title: ChIP-STAT5-Tr , Replicate 2

data_processing:
ChIP-seq data analysis: Single-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data, details and codes can be found in our previously publications(Yang, X. et al. Nat Neurosci. 2019).
After confirmed the quality were good, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks(normalized to 15M uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”).
Cut-and-Run data analysis: Paired-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5M fragments as suggested by Cut&Run protocols paper. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: Wild-type regulatory T cells

growth_protocol: Tn, Treg cells were sorted from the lymphocytes isolated from male Foxp3gfp mice by CD4+GFP- CD25-CD44loCD62Lhi and CD4+GFP+, respectively. iTreg cells were induced from CD4 Tn cells with TCR agonists, IL-2, TGF-beta for 4 days in the presence or absence of 0.25mM ascorbic acid 2-phosphate, or in the presence of DMSO or JQ1. At the end of induction, live GFP+ cells were FACS sorted. Tn cells were cultured in the Treg induction condition for 24 hours with DMSO or JQ1 as 24h induced cells.

extract_protocol:
A two-step protocol was used to fix the cells for Stat5 ChIP-seq as we previously described (PMID: 25126783). Cut&Run was performed according to a method recently described (PMID: 28079019).
Libraries were constructed according to standard protocols for ChIP or Cut&Run sequencing.

treatment_protocol: Natural Treg (nTreg) cells from Foxp3gfp male mice were FACS sorted and expanded in vitro for 5 days with Dynabeads® Mouse T-Activator CD3/CD28 in the presence of 500-1000 U/ml recombinant IL-2. To perform Stat5 ChIP, iTreg or nTreg cells were starved for 4 hours in complete RPMI 1640 without cytokines. Cells were then restimulated with 100 U/ml (iTreg) or 500 U/ml (nTreg) IL-2 for 30 min before being fixed for ChIP experiments.

value: Wild-type regulatory T cells

tag: chip antibody

value: Stat5 (CellSignalingTechnology,94205)


title: LL10LR

status: Public on Dec 14 2021

type: SRA

city: New Haven

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10 Amistad Street

department: Biomedical Engineering

country: USA

institute: Yale University

description: Bulk RNAseq

library_source: transcriptomic

data_processing:
For scRNAseq, FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
For scRNAseq, downstream processing was conducted with Cellranger 3.0.2 with the default parameters.
For scRNAseq, cells were accepted with greater than 500 and fewer than 10000 unique mapped genes, and fewer than 100000 gene transcripts. Analysis was performed on cells with less than 5% mitochondrial mapping for P4PMEC, Engineered lung, Preseeded iPSC, and iPSC-ECFC lung samples and less than 20% for the P7native sample.
Genome_build: Reads were aligned to rat reference genome Ensembl Rnor6.0 release 95 an human reference genome GRCh38 release 31 (GRCh38.p12), respectively.
Supplementary_files_format_and_content: *.mtx: sparse matrix file of raw counts, *genes.tsv: genelist (rownames for .mtx file), *barcodes.tsv: barcodes (column names for .mtx file), *.idents.tsv: celltype idents (metadata)

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Lung Endothelium

growth_protocol: Rodent pulmonary microvascular endothelial cells were isolated from postnatal day 7 rat lungs. The isolated cells were cultured on fibronectin-coated 6 well-plate at a density of 5000 cells/cm2 in endothelial culture medium (Vasculife (VEGF) medium (Lifeline cell technology) supplemented with 10 % FBS and 1.5% antibiotic/antimycotic (A/A)) for 7 days with daily complete medium change.  Human iPSC-derived endothelial colony forming cells were cultured on collagen I-coated flasks (50 μg/mL) in endothelial culture medium.

extract_protocol:
Lungs were extracted from the animals and transferred into 60mm petri dish. A syringe fitted with 25G needle was injected into lung pieces with enzyme solution (DMEM (low glucose) + 1 mg/mL Collagenase/Dispase + 3 U/mL Elastase + 20 U/mL DNAse).  The tissue pieces were minces into small pieces and transfered to a 50 mL conical tube. Incubate the tissue pieces at 37C for 20 minutes at a agitation of ~75rpm. The tissue was dissociated through a wire mesh strainer and rinsed with medium, followed by centrifugation and filtration. The number of cells was counted and the cell solution was diluted to a final concentration of 1M cells/mL in 0.01% BSA in PBS.
scRNAseq libraries were generated with the Chromium Single Cell 3’ assay (10x Genomics). Samples were diluted for an expected cell recovery population of 10,000 cells per lane. Bulk RNAseq libraries were prepared using the Pair End Sequencing Prep Kit.
For scRNAseq, libraries sequenced on the HiSeq4000 platform to a depth of 180 to 500 million reads per library. Downstream processing was conducted with Cellranger 3.0.2 with the default parameters. For bulk RNAseq, libraries were sequenced through NovaSeq with sequencing read length of 100 base pairs (bp).

tag: tissue

value: Lung Endothelium

tag: age

value: Postnatal day 7


title: LL13LL

description: Bulk RNAseq


title: LL16LR

description: Bulk RNAseq


title: ChIP-STAT5-Tr , Replicate 1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: Sex

value: male

tag: cell type

tag: treatment


title: Cut-and-Run-PolII-iTreg-ASC-1

data_processing:
Library strategy: CUT&RUN
ChIP-seq data analysis: Single-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data, details and codes can be found in our previously publications(Yang, X. et al. Nat Neurosci. 2019).
After confirmed the quality were good, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks(normalized to 15M uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”).
Cut-and-Run data analysis: Paired-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5M fragments as suggested by Cut&Run protocols paper. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

source_name: In vitro induced wild-type regulatory T cells (ascorbic acid treated)

value: Ascorbic Acid

value: RNA polymerase II CTD repeat (Abcam, ab26721)


title: Cut-and-Run-PolII-iTreg-ASC-2

value: In vitro induced wild-type regulatory T cells


title: Total Stranded RNA-sequencing_CNTRL_CTX_1

first: Peter

middle: J

last: McKinnon

address: 262 Danny Thomas Place

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

description:
TS01_C1_CNTRL_CTX_1
processed data file: TotalStranded_FPKM_Cortex.xlsx

data_processing:
FASTQ sequences are mapped to the University of California Santa Cruz mouse reference genome (mm9)
RNA-seq reads were mapped by our in-house mapping pipeline STRONGARM developed for the PCGP (Downing et al., 2012).
Reads were aligned to four different databases using BWA (0.5.10): (i) the mouse MGSCv37 reference sequence; (ii) RefSeq; (iii) a sequence file representing all possible combinations of non-sequential pairs in RefSeq exons; and (iv) the AceView database flat file downloaded from the UCSC Genome Browser, representing transcripts constructed from mouse ESTs
Mapped reads were counted with HTseq and normalized to FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

molecule: total RNA

source_name: Whole Cortex_Control

extract_protocol:
Total RNA was isolated from mouse brain tissue with TRIzol (Invitrogen)
TruSeq Standed Total RNA Kit (Illumina) is used for library preparation: Double stranded cDNA fragments are ligated with Illumina paired end adaptors, followed by size selection (~200bp).

tag: tissue type

value: Cortex

tag: genotype

value: Control


title: Cut-and-Run-PolII-iTreg-Mock-2

source_name: In vitro induced wild-type regulatory T cells (control)

value: Mock


title: chronic NB73 231-R.1

city: Urbana

first: Yvonne

last: Ziegler

state: IL

address: 407 S Goodwin Ave.

department: MIP

institute: University of Illinois

description: chronic NB73

data_processing:
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36)
Reads were mapped to the Homo sapiens reference genome from Ensembl database (GRCh37) and aligned using the STAR alignment tool (Version 2.5.3)
Read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized expressions and differentially expressed genes

organism: Homo sapiens

source_name: MDA-MB-231 cells

growth_protocol: MCF-7 cells were cultured in RPMI medium +5%FBS+pen/strep.  MDA-MB-231 cells were cultured in DMEM+5%FBS + pen/strep

extract_protocol:
RNA was extracted using Trizol protocol, followed by DNase treatment.  RNA was then re-purified with an aqueous column-based protocol followed by gel analysis to analyze purity and quality of the RNA.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.
* The libraries were quantitated by qPCR and sequenced on two lanes for 101 cycles from one end of the fragments on a HiSeq 4000
using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: Cells were treated with vehicle or inhibitors while in growth phase, for times indicated.

tag: cell line


title: Total Stranded RNA-sequencing_APTXATM_CTX_6

description:
TS50_G2_APTXATM_CTX_6
processed data file: TotalStranded_FPKM_Cortex.xlsx

source_name: Whole Cortex_Atm Nes-cre; Aptx-/-

value: Atm Nes-cre; Aptx-/-


title: 24hr NB73 231 NB73.3

description: 24hr NB73


title: 24hr NB73 231 NB73.2

description: 24hr NB73


title: 24hr Vehicle 231 VEH.3

description: 24hr Vehicle


title: chronic NB73 231-R.2

description: chronic NB73


title: Case 11: Brain tumour_PXA

type: RNA

city: New Delhi

first: Vaishali

last: Suri

state: Delhi

address: Sri Aurobindo Marg, Ansari Nagar, Ansari Nagar East

department: Pathology

country: India

institute: AIIMS

description: Gene Expression_PXA

hyb_protocol: Cy3-labeled cRNA samples were hybridized onto whole human genome SurePrint G3 8X60K arrays using Agilent’s Surehyb Chambers in an Agilent hybridization oven set at 65°C for 17 hours.

scan_protocol: The slides were then washed and subsequently scanned by an Agilent G4900DA SureScan Microarray Scanner (Agilent Technologies).

data_processing: Images from the scanned array were analyzed using Agilent’s Feature Extraction software, version 11.5.1.1 and further analyzed for statistical evaluations using GeneSpring GX version-13.0 software (Agilent Technologies).

source_name: Tumour tissue_FFPE_PXA

label_protocol: Expression profiling was performed using a low-input QuickAmp labeling kit and human SurePrint G3 8x60K microarrays (Agilent Technologies, Santa Clara, CA). Briefly, 100 ng quality-checked total RNA was reverse transcribed using a Low Input Quick Amp labeling kit and then transcribed to Cy3-labeled cRNA according to the manufacturer’s protocol.

extract_protocol: RNA from the formalin-fixed paraffin-embedded (FFPE) blocks was extracted using the manufacturer’s protocol (RecoverAll™ Total Nucleic Acid Isolation Kit, Thermo Scientific). The extent of RNA fragmentation or quality and concentration were assessed via capillary chip electrophoresis using the RNA 6000 Nano Chip kit on Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with an integrity number above 5 were used for the further analysis.

treatment_protocol: Genome-wide expression profiling of 14 PXA and 6 APXAs was performed by microarray. Amongst differentially expressed genes ( DEGs), Cyclin Dependent Kinase 14 (CDK 14)  and Mitochondrial Fission Process 1  (MTFP 1) were validated by qRT-PCR.

value: Formalin Fixed Paraffin Embedded

tag: gender


title: Case 33: Brain tumour_APXA

description: Gene Expression_APXA

source_name: Tumour tissue_FFPE_APXA


title: chronic NB73 231-R.3

description: chronic NB73


title: 24hr Vehicle 231 VEH.1

description: 24hr Vehicle


title: 24hr Vehicle 231 VEH.2

description: 24hr Vehicle


title: Cut-and-Run-PolII-iTreg-Mock-1


title: Case 17: Brain tumour_APXA

description: Gene Expression_APXA


title: chronic NB73 MCF7-R.3

description: chronic NB73

source_name: MCF-7 cells


title: Case 22: Brain tumour_APXA

description: Gene Expression_APXA


title: Total Stranded RNA-sequencing_APTXATM_CTX_4

description:
TS53_G2_APTXATM_CTX_4
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: Total Stranded RNA-sequencing_APTXATM_CTX_3

description:
TS44_G2_APTXATM_CTX_3
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: Cut-and-Run-H3K4Me3-iTreg-ASC-1

value: H3K4me3(Active motif, 39159)


title: 24hr NB73 231 NB73.1

description: 24hr NB73


title: Total Stranded RNA-sequencing_APTXATM_CTX_2

description:
TS43_G2_APTXATM_CTX_2
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: chronic NB73 MCF7-R.1

description: chronic NB73


title: 24hr NB73 MCF7 NB73.2

description: 24hr NB73


title: 24hr NB73 MCF7 NB73.3

description: 24hr NB73


title: 24hr NB73 MCF7 NB73.1

description: 24hr NB73


title: Cut-and-Run-H3K4Me3-iTreg-Mock-1


title: Cut-and-Run-H3K4Me3-iTreg-ASC-2


title: Total Stranded RNA-sequencing_APTXATM_CTX_1

description:
TS42_G2_APTXATM_CTX_1
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: Total Stranded RNA-sequencing_APTXATM_CTX_5

description:
TS52_G2_APTXATM_CTX_5
processed data file: TotalStranded_FPKM_Cortex.xlsx


title: 24hr Vehicle MCF7 VEH.3

description: 24hr Vehicle


title: 24hr Vehicle MCF7 VEH.2

description: 24hr Vehicle


title: Cut-and-Run-H3K27ac-iTreg-ASC-2


title: Total Stranded RNA-sequencing_CNTRL_CB_4

description:
TS06_C1_CNTRL_CB_4
processed data file: TotalStranded_FPKM_Cerebellum.xlsx

source_name: Whole Cerebellum_Control

value: Cerebellum


title: 24hr Vehicle MCF7 VEH.1

description: 24hr Vehicle


title: Total Stranded RNA-sequencing_CNTRL_CB_3

description:
TS04_C1_CNTRL_CB_3
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Cut-and-Run-H3K27ac-iTreg-Mock-2


title: Cut-and-Run-H3K27ac-iTreg-ASC-1


title: Cut-and-Run-H3K4Me3-iTreg-Mock-2


title: 9hr NB73 NB73.3

description: 9hr NB73

growth_protocol: MCF-7 cells were cultured in RPMI medium +5%FBS+pen/strep.


title: 9hr NB115 NB115.1

description: 9hr NB115


title: 9hr NB115 NB115.3

description: 9hr NB115


title: 9hr NB73 NB73.2

description: 9hr NB73


title: Total Stranded RNA-sequencing_CNTRL_CB_1

description:
TS00_C1_CNTRL_CB_1
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: 9hr NB73 NB73.1

description: 9hr NB73


title: ChIP-S5P-iTreg-Mock-JQ1-2

source_name: In vitro induced wild-type regulatory T cells with JQ1

value: PolII CTD repeat phospho S5 (Abcam, ab5131)


title: 9hr Vehicle VEH.3

description: 9hr Vehicle


title: 9hr NB115 NB115.2

description: 9hr NB115


title: ChIP-S5P-iTreg-Mock-JQ1-1


title: Cut-and-Run-H3K27ac-iTreg-Mock-1


title: 9hr Vehicle VEH.1

description: 9hr Vehicle


title: 9hr Vehicle VEH.2

description: 9hr Vehicle


title: ChIP-S5P-iTreg-Mock-DMSO-2

source_name: In vitro induced wild-type regulatory T cells with DMSO

value: DMSO


title: Liver tissue of Control_rep9 [19069_D]

city: Changsha

first: Yongqiang

last: Ma

address: 139 Renmin Road

country: China

institute: Department of Liver Transplant, Second Xiangya Hospital, Central South University

data_processing:
Finally, the prepared RNA-seq libraries were qualified using a 2100 Bioanalyzer (Agilent, USA) and quantified using a qPCR absolute quantification method. The sequencing was performed using the Illumina Hi Seq 4000 platform. Raw sequencing data that passed the Illumina quality filter were used for the following analysis.
Trimmed reads are aligned to the reference genome (Human GRCh38/hg38). Based on alignment statistical analysis (mapping ratio, rRNA/mt RNA content, and fragment sequence bias), we determined whether the results could be used for subsequent data analysis. Subsequently, expression profiling, differentially expressed genes, and differentially expressed transcripts were calculated. Genes with P value <0.05 were considered differentially expression genes.
Genome_build: Human GRCh38/hg38
Supplementary_files_format_and_content: FPKM

source_name: Liver tissue of Control

extract_protocol:
Total RNA was extracted from liver tissue samples of patients with MAFLD and healthy controls using the Illustra RNA spin Mini Kit (GE Healthcare, USA). RNA samples were quantified using a Nano Drop instrument (Thermo Fisher Scientific, USA) and qualified by agarose gel electrophoresis.
Illumina kits which include procedures of RNA fragmentation, random hexamer primed first-strand cDNA synthesis, dUTP-based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation, and library PCR amplification, were used for RNA-seq library preparation.

tag: subject status

value: control

value: Liver cell

value: untreated


title: Total Stranded RNA-sequencing_APTX_CB_2

description:
TS51_G1_APTX_CB_2
processed data file: TotalStranded_FPKM_Cerebellum.xlsx

source_name: Whole Cerebellum_Aptx-/-

value: Aptx-/-


title: Total Stranded RNA-sequencing_ATM_CB_1

description:
TS45_G1_ATM_CB_1
processed data file: TotalStranded_FPKM_Cerebellum.xlsx

source_name: Whole Cerebellum_Atm Nes-cre

value: Atm Nes-cre


title: Total Stranded RNA-sequencing_ATM_CB_2

description:
TS54_G1_ATM_CB_2
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Total Stranded RNA-sequencing_CNTRL_CB_2

description:
TS02_C1_CNTRL_CB_2
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Liver tissue of Control_rep8 [19066_D1]


title: Total Stranded RNA-sequencing_APTX_CB_1

description:
TS41_G1_APTX_CB_1
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Liver tissue of Control_rep6 [19052_D1]


title: Total Stranded RNA-sequencing_APTXATM_CB_6

description:
TS50_G1_APTXATM_CB_6
processed data file: TotalStranded_FPKM_Cerebellum.xlsx

source_name: Whole Cerebellum_Atm Nes-cre; Aptx-/-


title: Liver tissue of Control_rep4 [19042_D1]


title: Liver tissue of Control_rep3 [19040_D1]


title: Total Stranded RNA-sequencing_APTXATM_CB_5

description:
TS52_G1_APTXATM_CB_5
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: ChIP-S5P-iTreg-Mock-DMSO-1

value: male


title: ChIP-S2P-iTreg-Mock-JQ1-1

value: PolII CTD repeat phospho S2 (Abcam, ab5095)


title: Liver tissue of Control_rep1 [19038_D1]


title: ChIP-S2P-iTreg-Mock-JQ1-2

value: In vitro induced wild-type regulatory T cells


title: Liver tissue of Control_rep2 [19039_D1]


title: ChIP-S2P-iTreg-Mock-DMSO-2


title: Liver tissue of Control_rep5 [19050_D]


title: ChIP-S2P-iTreg-Mock-DMSO-1


title: Liver tissue of MAFLD patient_rep7 [18095_D1]

source_name: Liver tissue of MAFLD patient

value: MAFLD patient


title: Liver tissue of MAFLD patient_rep5 [18131_D]


title: Total Stranded RNA-sequencing_APTXATM_CB_3

description:
TS44_G1_APTXATM_CB_3
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Total Stranded RNA-sequencing_APTXATM_CB_4

description:
TS53_G1_APTXATM_CB_4
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Liver tissue of Control_rep7 [19056_D1]


title: Liver tissue of MAFLD patient_rep4 [18210_D1]


title: ChIP-PolII-iTreg-Mock-JQ1-2

value: RNA polymerase II CTD repeat (Abcam, ab26721)


title: Total Stranded RNA-sequencing_APTXATM_CB_1

description:
TS42_G1_APTXATM_CB_1
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Liver tissue of MAFLD patient_rep2 [19054_D1]


title: Total Stranded RNA-sequencing_APTXATM_CB_2

description:
TS43_G1_APTXATM_CB_2
processed data file: TotalStranded_FPKM_Cerebellum.xlsx


title: Liver tissue of MAFLD patient_rep1 [19064_D]


title: ChIP-PolII-iTreg-Mock-JQ1-1


title: Liver tissue of MAFLD patient_rep3 [19025_D1]


title: 17 week Human Cochlea

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: Samples were collected as part of an UCSF IRB approval. The soft tissue was dissected out, minced with a scalpel, and washed with PBS. Dissociation: 20 minutes in thermolysin followed by 10 to 40 minutes in Accumax with trituration. Resulting cells were passed through a 40 μm cell strainer and pelleted, then red blood cells were lysed (Alfa Aesar), and the cells were processed using the Dead Cell Removal Kit and, when indicated, CD326 (EpCAM) MicroBeads, human, from Miltenyi Biotec.

data_processing:
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
the output matrix files are here and are included for postprocessing for R analysis
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
Genome_build: Genome_build: mm10 for mouse, and hg19 for human

source_name: cochlea

extract_protocol:
Cells were loaded onto the Chromium Controller from 10x Genomics for single cell capture.
10x Chromium

value: cochlea

tag: developmental stage

value: gestational age 17 weeks


title: ChIP-PolII-iTreg-Mock-DMSO-2


title: 15 week Epcam Positive Human Cochlea

value: gestational age 15 weeks


title: YUMASK, scRNA-seq

first: Ruth

last: Halaban

state: CT

address: 15 York St.

department: Dermatology

data_processing:
Single-cell RNA-seq reads from four acral melanoma patients were mapped to the GRCh38 human reference assembly and barcode-deduplicated using Cell Ranger (version 3.0.2 and 5.0.1).
The resulting data were imported into Seurat116 (version 4.0.4) and quality-control filtered for the number of expressed genes per cell and the fraction of reads mapped to mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each cell per gene

source_name: Tumor

extract_protocol:
For YUJASMIN, cryopreserved tumor cell suspension was sorted for viable singlets to target 10,000 cells. Cells were sorted in the following ratios prior to library preparation: 50% CD3+CD45+ T cells: 25% CD3–CD45+ non-T immune cells: 25% CD45– stromal/cancer cells. Cell viability was assessed by the LIVE/DEAD™ Fixable Red Dead Cell Stain Kit (catalog #L34971, Thermo Fisher). The following antibodies were used: Alexa Fluor® 488 anti-human CD45 antibody (clone H130, catalog #304019, BioLegend); APC anti-human CD3 antibody (clone HIT3a, catalog #300319, BioLegend). For the other three tumors,  cryopreserved tumor cell suspensions were used.
For YUJASMIN, the 10x Chromium 5’ expression profiling platform with V1 chemistry was applied  and  the 10x library was sequenced on an Illumina HiSeq 2500 instrument. For the other three tumors, the 10x Chromium 5’ assay with V2 chemistry was applied to cryopreserved tumor cell suspensions and sequenced on an Illumina NovaSeq 6000 instrument.

tag: individual

value: patient YUMASK

tag: disease state

value: acral melanoma

value: acral melanoma tumor

tag: 22q11.21 amplified

value: no


title: YUPARK, scRNA-seq

value: patient YUPARK


title: Liver tissue of MAFLD patient_rep6 [19003_D1]

value: Liver cell


title: ChIP-PolII-iTreg-Mock-DMSO-1

value: DMSO


title: 9-mo WT-CD11c- rep2

city: Chongqing

first: Yiguo

last: Qiu

state: Chongqing

address: 13 Tianchi Road, Banan Distri

institute: Chongqing International Institute for Immunology

data_processing:
After reviewing the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome (ENSEMBL) using STAR aligner v.2.5.2b, a splice aligner that detects and incorporates splice junctions to align the entire read sequences.
BAM files were generated, and unique gene hit counts were calculated using Counts (Subread package v.1.5.2).
Only unique reads that fell within exon regions were counted. Differential expression was considered significant with an FDR-adjusted p value < 0.05.
Genome_build: Mus musculus reference genome (ENSEMBL)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: microglia

extract_protocol:
Total RNA was extracted from FACS-sorted cell pellets using RNeasy Plus Universal Mini Kit, according to manufacturer’s instructions (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols and CD11c+ and CD11c- microglial samples of 9-mo old WT mice were processed with SMART-Seq v4 Ultra Low Input Kit for Sequencing for full-length cDNA synthesis and amplification

value: brain

value: microglia

tag: cell subset


title: 9-mo WT-CD11c+ rep1


title: 9-mo WT-CD11c+ rep2


title: 9-mo WT-CD11c- rep1


title: 8d_S_L_3_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Raw sequence WGBS paired-end reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v.0.6.5). Sequences were mapped to the mouse GRCm38 genome assembly using Bismark (v0.22.3), deduplicated with deduplicate_bismark, then CpG methylation calls were extracted and analysed with SeqMonk.
Raw, single-end RNA-seq reads were trimmed using Trim Galore (v.0.6.5) with default settings. Trimmed reads were mapped to the mouse GRCm38 genome assembly using HISAT2, and mappings with MAPQ scores <20 were discarded. Mapped RNA-seq data was quantitated over strand-specific mRNA probes using the Seqmonk RNA-seq Quantitation Pipeline to generate log2 RPM (reads per million mapped reads of library) expression values.
Genome_build: GRCm38
RNA-seq report: Tab-delimited text file of log2RPM values for each replicate sample individually (SeqMonk Annotated Probe report).
Bismark coverage report: A Bismark coverage file specific for either the top (OT) or bottom (OB) strand.

growth_protocol: E14 (XY) mouse embryonic stem cells (mESCs) were cultured feeder-free in normoxia on 0.1% gelatin-coated plates. 1.5 million cells were plated per 10cm plate in S/L media (DMEM supplemented with 15% fetal bovine serum, 1% Penicillin-Streptomycin, 1% MEM non-essential amino acids, 1% Glutamax, 50 μM β-mercaptoethanol [all Gibco] and 10^3 U LIF [Cambridge Stem Cell Institute]). The following day, cells were washed twice with PBS and the media changed to S/L, 2i/L, GSK3i/L or MEKi/L media. 2i/L, GSK3i/L and MEKi/L media had in common the basal N2B27 media with LIF (1:1 ratio DMEM/F12 to neurobasal medium, 0.5% 100X N-2 supplement, 1% 50X B-27 supplement without Vitamin A, 1% Glutamax, 1% Penicillin- Streptomycin, 50 μM β-mercaptoethanol [all Gibco] and 10^3 U LIF). 2i/L media was supplemented with 1μM PD03259010 and 3μM CHIR99021 (both Cambridge Stem Cell Institute), GSK3i/L media with 3μM CHIR99021 only, and MEKi/L with 1μM PD03259010 only. Cells were passaged every 2 days using TrypLE Express (Gibco), and 3 million cells were plated per 10cm plate.

extract_protocol:
For collection at designated time points for DNA and RNA extraction, cells were washed twice with cold PBS and then scraped from plates in RLT plus buffer (Qiagen). DNA and RNA was extracted using the DNA/RNA mini kit (Qiagen). RNA was subsequently DNase treated using the TURBO DNA-free kit ’Rigorous DNase treatment’ protocol.
For whole genome Bisulfite-Seq, DNA was fragmented to an average of 400bp using a Covaris sonicator, and 50ng of sonicated DNA together with a spike-in of 8ng lambda DNA was used for library preparation. Methylated adaptors were added using NEBNext Ultra II DNA Library Prep reagents, then samples were bisulfite converted using the Zymo EZ Methylation-Direct kit. Libraries were amplified using KAPA HiFi Uracil+ then analysed on a Bioanalyzer and by KAPA quantification. A 10nM pool of 26 duplicate samples was 100bp paired-end sequenced over two lanes of a NovaSeq S1 flowcell.
RNA-seq libraries were made using the NEBNext Poly(A) mRNA Magnetic Isolation Module combined with the NEBNext Ultra II Directional Library Prep Kit for Illumina. Final libraries were KAPA quantified and the library quality assessed with the Agilent Bioanalyser DNA High Sensitivity Kit. A 20nM pool of 17 libraries was sequenced over two lanes of HiSeq2500-RapidRun 50bp Single End.

value: Embryonic stem cells

value: 8d S/L


title: ChIP-S5P-iTreg-24h-JQ1-1

source_name: In vitro induced for 24 hours with JQ1

value: male

value: In vitro induced for 24 hours from Tn cells

tag: chip antibody

value: PolII CTD repeat phospho S5 (Abcam, ab5131)


title: ChIP-S5P-iTreg-24h-DMSO-2

source_name: In vitro induced for 24 hours with DMSO


title: Pt25

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description: Subglotic stenosis patient

data_processing:
Genome alignment single read: STAR --genomeDir ~/STAR_GENOME_DIR --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
Counting reads: featureCounts -t exon -g gene_id -a ~/genes.gtf -T 20
DGE with DESeq2.
Genome_build: hg38 (GRCh38) and mm10 (GRCm38)
Supplementary_files_format_and_content: *_SGS_counts.txt: featureCounts read counts for all samples.

source_name: human laryngotracheal swab

extract_protocol:
Tracheal tissues were placed in a vial 5ml conical tube containing RNAlater immediately after collection from the operating room. The tubes were vortex-mixed for 30 seconds, patties were removed, and the RNAlater solution decanted following 15 min of centrifugation at 16,000 x g. This step ensured maximum recovery of epithelial cells. The decanted RNAlater was collected in a fresh tube and centrifuged at 2,000 x g for 5 minutes. Pellets were resuspended in 500 μL of TRIzol. Samples were incubated for 1 hour at room temperature, before lysing the cells by repeated passage through a 29-G syringe. We then proceeded with the TRIzol RNA extraction protocol as suggested by the manufacturer’s instructions.
RNA libraries were prepared for sequencing per NEB protocol.

tag: diagnosis

value: Subglottic stenosis (SGS)

tag: tissue

value: Laryngotracheal swab


title: ChIP-S5P-iTreg-24h-JQ1-2

tag: strain


title: Pt26

description: Subglotic stenosis patient


title: Rat+Mouse

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: Rnor_6.0 / GRCm38
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

organism:
Mus musculus
Rattus norvegicus

source_name: Mediobasal hypothalamus

growth_protocol: Chow with ad libitum food

extract_protocol:
Rats were euthanized, the hypothalamus was dissected, nuclei were isolated and cleaned using FACS, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression

value: mediobasal hypothalamic cells


title: P5 WT-CD11c- rep3

tag: age

value: postnatal day 5


title: P5 WT-CD11c- rep2

tag: cell type


title: 23 week Epcam Positive Human Cochlea

value: cochlea

value: gestational age 17 weeks


title: Pt24

description: Subglotic stenosis patient


title: ChIP-S2P-iTreg-24h-JQ1-2

tag: Sex

tag: treatment

value: PolII CTD repeat phospho S2 (Abcam, ab5095)


title: 8d_S_L_2_RNAseq


title: 8d_S_L_1_RNAseq


title: ChIP-S2P-iTreg-24h-JQ1-1


title: P5 WT-CD11c+ rep3


title: 8d_GSK3i_L_3_RNAseq

value: 8 days GSK3i/L


title: P5 WT-CD11c+ rep2


title: Pt21

description: Subglotic stenosis patient


title: ChIP-S2P-iTreg-24h-DMSO-2


title: Pt13

description: Subglotic stenosis patient


title: 8d_GSK3i_L_2_RNAseq


title: YUGRUS, scRNA-seq

value: patient YUGRUS

value: acral melanoma

value: acral melanoma tumor

value: no


title: Pt10

description: Subglotic stenosis patient


title: 8d_GSK3i_L_1_RNAseq

value: Embryonic stem cells


title: Pt6

description: Subglotic stenosis patient


title: 8d_2i_L_3_RNAseq

value: 8 days 2i/L


title: Pt2

description: Subglotic stenosis patient


title: P5 WT-CD11c- rep1

value: brain

value: microglia


title: ChIP-S5P-iTreg-24h-DMSO-1

value: male

value: In vitro induced for 24 hours from Tn cells

value: DMSO

value: PolII CTD repeat phospho S5 (Abcam, ab5131)


title: 8d_2i_L_2_RNAseq


title: ChIP-PolII-iTreg-24h-JQ1-2

value: RNA polymerase II CTD repeat (Abcam, ab26721)


title: WT 300nM 5-azacytidine

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

data_processing:
Adapter were trimmed using TrimGalore! v0.6.6, with following settings --clip_r1 10 --clip_r2 15 --three_prime_clip_r1 15 --three_prime_clip_r2 10 --paired
Reads were aligned either to mm10 or lambda DNA (for spike-ins) reference genomes using BSMAPz v1.1.3 with parameters: -v 0.1 -q 20 -S 1 -w 500
Methylation calls were made using the methratio.py script with the -r flag to remove PCR duplicates
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph file containing DNA methylation percentage of each CpG alignment

source_name: murine embryonic stem cells

growth_protocol: Cells were grown in Knockout DMEM (Gibco) supplemented with 15% ES qualified FBS (Gibco), ESGRO mouse LIF 1000U/mL (Millipore), 1X PenStrep (Invitrogen), 1X Glutamax (Invitrogen), 55µM b-mercaptoethanol (Invitrogen), 1X non-essential amino acids.  (Invitrogen) and 1X Primocin (Invivogen) on plates coated with murine embryonic feeders (MEFs). Prior to the start of the experiment, murine embryonic stem cells were plated on plates pre-coated with 0.1% gelatin and no MEFs. During the experimental course, cells were passaged every 2-3 days.

extract_protocol:
Cell pellets were snap frozen and kept at –80 °C until extraction. RNA and DNA was isolated simultaneously using the AllPrep DNA/RNA kit (Qiagen)
Genomic DNA (500 ng) with spiked-in lambda DNA (1.25 ng) (NEB) was sheared using an M220 ultrasound sonicator (Covaris) to an average size of 350 bp. The size of the DNA fragments was confirmed by electrophoresis on an 1.5% agarose gel. 200 ng of sheared DNA was subjected to bisulfite conversion using EZ DNA Methylation-Gold Kit (Zymo Research) as per manufacturer’s instructions. Libraries were prepared using 50-100 ng of bisulfite-converted DNA and the Accel-NGS Methyl-Seq DNA Library prep kit (Swift Biosciences) according to manufacturer's instructions, with 8-11 cycles of PCR-amplification.

value: undifferentiated embryonic stem cells

value: serum+LIF, supplemented with 0.3microM 5-azacytidine for 48h and then cultured in serum+LIF for 46h

tag: genotype

value: wild type


title: WT 100nM 5-azacytidine

value: serum+LIF, supplemented with 0.1microM 5-azacytidine for 48h and then cultured in serum+LIF for 46h


title: WT DMSO (5-aza control)

value: serum+LIF, supplemented with 0.1percent DMSO for 48h and then cultured in serum+LIF for 46h


title: ChIP-PolII-iTreg-24h-JQ1-1


title: Control11

value: Healthy control

value: Laryngotracheal swab


title: ChIP-PolII-iTreg-24h-DMSO-2


title: 8d_2i_L_1_RNAseq

tag: cell line


title: WT 2μM GSK-3484862 d6 (MedChemExpress)

value: serum+LIF, supplemented with 2microM GSK-3484862 for 6 days


title: ChIP-PolII-iTreg-24h-DMSO-1


title: 8d_1uM_MEKi_L_3_RNAseq

value: Embryonic stem cells

value: 8 days 1uM MEKi/L


title: Control8


title: P5 WT-CD11c+ rep1

value: brain

value: postnatal day 5


title: ChIP-S2P-iTreg-24h-DMSO-1

value: male

value: PolII CTD repeat phospho S2 (Abcam, ab5095)


title: 8d_1uM_MEKi_L_2_RNAseq


title: ChIP-H3K27Ac-iTreg-24h-C646-2

source_name: In vitro induced for 24 hours with C646

value: In vitro induced for 24 hours from Tn cells


title: Control7


title: ChIP-H3K27Ac-iTreg-24h-C646-1


title: 24d_GSK3i_L_3_RNAseq

value: 24 days GSK3i/L


title: ChIP-H3K27Ac-iTreg-24h-JQ1-2


title: WT 10μM GSK-3484862 d6 (MedChemExpress)

value: serum+LIF, supplemented with 10microM GSK-3484862 for 6 days


title: 8d_1uM_MEKi_L_1_RNAseq


title: WT 2μM GSK-3484862 d6 (ChemieTek)

value: undifferentiated embryonic stem cells


title: WT 10μM GSK-3484862 d14 (MedChemExpress)

value: serum+LIF, supplemented with 10microM GSK-3484862 for 14 days


title: Control14


title: 24d_GSK3i_L_2_RNAseq


title: ChIP-H3K27Ac-iTreg-24h-JQ1-1


title: WT 2μM GSK-3484862 d14 (ChemieTek)

value: serum+LIF, supplemented with 2microM GSK-3484862 for 14 days

value: wild type


title: ChIP-H3K27Ac-iTreg-24h-DMSO-2

value: DMSO


title: Control4

value: Healthy control


title: scAR: Patient 41 scATAC-seq

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description: ID: UVA062

data_processing:
scATAC-seq data were pre-processed using Cell Ranger ATAC version 1.2.0 (genome version hg38). The ArchR package (version 1.0.1) was used for QC and basic analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Filtered peak barcode matrix in hdf5 format

source_name: Coronary artery

extract_protocol:
Frozen coronary artery segments were broken down using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Nuclei were washed and resuspended in 1X concentration Nuclei Buffer for single cell ATAC sequencing
Libraries were constructed according to the 10x Genomics Chromium Single Cell ATAC Reagent Kit protocol (v1 and v1.1 (Next GEM)). Each GEM (gel bead in emulsion) contains a unique 16 nucleotide 10x Barcode sequence. The sample index PCR step during library construction adds a P7 sequence and sample index barcode to each scATAC library. The amplified scATAC libaries contain the 16 nt 10x cell barcode, 8 nt sample index barcode, and P5 and P7 sequences necessary for Illumina sequencing bridge amplification. All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.

treatment_protocol: Human hearts were obtained from heart transplant recipients or rejected donor hearts. Hearts were all placed in cardioplegic solution prior to dissection of the left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA). All coronary artery samples were flash frozen in liquid nitrogen in the same manner

tag: subject

value: Patient 41

value: Coronary artery disease (CAD)

value: Coronary artery (LAD)

tag: ancestry

value: European


title: ChIP-1484802_iTr-AA2P-STAT5 , Replicate 2

source_name: In vitro induced wild-type regulatory T cells (ascorbic acid treated)

value: Ascorbic Acid

value: Stat5 (CellSignalingTechnology,94205)


title: scAQ: Patient 40 scATAC-seq

description: ID: UVA008

value: Patient 40

value: male

value: Mixed ancestry


title: ChIP-H3K27Ac-iTreg-24h-DMSO-1

value: In vitro induced for 24 hours from Tn cells


title: scAP: Patient 39 scATAC-seq

description: ID: UVA153

value: Patient 39

value: female


title: WT 10μM GSK-3484862 d6 (ChemieTek)

value: undifferentiated embryonic stem cells

value: serum+LIF, supplemented with 10microM GSK-3484862 for 6 days


title: WT 2μM GSK-3484862 d14 (MedChemExpress)

value: serum+LIF, supplemented with 2microM GSK-3484862 for 14 days

value: wild type


title: scAO: Patient 38 scATAC-seq

description: ID: UVA039

value: Patient 38

value: Coronary artery (RCA)


title: ChIP-1484800_iTr-AA2P-STAT5 , Replicate 1

value: In vitro induced wild-type regulatory T cells


title: Cut-and-Run-H3K27ac-Treg

source_name: Wild-type regulatory T cells

value: Wild-type regulatory T cells


title: scAN: Patient 20 scATAC-seq

description: ID: UVA030

value: Patient 20

value: Coronary artery disease (CAD)

value: Coronary artery (LAD)

value: European


title: ChIP-1484801_iTr-STAT5 , Replicate 2

source_name: In vitro induced wild-type regulatory T cells (control)

value: male

value: Mock

value: Stat5 (CellSignalingTechnology,94205)


title: WT 10μM GSK-3484862 d14 (ChemieTek)

value: serum+LIF, supplemented with 10microM GSK-3484862 for 14 days


title: Cut-and-Run-H3K27ac-Tnaive

source_name: Wild-type naive CD4 T cells

value: Wild-type naive CD4 T cells


title: WT DMSO d6 (GSK-3484862 control)

value: undifferentiated embryonic stem cells

value: serum+LIF, supplemented with 0.1percent DMSO for 6 days


title: WT DMSO d14 (GSK-3484862 control)

value: serum+LIF, supplemented with 0.1percent DMSO for 14 days


title: 1119045_iTregAA2P1

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm9 genome by BSMAP2.74
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

growth_protocol: Tn, Te, Treg cells were sorted from the lymphocytes isolated from male Foxp3gfp mice by CD4+GFP- CD25-CD44loCD62Lhi, CD4+GFP-CD44hiCD62Llo, and CD4+GFP+,respectively.  iTreg cells were induced from CD4 Tn isolated from male Foxp3gfp mice with TCR agonists, IL-2, TGF-beta for 4 days in the presence or absence of 0.25mM ascorbic acid 2-phosphate.  At the end of induction, live GFP+ cells were FACS sorted.

extract_protocol:
Genomic DNA was prepared from sorted cells with proteinase K digestion followed by phenol:chloroform:isoamyl alcohol extraction and 2-propanol precipitation.  More than 100ng of genomic DNA in each sample was converted by EpiTect Bisulfite Kits (Qiagen).
Libraries were prepared from converted DNA using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences)

treatment_protocol: iTreg cells were treated with or without 0.25mM ascorbic acid 2-phosphate for 4 days during Treg induction.

value: In vitro induced wild-type regulatory T cells (ascorbic acid treated)

tag: gender


title: Dnmt1/3a/3b TKO 0.1% DMSO 14d


title: Dnmt1/3a/3b TKO 0.1% DMSO 6d


title: F7_2

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
CITE-seq files: ADTs: ADT_F7_2_S13_L001_R1_001.fastq.gz
CITE-seq files: ADTs: ADT_F7_2_S13_L001_R2_001.fastq.gz
CITE-seq files: ADTs: ADT_F7_2_S13_L002_R1_001.fastq.gz
CITE-seq files: ADTs: ADT_F7_2_S13_L002_R2_001.fastq.gz
Hashing files: HTOs: HTO_F7_2_S14_L001_R1_001.fastq.gz
Hashing files: HTOs: HTO_F7_2_S14_L001_R2_001.fastq.gz
Hashing files: HTOs: HTO_F7_2_S14_L002_R1_001.fastq.gz
Hashing files: HTOs: HTO_F7_2_S14_L002_R2_001.fastq.gz

data_processing:
The sequencing data was processed using CellRanger software (version 3.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

source_name: Aortic Cells

extract_protocol:
Aortas from Ldlr-/- mice fed with a high fat, high cholesterol diet (Altromin, 15% milk fat, 1.25% cholesterol) for 13 weeks were collected, 2 aortas were pooled to generate each sample, and n=5 pools were analyzed. To exclude circulating leukocytes from analysis, mice were injected with 2.5µg anti-CD45.2 APC (clone 104, BioLegend) intravenously 5 minutes before sacrifice to label blood borne immune cells. Aortas were enzymatically digested in RPMI medium containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C with agitation, washed in PBS/1% FCS and passed through a 70µm cell strainer. Cells were labeled for 20 minutes at 37°C with CalceinViolet-AM (BioLegend 425203) according to the manufacturer’s instructions. Cells were washed and resuspended in PBS 1% FCS, plated in round bottom 96 well plates, and incubated for 10 minutes on ice with anti-CD16/32 (Biolegend, Clone 93, 10µg/ml) to block unspecific binding of antibodies to Fc receptor. Cells were subsequently labeled in a final volume of 100µl for 15 minutes at 4°C with anti-CD45.2 Alexa488 (2.5µg/ml, clone 104, BioLegend), anti-Ter119 PE-Cy7 (1µg/ml, clone TER119, BioLegend), 1:1000 Fixable Viability Dye, CITE-seq antibodies (see table), and hashtag antibodies. Each sample was labeled with a specific Hashtag antibody (Hashtag 1 to 5, final concentration 1:200, BioLegend). Cells were washed twice and all the sample were pooled. Viable Ter119negCD45.2-APC(i.v.)negCalceinAM+ cells were sorted using a BD FACS Aria III with a 100µm nozzle. The amount of sorted cells was adjusted so that ~50% of the total cells represent leukocytes (CD45-Alexa488+). Cells were sorted in PBS supplemented with 0.04% BSA, washed and counted in Trypan blue to assess viability (>85%). 18,000 cells were loaded at a concentration of 600 cells/µl in the 10x Genomics Chromium (Single Cell 3’ v3 reagents, 10x Genomics) and scRNA-seq ADT and HTO libraries were prepared.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.

value: Ldlr-/- (C57BL6/J background)


title: ChIP-seq_YD6_PolIICTD_AB1_ATMAPTX

data_processing:
The ChIP-seq raw reads were aligned to the mouse reference genome (mm9) using BWA (version 0.7.12; default parameter)
Duplicate reads were marked with Picard (version 1.65)
Only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’) were used for downstream analysis
R package SPP (version 1.11) was used to calculate relative strand correlation and estimate the fragment size
We used genomeCoverageBed (bedtools 2.25.0) to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig
The bigwig file was scaled by ChIP-seq library-size to allow comparison across samples and visualized by integrated genome viewer (IGV) (version 2.3.82).
MACS2 (version 2.1.1) was used to call RNA Pol II peaks by comparing the IP library file to input library file with default parameters and a FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig Files
Supplementary_files_format_and_content: Bed Files of Peak Calls

source_name: Whole Cerebellum PolIICTD

extract_protocol:
Cerebellar tissues were collected from WT and AtmNes-cre;Aptx-/- mice (10-12 month old) for RNA Pol II  ChIP-seq. Frozen tissues were powdered, suspended in PBS containing 1% PFA to crosslink, pelleted and then washed with ice cold PBS containing protease inhibitor cocktail (Sigma, P8340). Chromatin was extracted in lysis buffer (0.25% Triton X-100, 1mM EDTA pH8.0, 140mM NaCl, 50mM HEPES pH7.9, 10% Glycerol, and 0.5% NP-40) and then washed (in 1mM EDTA pH8.0, 200mM NaCl, 10mM Tris HCl pH8.0, and 0.5mM EGTA pH 8.0). Chromatin was then sheared (in 0.1% SDS, 1mM EDTA pH8.0, and 10mM Tris HCl pH8.0) to generate DNA fragments of 200-500bp using a Covaris M220 sonicator (Covaris). RNA pol II CTD repeat YSPTSPS (phospho S5) antibody (5μg, Abcam, #ab5131) and Magna ChIPTM Protein A+G Magnetic Beads (20μl, Millipore, #16-663) were added to the chromatin and incubated overnight at 4°C. Beads were washed 1x with low salt ChIP wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH8.0 and 150mM NaCl), 1x with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH8.0 and 500mM NaCl) and 1x with LiCl wash buffer (1mM EDTA, 10mM Tris HCl pH8.0, 250mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and finally in TE buffer (1% SDS, 1mM EDTA and 10mM Tris HCl pH8.0). Immunoprecipitated DNA was eluted using (0.1 M NaHCO3/1% SDS) followed by addition of 4μl of 5M NaCl2 per IP to dissociate DNA-protein complexes and incubated at 65°C overnight.
For library preparation, immunoprecipitated DNA was quantified using the Quant-iT RiboGreen assay (Life Technologies). Libraries were prepared with HyperPrep  Library Preparation Kits (Roche PN07962363001) and analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies,) 4200 TapeStation D1000 ScreenTape assay, or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies) or low pass sequencing with a MiSeq nano kit (Illumina).

tag: tissue type

value: Cerebellum

value: Atm Nes-cre; Aptx-/-

tag: antibody

value: RNA Pol II


title: ChIP-seq_YD7_PolIICTD_AB1_ATMAPTX


title: scAK: Patient 35 scATAC-seq

description: ID: UVA061

value: Patient 35

tag: disease state

value: Pacific Islander


title: 1119044_iTreg1

value: In vitro induced wild-type regulatory T cells (control)


title: scAJ: Patient 34 scATAC-seq

description: ID: UVA112

value: Patient 34

value: Coronary artery disease (CAD)

value: Coronary artery (LAD)

value: female

value: European


title: ATAC iTr-AA2P, Replicate2

data_processing:
2x100bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”) and aligned to mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) , duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2).
We also confirmed good reproducibility. All cell types have more than 15M nucleosome free reads after merge so we consider all important nucleosome free regions should be called.
At last, we merge replicates and adjust Tn5 shift (reads were offset were offset by +4 bp for the sense strand and -5 bp for the antisense strand) and we separated reads into nucleosome free, mononucleosome, dinucleosome, trinucleosome as described in Buenrostro et.al by fragment size and generated bigwig files by using the center 80bp of fragments and scale to 20 million nucleosome free reads. We observed good pattern that nucleosome tracks surrounding nucleosome free tracks and only provide nucleosome free tracks here.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig

growth_protocol: Tn cells were sorted from the lymphocytes isolated from male mice by CD4+GFP- CD25-CD44loCD62Lhi, then induced to iTreg cells with TCR agonists, IL-2, TGF-beta for 4 days in the presence or absence of 0.25mM ascorbic acid 2-phosphate. At the end of induction, live GFP+ cells were FACS sorted.

extract_protocol:
Sorted cells were harvested by centrifugation before being permeabilized for Tn5 transposition according to published protocols (PMID: 25559105).
Library was constructed according to published protocols (PMID: 25559105).

value: male

value: In vitro induced wild-type regulatory T cells

value: Ascorbic Acid


title: ChIP-seq_YD5_PolIICTD_AB1_ATMAPTX


title: ChIP-seq_YD4_PolIICTD_AB1_CNTRL

value: Control


title: ATAC iTr-AA2P, Replicate3


title: ATAC iTr-AA2P, Replicate1


title: scAH: Patient 32 scATAC-seq

description: ID: UVA069

value: Patient 32

value: Mixed ancestry


title: ChIP-seq_YD3_PolIICTD_AB1_CNTRL

value: Cerebellum


title: scAG: Patient 31 scATAC-seq

description: ID: UVA124

value: Patient 31


title: scAF: Patient 30 scATAC-seq

description: ID: UVA036

value: Patient 30

value: Coronary artery (RCA)


title: ChIP-1484799_iTr-STAT5 , Replicate 1

data_processing:
ChIP-seq data analysis: Single-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data, details and codes can be found in our previously publications(Yang, X. et al. Nat Neurosci. 2019).
After confirmed the quality were good, we extended reads to fragment size (detected by SPP v1.1) and generated bigwig tracks(normalized to 15M uniquely mapped reads) for visualization. We then called peaks using MACS2(version 2.1.1.20160309, parameters “--nomodel --extsize fragment size”).
Cut-and-Run data analysis: Paired-end reads of 50bp or 100bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5M fragments as suggested by Cut&Run protocols paper. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments.
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
A two-step protocol was used to fix the cells for Stat5 ChIP-seq as we previously described (PMID: 25126783). Cut&Run was performed according to a method recently described (PMID: 28079019).
Libraries were constructed according to standard protocols for ChIP or Cut&Run sequencing.

value: Mock

value: Stat5 (CellSignalingTechnology,94205)


title: ATAC iTr-noAA2P, Replicate3


title: Trophoblast organoid, EVT-differentiated CT30

city: Vancouver

first: Alexander

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

data_processing:
For all samples the 10X Genomics Cell Ranger version 3.0 software was used for read alignment by STAR and counting against the hg19 reference transcriptome, using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, three processed data files were generated as .tsv and .mtx files. These include one barcode file with cell barcode sequences that correspond to column indices, one feature file with gene counts that correspond to row indices, and one matrix file for the count matrix.

source_name: hTSC-derived trophoblast organoid

growth_protocol: Trophoblast organoid cultures were maintained in 100% growth-factor reduced matrigel submersed in trophoblast organoid media, as described in Shannon et al. 2021.

extract_protocol:
RNA from all samples was prepared using RiboZol reagent followed by Rneasy Mini Kit purification, following manufacturer protocol. RNA purity was confirmed by NanoDrop Spectrophotometry and integrity confirmed by Agilent BioAnalyzer. Only RNA with a RIN > 8.0 was used for sequencing.
Libraries were constructed using the 10X Genomics chromium single cell 3’ reagent v2 chemistry kit for all placental tissue samples and using the chromium single cell 3’ reagent v3 chemistry kit for all trophoblast organoid samples at a read depth of 50,000 reads/cell for placental villus samples and a read depth of 150,000 reads/cell for trophoblast organoid samples.
Single-cell RNA-seq

treatment_protocol: Trophoblast organoid differentiation into EVT was achevied by removing trophoblast organoid media, and replacing it with EVT differentiation media lacking CHIR99021 and R-spondin in the basal media

value: Trophoblast organoid

tag: gestational age

tag: culture day

tag: state

value: EVT-differentiated

tag: fetal sex

value: Female

tag: maternal age

tag: maternal bmi

tag: maternal smoking status

tag: maternal diabetes

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure

tag: sequencing batch


title: scAL: Patient 36 scATAC-seq

description: ID: UVA005

tag: subject

value: Patient 36

value: Coronary artery disease (CAD)

tag: tissue

tag: age

tag: Sex

value: female


title: ATAC iTr-noAA2P, Replicate2

tag: strain

value: male

tag: cell type

value: In vitro induced wild-type regulatory T cells

tag: treatment


title: Trophoblast organoid, Undifferentiated CT30

tag: cell line

tag: gestational age

tag: culture day

value: Regenerative


title: ChIP-seq_YD7_INPUT_ATMAPTX

source_name: Whole Cerebellum INPUT

tag: tissue type

tag: genotype

value: Atm Nes-cre; Aptx-/-

tag: antibody

value: input


title: scAE: Patient 29 scATAC-seq

description: ID: UVA015

value: Patient 29

tag: disease state

value: Coronary artery (LAD)

tag: ancestry

value: Asian


title: ChIP-seq_YD6_INPUT_ATMAPTX

value: Cerebellum


title: Trophoblast organoid, EVT-differentiated CT29

tag: state

tag: fetal sex

value: Male

tag: maternal age

tag: maternal bmi

tag: maternal smoking status

tag: maternal diabetes

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure


title: scAI: Patient 33 scATAC-seq

description: ID: UVA094

tag: subject

value: Patient 33

tag: tissue

tag: age

tag: Sex

value: European


title: scAD: Patient 28 scATAC-seq

description: ID: UVA080

value: Patient 28


title: Trophoblast organoid, Undifferentiated CT29

value: Trophoblast organoid

tag: cell line

tag: gestational age

tag: culture day

tag: sequencing batch


title: ChIP-seq_YD5_INPUT_ATMAPTX

tag: tissue type

tag: genotype

tag: antibody


title: ChIP-seq_YD4_INPUT_CNTRL

value: Control


title: ChIP-seq_YD2_PolIICTD_AB1_CNTRL

value: RNA Pol II


title: scAB: Patient 26 scATAC-seq

description: ID: UVA053

value: Patient 26

tag: disease state

value: Coronary artery disease (CAD)

value: female

tag: ancestry


title: ATAC-seq_ATAC69_C2_YD19_ATMAPTX_dKO_GranuleCell

data_processing:
Trim Galore (version 0.4.4) was used to trim 3’ adapters from ATAC-seq raw reads with a quality score cutoff of Q20
Then reads were aligned to the mouse reference genome (mm9) using BWA (version 0.7.12; default parameter)
Duplicate reads were marked and removed by Picard (version 1.65)
Only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1)
Mitochondrial reads were excluded from all downstream analysis
All mapped reads were offset by +4 bp for the + strand and -5 bp for the – strand
Finally, nucleosome free fragments (<100 bp) were extracted for calling peaks and generating bigwig file
Narrow peaks were called by MACS2 (version 2.2.7.1) with the following parameters; -q 0.01 -nomodel -extsize 200 -shift 100 -keep-dup all
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
Supplementary_files_format_and_content: BED

source_name: Granule Cell (Purified)

extract_protocol:
Nuclei were isolated according to Xu et. al., (2018), via minor modifications. Isolated  pooled cerebella tissue from 4 wild type mice were collected and snap frozen using liquid  nitrogen, and then thawed on ice for 30min. Cerebella were then transferred to 5ml of  homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH  pH 7.8, 0.15 mM spermine, 0.5 mM spermidine, 5 units EDTA-free protease inhibitor  cocktail, 1 mM DTT, 20 U/mL Superase-In RNase inhibitor, 40 U/mL RNasin ribonuclease  inhibitor) and homogenized by 30 strokes with a glass dounce homogenizer.  Subsequently, 4.6 ml of a 50% iodixanol solution (60% Iodixanol/Optiprep, 900 mM KCl,  30 mM MgCl2, 120 mM Tricine-KOH pH 7.8, 0.15 mM spermine, 0.5 mM spermidine, 4  units EDTA-free protease inhibitor cocktail, 1 mM DTT, 20 U/mL Superase-In RNase  inhibitor, 40 U/mL RNasin ribonuclease inhibitor) was added to tissue homogenates.  Tissue homogenates were then added to a cushion of 2 ml of 27% iodixanol solution in  the bottom of 13.2 ultraclear ultracentrifugation tube (Beckman Coulter; #41121703).  Ultracentrifugation was performed at 10,000 rpm for 45 min at 4°C to isolate nuclei in a  swinging bucket rotor (SW41) in a Beckman Coulter XL-70 ultracentrifuge.  Nuclei pellets were carefully resuspended with 500 ml of homogenization buffer  and fixed with 1 % formaldehyde for 8 min at room temperature. Fixation was stopped by  adding 0.125M glycine for 5 min. Then, fixed nuclei were centrifuged at 1000g, 4 min and  supernatant were discarded. Pellets were washed twice with wash buffer (PBS, 0.05%  TritonX-100, 50 ng/mL BSA, 1 mM DTT, 10 U/uL Superase-In RNase Inhibitor). Nuclei were blocked with blocking buffer (PBS, 0.05% TritonX-100, 50 ng/mL BSA, 1 mM DTT, 10 U/uL Superase-In RNase Inhibitor, and 50 ng/mL BSA) for 30 min. Then, nuclei were incubated with NeuN antibodies (Mouse; 1:250; Millipore, MAB377) and ITPR1 antibodies (Rabbit; 1:500; Invitrogen, PA1-901) for 16hrs at 4°C. Next day, nuclei were washed 3 times with wash buffer and secondary antibodies (1:500) for 30 min at room temperature. Alexa 594 [mouse; ab150116] and Alexa 488 [rabbit; ab150077] were used secondary antibodies. Right before flow cytometry sorting, nuclei were stained with 20uM final concentration of DyeCycle Ruby (Invtrogen; V10273) for 10min at room temperature. Cell type specific nuclei were independently collected using a BD Biosciences FACS Aria cell sorter, with excitation at 488nm, 561nm and 640nm. Gating on single nuclei using width  versus area signals for Dye Cycle Ruby was followed by gating of cell type specific nuclei based on NeuN and ITPR1 signals.
Flow sorted granule and Purkinje cell nuclei (5,000 each) were incubated for 10 min in nuclei lysis buffer (10 mM Tris-Cl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.05% NP-40), centrifuged for 5 min at 500g and resuspended in 50 ul of transposition reaction mix (25ul of 2xTD buffer, 2.5 ul of Nextera TDE1 enzyme [Illumina; #20034197], and 22.5ul nuclease-free water). The transposition reaction was incubated at 37°C for 30 min with mild shaking. Then, 200ul of reverse-crosslinking solution (50 mM Tris–Cl, 1 mM EDTA, 1% SDS, 0.2 M NaCl, 5 ng/ml proteinase K) was added to transposition reactants for overnight incubation at 65°C in a Thermomixer (Thermo Fisher) with shaking at 800rpm. DNA was then purified with QiaQuick MinElute columns (Qiagen; #28206). and amplified by PCR containing Q5 High Fidelity Polymerase (NEB; M0491S) for 12 cycles with ATACseq barcoded primers. PCR reaction conditions were 72°C for 5 min, 98°C for 30s, 12 cycles of (98°C for 10s, 63°C for 30s, and 72°C for 1 min), 65°C for 5 min, with a hold at 4°C. Amplified libraries were purified and size selected with AMPure XP beads (Beckman Coulter) and then sequenced on an Illumina HiSeq 4000, yielding 100bp paired-end reads.

value: Purified Granule Cells


title: ChIP-seq_YD3_INPUT_CNTRL


title: Trophoblast organoid, Undifferentiated CT27

tag: state

value: Regenerative

tag: fetal sex

value: Female

tag: maternal age

tag: maternal bmi

tag: maternal smoking status


title: ATAC-seq_ATAC69_C3_YD20_ATMAPTX_dKO_PurkinjeCell

source_name: Purkinje Cell (Purified)

value: Purified Purkinje Cells

value: Atm Nes-cre; Aptx-/-


title: scAA: Patient 25 scATAC-seq

description: ID: UVA050

tag: subject

value: Patient 25

tag: tissue

value: Coronary artery (LCX)

value: Pacific Islander


title: scAM: Patient 37 scATAC-seq

description: ID: UVA054

value: Patient 37

tag: age

tag: Sex


title: Placenta, Patient 899

source_name: Placenta

value: Fetal placenta

tag: cell line

tag: gestational age

value: Negative

tag: maternal diabetes

value: No

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure


title: Trophoblast organoid, EVT-differentiated CT27

value: Trophoblast organoid

tag: culture day

value: EVT-differentiated

tag: sequencing batch


title: ATAC-seq_ATAC68_C2_YD16_CNTRL_GranuleCell

tag: tissue type

tag: genotype

value: Control


title: ChIP-seq_YD2_INPUT_CNTRL

value: Cerebellum

tag: antibody

value: input


title: ATAC-seq_ATAC29_C2_ATMAPTX_dKO_WholeCB

source_name: Whole Cerebellum


title: scZ: Patient 24 scATAC-seq

description: ID: UVA058

value: Patient 24

tag: disease state

value: Coronary artery disease (CAD)

value: Coronary artery (LAD)

value: female

tag: ancestry

value: European


title: ChIP-Sequencing_YD7_PolIICTDS5p_AB1_ATMAPTX

data_processing:
The ChIP-seq raw reads were aligned to the mouse reference genome (mm9) using BWA (version 0.7.12; default parameter)
Duplicate reads were marked with Picard (version 1.65)
Only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’) were used for downstream analysis
R package SPP (version 1.11) was used to calculate relative strand correlation and estimate the fragment size
We used genomeCoverageBed (bedtools 2.25.0) to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig
The bigwig file was scaled by ChIP-seq library-size to allow comparison across samples and visualized by integrated genome viewer (IGV) (version 2.3.82).
MACS2 (version 2.1.1) was used to call RNA Pol II (pSer5) peaks by comparing the IP library file to input library file with default parameters and a FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig Files
Supplementary_files_format_and_content: Bed Files of Peak Calls

source_name: Whole Cerebellum PolIICTDS5p

extract_protocol:
Cerebellar tissues were collected from WT and AtmNes-cre;Aptx-/- mice (10-12 month old) for RNA Pol II p-Ser5 ChIP-seq. Frozen tissues were powdered, suspended in PBS containing 1% PFA to crosslink, pelleted and then washed with ice cold PBS containing protease inhibitor cocktail (Sigma, P8340). Chromatin was extracted in lysis buffer (0.25% Triton X-100, 1mM EDTA pH8.0, 140mM NaCl, 50mM HEPES pH7.9, 10% Glycerol, and 0.5% NP-40) and then washed (in 1mM EDTA pH8.0, 200mM NaCl, 10mM Tris HCl pH8.0, and 0.5mM EGTA pH 8.0). Chromatin was then sheared (in 0.1% SDS, 1mM EDTA pH8.0, and 10mM Tris HCl pH8.0) to generate DNA fragments of 200-500bp using a Covaris M220 sonicator (Covaris). RNA pol II CTD repeat YSPTSPS (phospho S5) antibody (5μg, Abcam, #ab5131) and Magna ChIPTM Protein A+G Magnetic Beads (20μl, Millipore, #16-663) were added to the chromatin and incubated overnight at 4°C. Beads were washed 1x with low salt ChIP wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH8.0 and 150mM NaCl), 1x with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH8.0 and 500mM NaCl) and 1x with LiCl wash buffer (1mM EDTA, 10mM Tris HCl pH8.0, 250mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and finally in TE buffer (1% SDS, 1mM EDTA and 10mM Tris HCl pH8.0). Immunoprecipitated DNA was eluted using (0.1 M NaHCO3/1% SDS) followed by addition of 4μl of 5M NaCl2 per IP to dissociate DNA-protein complexes and incubated at 65°C overnight.
For library preparation, immunoprecipitated DNA was quantified using the Quant-iT RiboGreen assay (Life Technologies). Libraries were prepared with HyperPrep Library Preparation Kits (Roche PN07962363001) and analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies,) 4200 TapeStation D1000 ScreenTape assay, or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies) or low pass sequencing with a MiSeq nano kit (Illumina).

value: Atm Nes-cre; Aptx-/-

tag: chip antibody

value: RNA pol II CTD repeat YSPTSPS (phospho S5) antibody (Abcam, #ab5131)


title: ATAC-seq_ATAC29_C1_CNTRL_WholeCB


title: scY: Patient 23 scATAC-seq

description: ID: UVA043

tag: subject

value: Patient 23

value: Asian


title: ChIP-Sequencing_YD6_PolIICTDS5p_AB1_ATMAPTX


title: Placenta, Patient 295

tag: tissue

value: Fetal placenta

tag: state

tag: fetal sex

value: Male

tag: maternal age

tag: maternal bmi

tag: maternal smoking status


title: ATAC iTr-noAA2P, Replicate1

tag: strain

tag: Sex

value: male

tag: cell type

value: In vitro induced wild-type regulatory T cells

tag: treatment

value: Mock


title: scX: Patient 22 scATAC-seq

description: ID: UVA016

value: Patient 22

value: Coronary artery (RCA)

tag: age


title: Placenta, Patient 244

tag: cell line

tag: gestational age

tag: culture day

value: Female

value: Negative

tag: maternal diabetes

value: No

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure

tag: sequencing batch


title: ATAC-seq_ATAC68_C3_YD17_CNTRL_PurkinjeCell

tag: tissue type

value: Purified Purkinje Cells

tag: genotype

value: Control


title: ChIP-Sequencing_YD5_PolIICTDS5p_AB1_ATMAPTX

value: Cerebellum

tag: chip antibody


title: scW: Patient 21 scATAC-seq

description: ID: UVA046

tag: subject

value: Patient 21

tag: disease state

value: Coronary artery disease (CAD)

tag: tissue

value: Coronary artery (LAD)

value: female

tag: ancestry

value: European


title: ChIP-Sequencing_YD4_PolIICTDS5p_AB1_CNTRL

value: RNA pol II CTD repeat YSPTSPS (phospho S5) antibody (Abcam, #ab5131)


title: ChIP-Sequencing_YD3_PolIICTDS5p_AB1_CNTRL


title: scV: Patient 20 scATAC-seq

description: ID: UVA030

value: Patient 20

tag: Sex

value: male


title: scU: Patient 19 scATAC-seq

description: ID: UVA040

value: Patient 19

value: Americas


title: KO_1

city: Davis

first: John

last: Yoon

state: CA

address: One Shields Avenue

institute: University of California Davis

data_processing:
All ChIP-seq libraries were sequenced on Illumina HiSeq 4000 (Illumina) with single-end 100 bp reads.
Sequencing reads were aligned to the UCSC mm10 using STAR.
Peaks were called using findPeaks in Homer.
Differential analysis was performed using EdgeR.
BigWig files were created using bedGraphToBigWig.
Genome_build: mm10

source_name: BAT

extract_protocol:
BAT tissues from Letmd1 KO and WT mice were dissected and processed for ChIP-sequencing using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) and Brg1 monoclonal antibody following manufacturer’s instructions.
Barcode-indexed sequencing libraries were generated with the KAPA Hyper DNA Library Prep Kit (Roche, KK8504) according to the manufacturer's protocol.

value: BAT

tag: strain

value: Letmd1 KO

value: anti-BRG1 [Cell Signaling Technology, Cat# 49360]


title: WT_2

value: WT


title: ChIP-Sequencing_YD2_PolIICTDS5p_AB1_CNTRL


title: Placenta, Patient 89

value: Fetal placenta

tag: state

tag: fetal sex

value: Female

tag: maternal age

tag: maternal bmi

tag: maternal smoking status

value: Negative

value: No


title: KO_2


title: WT_3


title: scT: Patient 18 scATAC-seq

description: ID: UVA017

value: Patient 18

value: Coronary artery disease (CAD)

value: Coronary artery (RCA)

tag: age


title: ChIP-Sequencing_YD7_INPUT_ATMAPTX

value: Cerebellum

value: Atm Nes-cre; Aptx-/-


title: Placenta, Patient 277

tag: cell line

tag: gestational age

tag: culture day

value: Male

tag: maternal diabetes

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure


title: WT_1

tag: genotype

tag: chip antibody


title: ChIP-Sequencing_YD6_INPUT_ATMAPTX

tag: tissue type


title: scS: Patient 17 scATAC-seq

description: ID: UVA057

tag: subject

value: Patient 17

tag: disease state

tag: tissue

tag: Sex

value: male

tag: ancestry


title: ChIP-Sequencing_YD5_INPUT_ATMAPTX


title: scQ: Patient 15 scATAC-seq

description: ID: UVA014

value: Patient 15

value: Coronary artery (LCX)

value: Asian


title: Placenta, Patient 130

tag: state

tag: fetal sex

tag: maternal age

tag: maternal bmi

tag: sequencing batch


title: KO_cold_3

city: Seoul

first: Kyung-Mi

last: Choi

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Chronic cold

data_processing:
The quality of raw reads were assessed using fastqc.
Ribosomal RNA content was determined by aligning the reads against a set of Mouse rRNA sequences using bowtie2 v.2.3.4.1.
Raw reads were processed and trimmed to remove phiX and adapter sequences, and to remove the first 20 bases from each read.
Processed reads were aligned to GRCm38.p6 primary genome assembly using GENCODE v21 annotation, with STAR v.2.7.0e, to generate counts per gene.
Tables of raw counts and counts-per-million (CPM) normalized counts were generated. Prior to analysis, genes with low expression (defined here as a those with mean CPM less than 0.3) were filtered, leaving 15,570 genes.  Differential expression analyses were conducted using the limma-voom Bioconductor pipeline
Supplementary_files_format_and_content: logFC

extract_protocol: Total RNA was extracted from BAT and purified using Zymo RNA clean & concentrate kit. The purified RNA was analyzed by using Bioanalyzer for quality control and used for library preparation.

tag: strain

value: BAT

value: Letmd1 KO

tag: condition

value: cold


title: KO_3

value: anti-BRG1 [Cell Signaling Technology, Cat# 49360]


title: KO_cold_2

description: Chronic cold


title: scAC: Patient 27 scATAC-seq

description: ID: UVA024

value: Patient 27

value: Coronary artery (LAD)

tag: age


title: Placenta, Patient 21

value: Fetal placenta

tag: cell line

tag: gestational age

tag: culture day

value: Female

tag: maternal smoking status

value: Negative

tag: maternal diabetes

value: No

tag: anti-hypertensive drug exposure

tag: anti-inflammatory drug exposure


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1176]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads  (Illumina) were aligned to reference genome hg38 (ENSEMBL) and Homo_sapiens.GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL) using STAR two-pass mode ( star 2.7).
GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL, release 98) was used for quantification, performed by RSEM 1.3.0, followed by TPM normalisation in RSEM-1.3.0.
Genome_build: hg38
Supplementary_files_format_and_content: output of rsem package: txt table with normalized counts
Supplementary_files_format_and_content: expected_count  TPM     FPKM

source_name: CD138+ cells

extract_protocol:
RNA extraction was performed using AllPrep Kit (Qiagen) according manufacturer instructions.
Library was generated using TruSeq RNA Exome Kit (Illumina) followed by sequencing on HiSeq2000 (Illumina).

tag: patient

value: Patient 1A

tag: group

value: relapse


title: ChIP-Sequencing_YD3_INPUT_CNTRL

first: Peter

last: McKinnon

tag: tissue type

value: Cerebellum

tag: genotype

value: Control


title: KO_cold_1

description: Chronic cold

tag: tissue


title: scP: Patient 6 scATAC-seq

description: ID: UVA066

tag: subject

value: Patient 6

tag: disease state

value: Coronary artery disease (CAD)

tag: Sex

value: male

tag: ancestry

value: European


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1881]

value: Patient 9A


title: scN: Patient 8 scATAC-seq

description: ID: UVA079

value: Patient 8

value: Coronary artery (RCA)

tag: age


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1938]

value: Patient 14A

value: diagnosis


title: KO_normal_3

description: Thermoneutrality

tag: strain

value: BAT

value: Letmd1 KO

tag: condition

value: normal


title: scO: Patient 14 scATAC-seq

description: ID: UVA023

value: Patient 14

value: Coronary artery (LCX)

value: female


title: ChIP-Sequencing_YD1_INPUT_CNTRL

value: Cerebellum


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1880]


title: scR: Patient 16 scATAC-seq

description: ID: UVA020

value: Patient 16

value: Asian


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM2103]

value: Patient 22A


title: KO_normal_1

description: Thermoneutrality


title: scM: Patient 13 scATAC-seq

description: ID: UVA045

value: Patient 13

value: Coronary artery disease (CAD)

value: male

value: Mixed ancestry


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM370]

value: Patient 1A


title: ChIP-Sequencing_YD1_IGG_AB5_CNTRL

source_name: Whole Cerebellum IGG

value: Control


title: scL: Patient 12 scATAC-seq

description: ID: UVA027

source_name: Coronary artery

value: Patient 12

value: Coronary artery (LAD)


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM2041]

value: Patient 16A

value: relapse


title: scK: Patient 11 scATAC-seq

description: ID: UVA064

value: Patient 11


title: ChIP-Sequencing_YD4_INPUT_CNTRL


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1989]

value: Patient 14A


title: WT_cold_2

description: Chronic cold

value: BAT

value: wildtype

value: cold


title: Saline 2

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: GRCm38
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

source_name: Mediobasal hypothalamus

extract_protocol:
Mice were euthanized, the hypothalamus was dissected, nuclei were isolated and cleaned using FACS, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression

treatment_protocol: Saline or insulin

tag: treatment

value: Saline


title: WT_cold_3

description: Chronic cold


title: ChIP-Sequencing_YD2_INPUT_CNTRL

value: Cerebellum


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM1958]

value: diagnosis


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells [MM2104]

value: Patient 22A


title: Insulin 2

value: Insulin


title: KO_normal_2

description: Thermoneutrality

value: Letmd1 KO

value: normal


title: scJ: Patient 10 scATAC-seq

description: ID: UVA068

value: Patient 10

value: Coronary artery disease (CAD)

value: female

value: African


title: WT_cold_1

description: Chronic cold


title: Insulin 1


title: scI: Patient 9 scATAC-seq

description: ID: UVA009

value: Patient 9

value: Coronary artery (RCA)

value: male

value: European


title: WT_normal_3

description: Thermoneutrality

value: BAT

value: wildtype


title: RMRP_SHAPE_70AG_TREATED_4

city: Edinburgh

first: Nic

last: Robertson

address: Swann Building, Max Born Crescent

department: Tollervey Lab

institute: University of Edinburgh

description:
SHAPE-MaP profile of 70AG RMRP
70AG_RMRP_4_RMRP_profile.txt

data_processing:
For each sample, modified vs. untreated files were analysed with ShapeMapper 2.1.5, using the following options: --target <RMRP.fa OR RMRP70A.fa> --amplicon --overwrite --modified --R1 <modified_read1> --R2 <modified_read2> --untreated -- R1 <untreated_read1> --R2 <untreated_read2>
Genome_build: RMRP sequences were aligned to NBCI sequence NR_003051.3 for wildtype cells, or this reference sequence adapted to include the a 71A->G mutation for mutant cells. Prior literature refers to this mutation as 70AG based on previous reference sequences, and we use 70AG for consistency in the paper.
Supplementary_files_format_and_content: For each modified/untreated pair, the ShapeMapper RNA profile is provided. This a tab-delimited text file, with columns as described at: https://github.com/Weeks-UNC/shapemapper2/blob/master/docs/file_formats.md. Also provided are PDFs showing the mapped death and graphs of per-nucleotide SHAPE reactivity.

source_name: K562 (70AG mutant clone F)

growth_protocol: Wildtype or CRISPR-generated RMRP 70->G K562 cells were grown in RMPI with 10% FBS, to a density of 0.5-0.7 x 10^6 cells / mL.

extract_protocol:
Total RNA was extracted using Trizol, following manufacturer’s phase separation protocol.
RNA was reversed transcribed using an RMRP specific RT primer (5’-ACAGCCGCGCTGAGA-3’). Two sequential PCRs were then performed to ligate adaptors for sequencing.

treatment_protocol: For treated samples, 1M7  (Sigma; cat. 908401) dissolved in DMSO was added to a final concentration of 10 mM. For untreated samples, the same volume of DMSO was used. In-cell acylation reaction left to proceed for 15 minutes at 37 degrees.

value: RMRP 70AG


title: Saline 1

value: Saline


title: chronic NB73 MCF7-R.2

first: Yvonne

last: Ziegler

description: chronic NB73

data_processing:
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36)
Reads were mapped to the Homo sapiens reference genome from Ensembl database (GRCh37) and aligned using the STAR alignment tool (Version 2.5.3)
Read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized expressions and differentially expressed genes

source_name: MCF-7 cells

extract_protocol:
RNA was extracted using Trizol protocol, followed by DNase treatment.  RNA was then re-purified with an aqueous column-based protocol followed by gel analysis to analyze purity and quality of the RNA.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.
* The libraries were quantitated by qPCR and sequenced on two lanes for 101 cycles from one end of the fragments on a HiSeq 4000
using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

tag: cell line


title: scG: Patient 7 scATAC-seq

description: ID: UVA083

value: Patient 7

value: Coronary artery (LCX)


title: sclamina-1

city: Los Angeles

first: Ying

last: Lin

state: California

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

data_processing:
bulk ATAC-seq: Raw fastq reads files were mapped to FlyBase reference genome (release 6.29) using Bowtie2 (2.2.9) and uniquely mapped genes were kept. All samples were pooled together prior to peak calling. Read start positions were shifted +4 or -5bp and used for peak calling using MACS2 (2.1.1) with parameters “-q 0.01 --nomodel --shift -100 --extsize 200”. Then bedtools multicov (2.27.1) was used to sum the total reads within each peak separately for each sample. Peaks with CPM ≥ 4 were used for counts normalization with edgeR.
bulk RNA-seq: fastq files were mapped to FlyBase reference genome (release 6.29) using STaR (2.6.0) and only uniquely mapped reads were collected. Genes with counts per million (CPM) ≥ 4 in more than 2 samples were used for normalization with R package edgeR (3.26.8). Gene expression was quantified using RPKM units (Reads Per Kilobase of exon per Million reads mapped), calculated based on reads in the sum of exons using customized scripts.
single cell RNA-seq: Fastq files were processed using Cell Ranger (3.1.0) pipeline using default parameters. Reference transcriptome package for Cell Ranger was generated using Drosophila melanogaster genome sequence and gene annotations from FlyBase (release 6.29). DGRP samples were demultiplexed based on parental genotypes using demuxlet (version 2).Downstream analysis including cell-type clustering was performed using Seurat package (3.1.2).
Genome_build: FlyBase 6.29
Supplementary_files_format_and_content: Bulk RNA-seq and bulk-ATAC-seq: abundance measurements in excel sheets; single cell RNA: cell-type cluster and counts in Seurat object.

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Maintenance and rearing of fly lines, as well as staging of pupae was done as described in Tan et al 2015

extract_protocol:
FACS-sorted cell suspension
Single cell RNA-seq: FACS-sorted cell suspension were loaded on 10X Genomics Chromium machine for single cell prepration. Single-cell RNA-Seq libraries were generated using Chromium Single Cell Reagent Kit V3 according to the manufacturer's protocol. Bulk RNA-seq: FACS sorted cell suspension were used for library prepration with SMART-seq2 protocol published by Picelli et al, 2014. Bulk ATAC-seq: FACS sorted cell suspension were used to library prep with modified protocol published by Buenrostro et al., 2013

value: brain

tag: cell type

value: FACS-sorted lamina neurons (L1-L5)


title: RMRP_SHAPE_70AG_UNTREATED_3

description:
SHAPE-MaP profile of 70AG RMRP
70AG_RMRP_3_RMRP_profile.txt

source_name: K562 (70AG mutant clone C)

value: DMSO


title: 1163351_iTregAA2P2

city: Memphis

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hosipital

source_name: In vitro induced wild-type regulatory T cells (ascorbic acid treated)

tag: gender


title: sclamina-2


title: RMRP_SHAPE_WT_UNTREATED_2

description:
SHAPE-MaP profile of wildtype RMRP
Wildtype_RMRP_2_RMRP_profile.txt

source_name: K562 (parental line)

value: Wildtype


title: Sun1

source_name: Hypothalamus

extract_protocol:
Mice were euthanized, the hypothalamus was dissected, nuclei were isolated and enriched using FACS, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression


title: 1163349_Te2

source_name: Wild-type CD4 effector T cells

value: Wild-type CD4 effector T cells


title: RMRP_SHAPE_WT_TREATED_2


title: RMRP_SHAPE_70AG_TREATED_2

description:
SHAPE-MaP profile of 70AG RMRP
70AG_RMRP_2_RMRP_profile.txt

source_name: K562 (70AG mutant clone H)


title: RMRP_SHAPE_70AG_TREATED_3


title: scH: Patient 8 scATAC-seq

description: ID: UVA079

extract_protocol:
Frozen coronary artery segments were broken down using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Nuclei were washed and resuspended in 1X concentration Nuclei Buffer for single cell ATAC sequencing
Libraries were constructed according to the 10x Genomics Chromium Single Cell ATAC Reagent Kit protocol (v1 and v1.1 (Next GEM)). Each GEM (gel bead in emulsion) contains a unique 16 nucleotide 10x Barcode sequence. The sample index PCR step during library construction adds a P7 sequence and sample index barcode to each scATAC library. The amplified scATAC libaries contain the 16 nt 10x cell barcode, 8 nt sample index barcode, and P5 and P7 sequences necessary for Illumina sequencing bridge amplification. All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-atac.

value: Patient 8

value: Coronary artery disease (CAD)


title: WT_normal_1

description: Thermoneutrality

value: normal


title: WT_normal_2

description: Thermoneutrality


title: scF: Patient 6 scATAC-seq

description: ID: UVA066

value: Patient 6


title: scHr3RNAi-1


title: 1119043_Te1

extract_protocol:
Genomic DNA was prepared from sorted cells with proteinase K digestion followed by phenol:chloroform:isoamyl alcohol extraction and 2-propanol precipitation.  More than 100ng of genomic DNA in each sample was converted by EpiTect Bisulfite Kits (Qiagen).
Libraries were prepared from converted DNA using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences)

value: male


title: RMRP_SHAPE_WT_TREATED_3

description:
SHAPE-MaP profile of wildtype RMRP
Wildtype_RMRP_3_RMRP_profile.txt


title: scE: Patient 5 scATAC-seq

description: ID: UVA007

value: Patient 5

value: Coronary artery (RCA)

value: European


title: scHr3RNAi-2


title: 1163350_iTreg2

source_name: In vitro induced wild-type regulatory T cells (control)


title: scEcRRNAi-1

value: EcRRNAi


title: scD: Patient 4 scATAC-seq

description: ID: UVA049

value: Patient 4

value: Coronary artery (LAD)


title: RMRP_SHAPE_70AG_UNTREATED_2

value: RMRP 70AG


title: scC: Patient 3 scATAC-seq

description: ID: UVA108

value: Patient 3

value: Asian


title: 1119041_Treg1

source_name: Wild-type regulatory T cells

value: Wild-type regulatory T cells


title: RMRP_SHAPE_70AG_UNTREATED_1

description:
SHAPE-MaP profile of 70AG RMRP
70AG_RMRP_1_RMRP_profile.txt

value: DMSO


title: scA: Patient 1 scATAC-seq

description: ID: UVA019

value: Patient 1


title: scEcRRNAi-2

value: brain

value: FACS-sorted lamina neurons (L1-L5)


title: scB: Patient 2 scATAC-seq

description: ID: UVA067

value: Patient 2

value: Coronary artery disease (CAD)

value: Pacific Islander


title: RMRP_SHAPE_70AG_TREATED_1


title: scEcRDN-1

value: EcRDN


title: scEcRDN-2


title: 1163347_Tn2

source_name: Wild-type naive CD4 T cells

value: Wild-type naive CD4 T cells

value: male


title: RMRP_SHAPE_WT_UNTREATED_1

description:
SHAPE-MaP profile of wildtype RMRP
Wildtype_RMRP_1_RMRP_profile.txt

value: Wildtype


title: 1163348_Treg2


title: RMRP_SHAPE_WT_TREATED_1


title: bort_3h_4

city: Mexico City

first: Luis

middle: Alonso

last: Herrera Montalvo

state: Mexico City

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan

department: Unidad de Investigacion Biomedica en Cancer

country: Mexico

institute: Instituto Nacional de Cancerología / Instituto Nacional de Medicina Genómica

description:
17W
total RNA (ribosomal RNA depleted)

data_processing:
Raw sequencing reads were checked for quality with fastqc, adapter removal and quality trimming was performed with cutadapt version 1.18 with parameters --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Mapping to the genome (assembly hg38) was performed with STAR aligner (1) version 2.7.1a with special parameters winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for multimapping reads.
Gene and subfamily repetitive elements quantification was performed with TEcount (version 2.1.3), part of the TEtranscripts package, using gencode v34 annotations for genes and the provided curated repeat annotations for hg38 found in (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF
Genome_build: hg38
Supplementary_files_format_and_content: tab separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts hg38 repeat ids)

source_name: Colorectal cancer

growth_protocol: HCT-116 cells (human colon cancer, ATCC CCL-247) were grown in 10% FBS supplemented McCoy's 5A medium at 37°C in 5% CO2 at 95% humidity and subcultured according to the supplier’s instructions.

extract_protocol:
After treatment, cells were washed with PBS, and RNA was extracted with TRIzol (Ambion, 15596018, Carlsbad, CA) according to the manufacturer’s instructions. DNA was digested with a TURBO DNA-Free kit (Ambion, AM1907, Vilnius, Lithuania) according to the manufacturer’s instructions.
TruSeq Stranded Total RNA Library Prep

treatment_protocol: A total of 1.3 x 104 cells per cm2 were seeded on 6-well plates, 24 h before the experiment. We synchronized cells (except the asynchronous controls) with a single, 16 h, 2 mM thymidine block (Sigma T1895, product of China) to obtain G1 cells. The cultures were subsequently incubated in fresh medium for 7 h to obtain G2/M cells. Once synchronized, the cells were treated for 3 h with the indicated drug or drug combination. The drug concentrations were the following: 50 µg/ml α-amanitin (Sigma A2263, product of Germany), 20 µM MG132 (Sigma C2211, product of Israel), and 100 nM bortezomib (Selleckchem, S1013).


title: 1119042_Tn1


title: bulkRNA-L1-72-1

description: L1 bulk RNA-seq expression.xlsx

value: FACS-sorted L1 neurons

value: wild type


title: bort_3h_2

description:
6P
total RNA (ribosomal RNA depleted)


title: KP3

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

data_processing:
Read trimming (Trimmomatic 0.38)
Alignment into chrimeric genome (STAR 2.6.0a)
Summation (featureCounts, subread 1.6.3)
Genome_build: Homo sapiens (release 94) and Klebsiella pneumoniae (ENSEMBL, release 41)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for six libraries

organism:
Klebsiella pneumoniae
Homo sapiens

source_name: Confluent human epithelial cell line (A549) co-incubated with Klebsiella pneumoniae

growth_protocol: Human epithelial cell line was cultured with no antibiotics into confluence, confluence was maintained for 10 more days before experiment

extract_protocol:
Total RNA isolation based on phenol-chloroform, gDNA treatment using RNase-free DNase
RNA libraries were prepared for sequencing using standard Illumina protocols with rRNA depletion

treatment_protocol: Klebsiella pneumoniae culture was co-incubated into the epithelial cells

value: wildtype strain

tag: human cell line


title: KP4

value: OmpR deletion strain


title: bulkRNA-L1-60-3

description: L1 bulk RNA-seq expression.xlsx


title: bort_3h_3

description:
2Q
total RNA (ribosomal RNA depleted)


title: bort_3h_1

description:
16O
total RNA (ribosomal RNA depleted)


title: KP5


title: bulkRNA-L1-60-2

description: L1 bulk RNA-seq expression.xlsx


title: Ctrl_0h_4

description:
1Q
total RNA (ribosomal RNA depleted)


title: bulkRNA-L1-60-1

description: L1 bulk RNA-seq expression.xlsx


title: Adult Epcam Negative Mouse Cochlea

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: After mincing with a scalpel and washing in PBS, the tissue was incubated in thermolysin (Sigma-Aldrich) at 37°C for 20 minutes. It was then transferred to Accumax (Innovative Cell Technologies) for 35 minutes, with trituration every 5-10 minutes. The dissociated tissue was diluted in PBS with 10% FBS and filtered through a 40 μm cell strainer. Cells were pelleted and dead cells and debris removed using the Dead Cell Removal Kit (Miltenyi Biotec) following the manufacturer’s instructions. When indicated, Epcam positive cells were next enriched in one fraction using CD326 (EpCAM) MicroBeads, mouse (Miltenyi Biotec).

data_processing:
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
the output matrix files are here and are included for postprocessing for R analysis
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
Genome_build: Genome_build: mm10 for mouse, and hg19 for human

source_name: cochlea

extract_protocol:
Cells were loaded onto the Chromium Controller from 10x Genomics for single cell capture.
10x Chromium

value: cochlea

value: Swiss Webster

tag: developmental stage

value: Adult (6 weeks old)

value: wildtype


title: Adult Epcam Positive v2 Mouse Cochlea


title: KP2


title: G2_0h_4

description:
13O
total RNA (ribosomal RNA depleted)


title: bulkRNA-L1-40-2

description: L1 bulk RNA-seq expression.xlsx

value: brain


title: P2 Mouse Cochlea

description: Mice were maintained under approval from the Institutional Animal Care and Use Committee at the University of California, San Francisco. The tissue was minced with a scalpel, collected in PBS, and pelleted by centrifugation. It was dissociated in TrypLE Select  (Life Technologies) at 37°C with trituration every five minutes. Once the tissue was dissociated (10-30 minutes), HBSS supplemented with 10% FBS and 2 mM EDTA was added and the suspension was passed through a 30 μm cell strainer. Cells were pelleted and then incubated with SYTOX Blue dead cell stain (Thermo Fisher Scientific) at a 1:1000 dilution for twenty minutes on ice. Cells were washed and then FACS used to collect only live cells. These cells were counted on a Moxi Flow (ORFLO Technologies) and resuspended at 1000 cells/μL in 0.04% BSA in PBS for single cell capture.

value: Embryonic P2 days


title: Adult Epcam Positive Mouse Cochlea