title: adult_R848

status: Public on Dec 31 2022

city: Aachen

first: Mathias

middle: W.

last: Hornef

address: Steppenbergallee 203

department: Medical Microbiology

institute: RWTH Áachen University

description: Cells were pooled from 4 mice.

data_processing:
Cell Ranger Software (Version 6.0.1) was used to process sequencing data
Seurat (Version 3.1.0) was used to integrate data
mm10
Genome_build: matrix: In hdf4 format. The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.
Supplementary_files_format_and_content: Molecule Info: The cellranger pipeline outputs an HDF5 file containing per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file 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: Summary : The cellranger pipeline outputs a summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. Rarely, an issue may also be detected during the pipeline run leading to an alert also appearing on this page, and more information about these is provided in the troubleshooting documentation.
Supplementary_files_format_and_content: Fig1_PND11VsAdult_withCorrectedAnnotations.rds is the R-object for generating Fig1 from the paper.
Supplementary_files_format_and_content: Fig6_R848_PND11vsAdult_withCorrectedAnnotations.rds is the R-object for generating Fig6 from the paper.
Supplementary_files_format_and_content: Figures_Natalia.et.all.html is the html file that contains aforementioned UAMPs (without the Pseudotime plots).

source_name: Peyer's patch

extract_protocol: Single Cell 3′ Reagent Kits (v2) User Guide (manual part no. CG00052, Rev D). All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://suppo

treatment_protocol: Peyer's patches were excised, enzymatically digested and mononuclear phagocytes  were MACS enriched using CD11c magnetic microbeads. Finally, the cells of interest were FACS sorted as CD11c+MHCII+CD45+live+IgA-TCRb-.

value: 8h post R848 gavage (0.4ug/g body weight)

tag: celltype

value: CD11c+MHCII+CD45+live+IgA-TCRb-  (mononuclear phagocytes)

tag: strain


title: adult_PBS

type: SRA

country: Germany

description: Cells were pooled from 4 mice.

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: treatment

value: 8h post PBS gavage


title: C097

status: Public on Jan 19 2023

type: RNA

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from human leukocytes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

molecule: total RNA

organism: Homo sapiens

source_name: leukocytes, whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: A total of 0.5 - 1.5 mL of whole blood were used for white blood cells (WBC) RNA extraction using the QIAamp RNA Blood Mini kit (Qiagen).

treatment_protocol: Whole blood samples were collected during hospitalization (average of 14 days after symptoms) or from volunteers (average of 9 days after symptoms). Whole blood was collected in an EDTA-containing tube as storage in maximum 6 hours for RNA extraction and plasma separation.

tag: gender

value: Male

tag: age (yr)

tag: group

value: Severe

tag: comorbidity

value: Pneumopathy


title: PND11_PBS

description: Cells were pooled from 1 litter (5-8 pups).


title: adult_1

description: Cells were pooled from 4 mice.

value: untreated


title: adult_2

description: Cells were pooled from 4 mice.


title: Med1_KO_3

status: Public on Jan 03 2023

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern Medical Center

data_processing:
Demultiplexed mRNA seq reads were  mapped  to  the  mm10 version of the mouse reference genome using STAR methods (v2.7.3a)  and  subsequent analyses  were  performed  using  samtools  (v1.6)  and  BEDtools  (v  2.29.2).
Per-transcript expression was quantified as RPKMs using featureCounts from the subread(v.1.6.3) package.
Bigwig files were generated using deeptools (v.3.5.0) with the following parameters -bs 50 --normalizeUsing CPM
Assembly: mm10
Supplementary files format and content: Bigwig files

growth_protocol: 3T3-L1 cells (ATCC CL-173) were cultured in full medium (DMEM (FisherScientific 11995) supplemented with 10% FBS (Sigma F0926), 1x GlutaMAX (FisherScientific 35050), 1x Penicillin-Streptomycin (FisherScientific 15140)). 293T cells were grown in full medium on plates coated with 0.001% poly-L-lysine (Sigma P4832).

extract_protocol:
RNA was extracted with RNeasy Plus Mini Kit (Qiagen 74136)
Samples are run on the Agilent 2100 Bioanalyzer to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher). The Qubit fluorometer is used to determine the concentration prior to staring library prep. 4 µg of total DNAse treated RNA are then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents."

treatment_protocol:
Adipocyte differentiatiton: Cells were grown to 100% confluence and then maintained for two days prior to initiating differentiation. Differentiation was induced by treatment with full medium supplemented with 0.5mM IBMX (Sigma I7018), 1μM dexamethasone (Sigma D1881), 5μg/ml insulin (Sigma I5500), 5μM troglitazone (Sigma T2573). Cells were treated with this differentiation medium for three days.
siRNA knockdown: 6 wells of 3T3-L1 cells at approximately 60% confluency were transfected with 30pmol of the indicated Dharmacon siRNAs using Lipofectamine RNAiMAX transfection reagent (FisherScientific 13-778-075) according to the manufacturer’s instructions. 48h post transfection, cells were treated with differentiation medium as described above for three days prior to harvesting for RNA extraction.
CRISPR editing: 6 wells of 293T cells (ATTC CRL-3216) at approximately 50% confluency were transfected with 3.3μg LentiCRISPR V2 (Addgene plasmid #52961) containing an sgRNA targeting exon 2, exon 3, or exon 17 of Med1, together with 2μg psPAX2-GAG-Pol-Rev (Addgene plasmid #12260), 0.85μg pAdVAntage (Promega E1711), and 1.3μg pCMV-VSV-G (Addgene plasmid #8454) using Lipofectamine 3000 transfection reagent FisherScientific L3000015) according to the manufacturer’s instructions. A LentiCRISPR V2  plasmid  containing  a  non-targeting  sgRNA  was  transfected  as  a  control. At  48-and  72-hours  post-transfection,  culture  medium containing  virus  was  collected  and passed  through  a  45μm  PVDF filter  onto  6  wells of 3T3-L1  cells  at  approximately  50%  confluency.  48h  after  the  second  addition  of  virus, infected 3T3-L1cells were selected using 2μg/ml puromycin (FisherScientific A11138), expanded, and frozen for future  use.  Med1  knockout and  Med1ΔIDR  cell  lines  were validated  by  probing  cell  extracts  for  MED1  protein  expression  using  an  antibody (Invitrogen, PA5-36200) that binds to an epitope located in Med1ΔIDR too and is found in the N-terminal domain of MED1.

tag: cell line

tag: cell type

value: mouse fibroblast

tag: genotype

value: adipogenic differentiation

tag: time

value: Day 3


title: DNMT3A GT Donor ATAC processed genomic DNA

status: Public on Dec 20 2022

city: Palo Alto

first: Jayakrishnan (Jk)

last: Gopakumar

state: CA

address: 240 Pasteur Dr Rm 4600

institute: Stanford

description: binary version of tab-delimited text file that contains sequence alignment data

library_source: genomic

data_processing:
Reads were trimmed and filtered using fastp and mapped to the hg38 reference genome using hisat2 with the --no-spliced-alignment option. Bam files were deduplicated using Picard. Only reads mapping to chromosomes 1-22 and chrX were retained -- chrY reads, mitochondrial reads, and other reads were discarded. Genome track files were created by loading the fragments for each sample into R, and exporting bigwig files normalized by reads in transcription start sites using `rtracklayer::export`. Coverage files were visualized using the Integrative Genomics Viewer.
Assembly: GRCh38
Supplementary files format and content: bigWig files

molecule: genomic DNA

source_name: Hematopoietic Cells

growth_protocol: Lin- CD34+ CD38- CD45RA- cells were sorted from the electroporated TET2 KO CD34+ cells using a BD FACS Aria III. Cells were allowed to culture for 5 days in HSPC media.

extract_protocol:
On Day 5 40,000 cells were harvested, and bulk Omni-ATAC was performed
Cells were lysed with ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 3 minutes, and then the transposition was performed for 30 minutes at 37 C using 100 nM of Illumina Tagment DNA TDE1 Enzyme and Buffer Kit per 50,000 cells. The fragmented DNA was then cleaned up using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014). The transposed fragments were amplified and indexed using NEBNext 2x Master Mix. The final PCR product was purified using the Zymo DNA Clean and Concentrator-5 Kit.
OMNI-ATAC

tag: tissue

value: Hematopoietic Cells

value: In vitro cultured CD34+

tag: condition

value: GT Donor DNMT3A Edited


title: DNMT3A GG Donor ATAC processed genomic DNA

value: GG Donor DNMT3A Edited


title: AAVS TT Donor ATAC processed genomic DNA

value: TT Donor AAVS Edited


title: AAVS GT Donor ATAC processed genomic DNA

value: GT Donor AAVS Edited


title: DNMT3A TT Donor ATAC processed genomic DNA

value: TT Donor DNMT3A Edited


title: AAVS GG Donor ATAC processed genomic DNA

value: GG Donor AAVS Edited


title: Med1_delIDR_1

value: Med1_IDR deletion


title: TET2 TT Donor ATAC processed genomic DNA

description: raw data format: binary version of tab-delimited text file that contains sequence alignment data

extract_protocol:
On Day 5 40,000 cells were harvested, and bulk Omni-ATAC was performed
Cells were lysed with ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 3 minutes, and then the transposition was performed for 30 minutes at 37 C using 100 nM of Illumina Tagment DNA TDE1 Enzyme and Buffer Kit per 50,000 cells. The fragmented DNA was then cleaned up using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014). The transposed fragments were amplified and indexed using NEBNext 2x Master Mix. The final PCR product was purified using the Zymo DNA Clean and Concentrator-5 Kit.

value: TT Donor TET2 Edited


title: TET2 GT Donor ATAC processed genomic DNA

value: GT Donor TET2 Edited


title: TET2 GG Donor ATAC processed genomic DNA

value: GG Donor TET2 Edited


title: PND11_R848

value: 8h post R848 gavage (0.4ug/g body weight)

value: CD11c+MHCII+CD45+live+IgA-TCRb-  (mononuclear phagocytes)


title: pbmc5

status: Public on Dec 15 2022

city: st louis

first: andrew

last: malone

state: MO

address: 4525 laclede ave

institute: Washington University

description:
single cell RNA-seq
TWDO-68-68_PBMC-lib1_S2_L002

data_processing:
scRNA-seq: The Illumina HiSeq platform was used to generate paired end read sequence (2x150) on the S4 flow cell to a depth of 50,000 reads per cell for gene expression and 5,000 reads per cell for VDJ sequence. The Cellranger 3.0 pipeline was used to generate BAM files and gene expression matrices for each biopsy. Matrices were used to generate Seurat objects using Seurat v3
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix

source_name: peripheral blood

extract_protocol:
Ficol gradient used for separation of PBMCs from blood
cDNA libraries were prepared per 10X Chromium standard protocol usig 5-prime kits

tag: tissue source

value: kidney transplant biopsies

value: peripheral blood

tag: days post transplant that the blood sample was taken


title: pbmc4

description:
single cell RNA-seq
TWDO-67-67_PBMC-lib1_S1_L004


title: pbmc1

description:
single cell RNA-seq
TWDO-62-62_PBMC-lib2_S3_L003


title: sgSTING_2

status: Public on Dec 12 2022

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: IMR90 E6E7 sgSTING, Experiment 3

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the hg19 genome assembly using STAR v2.5.3a
Reads were annotated to genes using Homer v4.10
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Normal lung tissue

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen #15596018) and purified with RNAeasy Mini Kit (Qiagen #74106). The quality of the isolated total RNA was assessed using Agilent TapeStation 4200.
Libraries were prepared with 500ng total RNA using the TruSeq stranded mRNA sample preparation kit according to the manufacturer’s protocol (Illumina). RNA-seq libraries were multiplexed, normalized, and pooled for sequencing. The libraries were sequenced on the HiSeq 4000 system (Illumina) at single read 50bp or NextSeq 500 system (Illumina) at single read 75bp.

value: Normal lung tissue

value: Human Papillomavirus E6 and E7, sgSTING

value: STING-targeting gRNA


title: pbmc3

description:
single cell RNA-seq
TWDO-65-65_PBMC-lib1_S7_L004


title: sgSTING_3

description: IMR90 E6E7 sgSTING, Experiment 3


title: PND11_1

value: untreated


title: PND11_2


title: pbmc2

description:
single cell RNA-seq
TWDO-64-64_PBMC-lib2_S6_L003


title: VP16_ZBP1 mutant_2

description: VP16-TRF1(DN)-ZBP1(S)DZa2-Flag, Experiment 2

value: Human Papillomavirus E6 and E7; VP16-TRF1(DN)-ZBP1(S)DZa2-Flag

value: Doxycycline


title: TRF1_ZBP1 mutant_2

description: TRF1(DN)-ZBP1(S)DZa2-Flag, Experiment 2

value: Human Papillomavirus E6 and E7; TRF1(DN)-ZBP1(S)DZa2-Flag


title: VP16_ZBP1 mutant_1


title: sgMAVS_2

description: IMR90 E6E7 sgMAVS, Experiment 3

value: Human Papillomavirus E6 and E7; sgMAVS

value: MAVS-targeting gRNA


title: sgMAVS_1

description: IMR90 E6E7 sgMAVS, Experiment 3


title: TRF1_ZBP1 mutant_3

description: TRF1(DN)-ZBP1(S)DZa2-Flag, Experiment 2


title: VP16_ZBP1 mutant_3


title: VP16_ZBP1 WT_1

description: VP16-TRF1(DN)-ZBP1(S)WT-Flag, Experiment 2

value: Human Papillomavirus E6 and E7; VP16-TRF1(DN); ZBP1(S)WT-Flag


title: VP16_ZBP1 WT_3


title: IP_ZBP1WT_TRF2_2

description: IP - shTRF2 - IMR90 E6E7 ZBP1(S)WT-Flag, Experiment 4 rep2

data_processing:
Basecalls were generated using CASAVA v1.8
Data quality was assessed using FastQC v0.11.8
Sequenced reads were aligned to the human subtelomere assembly using STAR v2.5.3a
Library sizes were normalized to 1 x 10^7 for comparison and the log2 ratio of enrichment of IP vs input was calculated at each base in the subtelomere using HOMER v4.10 and the assembly available of human subtelomeres (http://www.wistar.org/lab/harold-c-riethman-phd/page/subtelomere-assemblies)
Assembly: hg19 WISTAR subtelomeric assembly
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen #15596018) and purified with RNAeasy Mini Kit (Qiagen #74106). The quality of the isolated total RNA was assessed using Agilent TapeStation 4200.
Sequencing libraries were prepared with immunoprecipitated RNA using the TruSeq stranded total RNA sample preparation kit according to the manufacturer’s protocol (Illumina). RNA-seq libraries were multiplexed, normalized, and pooled for sequencing. The libraries were sequenced on the MiniSeq system (Illumina) at paired-end read 37bp.

value: Human Papillomavirus E6 and E7; ZBP1(S)WT-Flag

value: TRF2-targeting shRNA


title: VP16_ZBP1 WT_2


title: TRF1_ZBP1 WT_3

description: TRF1(DN)-ZBP1(S)WT-Flag, Experiment 2

value: Human Papillomavirus E6 and E7; TRF1(DN); ZBP1(S)WT-Flag


title: TRF1_ZBP1 mutant_1

description: TRF1(DN)-ZBP1(S)DZa2-Flag, Experiment 2


title: TRF1_ZBP1 WT_1

description: TRF1(DN)-ZBP1(S)WT-Flag, Experiment 2

value: No treatment


title: input_ZBP1WT_TRF2_1

description: Input - shTRF2 - IMR90 E6E7 ZBP1(S)WT-Flag, Experiment 4 rep1


title: input_ZBP1WT_TRF2_2

description: Input - shTRF2 - IMR90 E6E7 ZBP1(S)WT-Flag, Experiment 4 rep2


title: LT_PD87_JT21

description: WI38 SV40LT crisis, Experiment 1

value: Simian virus 40 large T antigen


title: sgGFP_3

description: IMR90 E6E7 sgGFP, Experiment 3

value: Human Papillomavirus E6 and E7; sgGFP

value: GFP-targeting gRNA


title: IP_ZBP1WT_TRF2_1

description: IP - shTRF2 - IMR90 E6E7 ZBP1(S)WT-Flag, Experiment 4 rep1

value: Normal lung tissue


title: sgGFP_2

description: IMR90 E6E7 sgGFP, Experiment 3


title: E6E7_siZBP1B_JT15

description: IMR90 E6E7 pre-crisis siZBP1#B, Experiment 1

value: Human Papillomavirus E6 and E7

value: ZBP1-targeting siRNA


title: E6E7_siZBP1B_JT13


title: LT_PD35_JT17

description: WI38 SV40LT growing, Experiment 1


title: LT_PD87_JT20

description: WI38 SV40LT crisis, Experiment 1


title: LT_PD35_JT16

description: WI38 SV40LT growing, Experiment 1


title: LT_PD35_JT18

description: WI38 SV40LT growing, Experiment 1


title: E6E7_siZBP1B_JT14


title: E6E7_siZBP1A_JT12

description: IMR90 E6E7 pre-crisis siZBP1#A, Experiment 1


title: E6E7_siCtrl_JT09

description: IMR90 E6E7 pre-crisis siCTR, Experiment 1

value: Non-targeting siRNA


title: E6E7_siZBP1A_JT10


title: TRF1_ZBP1 WT_2

description: TRF1(DN)-ZBP1(S)WT-Flag, Experiment 2


title: E6E7_PD105_JT04

description: IMR90 E6E7 crisis, Experiment 1


title: E6E7_PD105_JT06

description: IMR90 E6E7 crisis, Experiment 1


title: E6E7_siCtrl_JT07


title: E6E7_PD61_JT01

description: IMR90 E6E7 growing, Experiment 1


title: E6E7_siCtrl_JT08


title: E6E7_siZBP1A_JT11


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep3

status: Public on Oct 28 2022

city: San Francisco

first: Yizhu

last: Lin

address: 513 Parnassus

department: Cell and Tissue Biology

institute: University of California, San Francisco

description:
dual-S16_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxH_DP50_OR1_padj005.bed

data_processing:
Sequencing reads were aligned with STAR to GRCh38 human genome reference
Aligned bam files were processed with samtools, picard MarkDuplicates, and GATK SplitNCigarReads
Assembly: GRCh38
Supplementary files format and content: bed

source_name: kidney

growth_protocol: HEK 293T cells were cultured in DMEM with 4.5 g / L glucose, L-glutamine & sodium pyruvate (Corning #10-0130CV) and 10% FBS (Avantor #97068-085) at 37 ˚C, 5% CO2.

extract_protocol:
Cellular RNA extraction was performed with Direct-zol RNA miniprep Kit (Zymo Research #R2053) following manufacturer’s protocol
For Illumina high-through sequencing library preparation, we used NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E7405), NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7765) and NEBNext Multiplex Oligos for Illumina (NEB #E6440S and NEB #E6442S) following manufacturer’s protocol.

value: kidney

value: Human embryonic kidney

value: PUM1-rABE PUM2-APOBEC1

value: 1000 ng/ml dox


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep2


title: E6E7_PD61_JT03

description: IMR90 E6E7 growing, Experiment 1


title: PUM1-rABE PUM2-APOBEC1, 50 ng/ml dox, rep3

description:
dual-S16_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxL_DP50_OR1_padj005.bed

value: 50 ng/ml dox


title: LT_PD87_JT19

description: WI38 SV40LT crisis, Experiment 1


title: PUM1-rABE PUM2-APOBEC1, 1000 ng/ml dox, rep1


title: PUM1-rABE PUM2-APOBEC1, 50 ng/ml dox, rep1


title: PUM1-rABE PUM2-APOBEC1, DMSO control, rep3

description:
dual-S16_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S16_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxL_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxH_DP50_OR1_padj005.bed

value: DMSO control


title: PUM1-rABE PUM2-APOBEC1, 50 ng/ml dox, rep2


title: HSC7E1068 in SD-URA

status: Public on Nov 15 2022

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

description: Strand-sepcific RNA-seq using NEBNext Ultra II Directional RNA Library Prep Kit

data_processing:
RNA-seq reads were pre-processed using Trimmomatic v0.36 with the parameters “ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:true SLIDINGWINDOW:4:10 MINLEN:36”. The ILLUMINACLIP parameter identified and eliminated Illumina adapters specified in the Truseq3 library. Using SLIDINGWINDOW:4:10, reads were scanned in a 4 bp window and trimmed when the average quality dropped below 10. The default parameter MINLEN:36 dropped reads below 36 bases long.  After trimming, the quality of the reads were confirmed with FastQC v 0.11.8.
A reference genome was constructed by concatenating chromosome 7 from the human reference genome GrCH38 (GRCh38.p13) and the yeast S288C reference R64 (GCF_000146045.2_R64/). RNA-seq reads were aligned to the reference using STAR v2.7.10a. First, the reference genome was indexed using the following parameters: --runMode genomeGenerate --sjdbGTFfile --sjdbOverhang 60 --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases 12. Reads were then aligned to the reference using the following parameters: --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --alignIntronMax 5000.
PCR duplicates were marked using Picard tools v2.18.7 (Broad Institute).
A genome-guided transcriptome assembly from both evolved and naïve DNA was constructed using Cufflinks v0.17.0. The sorted BAM from the STAR alignment was used as input with the following parameters: --no-update-check --overlap-radius 1 --max-intron-length 5000 --library-type fr-firststrand. The output GTF file containing predicted transcripts was imported into the integrative genomics viewer (IGV) genome browser (Broad Institute) for visual analysis.
Assembly: R64 (yeast) and GRCh38.p13 (human)
Supplementary files format and content: GTF file containing cufflinks predicted transcripts
Supplementary files format and content: bigwig file containing RNA-seq read coverage

organism: Saccharomyces cerevisiae

growth_protocol: Yeast colonies containing HSC7E1068, as confirmed by colony PCR, were grown in liquid SD-URA to an OD600 of ~0.3 - 0.6.

extract_protocol:
Total RNA was extracted from liquid yeast cultures using the hot acid phenol method, described previously (https://www.protocols.io/view/rna-isolation-from-yeast-inwcdfe).
Extracted RNA was prepared for strand specific sequencing by the Biomedical Research Centre Sequencing Core (UBC, Vancouver) using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and polyA selection (NEB).

tag: media

value: SD-URA

value: yeast cells

tag: yac clone


title: PUM1-rABE PUM2-APOBEC1, DMSO control, rep2


title: E6E7_PD105_JT05

description: IMR90 E6E7 crisis, Experiment 1


title: PUM1-rABE PUM2-APOBEC1, DMSO control, rep1


title: PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep3

description:
dual-S15_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxH_DP50_OR1_padj005.bed

value: PUM1-APOBEC1 PUM2-rABE


title: PUM1-APOBEC1 PUM2-rABE, 50 ng/ml dox, rep2

description:
dual-S15_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep1


title: PUM1-APOBEC1 PUM2-rABE, 50 ng/ml dox, rep1


title: PUM1-APOBEC1 PUM2-rABE, DMSO control, rep3

description:
dual-S15_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S15_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxH_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: E6E7_PD61_JT02

description: IMR90 E6E7 growing, Experiment 1

value: No treatment


title: PUM1-APOBEC1 PUM2-rABE, 1000 ng/ml dox, rep2


title: PUM1-APOBEC1 PUM2-rABE, 50 ng/ml dox, rep3


title: PUM1-APOBEC1 PUM2-rABE, DMSO control, rep1


title: PUM2-APOBEC1, 50 ng/ml dox, rep2

description: PUM2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM2-APOBEC1, 1000 ng/ml dox, rep2

description: PUM2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed


title: PUM2-APOBEC1, DMSO control, rep2

description:
PUM2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
PUM2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM2-APOBEC1, 1000 ng/ml dox, rep3


title: PUM2-APOBEC1, DMSO control, rep3


title: PUM2-APOBEC1, 50 ng/ml dox, rep3


title: PUM2-APOBEC1, 50 ng/ml dox, rep1


title: PUM2-APOBEC1, 1000 ng/ml dox, rep1


title: PUM2-APOBEC1, DMSO control, rep1


title: PUM2-rABE, 1000 ng/ml dox, rep3

description: PUM2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed


title: PUM2-rABE, 1000 ng/ml dox, rep2


title: PUM1-APOBEC1 PUM2-rABE, DMSO control, rep2


title: PUM2-rABE, 50 ng/ml dox, rep1

description: PUM2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: PUM2-rABE, 1000 ng/ml dox, rep1


title: PUM2-rABE, 50 ng/ml dox, rep3


title: PUM2-rABE, 50 ng/ml dox, rep2


title: PUM2-rABE, DMSO control, rep3

description:
PUM2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
PUM2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: PUM2-rABE, DMSO control, rep2


title: PUM1-APOBEC1, 1000 ng/ml dox, rep3

description: PUM1-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed


title: PUM1-APOBEC1, 50 ng/ml dox, rep1

description: PUM1-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM1-APOBEC1, 50 ng/ml dox, rep3


title: PUM1-APOBEC1, 50 ng/ml dox, rep2


title: PUM2-rABE, DMSO control, rep1


title: PUM1-APOBEC1, DMSO control, rep2

description:
PUM1-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
PUM1-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM1-APOBEC1, DMSO control, rep1


title: PUM1-rABE, 1000 ng/ml dox, rep2

description: PUM1-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed


title: PUM1-APOBEC1, 1000 ng/ml dox, rep2


title: PUM1-APOBEC1, 1000 ng/ml dox, rep1


title: PUM1-rABE, 1000 ng/ml dox, rep3


title: PUM1-rABE, 50 ng/ml dox, rep3

description: PUM1-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: PUM1-rABE, 1000 ng/ml dox, rep1


title: PUM1-rABE, 50 ng/ml dox, rep2


title: RBFox2-APOBEC1, 1000 ng/ml dox, rep2

description: RBFox2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed


title: PUM1-rABE, DMSO control, rep3

description:
PUM1-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
PUM1-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: PUM1-rABE, 50 ng/ml dox, rep1


title: PUM1-rABE, DMSO control, rep2


title: RBFox2-APOBEC1, 1000 ng/ml dox, rep3


title: RBFox2-APOBEC1, 1000 ng/ml dox, rep1


title: RBFox2-APOBEC1, 50 ng/ml dox, rep3

description: RBFox2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: RBFox2-APOBEC1, 50 ng/ml dox, rep2


title: RBFox2-APOBEC1, DMSO control, rep2

description:
RBFox2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
RBFox2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: PUM1-APOBEC1, DMSO control, rep3


title: RBFox2-APOBEC1, 50 ng/ml dox, rep1


title: RBFox2-APOBEC1, DMSO control, rep3


title: RBFox2-APOBEC1, DMSO control, rep1


title: RBFox2-rABE, 50 ng/ml dox, rep3

description: RBFox2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: RBFox2-rABE, 50 ng/ml dox, rep2


title: RBFox2-rABE, 1000 ng/ml dox, rep3

description: RBFox2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed


title: RBFox2-rABE, DMSO control, rep1

description:
RBFox2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
RBFox2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: PUM1-rABE, DMSO control, rep1


title: APOBEC1, 1000 ng/ml dox, rep1

description:
bg_BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
RBFox2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
PUM1-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
PUM2-BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxH_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxH_DP50_OR1_padj005.bed


title: RBFox2-rABE, 50 ng/ml dox, rep1


title: RBFox2-rABE, 1000 ng/ml dox, rep1


title: RBFox2-rABE, DMSO control, rep2


title: RBFox2-rABE, DMSO control, rep3


title: rABE, 1000 ng/ml dox, rep3

description:
bg_rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
RBFox2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
PUM2-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S15_cmh_A-G-doxH_DP50_OR1_padj005.bed
PUM1-rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
dual-S16_cmh_A-G-doxH_DP50_OR1_padj005.bed

value: rABE


title: APOBEC1, DMSO control, rep2

description:
bg_BE4_cmh_C-T-doxH_DP50_OR1_padj005.bed
bg_BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: rABE, 50 ng/ml dox, rep3

description:
bg_rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed
RBFox2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed
PUM2-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S15_cmh_A-G-doxL_DP50_OR1_padj005.bed
PUM1-rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed
dual-S16_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: APOBEC1, 50 ng/ml dox, rep2

description:
bg_BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed
RBFox2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed
PUM1-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed
PUM2-BE4_cmh_C-T-doxL_DP50_OR1_padj005.bed
dual-S15_cmh_C-T-doxL_DP50_OR1_padj005.bed
dual-S16_cmh_C-T-doxL_DP50_OR1_padj005.bed


title: APOBEC1, 50 ng/ml dox, rep1


title: APOBEC1, DMSO control, rep3


title: rABE, 1000 ng/ml dox, rep2


title: APOBEC1, DMSO control, rep1


title: rABE, 50 ng/ml dox, rep2


title: rABE, DMSO control, rep2

description:
bg_rABE_cmh_A-G-doxH_DP50_OR1_padj005.bed
bg_rABE_cmh_A-G-doxL_DP50_OR1_padj005.bed


title: RBFox2-rABE, 1000 ng/ml dox, rep2


title: APOBEC1, 1000 ng/ml dox, rep3


title: APOBEC1, 1000 ng/ml dox, rep2


title: Neonate Ischemic B

status: Public on Sep 08 2022

city: Raleigh

first: Amanda

middle: L

last: Ziegler

state: NC

address: 1060 William Moore Drive

department: Clinical Science

institute: NC State University

data_processing:
Prior to analysis all non-transcribed genes were removed and all genes that had more than one count per million in two or more samples were analyzed.
Using raw counts data from NextSeq500, differential gene expression analyses between neonatal and juvenile injured and uninjured mucosal scrapings were performed using R software (R Foundation for Statistical Computing, Vienna, Austria) with the DESeq2 package (Bioconductor) and RStudio software (RStudio, Boston, MA, USA) to obtain log fold change (logFC), false discovery rates (FDR) and p-values.
Assembly: UCSC Sscrofa11.1
Supplementary files format and content: tab-delimited text files include raw count values for each Sample.
Supplementary files format and content: Gene_Results.txt files include differential expression analysis generated using DESeq2 in R.

organism: Sus scrofa

source_name: Jejunual mucosa

extract_protocol:
mRNA were isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and cDNA libraries were generated using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio, Inc., Kusatsu, Japan).
Libraries were high-output single-end sequenced on a NextSeq500 instrument (Illumina, Inc., San Diego, CA, USA) for 75 cycles using an 8 base pair index

treatment_protocol: Under general anesthesia, the distal jejunum of 2- or 6-week-old pigs was accessed via midline or paralumbar incision and 8-10 cm loops were ligated in segments and subjected to 30-minutes of ischemia via ligation of local mesenteric blood vessels with 2-0 braided silk suture. Adjacent loops not subjected to ischemia were used as control tissue. Jejunal mucosal scrapings were snap frozen in liquid nitrogen and stored at -80°C until further processing.

tag: breed

value: Yorkshire cross

tag: age

value: Jejunual mucosa

value: Ischemia


title: rABE, DMSO control, rep3

tag: treatment


title: rABE, DMSO control, rep1


title: rABE, 50 ng/ml dox, rep1


title: Neonate Ischemic A


title: Neonate Control A

value: Control


title: Neonate Control D


title: Neonate Control B


title: Neonate Ischemic D


title: Juvenile Control C


title: Juvenile Ischemic B


title: APOBEC1, 50 ng/ml dox, rep3


title: Juvenile Ischemic C


title: rABE, 1000 ng/ml dox, rep1


title: Y3,tumor,Day8

status: Public on May 29 2022

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Samples were multiplexed  in each lane, which yields target number of single-end 100-bp reads for each sample, as a fraction of 180 million reads for the whole lane.
After trimming, sequence reads were mapped to the Drosophila genome (FlyBase genome annotation version r6.39) using Tophat.
With the uniquely mapped reads, gene expression was quantified using Cufflinks (FPKM values) and HTseq (read counts per gene).
Assembly: Drosophila genome (FlyBase genome annotation version r6.39)
Supplementary files format and content: Counts.All.csv

organism: Drosophila melanogaster

source_name: Malpighian tubules

growth_protocol: All flies were grown on the food containing 5.5 g agar, 65 g sucrose, 25 g dry yeast, 65 g cornmeal, 4 mL propionic acid, and 1.25 g Methylparaben (dissolved in 95% ethanol) per liter under standard laboratory conditions

extract_protocol:
80 Malpighian tubules of each genotype were lysed with Trizol (ThermoFisher, 15596018) for RNA extraction. After assessing RNA quality with Agilent Bioanalyzer (RIN > 7), mRNAs were enriched by poly-A pull-down.
Sequencing libraries were prepared with Illumina Truseq RNA preparation kits and were sequenced using Illumina HiSeq 2000 by Benagen (Wuhan, China).

treatment_protocol: Virgin progenies were maintained at 18 C for 6-8 days and then switched to 29C to induce transgenes for 8 days.

tag: sample group

value: yki3SA tumor-bearing

value: esg-GAL4, UAS-GFP, tub-GAL80TS /+; UAS-yki3SA/+

value: Malpighian tubules

value: Day 8


title: Y2,tumor,Day8


title: Juvenile Control B


title: W2,control,Day8

value: control

value: esg-GAL4, UAS-GFP, tub-GAL80TS /+


title: Juvenile Control A


title: Foxp3 Treg ETOH 1

status: Public on May 02 2022

data_processing:
Sequenced reads were quality-tested using FASTQC and mapped to the mm10 mouse genome using the STAR aligner with default parameters. Reads were trimmed using Trim Galore.
Peaks were identified with findPeaks in HOMER, using default parameters and input condition as background reference.
Assembly: mm10
Supplementary files format and content: tag density file for each sample in bigWig format

source_name: Skin Treg cells

extract_protocol: Libraries were prepared using Illumina TruSeq ChIP Sample Preparation kit following manufacturer’s instructions.

treatment_protocol: Splenic Tregs and Tcon were cultured in vitro with 10 nM dexamethasone for 48 hours and fixed in 1% formaldehyde.

value: ETOH

tag: chip antibody


title: Foxp3 Input Treg ETOH


title: Y1,tumor,Day8


title: Foxp3 Treg DEX 2

value: DEX


title: W3,control,Day8


title: Foxp3 Treg DEX 1


title: W1,control,Day8


title: Foxp3 Treg ETOH 2


title: Juvenile Ischemic A


title: Foxp3 Input Treg DEX


title: Treg GR WT HD 24h rep1

data_processing:
Sequenced reads were quality-tested using FASTQC and mapped to the mm10 mouse genome using the STAR aligner with default parameters. Reads were trimmed using Trim Galore.
TPM gene expression was quantified across all the exons of RefSeq genes with analyzeRepeats.pl in HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each RNA-Seq sample

extract_protocol:
RNA from FACS-Sorted cells in Trizol was isolated according to the manufacturer’s instruction.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer’s instructions.

treatment_protocol:
For Treg RNAseq, Skin Treg cells were sorted by FACS from WT and Foxp3YFP-Cre GRfl/fl mice one day after hair depilation.
For HFSC RNAseq, CD34+ITGA6high HFSCs were isolated by FACS from the skin of WT and Foxp3YFP-Cre GRfl/fl mice 4 days after hair depilation.

value: hair dipilation

value: 24hr after treatment

tag: genotypes

value: wide type


title: Treg GR WT HD 24h rep3


title: HFSC GR KO HD day 4 rep3

source_name: Hair follicle stem cell (HFSC)

value: 4 days after treatment

value: GR knock out


title: HFSC GR KO HD day 4 rep2


title: HFSC GR KO HD day 4 rep1


title: HFSC GR WT HD day 4 rep3


title: HFSC GR WT HD day 4 rep2


title: HFSC GR WT HD day 4 rep1


title: Treg GR KO HD 24h rep5


title: RKd12_Pre-Infection

status: Public on Feb 09 2022

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) https://www.unmc.edu/rhesusgenechip/index.htm#NewRhesusGenome
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Pre-Infection samples were sequenced on an Illumina HiSeq3000, the remaining samples were sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: subjectid

tag: processinggroup

tag: processday

tag: timepoint

value: Pre-Infection


title: RHa10_Pre-Infection


title: RJp11_Pre-Infection


title: Treg GR KO HD 24h rep1

tag: time


title: Treg GR KO HD 24h rep4


title: ROe12_Pre-Infection


title: Treg GR KO HD 24h rep2


title: GR Input Treg ETOH

data_processing:
Sequenced reads were quality-tested using FASTQC and mapped to the mm10 mouse genome using the STAR aligner with default parameters. Reads were trimmed using Trim Galore.
Peaks were identified with findPeaks in HOMER, using default parameters and input condition as background reference.
Genome_build: mm10
Supplementary_files_format_and_content: tag density file for each sample in bigWig format


title: Treg GR KO HD 24h rep3


title: Treg GR WT HD 24h rep2


title: GR Treg ETOH

value: GR


title: GR Treg DEX


title: GR Input Treg DEX


title: RPu12_Pre-Infection


title: RHa10_T2 [reanalysis]

description:
re-analysis of GSM1889069
X47_RHa10_Gr4_day242_GTCCGC_L006


title: RPy8_Pre-Infection


title: RJw12_Pre-Infection


title: RPy8_T2 [reanalysis]

description:
re-analysis of GSM1889068
X46_RPy8_Gr4_day242_CCGTCC_L006


title: RCb12_Pre-Infection


title: RKg11_T2 [reanalysis]

description:
re-analysis of GSM1889065
X43_RKg11_Gr3_day241_AGTCAA_L006


title: RGe12_Pre-Infection


title: RBt12_Pre-Infection


title: RGv10_Pre-Infection


title: RLm12_Pre-Infection


title: RKd12_T2 [reanalysis]

description:
re-analysis of GSM1889067
X45_RKd12_Gr4_day242_ATGTCA_L006


title: RJp11_T2 [reanalysis]

description:
re-analysis of GSM1889059
X37_RJp11_Gr2_day240_CGATGT_L005


title: RGe12_T2 [reanalysis]

description:
re-analysis of GSM1889058
X36_RGe12_Gr1_day241_GTGAAA_L005


title: RBt12_T2 [reanalysis]

description:
re-analysis of GSM1889057
X35_RBt12_Gr1_day241_GTCCGC_L005


title: ROe12_T2 [reanalysis]

description:
re-analysis of GSM1889056
X34_ROe12_Gr1_day241_CCGTCC_L005


title: RPu12_T2 [reanalysis]

description:
re-analysis of GSM1889066
X44_RPu12_Gr3_day241_AGTTCC_L006


title: RTb12_T2 [reanalysis]

description:
re-analysis of GSM1889064
X42_RTb12_Gr3_day241_CTTGTA_L006


title: RPu12_T1 [reanalysis]

description:
re-analysis of GSM1889050
X28_RPu12_Gr3_day106_GCCAAT_L004


title: RVt10_T2 [reanalysis]

description:
re-analysis of GSM1889063
X41_RVt10_Gr3_day241_CAGATC_L006


title: ROc10_T1 [reanalysis]

description:
re-analysis of GSM1889051
X29_ROc10_Gr4_day105_CAGATC_L004


title: RKg11_T1 [reanalysis]

description:
re-analysis of GSM1889049
X27_RKg11_Gr3_day106_ACAGTG_L004


title: RPy8_T1 [reanalysis]

description:
re-analysis of GSM1889053
X31_RPy8_Gr4_day105_AGTCAA_L004


title: RKd12_T1 [reanalysis]

description:
re-analysis of GSM1889052
X30_RKd12_Gr4_day105_CTTGTA_L004


title: RCb12_T2 [reanalysis]

description:
re-analysis of GSM1889061
X39_RCb12_Gr2_day240_ACAGTG_L005


title: RGv10_T2 [reanalysis]

description:
re-analysis of GSM1889060
X38_RGv10_Gr2_day240_TGACCA_L005


title: RCb12_T1 [reanalysis]

description:
re-analysis of GSM1889045
X23_RCb12_Gr2_day105_GTCCGC_L003


title: RHa10_T1 [reanalysis]

description:
re-analysis of GSM1889054
X32_RHa10_Gr4_day105_AGTTCC_L004


title: RLm12_T2 [reanalysis]

description:
re-analysis of GSM1889055
X33_RLm12_Gr1_day241_ATGTCA_L005


title: RJp11_T1 [reanalysis]

description:
re-analysis of GSM1889043
X21_RJp11_Gr2_day105_ATGTCA_L003


title: RJw12_T1 [reanalysis]

description:
re-analysis of GSM1889046
X24_RJw12_Gr2_day105_GTGAAA_L003


title: ROe12_T1 [reanalysis]

description:
re-analysis of GSM1889040
X18_ROe12_Gr1_day107_CTTGTA_L003


title: RJw12_T2 [reanalysis]

description:
re-analysis of GSM1889062
X40_RJw12_Gr2_day240_GCCAAT_L005


title: RBt12_T1 [reanalysis]

description:
re-analysis of GSM1889041
X19_RBt12_Gr1_day107_AGTCAA_L003


title: RTb12_T1 [reanalysis]

description:
re-analysis of GSM1889048
X26_RTb12_Gr3_day106_TGACCA_L004


title: RGe12_T1 [reanalysis]

description:
re-analysis of GSM1889042
X20_RGe12_Gr1_day107_AGTTCC_L003


title: RLm12_T1 [reanalysis]

description:
re-analysis of GSM1889039
X17_RLm12_Gr1_day107_CAGATC_L003


title: RHa10_Pre-ART [reanalysis]

description:
re-analysis of GSM1889038
X16_RHa10_Gr4_day58_GCCAAT_L002

value: Pre-ART


title: RPy8_Pre-ART [reanalysis]

description:
re-analysis of GSM1889037
X15_RPy8_Gr4_day58_ACAGTG_L002

value: Control


title: RKg11_Pre-ART [reanalysis]

description:
re-analysis of GSM1889033
X11_RKg11_Gr3_day59_GTCCGC_L002


title: RTb12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889032
X10_RTb12_Gr3_day59_CCGTCC_L002


title: RKd12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889036
X14_RKd12_Gr4_day58_TGACCA_L002


title: RVt10_Pre-ART [reanalysis]

description:
re-analysis of GSM1889031
X9_RVt10_Gr3_day59_ATGTCA_L002


title: RPu12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889034
X12_RPu12_Gr3_day59_GTGAAA_L002


title: RJw12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889030
X8_RJw12_Gr2_day58_AGTTCC_L001


title: RVt10_T1 [reanalysis]

description:
re-analysis of GSM1889047
X25_RVt10_Gr3_day106_CGATGT_L004


title: RCb12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889029
X7_RCb12_Gr2_day58_AGTCAA_L001


title: RGv10_T1 [reanalysis]

description:
re-analysis of GSM1889044
X22_RGv10_Gr2_day105_CCGTCC_L003


title: RJp11_Pre-ART [reanalysis]

description:
re-analysis of GSM1889027
X5_RJp11_Gr2_day58_CAGATC_L001


title: RGv10_Pre-ART [reanalysis]

description:
re-analysis of GSM1889028
X6_RGv10_Gr2_day58_CTTGTA_L001


title: RGe12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889026
X4_RGe12_Gr1_day58_GCCAAT_L001


title: ROe12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889024
X2_ROe12_Gr1_day58_TGACCA_L001


title: Input - 3xTg

status: Public on Jan 29 2022

first: Jae Joon

last: Choi

address: 77 Avenue Louis Pasteur

department: Genetics

description: Input: 3xTg mouse cortex, age 11 months, 4 female cortices were pooled

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings).
Duplicate reads were removed, and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome.
Genome_build: mm10
Supplementary_files_format_and_content: The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Supplementary_files_format_and_content: Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.

source_name: Mouse cortex

growth_protocol: Age 11 months

extract_protocol:
The frozen tissue was sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, the tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (25 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against the C-terminal region of REST (generous gift from Gail Mandel, Vollum Institute). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

tag: tissue

value: mouse cortex, bulk tissue

value: 11 months

value: none (input)

tag: disease state

value: Alzheimer's Disease


title: RBt12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889025
X3_RBt12_Gr1_day58_ACAGTG_L001


title: REST ChIP-seq - WT_rep2

description: REST ChIP-seq: WT mouse cortex, age 11 months, 4 female cortices were pooled (replicate 2)

value: REST C-terminal antibody, gift from Dr. Gail Mandel, Vollum Institute, Oregon Health & Science University. References:Ballas, N., Grunseich, C., Lu, D.D., Speh, J.C. & Mandel, G. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121, 645-657 (2005).  McGann, J.C. et al. The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus. J Neurosci 41, 6582-6595 (2021).

value: Wildtype


title: Input - WT

description: Input: WT mouse cortex, age 11 months, 4 female cortices were pooled


title: REST ChIP-seq - 3xTg_rep1

description: REST ChIP-seq: 3xTg mouse cortex, age 11 months, 4 female cortices were pooled (replicate 1)


title: Fibroadipogenic progenitors Replicate C

status: Public on Jan 02 2022

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

country: Netherlands

institute: Mosa Meat

description: FAPs C

data_processing:
STAR aligner 2.7 was used to align single-end reads to the reference genome bosTau9 (ARS UCD1.2.98)
Gene counts based on the aligned reads were quantified using the FeatureCounts function of the Rsubread package
Genome_build: bosTau9
Supplementary_files_format_and_content: Comma-separated matrix table with raw gene counts for every gene (row) and every sample (column)

organism: Bos taurus

source_name: Semitendinosus muscle

growth_protocol: SCs and FAPs were cultured on collagen-coated flasks at a seeding density of 2000 cells/cm2 in GM (Ham’s F-10 Nutrient Mix supplemented with 20% Fetal Bovine serum, 1% PSA, and 5 ng/ml bFGF).

extract_protocol:
Cell lysates were harvested by adding TRK lysis buffer (Omega Bio-tek) to tissue culture samples after removing culture media and washing with PBS.
RNA was purified using the Omega MicroElute Total RNA Kit (Omega Bio-tek).  Sequencing libraries were prepared from harvested RNA samples using the TruSeq stranded mRNA kit (Illumina) and sequenced on a high-output 75bp NextSeq 500 (Illumina)

treatment_protocol: SCs and FAPs were cultured in GM for 72h prior to lysis.

tag: cell type

value: Fibroadipogenic progenitor

value: Belgian blue


title: REST ChIP-seq - 3xTg_rep2

description: REST ChIP-seq: 3xTg mouse cortex, age 11 months, 4 female cortices were pooled (replicate 2)


title: ROc10_Pre-ART [reanalysis]

description:
re-analysis of GSM1889035
X13_ROc10_Gr4_day58_CGATGT_L002


title: Satellite cells Replicate C

description: SCs C

value: Satellite cell


title: Satellite cells Replicate B

description: SCs B


title: REST ChIP-seq - WT_rep1

description: REST ChIP-seq: WT mouse cortex, age 11 months, 4 female cortices were pooled (replicate 1)


title: FGF control and mutant

status: Public on Jan 27 2022

city: New York

first: Revathi

last: Balasubramanian

state: NY

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

data_processing:
Approximately 11,000 cells were sequenced on the 10X platform. cDNA Libraries were sequenced on an Illumina NovaSeq 6000 sequencer. The data alignment, barcode processing and generation of cell gene matrices was performed by the Single Cell Analysis core facility at Columbia Genome Center using cellranger pipeline v2.0.0.
Count matrices were aggregated and filtered for further processing using Seurat v3.
Supplementary_files_format_and_content: There is no barcode file. The control and mutant cells are sequenced together. During processing and analysis, they can be separated based on TdTomato reporter expression. The manuscript (in preparation) details how the separate matrices were constructed using Seurat workflow in R.

source_name: Peripheral retina

extract_protocol:
E14 retinal tissue was harvested and pooled from 3 embryos each for mutant and control. Cells were dissociated using a Papain protocol. Cells were sorted according to fluorescent reporters and single cell suspension was transferred to the Columbia genome center for further processing.
Barcoded cDNA library was contructed using the 10X Genomics Chromium controller.

tag: developmental stage

tag: genotype

value: Control:a-Cre; FgfR1 f/+ ; FgfR2 f/+  Mutant:a-Cre; FgfR1 f/f ; FgfR2 f/f; Rosa26-TdTomato

tag: strain

value: Mixed


title: Fibroadipogenic progenitors Replicate A

description: FAPs A

tag: breed


title: Satellite cells Replicate A

description: SCs A


title: Fibroadipogenic progenitors Replicate B

description: FAPs B


title: X94_82_CTRL

status: Public on Jan 01 2022

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5
After quality control for adapter contamination and trimming, fastq files were mapped on human genome (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM gene counts for every gene and every sample

source_name: Lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen) from each core. according the manufacture protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station
20 ng RNA input was used for library preparation by AmpliSeq Transcriptome Human Gene Expression kit. The cDNA was then amplified and barcoded using the Ion Xpress RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485).  The Ion Chip Kit v2 BC (Life Technologies) 4484270) was then loaded using the Ion Chef System (Life Technologies 4484177) with the Ion PI IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI IC 200 Kit.

treatment_protocol: Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor. The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 4 cores were randomly selected per lung.

value: lung

tag: disease

value: DONOR

tag: subject

tag: surface density

tag: smoking ever

tag: age transplant

tag: gender

value: M

tag: cluster

value: CTRL


title: X94_95_CTRL


title: X94_48_CTRL


title: X63_98_CTRL


title: X94_42_CTRL


title: X63_63_CTRL


title: X222_65_CTRL

value: F


title: RLm12_Pre-ART [reanalysis]

description:
re-analysis of GSM1889023
X1_RLm12_Gr1_day58_CGATGT_L001

tag: subjectid

tag: treatment

tag: processinggroup

tag: processday

value: Pre-ART


title: X63_28_CTRL

tag: tissue


title: X63_69_CTRL


title: X222_56_CTRL


title: X222_42_CTRL


title: X191_95_CTRL


title: X222_77_CTRL


title: X175_67_CTRL


title: X191_30_CTRL


title: X145_49_CTRL


title: X175_22_CTRL


title: X175_45_CTRL


title: X191_71_CTRL


title: X175_58_CTRL


title: X145_4_CTRL


title: X145_27_CTRL


title: 1*_Control#5_C76_HC_HC05 lib8566_C6VF8ANXX

status: Public on Dec 15 2021

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCh38

source_name: Islet-reactive CD4+ sorted T-cell

extract_protocol:
Single cells were captured on a C1 system or plate sorted. C1 capture was done using a 5-10 um mRNA Seq IFC according to manufacturer’s instructions (Fluidigm, South San Francisco, CA). Full-length cDNA was prepared using SMARTer Ultra Low RNA Kit for the Fluidigm C1 System (Clontech, Mountain View, CA). For plate sorting, single cells were sorted into wells of a 96-well plate. Full-length cDNA was prepared using a SMARTer V4 kit with half-volume reactions.
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

tag: library id

tag: study group

value: HC

tag: donor

tag: age

tag: Sex

value: male

tag: lib prep method


title: 1*_Control#5_C94_HC_HC05 lib8567_C6VF8ANXX


title: 1_Control#5_C60_HC_HC05 lib8565_C6VF8ANXX


title: P105_Buildup_Double_negative

status: Public on Dec 31 2021

first: Ang

middle: Andy

last: Tu

address: 500 Main Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: scRNA + TCR-Seq
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: hg19
Supplementary_files_format_and_content: gene expression count (genes by cells)

source_name: Transcriptome of single cells

extract_protocol: Seq-Well

tag: timepoint

value: Buildup

value: Full tolerance

tag: sequencing platform

value: NovaSeq S2 100 cycles


title: P105_Avoidance_Double_negative

value: Avoidance


title: 1*_Control#5_C54_HC_HC05 lib8564_C6VF8ANXX


title: X191_37_CTRL

tag: disease

tag: subject

tag: surface density

tag: smoking ever


title: 1_Control#5_C96_HC_HC05 lib8562_C6VF8ANXX


title: 1_Control#5_C65_HC_HC05 lib8563_C6VF8ANXX


title: 1*_Control#5_C84_HC_HC05 lib8560_C6VF8ANXX


title: 1_Control#5_C90_HC_HC05 lib8561_C6VF8ANXX


title: 1*_Control#5_C78_HC_HC05 lib8559_C6VF8ANXX


title: 1_Control#5_C64_HC_HC05 lib8558_C6VF8ANXX


title: 1_Control#5_C52_HC_HC05 lib8557_C6VF8ANXX


title: 1*_Control#5_C36_HC_HC05 lib8556_C6VF8ANXX


title: 1*_Control#5_C30_HC_HC05 lib8555_C6VF8ANXX


title: X145_110_CTRL

tag: age transplant

tag: gender

tag: cluster


title: 1_Control#5_C22_HC_HC05 lib8554_C6VF8ANXX


title: P105_Baseline_Double_negative

value: Baseline


title: P105_Maintenance_Double_negative

value: Maintenance


title: 1_Control#5_C41_HC_HC05 lib8550_C6VF8ANXX


title: 1*_Control#5_C04_HC_HC05 lib8551_C6VF8ANXX


title: 1_Control#5_C16_HC_HC05 lib8553_C6VF8ANXX


title: 1*_Control#5_C29_HC_HC05 lib8548_C6VF8ANXX


title: 1_Control#5_C11_HC_HC05 lib8547_C6VF8ANXX


title: 1*_Control#5_C35_HC_HC05 lib8549_C6VF8ANXX


title: 1_Control#5_C05_HC_HC05 lib8546_C6VF8ANXX


title: 1_Control#5_C46_HC_HC05 lib8545_C6VF8ANXX


title: 1_Control#5_C24_HC_HC05 lib8543_C6VF8ANXX


title: 1_Control#5_C12_HC_HC05 lib8541_C6VF8ANXX


title: 1*_Control#5_C06_HC_HC05 lib8540_C6VF8ANXX


title: 1*_Control#5_C40_HC_HC05 lib8544_C6VF8ANXX


title: 1_Control#5_C69_HC_HC05 lib8539_C6VF8ANXX


title: 1_Control#5_C63_HC_HC05 lib8538_C6VF8ANXX


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title: 1*_Control#4_C43_HC_HC04 lib8497_C6VF8ANXX


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title: 1*_T1D#5_C37_T1D_T1D5 lib8445_C6VF8ANXX


title: 1_T1D#4_RO+_C17_T1D_T1D4 lib6794_C6VG0ANXX


title: 1*_T1D#5_C21_T1D_T1D5 lib8443_C6VF8ANXX


title: 1*_T1D#4_RO+_C46_T1D_T1D4 lib6792_C6VG0ANXX


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tag: alias

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description: 25160_B11_new onset T1D_25160


title: 25160_D4_new onset T1D_25160 lib34028_CCUWNANXX_tophat_alignments

description: 25160_D4_new onset T1D_25160


title: 25160_B10_new onset T1D_25160 lib34010_CCUWNANXX_tophat_alignments

description: 25160_B10_new onset T1D_25160


title: 25160_C7_new onset T1D_25160 lib34019_CCUWNANXX_tophat_alignments

description: 25160_C7_new onset T1D_25160


title: 25160_C6_new onset T1D_25160 lib34018_CCUWNANXX_tophat_alignments

description: 25160_C6_new onset T1D_25160


title: 25160_B3_new onset T1D_25160 lib34003_CCUWNANXX_tophat_alignments

description: 25160_B3_new onset T1D_25160


title: 25160_D10_new onset T1D_25160 lib34034_CCUWNANXX_tophat_alignments

description: 25160_D10_new onset T1D_25160


title: 25160_B5_new onset T1D_25160 lib34005_CCUWNANXX_tophat_alignments

description: 25160_B5_new onset T1D_25160


title: 25160_D7_new onset T1D_25160 lib34031_CCUWNANXX_tophat_alignments

description: 25160_D7_new onset T1D_25160


title: 25160_C9_new onset T1D_25160 lib34021_CCUWNANXX_tophat_alignments

description: 25160_C9_new onset T1D_25160


title: 25160_A12_new onset T1D_25160 lib34000_CCUWNANXX_tophat_alignments

description: 25160_A12_new onset T1D_25160


title: 1_T1D#4_RO+_C02_T1D_T1D4 lib6777_C6VG0ANXX


title: 25160_A11_new onset T1D_25160 lib33999_CCUWNANXX_tophat_alignments

description: 25160_A11_new onset T1D_25160


title: 25160_B9_new onset T1D_25160 lib34009_CCUWNANXX_tophat_alignments

description: 25160_B9_new onset T1D_25160


title: 25160_A10_new onset T1D_25160 lib33998_CCUWNANXX_tophat_alignments

description: 25160_A10_new onset T1D_25160


title: 25160_B8_new onset T1D_25160 lib34008_CCUWNANXX_tophat_alignments

description: 25160_B8_new onset T1D_25160


title: 25160_A7_new onset T1D_25160 lib33995_CCUWNANXX_tophat_alignments

description: 25160_A7_new onset T1D_25160


title: 25160_A5_new onset T1D_25160 lib33993_CCUWNANXX_tophat_alignments

description: 25160_A5_new onset T1D_25160


title: 25160_C10_new onset T1D_25160 lib34022_CCUWNANXX_tophat_alignments

description: 25160_C10_new onset T1D_25160


title: 25160_B6_new onset T1D_25160 lib34006_CCUWNANXX_tophat_alignments

description: 25160_B6_new onset T1D_25160


title: 25160_C11_new onset T1D_25160 lib34023_CCUWNANXX_tophat_alignments

description: 25160_C11_new onset T1D_25160


title: 25160_A2_new onset T1D_25160 lib33990_CCUWNANXX_tophat_alignments

description: 25160_A2_new onset T1D_25160


title: 25160_B4_new onset T1D_25160 lib34004_CCUWNANXX_tophat_alignments

description: 25160_B4_new onset T1D_25160


title: 25160_C1_new onset T1D_25160 lib34013_CCUWNANXX_tophat_alignments

description: 25160_C1_new onset T1D_25160


title: 25160_C5_new onset T1D_25160 lib34017_CCUWNANXX_tophat_alignments

description: 25160_C5_new onset T1D_25160


title: 25160_B2_new onset T1D_25160 lib34002_CCUWNANXX_tophat_alignments

description: 25160_B2_new onset T1D_25160


title: 25160_A8_new onset T1D_25160 lib33996_CCUWNANXX_tophat_alignments

description: 25160_A8_new onset T1D_25160


title: 25160_B1_new onset T1D_25160 lib34001_CCUWNANXX_tophat_alignments

description: 25160_B1_new onset T1D_25160


title: 27613_D10_new onset T1D_27613 lib33986_CCUWNANXX_tophat_alignments

description: 27613_D10_new onset T1D_27613


title: 25160_A6_new onset T1D_25160 lib33994_CCUWNANXX_tophat_alignments

description: 25160_A6_new onset T1D_25160


title: 27613_D7_new onset T1D_27613 lib33983_CCUWNANXX_tophat_alignments

description: 27613_D7_new onset T1D_27613


title: 25160_A4_new onset T1D_25160 lib33992_CCUWNANXX_tophat_alignments

description: 25160_A4_new onset T1D_25160


title: 25160_A9_new onset T1D_25160 lib33997_CCUWNANXX_tophat_alignments

description: 25160_A9_new onset T1D_25160


title: 27613_D5_new onset T1D_27613 lib33981_CCUWNANXX_tophat_alignments

description: 27613_D5_new onset T1D_27613


title: 25160_B7_new onset T1D_25160 lib34007_CCUWNANXX_tophat_alignments

description: 25160_B7_new onset T1D_25160


title: 25160_A1_new onset T1D_25160 lib33989_CCUWNANXX_tophat_alignments

description: 25160_A1_new onset T1D_25160


title: 27613_C12_new onset T1D_27613 lib33977_CCUWNANXX_tophat_alignments

description: 27613_C12_new onset T1D_27613


title: 27613_C10_new onset T1D_27613 lib33975_CCUWNANXX_tophat_alignments

description: 27613_C10_new onset T1D_27613


title: 27613_D8_new onset T1D_27613 lib33984_CCUWNANXX_tophat_alignments

description: 27613_D8_new onset T1D_27613


title: 27613_D4_new onset T1D_27613 lib33980_CCUWNANXX_tophat_alignments

description: 27613_D4_new onset T1D_27613


title: 27613_D12_new onset T1D_27613 lib33988_CCUWNANXX_tophat_alignments

description: 27613_D12_new onset T1D_27613


title: 27613_D3_new onset T1D_27613 lib33979_CCUWNANXX_tophat_alignments

description: 27613_D3_new onset T1D_27613


title: 27613_C7_new onset T1D_27613 lib33972_CCUWNANXX_tophat_alignments

description: 27613_C7_new onset T1D_27613


title: 27613_C5_new onset T1D_27613 lib33970_CCUWNANXX_tophat_alignments

description: 27613_C5_new onset T1D_27613


title: 27613_C9_new onset T1D_27613 lib33974_CCUWNANXX_tophat_alignments

description: 27613_C9_new onset T1D_27613


title: 27613_C3_new onset T1D_27613 lib33968_CCUWNANXX_tophat_alignments

description: 27613_C3_new onset T1D_27613


title: 27613_C11_new onset T1D_27613 lib33976_CCUWNANXX_tophat_alignments

description: 27613_C11_new onset T1D_27613


title: 27613_D9_new onset T1D_27613 lib33985_CCUWNANXX_tophat_alignments

description: 27613_D9_new onset T1D_27613


title: 27613_D11_new onset T1D_27613 lib33987_CCUWNANXX_tophat_alignments

description: 27613_D11_new onset T1D_27613


title: 27613_C4_new onset T1D_27613 lib33969_CCUWNANXX_tophat_alignments

description: 27613_C4_new onset T1D_27613


title: 27613_C1_new onset T1D_27613 lib33966_CCUWNANXX_tophat_alignments

description: 27613_C1_new onset T1D_27613


title: 27613_C6_new onset T1D_27613 lib33971_CCUWNANXX_tophat_alignments

description: 27613_C6_new onset T1D_27613


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description: 27613_D6_new onset T1D_27613


title: 27613_B11_new onset T1D_27613 lib33964_CCUWNANXX_tophat_alignments

description: 27613_B11_new onset T1D_27613


title: 27613_D2_new onset T1D_27613 lib33978_CCUWNANXX_tophat_alignments

description: 27613_D2_new onset T1D_27613


title: 25160_A3_new onset T1D_25160 lib33991_CCUWNANXX_tophat_alignments

description: 25160_A3_new onset T1D_25160


title: 27613_B9_new onset T1D_27613 lib33962_CCUWNANXX_tophat_alignments

description: 27613_B9_new onset T1D_27613


title: 27613_B12_new onset T1D_27613 lib33965_CCUWNANXX_tophat_alignments

description: 27613_B12_new onset T1D_27613


title: 27613_C2_new onset T1D_27613 lib33967_CCUWNANXX_tophat_alignments

description: 27613_C2_new onset T1D_27613


title: 27613_B10_new onset T1D_27613 lib33963_CCUWNANXX_tophat_alignments

description: 27613_B10_new onset T1D_27613


title: 27613_B6_new onset T1D_27613 lib33959_CCUWNANXX_tophat_alignments

description: 27613_B6_new onset T1D_27613


title: 27613_B4_new onset T1D_27613 lib33957_CCUWNANXX_tophat_alignments

description: 27613_B4_new onset T1D_27613


title: 27613_B5_new onset T1D_27613 lib33958_CCUWNANXX_tophat_alignments

description: 27613_B5_new onset T1D_27613


title: 27613_B8_new onset T1D_27613 lib33961_CCUWNANXX_tophat_alignments

description: 27613_B8_new onset T1D_27613


title: 27613_B3_new onset T1D_27613 lib33956_CCUWNANXX_tophat_alignments

description: 27613_B3_new onset T1D_27613


title: 27613_B7_new onset T1D_27613 lib33960_CCUWNANXX_tophat_alignments

description: 27613_B7_new onset T1D_27613


title: 27613_A7_new onset T1D_27613 lib33948_CCUWNANXX_tophat_alignments

description: 27613_A7_new onset T1D_27613


title: 27613_A9_new onset T1D_27613 lib33950_CCUWNANXX_tophat_alignments

description: 27613_A9_new onset T1D_27613


title: 27613_A8_new onset T1D_27613 lib33949_CCUWNANXX_tophat_alignments

description: 27613_A8_new onset T1D_27613


title: 27613_A12_new onset T1D_27613 lib33953_CCUWNANXX_tophat_alignments

description: 27613_A12_new onset T1D_27613


title: 27613_A11_new onset T1D_27613 lib33952_CCUWNANXX_tophat_alignments

description: 27613_A11_new onset T1D_27613


title: 27613_C8_new onset T1D_27613 lib33973_CCUWNANXX_tophat_alignments

description: 27613_C8_new onset T1D_27613


title: 27613_A10_new onset T1D_27613 lib33951_CCUWNANXX_tophat_alignments

description: 27613_A10_new onset T1D_27613


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description: 27613_B2_new onset T1D_27613


title: 27613_A6_new onset T1D_27613 lib33947_CCUWNANXX_tophat_alignments

description: 27613_A6_new onset T1D_27613


title: 27613_A5_new onset T1D_27613 lib33946_CCUWNANXX_tophat_alignments

description: 27613_A5_new onset T1D_27613


title: 27613_A4_new onset T1D_27613 lib33945_CCUWNANXX_tophat_alignments

description: 27613_A4_new onset T1D_27613


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description: 27613_B1_new onset T1D_27613


title: 22752_C11_new onset T1D_22752 lib33881_CCUWNANXX_tophat_alignments

description: 22752_C11_new onset T1D_22752


title: 27613_A3_new onset T1D_27613 lib33944_CCUWNANXX_tophat_alignments

description: 27613_A3_new onset T1D_27613


title: 22752_C10_new onset T1D_22752 lib33880_CCUWNANXX_tophat_alignments

description: 22752_C10_new onset T1D_22752


title: 27613_A2_new onset T1D_27613 lib33943_CCUWNANXX_tophat_alignments

description: 27613_A2_new onset T1D_27613


title: 22752_C9_new onset T1D_22752 lib33879_CCUWNANXX_tophat_alignments

description: 22752_C9_new onset T1D_22752


title: 22752_C8_new onset T1D_22752 lib33878_CCUWNANXX_tophat_alignments

description: 22752_C8_new onset T1D_22752


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description: 22752_C4_new onset T1D_22752


title: 22752_C7_new onset T1D_22752 lib33877_CCUWNANXX_tophat_alignments

description: 22752_C7_new onset T1D_22752


title: 22752_C1_new onset T1D_22752 lib33871_CCUWNANXX_tophat_alignments

description: 22752_C1_new onset T1D_22752


title: 22752_C3_new onset T1D_22752 lib33873_CCUWNANXX_tophat_alignments

description: 22752_C3_new onset T1D_22752


title: 22752_C2_new onset T1D_22752 lib33872_CCUWNANXX_tophat_alignments

description: 22752_C2_new onset T1D_22752


title: 22752_B12_new onset T1D_22752 lib33870_CCUWNANXX_tophat_alignments

description: 22752_B12_new onset T1D_22752


title: 22752_B10_new onset T1D_22752 lib33868_CCUWNANXX_tophat_alignments

description: 22752_B10_new onset T1D_22752


title: 22752_C5_new onset T1D_22752 lib33875_CCUWNANXX_tophat_alignments

description: 22752_C5_new onset T1D_22752


title: 22752_C6_new onset T1D_22752 lib33876_CCUWNANXX_tophat_alignments

description: 22752_C6_new onset T1D_22752


title: 22752_B11_new onset T1D_22752 lib33869_CCUWNANXX_tophat_alignments

description: 22752_B11_new onset T1D_22752


title: 22752_B9_new onset T1D_22752 lib33867_CCUWNANXX_tophat_alignments

description: 22752_B9_new onset T1D_22752


title: 22752_C12_new onset T1D_22752 lib33882_CCUWNANXX_tophat_alignments

description: 22752_C12_new onset T1D_22752


title: 22752_B6_new onset T1D_22752 lib33864_CCUWNANXX_tophat_alignments

description: 22752_B6_new onset T1D_22752


title: 22752_B5_new onset T1D_22752 lib33863_CCUWNANXX_tophat_alignments

description: 22752_B5_new onset T1D_22752


title: 22752_B8_new onset T1D_22752 lib33866_CCUWNANXX_tophat_alignments

description: 22752_B8_new onset T1D_22752


title: 22752_B7_new onset T1D_22752 lib33865_CCUWNANXX_tophat_alignments

description: 22752_B7_new onset T1D_22752


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description: 22752_B4_new onset T1D_22752


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description: 27613_A1_new onset T1D_27613


title: 22752_B3_new onset T1D_22752 lib33861_CCUWNANXX_tophat_alignments

description: 22752_B3_new onset T1D_22752


title: 22752_B1_new onset T1D_22752 lib33859_CCUWNANXX_tophat_alignments

description: 22752_B1_new onset T1D_22752


title: 22752_A11_new onset T1D_22752 lib33857_CCUWNANXX_tophat_alignments

description: 22752_A11_new onset T1D_22752


title: 22752_B2_new onset T1D_22752 lib33860_CCUWNANXX_tophat_alignments

description: 22752_B2_new onset T1D_22752


title: 22752_A8_new onset T1D_22752 lib33854_CCUWNANXX_tophat_alignments

description: 22752_A8_new onset T1D_22752


title: 22752_A10_new onset T1D_22752 lib33856_CCUWNANXX_tophat_alignments

description: 22752_A10_new onset T1D_22752


title: 22752_A9_new onset T1D_22752 lib33855_CCUWNANXX_tophat_alignments

description: 22752_A9_new onset T1D_22752


title: 22752_A7_new onset T1D_22752 lib33853_CCUWNANXX_tophat_alignments

description: 22752_A7_new onset T1D_22752


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description: 22752_A6_new onset T1D_22752


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description: 22752_A5_new onset T1D_22752


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description: 22752_A4_new onset T1D_22752


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description: 22752_A3_new onset T1D_22752


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description: 20729_H10_new onset T1D_20729


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description: 20729_H12_new onset T1D_20729


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description: 20729_H9_new onset T1D_20729


title: 22752_A1_new onset T1D_22752 lib33847_CCUWNANXX_tophat_alignments

description: 22752_A1_new onset T1D_22752


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description: 20729_H4_new onset T1D_20729


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description: 20729_G11_new onset T1D_20729


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description: 20729_H2_new onset T1D_20729


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description: 20729_G12_new onset T1D_20729


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description: 20729_G7_new onset T1D_20729


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description: 20729_G10_new onset T1D_20729


title: 20729_G8_new onset T1D_20729 lib33831_CCUWNANXX_tophat_alignments

description: 20729_G8_new onset T1D_20729


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description: 20729_H11_new onset T1D_20729


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description: 20729_H5_new onset T1D_20729


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description: 20729_H3_new onset T1D_20729


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description: 20729_G5_new onset T1D_20729


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description: 22752_A2_new onset T1D_22752


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description: 20729_H8_new onset T1D_20729


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description: 20729_G3_new onset T1D_20729


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description: 20729_G1_new onset T1D_20729


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description: 20729_G6_new onset T1D_20729


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description: 20729_G9_new onset T1D_20729


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description: 22752_A12_new onset T1D_22752


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description: 20729_G4_new onset T1D_20729


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description: 20729_H6_new onset T1D_20729


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description: 20729_F12_new onset T1D_20729


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description: 20729_F10_new onset T1D_20729


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description: 20729_F8_new onset T1D_20729


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description: 20729_H7_new onset T1D_20729


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description: 20729_F6_new onset T1D_20729


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description: 20729_F9_new onset T1D_20729


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description: 20729_F7_new onset T1D_20729


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description: 20729_F5_new onset T1D_20729


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description: 20729_F11_new onset T1D_20729


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description: 20729_E11_new onset T1D_20729


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description: 20729_F3_new onset T1D_20729


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description: 20729_F4_new onset T1D_20729


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description: 20729_E8_new onset T1D_20729


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description: 20729_G2_new onset T1D_20729


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description: 20729_F2_new onset T1D_20729


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description: 20729_F1_new onset T1D_20729


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description: 20729_E2_new onset T1D_20729


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description: 20729_E6_new onset T1D_20729


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description: 20729_D12_new onset T1D_20729


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description: 20729_E12_new onset T1D_20729


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description: 20729_E1_new onset T1D_20729


title: 20729_D11_new onset T1D_20729 lib33798_CCUWNANXX_tophat_alignments

description: 20729_D11_new onset T1D_20729


title: 20729_E9_new onset T1D_20729 lib33808_CCUWNANXX_tophat_alignments

description: 20729_E9_new onset T1D_20729


title: 20729_E5_new onset T1D_20729 lib33804_CCUWNANXX_tophat_alignments

description: 20729_E5_new onset T1D_20729


title: 20729_E3_new onset T1D_20729 lib33802_CCUWNANXX_tophat_alignments

description: 20729_E3_new onset T1D_20729


title: 20729_D10_new onset T1D_20729 lib33797_CCUWNANXX_tophat_alignments

description: 20729_D10_new onset T1D_20729


title: 20729_D9_new onset T1D_20729 lib33796_CCUWNANXX_tophat_alignments

description: 20729_D9_new onset T1D_20729


title: 20729_D7_new onset T1D_20729 lib33794_CCUWNANXX_tophat_alignments

description: 20729_D7_new onset T1D_20729


title: 20729_D8_new onset T1D_20729 lib33795_CCUWNANXX_tophat_alignments

description: 20729_D8_new onset T1D_20729


title: 20729_D5_new onset T1D_20729 lib33792_CCUWNANXX_tophat_alignments

description: 20729_D5_new onset T1D_20729


title: 20729_E7_new onset T1D_20729 lib33806_CCUWNANXX_tophat_alignments

description: 20729_E7_new onset T1D_20729


title: 20729_E10_new onset T1D_20729 lib33809_CCUWNANXX_tophat_alignments

description: 20729_E10_new onset T1D_20729


title: 20729_D6_new onset T1D_20729 lib33793_CCUWNANXX_tophat_alignments

description: 20729_D6_new onset T1D_20729


title: 20729_D2_new onset T1D_20729 lib33789_CCUWNANXX_tophat_alignments

description: 20729_D2_new onset T1D_20729


title: 20729_D4_new onset T1D_20729 lib33791_CCUWNANXX_tophat_alignments

description: 20729_D4_new onset T1D_20729