title: 3d acute pancreatitis biol rep3

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

hyb_protocol: For fragmentation and labeling 5.5µg single-stranded cDNA was used, hybridized to Mouse Clariom S array and washed according to manufacturer´s instructions.

scan_protocol: The arrays were scanned on a Affynetrix Gene Chip Scanner 3000 and CEL intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing: For probe set extraction and normalization (SST-RMA), expression raw data were transferred to Transcriptome Analysis Console (TAC, 4.0.2.15, Thermo Fisher Scientific, Waltham, MA, USA).  Statistical analysis of the case control study on 4 biological replicates for each group was performed using Anova with ebayes correction. Statistically significant differentially expressed genes were assumed with a fold change of > |2| and FDR <0.05.

source_name: duodenal tissue

label_protocol: After purification and quality assessment using Bioanalyzer (Agilent) transcriptional profiling of intestinal tissue was performed with 200 ng total RNA using the WT Plus Kit and ClariomTM S mouse arrays (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer´s instructions.

growth_protocol: duodenal tissue was prepared from wild type mice with pancreatitis and untreated controls

extract_protocol: Snap frozen intestinal tissue from each mouse was homogenized using the Retsch dismembrator in presence of 700µl Trizol ®. Total RNA was isolated following the manufacturer’s instructions for total RNA isolation from Phenol/ Guanidine-based RNA isolation methods (RNA_Clean-Up and Concentration Kit, Norgen®, Thorold, Canada).

treatment_protocol: acute pancreatitis was induced by partial duct ligation of the pancreatic duct, 3d after surgery animals were sacrificed

tag: strain

value: C57Bl/6-J mice

tag: disease state

value: acute pancreatitis


title: ds20181001-0010

status: Public on Feb 01 2023

type: SRA

city: Los Angeles

first: David

last: Cobrinik

state: CA

address: 4546 Sunset Blvd

country: USA

institute: Children's Hospital Los Angeles

library_source: transcriptomic single cell

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to grch38 using HISAT2
Transcript assembly and quantitation were performed using StringTie
Read count extraction was performed using tximport
Assembly: GRCh38

molecule: polyA RNA

organism: Homo sapiens

source_name: retinal organoid

extract_protocol:
Retinal organoids were cultured per published protocols (Kuwahara et al., 2015; Zhong et al., 2014) with small changes. At desired timepoints (54-55, 70-71, 76, 83-85, 98-99, 112-113, 126-127, 139-140, and 225 days in culture (DIC)), three organoids with bright and organized neuroepithelial layers when viewed with phase contrast microscopy were placed in 1 ml 10 u/ml papain at 37 o C for 10 min, followed by gentle pipetting with a 1000 ul tip to dissociate larger pieces every 5-10 min (at 37o C for an additional 20-30 min total) to obtain a mostly single-cell suspension. ~ 2 volumes of retina culture media (IMDM, 10% fetal bovine serum (FBS), 0.28 u/ml insulin, 55 uM β-mercaptoethanol, glutamine, penicillin-streptomycin] was added to halt dissociation. Cells were centrifuged at 300 x g for 10 min, resuspended for counting, then recentrifuged and resuspended at 10,000 cell/ul in PBS with 5% FBS and CD133-PE, CD44-FITC, and CD49b FITC antibodies. After 1 h at room temperature, samples were diluted in PBS + 5% FBS, centrifuged, and resuspended in PBS with 1% FBS and 10 ug/ml DAPI. Forward and side scatter and CD133+/CD44,CD49b-low gating was used to enrich for cone photoreceptors. Single cells were directly collected from FACS into 1.2 ul lysis buffer droplets on a parafilm-covered glass slide and transferred to low-adherence tubes for subsequent processing.
Full-length single cell cDNA transcripts were generated using SMART-SeqV4 chemistry from Clontech (now Takara Bio) at ~ 0.1x scale using a Mantis liquid handler. Library preparation was performed using the Nextera XT DNA Library Preparation Kit at reduced volume using Mantis liquid handler and otherwise as per the manufacturer instructions.

tag: tissue

value: retinal organoid

tag: cell line

value: human embryonic stem cell (H9)

tag: prep method

value: Kuwahara

tag: prep id

tag: age (dic)

tag: time group

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)

tag: final dataset

value: Y

tag: removal reason


title: ds20181001-0007

value: RPC/MG

value: cRPC


title: ds20181001-0006


title: 3d acute pancreatitis biol rep2

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Mus musculus


title: 3d acute pancreatitis biol rep5


title: 3d acute pancreatitis biol rep1


title: ds20181001-0015


title: ds20181001-0005


title: Tregs acute pancreatitis biol rep1

source_name: Tregs

growth_protocol: Lymphocytes were isolated from spleen of mice (n=4) and sorted regarding their GFP expression via FACS

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

treatment_protocol: Acute pancreatitis was induced by partial pancreatic duct ligation 3d before isolation of Tregs,  untreated animals refer as controls


title: Tregs acute pancreatitis biol rep3


title: 0d control biol rep4

value: control


title: 0d control biol rep1


title: Tregs acute pancreatitis biol rep4


title: Tregs acute pancreatitis biol rep2


title: ds20181001-0004


title: 0d control biol rep5


title: 0d control biol rep6


title: PC-3-TetOn-PARG-H6 exp "B" DOX Rep1

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

description: experiment "B"

library_source: transcriptomic

data_processing:
Illumina FQ sequencing files were imported into CLC Genomics Workbench version 12.0.
The reads were trimmed to remove adapters then the trimmed reads were mapped to the Mouse genome using CLC’s default parameters (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distanc-es, maximum number of hits per read = 10).
Differential expression for RNA-seq analyses was performed in CLC Genomics Workbench 12.0 on the gene-level expression tracks using whole transcriptome RNA-seq with TMM normalization.
Differential expression due to treatment (hPARG+ or control) was tested with the comparison against the control group.
Genome_build: HG38 human genome
Supplementary_files_format_and_content: csv, Maximum group expression value and expression changes

source_name: PC-3 cell line

growth_protocol: PC-3_pLVX_TetOne-Puro cells were cultured in RPMI-1640 (Bio-Whittaker, Walkersville, MD) supplemented with 10% FBS (Hyclone, Logan, UT), pen/strap (1x), non-essential amino acids (0.1mM)

extract_protocol:
RNeasy kit (Qiagen), mRNA was enriched via Poly(A) selection.
For experiment "N" Novogene libraries were prepared with NEB’s Ultra II RNA library kit (both strands), for experiment "B" QB3 libraries were prepared with Roche KAPA HyperPrep library kits (strand specific-reverse).

treatment_protocol: PC-3 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter, signle clones were generated. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml doxycycline and RNA isolated. 3 wells for untreated control group, 3 wells for treated inducible experimental group.

tag: parg

value: PARG overexpression

tag: type

value: prostate cancer

tag: treatment

value: 500ng/ml doxycycline


title: Tregs control biol rep1


title: ds20181001-0001


title: ds20181001-0003


title: Tregs control biol rep3


title: ds20181001-0002


title: PC-3-TetOn-PARG-I4 exp "B" DOX Rep3

description: experiment "B"


title: Tregs control biol rep2


title: PC-3-TetOn-PARG-I4 exp "B" DOX Rep2

description: experiment "B"


title: Tregs control biol rep4


title: PC-3-TetOn-PARG-H6 exp "B" DOX Rep3

description: experiment "B"


title: PC-3-TetOn-PARG-H6 exp "B" DOX Rep2

description: experiment "B"


title: SI2

city: Lincoln

first: Lise

last: Pingault

state: NE

address: 1700 East Campus Mall, 312F Entomology Hall

institute: University of Nebraska-Lincoln

data_processing:
Trimming: Trimmomatic v0.39
Mapping: Tophat2
Differential expression analysis: Cuffdiff v2.2.1
Genome_build: Chinese Sping v2.1
Supplementary_files_format_and_content: Matrix table with gene FPKM for every gene and every sample

organism: Triticum aestivum

source_name: leaf whorl tissue

growth_protocol: Seeds were planted individually in cone-tainers (4 cm top diameter and 20 cm length) with standard greenhouse mix. These cone-tainers (Steuwe and Sons Inc., Corvallis, Oregon, USA) were covered with tube cages and kept in the growth chamber with 14:10 (L:D) photoperiod at 25oC and ca. 60% relative humidity. Cages were made from clear cylindrical plastic tubes (5 cm diameter and 50 cm length), vented with three 5-cm diameter openings covered with Nitex® screen.

extract_protocol:
Wheat whorl tissues (80-100 mg) were ground using 2010 Geno/Grinder® (SPEX SamplePrep, NJ, USA) for 40 seconds at 1400 strokes min-1. Total RNA was extracted from the homogenized tissue using the kit NucleoSpin miRNA for miRNA and RNA purification (Macherey-Nagel, NucleoSpin miRNA, Mini kit for miRNA and RNA purification, ref 740971.50)
mRNA-seq libraries were constructed following the Illumina TruSeq protocol.

treatment_protocol: At 14 days after planting, wheat plants were checked for uniformity in phenotypic growth and health before being used for WCM infestation. The study was conducted as a randomized complete block design with a factorial arrangement of treatments consisting of two wheat varieties (WCM-resistant and WCM-susceptible) and two WCM treatments (infested and non-infested). For each treatment, three replicates were used, and for each treatment, a replicate consisted of three individual wheat plants

tag: cultivar

value: susceptible (Settler CL)

value: leaf whorl

value: wheat curl mite


title: PC-3-TetOn-PARG-H6 exp "B" noDOX Rep2

description: experiment "B"


title: SI3


title: PC-3-TetOn-PARG-H6 exp "B" noDOX Rep1

description: experiment "B"


title: PC-3-TetOn-PARG-I4 exp "B" noDOX Rep3

description: experiment "B"


title: LS174T parental bulk ATAC-seq

city: San Francisco

first: Hani

last: Goodarzi

address: 600 16th St, Office S312D

institute: University of California, San Francisco

library_source: genomic

data_processing:
scRNA-seq QC and alignment with cellranger (v4.0.0)
scRNA-seq processing with Seurat (v4.0.0)
scATAC-seq QC and alignment with cellranger atac (v1.2.0)
scATAC-seq processing with ArchR(v1.0.0)
Bulk ATAC-seq trimming and quality control with trim galore (v0.6.4) and fastqc (v0.11.9)
Bulk ATAC-seq alignment with bowtie2 (v2.4.1)
Bulk ATAC-seq QC with ATACQC(v1.12.5)
Bulk ATAC-seq peak calling with MACS2 (v2.2.6)
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: RDS and narrowPeak

molecule: genomic DNA

source_name: LS174T parental cell line bulk ATAC-seq

growth_protocol: DMEM, 10% FBS, 1% penicillin/streptomycin

extract_protocol: 10X Chromium (v3), 10X ATAC (V1), and bulk ATAC-seq OMNI-SEQ

tag: cell type

tag: sequencing protocol

value: bulk ATAC-Seq lbiraries made with OMNI-SEQ


title: SI1


title: PC-3-TetOn-PARG-I4 exp "B" noDOX Rep2

description: experiment "B"


title: LS174T LvM2 bulk ATAC-seq

source_name: LS174T metastatic LvM2 cell line bulk ATAC-seq


title: LS174T LvM1 bulk ATAC-seq

source_name: LS174T metastatic LvM1 cell line bulk ATAC-seq


title: SC3

value: untreated


title: SC1


title: PC-3-TetOn-PARG-I4 exp "B" noDOX Rep1

description: experiment "B"


title: SW480 LvM2 bulk ATAC-seq

source_name: SW480 metastatic LvM2 cell line bulk ATAC-seq


title: LS174T scRNA-seq

source_name: LS174T cell line and its sequential metastasis derivatives LvM1 and LvM2 scRNA-seq

value: 10X Chromium V3 single cell RNA-seq


title: BC3

value: resistant (Byrd)


title: SC2


title: PC-3-TetOn-PARG-I4 exp "B" DOX Rep1

description: experiment "B"


title: BC1


title: BI3


title: SW480 scRNA-seq

source_name: SW480 cell line and its sequential metastasis derivatives LvM1 and LvM2 scRNA-seq


title: SW480 LvM2 scATAC-seq

source_name: SW480 cell line metastative derivative LvM2 scATAC-seq

value: 10X ATAC-Seq V1


title: 2020.2.10.11: HeLa METTL3-/mut siEIF4A3-1 RNA rep 2

city: Chicago

first: Philip

middle: Cody

last: He

state: IL

address: 929 E 57th Street

institute: University of Chicago

description:
RNA-seq
HeLa_siEIF4A3_5_METTL3mut_DEanalysis.txt

data_processing:
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: HeLa

growth_protocol: DMEM, high glucose, pyruvate (Gibco 11995040), 9.1% FBS, Penicillin Streptomycin (100 U/mL), 47C 5% CO2

extract_protocol:
Trizol extraction of RNA
For m6A-seq and RNA-seq: Illumina Stranded Truseq. MPm6A: Custom library construction as described in methods.

value: HeLa

value: siEIF4A3-1 KD

tag: input or ip

tag: genotype


title: SW480 parental bulk ATAC-seq

source_name: SW480 parental cell line bulk ATAC-seq


title: BI1

tag: tissue


title: wt_cp25_3

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
Quality and adapter trimming was applied to fastq formatted read files with Trim Galore Version 0.6.5 with options: "--fastqc_args '--noextract'", "--illumina", "--length_1 35", "--length_2 35", "--stringency 1", "--length 20", and "--quality 20".
Gene and isoform expression was estimated with RSEM Version 1.3.3 using Ensembl release 101 of the Danio rerio genome for alignment and using command “rsem-calculate-expression” with options: "--keep-intermediate-files", "--star-gzipped-read-file", "-p 64", "--estimate-rspd", "--append-names", "--output-genome-bam", and "--star". This run used 64 threads with the option to estimate the read start position distribution (RSPD) from the data instead of the default uniform RPSD and the option to output a BAM-formatted file of read alignments in genomic coordinates.
Counts were formatted into a count matrix with tximport using default options.
Due to concerns regarding potential confounding experimental variables, this experiment was repeated with improved collection protocols, yielding two runs of RNAseq data. PCA of these two runs revealed high similarity between the two, so the two were "merged" into one by taking the sum of transcript counts from corresponding samples (with respect to time, replicate number, and genetics) from the two runs.
The transcripts from this experiment were aligned to Ensembl gene IDs (Danio rerio, 101). For downstream analysis, it is more valuable to refer to genes by their name to estimate expression. There were 581 genes that were associated with more than one ensembl ID, so the count matrix collapsed these distinct transcript counts by taking the sum of all transcript counts that correspond to the same gene name, effectively removing gene duplicates from the count matrix.
Principal Components Analysis (PCA) was run on the count matrix to identify dominant sources of variance in transcript counts between samples in this experiment. This analysis was conducted with the pipeline developed by Bianca M. Massacci for the MDIBL Bioinformatics Core (Massacci, 2020).
Differential Expression Analysis was performed between wildtype and klf9 -/- samples in the count matrix with the MDIBL Bioinformatics Core’s DESeq2 R script, using R version 4.0.3 and DESeq2 version 1.30.1.
In addition to PC1 being used as a covariate, time was used as a covariant to isolate the time-independent effect of the klf9-knockout. The time-dependent effect of klf9 loss was captured by separating samples by time and rerunning the analysis between wildtype and klf9 -/- samples.
Assembly: Zebrafish genome v11, as obtained from Ensembl release 101, and preprocessed with rsem-prepare-reference, using STAR’s genomeGenerate option, using STAR v 2.7.5c
Supplementary files format and content: tsv and txt files containing raw and transformed/normalized expression data corrected for listed conditions and principal components
Supplementary files format and content: jcoffman_008.ZTp2.5.DESeq2_out.tsv; tab-separated values, DESeq2 output table for comparison of Klf9 -/- vs Wildtype control (WT), at the time point 2.5 hours after lights on.  The first principal component, which was associated with a technical affect of replicates was included as a covariate in the regression.
Supplementary files format and content: jcoffman_008.ZTm3.DEseq2_out.tsv; tab-separated values, DESeq2 output table for comparison of Klf9 -/- vs Wildtype control (WT), at the time point 3 hours before lights on.  The first principal component, which was associated with a technical affect of replicates was included as a covariate in the regression.
Supplementary files format and content: jcoffman_008.gene.counts.tsv; tab-separated values.  RSEM estimated count matrix at the gene level, with removal of duplicate genes as described above
Supplementary files format and content: jcoffman_008.ZT.DESeq2_out.tsv; tab-separated values, DESeq2 output table for comparison of Klf9 -/- vs Wildtype control (WT), at lights on (zeitgeber time).  The first principal component, which was associated with a technical affect of replicates was included as a covariate in the regression.
Supplementary files format and content: jcoffman_008.PC1_time.DESeq2_out.tsv; tab-separated values, DESeq2 output table for comparison of Klf9 -/- vs Wildtype control (WT) across all time points.  The first principal component, which was associated with a technical affect of replicates was included as a covariate in the regression, as was the time of day.
Supplementary files format and content: jcoffman_008.rlog.tsv; DESeq normalized count matrix, using the rlog (regularized log2 function)

organism: Danio rerio

source_name: larvae

growth_protocol: Zebrafish were klf9-/- mutants derived from the AB strain, and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory, and all methods were performed in accordance with the relevant guidelines and regulations. Embryo culture and cortisol treatments were performed as previously described. Briefly, fertilized eggs were collected in the morning, disinfected and at ~4 hours post fertilization placed in dishes with embryo media. Embryos developed in a 28.5o C incubator with a 14/10 light/dark cycle synchronized with the core fish room. Media was changed daily.

extract_protocol:
At -3, 0, and 2.5 hours zeitgeber time (onset of the light phase in the incubator) on day 5 post-fertilization, four biological replicates of klf9-/- mutant and wildtype larvae were collected as follows. Each biological replicate from each genotype and timepoint consisted of six larvae in a 30mm dish in 4ml of media. Larvae were collected from the dish into Eppendorf tubes, media was removed, and larvae immediately snap frozen in liquid nitrogen. Collection of the 8 samples at each time point occurred over ~10 minutes. Frozen samples were stored at -80 deg C. RNA was prepared using the Qiagen RNeasy Plus mini kit (Qiagen 74134). For each set of four biological replicate samples, RLT Plus lysis buffer (plus beta-mercaptoethanol, per kit instructions) was added to each sample immediately upon its retrieval from the freezer, and the sample was then immediately homogenized with a motorized pestle and placed on ice before the next sample was retrieved from the freezer and subjected to the same procedure. Following pestle homogenization replicate samples received simultaneous processing—i.e., passed though Qiashredder columns (Qiagen 79654), bound, washed, and eluted per kit instructions.
RNA was quantified and sent to the Oklahoma State Genomics Facility for Illumina library preparation and single-end sequencing.

value: larvae

tag: genotype WT

tag: developmental stage

value: 5 dpf embryo

tag: time

tag: mdibl id

tag: conc ng_ul

tag: sequence count


title: SW480 LvM1 bulk ATAC-seq

source_name: SW480 metastatic LvM1 cell line bulk ATAC-seq


title: wt_cp25_2


title: 2020.2.10.10: HeLa METTL3-/mut siEIF4A3-1 RNA rep 1

tag: cell line


title: BC2


title: wt_cp25_4


title: 2020.2.10.8: HeLa METTL3-/mut siControl RNA rep 2

value: siControl KD


title: BI2


title: SW480 parental scATAC-seq

source_name: SW480 cell line scATAC-seq


title: ko_cp25_3

tag: genotype Klf9 -/-


title: ko_cp25_4


title: 2020.2.10.7: HeLa METTL3-/mut siControl RNA rep 1


title: 2020.2.10.6: HeLa WT siEIF4A3-1 RNA rep 3

value: WT


title: 2020.2.10.5: HeLa WT siEIF4A3-1 RNA rep 2


title: ko_cp25_2


title: 2020.2.10.12: HeLa METTL3-/mut siEIF4A3-1 RNA rep 3


title: 2020.2.10.4: HeLa WT siEIF4A3-1 RNA rep 1


title: 2020.2.10.3: HeLa WT siControl RNA rep 3


title: 2020.2.10.2: HeLa WT siControl RNA rep 2


title: wt_cp25_1


title: wt_bz00_4


title: ko_cp25_1


title: wt_bz00_3


title: 2020.2.10.9: HeLa METTL3-/mut siControl RNA rep 3


title: gfp.m6a.2.ip.combined: in vitro MPm6A MPm6A rep 2

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_invitro_gfp_m6a

data_processing:
Library strategy: MPm6A
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

value: MPm6A IVT library


title: 2020.2.10.1: HeLa WT siControl RNA rep 1


title: ko_bz00_4


title: gfp.m6a.3.ip.combined: in vitro MPm6A MPm6A rep 3


title: wt_bz00_1


title: gfp.m6a.1.ip.combined: in vitro MPm6A MPm6A rep 1


title: ko_bz00_3


title: ko_bz00_1


title: gfp.m6a.2.IN.combined: in vitro MPm6A input rep 2

description:
MPm6A input
mpm6a_oligo_ratios_invitro_gfp_m6a

value: input


title: wt_am30_4


title: gfp.m6a.1.IN.combined: in vitro MPm6A input rep 1


title: wt_bz00_2


title: gfp.5.4.IP.combined: HeLa 5'UTR MPm6A m6A-IP rep 4

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_gfp.5.txt

value: 5'UTR GFP MPm6A library


title: wt_am30_2


title: wt_am30_3


title: gfp.5.3.IP.combined: HeLa 5'UTR MPm6A m6A-IP rep 3


title: ko_am30_4


title: wt_am30_1


title: ko_am30_2


title: ko_am30_3


title: gfp.5.2.IP.combined: HeLa 5'UTR MPm6A m6A-IP rep 2


title: gfp.5.1.IP.combined: HeLa 5'UTR MPm6A m6A-IP rep 1


title: ko_am30_1


title: PCK33, IL-4

city: Nijmegen

first: Noa

middle: Johanna Maria

last: van den Brink

address: René Descartesdreef 1

department: Experimental Dermatology

country: Netherlands

institute: Radboudumc

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-IL-4-rep1-17555

data_processing:
Paired-end reads were trimmed with Trimgalore 0.6.5 with the options: --paired --quality 10 --length 20 --consider_already_trimmed 10
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using STAR 2.5.0a (Dobin et al., 2013) with default options
Data frames were generated and normalization was performed using DEseq2
Assembly: hg19
Supplementary files format and content: counts.txt contains counts per gene for each sample
Supplementary files format and content: resultsdesq.txt contains results from DEseq2
Supplementary files format and content: Pairwise_comparisons_complete_file.xlsx contains baseMean, Log2FoldChange, lfcSE, stat, pvalue and padj for pairwise comparisons between treatments
Supplementary files format and content: Heatmap_zvalues_per_cluster.xlsx contains z-values for differentially expressed genes from pairwise comparisons per cluster as used for the heatmap in manuscript

source_name: Population control keratinocyte 33

growth_protocol: HEEs were generated using 24-well cell culture inserts (ThinCert, Greiner Bio-One or Nunc, Thermo Fisher Scientific, Waltham, MA, USA) coated with rat tail collagen (100 µg/mL, BD Biosciences) at 4 °C for 1 h prior to seeding of 100.000–150.000 primary human keratinocytes in 100–150 µL CnT-prime medium (CELLnTEC). After 48 h, cell culture medium was switched to 3D differentiation medium for another 24 h, consisting of 60% CnT-Prime 3D Barrier medium (CELLnTEC) and 40% High Glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, St. Louis, MO, USA). Thereafter, the HEEs were lifted to the air–liquid interface (ALI), with the differentiation medium refreshed every other day

extract_protocol:
RNA was harvested using E.Z.N.A Total RNA kit (OMEGA bio-tek), 1µg of total RNA was used for library construction
Libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) following manufactor's protocol

treatment_protocol: AD-HEEs were first stimulated with IL-4 (10 ng/mL, Peprotech (supplemented with 0.05% bovine serum albumin, BSA, Sigma-Aldrich, St. Louis, MO, USA)) at day 4 of the ALI. After 24 h of disease initiation, HEEs were co-stimulated with the SGA derivatives (SGA360 (10 µM), SGA360f (10 µM) and SGA388 (10 µM) and TCDD (10 nM) for 72 h (re-stimulation after 48 h)

value: Population control keratinocyte 33

value: Keratinocyte


title: PCK33, IL4+SGA360

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-IL-4-SGA360-rep1-17556


title: ko_bz00_2


title: PCK33, IL4+SGA360f

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-IL-4-SGA360f-rep2-17385

value: IL-4 + SGA360f


title: gfp.cds.4.IP.combined: HeLa CDS MPm6A m6A-IP rep 4

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_gfp.cds.txt

value: CDS GFP MPm6A library


title: PCK16, IL-4+TCDD

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-IL-4-TCDD-rep1-17561

source_name: Population control keratinocyte 16

value: Population control keratinocyte 16

value: IL-4 + TCDD


title: PCK33, IL-4+TCDD

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-IL-4-TCDD-rep1-17558


title: gfp.m6a.3.IN.combined: in vitro MPm6A input rep 3


title: PCK16, IL4+SGA360f

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-IL-4-SGA360f-rep1-17384


title: DIAC019B

city: Pullman

first: Ryan

middle: Roy

last: Driskell

state: Washington

address: 100 Dairy Rd. BLS 202A

department: Molecular Biosciences

institute: Washington State University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: H5 matrix, seurat object and h5ad of combined processed files.

source_name: Chronic foot ulcer

extract_protocol:
Skin wounds specimens were collected in PBS with 1% Pen/Strep. Tissues were cleaned with 10% betadine, twice in 70% ethanol, and twice in PBS. Tissues digestion followed protocol in Sandoval-Schaefer & Phan et al. to achieve single cell suspensions in DMEM with 700-1200 cells per uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: skin

value: Chronic foot ulcer

tag: disease

value: Non-diabetic


title: DIAC019C


title: PCK33, control

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-control-rep1-17554

value: Control


title: PCK33, IL-4+SGA388

description: bulkRNAseq-KC-3dmodel-stimulated-PCK33-IL-4-SGA388-rep1-17557


title: PCK16, IL4+SGA360

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-IL-4-SGA360-rep1-17383


title: PCK16, IL-4

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-IL-4-rep1-17382


title: DIAC019


title: PCK16, control

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-control-rep1-17381


title: PCK16, IL-4+SGA388

description: bulkRNAseq-KC-3dmodel-stimulated-PCK16-IL-4-SGA388-rep1-17551


title: PCK15, IL-4+TCDD

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-IL-4-TCDD-rep1-17378

source_name: Population control keratinocyte 15

value: Population control keratinocyte 15


title: DIAC013

value: Diabetic


title: DIAC010


title: PCK15, IL-4+SGA388

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-IL-4-SGA388-rep1-17377


title: DIAC009


title: PCK15, IL4+SGA360f

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-IL-4-SGA360f-rep1-17550


title: DIAC007


title: PCK15, IL-4

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-IL-4-rep1-17375


title: sc9, time-course analysis of senescence, bio rep2

city: Seattle

first: Alexander

last: Mendenhall

address: 1959 NE Pacific St, HSB E072

institute: University of Washington

data_processing:
Illumina HiSeq, NovaSeq
Fastq files mapped using STARsolo RNA aligner, barcodes for whitelist were obtained from Rosenberg et al, 2018. The following parameters were used for handling combinatorial barcodes in STARsolo: --soloType CB_UMI_Complex --soloCBposition 0_10_0_17 0_48_0_55 0_86_0_93  --soloUMIposition 0_0_0_9
barcodes, features and matrix files were produced by STARsolo
h5ad files were produced by merging features, barcodes and matrix files and filtering out low read cells/cell debris by identifying an inflection point in UMI/barcode vs barcode rank plot. Barcode to sample conversion was performed via provided barcode-sample combinations in bc_samples.csv files, e.g. sc6_bc_samples.csv
Assembly: hg19
Supplementary files format and content: tab separated values, matrix files, and anndata object files containing cell x gene matrix with low count cells and rarely detected genes filtered out

source_name: lung

extract_protocol:
RNA was extracted following SPLIT-seq protocol: after 3 rounds of barcoding, cells were incubated at 55C in buffer containing SDS and proteinase K for 2 hours. Liberated cDNA/RNA hybrids were then further processed through SPLIT-seq protocol.
The libraries were prepared via SPLIT-seq method. Briefly the cells were barcoded through 3 rounds of combinatorial barcoding. Cells were then lyzed, the library was prepared via series of amplification, fragmentation, size selection, end repair and ligation and pcr-based indexing
SPLIT-seq scRNAseq

treatment_protocol: Senescence was induced with hydrogen peroxide, quiescence was induced with lower serum media, senescence-like arrest was induced with MDM2 inhibitor nutlin-3a.

value: lung

value: fibroblasts

value: oxidative stress (hydrogen peroxide)


title: PCK15, control

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-control-rep1-17374


title: sc7,8, single oxidative stress treatment, bio rep1 and bio rep2

data_processing:
Illumina HiSeq
Fastq files mapped using STARsolo RNA aligner, barcodes for whitelist were obtained from Rosenberg et al, 2018. The following parameters were used for handling combinatorial barcodes in STARsolo: --soloType CB_UMI_Complex --soloCBposition 0_10_0_17 0_48_0_55 0_86_0_93  --soloUMIposition 0_0_0_9
barcodes, features and matrix files were produced by STARsolo
h5ad files were produced by merging features, barcodes and matrix files and filtering out low read cells/cell debris by identifying an inflection point in UMI/barcode vs barcode rank plot. Barcode to sample conversion was performed via provided barcode-sample combinations in bc_samples.csv files, e.g. sc6_bc_samples.csv
Assembly: hg19
Supplementary files format and content: tab separated values, matrix files, and anndata object files containing cell x gene matrix with low count cells and rarely detected genes filtered out

value: oxidative stress (hydrogen peroxide), lower serum, nutlin-3a


title: sc5, time-course analysis of senescence, bio rep2


title: sc5, time-course analysis of senescence, bio rep1


title: scRNA-seq Human Breast Cancer replicate 2

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Human Breast Cancer

data_processing:
Base calls were converted to reads with the software Cell Ranger (10X Genomics; version 3.1)'s implementation mkfastq. These were then aligned against either the  mm10 v3.0.0 (mouse) or GRCh38-3.0.0 (human) genome using Cell Ranger’s count function (an implementation of STAR v2.7.0) with SC3Pv3 chemistry and 5,000 expected cells per sample.
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 1000 transcripts profiled and less than 10% of their transcriptome of mitochondrial origin.
UMIs from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Since samples were hashtagged and pooled, the cell barcodes for each mouse or human sample are kept in a separate assay embedded within the standard three 10X output files, which is the recommended storage format for HTO-indexed 10X data. Each samples contained tissue from a single mouse or human tumor sample and was not FACS sorted.     Values for each barcode for each cell can be found in the matrix.mtx file.  Please see the associated Seurat vignette for additional details: https://satijalab.org/seurat/v3.1/hashing_vignette.html
Hashtag oligos (HTOs) for samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a ‘negative’ HTO distribution is calculated. For each HTO,  the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Cells are then assigned to the HTO for which they have the strongest positive signal. This is accomplished using Seurat's workflow as described in this Vignette: https://satijalab.org/seurat/v3.1/hashing_vignette.html
Genome_build:  mm10 v3.0.0 (mouse) or GRCh38-3.0.0 (human)
Supplementary_files_format_and_content: Filtered 10X matrix counts

source_name: core needle biopsy

extract_protocol:
Tumor Tissue Processing  Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturers protocol. Cells were counted and re-suspended for further processing.
Single Cell Barcoding, Library Preparation, and Sequencing.   Cell suspensions from individual human and mouse samples were labeled with TotalSeq Series B hashtag oligonucleotide-labeled antibodies (BioLegend). Single-cell RNA-seq (scRNA-seq) was then performed at the Stanford Functional Genomics Facility (SFGF) for droplet-based microfluidics using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA). Droplets of the cellular suspensions, reverse transcription master mix, and partitioning oil were mixed, loaded onto a single cell chip, and processed on the Chromium Controller. Reverse transcription was performed, and cDNA was amplified using a BioRad C1000 Touch thermocycler, with cDNA size selected using SpriSelect beads (Beckman Coulter, USA). An Agilent Bioanalyzer High Sensitivity DNA chip was used to analyze cDNA for qualitative control purposes; cDNA was then fragmented using the proprietary fragmentation enzyme blend for 5min at 32°C, followed by end repair and A-tailing at 65°C for 30 min. DNA was double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

tag: strain

value: Human Breast Cancer

value: Unsorted


title: scRNA-seq Human Pancreatic Cancer replicate 2

description: Human Pancreatic Cancer

source_name: surgical resection

value: Human Pancreatic Cancer


title: scRNA-seq Human Breast Cancer replicate 1

description: Human Breast Cancer


title: PMacrophageM1_Mock1

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Basecalling was performed using HiSeq Control Software HD 3.4.0.38, RTA 2.7.7 and bcl2fastq2.17 v2.17.1.14.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.33.
Trimmed sequence reads were mapped to the Human genome (ensembl_release-101) using HISAT2 using default parameters.
Read count extraction was performed on exon features of the human genome (ensembl_release-101) using the featureCounts function of the subread v2 package.
Assembly: ensembl_release-101
Supplementary files format and content: tab-delimited text file include exon read count values of human protein coding genes for each Sample.

source_name: primary human macrophage cells

growth_protocol: Primary human monocytes were thawed and cultured in ImmunoCult™-SF Macrophage Medium (StemCell) with Recombinant M-CSF with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq and sequencing was performed by FASTERIS following Illumina protocols.

treatment_protocol:
Primary human macrophage M1 differentiation was achieved four days post-thaw by treatment with LPS and Interferon-gamma.
Treatment with vector solution or infection with virus was done 2 days post-differentiation for a total of 18h.

value: primary human macrophage cells

value: WT

tag: treatment

value: differentiation to M1, treatment with vector

value: Day 1


title: PMacrophageM1_STINGPOX

value: differentiation to M1, treatment with STINGPOX, MOI = 3


title: PMacrophageM1_Mock2


title: sc2, double oxidative stress treatment


title: PMacrophageM1_OncoVACV

value: differentiation to M1, treatment with OncoVACV, MOI = 3


title: BMDM_KO_Zymosan_3

city: Oxford

first: Sara

last: Danielli

state: Oxon

address: Roosevelt Dr, headington

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of rheumatology

description: AppendixTableS6_WTvsCalhm6KOZymosanDEGs_based_on_Log2fold_change_and_Pvalue

data_processing:
The sequence data quality was checked using FastQC and MultiQC software.
Raw sequence reads were processed to remove adapter sequences and low quality bases using fastp.
The QC passed reads were mapped onto indexed Mouse reference genome (GRCm 38.90) using STAR v2 alligner
The PCR and optical duplicates were marked and removed using Picard tools
Differential expression analysis was carried out using edgeR package after normalizing the data based on trimmed mean of M values.
Assembly: GRCm 38.90
Supplementary files format and content: Each table is an Excel file containig DEG (p value>0.05, log 2 fold change>2) between WT and CALHM6 KO BMDM. For each gene in the table we have: gene Id, p value, P value adjusted, gene name, gene description, gene biotype, ENTREZ number ID, and TF family

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells were differentiated for 7 days in M-CSF (50ng/ml)

extract_protocol:
RNA extracted with RNAeasy mini kit from Quiagen
.  0.5ug of purified total RNA was depleted of ribosomal RNA using NEB rRNA depletion kit (E6310X). NEBNest Ultra II Directional RNA library kit (E7760L) for Illumina was used for library preparation following manufacturers instruction. Briefly, rRNA depleted fraction was fragmented, converted to double stranded cDNA and adapter ligated following end-repair and dA-tailing. Adapter-ligated libraries were generated by PCR using Illumina PE primers and the resulting purified cDNA libraries were applied to an Illumina flow for cluster generation followed by sequencing on an Illumina instrument following manufacturer’s instructions.

treatment_protocol: BMDM were left unstimulated or cultured for 24 hours in the presence of Poly(I:C) (50 ug/ml), LPS (100 ng/ml), IFN-g (10 ng/ml), Zymosan  (100ug/ml) or a combination of the above

value: Bone marrow derived macrophages

value: Zymosan (100 ug/ml)


title: BMDM_KO_PolyIC_3

description: AppendixTableS2_WTvsCalhm6KOPolyICDEGs_based_on_Log2fold_change_and_Pvalue

value: Poly(I:C) (50 ug/ml


title: ds20181001-1040

source_name: retinal organoid

value: retinal organoid

value: human embryonic stem cell (H9)

tag: prep method

value: Zhong

tag: prep id

value: iPSC

tag: age (dic)

tag: time group

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)

tag: final dataset

value: N

tag: removal reason


title: ds20181001-1039

tag: tissue


title: BMDM_KO_LPS-IFNG_3

description: AppendixTableS5_WTvsCalhm6KOLPSAndIFNgDEGs_based_on_Log2fold_change_and_Pvalue

tag: cell type

tag: genotype

value: LPS (100 ng/ml) + IFN-g (10ng/ml)


title: PCK15, IL4+SGA360

description: bulkRNAseq-KC-3dmodel-stimulated-PCK15-IL-4-SGA360-rep1-17376

value: Population control keratinocyte 15

value: Keratinocyte


title: BMDM_KO_Zymosan-IFNg_3

description: AppendixTableS7_WTvsCalhm6KOZymosanAndIFNgDEGs_based_on_Log2fold_change_and_Pvalue

value: Zymosan (100 ug/ml) + IFN-g (10ng/ml)


title: BMDM_KO_IFNg_3

description: AppendixTableS3_WTvsCalhm6KOIFNgDEGs_based_on_Log2fold_change_and_Pvalue

value: IFN-g (10ng/ml)


title: ds20181001-1037


title: BMDM_KO_LPS_3

description: AppendixTableS4_WTvsCalhm6KOLPSDEGs_based_on_Log2fold_change_and_Pvalue

value: LPS (100 ng/ml)


title: BMDM_KO_UN_3

description: AppendixTableS1_WTvsCalhm6KOuntreatedDEGs_based_on_Log2fold_change_and_Pvalue

value: untreated


title: ds20181001-1038


title: scRNA-seq Human Pancreatic Cancer replicate 1

description: Human Pancreatic Cancer

value: Human Pancreatic Cancer

value: Unsorted


title: ds20181001-1036


title: BMDM_KO_PolyIC_2

value: Bone marrow derived macrophages


title: ds20181001-1035


title: BMDM_KO_Zymosan-IFNg_2


title: ds20181001-1034


title: BMDM_KO_Zymosan_2

value: Zymosan (100 ug/ml)


title: ds20181001-1032

value: Y


title: BMDM_KO_LPS-IFNG_2


title: ds20181001-1033

value: retinal organoid


title: BMDM_KO_IFNg_2


title: ds20181001-1030

value: human embryonic stem cell (H9)


title: BMDM_KO_UN_2


title: ds20181001-1031

value: Zhong


title: BMDM_KO_LPS_2


title: BMDM_KO_PolyIC_1

value: Poly(I:C) (50 ug/ml


title: ds20181001-1026


title: BMDM_KO_Zymosan-IFNg_1


title: BMDM_KO_Zymosan_1


title: ds20181001-1025


title: ds20181001-1027


title: ds20181001-1028


title: BMDM_KO_LPS-IFNG_1


title: BMDM_KO_IFNg_1


title: ds20181001-1023


title: ds20181001-1024


title: BMDM_KO_LPS_1


title: ds20181001-1022

value: RPC/MG


title: BMDM_WT_PolyIC_3

value: Wild type


title: ds20181001-1020


title: BMDM_WT_Zymosan-IFNg_3


title: ds20181001-1021


title: ds20181001-1019


title: BMDM_WT_Zymosan_3


title: BMDM_WT_LPS-IFNG_3

value: LPS (100 ng/ml) + IFN-g (10ng/ml)


title: ds20181001-1018


title: ds20181001-1029


title: ds20181001-1017


title: BMDM_WT_LPS_3


title: BMDM_KO_UN_1


title: BMDM_WT_PolyIC_2


title: BMDM_WT_UN_3


title: BMDM_WT_Zymosan-IFNg_2


title: ds20181001-1014

value: cRPC


title: BMDM_WT_Zymosan_2


title: ds20181001-1013


title: ds20181001-1012


title: DIAC016

value: skin

value: Chronic foot ulcer

value: Diabetic


title: BMDM_WT_LPS-IFNG_2


title: BMDM_WT_IFNg_2

value: IFN-g (10ng/ml)


title: ds20181001-1011


title: ds20181001-1009


title: ds20181001-1007


title: ds20181001-1008


title: ds20181001-1006


title: BMDM_WT_PolyIC_1


title: ds20181001-1016


title: ds20181001-1015


title: BMDM_WT_Zymosan_1


title: BMDM_WT_Zymosan-IFNg_1

value: Zymosan (100 ug/ml) + IFN-g (10ng/ml)


title: BMDM_WT_IFNg_1


title: ds20181001-1004


title: ds20181001-1005


title: BMDM_WT_LPS_1

value: LPS (100 ng/ml)


title: ds20181001-1001


title: ds20181001-1003


title: BMDM_WT_UN_1

value: Bone marrow derived macrophages

value: untreated


title: Maf flox/flox rep4

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
Sequencing reads were mapped to the Ensembl mouse genome (release GRCm38.102) using subread (version 2.0.2) (PMID:23558742) and the read counts  aligning to known genes were generated by featureCounts (PMID: 24227677).
The read counts were normalized with the iDEGES/edgeR method implemented in TCC (version 1.34.0) (PMID:12770646), and pairwise comparisons of gene expression between livers from WT control and Lmln KO were conducted with the edgeR (version 3.36.0) (PMID:19910308). The false discovery rate (FDR) adjustments (DOI:http://www.jstor.org/stable/2346101) were applied to correct for multiple testing, and differentially expressed genes (DEGs) were identified with an FDR cutoff of 0.05.
Assembly: GRCm38.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole kidney

extract_protocol:
Total RNA from the liver was isolated using the TRIZOL reagent (Thermo Fisher Scientific). RNA quality was examined by RNA 6000 Pico kit (Agilent, Santa Clara, CA). An amount of 50 ng total RNA was used for RNA-seq library preparation with NEB NEBNext rRNA Depletion Kit and ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA); 2x36 base paired-end sequencing was performed with NextSeq500 (Illumina, San Diego, CA) by Tsukuba i-Laboratory LLP (Tsukuba, Ibaraki, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole kidney

tag: age

value: post natal 8 weeks

value: Maf flox/flox


title: ds20181001-1000

value: retinal organoid

tag: cell line

value: human embryonic stem cell (H9)

value: Zhong

value: Y


title: ds20181001-1010

value: RPC/MG


title: Maf flox/flox rep3


title: BMDM_WT_LPS_2

value: Wild type


title: Maf flox/flox rep2


title: ds20181001-0998


title: Maf flox/flox rep1


title: ds20181001-0997


title: ds20181001-0996


title: Maf conditional KO rep4

value: Maf conditional KO


title: ds20181001-0999

value: cRPC


title: BMDM_WT_UN_2


title: BMDM_WT_LPS-IFNG_1

value: LPS (100 ng/ml) + IFN-g (10ng/ml)


title: Maf conditional KO rep3


title: ds20181001-0994


title: ds20181001-0995

value: ConeSG


title: Maf conditional KO rep1


title: ds20181001-0992


title: ds20181001-0991


title: scATAC-seq Mouse Breast Cancer

description: Mouse Breast Cancer

data_processing:
Fastq files were aligned to the mm10 mouse genome, peaks were called, fragements filtered, and peacks annoted in a single step using the 10X Genomics software CellRanger with the command "cellranger-atac count" using default parameters
Genome_build: mm10 v3.0.0
Supplementary_files_format_and_content: Standard 10X Genomics scATAC-seq filtered_peak_bc_matrix files

source_name: endogenous tumor

value: Black 6

value: Mouse Breast Cancer

value: Unsorted


title: ds20181001-0990


title: ds20181001-0988


title: MI_day_3_rep2

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

data_processing:
The Cell Ranger ATAC Software Suite (version 1.2.0) was used for processing sequencing information and single cell barcodes.
Female and male fragments for each timepoint was merged, then macs2(version 2.2.7.1) was used to do peakcalling.
Seurat (version 3.2.2) was used to integrate the snATAC-seq data and predict cell labels based on scOpen estimated matrix.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: fragments: a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay and positions are 0-based. The columns are defined as following: chrom, chromStart, chromEnd, barcode and duplicateCount.
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: peaks: a bed file contains the output of the peak calling algorithm. Each peak is an interval on the genome that has a local enrichment of transposase cut-sites.

source_name: Mouse Heart of Myocardial Infarction

extract_protocol: All protocols to generate snATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.

value: Heart

tag: Stage

value: Day 3

tag: gender

value: Male


title: MI_day_10_rep2

value: Day 10


title: MI_day_10_rep1

value: Female


title: ds20181001-0989

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to grch38 using HISAT2
Transcript assembly and quantitation were performed using StringTie
Read count extraction was performed using tximport
Assembly: GRCh38

value: retinal organoid

value: human embryonic stem cell (H9)


title: MI_day_3_rep1


title: ds20181001-0987

value: Zhong

value: Y


title: MI_day_0_rep2

value: Day 0


title: MI_day_0_rep1


title: ds20181001-0984


title: ds20181001-0985


title: ds20181001-0986


title: ds20181001-0983


title: Maf conditional KO rep2

tag: strain

value: Whole kidney

value: post natal 8 weeks

value: Maf conditional KO


title: ds20181001-0982


title: set104.ChIP-seq.WT.starvation.input.rep3.bw

city: Baltimore

first: Weidong

last: Wang

state: MD

address: 251 Bayview Blvd

department: National Institute on Aging

institute: Shuaikun Su

data_processing:
For RNA-seq, the reads were mapped to human genome (hg38) with HISAT2. The raw read counts were generated by HTSeq-Count. The differentially expressed genes (DEGs) and normalized read counts were generated by DESeq2. The genes with total read counts (untreated and treated groups) less than 10 were removed. The DEGs were identified by the thresholds (For starvation-induced DEGs, fold change > 2 and adjusted p-values < 0.05; For the DEGs caused by TOP3B-KO/TDRD3-KO/Y336F-KI mutants, fold change > 1.5 and adjusted p-values < 0.1).
For ChIP-seq, the reads were mapped to the genome using Bowtie2 allowing maximum of 2 mismatches. The bigwig files, heatmaps, metagene profile analysis were generated by deepTools. The bigwig files were visualized by Integrative Genomics Viewer (IGV). The TDRD3 binding peaks were identified by MACS2 using input samples as a control. Only the peaks identified by both replicates (WT groups) were used to extract reads counts by BEDTools. The normalized read counts from peak regions were used to calculate the fold changes in Excel. The enriched peaks (Fold change (WT/KO) > 1.5 in both replicates) were selected and annotated using HOMER. For RNAPII and RNAPII-ser2p ChIP-seq, raw read counts near transcription start site (TSS) regions (-500 - +500bp) and transcription end site (TES) regions (0 - -2000bp) were generated by BEDTools. The normalized read counts and DEGs (fold change > 1.5 and adjusted p-value < 0.1) were generated by DESeq2.
Assembly: hg38
Supplementary files format and content: bigwig files; Reads visualization across the genome.

source_name: human colorectal carcinoma cell line

growth_protocol: HCT116 cells were cultured in  DMEM with 10% fetal bovine serum (HyClone) and 1% antibiotics (Penicillin-Streptomycin, Sigma).

extract_protocol:
Different sequencing types have different protocols, please follow the protocols in the "Materials and Methods" part in the article. Briefly, for RNA-seq, total RNAs were extracted with TRizol. Then 10µg RNA were used to purify mRNAs by oligo dT beads. The mRNAs were used to generate library for Illumina sequencing.  For ChIP-seq, the starved or no treatment cells were crosslinked by formaldehyde (final 1%). Then the chromatins were sonicated by Bioruptor before pulling down by antibodies (TDRD3, RNAPII or RNAPII-ser2p). The DNAs were extracted from the immunoprecipitated chromatins  and were used for library generation. Finally, the libraries were sent for Illumina sequencing.
For RNA-seq and ChIP-seq, library construction protocol can be found here (Y. Joo et al., Topoisomerase 3beta knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity. Nat Commun 11, 3143 (2020).).

treatment_protocol: For starvation, HCT116 cells were washed once using 5mL warm (37 degree) PBS, then treated with warm (37degree) Earle’s Balanced Salt Solution (EBSS) for 6 hours before collecting cells.

value: Wild type

tag: treatment

value: starved with EBSS for 6 hours

tag: molecule type

value: DNA fragments


title: set104.ChIP-seq.WT.input.rep3.bw

value: non treatment


title: set104.ChIP-seq.WT.RNAPII.rep3.bw


title: set104.ChIP-seq.TOP3B-KO.starvation.input.rep3.bw


title: set104.ChIP-seq.TOP3B-KO.starvation.RNAPII.rep3.bw


title: ds20181001-0979

tag: prep method

tag: prep id


title: ds20181001-0980

tag: age (dic)

tag: time group

value: ConeSG


title: ds20181001-0978

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)


title: ds20181001-0981

tag: final dataset

tag: removal reason


title: set104.ChIP-seq.TOP3B-KO.input.rep3.bw


title: set101.ChIP-seq.WT.starvation.RNAPII-ser2p.rep3.bw


title: ds20181001-0977

tag: tissue

value: RPC/MG


title: set104.ChIP-seq.TOP3B-KO.RNAPII.rep3.bw

tag: genotype


title: ds20181001-0976


title: set104.ChIP-seq.WT.starvation.RNAPII.rep3.bw


title: set101.ChIP-seq.WT.input.rep3.bw


title: ds20181001-0975


title: ds20181001-0974


title: set101.ChIP-seq.TOP3B-KO.starvation.input.rep3.bw


title: ds20181001-0973


title: set92.ChIP-seq.wt.starvation.RNAPII.rep2.bw


title: ds20181001-0972


title: set101.ChIP-seq.TOP3B-KO.starvation.RNAPII-ser2p.rep3.bw


title: set92.ChIP-seq.wt.RNAPII.rep2.bw


title: set92.ChIP-seq.wt.RNAPII-ser2p.rep2.bw


title: set92.ChIP-seq.wt.starvation.RNAPII-ser2p.rep2.bw


title: ds20181001-0969


title: ds20181001-0968


title: ds20181001-0966


title: ds20181001-0964


title: ds20181001-0971


title: set91.HCT116.chip-seq.wt.starvation.RNAPII-ser2p.rep1.bw


title: set91.HCT116.chip-seq.wt.starvation.input.rep1.bw


title: set91.HCT116.chip-seq.wt.starvation.RNAPII.rep1.bw


title: ds20181001-0965


title: set101.ChIP-seq.WT.RNAPII-ser2p.rep3bw


title: ds20181001-0963


title: set91.HCT116.chip-seq.wt.input.rep1.bw


title: set91.HCT116.chip-seq.wt.RNAPII.rep1.bw


title: ds20181001-0961


title: ds20181001-0962


title: ds20181001-0960


title: ds20181001-0970


title: set91.HCT116.chip-seq.top3bko1.starvation.input.rep1.bw


title: set92.ChIP-seq.top3bko1.starvation.RNAPII.rep2.bw


title: ds20181001-0958


title: set91.HCT116.chip-seq.wt.RNAPII-ser2p.rep1.bw


title: set91.HCT116.chip-seq.top3bko1.starvation.RNAPII.rep1.bw


title: set91.HCT116.chip-seq.top3bko1.starvation.RNAPII-ser2p.rep1.bw


title: ds20181001-0956


title: set90.hct116.rna-seq.y336fki.starvation.rep3.bw

value: polyA RNAs


title: ds20181001-0955


title: set90.hct116.rna-seq.y336fki.starvation.rep2.bw


title: set90.hct116.rna-seq.y336fki.starvation.rep1.bw


title: ds20181001-0952


title: ds20181001-0967


title: set90.hct116.rna-seq.wt.rep3.bw


title: ds20181001-0948


title: ds20181001-0951


title: set90.hct116.rna-seq.wt.starvation.rep2.bw


title: set90.hct116.rna-seq.wt.starvation.rep1.bw


title: ds20181001-0949


title: ds20181001-0947


title: ds20181001-0959


title: ds20181001-0946


title: ds20181001-0945


title: set90.hct116.rna-seq.tdrd3ko.starvation.rep1.bw


title: set90.hct116.rna-seq.tdrd3ko.starvation.rep2.bw


title: ds20181001-0944


title: set89.RNA-seq.hct116.wt.starvation.rep3.bw


title: ds20181001-0942


title: set89.RNA-seq.hct116.wt.starvation.rep2.bw


title: ds20181001-0943


title: set89.RNA-seq.hct116.wt.rep3.bw


title: ds20181001-0941


title: set89.RNA-seq.hct116.top3b-ko.starvation.rep3.bw


title: set89.RNA-seq.hct116.wt.rep2.bw


title: set92.ChIP-seq.top3bko1.starvation.RNAPII-ser2p.rep2.bw


title: ds20181001-0940


title: set90.hct116.rna-seq.tdrd3ko.starvation.rep3.bw


title: set90.hct116.rna-seq.wt.starvation.rep3.bw


title: ds20181001-0939


title: ds20181001-0950


title: ds20181001-0938


title: set89.RNA-seq.hct116.top3b-ko.rep3.bw


title: set89.RNA-seq.hct116.top3b-ko.starvation.rep2.bw


title: ds20181001-0934


title: ds20181001-0933


title: set89.RNA-seq.hct116.top3b-ko.rep2.bw


title: ds20181001-0936


title: set89.ChIP-seq.hct116.wt.tdrd3.rep2.bw


title: set89.ChIP-seq.hct116.wt.starvation.tdrd3.rep2.bw


title: ds20181001-0932


title: set89.ChIP-seq.hct116.wt.starvation.input.rep2.bw


title: ds20181001-0930


title: set89.ChIP-seq.hct116.tdrd3-ko.tdrd3.rep2.bw


title: ds20181001-0926


title: ds20181001-0927


title: set89.ChIP-seq.hct116.tdrd3-ko.input.rep2.bw


title: set89.ChIP-seq.hct116.wt.input.rep2.bw


title: set89.ChIP-seq.hct116.tdrd3-ko.starvation.tdrd3.rep2.bw


title: ds20181001-0929


title: ds20181001-0925


title: set88.RNA-seq.hct116.wt.starvation.rep1.bw


title: set88.RNA-seq.hct116.wt.rep1.bw


title: ds20181001-0924


title: set88.RNA-seq.hct116.top3b-ko.rep1.bw


title: set88.RNA-seq.hct116.top3b-ko.starvation.rep1.bw


title: ds20181001-0922


title: set89.ChIP-seq.hct116.tdrd3-ko.starvation.input.rep2.bw


title: ds20181001-0923

value: MG


title: ds20181001-0921


title: set88.ChIP-seq.hct116.wt.tdrd3.rep1.bw


title: ds20181001-0931


title: set88.ChIP-seq.hct116.wt.starvation.tdrd3.rep1.bw


title: set88.ChIP-seq.hct116.wt.starvation.input.rep1.bw


title: ds20181001-0919


title: ds20181001-0928

value: cRPC


title: ds20181001-0917

value: retinal organoid


title: ds20181001-0916

value: human embryonic stem cell (H9)


title: set88.ChIP-seq.hct116.tdrd3-ko.starvation.tdrd3.rep1.bw


title: set88.ChIP-seq.hct116.wt.input.rep1.bw


title: set88.ChIP-seq.hct116.tdrd3-ko.starvation.input.rep1.bw


title: set88.ChIP-seq.hct116.tdrd3-ko.input.rep1.bw


title: ds20181001-0915

value: Zhong


title: ds20181001-0912

value: Kuwahara

value: Y


title: MCF7, RNA, siSET, E2, rep3

city: Mexico City

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

data_processing:
Reads were aligned to the Human Reference Genome hg19 (GRCh37/hg19) using Bowtie 2.3.4 with default parameters
Duplicated reads and reads with a MAPQ < 10 were discarded using macs2 filterdup and samtools v1.7, respectively
The remaining alignments were used as input for MACS 2.1.1 for peak calling, using their respective input as control with an FDR of 5e-4, except for SET, for which an FDR of 5e-2 was used
Peaks falling into blacklisted regions from the ENCODE project were discarded and bigwig files of normalized reads/input were generated for visualization from MACS2 with a window size of 150 bp.
Assembly: hg19
Supplementary files format and content: Bigwig files show normalized ChIP enrichment/Input (except for Input, which only shows normalized input)
Supplementary files format and content: txt tab-delimited includes raw read counts for all the samples in the RNA-seq experiment

growth_protocol: MCF7 cells were maintained in DMEM high glucose medium (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 2 mM L-glutamine and penicillin/streptomycin.

extract_protocol:
For ChIP ~2-4 X106 MCF7 cells treated with E2 for the indicated times were fixed with ChIP Cross-link Gold (Diagenode) according to the manufacturer's instructions. Nuclei were purified and fragmented using a nuclear Co-IP kit (Active Motif). After digestion, chromatin was sonicated to an average size of 250 bp. The fragmented chromatin was immunoprecipitated overnight by using the corresponding antibodies. For RNA-seq, total RNA was extracted with Trizol following manufacturer's instructions
For ChIP-seq, the NEBNext Ultra II DNA Library Prep Kit was used to produce high yield libraries from a small amount of purified DNA. For RNA-seq, the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used, using 1ug of total RNA as Input

treatment_protocol: For experiments related to estrogen stimulus, cells were washed with PBS and kept in phenol-red free DMEM for 2 hours and then cultured in phenol-red free DMEM supplemented with 5% charcoal:dextran stripped FBS (Hyclone) for at least 72 hr. For siRNA mediated SET knockdown (KD), MCF7 cells were transfected with siGENOME siRNA SMARTpool (Dharmacon) using the DhamaFECT transfection reagent (GE Dharmacon).

value: si SET

value: estrogen


title: ds20181001-0913

extract_protocol:
Retinal organoids were cultured per published protocols (Kuwahara et al., 2015; Zhong et al., 2014) with small changes. At desired timepoints (54-55, 70-71, 76, 83-85, 98-99, 112-113, 126-127, 139-140, and 225 days in culture (DIC)), three organoids with bright and organized neuroepithelial layers when viewed with phase contrast microscopy were placed in 1 ml 10 u/ml papain at 37 o C for 10 min, followed by gentle pipetting with a 1000 ul tip to dissociate larger pieces every 5-10 min (at 37o C for an additional 20-30 min total) to obtain a mostly single-cell suspension. ~ 2 volumes of retina culture media (IMDM, 10% fetal bovine serum (FBS), 0.28 u/ml insulin, 55 uM β-mercaptoethanol, glutamine, penicillin-streptomycin] was added to halt dissociation. Cells were centrifuged at 300 x g for 10 min, resuspended for counting, then recentrifuged and resuspended at 10,000 cell/ul in PBS with 5% FBS and CD133-PE, CD44-FITC, and CD49b FITC antibodies. After 1 h at room temperature, samples were diluted in PBS + 5% FBS, centrifuged, and resuspended in PBS with 1% FBS and 10 ug/ml DAPI. Forward and side scatter and CD133+/CD44,CD49b-low gating was used to enrich for cone photoreceptors. Single cells were directly collected from FACS into 1.2 ul lysis buffer droplets on a parafilm-covered glass slide and transferred to low-adherence tubes for subsequent processing.
Full-length single cell cDNA transcripts were generated using SMART-SeqV4 chemistry from Clontech (now Takara Bio) at ~ 0.1x scale using a Mantis liquid handler. Library preparation was performed using the Nextera XT DNA Library Preparation Kit at reduced volume using Mantis liquid handler and otherwise as per the manufacturer instructions.


title: MCF7, RNA, siSET, E2, rep2


title: ds20181001-0908


title: ds20181001-0909


title: MCF7, RNA, siSET, EtOH, rep3

value: control


title: ds20181001-0911


title: ds20181001-0920


title: MCF7, RNA, siCtrl, E2, rep3

value: si Control


title: MCF7, RNA, siCtrl, E2, rep1


title: MCF7, RNA, siSET, EtOH, rep2


title: MCF7, RNA, siSET, E2, rep1


title: ds20181001-0918


title: MCF7, RNA, siCtrl, E2, rep2


title: ds20181001-0907


title: ds20181001-0906


title: set88.ChIP-seq.hct116.tdrd3-ko.tdrd3.rep1.bw


title: ds20181001-0905


title: MCF7, RNA, siCtrl, EtOH, rep3


title: MCF7, RNA, siSET, EtOH, rep1


title: ds20181001-0904


title: ds20181001-0903


title: ds20181001-0914


title: ds20181001-0902


title: ds20181001-0910


title: MCF7, ChIP, ERa, siSET, E2

tag: antibody

value: ERa


title: MCF7, RNA, siCtrl, EtOH, rep1

tag: cell line


title: MCF7, ChIP, ERa, siCtl, E2


title: ds20181001-0900


title: MCF7, ChIP, ERa, siSET, EtOH


title: ds20181001-0899


title: ds20181001-0898


title: MCF7, ChIP, SET, E2

value: SET


title: MCF7, ChIP, SET, EtOH


title: ds20181001-0896


title: ds20181001-0897


title: ds20181001-0894


title: MCF7, ChIP, ERa, siCtl, EtOH


title: MCF7, ChIP, IgG

value: IgG


title: ds20181001-0895


title: MCF7, ChIP, Input


title: MCF7, RNA, siCtrl, EtOH, rep2


title: ds20181001-0893


title: ds20181001-0892


title: ds20181001-0901


title: ds20181001-0891


title: ds20181001-0890


title: ds20181001-0889


title: ds20181001-0888

value: N


title: ds20181001-0887


title: WT_Ctrl_3

city: Beijing

first: Zijun

last: Sun

address: No 8, Xishiku Street

country: China

institute: Peking University First Hospital

data_processing:
Quality control and mapping: Raw data (raw reads) were processed using Trimmomatic . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest.
Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Kidney

growth_protocol: Cfb knockout and WT male mice were housed in with a 12-hour light-dark cycle, pathogen-free condition, and bacteria-free diet.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500) and 125bp/150bp paired-end reads were generated.

treatment_protocol: HFD (60% of total calories from fat) was fed to diabetic groups for four weeks. Meanwhile, non-diabetic groups were fed a normal chow diet (10% of total calories from fat). After fasting for 4 hours, the diabetic groups received an intraperitoneal injection of STZ (S0130; Sigma-Aldrich, St Louis, USA) dissolved in 50 mM sodium citrate at 60 mg/kg for five consecutive days, while the non-diabetic groups were supplemented with an equivalent amount of 50 mM sodium citrate buffer.

value: Kidney

tag: Sex

value: male

value: WT

value: STZ/HFD induced diabetic mice

tag: diet

value: Normal chow diet (10% of total calories from fat)

tag: disease

value: Healthy control

tag: time

value: 34 weeks


title: ds20181001-0886

city: Los Angeles

last: Cobrinik

address: 4546 Sunset Blvd

institute: Children's Hospital Los Angeles

value: retinal organoid

value: human embryonic stem cell (H9)

value: Kuwahara


title: ds20181001-0885

value: Y


title: WT_Ctrl_1

tag: treatment

tag: strain


title: CFB_KO_Ctrl_3

value: Cfb knockdown


title: WT_Ctrl_2


title: CFB_KO_Ctrl_2


title: WT_STZ_4

value: High fat diet(HFD, 60% of total calories from fat)

value: Diabetic kidney disease


title: ds20181001-0884

tag: prep method

tag: prep id


title: ds20181001-0881

tag: age (dic)

tag: time group


title: WT_STZ_3


title: ds20181001-0882

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)


title: CFB_KO_Ctrl_1


title: WT_STZ_1


title: ds20181001-0878

tag: final dataset

tag: removal reason


title: WT_STZ_2

tag: tissue

tag: genotype


title: ds20181001-0879

tag: cell line


title: ds20181001-0876


title: CFB_KO_STZ_4

tag: Sex


title: Tao3+/+ RAW264.7 cells, untreated

city: Shanghai

first: Taoyong

last: Chen

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression data from wild type RAW264.7 cells

hyb_protocol: The hybridization was done at the Shanghai Biotechnology Corporation (Shanghai, China). Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat #900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat #00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat #00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: The scanning was done at the Shanghai Biotechnology Corporation (Shanghai, China). Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The genes in each Matrix template are arranged according to affymetrix probe set id.

label: Biotin

source_name: Tao3+/+ RAW264.7 cells, untreated

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’ IVT Express Kit (Cat #901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA at the Shanghai Biotechnology Corporation (Shanghai, China).

extract_protocol: Total RNA was isolated from the cells using the TRIZOL method (InVitrogen), followed by digestion with RNase-free DNase (Qiagen) and purification on RNeasy spin columns using RNeasy Minikit (Qiagen).

treatment_protocol: Wild type and Tao3−/− RAW264.7 cells were infected with Vesicular Stomatitis Virus (VSV, MOI=1) or herpes simplex virus 1 (HSV-1, MOI=5) for 6h.

tag: cell type

value: macrophage


title: ds20181001-0877

first: David


title: Tao3−/− RAW264.7 cells, untreated

description: Gene expression data from Tao3−/− RAW264.7 cells

source_name: Tao3−/− RAW264.7 cells, untreated


title: Tao3+/+ RAW264.7 cells infected with VSV

description: Gene expression data from wild type RAW264.7 cells infected with VSV


description: Gene expression data from Tao3−/− RAW264.7 cells infected with HSV-1


title: CFB_KO_STZ_3

tag: diet

tag: disease


description: Gene expression data from Tao3−/− RAW264.7 cells infected with VSV


title: ds20181001-0875


title: CFB_KO_STZ_2

tag: treatment

tag: time


title: ds20181001-0874

tag: prep method


title: ds20181001-0873

tag: prep id


title: ds20181001-0871

tag: age (dic)


title: ds20181001-0869

tag: time group


title: ds20181001-0883

tag: cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia, conesg = cone side group)


title: ds20181001-0870

tag: reduced data cluster cell type (crpc = cycling retinal progenitor cell, mg = muller glia)


title: CFB_KO_STZ_1

tag: strain


title: ds20181001-0880

tag: final dataset

tag: removal reason


title: Treg, CD18wt, stimulated, biol rep3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Primary sequencing results were processed according to the Illumina standard protocol.
Sequence reads were trimmed (deleting adapter sequences) and processed using the CLC Genomics Workbench software (v20.0, default settings; Qiagen).
Differentially regulated genes (> 2-fold) were sorted based on log2 [fold change] maximum-likelihood estimation with the P-value cut-off set to 0.05.
Assembly: Reads were aligned to GRCm38 genome.
Supplementary files format and content: tab deliminated text files include RPKM values for each sample

source_name: Spleen

growth_protocol: Splenic RFP-positive CD4+ T cells (each about 10e5 per sample) were sorted by flow cytometry using a FACSAriaII (BD Biosciences).

extract_protocol:
Total RNA was isolated using the RNeasy Plus mini kit (Qiagen, Hilden, Germany) as recommended and was quantified employing a Qubit 2.0 fluorometer (Thermo Fisher/Invitrogen, Waltham, MA). RNA quality was determined using a Bioanalyzer 2100 with a RNA 6000 Pico chip (both from Agilent, Santa Slara, CA).
10 ng of total RNA (integrity > 8) was used to generate barcoded mRNA-seq cDNA library using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (both from NEB, Ipswich, MA) with a final amplification of 15 PCR cycles. Afterwards, RNA was quantified using the Qubit HS assay kit (Thermo).
The library size distribution was determined using the Bioanalyzer HS DNA assay (Agilent). Then, barcoded RNA-Seq libraries were clustered using the HiSeq® Rapid SR Cluster Kit v2 (Illumina, San Diego, CA) using 8pM, and 59bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (59 cycles).

treatment_protocol: Cells were incubated overnight with recombinant human IL-2 (5 U/ml). In parallel assays, agonistic anti-CD3 (1 µg/ml) and anti-CD28 (2 µg/ml) antibody were applied.

tag: tissue

value: Spleen

value: Treg (FOXP3+)

tag: genotype

value: Stimulated


title: Treg, CD18Foxp3, stimulated, biol rep1


title: Treg, CD18Foxp3, stimulated, biol rep2


title: Treg, CD18Foxp3, stimulated, biol rep3


title: Treg, CD18wt, stimulated, biol rep1


title: ds20181001-0872

tag: cell line


title: Treg, CD18Foxp3, unstimulated, biol rep3

tag: cell type

value: Unstimulated


title: Treg, CD18wt, stimulated, biol rep2


title: ds20181001-0864

value: MG


title: Treg, CD18wt, unstimulated, biol rep3


title: ds20181001-0862


title: ds20181001-0865


title: Treg, CD18wt, unstimulated, biol rep2


title: Splenocytes_BbIsC1ql3_Rep3

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

data_processing:
Partek Flow
RNAseq data were trimmed and aligned to the mouse genome ( from Ensembl), with associated annotation file using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl transcripts using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The counts generated were processed by gene set analysis (GSA).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include baseMean for each gene

extract_protocol:
RNA was isolated using RNeasy Mini kit according to the manufacturer’s instructions (Qiagen, #74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The murine splenocytes were stimulated by the Lyme disease agent Borrelia burgdorferi, with or without IsC1ql3, for 6 hours.

value: Splenocytes

value: Borrelia and IsC1ql3


title: ds20181001-0867


title: ds20181001-0868


title: Splenocytes_Bb_Rep3

value: Borrelia


title: ds20181001-0858


title: ds20181001-0866


title: Treg, CD18Foxp3, unstimulated, biol rep2


title: Splenocytes_Bb_Rep2


title: Treg, CD18Foxp3, unstimulated, biol rep1


title: Treg, CD18wt, unstimulated, biol rep1


title: ds20181001-0861


title: Tao3+/+ RAW264.7 cells infected with HSV-1

description: Gene expression data from wild type RAW264.7 cells infected with HSV-1


title: ds20181001-0863


title: Splenocytes_BbIsC1ql3_Rep2


title: ds20181001-0852


title: ds20181001-0851


title: ds20181001-0860

value: RPC/MG

value: cRPC


title: Splenocytes_BbIsC1ql3_Rep1


title: ds20181001-0859

value: retinal organoid

value: human embryonic stem cell (H9)


title: ds20181001-0857

value: Kuwahara

value: Y


title: Splenocytes_Bb_Rep1


title: ds20181001-0855


title: ds20181001-0854


title: DEN-T-WD rep 5

city: London

first: Dimitrios

last: Anastasiou

address: 1 Midland Road

department: Cancer Metabolism Laboratory

institute: The Francis Crick Institute

data_processing:
Raw sequence quality checked with FastQC
Reference genome alignment with RSEM and STAR
RSEM/STAR used to generate raw counts, TPM and FPKM
Assembly: GRCm38
Supplementary files format and content: text files with processed gene counts, TPMs, FPKMs

source_name: Tumor

extract_protocol:
Total tissue was pulverized with mortar and pestle under a liquid nitrogen atmosphere and RNA was extracted from the equivalent of 20-30mg frozen tissue in TRIzol Reagent (Thermo Fisher Scientific, UK) followed by phenol removal with chloroform. RNA was further purified with the RNeasy Mini Kit (Qiagen, UK). DNase treatment was performed to avoid genomic DNA contamination. RNA quantification and quality controls for integrity and purity (Nanodrop, Qubit and Agilent 2100 Bioanalyzer).
Libraries were prepared using KAPA mRNA HyperPrep Kit (Kapa Biosystems)

treatment_protocol: Two-week old male mice were injected intraperitoneally with 25mg/kg of the liver cancer-inducing carcinogen diethylnitrosamine (DEN). From the time of weaning, mice were fed either a western-like diet or a control diet.

value: Tumor

value: DEN

tag: diet

value: Western diet


title: DEN-T-WD rep 3


title: DEN-T-WD rep 1


title: ds20181001-0849


title: DEN-PT-WD rep 8

source_name: Peritumoral

value: Peritumoral


title: ds20181001-0856


title: DEN-T-WD rep 4


title: ds20181001-0853


title: DEN-T-WD rep 6


title: ds20181001-0847


title: ds20181001-0848


title: DEN-PT-WD rep 4


title: ds20181001-0850


title: DEN-PT-WD rep 6


title: ds20181001-0846

value: N


title: DEN-PT-WD rep 5


title: DEN-PT-WD rep 3


title: ds20181001-0843


title: ds20181001-0842


title: ds20181001-0844

value: ConeSG


title: DEN-T-WD rep 2


title: DEN-PT-WD rep 1


title: DEN-PT-WD rep 2


title: DEN-L-CD rep 2

source_name: Liver

value: Liver

value: Control diet


title: DEN-L-CD rep 4


title: ds20181001-0840


title: DEN-PT-WD rep 7


title: DEN-L-CD rep 3


title: nonDEN-L-WD rep 2

value: untreated


title: ds20181001-0839


title: nonDEN-L-WD rep 4


title: DEN-L-CD rep 1


title: ds20181001-0834


title: ds20181001-0845


title: ds20181001-0835


title: ds20181001-0838


title: ds20181001-0833


title: ds20181001-0836


title: nonDEN-L-WD rep 1


title: nonDEN-L-WD rep 3


title: ds20181001-0837


title: nonDEN-L-CD rep 3


title: ds20181001-0832


title: ds20181001-0841


title: nonDEN-L-CD rep 2


title: ds20181001-0831


title: 15207X8 NIR WT

city: Salt Lake City

first: Christopher

middle: A

last: Reilly

state: UT

address: 30 S 2000 E, Room 201 Skaggs Hall

department: Pharmacology and Toxicology

institute: University of Utah

description: DRG no injury Contra (right)

data_processing:
Mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 92
Reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference using STAR in two pass mode
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts from FeatureCounts combined in a single tab-delimited matrix

source_name: Dorsal root ganglia (DRG)

growth_protocol: All mice were housed in an AAALAC-approved vivarium under controlled environmental conditions consisting of 12 h light/12 h dark cycles, a temperature of 23-26°C, and 40-50% relative humidity. Mice were fed standard lab chow and water ad libitum.

extract_protocol: Lumbar DRGs (L3-L5) were collected from the ipsa (injured) and the contra (uninjured) side of mice 0, 1, 3, and 7 days.  The 3 DRGs were immediately collected into RLT buffer (RNeasy kit Qiagen), homogenized, and stored at -80C.  DRGs from three mice per time point were pooled and RNA was isolated using RNeasy Kit (Qiagen) with on column DNaseI digestion.

treatment_protocol: male C57BL/6J mice were anesthetized with 4% isoflourane and maintained at 2.5% with 0.8 LPM of oxygen. Following a 1-cm incision in the midline of the dorsal skin, and removal of the left L5 transverse process, the left L4 spinal nerve was exposed and tightly ligated with a 5-0 silk suture (AD Surgical, USA). The incision was closed with 5-0 silk and Vetbond tissue adhesive (3M, USA). Animals were given a 50/50 mix of 2% lidocaine with 0.5% bupivacaine to the muscle layer after surgery and returned to their cages. Sham controls received the same surgical procedure except that their nerves were not ligated.

value: Dorsal root ganglia (DRG)

tag: protocol

value: no injury Contra (right)


title: ds20181001-0829


title: ds20181001-0830


title: ds20181001-0828


title: nonDEN-L-CD rep 1

tag: treatment


title: 15207X6 Contra 1D

description: DRG uninjured 1 day

value: uninjured 1 day


title: 15207X7 NIL WT

description: DRG no injury IPSA (left)

value: no injury IPSA (left)


title: 15207X5 IPSA 1D

description: DRG injured 1 day

value: injured 1 day


title: ds20181001-0827

value: retinal organoid

value: human embryonic stem cell (H9)


title: 15207X4 Contra 3D

description: DRG uninjured 3 day

value: uninjured 3 day


title: ds20181001-0826

value: Kuwahara


title: 15207X3 IPSA 3D

description: DRG injured 3 day

value: injured 3 day


title: 15207X2 Contra 7D

description: DRG uninjured 7 day

value: uninjured 7 day


title: ds20181001-0825

value: Y


title: ds20181001-0824


title: ds20181001-0820


title: ds20181001-0823


title: ds20181001-0819


title: ds20181001-0822


title: ds20181001-0817


title: ds20181001-0816


title: 15207X1 IPSA 7D

description: DRG injured 7 day

value: injured 7 day


title: ds20181001-0821


title: 524_8H_name

city: DC

first: Zachory

last: Park

state: Washington DC

address: 37th and O Streets NW

department: Biology

institute: Georgetown University

description: PzevIME1 PzevRIM4

hyb_protocol: Labeled cRNA was allowed to hybridze for 17 hours at 65 degrees C and 20 RPM. After hybridization, slides were washed sequentially with wash buffer 1 for 1 minute, 2 for 1 minute, and then acetonitrile for 30 seconds.

scan_protocol: Scanned on an Agilent G2505C

data_processing: Agilent Feature Extractor was used.

organism: Saccharomyces cerevisiae

label_protocol: Brauer et al. 2008

growth_protocol: Cells were grown in YPD and then back diluted to YPA at an OD of 0.1 and allowed to grow for 16-18 hours before being transferred to Spo media (1% Kac) at an OD of 0.5. 1 uM of estradiol was added to overexpression strains.

extract_protocol: Cells were lysed with bead beating. Phenol saturated with 0.1 M citrate was added. Lysates were incubated at 65 degrees C for 30 minutes vortexing every 5 minutes. Lysates were chilled on ice for 30 minutes. The aqueous phase was transferred and chlorofom was added. Samples were mixed lightly and centrifuged before being moved to a new tube containing sodium acetate. Samples were washed with 100% ethanol and left to incubate at -20 degrees C for 30 minutes to 16 hours. Samples were then spun at full speed for 5 minutes to pellet the RNA. Pellets were washed with 70% ethanol and pulse-spun. Remaining alcohol was aspirated and RNA was resuspending in 100 uL of water. Samples were further cleaned using the Qiagen Rneasy kit.

source_name: WT


title: ds20181001-0814


title: ds20181001-0813


title: 524_5H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0818


title: 524_7H_name

description: PzevIME1 PzevRIM4


title: 524_6H_name

description: PzevIME1 PzevRIM4


title: 524_4H_name

description: PzevIME1 PzevRIM4


title: 524_9H_name

description: PzevIME1 PzevRIM4


title: 524_3H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0812

value: MG


title: ds20181001-0810


title: ds20181001-0811

value: ConeSG


title: WT_0H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0815


title: ds20181001-0809


title: 524_1H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0808


title: ds20181001-0807


title: ds20181001-0806


title: 524_12H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0805


title: ds20181001-0803


title: ds20181001-0802


title: 528_11H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0801


title: 524_11H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0800


title: 528_12H_name

description: PzevIME1 PzevRIM4


title: 524_0H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0799


title: 524_10H_name

description: PzevIME1 PzevRIM4


title: 528_10H_name

description: PzevIME1 PzevRIM4


title: 524_2H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0798


title: 528_7H_name

description: PzevIME1 PzevRIM4


title: 528_6H_name

description: PzevIME1 PzevRIM4


title: 528_8H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0796

value: RPC/MG


title: ds20181001-0804

value: N


title: ds20181001-0795


title: 528_9H_name

description: PzevIME1 PzevRIM4


title: 528_1H_name

description: PzevIME1 PzevRIM4


title: 528_2H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0794


title: ds20181001-0797


title: PZEV_IME1_kar4d_8H

description: PzevIME1 pRIM4


title: ds20181001-0793


title: PZEV_IME1_kar4d_9H

description: PzevIME1 pRIM4


title: 528_5H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0791


title: 528_4H_name

description: PzevIME1 PzevRIM4


title: 528_3H_name

description: PzevIME1 PzevRIM4


title: ds20181001-0789


title: PZEV_IME1_kar4d_6H

description: PzevIME1 pRIM4


title: ds20181001-0788


title: ds20181001-0792


title: PZEV_IME1_kar4d_7H

description: PzevIME1 pRIM4


title: ds20181001-0790


title: PZEV_IME1_kar4d_5H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_3-5H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_3H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_4H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_2H

description: PzevIME1 pRIM4


title: ds20181001-0786


title: ds20181001-0785


title: ds20181001-0780


title: ds20181001-0781


title: ds20181001-0787


title: PZEV_IME1_kar4d_2-5H

description: PzevIME1 pRIM4


title: ds20181001-0783


title: ds20181001-0779


title: ds20181001-0784


title: PZEV_IME1_kar4d_13H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_1H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_14H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_15H

description: PzevIME1 pRIM4


title: ds20181001-0777


title: ds20181001-0776


title: PZEV_IME1_kar4d_10H

description: PzevIME1 pRIM4


title: ds20181001-0775


title: ds20181001-0782


title: PZEV_IME1_kar4d_1-5H

description: PzevIME1 pRIM4


title: ds20181001-0774


title: ds20181001-0773

value: cRPC


title: PZEV_IME1_kar4d_11H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_12H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_0H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_16H

description: PzevIME1 pRIM4


title: ds20181001-0778


title: ds20181001-0772


title: PZEV_IME1_26JUN2014_kar4d_8H

description: PzevIME1 pRIM4


title: ds20181001-0770


title: ds20181001-0771


title: PZEV_IME1_26JUN2014_kar4d_2H

description: PzevIME1 pRIM4


title: ds20181001-0769


title: ds20181001-0716

value: Zhong

value: iPSC


title: ds20181001-0715


title: PZEV_IME1_26JUN2014_kar4d_15H

description: PzevIME1 pRIM4


title: PZEV_IME1_kar4d_0-5H

description: PzevIME1 pRIM4


title: ds20181001-0714


title: PZEV_IME1_26JUN2014_kar4d_13H

description: PzevIME1 pRIM4


title: ds20181001-0713


title: ds20181001-0712


title: 23AUG2014_PZEV_IME1_kar4d_0H_26AUG2014

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_9H

description: PzevIME1 pRIM4


title: ds20181001-0710


title: ds20181001-0709


title: 23AUG2014_PZEV_IME1_kar4d_0H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_6H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_5H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_7H

description: PzevIME1 pRIM4


title: ds20181001-0708


title: PZEV_IME1_KAR4_4H

description: PzevIME1 pRIM4


title: ds20181001-0707


title: ds20181001-0706


title: ds20181001-0705


title: 528_0H_name

description: PzevIME1 PzevRIM4


title: PZEV_IME1_KAR4_2H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_3-5H

description: PzevIME1 pRIM4


title: ds20181001-0704


title: ds20181001-0711


title: PZEV_IME1_KAR4_3H

description: PzevIME1 pRIM4


title: ds20181001-0703


title: PZEV_IME1_KAR4_8H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_16H

description: PzevIME1 pRIM4


title: ds20181001-0702


title: ds20181001-0701


title: PZEV_IME1_KAR4_1H

description: PzevIME1 pRIM4


title: ds20181001-0700


title: ds20181001-0698


title: PZEV_IME1_KAR4_14H

description: PzevIME1 pRIM4


title: ds20181001-0696


title: PZEV_IME1_KAR4_15H

description: PzevIME1 pRIM4


title: ds20181001-0695


title: PZEV_IME1_KAR4_13H

description: PzevIME1 pRIM4


title: ds20181001-0694


title: F4/80+ cells isolated from medium-content tumor, Day11 [Y22_M_TAM_1]

city: ShenZhen

first: Huan

last: Ren

address: 1088 Xueyuan Avenue

institute: Southern university of science and technology

data_processing:
CASAVA base recognition.
Clean data were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome(GRCm38/mm10) using Hisat2 (v2.0.5)
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads as a matrix table for each sample.

source_name: liver

extract_protocol:
RNA was harvested using TRIzol Reagent (Life Technologies), total amounts and integrity of RNA were assessed using the Agilent 5400.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols, the effective concentration of the library is higher than that of 2nM.

value: liver

value: F4/80+ cells

value: WT

tag: time

value: Day 11


title: CD11b+ cells isolated from medium-content tumor, Day11 [Y22_M_MTAM_1]

value: CD11b+ cells


title: CD11b+ cells isolated from medium-content tumor, Day11 [Y22_M_MTAM_3]


title: F4/80+ cells isolated from medium-content tumor, Day11 [Y22_M_TAM_2]


title: ds20181001-0699

value: retinal organoid

value: human embryonic stem cell (H9)

tag: prep method


title: PZEV_IME1_KAR4_12H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_11H

description: PzevIME1 pRIM4


title: gfp.cds.3.IP.combined: HeLa CDS MPm6A m6A-IP rep 3

city: Chicago

first: Philip

last: He

address: 929 E 57th Street

institute: University of Chicago

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_gfp.cds.txt

data_processing:
Library strategy: MPm6A
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: HeLa

extract_protocol:
Trizol extraction of RNA
For m6A-seq and RNA-seq: Illumina Stranded Truseq. MPm6A: Custom library construction as described in methods.

value: HeLa

value: CDS GFP MPm6A library

tag: input or ip


title: CD11b+ cells isolated from medium-content tumor, Day11 [Y22_M_MTAM_2]


title: PZEV_IME1_KAR4_10H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_0H

description: PzevIME1 pRIM4


title: PZEV_IME1_KAR4_0-5H

description: PzevIME1 pRIM4