title: ATAC-seq_24h_dTAG_R1

city: Aachen

first: Mirna

last: Barsoum

state: North Rhine Westphalia

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Biology

country: Germany

institute: Uniklinik RWTH Aachen

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BIigWig files
Supplementary files format and content: Excel files

source_name: iMEF

growth_protocol: The cells ere cultured in humidified atmosphere with 5 % CO2 at 37 °C  in Dulbecco’s Modified Eagle Medium (DMEM; Gibco) without pyruvate, 10 % heat-inactivated FCS (Gibco) and 1 % penicillin/streptomycin. iMEFcells were used and transfected with a lentiviral construct, containing N-terminal tagged FKBP12F36V human ASH2L encoding gene

extract_protocol:
iMEF cells were cross-linked with 1% formaldehyde in cell culture medium on a shaking platform for 10 min at room temperature (RT). The cross-linking reaction was quenched by adding glycine to 125 mM and incubation for another 5 min at RT. Adherent cells were washed with PBS twice and collected in PBS by scraping the cells from the dish. Cells were centrifuged at 380 x g for 5 min at 4°C and resuspended in 1 ml Lysis Buffer B (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 0.25% (v/v) Triton X-100) per 2 x 107 cells and centrifuged. To the pellet 1 ml Lysis Buffer C (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 200 mM NaCl) was added per 2 x 107 cells, followed by an incubation on ice for 10 min. After a further centrifugation step, disruption of the pelleted nuclei was performed in 200 μl lysis buffer D (50 mM Tris pH 8, 10 mM EDTA, 1% (w/v) SDS, protease inhibitor cocktail (1xPIC, Merck, P8340) per 5 x 106 MEF cells for 30 min at 15°C.  200 μl aliquots were sonicated for a minimum of 10 cycles using a Bioruptor Pico (Diagenode) with 30-second on-off-cycles to achieve DNA fragment lengths of about 800 bp or 300 bp for ChIP-qPCR or ChIP-seqq, respectively. The size distribution of the resulting DNA fragments was assessed by agarose gel electrophoresis. To remove cell debris, lysates were centrifuged for 10 min at 10,000 x g (15°C), the supernatants pooled, and DNA concentrations were measured using a NanoDrop 1000 device (Peqlab). ChIP assays were performed using the OneDay ChIP Kit from Diagenode (C01010080) according to the manufacturer’s instructions. To capture protein-DNA complexes, 42 μl of Protein A beads per sample were pre-incubated in 1 x ChIP buffer for 2 hours at 4 °C with 2 μg of specific antibody or rabbit IgG (provided by the kit). The sheared chromatin (10 – 100 µg) was diluted 4.7-fold with 1 x ChIP buffer, setting aside 1/10 of the diluted chromatin for the input control, and mixed with the pre-incubated beads for 30 min at 4°C. Subsequently, the chromatin-antibody-bead complexes were washed three times with 1 x ChIP buffer and taken up in DNA purifying slurry. The diluted input control chromatin was precipitated by the addition of 5 volumes 100% ethanol and centrifuged at 16,000 x g, 4°C for 10 min. The dried pellets were resuspended in RNase-free H2O and mixed with DNA purifying slurry. The DNA of all samples was reverse crosslinked and further purified according to the manual.
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as single reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturers recommendations.

treatment_protocol: iMEF cells were treated with dTAG  for 30min, 4h, 8h or 24h

value: iMEF

tag: time point

tag: agent

value: dTAG treatment


title: ATAC-seq_8h_dTAG_R2

status: Public on Sep 12 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue


title: AAS_38_Atopic asthmatic_convalescent_visit_L006

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_38 sequenced on lane L006
AAS_38_C80BLANXX_CGATGT_L006
Barcode: CGATGT

library_source: transcriptomic

data_processing:
The Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Raw sequencing reads were aligned to the reference genome (hg19) using Rsubread and summarised at the gene-level with featureCounts. Genes were annotated using the genome wide annotation for human org.Hs.eg.db.
Genome_build: hg19
Supplementary_files_format_and_content: AAS_raw_counts.txt file includes raw-gene level counts. Sample were sequenced across two lanes and need to be collapsed prior to further downstream analysis (AAS_raw_counts_collapsed.txt). For differential expression analysis, the raw counts were used.
Supplementary_files_format_and_content: AAS_VST_transformed_counts.txt file includes DESeq2 vst transformed counts and samples need to be collapsed prior to further downstream analysis (AAS_VST_transformed_counts_collapsed.txt). For network analysis, the vst transformed data was used.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from viable PBMC employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany). The integrity of the RNA was 9.5 ± 0.3 (mean ± SD), as assessed on the Bioanalyzer (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subjectid

tag: visit

value: CV

tag: age at visit (years)

tag: gender

value: Male

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type

value: PBMC


title: K107228

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

country: USA

institute: Indiana University School of Medicine

description: normal breast tissue core

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded.

source_name: normal breast tissue core

growth_protocol: Breast tissue biospies are collected using a vacuum-assisted breast biopsy system (ATEC, Hologic) and fresh frozen whitin 10 min.

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA samples were first assessed using Agilent 2100 Bioanalyzer. Then cDNA library was prepared using the  KAPA RNA HyperPrep kit (Roche, Wilmington, MA)  on  a BiomeK Automated worstation (Beckman coulter, Indianapolis, IN)

value: normal breast tissue core

value: female

tag: age

tag: bmi

tag: racial background

value: WHITE

tag: tyrer-cuzick lifetime_risk_score


title: AAS_42_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_42 sequenced on lane L007
AAS_42_C80BLANXX_GCCAAT_L007
Barcode: GCCAAT


title: Young_2_mnth_mice_1_bulk_mRNAseq_hippocampus

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

data_processing:
From mRNA sequencing, low-quality raw sequence reads, reads with adapters, and reads with unknown bases were filtered by SOAPnuke software to yield clean reads.
Filtered clean reads were mapped into the reference mouse genome (mm10) using HISAT.
Novel genes predicted using StringTie and Cuffcompare to compare the reconstructed transcripts to the reference annotation and then used CPC tools to predict the novel transcripts.
Gene expression level for each sample was determined using the tools Bowtie2 and RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Young male C57BL/6J mice

extract_protocol:
The total RNA of the samples was extracted with the Trizol (Invitrogen) reagent and used for construction of sequencing libraries.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Hippocampus

tag: Sex

value: male

value: 2 months

tag: strain


title: AAS_37_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_37 sequenced on lane L007
AAS_37_C80BLANXX_ATCACG_L007
Barcode: ATCACG

source_name: AAS_37_Atopic asthmatic_acute_visit

value: AV

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: ATAC-seq_8h_dTAG_R1

tag: tissue

tag: time point

tag: agent


title: ATAC-seq_4h_dTAG_R2


title: RNAseq_Day14_3

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequenced libraries were evaluated with FastQC/0.11.3
Transcripts were quantified using Salmon.
Differential expression analysis was performed using DESeq2 package based on the criteria of more than two-fold change in expression value versus control and false discovery rates (FDR) <0.05.
Assembly: rn6
Supplementary files format and content: txt files include read counts for each sample

organism: Rattus rattus

source_name: Perigonadal fat

extract_protocol:
Samples were homogenized in Qiazol Lysis Reagent (Qiagen, Germantown, MD) using a TissueLyser II (Qiagen, Germantown, MD). RNA was isolated using a RNeasy Lipid Tissue Mini Kit (Qiagen, Germany).
RNA-seq libraries were constructed from total RNA using polyA selection followed by NEBNext UltraDirectional kit workflow (New England Biolabs, MA).

value: Perigonadal fat

value: Sprague-Dawley

tag: treatment

value: Injectable Ice Slurry

tag: time

value: Day 14


title: ATAC-seq_24h_dTAG_R2


title: K107174

description: normal breast tissue core

tag: gender


title: ATAC-seq_4h_dTAG_R1


title: AAS_37_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_37 sequenced on lane L006
AAS_37_C80BLANXX_ATCACG_L006
Barcode: ATCACG

tag: subjectid

tag: visit

tag: age at visit (years)

tag: hdm-specific ige

tag: total ige


title: K107230

description: normal breast tissue core

tag: age

tag: bmi


title: RNAseq_Day14_2


title: AAS_36_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_36 sequenced on lane L007
AAS_36_C80BLANXX_ATTCCT_L007
Barcode: ATTCCT

value: Female

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: K107148

description: normal breast tissue core

tag: racial background

tag: tyrer-cuzick lifetime_risk_score


title: AAS_36_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_36 sequenced on lane L006
AAS_36_C80BLANXX_ATTCCT_L006
Barcode: ATTCCT


title: RNAseq_Day14_1

tag: tissue

tag: strain


title: K107145

description: normal breast tissue core


title: RNAseq_Day3_3

tag: treatment

value: Day 3


title: AAS_35_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_35 sequenced on lane L007
AAS_35_C80BLANXX_ACTGAT_L007
Barcode: ACTGAT

source_name: AAS_35_Atopic asthmatic_acute_visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: ATAC-seq_30min_dTAG_R1

value: iMEF

tag: time point

tag: agent

value: dTAG treatment


title: K107147

description: normal breast tissue core

tag: gender


title: ATAC-seq_WT_R2

value: No dTAG treatment


title: ATAC-seq_30min_dTAG_R2


title: RNAseq_Day3_2

tag: time


title: AAS_35_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_35 sequenced on lane L006
AAS_35_C80BLANXX_ACTGAT_L006
Barcode: ACTGAT

tag: subjectid

tag: visit

tag: age at visit (years)

tag: hdm-specific ige

value: PBMC


title: RNAseq_Day3_1


title: K107132

description: normal breast tissue core

value: normal breast tissue core

tag: age

tag: bmi


title: ATAC-seq_WT_R1


title: K107133

description: normal breast tissue core

value: female


title: RNAseq_Day1_3


title: AAS_34_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_34 sequenced on lane L007
AAS_34_C80BLANXX_GAGTGG_L007
Barcode: GAGTGG

value: CV

value: Male

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: RNAseq_Day1_2

tag: tissue

tag: strain


title: K107120

description: normal breast tissue core

tag: racial background

value: WHITE

tag: tyrer-cuzick lifetime_risk_score


title: K107104

description: normal breast tissue core


title: RNAseq_Day1_1

tag: treatment


title: RNAseq_NC_3

value: Control


title: AAS_33_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_33 sequenced on lane L006
AAS_33_C80BLANXX_CGTACG_L006
Barcode: CGTACG

source_name: AAS_33_Atopic asthmatic_acute_visit

value: AV

tag: gender

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: ChIP-seq_Ash2l_WT_R2

treatment_protocol: iMEF cells were treated with dTAG  for 1h

tag: agent

tag: antibody


title: K107111

description: normal breast tissue core


title: ChIP-seq_Ash2l_1h_dTAG_R1

tag: time point


title: ChIP-seq_Ash2l_WT_R1


title: AAS_32_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_32 sequenced on lane L007
AAS_32_C80BLANXX_GTTTCG_L007
Barcode: GTTTCG

tag: subjectid

tag: visit

tag: age at visit (years)

tag: hdm-specific ige


title: ChIP-seq_Ash2l_Input_dTAG_R2


title: RNAseq_NC_2

value: Perigonadal fat

tag: time


title: ChIP-seq_Ash2l_Input_WT_R2


title: AAS_31_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_31 sequenced on lane L007
AAS_31_C80BLANXX_GTGGCC_L007
Barcode: GTGGCC

source_name: AAS_31_Atopic asthmatic_acute_visit

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)


title: AAS_32_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_32 sequenced on lane L006
AAS_32_C80BLANXX_GTTTCG_L006
Barcode: GTTTCG

tag: cell type


title: K107431

description: normal breast tissue core

tag: tissue

tag: age

tag: bmi

tag: racial background


title: ChIP-seq_Ash2l_Input_dTAG_R1


title: AAS_31_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_31 sequenced on lane L006
AAS_31_C80BLANXX_GTGGCC_L006
Barcode: GTGGCC

tag: gender

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: K107101

description: normal breast tissue core

tag: tyrer-cuzick lifetime_risk_score


title: ChIP-seq_Ash2l_1h_dTAG_R2

tag: agent

tag: time point

tag: antibody


title: AAS_34_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_34 sequenced on lane L006
AAS_34_C80BLANXX_GAGTGG_L006
Barcode: GAGTGG

tag: subjectid

tag: visit

tag: age at visit (years)


title: Setd8-LKO2, TCPOBOP 24h, Mouse liver nuclei, ATAC-seq

city: Heraklion

first: Dimitrios

last: Botskaris

address: Nikolaou Plastira 100

country: Greece

institute: IMBB FORTH

data_processing:
To remove low-quality bases and adapter sequences from the raw FASTQ files, we employed Trimmomatic (version 0.39). The FASTQ files were mapped on the UCSC mm10 genome using hisat2 with default settings. We retained only the reads with a mapping quality score greater than 30 and removed blacklisted regions from our BAM files which are known to be susceptible to technical artifacts and spurious signals. The resulting BAM files were converted to bigwig files using deeptools (version 3.3.2). Before identifying peak regions and to account for variations in the number of sequencing reads between ChIP and CUT&Tag samples, we standardized the total read count for each sample by equally reducing reads proportionally based on the sample with the fewer reads. Peaks for ChIP-seq data were initially identified using MACS2 (version 2.2.7.1) with a stringent p-value cutoff of 1.00e-13. Additionally, for CUT&TAG data, peak calling was performed using SICER2.  Differential expression analysis of RNA-seq data performed with metaseqR2.
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeak, output of metaseqR2, output of SICER2

source_name: Liver

growth_protocol: We used livers dissected from 45-50 days old mice

extract_protocol:
For RNA: Total RNAs were purified from liver tissues by brief homogenization in 10 volumes of Trizol reagent using Polytron device, followed by incubation at room temperature for 5 min and the addition of 0.2 volumes of chloroform and further incubation at room temperature for 3 minutes. The samples were centrifuged at 12000 g for 15 minutes at 40C and the aqueous phase was collected, precipitated by the addition of equal volume of isopropanol. After 10 minutes at room temperature, the RNA was collected by centrifugation at 12000g for 15 minutes. The pellet was resuspended in H2O and re-precipitated with ethanol. The RNA samples were further purified by digestion with 10 units of DNase-I for 10 min at 370C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. For ChIP: Livers were minced to small pieces and crosslinked with 1% formaldehyde for 10 min. After the addition of glycine at 0.125 M final concentration, the cross-linked cells were washed with a buffer containing 50 mM Hepes pH 7.9, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and sequentially treated with a buffer containing 0.25% Triton-X100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES and a buffer containing 0.15M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES for 10 minutes each. The resulting crosslinked nuclei were resuspended in 10 volumes of 50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 0.5% Sarkosyl, and protease inhibitor cocktail (CompleteTM Roche), sonicated for 10 minutes in Covaris Sonicator instrument with maximum setting. After sonication, samples were supplemented with 0.5 volume of 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 3% Triton X-100, 0.1% Sodium deoxycholate, and protease inhibitor cocktail, and centrifuged for 15 minutes at 20.000g. The soluble chromatin was incubated overnight with Dynabeads Protein G (Invitrogen), that were prebound by 5 mg of the primary antibodies recognizing H3K27ac-modified histones, CTCF and Smc3. The beads were washed twice with a buffer containing 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 0.5 mM PMSF, 2 mg/ml aprotinin, once with the same buffer but containing 500 mM NaCl, once with a buffer containing 20 mM Tris, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5 % NP-40, 0.5 % Na-deoxycholate, 0.5 mM PMSF, 2 mg/ml aprotinin and once with a buffer containing 10 mM Tris pH 8.0, 0.1 mM EDTA, 0.5 mM PMSF, 2 mg/ml aprotinin.  Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation in a buffer containing 50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS and 50 mM NaHCO3 at 65oC. The samples were then incubated with 20 mg/ml RNase-A for 30 minutes at 37oC, followed by incubation with 20 mg/ml Proteinase-K for 2 hours at 42oC. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. For CUT&Tag and ATAC-seq: Hepatocyte nuclei were prepared as follows: liver tissue was minced into small pieces in 20 volumes of ice cold buffer containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2 and protease inhibitor cocktail (CompleteTM EDTA-free, Roche), and homogenized by 10 strokes using Dounce device. The suspension was filtered through 100 m mesh strainer and centrifuged for 5 min. at 400g. The resulting pellet was resuspended in a buffer containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 1% NP40 and protease inhibitor cocktail (CompleteTM EDTA-free, Roche). After incubation in ice for 3 min the nuclei were collected by centrifugation for 5 min at 400g, washed twice with PBS and used for downstream applications. CUT&Tag assays were performed as follows: 105 nuclei were resuspended in a buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, protease inhibitor cocktail (CompleteTM EDTA-free, Roche) and incubated for 10 min with Concanavalin A-conjugated magnetic beads (Epicypher) that were previously activated by repeated washings with a buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2. The reactions were supplemented with 0.5 volume of a buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin, 2 mM EDTA and 0.5 g of the anti-Lamin A/C or anti-H4K20Me3 or IgG negative control primary antibodies (see Reporting Summary). The samples were incubated overnight at 40C by gentle agitation. The beads were collected and supplemented with a buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin and 0.5 g of anti-rabbit or anti-mouse secondary antibodies (Epicypher). After incubation for 30 min at room temperature, the beads were washed twice with the same buffer and resuspended in the same buffer containing 300 mM NaCl. Protein A/G-fused Tn5 transposase protein (CUTANA pA/G-Tn5, Epicypher) was added and the samples were incubated for 1 hour at room temperature followed by washing with a buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin. The beads were collected and resuspended in the above buffer containing 10 mM MgCl2, and incubated for 1 hour at room temperature. The beads were collected and washed once with 10 mM TAPS, pH 8.5, 0.2 mM EDTA. DNA was released from the beads by incubation in 10 mM TAPS, pH 8.5, 0.1% SDS for 1 hour at 580C. After quenching by the addition of 3 volumes of 0.67% Triton-X100, the samples were used for PCR reaction (15 cycles) using universal i5 primers and barcoded i7 primers. For ATAC-seq reactions we used the ATAC-seq kit from Active Motif. Tagmentation reactions using 105 nuclei, DNA purification and PCR amplifications using combinations of indexed i5 and i7 primers were performed according to the manufacturer’s instructions.
RNA-seq libraries were generated using NEBNext Ultra II RNA Library preparation kit from New England Biolabs using Poly-A selection. ChIp-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit of New England Biolabs. CUT&Tag and ATAC-seq libraries corresponded to the above-described PCR reactions with i5 and i7 primers, which were cleaned-up by AMPure.

treatment_protocol: Mice were treated with intraperitoneal injection of TCPOBOP mitogen (3mg/kg) for 24 hours

value: Liver

value: Whole Liver

tag: genotype

tag: treatment

value: TCPOBOP


title: K107095

description: normal breast tissue core


title: AAS_33_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_33 sequenced on lane L007
AAS_33_C80BLANXX_CGTACG_L007
Barcode: CGTACG

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)


title: ChIP-seq_Ash2l_Input_WT_R1

tag: tissue


title: ChIP-seq_H3K27me3_Second_48h_R2

data_processing:
Alignment by BWA
Filtering by Samtools
Broad peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BIigWig files
Supplementary files format and content: Excel files

treatment_protocol: iMEF cells were treated with dTAG for 16h, 24h or 48h


title: AAS_30_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_30 sequenced on lane L006
AAS_30_C80BLANXX_GTGAAA_L006
Barcode: GTGAAA

tag: cell type


title: ChIP-seq_H3K27me3_Second_48h_R1


title: K107096

description: normal breast tissue core

tag: gender

tag: age

tag: bmi

tag: racial background


title: K107085

description: normal breast tissue core

tag: tyrer-cuzick lifetime_risk_score


title: K107108

description: normal breast tissue core


title: RNAseq_NC_1

tag: strain

value: Sprague-Dawley

tag: time


title: AAS_29_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_29 sequenced on lane L007
AAS_29_C80BLANXX_GTCCGC_L007
Barcode: GTCCGC

source_name: AAS_29_Atopic asthmatic_acute_visit

tag: subjectid

tag: visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: AAS_28_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_28 sequenced on lane L007
AAS_28_C80BLANXX_CCGTCC_L007
Barcode: CCGTCC

tag: age at visit (years)


title: K107039

description: normal breast tissue core


title: ChIP-seq_H3K27me3_Second_24h_R2

tag: antibody

tag: agent

tag: time point


title: K107034

description: normal breast tissue core


title: AAS_30_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_30 sequenced on lane L007
AAS_30_C80BLANXX_GTGAAA_L007
Barcode: GTGAAA

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)


title: AAS_29_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_29 sequenced on lane L006
AAS_29_C80BLANXX_GTCCGC_L006
Barcode: GTCCGC

tag: gender

tag: cell type


title: AAS_28_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_28 sequenced on lane L006
AAS_28_C80BLANXX_CCGTCC_L006
Barcode: CCGTCC


title: Serum_AD_15

type: RNA

city: Washington

first: Rachael

last: Batabyal

address: 111 Michigan Ave NW

institute: Children's National Hospital

description: miRNA expression data

hyb_protocol: Following labeling RNA was hybridized to affymetrix miRNA 4.0 GeneChips for 16 hours and washed and stained on the GeneChip Fluidics Station 450 using protocol FS450_0002.

scan_protocol: GeneChips were scanned on the Affymetrix GeneChip Scanner 3000

data_processing:
Resulting data were normalized in Affymetrix Expression Console software using RMA-DABG and exported into Partek Genomics Suite version 6.6 for analysis.
intensity signals after normalization with RMA-DABG

label: Biotin

source_name: AD Serum 15

label_protocol: 1,000 ng of RNA was labeled using Affymetrix FlashTag Biotin HSR RNA labeling kit.

extract_protocol: adipocyte-derived small extracellular vesicles were isolated from serum and CSF using Exoquick and Exoquick TC precipitation reagents followed by immunoselection. Total RNA was extracted using mirVana RNA isolation kits. Total RNA was amplified with the complete Seramir Exosome RNA amplification kit.

tag: tissue

tag: disease state

value: Alzheimer Disease


title: ChIP-seq_H3K27me3_Second_24h_R1

value: iMEF


title: K107473

description: normal breast tissue core

tag: age

tag: bmi

tag: racial background

tag: tyrer-cuzick lifetime_risk_score


title: Serum_AD_16

description: miRNA expression data

source_name: AD Serum 16


title: ChIP-seq_H3K27me3_Second_16h_R2

value: dTAG treatment


title: Serum_AD_14

description: miRNA expression data

source_name: AD Serum 14


title: K107038

description: normal breast tissue core


title: K107040

description: normal breast tissue core


title: ChIP-seq_H3K27me3_Second_16h_R1


title: Serum_AD_12

description: miRNA expression data

source_name: AD Serum 12


title: Serum_AD_17

description: miRNA expression data

source_name: AD Serum 17


title: AAS_27_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_27 sequenced on lane L007
AAS_27_C80BLANXX_ATGTCA_L007
Barcode: ATGTCA

source_name: AAS_27_Atopic asthmatic_acute_visit

tag: subjectid

tag: visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: Serum_AD_13

description: miRNA expression data

source_name: AD Serum 13


title: ChIP-seq_H3K27me3_Second_WT_R2

source_name: iMEF

tag: antibody

tag: agent

value: No dTAG treatment


title: AAS_26_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_26 sequenced on lane L007
AAS_26_C80BLANXX_AGTTCC_L007
Barcode: AGTTCC

tag: age at visit (years)

tag: hdm-specific ige

value: PBMC


title: AAS_27_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_27 sequenced on lane L006
AAS_27_C80BLANXX_ATGTCA_L006
Barcode: ATGTCA

tag: total ige

tag: cat-specific ige


title: Serum_AD_11

description: miRNA expression data

source_name: AD Serum 11


title: Serum_AD_10

description: miRNA expression data

source_name: AD Serum 10


title: K107027

description: normal breast tissue core

source_name: normal breast tissue core

value: normal breast tissue core

tag: gender


title: ChIP-seq_H3K27me3_Second_WT_R1


title: Serum_AD_9

description: miRNA expression data

source_name: AD Serum 9


title: K107468

description: normal breast tissue core

value: female


title: K107004

description: normal breast tissue core


title: K107462

description: normal breast tissue core


title: Serum_AD_8

description: miRNA expression data

source_name: AD Serum 8


title: ChIP-seq_H3K27me3_Second_Input_dTAG_R2

tag: time point


title: ChIP-seq_H3K27me3_Second_Input_dTAG_R1

tag: tissue


title: ChIP-seq_H3K27me3_Second_Input_WT_R2


title: AAS_24_Atopic asthmatic_convalescent_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_24 sequenced on lane L007
AAS_24_C80BLANXX_CTTGTA_L007
Barcode: CTTGTA

value: CV

value: Female

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: AAS_26_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_26 sequenced on lane L006
AAS_26_C80BLANXX_AGTTCC_L006
Barcode: AGTTCC

value: Male


title: K107472

description: normal breast tissue core

tag: age

tag: bmi

value: AFRNAMER


title: AAS_24_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_24 sequenced on lane L006
AAS_24_C80BLANXX_CTTGTA_L006
Barcode: CTTGTA


title: AAS_23_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_23 sequenced on lane L007
AAS_23_C80BLANXX_GGCTAC_L007
Barcode: GGCTAC

source_name: AAS_23_Atopic asthmatic_acute_visit

value: AV


title: Serum_AD_7

description: miRNA expression data

source_name: AD Serum 7

tag: disease state


title: ChIP-seq_H3K27me3_First_16h_dTAG_R2

treatment_protocol: iMEF cells were treated with dTAG  for 30min, 2h, 4h, 8h or 16h


title: ChIP-seq_H3K27me3_First_8h_dTAG_R2


title: ChIP-seq_H3K27me3_Second_Input_WT_R1


title: AAS_25_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_25 sequenced on lane L006
AAS_25_C80BLANXX_AGTCAA_L006
Barcode: AGTCAA

source_name: AAS_25_Atopic asthmatic_acute_visit

tag: subjectid


title: AAS_23_Atopic asthmatic_acute_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_23 sequenced on lane L006
AAS_23_C80BLANXX_GGCTAC_L006
Barcode: GGCTAC

tag: visit


title: ChIP-seq_H3K27me3_First_16h_dTAG_R1


title: AAS_25_Atopic asthmatic_acute_visit_L007

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_25 sequenced on lane L007
AAS_25_C80BLANXX_AGTCAA_L007
Barcode: AGTCAA

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: K107463

description: normal breast tissue core

tag: racial background

value: WHITE

tag: tyrer-cuzick lifetime_risk_score


title: AAS_22_Atopic asthmatic_convalescent_visit_L006

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_22 sequenced on lane L006
AAS_22_C80BLANXX_TAGCTT_L006
Barcode: TAGCTT

tag: age at visit (years)


title: K107444

description: normal breast tissue core


title: ChIP-seq_H3K27me3_First_4h_dTAG_R2

tag: agent

tag: antibody


title: ChIP-seq_H3K27me3_First_8h_dTAG_R1


title: AAS_21_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_21 sequenced on lane L005
AAS_21_C80BLANXX_GATCAG_L005
Barcode: GATCAG

source_name: AAS_21_Atopic asthmatic_acute_visit

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige


title: Serum_Control_11

description: miRNA expression data

source_name: Control Serum 11

tag: tissue

value: Control


title: Serum_Control_10

description: miRNA expression data

source_name: Control Serum 10


title: Serum_Control_12

description: miRNA expression data

source_name: Control Serum 12


title: ChIP-seq_H3K27me3_First_4h_dTAG_R1

tag: time point


title: K107451

description: normal breast tissue core

tag: gender


title: AAS_22_Atopic asthmatic_convalescent_visit

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_22 sequenced on lane L007
AAS_22_C80BLANXX_TAGCTT_L007
Barcode: TAGCTT

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: Serum_Control_9

description: miRNA expression data

source_name: Control Serum 9

tag: disease state


title: Serum_AD_6

description: miRNA expression data

source_name: AD Serum 6


title: K107436

description: normal breast tissue core

tag: age

tag: bmi


title: Serum_Control_6

description: miRNA expression data

source_name: Control Serum 6


title: ChIP-seq_H3K27me3_First_2h_dTAG_R2


title: K107414

description: normal breast tissue core


title: K107423

description: normal breast tissue core

value: ASIAN,~~OTHASIAN


title: Serum_Control_4

description: miRNA expression data

source_name: Control Serum 4


title: Serum_Control_7

description: miRNA expression data

source_name: Control Serum 7


title: K107403

description: normal breast tissue core

value: ASIAN


title: AAS_20_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_20 sequenced on lane L005
AAS_20_C80BLANXX_ACTTGA_L005
Barcode: ACTTGA

tag: subjectid

tag: visit


title: AAS_21_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_21 sequenced on lane L004
AAS_21_C80BLANXX_GATCAG_L004
Barcode: GATCAG

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: AAS_20_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_20 sequenced on lane L004
AAS_20_C80BLANXX_ACTTGA_L004
Barcode: ACTTGA

tag: age at visit (years)


title: Serum_Control_5

description: miRNA expression data

source_name: Control Serum 5


title: ChIP-seq_H3K27me3_First_2h_dTAG_R1

source_name: iMEF

tag: agent


title: K107380

description: normal breast tissue core

source_name: normal breast tissue core

tag: racial background

tag: tyrer-cuzick lifetime_risk_score


title: Serum_Control_8

description: miRNA expression data

source_name: Control Serum 8


title: K107422

description: normal breast tissue core

value: WHITE,~~OTHRACE


title: Serum_Control_2

description: miRNA expression data

source_name: Control Serum 2


title: K107420

description: normal breast tissue core


title: ChIP-seq_H3K27me3_First_30min_dTAG_R2

tag: antibody


title: AAS_19_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_19 sequenced on lane L005
AAS_19_C80BLANXX_CAGATC_L005
Barcode: CAGATC

source_name: AAS_19_Atopic asthmatic_acute_visit

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige


title: K107330

description: normal breast tissue core

tag: tissue

tag: gender


title: Serum_Control_3

description: miRNA expression data

source_name: Control Serum 3


title: K107377

description: normal breast tissue core


title: AAS_18_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_18 sequenced on lane L005
AAS_18_C80BLANXX_GCCAAT_L005
Barcode: GCCAAT

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: ChIP-seq_H3K27me3_First_WT_R2


title: K107344

description: normal breast tissue core

tag: age


title: AAS_18_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_18 sequenced on lane L004
AAS_18_C80BLANXX_GCCAAT_L004
Barcode: GCCAAT


title: ChIP-seq_H3K27me3_First_WT_R1


title: ChIP-seq_H3K27me3_First_Input_dTAG

tag: time point


title: ChIP-seq_H3K27me3_First_Input_WT


title: ChIP-seq_H3K27me3_First_30min_dTAG_R1


title: Serum_AD_4

description: miRNA expression data

source_name: AD Serum 4

tag: disease state

value: Alzheimer Disease


title: K107342

description: normal breast tissue core

tag: bmi


title: K107314

description: normal breast tissue core

value: not available


title: ChIP-seq_H3K4me3_16h_dTAG_R2

value: iMEF

value: dTAG treatment


title: AAS_17_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_17 sequenced on lane L004
AAS_17_C80BLANXX_ACAGTG_L004
Barcode: ACAGTG

source_name: AAS_17_Atopic asthmatic_acute_visit

tag: subjectid

tag: visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

value: PBMC


title: K107302

description: normal breast tissue core

value: normal breast tissue core

tag: racial background

value: ~~OTHRACE


title: AAS_16_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_16 sequenced on lane L005
AAS_16_C80BLANXX_TGACCA_L005
Barcode: TGACCA

value: CV

tag: age at visit (years)


title: ChIP-seq_H3K4me3_16h_dTAG_R1

tag: agent

tag: antibody


title: AAS_19_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_19 sequenced on lane L004
AAS_19_C80BLANXX_CAGATC_L004
Barcode: CAGATC

tag: hdm-specific ige

tag: total ige


title: ChIP-seq_H3K4me3_8h_dTAG_R2

tag: tissue


title: K107311

description: normal breast tissue core

tag: gender

value: female

value: NATHAWPI

tag: tyrer-cuzick lifetime_risk_score


title: K107309

description: normal breast tissue core


title: ChIP-seq_H3K4me3_8h_dTAG_R1


title: AAS_16_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_16 sequenced on lane L004
AAS_16_C80BLANXX_TGACCA_L004
Barcode: TGACCA

value: Male

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: AAS_15_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_15 sequenced on lane L005
AAS_15_C80BLANXX_TTAGGC_L005
Barcode: TTAGGC

source_name: AAS_15_Atopic asthmatic_acute_visit

value: AV


title: K107305

description: normal breast tissue core

tag: age

value: WHITE


title: Serum_Control_1

description: miRNA expression data

source_name: Control Serum 1

tag: disease state

value: Control


title: ChIP-seq_H3K4me3_4h_dTAG_R2

tag: time point


title: AAS_15_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_15 sequenced on lane L004
AAS_15_C80BLANXX_TTAGGC_L004
Barcode: TTAGGC

tag: subjectid

tag: visit


title: CSF_AD_14

description: miRNA expression data

source_name: AD CSF 14


title: AAS_17_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_17 sequenced on lane L005
AAS_17_C80BLANXX_ACAGTG_L005
Barcode: ACAGTG

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: Serum_AD_5

description: miRNA expression data

source_name: AD Serum 5


title: ChIP-seq_H3K4me3_4h_dTAG_R1


title: K106948

description: normal breast tissue core

tag: bmi

tag: racial background


title: CSF_AD_12

description: miRNA expression data

source_name: AD CSF 12


title: Serum_AD_3

description: miRNA expression data

source_name: AD Serum 3


title: Serum_AD_1

description: miRNA expression data

source_name: AD Serum 1


title: Serum_AD_2

description: miRNA expression data

source_name: AD Serum 2


title: AAS_14_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_14 sequenced on lane L005
AAS_14_C80BLANXX_CGATGT_L005
Barcode: CGATGT

tag: age at visit (years)

value: Female


title: CSF_AD_11

description: miRNA expression data

source_name: AD CSF 11


title: K106931

description: normal breast tissue core


title: ChIP-seq_H3K4me3_2h_dTAG_R1

source_name: iMEF

tag: agent

tag: antibody


title: ChIP-seq_H3K4me3_2h_dTAG_R2

tag: tissue


title: K106922

description: normal breast tissue core

source_name: normal breast tissue core

tag: gender


title: K106923

description: normal breast tissue core

tag: tyrer-cuzick lifetime_risk_score


title: CSF_AD_10

description: miRNA expression data

source_name: AD CSF 10


title: ChIP-seq_H3K4me3_30min_dTAG_R2


title: AAS_13_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_13 sequenced on lane L004
AAS_13_C80BLANXX_ATCACG_L004
Barcode: ATCACG

source_name: AAS_13_Atopic asthmatic_acute_visit

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige


title: K106929

description: normal breast tissue core

tag: age


title: CSF_AD_8

description: miRNA expression data

source_name: AD CSF 8

tag: disease state


title: CSF_AD_9

description: miRNA expression data

source_name: AD CSF 9


title: CSF_AD_13

description: miRNA expression data

source_name: AD CSF 13


title: AAS_12_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_12 sequenced on lane L005
AAS_12_C80BLANXX_ATTCCT_L005
Barcode: ATTCCT

tag: pbmc processing day (1=sameday, 2=overnight)

tag: cell type


title: K106924

description: normal breast tissue core


title: AAS_12_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_12 sequenced on lane L004
AAS_12_C80BLANXX_ATTCCT_L004
Barcode: ATTCCT

tag: subjectid

tag: visit


title: CSF_AD_7

description: miRNA expression data

source_name: AD CSF 7


title: ChIP-seq_H3K4me3_WT_R2

value: No dTAG treatment


title: ChIP-seq_H3K4me3_WT_R1


title: AAS_11_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_11 sequenced on lane L005
AAS_11_C80BLANXX_ACTGAT_L005
Barcode: ACTGAT

source_name: AAS_11_Atopic asthmatic_acute_visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: AAS_11_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_11 sequenced on lane L004
AAS_11_C80BLANXX_ACTGAT_L004
Barcode: ACTGAT


title: AAS_14_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_14 sequenced on lane L004
AAS_14_C80BLANXX_CGATGT_L004
Barcode: CGATGT


title: ChIP-seq_H3K4me3_Input_dTAG

tag: time point


title: ChIP-seq_H3K4me3_Input_WT.fastq.gz


title: CSF_AD_6

description: miRNA expression data

source_name: AD CSF 6


title: AAS_13_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_13 sequenced on lane L005
AAS_13_C80BLANXX_ATCACG_L005
Barcode: ATCACG

tag: age at visit (years)


title: AAS_10_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_10 sequenced on lane L005
AAS_10_C80BLANXX_GAGTGG_L005
Barcode: GAGTGG


title: K106878

description: normal breast tissue core

tag: bmi

tag: racial background

value: ASIAN


title: ChIP-seq_H3K4me1_16h_dTAG_R2

tag: tissue

tag: agent

tag: antibody


title: K106879

description: normal breast tissue core

tag: gender

value: ASIAN,JAPANESE

tag: tyrer-cuzick lifetime_risk_score


title: ChIP-seq_H3K4me3_30min_dTAG_R1


title: CSF_Control_10

description: miRNA expression data

source_name: Control CSF 10


title: CSF_AD_4

description: miRNA expression data

source_name: AD CSF 4

value: Alzheimer Disease


title: AAS_10_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_10 sequenced on lane L004
AAS_10_C80BLANXX_GAGTGG_L004
Barcode: GAGTGG

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige


title: AAS_09_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_09 sequenced on lane L005
AAS_09_C80BLANXX_CGTACG_L005
Barcode: CGTACG

source_name: AAS_09_Atopic asthmatic_acute_visit

tag: pbmc processing day (1=sameday, 2=overnight)


title: ChIP-seq_H3K4me1_16h_dTAG_R1

value: iMEF


title: K106913

description: normal breast tissue core

tag: age

value: not available


title: CSF_Control_8

description: miRNA expression data

source_name: Control CSF 8

tag: disease state


title: K106892

description: normal breast tissue core


title: K106877

description: normal breast tissue core


title: ChIP-seq_H3K4me1_8h_dTAG_R2

value: dTAG treatment


title: AAS_09_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_09 sequenced on lane L004
AAS_09_C80BLANXX_CGTACG_L004
Barcode: CGTACG

tag: subjectid

tag: visit

tag: cell type

value: PBMC


title: CSF_Control_7

description: miRNA expression data

source_name: Control CSF 7


title: ChIP-seq_H3K4me1_8h_dTAG_R1

tag: time point


title: CSF_Control_6

description: miRNA expression data

source_name: Control CSF 6


title: AAS_06_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_06 sequenced on lane L005
AAS_06_C80BLANXX_GTGAAA_L005
Barcode: GTGAAA

tag: age at visit (years)


title: K106910

description: normal breast tissue core

value: normal breast tissue core

tag: bmi

tag: racial background


title: ChIP-seq_H3K4me1_4h_dTAG_R2

tag: tissue

tag: agent


title: K107127

description: normal breast tissue core

tag: gender


title: CSF_AD_5

description: miRNA expression data

source_name: AD CSF 5


title: K106856

description: normal breast tissue core

tag: tyrer-cuzick lifetime_risk_score


title: AAS_05_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_05 sequenced on lane L005
AAS_05_C80BLANXX_GTCCGC_L005
Barcode: GTCCGC

source_name: AAS_05_Atopic asthmatic_acute_visit

tag: hdm-specific ige

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)


title: ChIP-seq_H3K4me1_4h_dTAG_R1

source_name: iMEF

tag: antibody


title: AAS_06_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_06 sequenced on lane L004
AAS_06_C80BLANXX_GTGAAA_L004
Barcode: GTGAAA

value: CV

tag: total ige

tag: cat-specific ige

tag: pbmc processing day (1=sameday, 2=overnight)


title: K106887

description: normal breast tissue core

source_name: normal breast tissue core

value: female

tag: age


title: K106835

description: normal breast tissue core


title: CSF_Control_5

description: miRNA expression data

source_name: Control CSF 5

tag: disease state


title: CSF_Control_9

description: miRNA expression data

source_name: Control CSF 9


title: K106848

description: normal breast tissue core


title: AAS_05_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_05 sequenced on lane L004
AAS_05_C80BLANXX_GTCCGC_L004
Barcode: GTCCGC

tag: subjectid

tag: visit

tag: cell type


title: ChIP-seq_H3K4me1_2h_dTAG_R1

tag: time point


title: ChIP-seq_H3K4me1_30min_dTAG_R2


title: ChIP-seq_H3K4me1_2h_dTAG_R2


title: AAS_04_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_04 sequenced on lane L005
AAS_04_C80BLANXX_CCGTCC_L005
Barcode: CCGTCC

tag: age at visit (years)


title: K106996

description: normal breast tissue core

tag: tissue

tag: bmi

tag: racial background


title: CSF_Control_2

description: miRNA expression data

source_name: Control CSF 2


title: CSF_Control_4

description: miRNA expression data

source_name: Control CSF 4


title: ChIP-seq_H3K4me1_30min_dTAG_R1

tag: agent


title: AAS_04_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_04 sequenced on lane L004
AAS_04_C80BLANXX_CCGTCC_L004
Barcode: CCGTCC

tag: gender

tag: hdm-specific ige


title: K106971

description: normal breast tissue core

tag: tyrer-cuzick lifetime_risk_score


title: CSF_AD_2

description: miRNA expression data

source_name: AD CSF 2


title: CSF_Control_3

description: miRNA expression data

source_name: Control CSF 3


title: K108034

description: normal breast tissue core


title: ChIP-seq_H3K4me1_WT_R2

tag: antibody


title: AAS_02_Atopic asthmatic_convalescent_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_02 sequenced on lane L005
AAS_02_C80BLANXX_AGTTCC_L005
Barcode: AGTTCC

tag: total ige

tag: cat-specific ige


title: AAS_03_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_03 sequenced on lane L005
AAS_03_C80BLANXX_ATGTCA_L005
Barcode: ATGTCA

source_name: AAS_03_Atopic asthmatic_acute_visit

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

tag: pbmc processing day (1=sameday, 2=overnight)


title: Induced endometrial stromall cells, Day4

city: Beijing

first: Min

last: Yang

state: Beijing

address: No. 5, yiheyuan road, haidian district,

country: China

institute: Peking University

data_processing:
For PolyA(+) RNA-seq, Trimmomatic software was used to trim the adapters. Hisat2 software was used for the alignment to the hg38 reference genome with default parameters.
The expression count matrix was obtained by FeatureCounts.
Data were normalized by total mapped reads of each library (CPM: count per million).
Assembly: mm10
Supplementary files format and content: counts

source_name: Induced endometrial stromall cells

extract_protocol:
DNA and RNA extracted according to the manufacturer’s instructions.
RNA-seq libraries preparation using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: Induced endometrial stromall cells

tag: treatment

value: 1 μM P4 and 0.5 μM cAMP

tag: time

value: 4 Day


title: AAS_03_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_03 sequenced on lane L004
AAS_03_C80BLANXX_ATGTCA_L004
Barcode: ATGTCA

tag: subjectid

tag: visit

value: AV

value: Male

tag: cell type


title: ChIP-seq_H3K4me1_WT_R1

tag: tissue


title: CSF_Control_1

description: miRNA expression data

source_name: Control CSF 1

tag: disease state

value: Control


title: Induced endometrial stromall cells, Day5

value: 5 Day


title: K106991

description: normal breast tissue core

tag: age

tag: bmi

tag: racial background

value: WHITE


title: ChIP-seq_H3K27ac_16h_dTAG_R2

tag: agent

tag: time point


title: Induced endometrial stromall cells, Day2

value: 2 Day


title: Induced endometrial stromall cells, Day3

value: 3 Day


title: K106847

description: normal breast tissue core

tag: gender

value: WHITE,AFRNAMER

tag: tyrer-cuzick lifetime_risk_score


title: ChIP-seq_H3K4me1_Input_WT.fastq.gz

value: iMEF

value: No dTAG treatment

tag: antibody


title: AAS_01_Atopic asthmatic_acute_visit_L005

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_01 sequenced on lane L005
AAS_01_C80BLANXX_AGTCAA_L005
Barcode: AGTCAA

source_name: AAS_01_Atopic asthmatic_acute_visit

tag: age at visit (years)

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

value: PBMC


title: K106969

description: normal breast tissue core

value: normal breast tissue core

value: not available


title: K106967

description: normal breast tissue core

value: female


title: ChIP-seq_H3K4me1_Input_dTAG

value: dTAG treatment


title: AAS_02_Atopic asthmatic_convalescent_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_02 sequenced on lane L004
AAS_02_C80BLANXX_AGTTCC_L004
Barcode: AGTTCC

tag: subjectid

tag: visit

value: CV

tag: pbmc processing day (1=sameday, 2=overnight)


title: K108750

description: normal breast tissue core

tag: tissue


title: ChIP-seq_H3K27ac_16h_dTAG_R1


title: Induced endometrial stromall cells, Day1

tag: cell type

value: Induced endometrial stromall cells

tag: treatment

value: 1 μM P4 and 0.5 μM cAMP

tag: time

value: 1 Day


title: K108867

description: normal breast tissue core

tag: age

tag: bmi

tag: racial background


title: Primary endometrial stromall cells, Control

source_name: Primary endometrial stromall cells

value: Primary endometrial stromall cells

value: No treatment

value: 0 Day


title: CSF_AD_3

description: miRNA expression data

source_name: AD CSF 3

tag: disease state

value: Alzheimer Disease


title: CSF_AD_1

description: miRNA expression data

source_name: AD CSF 1


title: Uterus, CBA

description:
10x Genomics
CBA_seurat.RData

library_source: transcriptomic single cell

data_processing:
For single-cell RNA seq, cellranger was used for the pre-processing and Seurat was used for the downstream analysis.
Assembly: mm10
Supplementary files format and content: RData

source_name: Uterus (CBA/J disease model)

extract_protocol:
The dissections were executed on ice in cold PBS supplemented with 10% (v/v) fetal bovine serum (FBS; Gemini) using fine-pointed forceps. For each gestational time point, except for E5.5, the uterus wall surrounding the implantation sites was removed. Subsequently, the E6.5 and E7.5 embryos were dissected out of the decidua and digested using 1 mg/ml collagenase type I (Worthington Biochemical) containing 20% (v/v) FBS at 37°C for 5-10 min. The embryos at E8.5, E9.5 and E10.5 were removed and excluded from the study.   Yolk sacs of the embryos at E8.5, E9.5 and E10.5, and the E10.5 placentas were washed in PBS and minced into small pieces of approximately 1-2 mm3 using scissors. The cells were then dissociated at 37°C for 20-30 min using 1 mg/ml collagenase type I (Worthington Biochemical) supplemented with 20% (v/v) FBS.  The decidua of E5.5, E6.5, E7.5, E8.5 and E9.5 embryos were washed in PBS and minced into small pieces of approximately 1-2 mm3 using scissors. The tissues were then repeatedly digested using 0.5% (w/v) collagenase type I (Worthington Biochemical) dissolved in PBS with 5 mM glucose and 20 µl/ml deoxyribonuclease I (Promega) for 10 min and 0.25% trypsin (Gibco) for 5 min at 37°C on a rotator. Trypsin was deactivated using PBS containing 10% (v/v) FBS.  The dissociated cells were filtered through a 40 µm cell strainer (Corning Falcon™, Cat# 352340) and centrifuged at 230 g for 5 min at 4°C. Subsequently, the dissociated cells were washed two times in ice-cold PBS supplemented with 10% (v/v) FBS and resuspended in PBS supplemented with 2% (v/v) FBS.
To generate Gel Bead-InEMulsions (GEMs), 12,000 living cells, Chromium Single Cell 3’ GEM Kit v3 and Chromium Single Cell 3’ Gel Bead Kit v3 were used and loaded on a Chromium Single Cell Controller (10x Genomics). Recovered cDNA was used to construct library using the Single Cell 3’ Library kit (10x Genomics), according to the manufacturer’s protocol. The libraries were subjected to Illumina HiSeq X Ten and Nova-seq 6000 sequencing system.

value: Uterus (CBA/J disease model)

value: embryonic 8.5/9.5 day tissue


title: SGC7901-R Cells, siLinc00942#2, Rep2

city: Hangzhou

first: Liyuan

last: Zhu

state: Zhejiang

address: NO.3, East Qingchun Road, Shangcheng Distinct

department: Sir Run Run Shaw Hospital, School of Medicine

institute: Zhejiang University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8)
Adaptor removal using cutadapt and Quality Control using FastQC
Trimmed sequence reads were mapped to GRCh37 using Hisat2 and annotation was operated using StringTie.
Read count extraction, RPKM calculation, differential analysis and normalization were performed using Ballgown
The mRNA reads were aligned to reference genome using STAR(2.5.2b). Custom program python/R/shell was used to cluster analysis
Assembly: GRCh37 hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

growth_protocol: Human gastric cancer cell line (Multidrug-resistant) SGC7901-R was induced from SGC7901. Cells were all cultured in RPMI-1640 or DMEM medium (Invitrogen) medium supplemented with 10% FBS and 100 U/mL Penicillin-Streptomycin at 37°C in a 5% CO2 atmosphere. This cell line was handled with Plasmocin® treatment and Plasmocin® prophylactic (InvivoGen, ant-mpt & ant-mpp) to eliminate or prevent Mycoplasma contamination.

extract_protocol:
Total RNA was extracted using TrizoL-chloroform, then oligo dT enrichment and rRNA removal both were performed. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-seq Library Prep Kit (Illumina) following manufacturer's protocols. Briefly, RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.
RNA-seq after Quality Control using Agilent 2100 Bioanalyzer

treatment_protocol: siNC, siLinc00942#1 and siLinc00942#2 were transfected to SGC7901-R using Lipo RNAiMAX (Invitrogen) for 48h, respectively.

tag: cell line

value: Gastric cancer cells (Multidrug resistant)

tag: genotype

value: Linc00942 knockdown

value: siLinc00942#2 transfection


title: K108838

description: normal breast tissue core

value: normal breast tissue core

tag: gender

value: WHITE

tag: tyrer-cuzick lifetime_risk_score


title: ChIP-seq_H3K27ac_8h_dTAG_R1

value: iMEF

tag: agent

tag: time point

tag: antibody


title: SGC7901-R Cells, siLinc00942#2, Rep3


title: SGC7901-R Cells, siLinc00942#1, Rep3

value: siLinc00942#1 transfection


title: AAS_01_Atopic asthmatic_acute_visit_L004

description:
There are 38 samples; each sample was sequenced across two lanes.
AAS_01 sequenced on lane L004
AAS_01_C80BLANXX_AGTCAA_L004
Barcode: AGTCAA

tag: subjectid

tag: visit

value: AV

tag: age at visit (years)

value: Male

tag: hdm-specific ige

tag: total ige

tag: cat-specific ige

tag: rhinovirus positive at av (1=yes, 0=no, 9=not measured)

value: PBMC


title: SGC7901-R Cells, siLinc00942#2, Rep1

tag: cell type

tag: treatment


title: K108892

description: normal breast tissue core

tag: tissue

value: female

tag: age

tag: bmi

tag: racial background


title: Uterus, E105_tdTomato_neg

description:
10x Genomics
UE_all.RData
UE_DSC.RData
UE_EC.RData
UE_immune.RData
UE_trophoblast.RData
iDSC.RData

source_name: Uterus

value: Uterus

value: embryonic 10.5 day tissue


title: ChIP-seq_H3K27ac_4h_dTAG_R1

source_name: iMEF

value: dTAG treatment


title: Yolk sac , Placenta, E105_tdTomato_pos

source_name: Yolk sac and Placenta

value: Yolk sac and Placenta


title: ChIP-seq_H3K27ac_4h_dTAG_R2


title: SGC7901-R Cells, siLinc00942#1, Rep1

tag: cell line

tag: genotype


title: SGC7901-R Cells, siLinc00942#1, Rep2


title: ChIP-seq_H3K27ac_2h_dTAG_R2

tag: agent

tag: time point


title: Yolk sac , Placenta, E95_tdTomato_pos

value: embryonic 9.5 day tissue


title: ChIP-seq_H3K27ac_8h_dTAG_R2

tag: antibody


title: Uterus, E95_tdTomato_neg


title: K108898

description: normal breast tissue core

source_name: normal breast tissue core

tag: gender

tag: tyrer-cuzick lifetime_risk_score


title: K108890

description: normal breast tissue core


title: Yolk sac , Placenta, E85_tdTomato_pos

value: embryonic 8.5 day tissue


title: ChIP-seq_H3K27ac_2h_dTAG_R1


title: ChIP-seq_H3K27ac_30min_dTAG_R2


title: K108836

description: normal breast tissue core


title: SGC7901-R Cells, siNC, Rep3

value: Gastric cancer cells (Multidrug resistant)

value: Mock

value: siNC transfection


title: K108913

description: normal breast tissue core

value: normal breast tissue core


title: Uterus, E85_tdTomato_neg_2


title: ChIP-seq_H3K27ac_WT_R2

value: No dTAG treatment


title: Uterus, E85_tdTomato_neg_1


title: SGC7901-R Cells, siNC, Rep1


title: K108894

description: normal breast tissue core

value: WHITE


title: K108703

description: normal breast tissue core


title: SGC7901-R Cells, siNC, Rep2


title: ChIP-seq_H3K27ac_30min_dTAG_R1

value: iMEF


title: Uterus, Yolk sac , Placenta, E75_tdTomato_pos_neg

source_name: Uterus, Yolk sac and Placenta

value: Uterus, Yolk sac and Placenta

value: embryonic 7.5 day tissue


title: ChIP-seq_H3K27ac_WT_R1


title: K108809

description: normal breast tissue core

value: WHITE,ASIAN,~~OTHASIAN


title: Uterus, E65_tdTomato_neg

value: embryonic 6.5 day tissue


title: ND7/23, 100 μM menthol+100 ng/ml Wnt3a, 6h, rep2

city: Shanghai

first: Zehua

last: Zhang

state: --- Select One ---

address: No. 150 Jimo Road

institute: Tongji University School of Medicine

data_processing:
Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
The radar map of top 30 genes was drawn to show the expression of up-regulated or down-regulated DEGs using R packet grader. Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples.
Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: mRatBN7.2
Supplementary files format and content: Excel format
Supplementary files format and content: Expression data for all samples exists at gene_sample_FPKM_with_symbol.

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: 100 microM menthol and 100 ng/ml Wnt3a


title: ND7/23, 100 μM menthol+100 ng/ml Wnt3a, 6h, rep3


title: ChIP-seq_H3K27ac_Input_dTAG


title: ND7/23, 100 μM menthol+100 ng/ml Wnt3a, 6h, rep1


title: K108912

description: normal breast tissue core

value: female

value: AFRNAMER


title: K108704

description: normal breast tissue core


title: ChIP-seq_H3K27ac_Input_WT.fastq.gz


title: Uterus, Yolk sac , Placenta, E55_tdTomato_neg_E65_tdTomato_pos

value: embryonic 5.5 day tissue


title: ND7/23, 100 ng/ml Wnt3a, 6h, rep3

value: 100 ng/ml Wnt3a


title: K107764

description: normal breast tissue core

value: ASIAN,~~OTHASIAN


title: K107714

description: normal breast tissue core


title: RNA-seq_24h_dTAG_R3

molecule: polyA RNA

extract_protocol:
Total RNA was isolated with the High Pure RNA Isolation Kit (Roche, 11828665001) and cDNA synthesized with the QuantiTect Reverse Transcription Kit (Qiagen, 205314).]
The cell number was used to adjust the amount of ERCC RNA Spike-In Mix (ThermoFisher Scientific, 4456740). Generation of RNA-seq libraries (TruSeq Stranded Total RNA Sample Library Prep, Illumina, 20020596) and next-generation sequencing (NextSeq 500/550 High Output Kit v2.5, 150 cycles, Illumina, 20024907) were performed.

value: dTAG treatment


title: K107800

description: normal breast tissue core


title: RNA-seq_24h_dTAG_R2


title: ND7/23, 100 ng/ml Wnt3a, 6h, rep1


title: RNA-seq_24h_dTAG_R1


title: ND7/23, 100 μM menthol, 6h, rep3

value: 100 microM menthol


title: ND7/23, 100 ng/ml Wnt3a, 6h, rep2


title: T-LCDM-P9-1

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
Library strategy: Exome-seq
Variant calling was performed as previously described (Bhutani et al., 2016; Gore et al., 2011). Briefly, paired-end clean reads in FastQ format generated by the Illumina pipeline were aligned to the mouse reference genome mm10 by Burrows-Wheeler Aligner (BWA) to obtain the original mapping results stored in BAM format.
SAMtools (http://broadinstitute.github.io/picard/) were used to sort BAM files and generate final BAM files for computation of the sequence coverage and depth.
BCF tools were used to call var- iants, and variants annotation and variant positions were obtained using Variant Annotation software.
RefSeq was applied for annotation to determine amino acid alternations.
Variants obtained from previous steps were compared against SNPs present in the dbSNP database to discard background SNPs
Genome_build: mm10
Supplementary_files_format_and_content: text file for Single nucleotides variations of each sample (mESCs compared with MEF; tumors compared with WT blood cells)

extract_protocol:
Genome DNA was prepared using DNeasy Blood & Tissue Kit (QIAGEN, Valencia, CA)
For population cells, paired-end DNA library were prepared according to manufacturer’s instructions (Agilent). Genomic DNAs (gDNA) from cell samples were sheared into 180$280 bp fragments by Covaris S220 sonicator. Ends of gDNA fragments were re- paired and 30 ends were adenylated. Both ends of gDNA fragments were ligated at the 30 ends with paired-end adaptors (Illumina) with a single ‘T’ base overhang and purified using AMPure SPRI beads from Agencourt. The adaptor-modified gDNA fragments were enriched by six cycles of PCR using SureSelect Primer and SureSelect ILM Indexing PreCapture PCR Reverse Primer. The concen- tration and size distribution of the libraries were determined on an Agilent Bioanalyzer DNA 1000 chip.

treatment_protocol: SL: KO-DMEM medium+15%FBS+1000 IU mLIF, with Feeder; 2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, with feeder; a2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1.5 μM CGP77675, with feeder; LCDM: N2B27 medium+1000 IU mLIF+3 μM Chir99021+2 μM Dim+ 2 μM Mih, with feeder; 2iL-F: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, without feeder. Blood cells and turmors isolated from mice.

tag: strain

value: tumour


title: T-LCDM-P9-2


title: RNA-seq_WT_R3


title: T-A2iL-P9-3


title: ND7/23, 100 μM menthol, 6h, rep2


title: T-A2iL-P14-1


title: K107577

description: normal breast tissue core

value: normal breast tissue core


title: RNA-seq_WT_R2

value: No dTAG treatment


title: ND7/23, 100 μM menthol, 6h, rep1


title: K107234

description: normal breast tissue core


title: T-A2iL-P9-2


title: RNA-seq_WT_R1


title: T-A2iL-P9-1


title: K107206

description: normal breast tissue core

value: WHITE


title: ND7/23, CON, 6h, rep3

value: control


title: T-2iL-P9


title: T-2iL-F-P9


title: Click-it_8h_dTAG_R1

extract_protocol:
As described in this start Protocol: https://star-protocols.cell.com/protocols/961
The cell number was used to adjust the amount of ERCC RNA Spike-In Mix (ThermoFisher Scientific, 4456740). Generation of Click-it libraries (TruSeq Stranded Total RNA Sample Library Prep, Illumina, 20020596) and next-generation sequencing (NextSeq 500/550 High Output Kit v2.5, 150 cycles, Illumina, 20024907) were performed.

treatment_protocol: iMEF cells were treated with dTAG  for 4h or 8h

value: iMEF


title: WT-2

value: Blood cells


title: Click-it_4h_dTAG_R2


title: K107509

description: normal breast tissue core


title: K107286

description: normal breast tissue core


title: 2iL-F-5

value: Embryonic stem cell line


title: 4T

city: Wenzhou

first: Meng

last: Zhou

address: 270 Xueyuan Xi Road

institute: Wenzhou Medical University

data_processing:
Raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.
Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a to map reads to the reference genome GRCh38 (ensembl version 92 annotation).
UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCh38 (ensembl version 92 annotation)
Supplementary files format and content: tab-delimited text files include raw count values of each cell for each Sample

source_name: MVI absent Hepatocellular carcinoma

extract_protocol:
Inclusion criteria for patients comprised the absence of apparent metastases, a singular tumor of dimensions between 3 and 5 cm, and no prior therapeutic intervention. Ten independent surgical resected specimens were collected from five HCC patients. The collected samples were rapidly stored in sCelLiveTM Tissue Preservation Solution (Singleron) after isolation at low temperature, followed by washing with normal saline to remove blood and impurities. Following surgical excision, fresh tissues were stored in the sCelLiveTMTissue Preservation Solution (Singleron) on ice for 30 minutes. The specimens were thoroughly washed three times with Hank’s Balanced Salt Solution (HBSS), then minced into small pieces, and subjected to enzymatic digestion with 3 mL of sCelLiveTM Tissue Dissociation Solution (Singleron) using the Singleron PythoN™ Tissue Dissociation System (Singleron) at 37°C for 15 minutes. The resulting cell suspension was collected and filtered through a 40-micron sterile strainer and incubated with GEXSCOPE® red blood cell lysis buffer (RCLB, Singleron) for 5-8 minutes at room temperature with a Cell: RCLB ratio of 1:2 (volume ratio) to eliminate red blood cells. The mixture was then centrifuged at 300× g at 4 ℃ for 5 minutes and the supernatant was removed, leaving behind a gentle PBS suspension.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix®Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads. Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope(https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a to map reads to the reference genome GRCh38 (ensembl version 92 annotation. UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.

tag: disease state

value: Hepatocellular carcinoma


title: 3T

source_name: MVI present Hepatocellular carcinoma


title: WGBS in nrpe1 rep2

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
ChIP-seq data were aligned to the TAIR10 reference genome with Bowtie2 (v2.1.0) (Langmead and Salzberg, 2012) allowing only uniquely mapping reads with 0 mismatches. Duplicated reads were removed by Samtools. ChIP-seq peaks were called by MACS2 (v2.1.1) and annotated with ChIPseeker (Yu et al., 2015). Differential peaks were called by bdgdiff function in MACS2 (Zhang et al., 2008). ChIP-seq data metaplots were plotted by deeptools (v2.5.1) (Ramírez et al., 2016).
Previously published whole-genome bisulfite sequencing data for mutants and wild type were reanalyzed from previous paper (Stroud et al., 2012). Briefly, Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim adapters. BS-seq reads were aligned to TAIR10 reference genome by BSMAP (v2.90) and allowed 2 mismatches and 1 best hit (-v 2 -w 1) (Xi and Li, 2009). Reads with three or more consecutive CHH sites were considered as unconverted reads and filtered. DNA methylation levels were defined as #C/ (#C + #T). DMR overlapping analysis were conducted by mergePeaks (-d 100) of Homer (Heinz et al., 2010)
Assembly: TAIR10
Supplementary files format and content: bigwig: methylation or ChIP-seq intensity.
Supplementary files format and content: narrowPeak: peak file

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under 16h light: 8h dark condition (on soil), or under constant light (on plates).

extract_protocol:
All the material for ChIP used in this paper were from pooled 10-12 day old seedlings grown on Murashinge and Skoog agar plates (1/2X MS, 1.5% agar, pH5.7). 2-4g of seedling tissue was used for each sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer (50mM Hepes pH8, 1M sucrose, 5mM KCl, 5mM MgCl2, 0.6% triton X-100, 0.4 mM PMSF, 5 mM benzamidine hydrochloride, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)) containing 1% formaldehyde. The crosslinking reactions were stopped with 125 mM glycine by incubation at room temperature for 10 minutes. Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol (Villar and Kohler, 2018)). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with antibody. anti-NRPE1 (endogenous antibody, described in (Liu et al., 2018)), anti-H1 (AS11 1801 Agrisera), anti-H3K9me2 (abcam1220), anti-H3 (abcam1791), anti-FLAG (for both the SUVH1-3xFLAG and the DMS3-ZF ChIPs, we used Anti-FLAG M2 (Sigma, F1804)). 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers, for 5 minutes each at 4°C (buffer compositions are described in the published protocol (Villar and Kohler, 2018)) and eluted twice with 250 µl of elution buffer (1% SDS and 0.1 M NaHCO3) in a thermomixer at 65°C and 1000 rpm, 20 minutes for each elution. Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN, 0344NB-A01) following the manufacturer’s instructions, with 15 cycles of PCR. Libraries were sequences on a Novaseq 6000 using either single- or paired-end 50bp reads. Whole genome bisulfite sequencing libraries were generated as previously described (Harris et al., 2016), with minor modifications. The DNeasy Plant Mini Kit (Qiagen #69104) was used to isolate genomic DNA. 150 ug of genomic DNA was used as input, a Covais S2 instrument was used for shearing (2 minutes), the Epitect Kit (QIAgen #59104) was used for bisulfite conversion, and the Nugen Ultralow Methyl Kit was used for library preparation and paired-end libraries were sequences on a Novaseq 6000 instrument.

value: floral tissue

tag: ecotype

value: nrpe1 mutant


title: WGBS in nrpe1 rep1


title: Click-it_WT_R2


title: WGBS in h1 rep2

value: h1 mutant


title: 2iL-F-3


title: ND7/23, CON, 6h, rep2


title: WGBS in h1 rep1


title: Click-it_WT_R1


title: Click-it_8h_dTAG_R2


title: LCDM-5


title: 2T


title: LCDM-3


title: polyA RNA from wildtype mouse kidneys, replicate 4 [ZYY_003_WT_AD014]

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: polyA RNA extracted from  tissue

data_processing:
Sequencing reads were aligned to the mouse genome (version mm10) using hisat2 (Kim et al., 2015, doi: 10.1038/s41587-019-0201-4), and reads counted using quasR (Gaidatzis et al., 2015, doi: 10.1093/bioinformatics/btu781)
Assembly: mm10
Supplementary files format and content: tab separated values

source_name: Kidney tissue

growth_protocol: In this study, wild-type mice refers toR26StopFLMYC;Grhl2 flox/flox.Grhl2 knockout mice were described previously (doi: 10.1681/ASN.2017030353). Grhl2 knockout; Myc overexpression mice were generated by crossing HoxB7-Cre; Grhl2flox/+ with R26StopFLMYC; Grhl2flox/flox mice.

extract_protocol:
For RNA extraction, the entire right kidney was removed and kept in Qiazol until used, and then lysed using a tissue homogenizer. Total RNA extraction was performed using the RNeasy Mini Kit (74104, Qiagen).  For RNA purity, DNase digestion was performed using the RNase Free DNase Set (79254, Qiagen) according to the manufacturer’s instructions. RNA was eluted in 30 μl RNase-free H2O.
RNA-sequencing libraries were constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina)

treatment_protocol: There was no treatment of the mice in this experiment.

value: wildtype

value: Kidney tissue

tag: illumina adapter


title: WGBS in h1 nrpe1 CRKOn63

value: h1 nrpe1 mutant


title: 5NT

source_name: adjacent tissues


title: polyA RNA from wildtype mouse kidneys, replicate 5 [ZYY_003_WT_AD016]

description: polyA RNA extracted from  tissue


title: ND7/23, CON, 6h, rep1


title: WGBS in h1 nrpe1 CRKOn49


title: WT-1

tag: cell type


title: Click-it_4h_dTAG_R1

value: dTAG treatment


title: 5T


title: polyA RNA from wildtype mouse kidneys, replicate 3 [ZYY_003_WT_AD006]

description: polyA RNA extracted from  tissue


title: A2iL-5


title: 4NT


title: A2iL-3


title: polyA RNA from wildtype mouse kidneys, replicate 2 [ZYY_003_WT_AD004]

description: polyA RNA extracted from  tissue


title: 3NT


title: 2iL-5


title: WGBS in WT rep2

value: WT


title: polyA RNA from wildtype mouse kidneys, replicate 1 [ZYY_003_WT_AD002]

description: polyA RNA extracted from  tissue


title: 2NT


title: antiH3 ChIP in nrpe1 rep2

tag: chip antibody

value: anti-H3 (abcam1791)


title: 1T


title: 2iL-3


title: 1NT


title: SL-5


title: polyA RNA from Grhl2 knockout; Myc overexpression mouse kidneys, replicate 4 [ZYY_003_KO_AD019]

description: polyA RNA extracted from  tissue

value: Grhl2 knockout; Myc overexpression

tag: tissue


title: antiH1 ChIP in nrpe1 rep2

value: anti-H1 (AS11 1801 Agrisera)


title: SL-3


title: antiH3 ChIP in nrpe1 rep1


title: polyA RNA from Grhl2 knockout; Myc overexpression mouse kidneys, replicate 3 [ZYY_003_KO_AD018]

description: polyA RNA extracted from  tissue


title: MEF

description: MEF

source_name: MEF

value: Mouse fibroblasts


title: polyA RNA from Grhl2 knockout; Myc overexpression mouse kidneys, replicate 2 [ZYY_003_KO_AD012]

description: polyA RNA extracted from  tissue


title: antiH1 ChIP in nrpe1 rep1


title: polyA RNA from Grhl2 knockout; Myc overexpression mouse kidneys, replicate 1 [ZYY_003_KO_AD007]

description: polyA RNA extracted from  tissue


title: RNA-seq_2iL-F-5

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population).
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: All_TPM.csv. This file contains all samples TPM value of all genes

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: SL: KO-DMEM medium+15%FBS+1000 IU mLIF, with Feeder; 2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, with feeder; a2iL: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1.5 μM CGP77675, with feeder; LCDM: N2B27 medium+1000 IU mLIF+3 μM Chir99021+2 μM Dim+ 2 μM Mih, with feeder; 2iL-F: N2B27 medium+1000 IU mLIF+3 μM Chir99021+1 μM PD0325901, without feeder.


title: WGBS in WT rep1


title: antiH3 ChIP in h1 rep2


title: polyA RNA from Myc overexpression mouse kidneys, replicate 3 [ZYY_003_HET_AD015]

description: polyA RNA extracted from  tissue

value: Myc overexpression


title: MV4-11 sh-ANP32B-1

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description: MV4-11 sample with ANP32B knockdown

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA

value: ANP32B knockdown


title: MV4-11 NC-1

description: MV4-11 sample with no treatment


title: antiH3K9me2 ChIP in h1 rep2

value: anti-H3K9me2 (abcam1220)


title: polyA RNA from Myc overexpression mouse kidneys, replicate 2 [ZYY_003_HET_AD013]

description: polyA RNA extracted from  tissue


title: sh-ANP32B-2

description: Kasumi-1 sample with ANP32B knockdown


title: antiNRPE1 ChIP in h1 rep2

value: Anti-NRPE1 (Covance)


title: RNA-seq_2iL-F-3

value: Embryonic stem cell line


title: polyA RNA from Myc overexpression mouse kidneys, replicate 1 [ZYY_003_HET_AD005]

description: polyA RNA extracted from  tissue


title: MV4-11 NC-2

description: MV4-11 sample with no treatment


title: MV4-11 sh-ANP32B-2

description: MV4-11 sample with ANP32B knockdown


title: RNA-seq_LCDM-5


title: sh-ANP32B-1

description: Kasumi-1 sample with ANP32B knockdown


title: antiH3 ChIP in h1 rep1

value: floral tissue


title: Ventricular_Myocytes_9

city: New York

first: Akshay

last: Shekhar

state: NY

address: 564 1st Ave Apt 11S

department: Medicine - Cardiology

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.4
Calculating insert size and standard deviation performed using Picard v.1.126
Reads were mapped using the STAR aligner (v2.5.0c)
read counting performed using HT-seq v0.6.0
Normalization and Deferential expression analysis performed using DEseq2 v3.0
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Heart

extract_protocol: Cells were harvested and total RNAs were extracted using the RNeasy kit (Qiagen) according to the manufacture's protocol. Sequencing libraries were prepared using the TruSeq RNALibrary Prep Kit v2 (Illumina) according to the manufacture's protocol.

value: Heart

value: Ventricular myocytes

value: Wild Type

tag: treatment


title: RNA-seq_LCDM-3


title: NC-2

description: Kasumi-1 sample with no treatment


title: RNA-seq_A2iL-5


title: Ventricular_Myocytes_8


title: antiNRPE1 ChIP in h1 rep1

value: h1 mutant


title: Ventricular_Myocytes_7


title: RNA-seq_A2iL-3


title: antiH3K9me2 ChIP in h1 rep1


title: infusion product patient 4, scRNA-seq

city: Geneva

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: 10x Genomics

data_processing:
demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger Software v2.0.1/v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: matrix files and tab-separated values files

source_name: blood

extract_protocol:
Before running single cell sequencing on brain samples, brain dissociation tissues were enriched using the EasySepTM Release Human CD45 Positive Selection Kit (Stemcell#100-0105). CD45 positive cells fraction were resuspended in 1× PBS with 0.04% bovine serum albumin. Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) as well as classical hemocytometer and trypan blue. Before running single cell on blood samples, PBMCs were enriched using the EasySep™ Human T Cell Enrichment Kit StemCell #19051. CD3 positive cells fraction were resuspended in 1× PBS with 0.04% bovine serum albumin. Cell numbers and viability were measured using a Countess II Automated Cell Counter (Thermo Fisher Scientific) as well as classical hemocytometer and trypan blue.
Library was performed according to manufacturer instructions (Single Cell 5', 10x Genomics protocol and Single Cell V(D)J for TCR sequencing).Single-cell suspensions were loaded onto a Chromium Single Cell Chip (5’ RNAseq Chromium Single Cell 5' Reagent Kit v2 Chemistry Dual Index, 10X Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded gel beads at a target capture rate of 10,000 individual cells per sample, based on the initial number of cells per sample. For all patients, RNA and TCR libraries were synthetized by following the Chromium Single Cell 5′ V(D)J Enrichment Kit, Human T Cell (10X Genomics, Chromium Single Cell Human TCR Amplification Kit)

value: blood

value: immune

tag: time

value: pre-treatment

value: CART-EGFRvIII +Pembro

tag: individual

value: patient 4


title: RNA-seq_2iL-5


title: antiNRPE1 ChIP in ZF108DMS3 rep2

tag: genotype


title: infusion product patient 1, scRNA-seq

description: 10x Genomics

value: patient 1


title: antiH3 ChIP in ZF108DMS3 rep2

value: anti-H3 (abcam1791)


title: RNA-seq_2iL-3


title: Ventricular_Myocytes_5


title: Ventricular_Myocytes_6


title: sample 8993, patient 8 post-treatment biopsy, scTCR-seq

description: 10x Genomics

data_processing:
demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger Software v2.0.1/v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: matrix files and tab-separated values files
Library strategy: scTCR-seq

source_name: brain

value: brain

value: post-treatment

value: patient 8


title: sample 8990, patient 8 post-treatment biopsy, scTCR-seq

description: 10x Genomics


title: Ventricular_Myocytes_4


title: RNA-seq_SL-5


title: RNA-seq_SL-3


title: Ventricular_Myocytes_3


title: ATAC-seq_2iL-F-5

data_processing:
Clean reads were mapAll ATAC-seq reads were first mapped to the mm10 genome. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. ped to the Mus musculus mm10 reference genome using Bowtie2 (population) or Hisat2 (a few cells).
Normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads.
To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250 bp and counted the coverage for each base. The ATAC-seq enrichment was then summed within each 3-kb-window for the entire genome and was compared across different samples.
Pearson correlation was used for all analyses. All the ATAC-seq peaks were called by MACS with the parameters nolambda-nomodel. ATAC-seq peaks that are at least 2.5 kb away from annotated promoters (RefSeq, Ensemble and UCSC Known Gene databases combined) were selected as distal ATAC-seq peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells (500 to 3000 cells per reaction) were centrifuged to remove the supernatant. 20 μl of lysis buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 0.2% N-P40) was added, followed by pipetting 6-10 times to release the nuclei without purification, and 30 μl reaction buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 1000 unit Tn5) was mixed on a Vortex for 5 seconds. The reaction was incubated at 37 °C for 20 minutes, followed by addition of 350 μl ERC buffer (MiniElute, Qiagen) to stop the reaction. After DNA purification (MiniElute, Qiagen) and then performing ATAC-seq libraries construction.
Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: sample 8986, patient 6 post-treatment biopsy, scTCR-seq

description: 10x Genomics

value: patient 6


title: antiH3 ChIP in ZF108DMS3 rep1


title: antiNRPE1 ChIP in ZF108DMS3 rep1

value: Anti-NRPE1 (Covance)


title: sample 8945, patient 5 post-treatment biopsy, scTCR-seq

description: 10x Genomics

value: patient 5


title: Ventricular_Myocytes_1

value: Heart


title: NC-1

description: Kasumi-1 sample with no treatment

tag: cell line


title: Ventricular_Myocytes_10

value: Ventricular myocytes


title: sample 8944, patient 7 post-treatment biopsy, scTCR-seq

description: 10x Genomics

value: patient 7


title: ATAC-seq_LCDM-5

value: Embryonic stem cell line


title: sample 8862, patient 7 pre-treatment biopsy, scTCR-seq

description: 10x Genomics


title: Ventricular_Myocytes_2

value: Wild Type


title: antiH1 ChIP in ZF108DMS3 rep1

value: floral tissue

value: anti-H1 (AS11 1801 Agrisera)


title: antiH1 ChIP in ZF108DMS3 rep2


title: antiNRPE1 ChIP in WT rep2

value: WT


title: ATAC-seq_LCDM-3


title: Purkinje_cells_7

value: Cardiac Purkinje Cells


title: sample 8761, patient 2 post-treatment blood, scTCR-seq

description: 10x Genomics

value: blood

value: immune

value: CART-EGFRvIII +Pembro

value: patient 2


title: antiH3 ChIP in WT rep2

value: anti-H3 (abcam1791)


title: sample 8761, patient 2 post-treatment biopsy, scTCR-seq

description: 10x Genomics

value: brain

value: post-treatment


title: ATAC-seq_A2iL-5


title: Purkinje_cells_6


title: antiH1 ChIP in WT rep2


title: Purkinje_cells_5


title: sample 8742, patient 6 pre-treatment biopsy, scTCR-seq

description: 10x Genomics

value: pre-treatment

value: patient 6


title: ATAC-seq_2iL-F-3


title: Purkinje_cells_4

value: Heart


title: antiH1 ChIP in WT rep1


title: ATAC-seq_2iL-5


title: sample 8688, patient 4 post-treatment blood, scTCR-seq

description: 10x Genomics

value: patient 4


title: antiH3 ChIP in WT rep1


title: antiH3K9me2 ChIP in WT rep2

value: anti-H3K9me2 (abcam1220)


title: ATAC-seq_2iL-3

value: Embryonic stem cell line


title: sample 8688, patient 4 post-treatment biopsy, scTCR-seq

description: 10x Genomics


title: antiH3K9me2 ChIP in WT rep1

value: floral tissue


title: sample 8510, patient 1 post-treatment blood, scTCR-seq

description: 10x Genomics

value: patient 1


title: ATAC-seq_SL-5


title: antiNRPE1 ChIP in WT rep1

value: Anti-NRPE1 (Covance)

value: WT


title: Purkinje_cells_1

value: Cardiac Purkinje Cells

value: Wild Type


title: sample 8510, patient 1 post-treatment biopsy, scTCR-seq

description: 10x Genomics

value: immune

value: CART-EGFRvIII +Pembro


title: SUVH1 ChIP in h1 rep2

value: Anti-FLAG M2 (Sigma, F1804)

value: h1 mutant


title: sample 8167, patient 1 pre-treatment biopsy, scTCR-seq

description: 10x Genomics

value: brain


title: O3 TAM-6

city: Charlestown

first: Mei

last: Huang

address: Building 149 13th Street

institute: Massachusetts General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor

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

value: tumor

value: macrphages sorted from tumors

value: DMSO exposure


title: ATAC-seq_A2iL-3


title: sample 8993, patient 8 post-treatment biopsy, scRNA-seq

description: 10x Genomics

value: post-treatment

value: patient 8


title: SUVH1 ChIP in h1 rep1


title: O3 TAM-4


title: sample 8990, patient 8 post-treatment biopsy, scRNA-seq

description: 10x Genomics