 21 hours post fert.


title: 15_Ethanol bio rep 3


title: 15_Control bio rep 2


title: 15_Control bio rep 3


title: 21_Ethanol bio rep 2


title: 21_Ethanol bio rep 3


title: 18_Ethanol bio rep 3


title: 21_Control bio rep 2


title: 21_Control bio rep 3


title: 18_Ethanol bio rep 1


title: 18_Control bio rep 1


title: 15_Control bio rep 1


title: HTS4

city: Bin Zhou

first: Shuai

last: Shang

address: Huang he road  391

institute: Binzhou university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Spirodela polyrhiza/JGI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Spirodela polyrhiza

source_name: Leaf

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Leaf

value: High temperature


title: MTS2

value: Middle temperature


title: MTS4


title: MTS1


title: HTS3


title: MTS3


title: HTS2


title: HTS1


title: CK4

value: indoor temperature


title: 21_Control bio rep 1


title: CK3


title: 15_Ethanol bio rep 1


title: CK1


title: CK2


title: Tumor patient 10

city: Ulm

first: Linda

last: Hofmann

state: Deutschland

address: Frauensteige 14a, Haus 18

institute: University of Ulm

description: Exosomal miRNA was analyzed using the Human v3 miRNA Assay

hyb_protocol: Samples were denatured at 85°C for 5 min and then hybridized at 65°C for 12 h.

scan_protocol: Fluorescent reporter tags were scanned by an automated multi-channel epifluorescence scanner, generating the raw counts.

data_processing: Raw counts were normaliezd using the positive ligation and negative controls present on the chip.

label: Nanostring

source_name: Saliva-derived exosomes

extract_protocol: Exosomes were isolated from saliva by differential ultracentrifugation and RNA was isolated from exosomes using miRNeasy micro Kit (Qiagen).

tag: gender

value: male

tag: tumor site

value: Oropharynx

tag: uicc stage

value: IV

tag: hpv


title: Tumor patient 11

value: female

value: II

value: positive


title: Tumor patient 13

value: Oral cavity

value: III


title: Tumor patient 4

value: Larynx


title: Tumor patient 6

value: negative


title: Tumor patient 8

value: I


title: Tumor patient 5


title: Tumor patient 9


title: Tumor patient 1


title: Healthy donor 7

value: not applicable


title: Tumor patient 7


title: Healthy donor 2


title: Healthy donor 4


title: Kc_MOD_GFP_cell_Input_R1

city: Bethesda

first: Elissa

last: Lei

state: Montgomery

address: 9000 rockville pike

institute: NIDDK

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the Flybase r6-28 genome assembly  using Bowtie2 v2.4.2
Multimapping reads removed with samtools v1.12 using “view” subcommand and the additional argument “-q 20”, duplicated reads were removed with Picard v2.25.2
peaks were called using  MACS2 version 2.2.7.1

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Kc-MOD-GFP

growth_protocol: Kc167 cells-derived from Drosophila embryo, were routingly maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.

extract_protocol:
ChIP-seq was performed as described previously (Bag et al., 2019).
ChIP-seq library was performed as described previously (Bag et al., 2019, Matzat et al., 2012).

treatment_protocol: 0.7 x 10 million Kc167 cells were transfected with 5 ug of dsRNA against Cp190, su(Hw), Nurf301 by using Amexa cell line Nucleofector kit V (Lonza) and incubated 4 days at 25°C to obtain significant knockdown of  CP190, Su(Hw) and NURF301.

value: Kc-MOD-GFP cells

tag: developmental stage

value: embryo

value: tranfected

tag: chip antibody


title: Tumor patient 14


title: Healthy donor 3


title: Kc167_suhwkd_CP190_3

value: Kc167 cells

value: su(Hw)kd


title: Kc167_suhwkd_NURF_3

value: NURF


title: Kc_MOD_GFP_cell_Input_R3


title: Kc_MOD_GFP_cell_GFP_R1

value: GFP


title: Tumor patient 2

value: male

value: Hypopharynx

value: IV


title: Healthy donor 6

value: female


title: Tumor patient 3


title: Tumor patient 12

value: Oropharynx

value: positive


title: Kc_MOD_GFP_cell_GFP_R2


title: Kc167_suhwkd_SuHw_3

value: SuHw


title: Kc_MOD_GFP_cell_GFP_R3


title: Kc167_suhwkd_SuHw_2


title: Kc167_suhwkd_Input_3


title: Kc167_suhwkd_SuHw_1


title: Healthy donor 1


title: Kc167_suhwkd_NURF_1


title: Kc167_suhwkd_Input_2


title: Kc167_suhwkd_Input_1


title: Kc167_mock2_CP190_3

value: mock


title: Kc167_mock2_SuHw_2


title: Kc167_mock2_CP190_2


title: Kc167_suhwkd_CP190_1


title: Kc167_mock2_Input_3


title: Kc167_mock2_NURF_3


title: Kc167_mock2_SuHw_3


title: Kc167_mock2_CP190_1


title: Healthy donor 5


title: Kc_MOD_GFP_cell_Input_R2


title: Kc167_suhwkd_NURF_2


title: Kc167_mock2_SuHw_1


title: Kc167_mock2_Input_2


title: Kc167_mock2_NURF_2


title: Kc167_mock2_Input_1


title: Kc167_cp190kd_Input_R2


title: Kc167_mock2_NURF_1


title: Kc167_cp190kd_CP190_R2


title: Kc167_cp190kd_NURF_R2


title: Kc167_suhwkd_CP190_2


title: Kc167_cp190kd_NURF_R1


title: Kc167_nurfkd_CP190_R3


title: Kc167_cp190kd_CP190_R1


title: Kc167_nurfkd_NURF_R3


title: Kc167_nurfkd_NURF_R2


title: Kc167_mock_MOD_R3


title: Kc167_nurfkd_SuHw_R2


title: Kc167_nurfkd_CP190_R2


title: Kc167_nurfkd_CP190_R1


title: Kc167_nurfkd_SuHw_R1


title: Kc167_mock_CP190_R3


title: Kc167_nurfkd_Input_R3


title: Kc167_mock_SuHw_R2


title: Kc167_cp190kd_Input_R1


title: Kc167_nurfkd_NURF_R1


title: Kc167_nurfkd_Input_R2


title: Kc167_mock_NURF_R1


title: Kc167_mock_Input_R1


title: Kc167_mock_CP190_R1


title: Kc167_mock_MOD_R1


title: PimaS-7-30 rep3

city: Urumqi

first: Yajie

last: Duan

state: Xinjiang

address: Nongda East Road No. 311

department: College of Agronomy

institute: Xinjiang Agricultural University

data_processing:
Illumina  software used for basecalling.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
String Tie was used to produce the FPKM data.
Genome_build: Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1
https://www.cottongen.org/species/Gossypium_barbadense/HAU-AD2_genome_v2.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Gossypium barbadense

source_name: cotton fiber

extract_protocol:
contton fiber were removed, flash frozen on dry ice, and RNA was harvested using RNAprep Pure Plant kit reagent. NEBNext UltraTM RNA Library Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

tag: tissue

value: cotton fiber

value: post anthesis day 30


title: PimaS-7-35 rep2

tag: age

value: post anthesis day 35


title: Kc167_mock_NURF_R3

value: embryo

tag: Sex


title: Kc167_mock_MOD_R2


title: Kc167_nurfkd_Input_R1


title: PimaS-7-20 rep3

value: post anthesis day 20


title: Kc167_mock_Input_R2

value: Kc167 cells


title: Kc167_mock_Input_R3


title: PimaS-7-20 rep2


title: Kc167_mock_SuHw_R3


title: PimaS-7-15 rep3

value: post anthesis day 15


title: PimaS-7-15 rep1


title: Kc167_nurfkd_SuHw_R3


title: PimaS-7-35 rep3


title: Kc167_mock_CP190_R2


title: Kc167_mock_SuHw_R1


title: PimaS-7-30 rep1


title: PimaS-7-05 rep3

value: post anthesis day 05


title: PimaS-7-35 rep1


title: Kc167_mock_NURF_R2

value: NURF


title: PimaS-7-00 rep3

value: post anthesis day 00


title: PimaS-7-00 rep2


title: PimaS-7-25 rep1

value: post anthesis day 25


title: 5917-35 rep1


title: PimaS-7-10 rep3

value: post anthesis day 10


title: PimaS-7-25 rep2


title: 5917-30 rep3


title: PimaS-7-30 rep2


title: PimaS-7-25 rep3


title: 5917-30 rep1


title: PimaS-7-20 rep1


title: 5917-25 rep1


title: 5917-20 rep2


title: 5917-15 rep2


title: PimaS-7-15 rep2


title: PimaS-7-05 rep2


title: 5917-25 rep3


title: 5917-00 rep1


title: PimaS-7-10 rep2


title: PimaS-7-00 rep1


title: 5917-15 rep1


title: 5917-05 rep3


title: 5917-05 rep2


title: PimaS-7-05 rep1


title: 5917-15 rep3


title: 5917-00 rep2


title: 5917-35 rep3


title: PimaS-7-10 rep1


title: 5917-30 rep2


title: BMDMs, IL-10 + IL-18, a

city: Cincinnati

first: Yuting

last: Tang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Trim Galore for reads trimming
Sequence reads were aligned to the mm10 reference genome using HISAT2 algorithm
The aligned reads to each known transcript were counted using featureCounts algorithm
Pairwise analyses of differentially expressed genes between groups were performed using the edgeR algorithm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files were generated using FeatureCounts algorithm; Scores represent counted reads, per gene, per row

source_name: Bone marrow-derived macropahges

growth_protocol: Femurs and tibias from 8-12 week-old C57BL/6 mice were isolated and flushed with 3 ml cold Hanks' Balanced Salt Solution. Bone marrow cells were resuspended into a homogenous solution and passed through a 70 µm filter to eliminate debris. After centrifugation for 5 min at 1300rpm, cells were resuspended in bone marrow derived macrophage (BMDM) medium, which was prepared with Dulbecco's Modified Eagle Medium, 10% Fetal Bovine Serum, 1% GlutaMAX™ Supplement, 1% Non-Essential Amino Acids Solution, 1% Sodium Pyruvate, and 0.1% 2-Mercaptoethanol. The bone marrow cells were cultured in 37℃, 5% CO2 incubator for four hours to remove adherent mesenchymal cells and mature macrophages. Then cells were resuspended with BMDM medium containing 20 ng/ml M-CSF and plated at a density of 1 × 10^6 cells/ml in 6-well plates. Mediums were changed every 3 days.

extract_protocol:
Polarized BMDMs were washed with DPBS for three times and lysed directly with RLT buffer from the RNeasy Mini Kit (74104, Qiagen, Hilden, Germany) supplemented with 1% 2-mercaptoethanol. Total RNA was isolated using RNeasy Mini Kit (74104, Qiagen, Hilden, Germany) according to the manufacturer’s instructions and submitted for RNA-seq analysis.
Isolated RNA sample quality was determined by BioAnalyzer Nano Total RNA Assay (Agilent Technologies Inc., California, USA), and quantified by Qubit 2.0 RNA HS assay (Thermo Fisher, Massachusetts, USA). 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., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5 ́ d(N6) 3 ́ [N= A, C, G, T]) and fragmented based on the manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42 °C. All remaining steps for library construction were performed according to the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries were quantified by Qubit 2.0 (Thermo Fisher, Massachusetts, USA) and the quality was determined by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 400bp with an insert size of about 250bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Hiseq X (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction).

treatment_protocol: At day 7, IFN-γ (20ng/ml), IL-4 (20ng/ml), IL-10 (2000ng/ml), IL-18 (2000ng/ml), or IL-10 plus IL-18 (2000ng/ml each) were added to culture medium for 72 hours to generate polarized macrophages. Experiments were performed with triplicates. The doses of excessive IL-18 and IL-10 used (2000ng/ml) were comparable to the serum concentrations detected in the Dual-tg mice.

tag: strain

tag: cell type

value: Bone marrow-derived macropahges


title: BMDMs, IL-18, c


title: 5917-35 rep2


title: 5917-20 rep3


title: 5917-00 rep3


title: BMDMs, IL-18, a


title: 5917-25 rep2


title: BMDMs, IL-10, b


title: BMDMs, IL-4, c

value: IL-4 20ng/ml


title: BMDMs, PBS, a

value: PBS


title: 5917-10 rep3


title: 5917-20 rep1


title: meRIP_Scr_Rep3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed to remove reads with low alignment quality.
BAM files were converted to TDF format using IGVTools for visualization. The m6A enrichment peaks were called using MeTPeak package.
Genome_build: hg19
Supplementary_files_format_and_content: The processed MePeak files are 12-column BED format with column header. The tiled data files (.tdf or TDF) are binary files that contain data that has been preprocessed for faster display in IGV

source_name: Osteosarcoma

growth_protocol: 143B cells were cultured in minimum essential medium (Eagle)  supplemented with 10% fetal bovine serum and 1% penicillin/streptamycin. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from scrambled and ALKBH5-siRNA transfected 143B cells using Trizol (Thermo 15596018) followed by mRNA isolation using a Dynabeast Direct Kit (Life Tech 61012). 2 μg of polyadenylated mRNA was diluted to 100 ml in water and fragmented to 100 to 200 nucleotides using Bioruptor (Diagenode). 5 ml of RNA was used for input preparation. 2 μg of fragmented mRNA was used for immunoprecipitation (IP) using rabbit anti-m6A antibody (Synaptic Systems #202003) in IP buffer (10 mM Tris pH 7.4, 150 mM NaCl, 0.1% NP-40) for 2 hours at 4°C. After incubation, samples were added to Protein A beads and incubated for 2 more hours at 4°C with rotation. After washing, samples were eluted using elution buffer containing m6A nucleoside and elute was concentrated using a Zymo RCC-5 column. The resultant final product was used for RNA-seq. 0.1 μg of fragmented mRNA was used as input control for RNA-seq. For replicate 3: same protocol was followed with another m6A antibodiy (ABE572, Millipore, Germany).  .For rep2, meRIP-seq was done with total RNA using the Magna MeRIP m6A kit (catalog no.17-10499, Millipore) according to the manufacture’s protocol and it employed  MABE1006 (Millipore-Sigma) m6a antibody for IP.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: 143B cells were grown in 150 mm tissue culture plates and transfected with with either scrambled-siRNA or ALKBH5-siRNAs (Sigma-Aldrich) for 48 hours. Transfection was carried out using the RNAiMAX Reagent (Thermofisher) according to the manufacturer’s protocol.

tag: cell line

value: Osteosarcoma

tag: sample type

value: fragmented meRIP

value: scrambled-siRNA control

tag: harvest time

value: 48 hour

value: anti-m6A (Synaptic Systems #202003)


title: meRIP_ALKBH5_Rep2

tag: treatment

value: ALKBH5 knockdown

tag: rip antibody


title: 5917-10 rep2

value: cotton fiber


title: BMDMs, IL-10 + IL-18, b


title: Input_Scr_Rep1

value: fragmented input RNA

value: none (input)


title: 5917-05 rep1

value: post anthesis day 05


title: BMDMs, IL-10 + IL-18, c


title: 5917-10 rep1


title: Input_ALKBH5_Rep3


title: Input_ALKBH5_Rep2


title: Input_ALKBH5_Rep1


title: ALKBH5 KD Rep#1

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

extract_protocol:
Total RNA was extracted  from 143B cell lines 48 hours after transfection ,  using RNeasy Mini Kit (Qiagen)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: 143B cells were grown in 6-well plates and transfected with with either scrambled-siRNA or ALKBH5-siRNAs (Sigma-Aldrich) for 48 hours. Transfection was carried out using the RNAiMAX Reagent (Thermofisher) according to the manufacturer’s protocol.


title: BMDMs, IL-4, b


title: sc_Donor_14_GEX

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

data_processing:
Sequencing was performed on the Illumina HiSeq 3000/4000 flowcell (model #). Read 1, Read 2, and sample index were sequenced to 26, 98, and 8 basepairs, respectively.
The 10x Genomics cellranger 2.0.1 software was used to analyze raw base calls for this project. Cellranger MKFASTQ was used to demultiplex raw base calls by sample index. Cellranger COUNT was used to obtain UMI counts for each individual sample. Lastly, Cellranger AGGR was used to pool the individual samples together after depth normalization. It was noted that there were clusters of CD19+ and CD14+ in the default AGGR output. These two small clusters were thought to be comprised of B-lymphocyte and macrophage cells and were subsequently removed. Cells with above 2000 genes were thought to represent doublets in the drop-seq protocol and were removed.
The output from CellRanger AGGR was parsed by Seurat V3.0.0 as a cell barcode by gene matrix. Cells with mitochondrial DNA above 0.25% were removed.
Genome_build: Hg38 ENSEMBL 84
Supplementary_files_format_and_content: The processed data file, an .Rds file, was exported from the Seurat package. This file lists the cell barcodes (cell IDs) that remained after filtering out B cells, macrophages, and cells with more than 0.25% mitochondrial DNA. For each cell barcode, the associated donor number is listed as well as the UMI counts for each gene found in the cell.

source_name: Peripheral Blood

growth_protocol: Fresh CD8+ cells were enriched from PBMC by using EasySep™ Human CD8 Positive Selection Kit II (Stem cells technologies) according to manufacturer’s instructions. Cells were resuspended in PBS containing 0.04% BSA. CD8+ cells were sorted as CD3+/CD19-/CD8+/CD4- cells into PBS containing 0.04% BSA. Purities of CD8+ T cells were 97 - 98%.

extract_protocol:
For single-cell RNA seq library construction, cells were diluted to ~    1X10^6/mL in 100 uL PBS containing 0.04% BSA and processed within hours after they were obtained. Briefly, freshly sorted CD8+ T cells were kept on ice before processing. Viable cells counted and about 8700 cells were used for Gel bead-in-emulsion (GEM) generation (targeted recovery ~5000 cells).
Single-cell RNA seq libraries were constructed using Single Cell 3’ library (v2 Chemistry) and Gel beads kits (10x genomics) according to the manufacturer’s protocol. After template switching reverse transcription in beads, cDNA was amplified in bulk. Subsequent fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR generated P5- and P7- capped, cell- and sample-indexed single-cell 3’ libraries. Libraries were quantified using both bioanalyzer (Agilent) and Kapa library quantification kit (Roche) before sequencing.

tag: donor age

tag: donor gender

value: M

value: Peripheral Blood

value: CD8+ T-cells

tag: pbmc type

value: Fresh


title: BMDMs, IL-4, a

value: Bone marrow-derived macropahges


title: sc_Donor_15_GEX


title: BMDMs, IL-18, b


title: BMDMs, IFN-γ, c

value: IFN-γ 20ng/ml


title: sc_Donor_9_GEX

value: F


title: sc_Donor_10_GEX


title: meRIP_Scr_Rep2

value: Osteosarcoma


title: BMDMs, IL-10, a


title: sc_Donor_8_GEX


title: BMDMs, IFN-γ, a


title: BMDMs, IFN-γ, b


title: BMDMs, IL-10, c


title: BMDMs, PBS, b

value: PBS


title: Input_Scr_Rep3

value: fragmented meRIP

value: scrambled-siRNA control


title: sc_Donor_5_GEX


title: sc_Donor_4_GEX


title: meRIP_ALKBH5_Rep3

value: 48 hour

value: anti-m6A (Synaptic Systems #202003)


title: meRIP_Scr_Rep1


title: sc_Donor_7_GEX


title: BMDMs, PBS, c


title: Input_Scr_Rep2


title: Scrambled Rep#2


title: Scrambled Rep#1


title: sc_Donor_16_GEX


title: TFR-D1D8-2

city: Indianapolis

address: 332/333 RESEARCH II, 950 W Walnut Street

department: Microbiology and Immunology

institute: Indiana University School of Medicine

data_processing:
Sequence reads were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
featureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 0 -p –Q 10")
Assembly: mm10
Supplementary files format and content: excel tables with raw counts included

source_name: T follicular regulatory cells

extract_protocol:
Total RNA was harvested using RNeasy Plus Micro kit (QIAGEN) (Cat#: 74034).
The RNA-seq libraries were prepared using the Clontech SMART-Seq HT kit and Illumina Nextera XT DNA Lib Kit.

value: spleen

tag: group


title: b-SVZ

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 10%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38Ensembl92
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: The subventricular zone (SVZ)

growth_protocol: All mice were housed in cages with ad libitum access to food and water and acclimated to standard conditions (12 h light/dark cycle, temperature: 22 °C, relative humidity: 50%) for at least one week before the experiment.

extract_protocol:
Mice were sacrificed 48 hours post injury, and the SVZ was micro-dissected and washed in precooled PBS to remove residual blood. Then, the tissue was flash-frozen in liquid nitrogen and transferred to -80 ℃ until further use.NLB buffer (X-100 (Sigma-Aldrich, St Louis, MO, USA), 0.2 U/μL RNase Inhibitor (Takara, Kyoto, Japan), 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton 0.1 mM EDTA) was used to homogenize the frozen tissue. Different concentrations of sucrose were applied to purify the nuclei using sucrose density gradient centrifugation. A final concentration of around 1000 nuclei/μL was used for scRNA-Seq.
The scRNA-Seq libraries were built using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, CA, USA). Briefly, the acquired cell nuclei were loaded into several channels to obtain single-cell Gel Bead-In-Emulsions (GEMs). After reverse transcription, barcoded cDNA was released from the GEM and then purified. After amplification, the barcoded cDNA went through fragmentation, ligation with adaptors, and amplified with index PCR. The Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, Waltham, MA, USA) was applied to quantify the final libraries, and the size distribution was determined by the High Sensitivity DNA chip using Bioanalyzer 2200 (Agilent Technologies, Santa Clara, CA, USA). Novaseq6000 (Illumina, San Diego, CA, USA) was used for sequencing on a 150 bp paired-end run.

treatment_protocol: Each bTBI mouse received blast injury through BST explosion wave generator.

value: The subventricular zone (SVZ)

value: 7 weeks

value: SVZ


title: TFR-D1D3-1


title: meRIP_ALKBH5_Rep1

value: ALKBH5 knockdown


title: sc_Donor_13_GEX

value: Peripheral Blood


title: sc_Donor_2_GEX

growth_protocol: Thawed PBMCs were rested for 1 hr in warm medium and wash once with BSM (HBSS containing 0.2% of BSA, 1XHEPES, 1X Penicillin-Streptomycin-Glutamine) and stained with fluorescence antibodies against CD3, CD19, CD4, and CD8. CD8+ cells were sorted as CD3+/CD19-/CD8+/CD4- cells into PBS containing 0.04% BSA. Purities of CD8+ T cells were 97 - 98%.

value: M

value: CD8+ T-cells

value: Frozen


title: sc_Donor_1_GEX


title: sc_Donor_3_GEX

value: Fresh


title: TFH-D1D8-4

source_name: T follicular helper cells


title: sc_Donor_12_GEX


title: ALKBH5 KD Rep#2


title: sc_Donor_11_GEX


title: TFH-D1D8-1


title: TFR-D1D8-4


title: genomic DNA from CD14+ monocytes_V114M

type: genomic

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

hyb_protocol: Five hundred nanograms of each DNA sample was bisulfite-converted with the EZ DNA MethylationTM kit (Zymo Research, Irvine, CA, USA), following the manufacturer's instructions. Samples were hybridized onto an Infinium MethylationEPIC Bead Chip array

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
DNA methylation raw data (IDAT files) were processed using ShinyÉPICo, a graphical pipeline based on minfi and limma R packages.
Samples showing poor bisulfite conversion and those with gender discordance between prediction and demographic information were filtered out from further analyses. In addition, we used the 59 single nucleotide polymorphisms (SNPs) probes included in the array to check for sample duplication. One individual from each pair of duplicates was excluded.
Probes with a detection p-value < 0.01 were removed. To avoid technical and biological bias, we also excluded CpGs from X and Y chromosomes as well as those probes containing either a SNP at the CpG interrogation site or at the single base extension site. Probes were annotated using IlluminaHumanMethylationEPICmanifest v0.4.0
Raw methylation values were normalized using the Noob+Quantile method, and DNA methylation was measured as beta and M values.
To identify associations between DNA methylation levels and GCA disease state or clinical status along the genome, we applied a eBayes moderated t-test with trend and robust options enabled. We used a false discovery rate (FDR) to correct for multiple testing and those probes with a FDR < 0.05 were considered as differentially methylated positions (DMPs).
Sensitivity analyses were realized for each comparison to examine the contribution of all potential confounders (sex, age, slide, array and sample plate). Pearson correlation or Wilcoxon signed-rank test was applied depending on whether the variable of interest was continuous or categorical. Variables with a p-value < 0.05 were considered to significantly contribute to DNA methylation and were therefore included as covariates in the model. Average Beta values provided in matrix table.

label: Cy5 and Cy3

source_name: CD14+ Monocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were first obtained from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). For subsequent CD14+ monocytes isolation, PBMCs were incubated with CD14-PE and CD15-FITC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes in the dark. Pure monocytes were next isolated by positive selection as CD14+CD15- cells using flow cytometry sorting and were pelleted and stored at -80ºC. Genomic DNA were extracted  the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. DNA were quantified with Nanodrop ND-2100 and Qubit® DNA assay kit (invitrogen).

tag: classification

value: RNT

value: F

tag: sorter day


title: sc_Donor_6_GEX


title: TFR-D1D3-4


title: TFH-D1D3-4


title: genomic DNA from CD14+ monocytes_V113M

value: HD


title: TFR-D1D8-1


title: TFR-D1D3-2


title: genomic DNA from CD14+ monocytes_V115M


title: TFH-D1D8-3


title: TFR-D1D3-3


title: TFR-D1D8-3


title: TFH-D1D3-2


title: TFH-D1D3-1


title: genomic DNA from CD14+ monocytes_V112M


title: genomic DNA from CD14+ monocytes_V111M

value: RT


title: genomic DNA from CD14+ monocytes_V106M


title: genomic DNA from CD14+ monocytes_V105M


title: genomic DNA from CD14+ monocytes_V109M


title: PSCCreMRpos_R_H8_S324

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description: retrogradely labeled regenerating RGCs in PtenSocs3CKO+CNTF 21pdc

data_processing:
Sequencing reads were first trimmed using Trimmomatic-0.39. Reads were then aligned to mouse genome GRCm38.81 using hisat2, reads per gene per cell were counted using featureCounts.
Assembly: GRCm38
Supplementary files format and content: Gene count matrix in .csv format

source_name: Mouse retina, 6-8 wk old

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90,  (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP and mCherry (for MR+) or without mCherry (MR-)co-expression. Cells were collected directly into 96well plates, 1 cell/well and frozen at -80C.
Cells were processed following published SS2 protocols, using pre-beads clean up and purification and Nextera XT kit from Illumina. Libraries were sequenced on NovaSeq-SP

treatment_protocol: YFP17het-Ptenfl/fl, YFP17het-PtenSocs3fl/fl mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

value: Retina

value: Pten fl/fl - Socs3 fl/fl - YFP17 het

tag: aav infection

value: AAV2-Cre / AAV-CNTF

tag: intervention

value: PSCCreMRpos

value: 6-8 wk old


title: genomic DNA from CD14+ monocytes_V110M

tag: age


title: PSCCreMRpos_R_H3_S319

tag: tissue


title: genomic DNA from CD14+ monocytes_V108M

tag: Sex


title: genomic DNA from CD14+ monocytes_V102M

value: ACT


title: TFH-D1D8-2

first: Qiang

tag: strain

value: spleen


title: PSCCreMRpos_R_H7_S323


title: TFH-D1D3-3


title: PSCCreMRpos_R_G8_S312


title: genomic DNA from CD14+ monocytes_V104M


title: PSCCreMRpos_R_H4_S320


title: genomic DNA from CD14+ monocytes_V103M


title: genomic DNA from CD14+ monocytes_V101M


title: genomic DNA from CD14+ monocytes_V97M


title: PSCCreMRpos_R_G3_S307


title: PSCCreMRpos_R_G4_S308


title: genomic DNA from CD14+ monocytes_V99M


title: PSCCreMRpos_R_G7_S311


title: PSCCreMRpos_R_G10_S314


title: PSCCreMRpos_R_G6_S310


title: genomic DNA from CD14+ monocytes_V96M


title: genomic DNA from CD14+ monocytes_V93M


title: PSCCreMRpos_R_G1_S305


title: PSCCreMRpos_R_H2_S318


title: genomic DNA from CD14+ monocytes_V94M


title: PSCCreMRpos_R_H5_S321


title: genomic DNA from CD14+ monocytes_V92M


title: genomic DNA from CD14+ monocytes_V100M


title: PSCCreMRpos_R_F9_S301


title: genomic DNA from CD14+ monocytes_V98M


title: PSCCreMRpos_R_F6_S298


title: genomic DNA from CD14+ monocytes_V91M


title: PSCCreMRpos_R_F5_S297


title: genomic DNA from CD14+ monocytes_V90M


title: genomic DNA from CD14+ monocytes_V89M


title: PSCCreMRpos_R_F8_S300


title: PSCCreMRpos_R_F2_S294


title: genomic DNA from CD14+ monocytes_V107M


title: PSCCreMRpos_R_F3_S295


title: PSCCreMRpos_R_F11_S303


title: PSCCreMRpos_R_F10_S302


title: genomic DNA from CD14+ monocytes_V86M


title: genomic DNA from CD14+ monocytes_V87M


title: PSCCreMRpos_R_E6_S286


title: genomic DNA from CD14+ monocytes_V84M


title: PSCCreMRpos_R_E4_S284


title: PSCCreMRpos_R_E11_S291


title: genomic DNA from CD14+ monocytes_V83M

value: H


title: genomic DNA from CD14+ monocytes_V81M


title: PSCCreMRpos_R_E10_S290


title: genomic DNA from CD14+ monocytes_V88M


title: genomic DNA from CD14+ monocytes_V80M


title: genomic DNA from CD14+ monocytes_V78M


title: PSCCreMRpos_R_E2_S282


title: PSCCreMRpos_R_D9_S277


title: genomic DNA from CD14+ monocytes_V79M


title: PSCCreMRpos_R_E7_S287


title: PSCCreMRpos_R_D7_S275


title: genomic DNA from CD14+ monocytes_V76M


title: genomic DNA from CD14+ monocytes_V73M


title: PSCCreMRpos_R_D5_S273


title: genomic DNA from CD14+ monocytes_V75M


title: genomic DNA from CD14+ monocytes_V85M


title: PSCCreMRpos_R_D8_S276


title: genomic DNA from CD14+ monocytes_V77M


title: PSCCreMRpos_R_D6_S274


title: PSCCreMRpos_R_D2_S270


title: genomic DNA from CD14+ monocytes_V72M


title: PSCCreMRpos_R_E12_S292


title: PSCCreMRpos_R_D11_S279


title: PSCCreMRpos_R_D12_S280


title: genomic DNA from CD14+ monocytes_V82M


title: genomic DNA from CD14+ monocytes_V71M


title: PSCCreMRpos_R_D10_S278


title: genomic DNA from CD14+ monocytes_V70M


title: genomic DNA from CD14+ monocytes_V69M


title: PSCCreMRpos_R_C9_S265


title: PSCCreMRpos_R_C4_S260


title: PSCCreMRpos_R_C8_S264


title: PSCCreMRpos_R_C5_S261


title: genomic DNA from CD14+ monocytes_V68M


title: genomic DNA from CD14+ monocytes_V74M


title: PSCCreMRpos_R_C7_S263


title: genomic DNA from CD14+ monocytes_V66M


title: genomic DNA from CD14+ monocytes_V64M


title: genomic DNA from CD14+ monocytes_V65M


title: genomic DNA from CD14+ monocytes_V67M


title: PSCCreMRpos_R_D1_S269


title: genomic DNA from CD14+ monocytes_V63M


title: genomic DNA from CD14+ monocytes_V62M


title: PSCCreMRpos_R_C12_S268


title: PSCCreMRpos_R_C1_S257


title: genomic DNA from CD14+ monocytes_V60M


title: PSCCreMRpos_R_B6_S250


title: genomic DNA from CD14+ monocytes_V58M


title: PSCCreMRpos_R_B7_S251


title: PSCCreMRpos_R_B9_S253


title: PSCCreMRpos_R_B5_S249


title: PSCCreMRpos_R_B3_S247


title: genomic DNA from CD14+ monocytes_V57M


title: genomic DNA from CD14+ monocytes_V56M


title: PSCCreMRpos_R_B2_S246


title: PSCCreMRpos_R_C2_S258


title: genomic DNA from CD14+ monocytes_V61M


title: PSCCreMRpos_R_B1_S245


title: PSCCreMRpos_R_B10_S254


title: genomic DNA from CD14+ monocytes_V53M


title: PSCCreMRpos_R_A3_S235


title: PSCCreMRpos_R_B11_S255


title: PSCCreMRpos_R_A2_S234


title: genomic DNA from CD14+ monocytes_V51M


title: genomic DNA from CD14+ monocytes_V52M


title: genomic DNA from CD14+ monocytes_V50M


title: PSCCreMRpos_R_A11_S243


title: PSCCreMRpos_R_A1_S233


title: genomic DNA from CD14+ monocytes_V54M


title: genomic DNA from CD14+ monocytes_V47M


title: genomic DNA from CD14+ monocytes_V59M


title: PSCCreMRpos_G5


title: genomic DNA from CD14+ monocytes_V49M


title: PSCCreMRpos_H9


title: PSCCreMRpos_R_A10_S242


title: PSCCreMRpos_F_H9_S421


title: genomic DNA from CD14+ monocytes_V45M


title: genomic DNA from CD14+ monocytes_V55M


title: genomic DNA from CD14+ monocytes_V44M


title: genomic DNA from CD14+ monocytes_V43M


title: PSCCreMRpos_F_H6_S418


title: PSCCreMRpos_F_H7_S419


title: genomic DNA from CD14+ monocytes_V42M


title: genomic DNA from CD14+ monocytes_V41M


title: PSCCreMRpos_F_H5_S417


title: genomic DNA from CD14+ monocytes_V40M


title: PSCCreMRpos_F_H4_S416


title: PSCCreMRpos_F_H1_S413


title: PSCCreMRpos_F_H8_S420


title: genomic DNA from CD14+ monocytes_V46M


title: genomic DNA from CD14+ monocytes_V39M


title: PSCCreMRpos_F_H2_S414


title: genomic DNA from CD14+ monocytes_V48M


title: PSCCreMRpos_F_H12_S424


title: PSCCreMRpos_F_H11_S423


title: genomic DNA from CD14+ monocytes_V38M


title: genomic DNA from CD14+ monocytes_V34M


title: genomic DNA from CD14+ monocytes_V37M


title: genomic DNA from CD14+ monocytes_V35M


title: PSCCreMRpos_F_H10_S422


title: genomic DNA from CD14+ monocytes_V33M


title: PSCCreMRpos_F_G6_S406


title: genomic DNA from CD14+ monocytes_V31M


title: PSCCreMRpos_F_G8_S408


title: genomic DNA from CD14+ monocytes_V30M


title: PSCCreMRpos_F_G2_S402


title: genomic DNA from CD14+ monocytes_V29M


title: PSCCreMRpos_F_G10_S410


title: PSCCreMRpos_F_F7_S395


title: genomic DNA from CD14+ monocytes_V28M


title: PSCCreMRpos_F_F5_S393


title: genomic DNA from CD14+ monocytes_V27M


title: PSCCreMRpos_F_F4_S392


title: genomic DNA from CD14+ monocytes_V24M


title: PSCCreMRpos_F_E6_S382


title: genomic DNA from CD14+ monocytes_V25M


title: PSCCreMRpos_F_F2_S390


title: PSCCreMRpos_F_E12_S388


title: genomic DNA from CD14+ monocytes_V22M


title: genomic DNA from CD14+ monocytes_V32M


title: PSCCreMRpos_F_E5_S381


title: PSCCreMRpos_F_E10_S386


title: genomic DNA from CD14+ monocytes_V26M


title: PSCCreMRpos_F_G4_S404


title: genomic DNA from CD14+ monocytes_V16M


title: PSCCreMRpos_F_E7_S383


title: PSCCreMRpos_F_F1_S389


title: genomic DNA from CD14+ monocytes_V14M


title: genomic DNA from CD14+ monocytes_V21M


title: genomic DNA from CD14+ monocytes_V20M


title: PSCCreMRpos_F_D1_S365


title: genomic DNA from CD14+ monocytes_V17M


title: PSCCreMRpos_F_E1_S377


title: PSCCreMRpos_F_E3_S379


title: genomic DNA from CD14+ monocytes_V13M


title: genomic DNA from CD14+ monocytes_V19M


title: PSCCreMRpos_F_E11_S387


title: genomic DNA from CD14+ monocytes_V23M


title: PSCCreMRpos_F_C7_S359


title: PSCCreMRpos_F_D7_S371


title: genomic DNA from CD14+ monocytes_V11M


title: PSCCreMRpos_F_D10_S374


title: PSCCreMRpos_F_D2_S366


title: PSCCreMRpos_F_C2_S354


title: genomic DNA from CD14+ monocytes_V18M


title: PSCCreMRpos_F_C1_S353


title: genomic DNA from CD14+ monocytes_V5M


title: PSCCreMRpos_F_B8_S348


title: PSCCreMRpos_F_B5_S345


title: PSCCreMRpos_F_C6_S358


title: genomic DNA from CD14+ monocytes_V3M


title: genomic DNA from CD14+ monocytes_V9M


title: genomic DNA from CD14+ monocytes_V4M


title: genomic DNA from CD14+ monocytes_V2M


title: PSCCreMRpos_F_B4_S344


title: genomic DNA from CD14+ monocytes_V12M


title: genomic DNA from CD14+ monocytes_V1M


title: PSCCreMRpos_F_C3_S355


title: PSCCreMRpos_F_B10_S350


title: genomic DNA from CD14+ monocytes_V10M


title: genomic DNA from CD14+ monocytes_V15M


title: PSCCreMRpos_F_C5_S357


title: genomic DNA from CD14+ monocytes_V8M


title: PSCCreMRpos_F_A9_S337


title: PSCCreMRpos_F_D12_S376


title: GLU, STA, REP3 (control for STAR samples)

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description:
GSM2418316
STAR_vs_GLU_STA.xlsx
glu_STA - 6
re-analysis of GSM2418316

data_processing:
RNA sequencing was performed using an Illumina HiSeq2500 (50bp single-end reads; >10 million reads per sample) by GeneWiz.
The FASTQ files were uploaded to the GALAXY web-based platform for analysis. Aligments of the reads against the C. japonicus genome was perfomed using the HISAT2 and the transcript quantification was performed with HTSeq.
These counts were then used to generate the differential expression analyses using DESeq2.
Assembly: GCA_000019225.1
Supplementary files format and content: Excel Sheet (The following parameters were calculated: base mean, log2 (fold change), standard error of the log2(fold change), and a Benjamini-Hochberg adjusted p-value).

organism: Cellvibrio japonicus

source_name: bacterial cell

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Standard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

tag: cell type

value: bacterial cell

tag: genotype

value: WT

value: glucose (GLU)

tag: phase

value: Stationary phase (STA)


title: GLU, STA, REP2 (control for STAR samples)

description:
GSM2418315
STAR_vs_GLU_STA.xlsx
glu_STA - 5
re-analysis of GSM2418315

tag: treatment


title: genomic DNA from CD14+ monocytes_V6M


title: PSCCreMRpos_F_A7_S335


title: GLU, STA, REP1 (control for STAR samples)

description:
GSM2418314
STAR_vs_GLU_STA.xlsx
glu_STA - 4
re-analysis of GSM2418314


title: GLU, EXP, REP3 (control for STAR samples)

description:
GSM2418313
STAR_vs_GLU_EXP.xlsx
glu_LOG - 3
re-analysis of GSM2418313

value: Exponential growth (EXP)


title: PSCCreMRpos_F_A3_S331


title: PSCCreMRpos_F_B12_S352


title: PSCCreMRpos_F_A2_S330


title: PSCCreMRpos_F_A12_S340


title: genomic DNA from CD14+ monocytes_V7M

value: RNT


title: PSCCreMRpos_F_C10_S362


title: PSCCreMRpos_F_A10_S338


title: PSCCreMRpos_E7


title: PSCCreMRpos_E9


title: GLU, EXP, REP2 (control for MAN samples)

description:
MAN_vs_GLU_EXP.xlsx
glu_LOG - 2
re-analysis of GSM2418312


title: GLU, STA, REP2 (control for MAN samples)

description:
MAN_vs_GLU_STA.xlsx
glu_STA - 5
re-analysis of GSM2418315


title: PSCCreMRpos_F_A11_S339


title: GLU, EXP, REP1 (control for MAN samples)

description:
MAN_vs_GLU_EXP.xlsx
glu_LOG - 1
re-analysis of GSM2418311


title: PSCCreMRpos_E6


title: GLU, EXP, REP3 (control for MAN samples)

description:
MAN_vs_GLU_EXP.xlsx
glu_LOG - 3
re-analysis of GSM2418313


title: GLU, STA, REP3 (control for MAN samples)

description:
MAN_vs_GLU_STA.xlsx
glu_STA - 6
re-analysis of GSM2418316


title: PSCCreMRpos_E2


title: GLU, EXP, REP1 (control for STAR samples)

description:
GSM2418311
STAR_vs_GLU_EXP.xlsx
glu_LOG - 1
re-analysis of GSM2418311


title: PSCCreMRpos_D_H9_S229


title: CP2A 3.3-derived NSC

city: Bergen

first: Kristina Xiao

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
RNA quality and concentration were checked using Bioanalyzer and QubitTM. RNA-seq libraries were established by the PolyA enrichment method. For iPSCs and NSCs, sequencing was performed by HudsonAlpha. FASTQ files were trimmed using Trimmomatic version 0.39 to remove potential Illumina adapters and low quality bases with the following parameters: ILLUMINACLIP:truseq.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15. FASTQ files were assessed using fastQC version 0.11.8 prior and following trimming. We used Salmon version 1.0.0 to quantify the abundance at the transcript level with the fragment-level GC bias correction option (gcBiasflag) and the appropriate option for the library type (lflag set to A) against the GENCODE release 32 of the human transcriptome (GRCh38.p13). Transcript-level quantification was imported into R and collapsed onto gene-level quantification using the tximport R package version 1.8.0 according to the gene definitions provided by the same GENCODE release. We filtered out genes in non-canonical chromosomes and scaffolds, and transcripts encoded by the mitochondrial genome. Genes were filtered out if their level of expression was below 10 reads in more than 75% of the samples based on CPM (counts per million), which resulted in a total of 20,565 genes for downstream analyses. Transcripts counts were aggregated into gene counts. Sample correlations were calculated with the information of DV200, library size, cell type and mutation, and sample outliers were excluded (Figure S1). Differential expression analysis was conducted using DEseq2. Multiple comparisons were adjusted by using the false discovery rate method. Adjusted P value (q value) <0.05 was considered as statistical significance. KEGG pathway and KEGG module enrichment analysis were conducted using Clusterprofiler. Human MitoCarta 2.0 was used as a reference database of collections of genes with mitochondrial related function and localization. For astrocytes, RNA sequencing was performed by Beijing Genomics Institute (BGI, Shenzhen, China). Library preparation was conducted at BGI following the guide of the standard protocol. The sequencing was performed at BGI-Shenzhen using BGISEQ-500. Low-quality reads and adapter contaminated reads were removed using SOAPnuke software. The processed fastq files were mapped to the human genome using HISAT. The genome version was GRCh38, with annotations from Bowtie2. Then the expression level of the gene was calculated by RSEM (v1.2.12). Differential expression was conducted using the DEseq2 package.
Assembly: NCBI: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: NSC

growth_protocol: iPSCs were grown under feeder-free condition using E8 medium (Invitrogen, cat. no. A1517001) on 6 well Geltrex-coated plates. NSCS were cultured using StemPro™ NSC medium plus bFGF, EGF (Thermo Fisher, cat. no. A1050901) and 1X GlutaMAX™.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Kit (QIAGEN, 74104) following manufacturer’s instructions.
RNA-seq libraries were established by the PolyA enrichment method
Library preparation, hybridization and sequencing were performed according to the manufacturer's standard procedure provided by BGI (BGI-Shenzhen).

value: iPSC-derived NSC

value: POLG mutate (heterozygous c.1399G>A/c.2243G>C; p.A467T/W748S)

tag: Stage

value: Adult


title: GLU, EXP, REP2 (control for STAR samples)

description:
GSM2418312
STAR_vs_GLU_EXP.xlsx
glu_LOG - 2
re-analysis of GSM2418312


title: CP2A 3.1-derived NSC


title: CP2A 3.2-derived NSC


title: CP2A 3.3

source_name: iPSC

value: IPSC


title: GLU, STA, REP1 (control for MAN samples)

description:
MAN_vs_GLU_STA.xlsx
glu_STA - 4
re-analysis of GSM2418314


title: PSCCreMRpos_D_H2_S222

value: Retina

value: Pten fl/fl - Socs3 fl/fl - YFP17 het


title: PSCCreMRpos_D_G8_S216

value: AAV2-Cre / AAV-CNTF

value: PSCCreMRpos


title: PSCCreMRpos_D_G9_S217

value: 6-8 wk old


title: PSCCreMRpos_D_H7_S227


title: CP2A 2.3-derived NSC


title: CP2A 3.2


title: PSCCreMRpos_D_H1_S221


title: CP2A 2.2-derived NSC


title: PSCCreMRpos_D_H6_S226


title: CP2A 3.1


title: PSCCreMRpos_D_H10_S230


title: PSCCreMRpos_D_G7_S215


title: PSCCreMRpos_D_G6_S214


title: CP2A 2.3


title: CP2A 2.2


title: CP2A 2.1-derived NSC


title: PSCCreMRpos_D_G5_S213


title: PSCCreMRpos_D_G3_S211


title: CP2A 1.3-derived NSC


title: CP2A 1.2-derived NSC


title: CP2A 1.1-derived NSC


title: PSCCreMRpos_D_F9_S205


title: PSCCreMRpos_D_F7_S203


title: CP2A 1.3


title: CP2A 1.1


title: PSCCreMRpos_D_F6_S202


title: CP2A 1.2


title: WS5A 3.3-derived NSC

value: POLG mutate (homozygous for c.2243G>C; p.W748S)


title: CP2A 2.1


title: PSCCreMRpos_D_F3_S199


title: WS5A 3.2-derived NSC


title: PSCCreMRpos_D_F1_S197


title: PSCCreMRpos_D_F12_S208


title: WS5A 3.3


title: PSCCreMRpos_D_F4_S200


title: PSCCreMRpos_D_E7_S191


title: WS5A 3.2


title: PSCCreMRpos_D_E8_S192


title: PSCCreMRpos_D_G10_S218


title: PSCCreMRpos_D_F10_S206


title: WS5A 2.1-derived NSC


title: WS5A 2.3


title: PSCCreMRpos_D_D5_S177


title: WS5A 2.2-derived NSC


title: WS5A 3.1


title: PSCCreMRpos_D_D8_S180


title: PSCCreMRpos_D_E10_S194


title: PSCCreMRpos_D_D1_S173


title: PSCCreMRpos_D_D10_S182


title: PSCCreMRpos_D_D7_S179


title: WS5A 1.3


title: WS5A 2.1


title: PSCCreMRpos_D_C5_S165


title: WS5A 1.3-derived NSC


title: PSCCreMRpos_D_D11_S183


title: WS5A 3.1-derived NSC


title: WS5A 1.2-derived NSC


title: WS5A 2.3-derived NSC


title: PSCCreMRpos_D_C2_S162


title: PSCCreMRpos_D_C6_S166


title: WS5A 1.1-derived NSC


title: WS5A 2.2


title: PSCCreMRpos_D_C1_S161


title: PSCCreMRpos_D_C4_S164


title: WS5A 1.2


title: WS5A 1.1


title: CRTL 3.3-derived NSC

value: CTRL

value: Fetal


title: CRTL 3.2-derived NSC


title: PSCCreMRpos_D_B2_S150


title: CRTL 3.1-derived NSC


title: PSCCreMRpos_D_B6_S154


title: CRTL 3.2


title: PSCCreMRpos_D_B3_S151


title: PSCCreMRpos_D_B4_S152


title: PSCCreMRpos_D_B10_S158


title: CRTL 3.1


title: CRTL 2.3-derived NSC


title: PSCCreMRpos_D_A6_S142


title: CRTL 2.2-derived NSC


title: CRTL 2.3


title: PSCCreMRpos_D_A5_S141


title: PSCCreMRpos_D_C11_S171


title: PSCCreMRpos_D9


title: PSCCreMRpos_D5


title: PSCCreMRpos_D6


title: PSCCreMRpos_D3


title: PSCCreMRpos_C8


title: CRTL 2.1


title: CRTL 2.2


title: CRTL 1.2-derived NSC


title: CRTL 3.3


title: PSCCreMRpos_C2


title: CRTL 1.3-derived NSC


title: PSCCreMRpos_C10


title: PSCCreMRpos_B9


title: CRTL 1.1-derived NSC


title: PSCCreMRpos_C6


title: CRTL 1.3


title: CRTL1.2


title: CRTL 2.1-derived NSC


title: ESC 3.3

source_name: ESC

value: ESC

value: Embryo


title: CRTL 1.1


title: PSCCreMRpos_B8


title: PSCCreMRpos_A9


title: ESC 3.3-derived NSC

value: ESC-derived NSC


title: ESC 3.1


title: ESC 3.1-derived NSC


title: ESC 3.2-derived NSC


title: PSCCreMRpos_B5


title: ESC 3.2


title: ESC 2.1-derived NSC


title: ESC 2.3-derived NSC


title: PSCCreMRpos_C7


title: ESC 2.2-derived NSC


title: PSCCreMRpos_A5


title: PSCCreMRneg_B_H8_S132

description: NOT retrogradely labeled surviving RGCs in PtenSocs3CKO+CNTF 21pdc

value: PSCCreMRneg


title: PSCCreMRneg_B_H9_S133


title: PSCCreMRpos_A7


title: ESC 2.3


title: PSCCreMRneg_B_H7_S131


title: ESC 2.2


title: PSCCreMRneg_B_H6_S130


title: PSCCreMRneg_B_H5_S129


title: PSCCreMRpos_B10


title: PSCCreMRneg_B_H4_S128


title: ESC 1.3-derived NSC


title: ESC 2.1


title: PSCCreMRneg_B_H12_S136


title: ESC 1.1-derived NSC


title: PSCCreMRneg_B_H3_S127


title: PSCCreMRneg_B_H1_S125


title: ESC 1.1


title: PSCCreMRneg_B_H2_S126


title: PSCCreMRneg_B_G7_S119


title: ESC 1.3


title: PSCCreMRneg_B_G6_S118


title: iPSC-CM, empty adenovirus, Dox 4

city: Los Angeles

first: Junjie

state: California

address: 650 Charles E Young Dr

department: medicine

institute: UCLA

data_processing:
Salmon 1.8 for alignment
Supplementary files format and content: tab-delimited text files include raw counts

extract_protocol:
RNeasy Mini Kits (Qiagen)
RNAseq with Ribo-Zero Plus rRNA Depletion Kit

value: iPSC

value: cardiomyocyte

value: Doxorubicin


title: ESC 1.2-derived NSC


title: ESC 1.2


title: iPSC-CM, Igfbp3 adenoviral shRNA, Dox 4


title: PSCCreMRneg_B_F7_S107


title: PSCCreMRneg_B_H10_S134


title: PSCCreMRneg_B_G9_S121


title: PSCCreMRneg_B_G8_S120


title: PSCCreMRneg_B_F5_S105


title: iPSC-CM, Igfbp3 adenoviral overexpression, Dox 4


title: iPSC-CM, empty adenovirus, Dox 3


title: PSCCreMRneg_B_F3_S103


title: iPSC-CM, Igfbp3 adenoviral overexpression, Dox 3


title: iPSC-CM, empty adenovirus, Dox 2


title: PSCCreMRneg_B_G10_S122


title: iPSC-CM, Igfbp3 adenoviral shRNA, Dox 1


title: iPSC-CM, empty adenovirus, Dox 1


title: PSCCreMRneg_B_F6_S106


title: PSCCreMRneg_B_F1_S101


title: iPSC-CM, Igfbp3 adenoviral overexpression, Dox 2


title: PSCCreMRpos_D_G4_S212


title: PSCCreMRneg_B_G1_S113


title: iPSC-CM, Igfbp3 adenoviral overexpression, Dox 1


title: iPSC-CM, empty adenovirus, control 4

value: control


title: iPSC-CM, Igfbp3 adenoviral shRNA, Dox 3


title: PSCCreMRneg_B_F2_S102


title: PSCCreMRneg_B_F10_S110


title: PSCCreMRneg_B_E7_S95


title: PSCCreMRneg_B_F12_S112


title: iPSC-CM, empty adenovirus, control 1


title: PSCCreMRneg_B_E5_S93


title: iPSC-CM, Igfbp3 adenoviral shRNA, control 4


title: iPSC-CM, empty adenovirus, control 2


title: PSCCreMRneg_B_E8_S96


title: PSCCreMRneg_B_E9_S97


title: PSCCreMRneg_B_E6_S94


title: PSCCreMRneg_B_E2_S90


title: PSCCreMRneg_B_E11_S99


title: iPSC-CM, Igfbp3 adenoviral shRNA, control 3


title: iPSC-CM, Igfbp3 adenoviral overexpression, control 3


title: PSCCreMRneg_B_D9_S85


title: iPSC-CM, Igfbp3 adenoviral overexpression, control 2


title: PSCCreMRneg_B_D8_S84


title: iPSC-CM, empty adenovirus, control 3


title: iPSC-CM, Igfbp3 adenoviral overexpression, control 1


title: iPSC-CM, Igfbp3 adenoviral shRNA, control 1


title: iPSC-CM, Igfbp3 adenoviral overexpression, control 4


title: wt, ip, 1

city: princeton

first: Ang

last: Li

state: NJ

address: Washington Road

department: chemistry

institute: princeton university

description: wt, ip, 1

data_processing:
NovaSeq Control Software (NVCS) v1.7 was used for the sequencing run and base calling
alignment(STAR), filtering and peak-calling(Paraclu) were performed by using ICOUNT version2.0.0
Assembly: GRCh38
Supplementary files format and content: bed peaks file

source_name: wt, ip

growth_protocol: 5 x 10 cm dish WT or ALKBH1 ko 293 cells.

extract_protocol:
TotalRNA extracted from WT and ALKBH1 knock out cells were first treated with 2 μl DNase I (NEB) to remove DNA contamination. The total RNA was then fragmented into 150 nt fragments using RNA Fragmentation Reagents (Thermo). 100 ng f5C containing oligo was first added into 100 μg fragmented RNA, the mix was then incubated with 2 mM ARP in a 40 mM aqueous NH4OAc buffer pH 5.0 supplemented with 100 mM anisidine for 24 h at 25°C. RNA was then purified using phenol/chloroform extraction. 200 ng RNA was taken out as input, the rest of the samples were incubated with 50 μl pre-washed streptavidin beads in 400 μl IP -buffer (200 mM NaCl, 0.4 mM EDTA, 50 mM PH=7.4 Tris-HCl pH 7.4, and 0.1% NP-40) for 2 hours at 4 °C. The beads were then washed twice with IP -wash buffer (500 mM NaCl, 0.4 mM EDTA, 50mM PH=7.4 Tris-HCl pH 7.4, and 0.1% NP-40). The beads and input samples were treated with Quick-CIP (NEB) at 37 °C for 30 mins with rotation, the input samples were purified using RNA Zymo Clean kit (Zymo Research), and the beads were washed twice with wash buffer.
Reverse transcription was performed using oligonucleotides containing randomized barcodes (UMIs) and two inversely oriented adaptor regions separated by a BamHI restriction site. cDNAs were size-purified on TBE-Urea gels and then circularized by CircLigase II (Epicentre). Circularized cDNAs were digested with BamHI and linearized cDNAs were amplified using Solexa primers and submitted for Illumina sequencing.
Iclip-seq

tag: cell line

value: human embryonic kidney cell

value: WT

tag: fraction

value: IP


title: wt, ip, 2

description: wt, ip, 2


title: ALKBH11ko, ip, 2

description: ALKBH11ko, ip, 2

source_name: ALKBH11ko, ip

value: ALKBH1 knock out


title: ALKBH11ko, ip, 1

description: ALKBH11ko, ip, 1


title: PSCCreMRneg_B_D11_S87

value: Retina

value: Pten fl/fl - Socs3 fl/fl - YFP17 het

value: AAV2-Cre / AAV-CNTF


title: PSCCreMRneg_B_D12_S88

value: 6-8 wk old


title: PSCCreMRneg_B_D10_S86


title: PSCCreMRneg_B_D1_S77


title: ALKBH11ko, input, 2

description: ko, input, 2

source_name: ko, input

value: input


title: PSCCreMRneg_B_C8_S72


title: PSCCreMRneg_B_D5_S81


title: PSCCreMRneg_B_C7_S71


title: PSCCreMRneg_B_C4_S68


title: wt, input, 1

description: wt, input, 1

source_name: wt, input


title: PSCCreMRneg_B_D4_S80


title: PSCCreMRneg_B_C3_S67


title: PSCCreMRneg_B_C6_S70


title: PSCCreMRneg_B_C1_S65


title: PSCCreMRneg_B_C12_S76


title: ALKBH1 without 5EC treatment rep2

source_name: ALKBH1 without 5EC treatment

growth_protocol: 30 x 10 cm dish Flp-In T-Rex 293 cells expressing 3xFlag-ALKBH1 were treated with 1 mg/mL tetracycline once the cells reached 60% confluency.

extract_protocol:
Cells were washed twice with cold PBS and then 500 µl lysis buffer (50 mM Tris–HCL pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate) was added to each dish. Lysates were treated with Turbo DNase (AM2239) and a low (1:200) or high (1:50) concentration of RNaseI (AM2295) at 37 °C for 3 mins with rotation after which they were centrifuged at 13000  rpm for 15 min at 4°C. The supernatant was incubated with anti-FLAG beads (200 μl Protein G beads and 15 µg anti-Flag M2 antibody) at 4 °C overnight with rotation, and the immunoprecipitated material was then washed 3 times with high-salt buffer and then once with CutSmart buffer (NEB) washing. The beads were treated with Quick-CIP (NEB) at 37 °C for 30 mins with rotation, washed twice with high-salt buffer, and then incubated with preadenylated and biotin labeled L3 linker by using T4 RNA ligase I (NEB) at 16 °C overnight. After washing 3 times with high-salt buffer, the beads were boiled with 60 μl sample buffer and 3 μl was analyzed by Western blot for biotinylation with the chemiluminescent nucleic acid detection module (Thermo). The rest of the sample was gel purified based on the position of the biotin signal. Immunoprecipitated RNA was recovered using D-tube dialyzer midi (Merck-Millipore) and digested with proteinase K (NEB).
Reverse transcription was performed using oligonucleotides containing randomized barcodes (UMIs) and two inversely oriented adaptor regions separated by a BamHI restriction site. cDNAs were size-purified (70-80nt, 80-100nt and 100-150nt) on TBE-Urea gels and then circularized by CircLigase II (Epicentre). Circularized cDNAs were digested with BamHI and linearized cDNAs were amplified using Solexa primers and submitted for Illumina sequencing.
Iclip-seq

treatment_protocol: After 12 hr,the medium was changed to fresh medium containing 1 mg/mL tetracycline (Control) or 1 mg/mL tetracycline and 100 mM 5-EC (5-EC-iCLIP) and cultured for another 12 hr.

value: no 5EC (ctrl)


title: PSCCreMRneg_B_C2_S66


title: B cells isolated from donor 7 at visit 14 (setpoint) [ATH006641]

city: Silver Spring

first: Rasmi

last: Thomas

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

data_processing:
FASTQ files were generated from BCL files using bcl2fastq
Trimmomatic v0.36 was used to trim low-quality bases from both ends of each read
Trimmed reads were aligned to the human genome using HISAT2 v2.1.0
Read counts per protein-coding gene were determined using subread featureCounts v1.6.4
The trimmed mean of M-values normalization method (TMM), as implemented in the R package edgeR v3.34.0, was used for normalization
Genome_build: GRCh38 build 97
Supplementary_files_format_and_content: matrix file with read counts for each gene and sample
Supplementary_files_format_and_content: matrix file with TMM normalized expression for each gene and sample

source_name: B cells

extract_protocol:
Total RNA from sorted peripheral blood cells was extracted using the Single Cell RNA Purification kit from Norgen Biotek Corp
RNA libraries were prepared for sequencing using the Illumina Nextera XT kit

tag: timepoint

value: setpoint

value: B cells

tag: pid


title: ALKBH1 without 5EC treatment rep1


title: B cells isolated from donor 7 at visit 1 (prepeak) [ATH006639]

value: prepeak


title: PSCCreMRneg_B_C11_S75

value: PSCCreMRneg


title: B cells isolated from donor 6 at visit 14 (setpoint) [ATH006638]


title: ALKBH11ko, input, 1

description: ko, input, 1


title: PSCCreMRneg_B_C10_S74


title: B cells isolated from donor 5 at Visit 14 (setpoint) [ATH006635]


title: B cells isolated from donor 6 at visit B (HIV-) [ETH006591]

value: HIV-


title: B cells isolated from donor 6 at visit 2 (prepeak) [ATH006636]


title: PSCCreMRneg_B_B3_S55


title: wt, input, 2

description: wt, input, 2


title: PSCCreMRneg_B_B6_S58


title: B cells isolated from donor 5 at Visit 2 (prepeak) [ATH006633]


title: B cells isolated from donor 6 at visit 5 (peak) [ATH006637]

value: peak


title: B cells isolated from donor 5 at Visit 6 (peak) [ATH006634]


title: PSCCreMRneg_B_B2_S54


title: PSCCreMRneg_B_B1_S53


title: B cells isolated from donor 5 at Visit A (HIV-) [ETH006590]


title: B cells isolated from donor 7 at visit B (HIV-) [ETH006592]


title: PSCCreMRneg_B_B11_S63


title: PSCCreMRneg_B_B10_S62


title: B cells isolated from donor 4 at visit 14 (setpoint) [ATH006632]


title: PSCCreMRneg_B_A7_S47


title: PSCCreMRneg_B_A8_S48


title: B cells isolated from donor 4 at visit 4 (peak) [ATH006631]


title: PSCCreMRneg_B_A6_S46


title: B cells isolated from donor 4 at visit 2 (prepeak) [ATH006630]


title: B cells isolated from donor 3 at visit 14 (setpoint) [ATH006629]


title: B cells isolated from donor 7 at visit 5 (peak) [ATH006640]


title: PSCCreMRneg_B_B4_S56


title: B cells isolated from donor 3 at visit 6 (peak) [ATH006628]


title: B cells isolated from donor 4 at visit B (HIV-) [ETH006589]


title: PSCCreMRneg_B_B9_S61


title: B cells isolated from donor 3 at visit 2 (prepeak) [ATH006627]


title: PSCCreMRneg_B_A5_S45


title: PSCCreMRneg_B_A3_S43


title: B cells isolated from donor 3 at visit B (HIV-) [ETH006588]


title: PSCCreMRneg_B_A2_S42


title: PSCCreMRneg_B_A9_S49


title: PSCCreMRneg_B_A12_S52


title: PCreMRpos_H9

description: retrogradely labeled regenerating RGCs in PtenCKO 21pdc

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre

value: PCreMRpos


title: B cells isolated from donor 2 at visit 14 (setpoint) [ATH006626]


title: B cells isolated from donor 2 at visit 2 (prepeak) [ATH006624]


title: PCreMRpos_H7


title: BT549 cells, AZD-Day7

first: Jing

last: Yu

state: Sichuan

address: No.17, Section 3, Renmin South Road

institute: Sichuan university

data_processing:
Using the MAGeCK (v0.5.9.4) count function to obtain the sgRNA read counts of different screening groups (DMSO-Day0, DMSO-Day7, and AZD-Day7)
Assembly: Human GeCKO v2 library A_and_B
Supplementary files format and content: .txt format file includes sgRNA counts

source_name: BT549 cell line AZD day 7

growth_protocol: All cells were cultured in a humidified of 5% CO2 at 37°C in RPMI (Gibco) medium supplementing with 10% fetal bovine serum (FBS) (NATOCOR) and 1% penicillin-streptomycin (100μg/mL, Hyclone)

extract_protocol:
Finally, cells were harvested and snap-frozen in liquid nitrogen to extract genomic DNA (gDNA) using Phenol-Chloroform.
Using genomic DNA as a template, the target product is obtained through two rounds of PCR for High-throughput sequencing

treatment_protocol: Construct the cancer cell lines with constitutive Cas9 expression. Cells were seeded into the cell culture dish. The next day, cells were transduced with Cas9 lentivirus particles  in the presence of 2μg/mL protamine. After transduction, the target cells were treated with 5μg/ml blasticidin for 7 days to select cells that stably express the Cas9 plasmid. Stable Cas9-expressing cells were transduced with the lentiviral sgRNA library at a multiplicity of infection (MOI) of ≈ 0.3 and an average of 500-fold coverage of the library.   Since the library contains 123,411 sgRNAs, at least 2×108 cells were infected to achieve 500-fold coverage. Cells were selected in puromycin (0.5μg/mL) for 5 days after 24h of infection. When the cells have multiplied to 4×108 , the cells are divided into three groups. One group of cells were directly harvested, and the other two groups were treated with DMSO or 1μM AZD6244 for 7 days, respectively.

value: TNBC

value: AZD

tag: time

value: day 7


title: BT549 cells, DMSO-Day7

source_name: BT549 cell line DMSO day 7

value: DMSO


title: BILs, Control, 72 h, rep1

first: Sean

last: Lawler

address: 75 Francis St

institute: Brigham and Women's Hospital

data_processing:
Sequencing reads were aligned to mm10 reference genome using STAR (v2.5)
Raw gene counts calculated by STAR
Rlog normalized counts generated by DESeq2
Assembly: mm10
Supplementary files format and content: STAR_Gene_Counts.csv
Supplementary files format and content: Rlog_Normalized_Counts.csv

source_name: brain infiltrating leukocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries were prepared from 500pg of total RNA using Takara SMARTer Stranded Total RNAseq v2 Pico Mammalian sample preparation reagents according to manufacturers protocols.

value: brain infiltrating leukocytes

value: Control


title: PCreMRpos_H6

value: Retina

value: 6-8 wk old


title: BILs, Control, 72 h, rep2


title: BILs, ADU-S100, 72 h, rep1


title: BILs, ADU-S100, 72 h, rep3


title: BILs, ADU-S100, 72 h, rep2


title: B cells isolated from donor 2 at visit B (HIV-) [ETH006587]


title: BILs, Control, 72 h, rep3


title: B cells isolated from donor 1 at visit 14 (setpoint) [ATH006622]

value: setpoint


title: PCreMRpos_H5


title: PCreMRpos_H4


title: B cells isolated from donor 1 at visit 5 (peak) [ATH006623]

value: B cells


title: Group 3 innate lymphoid cell, WT rep2, scRNAseq

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

description:
BD Rhapsody
sample tag 8

library_source: transcriptomic single cell

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
First of all, read pairs with low mean base quality scores (less than 20) were removed. The filtered R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers(UMIs). R2 reads were aligned to the mice reference genome(GRCm38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence, and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts. The final single-cell expression matrices containing DBEC-adjusted molecules were used for downstream analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Csv files include readcount values for each Sample with different sample tag

source_name: small intestine

extract_protocol:
Intestinal ILC3s were sorted from siLP of wild-type and ThPOK-deficient mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.

value: Group 3 innate lymphoid cell

value: small intestine

value: 6-8 weeks old


title: Group 3 innate lymphoid cell, ThPOK-deficient rep1 and 2, scRNAseq

description:
BD Rhapsody
rep 1 sample tag 2, rep 2 sample tag 10


title: B cells isolated from donor 2 at visit 5 (peak) [ATH006625]

value: peak


title: BT549 cells, DMSO-Day0

source_name: DMSO day 0

value: day 0


title: PCreMRpos_H3

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre


title: B cells isolated from donor 1 at visit 1 (prepeak) [ATH006621]

value: prepeak