title: MED13-13lfl_ES_UNT_rep4_CapC_set1

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title: IP brain tissue of  sham group replicate 2

status: Public on May 23 2022

type: RNA

city: Shenzhen

first: Li

last: Yudi

address: No. 1098 Xueyuan Avenue, 518060 Shenzhen, Guangdong, China.

country: China

institute: Shenzhen Hospital, Southern Medical University

description: Biological replicate 2 of 3. the brain tissue of sham group was collected

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse circRNA Epitranscriptomic Arrays (8x15K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent Scanner G2505C scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images

molecule: total RNA

organism: Mus musculus

source_name: Cerebral cortex tissue  in mice

label_protocol: The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit

growth_protocol: C57BL/6J mice weighing 23–26 g were raised in an SPF laboratory, at room temperature of 24˚C, and were kept on a 12-hour dark/ light cycle.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

treatment_protocol: They were randomized to three groups: the 3d after MCAO, 7d after MCAO, and sham groups The 3d and 7d groups were sacrificed 3 and 7 days after the operation, respectively, and the sham group underwent the same surgical procedure without the MCAO. During surgery and recovery, the body temperatures of the mice were maintained at 37℃.

tag: tissue

value: brain

tag: age

tag: strain

tag: treatment

value: sham


title: IP brain tissue of  sham group replicate 1

description: Biological replicate 1 of 3. the brain tissue of sham group was collected


title: input-(3xFLAG-Scr(YPWM*)/+)-T1-rep2

type: SRA

city: New York

first: Siqian

last: Feng

state: New York

address: 625 W. 130th Street

country: USA

institute: Columbia University

library_source: genomic

data_processing:
For ChIP-seq and ATAC-seq, mapping was done against dm3 with the “Map with Bowtie for Illumina” tool on usegalaxy.org, and only uniquely mapped reads were kept.
ChIP-seq peak calling was performed using the galaxy version of MACS2 (“MACS2 callpeak” on usegalaxy.org), with the following setting: --nomodel –extsize 200, and all other parameters were default
ATAC-seq peak calling was also performed with the galaxy version of MACS2, with the following setting: --nomodel –extsize 200 - -shift -100.
For RNA-seq, the cutadaptor tool on usegalaxy.eu was used to trim reads and remove reads shorter than 100bp. The filtered reads were then mapped to the genome build dm6 using the RNA STAR tool with the following parameters: --sjdbOverhang 149. The featurecount tool was used to obtain the transcript count tables.
Selex-seq data were processed using the NRLB algorithm
When analysing the Selex-seq raw data, the algorithm we used took the R0 and R1 data, and output the motifs enriched in the R1 data. This is somewhat similar to de novo motif search. The algorithm didn't output any intermediate quantitative data, and the motif logos were the only data it generated.
Genome_build: dm3 for ChIP-seq and ATAC-seq, dm6 for RNA-seq
Supplementary_files_format_and_content: bigwig (ChIP-seq and ATAC-seq) and count table (RNA-seq)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: T1 leg imaginal discs, wandering larvae

growth_protocol: Drosophila larvae were grown on standard cornmeal or molasses food at 25°C.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde for 10 minutes at RT, and were sonicated. DNA was purified from input and ChIP samples.
ChIP-seq libraries were constructed using illumina TruSeq ChIP Library Preparation Kit

tag: genotype

value: isogenic 3xFLAG-Scr(YPWM*)/+

tag: chip antibody

tag: genome build


title: JE_RNA_MV411_dTAG13_06h_R2

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

library_source: transcriptomic

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The spiked-in human reads were mapped to the GRCh37/hg19 human genome using STAR v2.7.3  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend.
The ERCC92 Mix1 Spike-in sequences were mapped using STAR v2.7.3 according to the standard ThermoFisher protocol https://www.thermofisher.com/order/catalog/product/4456740#/4456740.
Gene level reads were summarized by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net) ref FeatureCounts. The technical quality metrics of the spiked-in mapped reads   were investigated using the standard methods   implemented  in the  erccdashboard package. Additional quality control tests for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.
Gene counts were normalized and used to quantify differential  genes between the experimental and control conditions using the DESeq2 v1.24.0 method implemented in Bioconductor v3.9. Genes with at least 10 reads across at least 3 samples were annotated  as "expressed".
Differentiability for the expressed genes  was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients  method for effect size. The cutoffs for differentially expressed genes were |fold change expression|>1.5 and adjusted p-value < 0.10.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: MV4-11 treated with dTAG-13 IRF2BP2 degrader for 6h

extract_protocol:
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:  these experiments were performed in three technical replicates for each time point and condition. ERCC RNA spike-in mix was added to all samples following the manufacturer’s instructions (ThermoFischer, 4456740).  RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
PDX AML parental: these experiments were performed in a single replicate. RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen), except for PDX 2017-63 and PDX 2017-94 for which RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with the total RNA extraction protocol.
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:   PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX AML parental (except PDX 2017-63 and PDX 2017-94):  PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX 2017-63 and PDX 2017-94 parental: NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for poly(A) RNA purification with 50 uL total RNA as input. SMARTer Apollo NGS library prep system (Takara, Mountain View, CA) was used for automated poly(A) RNA isolation. The library for RNA-Seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell v3 using Illumina TruSeq SR Cluster kit v3 and sequenced to 51 bp using TruSeq SBS kit v3 on Illumina HiSeq system.

tag: cell line

tag: cell type

value: Acute Myeloid Leukemia

value: dTAG-13 IRF2BP2 degrader for 6h

tag: disease state


title: IP brain tissue of 7d after MCAO group replicate 3

description: Biological replicate 1 of 3. At 7day after cerebral infarction operation, the brain tissue was collected

source_name: Cerebral cortex tissue around infarction in mice

value: cerebral infarction operation


title: MED13-13lfl_ES_UNT_rep3_CapC_set1

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis interactions called by chicago (score >= 5) across all samples were aggregated and interactions with a distance of less than 4 DpnII fragments were merged to a single interaction peak. For each interaction peak we then quantified mean normalized read count and chicago score of all overlapping DpnII fragments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage of normalized read counts for each sample and each promoter were generated from chicago data object.

source_name: Mouse embryonic stem cells , untreated control, CaptureC

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureX beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext DNA library Prep Reagent Set (New England Biolabs: E6040S/L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in teh following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq.
CaptureC

treatment_protocol: To induce conditional removal of Med13 and Med13l in MED13/13lfl ESC line or Pcgf2 in Pcgf2fl ESC line, cells were treated with 800nM 4-hydroxytamoxifen (TAM) for 96 hours or 72 hours, respectively.

value: Med13;Med13l flfl

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr


title: JE_RNA_MV411_dTAG13_06h_R1


title: input-(3xFLAG-Scr(YPWM*)/+)-T1-rep1


title: MED13-13lfl_ES_UNT_rep2_CapC_set1


title: ChIP-(3xFLAG-Scr(YPWM*)/+)-T1-rep2

value: anti-FLAG monoclonal M2


title: IP brain tissue of 7d after MCAO group replicate 2


title: JE_RNA_MV411_DMSO_06h_R2

source_name: MV4-11 treated with DMSO for 6h

value: DMSO for 6h


title: input-(3xFLAG-Scr/+)-T1-rep2

value: isogenic 3xFLAG-Scr/+


title: JE_RNA_MV411_DMSO_06h_R3


title: WT.4.naive

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

country: Germany

institute: Helmholtz Center Munich

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Sequencing reads were pre-processed with bbduk (BBmap 2020) to remove adapters still present in the raw reads and for quality trimming.
Preprocessed reads were aligned to the mouse genome assembly (mm10) using GSNAP (2020-03-12 ; parameters: -t 96 -n 1 -Q --gunzip -A sam -s Mus_musculus.GRCm38.99.spliceSites.iit) with known splice sites from Ensembl (v99) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v99) were used for featureCounts (v2.0.0 ; parameters: -a Mus_musculus.GRCm38.99.collapsed.gtf -s 0 -Q 1 -T 64) to obtain a table with read counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: run1_steadyState_naive_counts.csv.gz and run2_allergyState_HDM_counts.csv.gz are tab-delimited files with the first columns showing the Ensembl Gene ID and the remaining column the counts per sample

growth_protocol: Primary lung cells of the indicated genotype were sorted with a FACS AriaIII as singlets, alive, CD45-EpCAM+ cells

extract_protocol:
Total RNA was isolated using Rneasy Micro Kit (Qiagen) and eluted in nuclease-free water.
RNA was desiccated to 3 µl and denatured for 3 minutes at 72 °C in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer* and 4 U RNase Inhibitor (NEB). Reverse transcription and addition of the template switch oligo was performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase was inactivated at 70 °C for 15 min and single stranded cDNA was subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 250 nM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 10 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration was determined with the Fragment Analyzer (Agilent). For library preparation, 1.5 ng cDNA was tagmented using 0.5 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 10 min. Next, Illumina indices were added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries were purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer, followed by Illumina sequencing on a Nextseq500 with a sample sequencing depth of 30 mio reads on average.

treatment_protocol: Cells were isolated after digestion of lungs with enzymes forced to digest lung epithelium with a protocol using low-melt agarose

value: CD45-EpCAM+ lung epithelial cells

value: wildtype

value: naive


title: ChIP-(3xFLAG-Scr(YPWM*)/+)-T1-rep1


title: IP brain tissue of 3d after MCAO group replicate 3

description: Biological replicate 3 of 3. At 3day after cerebral infarction operation, the brain tissue was collected


title: IP brain tissue of 7d after MCAO group replicate 1


title: JE_RNA_MV411_DMSO_06h_R1


title: ConAFICZ_Liver

city: Columbia

first: Alkeiver

last: Cannon

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

library_source: transcriptomic single cell

data_processing:
Base call files generated from the Illumina NextSeq 550 were demultiplexed using the cellranger mkfastq command. This pipeline uses bcl2fastq
Single cell feature counts files for each library were generated by running the cellranger count command on the demultiplexed fastq files.
Samples were aggregated by running the cellranger aggr command on the molecule.h5 files generated by the count command.
cloupe files generated by the cellranger aggr command were viewed in Loupe Browser 6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Liver mononuclear cells were extracted using the mouse Liver Dissociation Kit from Miltenyi Biotec followed by a 40/80 Percoll gradient for enrichment. Single cell suspensions were processed for single-cell RNA-sequencing by 10X Genomics Chromium Controller and 5' Gene Expression Kit.
Libraries were generated with 10X Genomics Chromium Single Cell 5' Library Construction kit.

value: Liver

value: 8-10 weeks


title: IP brain tissue of 3d after MCAO group replicate 2

description: Biological replicate 2 of 3. At 3day after cerebral infarction operation, the brain tissue was collected


title: input-(3xFLAG-Scr/+)-T1-rep1


title: ConATCDD_Liver


title: ChIP-(3xFLAG-Scr/+)-T1-rep2


title: MV411_dTAG13_input_24h

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The H3K27ac ChIP-Seq sequences were spiked-in with Drosophila Melanogaster based on the Active Motif kit protocol. The human ChIP-Seq sequences for IRF2BP2, H3K27ac, H3K4me3 and H3K4me1 antibodies were aligned to the GRCh37/hg19 genome and the Drosophila Melanogaster sequences were aligned to the dm6 genome using bowtie2-2.3.5  with the standard options.
PCR duplicates were removed with the Picard v2.18.2 MarkDuplicates tool (https://broadinstitute.github.io/picard/). The Active Motif Spike-in Normalization protocol (https://www.activemotif.com/catalog/1091/chip-normalization)  was applied to the H3K27ac samples by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.
The mapped reads were normalized in units of Reads Per Kilobase per Million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools v2.5.3.  Peak calling was performed against input control using the model-based MACS2 v2.1.1.20160309 software, with the cut-off FDR ≤ 0.01.  Area under Curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software ref bwtool. Peaks with low area under curve coverage (< 300 RPKM)  were disregarded and the ENCODE black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/) were removed from each set of peak regions. Quality control tests for the mapped reads were performed by using the ChIPQC library available from Bioconductor v3.9.
The ChIP-Seq IRF2BP2 data was produced for three different IRF2BP2 antibodies (r1: Abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A).  The pairwise correlations between IRF2BP2 replicates were estimated based on the multiBamSummary function available from the deepTools v2.5.3  and visualized on correlation heatmaps and PCA plots. The IRF2BP2 replicates were found significantly correlated (Spearman R > 0.90) and they were merged into a single IRF2BP2 ChIP-Seq sample. The  IRF2BP2 binding sites was identified for the merged data (macs2, FDR ≤ 0.01).
The peaks were annotated with the closest hg19 genes by using the annotatePeaks function implemented in the Homer v4.11 platform  and the GREAT annotation platform.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp).  Coverage was computed for  bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.  The Active Motif Spike-in Normalization protocol was  applied by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.

source_name: Input on MV4-11 treated with dTAG-13 IRF2BP2 degrader for 24h

extract_protocol:
25 million (for histone marks) to 100 million AML cells (for IRF2BP2) per condition were crosslinked with 1% formaldehyde in cell culture media for 10 minutes and then quenched with 0.125 mM glycine. Cells were lysed in Nuclei EZ Isolation buffer (Sigma EZ Prep Nuclear Isolation Kit, Cat No. NUC-101) supplemented with protease inhibitor. Chromatin was sheared using a Covaris instrument. Subsequently, 0.5% of the lysate was removed as the input control. The remaining lysate was incubated with 30 ul (for histone marks) or 100 ul (for IRF2BP2) of protein G dynabeads (Thermofisher) and 5 ug of H3K27Ac: ab4729 abcam,  H3K4me1: ab8895, H3K4me3: ab8580,  or 10 ug of IRF2BP2 antibody (r1: abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A) and HA (Cell Signaling Technology_3724S),  at 4 degrees C overnight (antibodies and beads were incubated together for 30 minutes at 4 degrees C prior to the addition of cell lysate).
The precipitated lysate was then washed sequentially in two washes of each of the following buffers: ice cold low salt buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 nM EDTA, 1% Triton-X100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% desoxycholic acid, 1% IGEPAL CA-630) and TE buffer (10 mM Tris-HCl ph8.1, 1 mM EDTA). Samples were eluted in elution buffer (1x TE pH 7.4, 1% SDS, 150 mM NaCl, 5 mM DTT). RNase A, proteinase K, and 0.2 M NaCl was added to the elution buffer and samples were incubated at 65 degrees Celsius for at least four hours to reverse cross-linking. DNA was purified using AMPure XP beads (Agencourt). ChIP-seq libraries were prepared using Swift S2 Acel reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq.

treatment_protocol: H3K27Ac: ab4729 abcam, H3K4me1: ab8895, H3K4me3: ab8580, IRF2BP2 (r1: abcam_ab114997, r2: Bethyl_A303-189A-T, r3: Bethyl_A303-190A), HA (Cell Signaling Technology_3724S)

value: none (input)


title: WT.2.naive


title: WT.1.naive


title: ConA_Liver


title: ChIP-(3xFLAG-Scr/+)-T1-rep1


title: Naïve_Liver


title: MV411_dTAG13_H3K27ac_24h

source_name: H3K27ac on MV4-11 treated with dTAG-13 IRF2BP2 degrader for 24h

value: H3K27ac (ab4729 abcam)


title: WT.3.naive


title: IP brain tissue of 3d after MCAO group replicate 1

description: Biological replicate 1 of 3. At 3day after cerebral infarction operation, the brain tissue was collected

value: brain


title: AG from female a-CD115 treated 4

city: Saint-Petersburg

first: Maria

last: Firulyova

address: Kronverksky Pr. 49

department: Department of Computer Technologies

country: Russia

institute: Information Technologies, Mechanics, and Optics University

data_processing:
quality control, FastQC v0.11.9
alignment, hisat2 v2.2.1
bam sorting, samtools v1.3.1
bam indexing, samtools v1.3.1
counting step, featureCounts v2.0.1
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: Adrenal gland

growth_protocol: All mice were bred and housed in specific pathogen-free conditions maintained by animal facilities in either the Mediterranean Center of Molecular Medicine (INSERM U1065, Université Côte d’Azur), facilitie were maintained at ambient temperature of ~20-23 °C, with 12/12-hour light/dark cycle and food available ad libitum

extract_protocol:
RNA was extracted from adrenal glands using RNA extraction kit (QIAGEN cat No. 7413). Both adrenals were crushed using 0,1 mm glass beads in a precellys homogenizer (Biospec cat No. 11079101) containing RLT buffer from the RNA extraction kit. Total RNAs were extracted in RNase-free water from adrenals and were analyzed in DNBseqTM sequencing plateform using DNBSEQ stranded mRNA library.
Paired RNA-seq reads were aligned to the Ensembl 84 Mus musculus reference genome with hisat2 (version 2.2.1) (Kim et al., 2019).

treatment_protocol: C57BL/6 mice received an intraperitoneal injection of 500 µg InVivoMAb anti-mouse CSF1R (CD115) antibody (Clone AFS98, BioXCell cat No. BE0213) or isotype control (Clone 2A3, BioXCell cat No. BE0089). The injection was repeated 2 days later. Mice were sacrificed 16 hours after the second injection. For cold exposure, macrophage depleted, and control mice were housed for 12 hours at 4°C. Mice were single housed with identical light/dark cycle and food available ad libitum.

value: Adrenal gland

value: Whole adrenal gland cells

value: C57Bl/6 J wild type


title: MV411_DMSO_Input_24h

source_name: Input on MV4-11 treated with DMSO for 24h

value: treated with DMSO for 24h

value: Acute Myeloid Leukemia


title: CypKO.3.naive


title: MV411_DMSO_H3K27ac_24h

source_name: H3K27ac on MV4-11 treated with DMSO for 24h


title: CypKO.2.naive


title: ChIP-negative control-rep2

value: isogenic w1118 (BL5905)


title: AG from female a-CD115 treated 3

description: C57BL/6 mice received an intraperitoneal injection of 500 µg InVivoMAb anti-mouse CSF1R (CD115) antibody (Clone AFS98, BioXCell cat No. BE0213) or isotype control (Clone 2A3, BioXCell cat No. BE0089). The injection was repeated 2 days later. Mice were sacrificed 16 hours after the second injection


title: AhR.3.naive

value: AhR-KO


title: input-negative control-rep1


title: AhR.4.naive


title: MV411_Input

source_name: Input on MV411

value: untreated


title: CypKO.4.naive


title: MV411_IRF2BP2_r3

source_name: IRF2BP2 on MV4-11  rep 3 (Bethyl_A303-190A)

value: IRF2BP2  (Bethyl_A303-190A)


title: ChIP-3xFLAG-Ubx-T3-rep2

source_name: T3 leg imaginal discs, wandering larvae

value: isogenic 3xFLAG-Ubx

value: anti-FLAG monoclonal M2


title: AG from female a-CD115 treated 1


title: MV411_H3K4me3

source_name: H3K4me3 on MV4-11

value: H3K4me3 (Abcam, ab8580)


title: input-negative control-rep2


title: AhR.1.naive

value: CD45-EpCAM+ lung epithelial cells

value: naive


title: input-3xFLAG-Ubx-T3-rep1


title: AG from female isotype treated 3

value: Isotype


title: MV411_IRF2BP2_r2

source_name: IRF2BP2 on MV4-11  rep 2 (Bethyl_A303-189A-T)

value: IRF2BP2  (Bethyl_A303-189A-T)


title: AG from female isotype treated 2


title: MV411_IRF2BP2_r1

source_name: IRF2BP2 on MV4-11  rep 1 (Abcam_ab114997)

value: IRF2BP2 (Abcam_ab114997)


title: AG from female isotype treated 1

value: Adrenal gland


title: WT.2.hdm

value: wildtype

value: HDM-sensitized


title: WT.3.hdm


title: AG from female a-CD115 treated 2

value: Whole adrenal gland cells

value: C57Bl/6 J wild type


title: Luc-3

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

description: RNA-seq of GIST cell line

data_processing:
RNA-seq data were aligned using STAR with expression quantification using Cufflinks to generate gene expression values in FPKM units.
Genome_build: hg19
Supplementary_files_format_and_content: Processed RNA-seq data files with FPKM values are in text format

source_name: Luciferase sgRNA RNA-seq

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Libraries for Illumina NovaSeq6000 sequencing were prepared using NEBNext Ultra II non-stranded library prep kit

value: gastrointestinal stromal tumor (GIST)

tag: knockdown

value: Luciferase sgRNA


title: ChIP-negative control-rep1

source_name: T1 leg imaginal discs, wandering larvae

value: isogenic w1118 (BL5905)


title: Luc-2

description: RNA-seq of GIST cell line


title: AG from Male a-CD115 treated 4


title: WT.1.hdm


title: input-3xFLAG-Scr-T1-rep2

value: isogenic 3xFLAG-Scr


title: AG from Male a-CD115 treated 3


title: CypKO.3.hdm


title: Luc-1

description: RNA-seq of GIST cell line


title: WT.4.hdm


title: AG from Male a-CD115 treated 2


title: CypKO.2.hdm


title: CypKO.4.hdm


title: ChIP-3xFLAG-Scr-T1-rep1


title: input-3xFLAG-Scr-T1-rep1


title: HAND1-2

description: RNA-seq of GIST cell line

source_name: HAND1 sgRNA RNA-seq

value: HAND1 sgRNA


title: AG from Male a-CD115 treated 1


title: ChIP-3xFLAG-Ubx-T3-rep1

value: isogenic 3xFLAG-Ubx

value: anti-FLAG monoclonal M2


title: AG from males isotype treated 4


title: HAND1-3

description: RNA-seq of GIST cell line


title: AhR.3.hdm

value: CD45-EpCAM+ lung epithelial cells

value: AhR-KO


title: FaDu control

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HNSCC cells

growth_protocol: 10% FBS in DMEM

extract_protocol:
Total RNA was isolated from cells using NucleoSpin® RNA II RNA purification kit (Machery-Nagel; #740955.20).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: cells were treated with FOSL1 siRNA or control siRNA for 48 hours

value: FaDu

value: control


title: AG from males isotype treated 3

value: Isotype


title: CypKO.1.hdm


title: ChIP-3xFLAG-Scr-T1-rep2


title: ETV1-3

description: RNA-seq of GIST cell line

source_name: ETV1 sgRNA RNA-seq

value: ETV1 sgRNA


title: FaDu FOSL1 depletion

value: FOSL1 depletion


title: HAND1-1

description: RNA-seq of GIST cell line


title: SCC1 FOSL1 depletion


title: AG from males isotype treated 2

value: Adrenal gland


title: AhR.2.hdm

value: HDM-sensitized


title: SCC1 control


title: ETV1-2

description: RNA-seq of GIST cell line


title: AhR.4.hdm


title: AG from males isotype treated 1

value: Whole adrenal gland cells

value: C57Bl/6 J wild type


title: AhR.1.hdm


title: ETV1-1

description: RNA-seq of GIST cell line

value: gastrointestinal stromal tumor (GIST)


title: EC neurons, shDEK, ATACseq [shdek1_ATAC]

status: Public on May 22 2022

city: Boston

first: Jean-Pierre

last: Roussarie

address: 72 E Concord Street

department: Anatomy & Neurobiology

institute: Boston University School of Medicine

data_processing:
For ATACseq: Reads were aligned to the mm10 genome from the Bsgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0) using Rsubread’s align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired (Liao et al., 2019). Normalized, fragment signal bigWigs were created using the rtracklayer package (Lawrence et al., 2009). Peak calls for each replicate were made with MACS2 software in BAMPE mode (Feng et al., 2012; Zhang et al., 2008). Deeptools (version 3.1.2) bamcompare was used to generate log2 ratio Bigwigs of shdek/ cont bam files. Differential analysis of signal was then performed using DESeq2 (v. 1.28.1) (Love et al., 2014). Briefly, count matrices were generated by measuring ATAC signal from each replicate over a non-redundant union ATAC peak set representing peak calls across all conditions.
For cut&tag: Genomic regions with high levels of transposition/tagging events were determined using the MACS2 peak calling algorithm. To identify the density of transposition events along the genome, the genome was divided into 32 bp bins and the number of fragments in each bin was determined by extending the reads to 200 bp, which is close to the average length of the sequenced library inserts. To compare peak metrics between samples, overlapping intervals were grouped into “merged regions” which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval. In locations where only one samples has an interval, that interval defined the merged region.
Assembly: mm10

source_name: primary cultures of EC from mouse E17 embryo

growth_protocol: 7 days in vitro at 37°C before transduction in Neurobasal medium with 2% B27 supplement

extract_protocol:
For ATACseq, primary neurons were pelleted by centrifugation (5 min, 500 xg at 4°C) and lysed in 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin. Nuclei where then pelleted by centrifugation (10 min, 1000 xg at 4°C). For the Cut&Tag, cells were pelleted, frozen and sent to Active Motif, where they were washed and incubated overnight with Concanavalin A beads and 1.3 µl/reaction of primary antibodies against H3K27Ac (#39133, Active Motif), H3.3 (#91191, Active Motif) and H3K36Ac (#39379, Activ Motif). After incubation with the secondary anti-rabbit antibody (1:100), cells were washed once more before tagmentation
Nextera DNA Library prep kit for ATAC, and Active Motif Cut&Tag kit for the Cut & Tag.

treatment_protocol: treatment with 10^10 viral genomes of AAV per ml of medium in a fresh change of medium

value: primary neurons

value: 4 days posttransduction


title: EC neurons, shDEK, ATACseq [shdek2_ATAC]

value: primary cultures of EC from mouse E17 embryo


title: EC neurons, control, ATACseq [ctrl3_ATAC]


title: EC neurons, control, ATACseq [ctrl2_ATAC]


title: EC neurons, shDEK, H3K36ac [shdek_H3K36ac]

data_processing:
library strategy: CUT&TAG
For ATACseq: Reads were aligned to the mm10 genome from the Bsgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0) using Rsubread’s align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired (Liao et al., 2019). Normalized, fragment signal bigWigs were created using the rtracklayer package (Lawrence et al., 2009). Peak calls for each replicate were made with MACS2 software in BAMPE mode (Feng et al., 2012; Zhang et al., 2008). Deeptools (version 3.1.2) bamcompare was used to generate log2 ratio Bigwigs of shdek/ cont bam files. Differential analysis of signal was then performed using DESeq2 (v. 1.28.1) (Love et al., 2014). Briefly, count matrices were generated by measuring ATAC signal from each replicate over a non-redundant union ATAC peak set representing peak calls across all conditions.
For cut&tag: Genomic regions with high levels of transposition/tagging events were determined using the MACS2 peak calling algorithm. To identify the density of transposition events along the genome, the genome was divided into 32 bp bins and the number of fragments in each bin was determined by extending the reads to 200 bp, which is close to the average length of the sequenced library inserts. To compare peak metrics between samples, overlapping intervals were grouped into “merged regions” which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval. In locations where only one samples has an interval, that interval defined the merged region.
Assembly: mm10

tag: antibody

value: H3K36Ac (#39379, Activ Motif)


title: EC neurons, control, ATACseq [ctrl1_ATAC]


title: EC neurons, control, H3K36ac [ctrl_H3K36ac]

value: non transduced


title: mouse ECII RNA, shRNA DEK 4 [shdek4]

data_processing:
reads were aligned using Salmon
DEseq2 was performed on the salmon counts
Assembly: mm10
Supplementary files format and content: salmon counts

source_name: ECII-bacTRAP male, EC

growth_protocol: Mice were injected stereotaxically in the EC, bilaterally, at coordinates AP: -3.70; ML: ±4.65; DV: -4.50 with nanoinjector tilt of ±4.05°, with 2E10 viral genomes  in 2ul)

extract_protocol:
we purified RNA from immunoprecipitated polysomes using Rneasy micro plus kit
bacTRAP RNA-seq; 5ng of RNA was used to generate cDNA using Ovation RNAseq v2 kit; cDNA were sonicated using a covaris ultrasonicator and 200ng of sonicated cDNA were used for library generation using Truseq RNA sample prep kit

treatment_protocol: 1 week post injection, we performed polysome immunoprecipitation using the bacTRAP protocol

value: ECII-bacTRAP male, EC

value: principal neurons from layer II of EC

value: stereotaxic injection within the EC


title: corticohippocampal neurons, shRNA DEK, H3-3, 2 [shdek2_H3-3]

source_name: primary cultures of cortex/hippocampus of mouse E17 embryos

value: H3.3 (#91191, Active Motif)


title: corticohippocampal neurons, shRNA DEK, H3-3, 1 [shdek1_H3-3]

value: primary cultures of cortex/hippocampus of mouse E17 embryos


title: mouse ECII RNA, shRNA DEK 5 [shdek5]


title: corticohippocampal neurons, control, H3-3, 2 [ctrl2_H3-3]


title: mouse ECII RNA, shRNA DEK 3 [shdek3]


title: corticohippocampal neurons, control, H3-3, 1 [ctrl1_H3-3]


title: Input_rep2

city: Nanjing

first: Jia-Yu

last: Chen

state: CA

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

institute: Nanjing University

description: ssDNA

data_processing:
Sequencing data were mapped to human genome (hg38) via Bowtie2. Only uniquely-mapped non-redundant sequencing reads were kept with Samtools. Sequencing reads were extended to the estimated average size of sequenced fragments and normalized to 1M reads for generation of bigWig files.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files: reads density normalized to 1M reads.

growth_protocol: HEK293T cells were from a common laboratory stock (gift of Dr. Steve Dowdy’s lab); K562 cells were purchased from ATCC (ATCC#: CCL-243). HEK293T cells were grown in DMEM supplemented with 10% FBS and 1 X penicillin-streptomycin (GIBCO); K562 cells were cultured in RPMI1640 (CORNING) with 10% fetal bovine serum (FBS; Omega Scientific), and 100 U/ml penicillin-streptomycin (GIBCO) at 37 °C in a 5% of CO2 incubator.

extract_protocol:
For DRIP-seq, genomic DNA (gDNA) was purified from 8M of K562 cells. The purified gDNA was digested at 37 °C with five restriction enzymes (EcoRI, BsrGI, XbaI, SspI, and HindIII; NEB). Ten micrograms of digested gDNA was incubated with 7ug of S9.6 antibody (Millipore) for IP and the IPed gDNA was recovered by proteinase K (Thermo Fisher Scientific) treatment. Before sonication, the purified gDNA was incubated at 37 °C for 1 h with RNase H (Thermo Fisher Scientific) to remove hybridized RNA for RNase H-treated DRIP-seq library. For RPA ChIP-seq, approximately 10M HEK293T cells were crosslinked with 1% formaldehyde for 15 min at room temperature. Fixation was stopped by adding Glycine at the final concentration 125 mM followed by incubation on a rotating platform for 15 min at room temperature. After washing plates twice with PBS, cells were scraped off and incubated in cell lysis buffer (10 mM Tris-HCl pH 8.0, 10mM NaCl, 0.5% NP-40 and 1× protease inhibitor cocktail) for 15 min on ice. After centrifugation at 12,000 rpm for 10 min at 4 °C , the supernatant was aspirated and discarded. The cell pellet was then suspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and 1 X protease inhibitor cocktail) and incubated for 10 min on ice. Chromatin DNA was sheared to 250-600 bp in size by sonication. 5% chromatin fragment was saved as input and the remaining was incubated with magnetic beads conjugated with anti-RPA32 antibody (Millipore, NA19L) overnight at 4°C . On the next day, beads were sequentially washed three times with TSEI (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA and 1 X protease inhibitor cocktail), three times with TSEII (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA and 1× protease inhibitor cocktail), once with TSEIII (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% NP-40, 1% Deoxycholate, 1 mM EDTA and 1× protease inhibitor cocktail) and once with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). The protein-chromatin complex was eluted with elution buffer (10 mM Tris-HCl pH 8.0, 1% SDS and 1 mM EDTA) and reverse-crosslinked on a thermomixer with agitation overnight at 65 °C . After sequential treatments of RNase A and Proteinase K to remove any residual RNA and protein, the precipitated DNA fragment was cleaned twice with phenol and once with phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. The recovered DNA fragment was subjected to library construction.
For DRIP-seq, the recovered DNA were fragmented by sonication, and them repaired using Quick Blunting Kit (NEB). For TA ligation, dA was added to the 3’-end of DNA using Klenow fragment exo- (NEB) and then the adapter was ligated to the end of DNA. After PCR amplification, DNA was loaded onto acrylamide gel to select library with 200-500 bp in length. DNA library was eluted from the gel fragments for 12 h in elution buffer (10 mM Tris-Cl, pH 8.0, 1 mM EDTA, 0.1% Tween-20, and 300 mM NaCl) and purified using DNA Clean and Concentrator-5 Kit (Zymo Research).  For RPA ChIP-seq, the recovered DNA fragment was subjected to random priming using a primer ended with 9-mer random sequences (5’- /invddt/CAAGCAGAAGACGGCATACGAGNNNNNNNNN-3’). An “A” base was then added to the 3’ end and the adaptor from Illumina was ligated only to one end of the resultant dsDNA as the other end contained a 5’ overhang introduced by the N9 primer. After purification, 16-18 cycles of PCR were performed and PCR products in the size range of 130-350 bp were gel-isolated and purified.

value: input


title: EC neurons, shDEK, ATACseq [shdek3_ATAC]


title: mouse ECII RNA, shRNA DEK 1 [shdek1]

source_name: ECII-bacTRAP female, EC

value: ECII-bacTRAP female, EC


title: Input_rep1

description: ssDNA


title: mouse ECII RNA, control, 5 [shcnt5]


title: ChIP_RPA_rep2

description: ssDNA

value: Replication protein A (RPA)


title: corticohippocampal neurons, control, H3K27ac [ctrl_H3K27Ac]

value: H3K27Ac (#39133, Active Motif)


title: ChIP_RPA_rep1

description: ssDNA


title: corticohippocampal neurons, shRNA DEK, H3K27ac [shdek_H3K27ac]


title: Vip rep2

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description: Viperin-transfected 293T cells Rep2

data_processing:
The sequences were basecalled by Illumina RTA embedded in HiSeq Control Software.
Illumina reads were mapped to the hg38 genome using STAR (Dobin et al., 2013) and transcripts were counted using BEDTools multicov (Quinlan and Hall, 2010).
Genome_build: hg38
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, transcript counts

source_name: tissue culture cells

growth_protocol: 293T cells were cultured in 10% FBS/DMEM.

extract_protocol:
Cells were harvested on ice, and RNA was harvested using Trizol reagent. rRNAs were depleted by NEBNext rRNA Depletion Kit (NEB). Illumina TruSeq Stranded mRNA Library Prep (Cat#20020594) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with mock or pcDNA3.1 containing viperin using Lipofectamine 2000 for 48 hours

tag: transfection

value: pcDNA3.1 containing viperin


title: mouse ECII RNA, control, 3 [shcnt3]


title: mouse ECII RNA, control, 4 [shcnt4]


title: mouse ECII RNA, control, 2 [shcnt2]


title: EC, DEK overexpression, control 3 [DEKOE_ctrl3]

extract_protocol:
we lysed cells and purified RNA using Purelink RNA with in-column digestion
bacTRAP RNA-seq; 200ng of RNA was used to generate libraries with Truseq RNA sample prep kit

value: primary EC neurons


title: Vip rep1

description: Viperin-transfected 293T cells Rep1


title: Mock rep2

description: Mock-transfected 293T cells Rep2

value: mock


title: Mock rep1

description: Mock-transfected 293T cells Rep1


title: EC, DEK overexpression, control 2 [DEKOE_ctrl2]


title: EC, DEK overexpression, overexpression 3 [DEKOE_OE3]


title: EC, DEK overexpression, control 1 [DEKOE_ctrl1]


title: EC, DEK overexpression, overexpression 2 [DEKOE_OE2]


title: CD8+ T cell, poly (I:C) plus CSP-injected mice (n=6), 14 days after last immunization

city: Sao Paulo

first: Filipe

last: Menegatti de Melo

state: Sao Paulo

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

country: Brazil

institute: University of Sao Paulo

data_processing:
Demultiplexed FastQ files were aligned against the UCSC Genome Browser Assembly GRCm38/mm10 Mus musculus genome with Hisat2.
Reads that aligned in more than one site, aligned to mitochondrial DNA, or were unaligned, were excluded using the Linux command line: sed '/chrM/d;/random/d;/chrUn/d;/XS:/d'.
Resulting SAM files were converted to BAM using Samtools.
BAM files were loaded to SeqMonk (Babraham Institute) and read quantification was performed against a probe that contained all the exons from mm10 mouse genome assembly
Genes were annotaded according to NCBI RefSeq.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files. Each file contains the raw reads from all the samples (immunization groups) for each lymphocyte population.

source_name: spleen

extract_protocol:
Total RNA was DNAse I treated and purified using the Qiagen RNeasy Mini Kit.
cDNA library was prepared by the company Quick Biology (Pasadena, CA, USA) using the KAPA Stranded RNA-Seq Kit with RiboErase system (KAPA Biosystems, Wilmington, MA)

value: spleen

value: CD8+ T cells enriched by positive selection from pooled splenocytes

value: WT

value: three immunizations with poly (I:C) plus CSP recombinant protein, one week apart


title: CD4+ T cell, poly (I:C) plus CSP-injected mice (n=6), 14 days after last immunization

value: CD4+ T cells enriched by positive selection from pooled splenocytes


title: CD8+ T cell, naive mice (n=6)

value: naive


title: CD8+ T cell, Montanide plus CSP-injected mice (n=6), 14 days after last immunization

value: three immunizations with Montanide plus CSP recombinant protein, one week apart


title: CD8+ T cell, Montanide-injected mice (n=6), 14 days after last immunization

value: three immunizations with Montanide ISA 720, one week apart


title: CD8+ T cell, poly (I:C)-injected mice (n=6), 14 days after last immunization

value: three immunizations with poly (I:C), one week apart


title: EC, DEK silencing, control 2 [DEKSh_scr2]

value: primary cultures of EC from mouse E17 embryo

value: 4 days posttransduction


title: EC, DEK silencing, silencing 3 [DEKSh_sh3]


title: EC, DEK overexpression, overexpression 1 [DEKOE_OE1]


title: CD4+ T cell, Montanide-injected mice (n=6), 14 days after last immunization


title: CD4+ T cell, poly (I:C)-injected mice (n=6), 14 days after last immunization


title: mouse ECII RNA, control, 1 [shcnt1]

value: ECII-bacTRAP male, EC

value: principal neurons from layer II of EC

value: stereotaxic injection within the EC


title: EC, DEK silencing, control 1 [DEKSh_scr1]


title: EC, DEK silencing, silencing 2 [DEKSh_sh2]


title: CD4+ T cell, naive mice (n=6)


title: B lymphocyte, Montanide-injected mice (n=6), 14 days after last immunization

value: B cells enriched by negative selection from pooled splenocytes


title: EC, DEK silencing, silencing 1 [DEKSh_sh1]

value: primary EC neurons


title: B lymphocyte, poly (I:C) plus CSP-injected mice (n=6), 14 days after last immunization


title: input-3xFLAG-Ubx-T3-rep2

value: isogenic 3xFLAG-Ubx


title: eCLIP_C2C12diff_A2B1_A

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

data_processing:
Library strategy: eCLIP-seq
3' barcodes and adapter sequences were removed using standard eCLIP scripts.
Reads were trimmed, filtered for repetitive elements, and aligned to the mm9 reference sequence using STAR.
PCR duplicate reads were removed based on the read start positions and randomer sequence.
Bigwig files for genome browser display were generated based on the location of the second of the paired end reads.
Peaks were identified using encode_branch version of CLIPPER (Lovci et al. 2013) using the parameter -s mm9
Peaks were normalized against size matched input by calculating fold enrichment of reads in IP versus input, and were designated as significant if the number of reads in IP was greater than in the input, with a Bonferroni corrected Fisher exact p-value smaller than 10^–5
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed and bigwig

source_name: Differentiated C2C12 cells

growth_protocol: C2C12 cells were grown in DMEM supplemented with 20% FBS and 1x penicillin-streptomycin. For differentiation, confluent cells were passaged in differentiation media (DMEM supplemented with 5% horse serum, 1x penicillin-streptomycin, and 1x ITS) for 8-10 days.

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al. 2016) with minor modifications. Briefly, confluent cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 13 mL of PBS in 15 cm plates; these cells were then spun down, flash frozen in liquid nitrogen, and stored at –80ºC. Nuclear isolation was performed as previously described (Kung et al. 2015), followed by further digestion by Bioruptor, RNase I, and Turbo DNase as specified in the original eCLIP protocol. Overnight immunoprecipitation was performed using 2 mg Protein G Dynabeads per 10 µg antibody, and appropriate antibody for hnRNP A2/B1 (10 µg/IP). Following end repair and 3′ adaptor ligation (using X1A and X1B adaptors as previously described), size selection was carried out using Nupage 4-12% Bis-Tris protein gels followed by overnight transfer at 30V to nitrocellulose membranes.
Protein-RNA complexes on nitrocellulose were then digested with Proteinase K (Roche) and reverse transcribed using SuperScript IV (Thermo Fisher). These cDNAs were then prepared for sequencing as described using Illumina TruSeq HT dual indexed primers, and sequenced on an Illumina HiSeq 2500 for high-output 2x150 bp run.

value: Differentiated C2C12 cells

value: hnRNP A2B1

tag: antibody vendor

value: abcam


title: eCLIP_C2C12diff_A2B1_input

tag: tissue


title: eCLIP_C2C12diff_A2B1_B


title: CD4+ T cell, Montanide plus CSP-injected mice (n=6), 14 days after last immunization

value: spleen

value: WT


title: NC 4

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

data_processing:
After Illumina sequencing, image analysis, and base recognition, the original reads after quality control were harvested. First use Q30 for quality control. Use cutadapt software (v1.9.3) to de-join the original reads, remove low-quality reads, and keep the reads with length> = 15 nt to get the de-connected reads (ie trimmed reads).
Then, the trimmed reads of all samples were combined, and new miRNA prediction was performed using miRDeep2 software (v2.0.0.5). Use Novoalign software (v3.02.12) to compare the trimmed reads of each sample to the combined human pre-miRNAs database (miRBase pre-miRNAs (v21) + newly predicted pre-miRNAs), allowing up to 1 mismatch.
Statistically compare the number of tags on each mature miRNA as the original expression level of the miRNA, and use TPM (tag counts per million aligned miRNAs) method for standardization. Calculate the Fold change between the two samples and screen for differentially expressed miRNAs. Calculate the P-value and Fold Change between the two groups of samples (with duplicates), and screen for differentially expressed miRNAs.
Genome_build: human NBCI genobuild 36
Supplementary_files_format_and_content: Number of alignment tags per mature miRNA

source_name: Blood

extract_protocol:
Human PBMCs were isolated by density-gradient centrifugation over Ficoll-Hypaque solution (Tianjin Haoyang Biological Technology Co., Tianjin, China) according to the manufacturer’s instructions and stored at -80 °C   until use for miRNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood mononuclear cells

tag: age

value: Adult

value: Blood

tag: gender

value: female

value: healthy control


title: EC, DEK silencing, control 3 [DEKSh_scr3]

value: primary cultures of EC from mouse E17 embryo

value: 4 days posttransduction

tag: treatment


title: eCLIP_C2C12_A2B1_A

source_name: C2C12 cells

value: C2C12 cells


title: eCLIP_C2C12_A2B1_input


title: NC 1


title: Asagrei17leg

city: Vermillion

first: Andrea

middle: Lyn

last: Liebl

state: SD

address: 414 E Clark Street

department: Biology

institute: University of South Dakota

data_processing:
Adaptors trimmed, low quality ends removed and pair ends overlapped with HTStream
Sequences mapped to Anolis carolinensis using STAR
genes counted using STAR
Assembly: Anolis carolinensis genome
Supplementary files format and content: tab deliminated .txt file with raw read counts per loci

organism: Anolis sagrei

source_name: leg muscle

extract_protocol:
Total RNA was extracted from whole muscle using Trizol extractions
Libraries were constructed using BGI

value: leg muscle

tag: Sex

value: male


title: B lymphocyte, Montanide plus CSP-injected mice (n=6), 14 days after last immunization

value: B cells enriched by negative selection from pooled splenocytes

tag: genotype

value: three immunizations with Montanide plus CSP recombinant protein, one week apart


title: GD-4

value: Graves Disease


title: Asagrei16leg


title: GD-3


title: Asagrei17jaw

source_name: jaw muscle

value: jaw muscle


title: B lymphocyte, naive mice (n=6)

value: naive


title: NC 3


title: GD-5


title: B lymphocyte, poly (I:C)-injected mice (n=6), 14 days after last immunization

value: spleen

value: three immunizations with poly (I:C), one week apart


title: Asagrei16jaw


title: eCLIP_C2C12_A2B1_B

value: hnRNP A2B1

value: abcam


title: NC 5

value: peripheral blood mononuclear cells

value: Adult

value: Blood


title: Asagrei15leg


title: GD-1

value: female


title: R28d_T3

first: Fangfang

last: Wu

state: Jiangsu

address: Dingjia Qiao 87#

department: Department of Pharmacology

institute: Southeast University

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the UCSC (http://genome.ucsc.edu/) C57BL_6NJ mouse reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: ipsilateral cortex

growth_protocol: Adult male C57BL/6J mice (24.0–26.0 g, 8–10 weeks old) were purchased from the Model Animal Research Center of Nanjing University (Nanjing, China) and randomly assigned to experimental groups. All animals were housed under a constant temperature and humidity and a 12-h light/12-h dark cycle, with the lights turned on at 7:00 AM. Food and water were available ad libitum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, then ligated to modified Illumina multiplex barcode adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012), and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Novaseq TM 6000 following the vendor's recommended protocol.

treatment_protocol: Mice were microinjected with neuron-specific shRNA-TIPARP or shRNA scramble control AAVs in left lateral ventricle. Four weeks later,  mice were  subjected to sham or tMCAO model. Mice subjected to tMCAO were sacrificed at 24 h and 28 d after tMCAO.

tag: strain

value: brain

tag: aav type

value: AAV-SYN-shRNA-TIPARP

value: 28d after tMCAO


title: R28d_T1


title: Asagrei15jaw

value: male


title: R28d_T2


title: DRIP_H_rep2

description: RNA:DNA hybrids

tag: cell line

value: RNase H


title: DRIP_H_rep1

description: RNA:DNA hybrids


title: Acyb08leg

organism: Anolis cybotes

value: leg muscle


title: Acyb08jaw


title: Acyb03leg


title: R28d_C3

value: AAV-SYN-shRNA-Con


title: DRIP_Nor_rep2

description: RNA:DNA hybrids


title: GD-2

tag: cell type

tag: disease state

value: Graves Disease


title: R28d_C1


title: AG from female isotype treated 4

source_name: Adrenal gland

value: Adrenal gland

value: Whole adrenal gland cells

value: C57Bl/6 J wild type

value: Isotype


title: Aosa07leg

organism: Anolis osa


title: Acyb01leg


title: R28d_C2


title: DRIP_Nor_rep1

description: RNA:DNA hybrids


title: Acyb01jaw

value: jaw muscle


title: Aosa07jaw


title: R24h_T2

value: 24h after tMCAO


title: Acyb03jaw


title: MV411_H3K4me1

source_name: H3K4me1 on MV4-11

value: untreated

value: Acute Myeloid Leukemia

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: Aosa05jaw


title: Aosa05leg


title: R24h_T3

value: brain


title: R24h_C1


title: R24h_T1

value: AAV-SYN-shRNA-TIPARP


title: R24h_C2


title: R24h_C3


title: Sham_T3

value: Sham


title: Achloro08jaw

organism: Anolis chlorocyanus

value: male


title: Achloro06leg


title: Achloro08leg


title: H1_VM_iAst_rep3

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw FASTQ files were trimmed for adapters using BBDuk, and quntified their transcripts with Salmon using the reference transcript GENCODEV32 (GRCh38.p13)
Normalized abundance measurements was conducted with DESeq2 (1.27.12)
Assembly: GENCODEV32
Supplementary files format and content: Normalized abundance measurements, Salmon quantification file

source_name: Astrocyte

extract_protocol:
The total RNAs were extracted using TRIzol® (Thermo Fisher Scientific) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using QuantSeq 3' mRNA-Seq Library Prep Kit FWD

tag: regional character

value: Ventral midbrain

value: hESC


title: H1_Control_iAst_rep4

value: Control (Forebrain)


title: H1_VM_iAst_rep4


title: Sham_T2


title: Sham_T1


title: C4D14 (C4D15)

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
Post-processing including demultiplexing, read alignment and quality control was performed using the 10X Genomics Cell Ranger package (v3.1.0).
TCR clonotype data including clonotype ID and CDR3 amino acid sequences were added to the metadata for each cells, and data of C1D0, C4D7 and C4D14 were merged.
Unsupervised clusering of scRNA-seq data was performed with Seurat software and CD8+ T cell clusters were selected and subclustered.
Genome_build: GRCh38
Supplementary_files_format_and_content: expression_matrix_normalized_cd8.csv: Normalized expression matrix of peripheral blood CD8 T cells from C1D0, C4D7 and C4D14
Supplementary_files_format_and_content: sample_information.csv: Metadata for each cells including sample names and TCR sequence

source_name: Peripheral blood lymphocytes

extract_protocol:
T and B cells from cycles 1 and 4 of the responder patient were enriched using CD3 and CD19 microbeads (Miltenyi Biotec). Enriched lymphocytes were run on a Chromium controller (10X Gemomics).
scRNA-seq and TCRab-libraries were prepared according to the manufacturer’s instructions using Chromium™ Next GEM Single Cell 5' Library & Gel Bead Kit (10X Genomics).

tag: time points

value: Cycle 4, day 14

value: Blood

value: CD3+ T and CD19+ B cells


title: H1_VM_iAst_rep2


title: H1_Control_iAst_rep2


title: NC group rep2

status: Public on May 21 2022

city: Guangzhou

first: YISHEN

last: WANG

address: No.54 Xianlie South Road, Yuexiu District

institute: State Key Laboratory of Ophthalmology, Image Reading Center, Zhongshan Ophthalmic Center, Sun Yat-Sen University

data_processing:
Paired-end sequencing was performed with Illumina HiSeq 3000.
HISAT2 alignment program was used for mapping sequencing reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Assembly: mm9
Supplementary files format and content: Matrix with raw gene counts and RPKM for every gene and every sample

source_name: retina

growth_protocol: Mice were housed under a controlled temperature with a 12-h light/dark cycle, and their health and behaviour were monitored daily.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) and purified with the RNeasy Mini kit (Exiqon; Qiagen GmbH,  Hilden, Germany.), according to the manufacturer’s instructions.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L).

treatment_protocol: Antagomirs and antagomir negative controls (Ribobio Co., Ltd.) were dissolved in normal saline. At P3, following anaesthesia in all mice using 3-5% induction and 1-3% maintenance (0.5-1 l/min) isoflurane, a Hamilton syringe (Hamilton Robotics) with a 34-gauge needle was used for intravitreal injection. The left eye was intravitreally injected with 1 μl 0.6 nmol miR-124-3p antagomir, labelled the miR-124-3p knockdown group (anti-miR-124 group), while the right eye was intravitreally injected with an equal volume and concentration of the scrambled control sequence, labelled the negative control group (NC group). to increase the heterogeneity of the sample, the samples in each group were from at least two different litters.

value: wide type

value: postnatal day 9


title: Sham_C3

value: AAV-SYN-shRNA-Con


title: C4D7 (C4D8)

value: Cycle 4, day 7


title: Aosa04leg

value: leg muscle


title: Achloro04leg


title: anti-miR-124 group rep1


title: Sham_C2


title: Aosa04jaw

value: jaw muscle


title: Achloro04jaw


title: C1D0 (C1D1)

value: Cycle 1, day 0


title: H1_Control_iAst_rep3


title: anti-miR-124 group rep2


title: Sham_C1

value: brain


title: NC group rep1


title: mouse ECII RNA, shRNA DEK 2 [shdek2]

value: ECII-bacTRAP female, EC

value: principal neurons from layer II of EC

value: stereotaxic injection within the EC


title: Achloro06jaw

value: male


title: 0.5 µM imatinib R2

type: genomic

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

institute: University Hospital Schleswig-Holstein, Campus Kiel

hyb_protocol: Probes were hybridized on Infinium MethylationEPIC BeadChips ccording to the manufacturer's recommendations.

scan_protocol: The arrays were scanned according to the manufacturer's recommendations.

data_processing: Data analysis was performed using Genome Studio v2.0 with MethylationEPIC v.1.0_B4 and 1 % false discovery rate.

label: Cy5 and Cy3

source_name: K-562 cells

label_protocol: 250 ng DNA was bisulfite-converted and labeled according to the manufacturer's recommendations.

growth_protocol: Cells were grown in RPMI 1640 + 10% v/v FCS + 1 % v/v Pen/Strep w/o imatinib or nilotinib.

extract_protocol: DNA was isolated using Gentra Puregene Kit (Qiagen)

treatment_protocol: Resistant cells were generated by step-wise increase of imatinib concentration to 0.5 and 2 µM imatinib or 0.1 µM nilotinib.

tag: cel line

tag: resistance

value: resistant to 0.5 uM imatinib


title: ST-01008271

first: Vrushali

middle: Dipak

last: Fangal

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

institute: Harvard Medical School

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Whole-blood gene expression profiles were generated with 47,323 probes from the HumanHT-12 v4 Expression BeadChip (Illumina, Inc.) that passed stringent and commonly used quality control (QC) metrics. Expression data were log2-transformed and quantile-normalized as a single batch using the lumiT() and lumiN() functions, respectively, from the R package lumi (version 2.22; The R Foundation). Principal components of gene expression were generated using the getPCAFunc function from the R package iCheck (version 0.6). Prior to downstream statistical analyses, we applied a standard nonspecific variance filter to the expression data using the nsFilter function from the R package genefilter (version 1.52). Probes not annotated with a valid Entrez gene identifier or Human Genome Organization gene symbol and probes with interquartile ranges of expression variance below the 50th percentile were removed to select only the most informative probes. Data were then collapsed to a single probe per gene based on the largest interquartile range of expression variance.

source_name: children between 6 to 14 years of age with moderate persistent asthma

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted from subset of 321 children and blood samples were processed within 4 hrs. of extraction. RNA was stored in PAXgene tubes (Qiagen).

tag: condition

value: asthma

value: M


title: 2 µM imatinib R1

value: resistant to 2 uM imatinib


title: ST-01008179

tag: tissue

value: Blood

value: F


title: ST-01008277


title: ST-01008173


title: ST-01008274


title: ST-01008215


title: 2 µM imatinib R2


title: ST-01008268


title: ST-01008150


title: 0.1 µM nilotinib R2

value: resistant to 0.1 uM nilotinib


title: native

value: treatment-naive


title: ST-01008096


title: ST-01008183


title: ST-01008140


title: ST-01008104


title: ST-01008090


title: ST-01008189


title: ST-01008212


title: ST-01008203


title: ST-01008129


title: ST-01008046


title: ST-01008132


title: ST-01008126


title: ST-01008100


title: NC 2

value: peripheral blood mononuclear cells

tag: age

value: Adult

value: female

value: healthy control


title: 0.1 µM nilotinib R1


title: 0.5 µM imatinib R1


title: ST-01008088

tag: gender


title: ST-01008003


title: ST-01007947


title: ST-01007953


title: ST-01007629


title: ST-01007950


title: ST-01007997


title: ST-01008040


title: ST-01008009


title: ST-01008043


title: ST-01007917


title: ST-01007632


title: ST-01008012


title: ST-01008000


title: ST-01007923


title: ST-01007920


title: ST-01008006


title: ST-01006609


title: ST-01007626


title: ST-01006597


title: ST-01006630


title: ST-01006535


title: ST-01006542


title: ST-01006545


title: ST-01006600


title: ST-01006491


title: ST-01006539


title: ST-01006494


title: ST-01006606


title: ST-01006603


title: ST-01006455


title: ST-01006327


title: ST-01006279


title: ST-01006360


title: ST-01006449


title: ST-01006405


title: ST-01006305


title: ST-01006314


title: ST-01006002


title: ST-01006106


title: ST-01006008


title: ST-01006094


title: ST-01006408


title: ST-01006414


title: ST-01006323


title: ST-01006411


title: ST-01006363


title: ST-01006200


title: ST-01005687


title: ST-01006270


title: ST-01005721


title: ST-01006011


title: ST-01006283


title: ST-01005918


title: ST-01006273


title: ST-01006254


title: ST-01006097


title: ST-01006005


title: ST-01005999


title: ST-01005831


title: ST-01005684


title: ST-01005662


title: ST-01005553


title: ST-01005627


title: ST-01005611


title: ST-01003820


title: ST-01003817


title: ST-01005681


title: ST-01005630


title: ST-01004867


title: ST-01005567


title: ST-01005550


title: ST-01004864


title: ST-01003791


title: ST-01003814


title: ST-01003804


title: ST-01003808


title: ST-01005605


title: ST-01003799


title: ST-01003790


title: ST-01003809


title: ST-01003771


title: ST-01003781


title: ST-01003785


title: ST-01003796


title: ST-01003777


title: ST-01003675


title: ST-01003764


title: ST-01003775


title: ST-01003678


title: ST-01003668


title: ST-01003758


title: ST-01003609


title: ST-01003672


title: ST-01003769


title: ST-01003601


title: ST-01003604


title: ST-01003754


title: ST-01003800


title: ST-01003556


title: ST-01003571


title: ST-01003565


title: ST-01003559


title: ST-01003568


title: ST-01003598


title: ST-01003513


title: ST-01003550


title: ST-01002390


title: ST-01002211


title: ST-01002171


title: ST-01003509


title: ST-01003503


title: ST-01003506


title: ST-01002168


title: ST-01002146


title: ST-01002097


title: ST-01003553


title: ST-01002442


title: ST-01001852


title: ST-01002149


title: ST-01002122


title: ST-01005665


title: ST-01000797


title: ST-01000719


title: ST-01000598


title: ST-01000673


title: ST-01000489


title: ST-01000794


title: ST-01001899


title: ST-01000760


title: ST-00080842


title: ST-00080899


title: ST-01000757


title: ST-00080856


title: ST-00080845


title: ST-01003617


title: ST-00080626


title: ST-00080611


title: ST-00080541


title: ST-00080470


title: ST-00080367


title: ST-00080473


title: ST-00080343


title: ST-01003614


title: ST-00080337


title: ST-00080467


title: ST-00080364


title: ST-00070277


title: ST-00080287


title: ST-00068499


title: ST-00068470


title: ST-00068380


title: ST-00069053


title: ST-00080340


title: ST-00080174


title: ST-00080334


title: ST-00080284


title: ST-00068498


title: ST-00068436


title: ST-00069776


title: ST-00068276


title: ST-01003681


title: ST-00068504


title: ST-00068371


title: ST-00080261


title: ST-00068264


title: ST-00068405


title: ST-00068416


title: ST-00068246


title: ST-01002119


title: ST-00068162


title: ST-00068211


title: ST-00068156


title: ST-00068254


title: ST-00068192


title: ST-00068134


title: ST-00068153


title: ST-00068122


title: ST-00068004


title: ST-00068036


title: ST-00068137


title: ST-00067990


title: ST-00068129


title: ST-00068012


title: ST-00068066


title: ST-00068136


title: ST-00068068


title: SK-CTBP1/2-DKD-2

city: kunming

first: shubai

last: Liu

state: yunnan

address: 132 lanhei road,

institute: kunming institute of botany, chinese academic of science

hyb_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas hyberzation station according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the  Affymetrix GeneAtlas Fluidic station according to the manufacturer's instructions.

data_processing: The data were analyzed with Affymetrix Expression Console  using Robust Mutichip Average (RMA) preprocessing followed by “per chip” normalization across all samples. All Affymetrix control genes were removed from the expression data and the remaining Affymetrix probe clusters were imported into the Affymetrix Power Tools software (APT package).

label: biotin

label_protocol: The quality and quantity of the RNA were tested using Bioanalyzer (Agilent Technologies, Santa Clara, CA). 4.5 μg of RNA from each sample was used for target labeling by a two-round amplification protocol (Expression Analysis Technical Manual, 20012, Affymetrix).

growth_protocol: The human macrophages derived by PMA induced were cultured as descripted in the manuscipt.

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

treatment_protocol: the cell lines  were treated with control and HMEOs  as descripted in the manuscript.

value: Cell line with


title: ST-00068013


title: SK-CTBP1/2-DKD-1


title: ST-00067988


title: ST-00067980


title: ST-00068015


title: SK-CTBP2-KD-2


title: ST-00067831


title: SK-CTBP2-KD-1


title: ST-00067960


title: ST-00067911


title: ST-00067814


title: ST-00067883


title: ST-00067875


title: ST-00067956


title: ST-00067823


title: ST-00067794


title: ST-00067776


title: ST-00067916


title: 736P

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary files format and content: tab-delimited text files include raw values for each sample.

organism: Rattus norvegicus

source_name: Thyroarytenoid muscle, vocal fold

extract_protocol:
Muscles were removed, bissected, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long Evans

value: Thyroarytenoid muscle, vocal fold

value: 8 months

value: Female


title: 602P


title: 195P


title: SK-CTBP1-KD-2


title: 321WT

value: WT


title: 389WT


title: 147WT


title: 111WT


title: SK-Sham Ctrl-2


title: ST-00067759

value: asthma


title: SK-CTBP1-KD-1


title: ST-00067770

value: M


title: SK-Sham Ctrl-1


title: ST-00067746


title: ST-00067735


title: ST-00067595


title: ST-00067586


title: ST-00067744


title: ALI_SB_Flagellin_24h_3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Preincubated 1h with 20 µM SB203580, then 100 ng/ml Flagellin for 24 h.

data_processing:
STAR_2.4.0a paired-end mapping versus Sscrofa11.2.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Sus_Crofa.GRCm38.77 Ensembl GTF annotation file.
Genome_build: Sscrofa11.2
Supplementary_files_format_and_content: featurecounts.txt: Tab-delimited text file; Feature Counts.

organism: Sus scrofa

source_name: Pig bronchial epithelial cells

growth_protocol: Epithelial cells were dissected from the bronchi 1-month-old pigs by enzymatic digestion (0.1% proteases mix and 0.01% deoxyribonuclease I) during 24h at 4°C. The enzymatic digestion was stopped by the addition of a 10% volume of foetal bovine serum and cells were recovered and seeded onto 0.4 μm semi-permeable membranes (Greiner bio-one, Les Ulis, France) treated with collagen type 1. Cells were cultured until confluency and then cultured in an air-liquid-interface (ALI) at 37°C in 5% CO2 atmosphere. Culture medium was DMEM/F12 supplemented with SupplementMix (PromoCell C-39165), Glutamine (2 mM) and penicillin/streptomycin (100U/µg/ml).

extract_protocol: Paired-end

treatment_protocol: 20 µM SB203580 or the vehicle (DMSO) for 1 h and then 100 ng/ml Flagellin or not (PBS) for 2 h or 24 h.

value: Bronchial epithelial cells differentiated under air-liquid condition

value: Wild type

value: 1 month

tag: treatment 1

tag: treatment 2

value: 100 ng/ml Flagellin for 24 h


title: ALI_SB_Flagellin_24h_4

tag: genotype


title: ALI_SB_Flagellin_24h_2


title: ST-00067648

value: Blood


title: ALI_SB_Flagellin_2h_4

description: Preincubated 1h with 20 µM SB203580, then 100 ng/ml Flagellin for 2 h.

value: 100 ng/ml Flagellin for 2 h


title: ST-00067589

value: F


title: ST-00067577


title: ALI_SB_Flagellin_2h_3


title: ALI_SB_Flagellin_24h_1


title: ST-00067462


title: ST-00067340


title: ST-00067545


title: ST-00067249


title: ST-00067112


title: ST-00067271


title: T47D_VC1_3

city: Itabashi-ku

first: Miho

last: Akimoto

state: Tokyo

department: Department of Biochemistry

country: Japan

institute: Teikyo University

description: Gene expression in T47D cells transfected with empty vector

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: T47D cell, vector control

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)  according to the manufacturer's instructions.

value: breast cancer cell  line T47D

value: control


title: ST-00067318


title: ALI_SB_Flagellin_2h_2


title: T47D_PA6_3_1

description: Gene expression in T47D cells expressing full-length PTH-AS

source_name: T47D cell, full-length PTH-AS

value: expressing full-length PTH-AS


title: ST-00067254


title: ST-00067117


title: T47D_PA6_3_1_2


title: ST-00067105


title: T47D_PA5_8_4_3

description: Gene expression in T47D cells expressing incomplete PTH-AS

source_name: T47D cell, trancated PTH-AS

value: expressing incomplete PTH-AS


title: T47D_PA5_8_4_2


title: T47D_VC1


title: ALI_SB_Flagellin_2h_1


title: T47D_PA6_3_1_3


title: ST-00067145


title: T47D_VC1_2


title: ST-00067036


title: T47D_PA5_8_4


title: ST-00067019


title: ST-00067012


title: ST-00067042


title: ALI_DMSO_PBS_24h_4

description: Preincubated 1h DMSO, PBS for 24 h.

value: DMSO for 1h

value: PBS for 24 h


title: ALI_DMSO_PBS_24h_2

description: Preincubated 1h DMSO, PBS for 24 h.


title: ST-00067055


title: ST-00067021


title: ALI_DMSO_PBS_24h_1

description: Preincubated 1h DMSO, PBS for 24 h.


title: ALI_DMSO_PBS_2h_4

description: Preincubated 1h DMSO, PBS for 2 h.

value: PBS for 2 h


title: ALI_DMSO_PBS_2h_3

description: Preincubated 1h DMSO, PBS for 2 h.


title: ALI_DMSO_PBS_2h_2

description: Preincubated 1h DMSO, PBS for 2 h.


title: ALI_DMSO_PBS_24h_3

description: Preincubated 1h DMSO, PBS for 24 h.


title: ALI_DMSO_PBS_2h_1

description: Preincubated 1h DMSO, PBS for 2 h.


title: ALI_DMSO_Flagellin_24h_4

description: Preincubated 1h DMSO, 100 ng/ml Flagellin for 24 h.


title: ALI_DMSO_Flagellin_24h_2


title: ST-00066997


title: ST-00066985


title: ST-00066989


title: ALI_DMSO_Flagellin_2h_4

description: Preincubated 1h DMSO, 100 ng/ml Flagellin for 2 h.


title: ALI_DMSO_Flagellin_24h_1


title: ST-00066965


title: ST-00066936


title: ALI_DMSO_Flagellin_2h_3


title: ALI_DMSO_Flagellin_24h_3


title: ALI_DMSO_Flagellin_2h_2


title: ST-00066951


title: ST-00066833


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_8 hour_replicate_3

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

country: United Arab Emirates

institute: NYUAD

data_processing:
Raw sequencing reads were quality controlled using the FASTQC tool prior to processing using Trimmomatic v0.36 to remove barcodes, adapter sequences and low-quality bases (Phred quality score <22).
Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.2a.
Genes not expressed or with very low expression levels (less than five reads in 2 or more samples in any given condition) were removed.
Filtered raw counts were log2 transformed prior to normalization using JMP Genomics 8 (SAS Institute). Data were batch normalized to reduce any potential technical batch effects.

source_name: Human Aortic Endothelial Cell

growth_protocol: Human aortic endothelial cells (HAECs) obtained from Lonza were grown in normal physiological levels of glucose (NG) (5.5 mM D-glucose) EGM™ 2 Endothelial Cell Growth Medium-2 BulletKit™ (Lonza) containing 2 % fetal bovine serum (FBS) as per manufacturer’s instructions, and maintained at 37°C, 5% CO2

extract_protocol:
Total RNA was isolated from HAECs using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
KAPA Stranded RNA-Seq kit with RiboErase

treatment_protocol: HAECs were then exposed to NG EGM™ 2 Endothelial Cell Growth Medium-2 BulletKit™ (Lonza) containing reduced serum (0.2 % FBS) overnight (growth factors and supplements remained in the media). HAECs were then treated with EGM™ 2 Endothelial Cell Growth Medium-2 BulletKit™ (Lonza) containing 2 % FBS and either 5.5 mM D-glucose or 25 mM D-glucose. HAECs were then harvested at 0, 0.5, 1, 4 and 8 h post treatment.

value: Endothelial cell

tag: treatment

value: Normal Glucose (5.5 mM D-glucose)

tag: time

value: 8 hour


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_8 hour_replicate_2


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_4 hour_replicate_3

value: 4 hour


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_4 hour_replicate_2


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_4 hour_replicate_4


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_8 hour_replicate_1


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_8 hour_replicate_4


title: ST-00066830

value: asthma


title: ALI_DMSO_Flagellin_2h_1

value: Bronchial epithelial cells differentiated under air-liquid condition

value: Wild type

value: 1 month


title: ST-00066749

value: Blood

value: M


title: ST-00066795

value: F


title: ST-00066745


title: ST-00066785


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_4 hour_replicate_1


title: ST-00066566


title: ST-00066820


title: Donor 6 CD8 Day 2

city: San Francisco

first: Vivasvan

last: Vykunta

address: 513 Parnassus Avenue HSW901

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
PE reads processed with kallisto using GRCh37 (hg19) cDNA annotation from ensembl
Transcript counts aggregated at the gene level (ensembl transcript IDs mapped to ensembl gene IDs)
Genes of interest were selected from the normalized and aggregated counts table
Genes with multiple ensembl IDs were merged (summed) based on gene symbol; these "isoforms" showed extremely high correlation (see plots)
Output matrix of TPM values of samples vs gene symbols
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: CD8 T cell

extract_protocol:
CD4 and CD8 T cells from each donor were sorted by FACS and then frozen in RNAlater (QIAGEN) for bulk RNA sequencing. Total RNA from frozen samples was extracted using Rneasy Mini Kit (Qiagen) based on manufactuter protocols.
RNA libraries were contructed with Illumina TruSeq RNA Sample Prep Kit v2 (cat. no. RS-122-2001) according to the manufacturer’s protocol.
Bulk RNA Sequencing

tag: individual

value: Donor 6

value: CD8 T cell

value: Day 2

value: after electroporation


title: Donor 6 CD4 Day 2

source_name: CD4 T cell

tag: cell type

value: CD4 T cell


title: ST-00066678

city: Boston


title: ST-00066602


title: ST-00066659


title: ST-00066686


title: ST-00066995


title: ST-00066644


title: ST-00066707


title: ST-00066580


title: ST-00066560


title: ST-00066710


title: ST-00066563


title: ST-00066555


title: Donor 6 CD4 Day 0

value: Day 0

value: day of electroporation


title: Donor 6 CD8 Day 0


title: Donor 6 CD8 Day -2

value: Day -2

value: pre-stimulation


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_24 hour_replicate_4

value: Endothelial cell

value: Normal Glucose (5.5 mM D-glucose)

value: 24 hour


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_24 hour_replicate_2


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_24 hour_replicate_3


title: Donor 6 CD4 Day -2


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_24 hour_replicate_1


title: Donor 5 CD8 Day 2

value: Donor 5


title: Human Aortic Endothelial Cell_Normal Glucose (NG)_1 hour_replicate_3

value: 1 hour


title: Donor 5 CD8 Day 0


title: Donor 5 CD4 Day 2