title: rh2527, Group_2, D0

value: Whole blood PAXgene

value: female


title: EP17,Psoriasis,H3K27ac

status: Public on Oct 07 2024

type: SRA

city: Heidelberg

first: Nila

middle: Hendrika

last: Servaas

address: Meyerhofstrasse 1

department: Structural and Computational Biology

country: Germany

institute: EMBL

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic v0.36 for illumina TruSeq3-SE adaptors. FASTQC was performed on samples before and after trimming and those samples which passed quality control were used for alignment.
The ChIP-seq reads were then aligned to human genome assembly hg38 using Bowtie2 with default parameters in “—very-sensitive” mode.
Aligned reads mapping to ChrM, other unassembled contigs and also reads with minimum mapping quality score < 10 were filtered out using SAMtools v1.5. Additionally, duplicates were removed using Picard tool v2.17.6 using the “MarkDuplicates” function.
Peak calling was done per sample using MACS292 v.2.0.1 using default parameters and “--keep-dup all”.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (excluding Input samples)

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
30mL of peripheral blood was collected in EDTA tubes from patients with SLE (n=11) and psoriasis (n=15) and from age- and sex-matched healthy donors (n=11 and n=15 respectively) from The University of Tartu, Estonia. PBMCs were obtained by Ficoll Paque (GE Healthcare) density gradient centrifugation. CD4+ T cells were collected by magnetic isolation using CD4 MicroBeads (Miltenyi) on the AutoMACs (Miltenyi) according to the manufacturer's instructions. 1 million isolated CD4+ T cells were cross-linked with an 11% formaldehyde buffer, lysed and subjected to sonication using a Bioruptor sonicator UCD-200 (Diagenode) to obtain chromatin fragments of 100–500 bp. Sheared chromatin was immunoprecipitated with 2 μL of anti-H3K27ac antibody (Abcam, ab4729) and 2 μL of Dynabeads M-280 magnetic beads (Sheep Anti-Mouse IgG, Sheep Anti-Rabbit IgG, Invitrogen) using the SX-8G IP-Star Automated System (Diagenode). ChIP samples were decrosslinked at 65°C for 4 hours. After incubation, the samples were treated with 0.2 mg/mL RNaseA (RNase Cocktail Enzyme Mix, Ambion, Life Technologies) and 0.4 mg/mL Proteinase K (Thermo Scientific). DNA was purified with the MinElute PCR Purification Kit (Qiagen) according to the manufacturer's protocol.
ChIP-Seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Library quality and concentration were determined using an Agilent Bioanalyzer DNA1000 chip. Libraries were sequenced on an Illumina NextSeq 500 Sequencer (75-bp single-end mode).

tag: tissue

value: Peripheral blood

tag: cell type

value: CD4 T cell

tag: Sex

value: Female

tag: age

tag: condition

value: Psoriasis


title: RNAseq_U2OS_G3BPKO_Thaps_Rep2

city: San Francisco

first: José

middle: M.

last: Liboy-Lugo

state: CA

address: 513 Parnassus Ave.

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
FASTQ files were converted to FASTA format. Reads were aligned with bowtie2 2.4.1 and filtered against a collection of repeat RNAs like tRNA, rRNA, snRNA, scRNA, srpRNA, among others (RMSK). Filtered reads were mapped to the hg38 version of the human genome using STAR 2.7.5a with --sjdbOverhang set to 64. Quality control of mapped reads was performed with MultiQC tool (doi: 10.1093/bioinformatics/btw354).
We used bamCoverage from deeptools to convert RNA-seq pre-processed .bam files to .bigwig files. Raw counts of sequencing reads from exons were stored in a .csv file.
Assembly: hg38
Supplementary files format and content: Coverage tracks were stored in .bw files.
Supplementary files format and content: Raw counts of sequencing reads from exons were stored in .csv files.

molecule: total RNA

source_name: Bone

growth_protocol: Cells were grown in Dubelcco’s Modified Eagle Medium/Ham’s F-12 media, supplemented with 10% Fetal Bovine Serum and 1x of a penicillin streptomycin solution (100x, 10,000 I.U. penicillin (per mL), 10,000 mg/mL streptomycin)  at 37°C, 5% CO2.

extract_protocol:
Cells at 80-90% confluency were harvested from a 15 cm dish. Cells were incubated with 1 µM thapsigargin for 2hrs, and then treated with 50 µg/mL cyclohexamide (CHX) for 1 minute. Then, cells were washed gently with PBS containing 50 µg/mL CHX and lysed in ice-cold lysis buffer (20mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% v/v Triton x-100, 1mM DTT, 20-25 U/mL TURBO DNAse (Thermo Fisher Scientific, AM2238), 100 µg/mL CHX). Cells were triturated with a 26-gauge needle. Lysate was recovered after spinning for 10 min, 20,000g, at 4°C. Total RNA was extracted from 25 µL of lysate with a Direct-zol kit.
rRNA was depleted with a NEBNext rRNA Depletion Kit (NEB, E7400), and following manufacturer’s instructions. Libraries were prepared with a NEBNext Ultra II Directional RNA Library Prep Kit of Illumina (E7760), and following manufacturer’s instructions. cDNA libraries were amplified with multiplex oligos for Illumina sequencing (NEB, E6609S).

value: Bone

tag: cell line

value: epithelial

tag: genotype

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)

tag: treatment

value: Thapsigargin for 2 hours


title: rh2494, Group_2, D7

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Sequenced reads were trimmed with Trim galore using default parameters version 0.6.10
Globin and rRNA reads filtered out with bowtie2 version 2.5.1
Reads aligned and quantified using STAR v 2.7.10b to Mmul_10
Ensembl annotation version 109
Assembly: Mmul_10
Supplementary files format and content: Comma separated value file of raw counts provided in count_matrix.csv

molecule: polyA RNA

organism: Macaca mulatta

source_name: Whole blood PAXgene

extract_protocol:
Whole blood was collected from cynomolgus macaques in PAXgene RNA tubes (PreAnaytiX) to manufacturers instrucruction. RNA was isolated using RNAdvance Blood Kit with the manufacter's instructions
RNA was extracted using the PAXgene Blood miRNA Kit 96, enriched for mRNA with Thermofisher Dynabeads, and libraries prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin depletion kit.

treatment_protocol: Indian rhesus macaques were unvaccinated or received heterologous prime-boost of recombinant vectors expressing SIVmac239 Vif and Nef (rAd5-Vif and rAD5-Nef; rVSV-Nef-Tat-Vif; rRRV-Rev-Tat-Nef, rRRV-Nef, rRRV-Vif), then challenged with a minimal dose of SIVmac239 until productive infection was measured. D0 samples represent baseline prior to the qualifying challenge, with samples then collected at days 3,7,10 and 14 after qualifying challenge dose.

tag: animal id

value: male

value: Unvaccinated

tag: time

tag: outcome

tag: num challenges

tag: final virus_dose


title: NIPBL-D7_DMSO_0min_4sU_15min_R3_SLAM

city: La Jolla

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
Alignment was performed using HISAT-3N with a HISAT-3N index built to account for T>C conversions and with RPE-1 SNPs substituted with N. For alignment purposes, read2 was treated as read1, and read1 was treated as read2.
Aligned data was de-duplicated using Picard MarkDuplicates.
A custom HTSeq Python script (SLAM_HTSeq.py) was used count read pairs that align to a gencode.v25 gene. Read pairs that HISAT-3N determine contain a T>C conversion (Yf>0) are counted as nascent, while all nascent and non-converted read pairs are counted as total.
Assembly: hg38
Supplementary files format and content: Nascent and total gene (gencode.v25) counts in .txt format
Library strategy: SLAM-seq

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin, and grown at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using TRIzol and purified using Direct-zol RNA Miniprep Kit (Zymo #R2052). Iodoacetamide conversion was performed using SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen #061), with subsequent purification using either ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo #R1013).
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Zymo #R3003), according to manufacturer’s instructions.

treatment_protocol: Asynchronous cells were actively cycling when treated with DMSO or dTAGV-1 for the stated times. For synchronization using a double thymidine block/nocodazole, engineered hTERT RPE-1 cells were treated with 2 mM thymidine for 14 hours, released for 10 hours, treated again with 2 mM thymidine for 14 hours, then released for 8 hours. Cells were then treated with 20 ng/ml nocodazole simultaneous with DMSO or dTAGV-1 for 120 minutes. Following this time, mitotic shake-off was used to enrich for cells synchronized to prometaphase, before being released into DMSO or dTAGV-1-containing media for the stated times. Four-thiouridine (4sU) was added to cells to a final concentration of 100 μM. Labeling periods are stated, and are included in the treatment time (e.g. DMSO/dTAG 4 hr would be DMSO/dTAG-only for 3:15 hr, then DMSO/dTAG + 4sU for an additional 45 minutes)

value: hTERT RPE-1

tag: clone name

value: DMSO 120min + 0min

tag: synchronization

tag: 4su labeling_period

value: 15 minutes


title: NIPBL-D7_dTAG_30min_4sU_15min_R3_SLAM

value: dTAGV-1 120min + 30min


title: RNAseq_U2OS_G3BP1wt_DMSO_Rep1

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1

value: DMSO for 2 hours


title: rh2504, Group_2, D10

value: Whole blood PAXgene


title: NIPBL-D7_DMSO_60min_4sU_15min_R3_SLAM

value: DMSO 120min + 60min


title: rh2504, Group_2, D3


title: NIPBL-D7_DMSO_60min_4sU_15min_R2_SLAM


title: NIPBL-D7_dTAG_0min_4sU_15min_R3_SLAM

value: dTAGV-1 120min + 0min


title: RNAseq_U2OS_G3BP2B_DMSO_Rep2

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B


title: EP15,Psoriasis,H3K27ac

value: Peripheral blood

value: CD4 T cell

value: Female

value: Psoriasis


title: rh2504, Group_2, D0


title: RNAseq_U2OS_G3BP2B_DMSO_Rep1

value: Bone

value: epithelial


title: EK7,Healthy,H3K27ac

value: Healthy


title: NIPBL-D7_dTAG_30min_4sU_15min_R2_SLAM

value: hTERT RPE-1


title: EK9,Healthy,H3K27ac


title: rh2494, Group_2, D0

value: male

value: Unvaccinated


title: RNAseq_U2OS_G3BP2A_DMSO_Rep2

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2A


title: RNAseq_U2OSwt_DMSO_Rep2

value: wild type


title: EP11,Psoriasis,H3K27ac


title: rh2494, Group_2, D10


title: NIPBL-D7_dTAG_90min_4sU_15min_R2_SLAM

value: dTAGV-1 120min + 90min

value: 15 minutes


title: NIPBL-D7_DMSO_30min_4sU_15min_R2_SLAM

value: DMSO 120min + 30min


title: EK6,Healthy,H3K27ac

value: Male


title: EK8,Healthy,H3K27ac


title: r18066, Group_2, D7

value: Whole blood PAXgene

value: female


title: NIPBL-D7_dTAG_0min_4sU_15min_R2_SLAM

value: dTAGV-1 120min + 0min


title: EP1,Psoriasis,Input

value: Peripheral blood

value: CD4 T cell


title: lncap_LINC01518 overexpression vector [OE3]

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

country: China

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome using Hisat2 software with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then TPM were calculated.
Genes differentially expressed between groups were identified using the DESeq. A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Used clusterProfiler for GO enrichment analysis, if the adjusted P-value (Qvalue) is less than 0.05,it isconsidered that the function has a significant enrichment situation.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: prostate

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
The RNA was used for library construction using the Illumina HiSeq RNA kit, according to the manufacturer’s recommendations.

value: prostate

value: lncap

value: Hormone-dependent prostate cancer cell

value: LINC01518 overexpression


title: NIPBL-D7_DMSO_90min_4sU_15min_R2_SLAM

value: hTERT RPE-1

value: DMSO 120min + 90min


title: rh2494, Group_2, D3

value: male

value: Unvaccinated


title: EK28,Healthy,H3K27ac

value: Female

value: Healthy


title: NIPBL-D7_dTAG_60min_4sU_15min_R2_SLAM

value: dTAGV-1 120min + 60min

value: 15 minutes


title: NIPBL-D7_dTAG_120min_4sU_15min_R1_SLAM

value: dTAGV-1 120min + 120min


title: lncap_empty vector [NC3]

value: empty vector control


title: RNAseq_U2OS_G3BPKO_DMSO_Rep2

value: Bone

value: epithelial

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)

value: DMSO for 2 hours


title: EK25,Healthy,H3K27ac

value: Peripheral blood

value: CD4 T cell


title: NIPBL-D7_dTAG_90min_4sU_15min_R1_SLAM

value: dTAGV-1 120min + 90min


title: RNAseq_U2OS_G3BP1wt_DMSO_Rep2

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1


title: r18066, Group_2, D14

value: Whole blood PAXgene

value: female


title: RNAseq_U2OS_G3BPKO_DMSO_Rep1


title: EP1,Psoriasis,H3K27ac

value: Male

value: Psoriasis


title: r18066, Group_2, D10

value: Unvaccinated


title: EK26,Healthy,H3K27ac

value: Female

value: Healthy


title: RNAseq_U2OSwt_DMSO_Rep1

value: wild type


title: EK24,Healthy,H3K27ac


title: Achilles tendon, control, rep4

city: Zhuhai

first: Dantian

last: Zhu

address: No. 52, Meihua East Road, Meihua Street, Xiangzhou District, Zhuhai City, Guangdong Province, China

institute: Department of Radiology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai

data_processing:
Reads were aligned to the rat Ensemble genome Rnor_6.0 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. Read counts and gene length were calculated using featureCounts (v1.6.3). Normalization and Differential gene expression (DEGs) analysis was conducted using DESeq2 v1.30.1.
Assembly: rat Ensemble genome Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: tissue

extract_protocol:
Fresh Achilles tendon tissues from the right legs of the running and naïve control rats were immediately dissected and placed in RNALater™ (Beyotime) to prevent RNA degradation. The total RNA was extracted after the tissues were mechanically pulverized in TRIzol (Thermo Scientific). After verification of the RNA integrity by Qsep100 (BIOptic; RNA integrity number > 7.0), polyA mRNAs was purified from total RNA using mRNA capture beads (Vazyme, N401). Then the mRNA was reverse-transcribed to create a cDNA library. VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02) was used for library preparation.
RNA sequencing was performed using the Illumina NovaSeq 6000 sequencer.

treatment_protocol: Rats in the running group (12 h p.r. group) sacrificed 12 h after 1 h of treadmill running. Control rats rested in cages and were sacrificed at the same time as the running group.

value: tissue

value: WT

value: control,  rested in cages


title: NIPBL-D7_DMSO_0min_4sU_15min_R2_SLAM

value: hTERT RPE-1

value: DMSO 120min + 0min

value: 15 minutes


title: r18066, Group_2, D3


title: r17100, Group_2, D14

value: male


title: EK4,Healthy,H3K27ac

value: Peripheral blood

value: CD4 T cell


title: EK24,Healthy,Input


title: NIPBL-D7_DMSO_60min_4sU_15min_R1_SLAM

value: DMSO 120min + 60min


title: EK3,Healthy,H3K27ac


title: EK23,Healthy,H3K27ac


title: NIPBL-D7_dTAG_30min_4sU_15min_R1_SLAM

value: dTAGV-1 120min + 30min


title: r18066, Group_2, D0

value: Whole blood PAXgene

value: female


title: r17100, Group_2, D10

value: Unvaccinated


title: lncap_LINC01518 overexpression vector [OE2]

value: prostate

value: lncap

value: Hormone-dependent prostate cancer cell

value: LINC01518 overexpression


title: r17115, Group_1, D14

value: Vaccinated


title: NIPBL-D7_DMSO_120min_4sU_15min_R1_SLAM

value: DMSO 120min + 120min


title: lncap_LINC01518 overexpression vector [OE1]


title: r17100, Group_2, D7


title: Achilles tendon, control, rep1

value: tissue

value: WT

value: control,  rested in cages


title: EK21,Healthy,Input

value: Female

value: Healthy


title: Achilles tendon, exercised 1 h and  sacrificed 12 h after running, rep4

value: sacrificed 12 h after 1 h of treadmill running


title: r17100, Group_2, D0

value: male


title: r17115, Group_1, D7


title: EK2,Healthy,H3K27ac

value: Peripheral blood

value: CD4 T cell


title: EK21,Healthy,H3K27ac


title: lncap_empty vector [NC2]

value: empty vector control


title: NIPBL-D7_dTAG_8hr_R1_HiC

data_processing:
HiC data was first aligned to the hg38 reference genome using BWA-MEM and processed with in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Aligned data was de-duplicated using Picard MarkDuplicates.
Contact files were generated from bam files using in-house perl scripts (see https://github.com/dixonlab/HiC_alignment_basic_scripts).
Juicer was used to create .hic files from contact files, while cooler was used to create multi-resolution cool (mcool) files.
Assembly: hg38
Supplementary files format and content: Multi-resolution cool file
Supplementary files format and content: hic file

extract_protocol:
Cells were fixed and processed according to the Arima Genomics HiC+ Kit protocol. For HiC of the RAD21 degron cell lines, cells were fixed and processed as-normal until prior to decrosslinking. At this stage, samples were stained with propidium iodide, and the G1/2N population was sorted in bulk. G1/2N sorted cells then reentered the HiC protocol.
Proximity-ligated DNA was first sonicated to ~400 bp using a Covaris M220 with 50 W power, 10% duty factor and 200 cycles per burst for 78 seconds, and then size-selected using AMPure beads. For high-input HiC samples, library preparation was performed using KAPA HyperPrep (Roche #KK8502) according to instructions provided with the Arima Genomics HiC+ Kit, with library preparation done on streptavidin beads. For low-input HiC samples, library preparation was performed using 2S Plus DNA Library Kit (IDT #10009878), with pre-PCR library preparation done in solution before biotin enrichment using Dynabeads MyOne Streptavidin T1 beads, and PCR on bead-bound DNA.

treatment_protocol: Asynchronous cells were actively cycling when treated with DMSO or dTAGV-1 for the stated times. For synchronization using a double thymidine block/nocodazole, engineered hTERT RPE-1 cells were treated with 2 mM thymidine for 14 hours, released for 10 hours, treated again with 2 mM thymidine for 14 hours, then released for 8 hours. Cells were then treated with 20 ng/ml nocodazole simultaneous with DMSO or dTAGV-1 for 120 minutes. Following this time, mitotic shake-off was used to enrich for cells synchronized to prometaphase, before being released into DMSO or dTAGV-1-containing media for the stated times.

value: hTERT RPE-1

value: dTAGV-1 120min + 8hr


title: r17082, Group_2, D10

value: Whole blood PAXgene

value: female

value: Unvaccinated


title: NIPBL-D7_DMSO_90min_4sU_15min_R1_SLAM

value: DMSO 120min + 90min

value: 15 minutes


title: lncap_empty vector [NC1]

value: prostate

value: lncap

value: Hormone-dependent prostate cancer cell


title: r17115, Group_1, D3

value: Vaccinated


title: NIPBL-D7_dTAG_60min_4sU_15min_R1_SLAM

value: dTAGV-1 120min + 60min


title: r17115, Group_1, D10


title: Achilles tendon, control, rep3

value: tissue

value: WT

value: control,  rested in cages


title: NIPBL-D7_dTAG_120min_R2_HiC

value: dTAGV-1 120min + 120min


title: r17115, Group_1, D0

value: male


title: r16007, Group_1, D7


title: Achilles tendon, control, rep2


title: EK16,Healthy,H3K27ac

value: Peripheral blood

value: CD4 T cell

value: Male

value: Healthy


title: NIPBL-D7_DMSO_120min_R2_HiC

value: hTERT RPE-1

value: DMSO 120min + 120min


title: NIPBL-D7_dTAG_0min_4sU_15min_R1_SLAM

value: dTAGV-1 120min + 0min

value: 15 minutes


title: r16007, Group_1, D3

value: Whole blood PAXgene

value: female


title: EK22,Healthy,H3K27ac

value: Female


title: r17100, Group_2, D3

value: Unvaccinated


title: NIPBL-D7_DMSO_8hr_R2_HiC

value: DMSO 120min + 8hr


title: Achilles tendon, exercised 1 h and  sacrificed 12 h after running, rep3

value: tissue

value: WT

value: sacrificed 12 h after 1 h of treadmill running


title: NIPBL-D7_dTAG_8hr_R2_HiC

value: dTAGV-1 120min + 8hr


title: Achilles tendon, exercised 1 h and  sacrificed 12 h after running, rep2


title: EK14,Healthy,H3K27ac

value: Peripheral blood


title: NIPBL-D7_DMSO_8hr_R1_HiC


title: EK17,Healthy,H3K27ac

value: CD4 T cell


title: r16007, Group_1, D14

value: Vaccinated


title: EK16,Healthy,Input

value: Male

value: Healthy


title: Achilles tendon, control, rep1

source_name: Achilles tendon

treatment_protocol: Rats in the 1 h treadmill running group (0 h p.r. group) and control (NC group) were sacrificed immediately.

value: Achilles tendon

value: control


title: EK19,Healthy,H3K27ac


title: r16007, Group_1, D10


title: Achilles tendon, control, rep4


title: EK13,Healthy,H3K27ac


title: EK12,Healthy,Input


title: NIPBL-D7_dTAG_90min_R2_HiC

value: hTERT RPE-1

value: dTAGV-1 120min + 90min


title: EK15,Healthy,H3K27ac


title: Achilles tendon, control, rep2


title: Achilles tendon, exercised 1 h and  sacrificed immediately, rep2


title: NIPBL-D7_DMSO_90min_R2_HiC

value: DMSO 120min + 90min


title: EK12,Healthy,H3K27ac

value: Female


title: NIPBL-D7_DMSO_30min_R2_HiC

value: DMSO 120min + 30min


title: r16007, Group_1, D0

value: Whole blood PAXgene

value: female


title: Achilles tendon, exercised 1 h and  sacrificed 12 h after running, rep1

value: tissue

value: WT


title: Achilles tendon, control, rep3


title: r15093, Group_2, D0

value: Unvaccinated


title: NIPBL-D7_DMSO_0min_R2_HiC

value: DMSO 120min + 0min


title: r15093, Group_2, D14


title: BLaER1 Mo internalizing Mito+ RBCs

city: New York

first: Simone

last: Caielli

state: NY

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

data_processing:
Adapter and quality trimming of sequencing reads were performed using TrimGalore
HISAT2 was used for aligning sequncing reads against the human genome GRCh38
Gene quantification was done using feature-counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited file with raw gene counts for each sample

source_name: Cell Line

growth_protocol: Human Mo were sorted from blood

extract_protocol:
Total RNA was isolated from cell lysates using the RNeasy Micro Kit (QIAGEN)
Poly(A)-enriched next-generation sequencing library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) with 100 ng of input total RNA and 15 amplification cycles
The quality and quantity of the individual libraries was assessed using the High Sensitivity DNA Kit (Agilent). The libraries were equimolar pooled, and an additional 1X bead clean-up was used to remove adaptor dimer. The pooled libraries were quantitated using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and sequenced on an Illumina NextSeq 500 with paired-end 75-base-pair (bp) read lengths.

treatment_protocol: Cells were co-cultured with Mito- or Mito+ RBCs for 18 hr

value: Cell Line

value: BLaER1 cells

value: culture with Mito+ RBCs


title: Achilles tendon, exercised 1 h and  sacrificed immediately, rep4


title: r15057, Group_2, D10

value: male


title: BLaER1 Mo internalizing Mito- RBCs

value: culture with Mito- RBCs


title: NIPBL-D7_DMSO_60min_R2_HiC

value: DMSO 120min + 60min


title: r15057, Group_2, D3


title: NIPBL-D7_dTAG_90min_R1_HiC

value: hTERT RPE-1


title: r15093, Group_2, D10


title: Human Mo internalizing Mito- RBCs

source_name: Blood

value: Blood

value: Human Blood Mo


title: r14095, Group_2, D10


title: NIPBL-D7_dTAG_30min_R2_HiC

value: dTAGV-1 120min + 30min


title: NIPBL-D7_dTAG_30min_R1_HiC


title: Achilles tendon, exercised 1 h and  sacrificed immediately, rep3

value: Achilles tendon


title: r15093, Group_2, D3

value: Whole blood PAXgene


title: r15093, Group_2, D7

value: female


title: EK11,Healthy,H3K27ac

value: Peripheral blood

value: CD4 T cell

value: Female

value: Healthy


title: Achilles tendon, exercised 1 h and  sacrificed immediately, rep1

value: WT


title: NIPBL-D7_dTAG_0min_R2_HiC

value: dTAGV-1 120min + 0min


title: Sample_340ctx

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

data_processing:
Bisulfite sequencing reads were processed using CASAVA for base calling and demultiplexing, followed by quality control with NGSQCtoolkit. Trim Galore! was used for adapter and low-quality read trimming. Differentially methylated regions were identified using the methylKit and BiSeq Bioconductor packages.
RNA-seq data were normalized and analyzed using GenomeStudio software. Differential expression was calculated using the Illumina custom model with a false discovery rate (FDR) threshold of p<0.05.
miRNA sequencing data were processed using CASAVA, followed by adapter trimming with cutadapt. Trimmed sequences were aligned with bowtie, and differential expression was analyzed using DESeq Bioconductor package.
Assembly: Reference genome used for alignment and analysis was the Rattus norvegicus assembly (UCSC rn6).
Supplementary files format and content: Processed data files include methylation data, mRNA expression data, and miRNA expression data in XLSX format. DMRs are provided as BED files with genomic coordinates and methylation levels.

source_name: Cortex

growth_protocol: Lineages of Long-Evans hooded rats were locally bred to avoid transportation stress. Nulliparous, pair-housed female rats (90-120 days old) were paired with naïve breeder males until pregnancy was confirmed. On gestational days 12-18, pregnant females were subjected to a daily semi-random stress paradigm including 20 minutes of restraint stress and 5 minutes of swimming. Stress procedures were performed in separate rooms to avoid bystander stress.

extract_protocol:
Cortical and placental tissue was collected from euthanized gestating dams on gestational day 21 via caesarean section. Fetal cortices were dissected and isolated for analysis. Genomic DNA was extracted and digested with restriction enzyme MspI, followed by blunt-ending, adapter ligation, and bisulfite conversion. RNA was isolated using TRIzol reagent and treated with DNase I. Small RNA libraries were prepared from total RNA.
For bisulfite sequencing, bisulfite-converted DNA libraries were prepared by ligating methylated adapters to digested DNA fragments, followed by size selection and purification. For RNA sequencing, mRNA libraries were prepared using the Illumina TotalPrep RNA Amplification Kit, and small RNA libraries were prepared using the TruSeq small RNA library construction kit.
Whole genome bisulfite sequencing (WGBS) was used for DNA methylation analysis, RNA sequencing (RNA-seq) was employed for mRNA expression analysis, and small RNA sequencing was used for miRNA expression analysis.

treatment_protocol: Pregnant females (F0 generation) were exposed to a stress paradigm consisting of restraint stress (20 minutes) and swim stress (5 minutes) daily on gestational days 12-18. Lineages were bred to the F3 generation with varying exposure to stress across generations. The transgenerational lineage received stress only in the F0 generation, while the multigenerational lineage received stress across F0, F1, and F2 generations. The control lineage did not receive any stress.

value: Cortex


title: r14095, Group_2, D3

value: Unvaccinated


title: NIPBL-D7_dTAG_60min_R2_HiC

value: dTAGV-1 120min + 60min


title: EK18,Healthy,Input


title: NIPBL-D7_dTAG_0min_R1_HiC


title: EK18,Healthy,H3K27ac


title: r15057, Group_2, D14

value: male


title: NIPBL-D7_dTAG_120min_R1_HiC

value: hTERT RPE-1

value: dTAGV-1 120min + 120min


title: Human Mo internalizing Mito+ RBCs

value: Blood

value: Human Blood Mo

value: culture with Mito+ RBCs


title: r15057, Group_2, D7

value: Whole blood PAXgene


title: r15057, Group_2, D0


title: NIPBL-D7_DMSO_90min_R1_HiC

value: DMSO 120min + 90min


title: r14065, Group_1, D14

value: female

value: Vaccinated


title: Sample_338pl

source_name: Placenta

value: Placenta


title: Sample_309pl


title: NIPBL-D7_dTAG_24hr_HiC

value: dTAGV-1 24hr

value: Asynchronous


title: r14065, Group_1, D10


title: Sample_338ctx


title: Sample_348pl


title: NIPBL-D7_dTAG_60min_R1_HiC


title: r14095, Group_2, D14


title: Sample_309ctx


title: NIPBL-D7_DMSO_120min_R1_HiC

value: DMSO 120min + 120min


title: r14065, Group_1, D3


title: r14065, Group_1, D0


title: Sample_348ctx

value: Cortex


title: NIPBL-A2_dTAG_4hr_HiC

value: dTAGV-1 4hr


title: Sample_340pl


title: r14095, Group_2, D7

value: Unvaccinated


title: r14095, Group_2, D0


title: NIPBL-D7_DMSO_60min_R1_HiC

value: DMSO 120min + 60min


title: human venous blood astnmatic 5

city: Shenyang

first: Bing

last: Wei

address: No.83 Wenhua Road

institute: General Hospital of Northern Theater Command

data_processing:
The quality of the sequencing data was first evaluated using FastQC software. We then preprocessed the sequencing data using fastp software.For the categorization and annotation of Small RNAs in the processed data,BLAST and Bowtie software were applied.This step included comparison with relevant databases.Subsequently, miRNAs were quantitatively analyzed using MiRDeep2.For differential expression analysis of miRNAs,DESeq software was utilized,setting the thresholds at P<0.05 and |log2(fold change)|>1 to identify differential genes.miRNAs with a log2(fold change) greater than 1 were classified as upregulated (Up),while those with a log2(fold change) less than -1 were marked as downregulated (Down).MiRNAs that did not meet these criteria were categorized as non-significantly differentially expressed genes (Not DEG).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

extract_protocol:
2.5ml of children's venous blood was drawn from fasting subjects using a PAX-gene Blood RNA tube(BD Company,USA).RNA was harvested using PAXgene Blood miRNA Kit(PreAnalytiX, Switzerland),RNA sample concentration ≥ 100 ng/µL, total amount ≥ 2μg, OD260/280 value between 1.8 and 2.2, OD260/230 ≥ 2.0, and RIN ≥ 7 detected by Agilent 2100 Bioanalyzer.
High-resolution polyacrylamide gel electrophoresis (PAGE) was used to isolate miRNA libraries with insert fragment sizes of 22-24 NT

value: blood

tag: disease state

value: asthmatic


title: Sample_265pl

tag: tissue


title: human venous blood astnmatic 4


title: Sample_265ctx


title: r14010, Group_2, D3

value: male


title: human venous blood astnmatic 3


title: NIPBL-D7_DMSO_0min_R1_HiC

value: hTERT RPE-1

value: DMSO 120min + 0min


title: r14010, Group_2, D0

value: Whole blood PAXgene


title: Sample_263ctx


title: NIPBL-A2_dTAG_24hr_HiC


title: rh3033, Group_1, D3


title: r14065, Group_1, D7


title: Sample_304pl


title: NIPBL-D7_dTAG_4hr_HiC


title: Sample_261ctx


title: Sample_304ctx


title: rh3032, Group_1, D3


title: human venous blood healthy 4

value: healthy


title: Sample_301pl


title: NIPBL-D7_DMSO_24hr_HiC

value: DMSO 24hr


title: r14010, Group_2, D14


title: NIPBL-A2_DMSO_24hr_HiC


title: Sample_301ctx


title: Sample_213ctx


title: r14010, Group_2, D10


title: human venous blood healthy 2

value: female


title: Sample_213pl

value: Placenta


title: Sample_263pl


title: human venous blood astnmatic 2


title: human venous blood astnmatic 1


title: r14010, Group_2, D7


title: Sample_207ctx


title: human venous blood healthy 5


title: NIPBL-D7_DMSO_30min_R1_HiC

value: DMSO 120min + 30min


title: r12048, Group_2, D7


title: Riboseq_V11A_Tg_Rep2

description: Ribosomal footprint RNA

data_processing:
FASTQ files were converted to FASTA format. Ribo-seq footprint reads were trimmed of adapter sequences with cutadapt and filtered based on a 32 nt cutoff. UMI sequences were collapsed and removed. Reads were aligned with bowtie2 2.4.1 and filtered against a collection of repeat RNAs like tRNA, rRNA, snRNA, scRNA, srpRNA, among others (RMSK). Filtered reads were mapped to the hg38 version of the human genome using STAR 2.7.5a with --sjdbOverhang set to 29. Quality control of mapped footprint reads was performed with R package Ribo-seQC (doi: doi:10.1101/601468) and MultiQC tool (doi: 10.1093/bioinformatics/btw354).
We used bamCoverage from deeptools to convert Ribo-seq pre-processed .bam files to .bigwig files. Raw counts of sequencing reads from exons were stored in a .csv file.
Assembly: hg38
Supplementary files format and content: Coverage tracks were stored in .bw files.
Supplementary files format and content: Raw counts of sequencing reads from exons were stored in .csv files.
Library strategy: Ribo-seq

extract_protocol:
Cells at 80-90% confluency were harvested from a 15 cm dish. Cells were incubated with 1 µM thapsigargin for 2hrs, and then treated with 50 µg/mL cyclohexamide (CHX) for 1 minute. Then, cells were washed gently with PBS containing 50 µg/mL CHX and lysed in ice-cold lysis buffer (20mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% v/v Triton x-100, 1mM DTT, 20-25 U/mL TURBO DNAse (Thermo Fisher Scientific, AM2238), 100 µg/mL CHX). Cells were triturated with a 26-gauge needle. Lysate was recovered after spinning for 10 min, 20,000g, at 4°C. Lysates were treated with RNAse I (Ambion, 100 U/µL) at room temperature for 45 minutes in slow agitation. Then, treated with SUPERase Inhibitor (Ambion, 20 U/µL) on ice. Monosomes were recovered by size exclusion chromatography (Illustra MicroSpin Columns, S-400 HR, VWR, 95017-619), and footprint RNA fragments were extracted from the flow-through using a Direct-zol kit (Zymo Research).
Gel slices of RNA fragments with sizes between 26-34 nt were excised from a 15% polyacrylamide TBE-Urea gel (Thermo Fisher Scientific, EC68855BOX). Eluted RNA was treated with T4 PNK and preadenylated linker was ligated to the 3’ end using T4 RNA ligase 2 truncated KQ (NEB, M0373L). Linker-ligated RNA was reverse transcribed with Protoscript II (NEB, M0368L) for 30 minutes at 50°C. Template RNA was hydrolyzed with 1M NaOH for 20 minutes at 70°C. Gel slices of reverse transcribed cDNA around 105 nt long, were excised from 15% polyacrylamide TBE-Urea gel. Eluted cDNA was circularized with CircLigase II ssDNA ligase (Lucigen, CL9021K) for 1 hr at 60°C. rRNA was depleted with biotinylated oligos18. cDNA libraries were amplified with different reverse indexing primers per sample.

value: Bone

tag: cell type

value: epithelial

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B V11A

value: Thapsigargin for 2 hours


title: r12048, Group_2, D10

tag: Sex

value: Unvaccinated


title: Sample_202ctx

value: Cortex


title: Sample_189pl


title: rh3033, Group_1, D0

value: Vaccinated


title: rh3032, Group_1, D0


title: Sample_207pl


title: human venous blood healthy 3

value: blood


title: Riboseq_KO_Tg_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: Riboseq_V11A_DMSO_Rep2

description: Ribosomal footprint RNA

value: DMSO for 2 hours


title: Sample_187ctx


title: human venous blood healthy 1


title: Sample_202pl


title: Sample_179pl


title: Riboseq_V11A_Tg_Rep1

description: Ribosomal footprint RNA


title: Sample_189ctx


title: r12048, Group_2, D3

value: male


title: r12048, Group_2, D0

value: Whole blood PAXgene


title: Riboseq_G3BP2B_Tg_Rep2

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B WT


title: r17017, Group_1, D7


title: r17017, Group_1, D14


title: r17039, Group_2, D14


title: Riboseq_G3BP2B_Tg_Rep1

description: Ribosomal footprint RNA


title: Sample_187pl


title: Riboseq_KO_Tg_Rep2

description: Ribosomal footprint RNA


title: r17039, Group_2, D10


title: Sample_172ctx


title: r17017, Group_1, D10


title: r17103, Group_2, D14


title: r17039, Group_2, D7


title: r17039, Group_2, D3


title: Sample_163pl


title: Sample_179ctx


title: Sample_163ctx


title: Riboseq_V11A_DMSO_Rep1

description: Ribosomal footprint RNA


title: Riboseq_V11A_NaAs_Rep1

description: Ribosomal footprint RNA

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 V11A

value: Arsenite for 2 hours


title: Sample_172pl

value: Placenta


title: Riboseq_G3BP2B_DMSO_Rep2

description: Ribosomal footprint RNA


title: r18067, Group_2, D14

value: female


title: Riboseq_G3BP1_NaAs_Rep2

description: Ribosomal footprint RNA

value: Bone

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 WT


title: Riboseq_G3BP2B_DMSO_Rep1

description: Ribosomal footprint RNA

value: epithelial


title: Riboseq_V11A_NaAs_Rep2

description: Ribosomal footprint RNA


title: Riboseq_KO_DMSO_Rep2

description: Ribosomal footprint RNA


title: Sample_168pl


title: r17017, Group_1, D3


title: r17017, Group_1, D0


title: Sample_143ctx


title: r18067, Group_2, D10


title: Riboseq_G3BP1_NaAs_Rep1

description: Ribosomal footprint RNA


title: Sample_141pl


title: Riboseq_KO_NaAs_Rep1

description: Ribosomal footprint RNA


title: r18067, Group_2, D7


title: r17103, Group_2, D10


title: r17039, Group_2, D0


title: r17103, Group_2, D7


title: Sample_143pl


title: r12048, Group_2, D14


title: Riboseq_V11A_water_Rep2

description: Ribosomal footprint RNA

value: water for 2 hours


title: Riboseq_KO_NaAs_Rep2

description: Ribosomal footprint RNA


title: Riboseq_KO_DMSO_Rep1

description: Ribosomal footprint RNA


title: Sample_168ctx


title: s42_cortex_NNN_F3

description: small RNA

source_name: cortex

value: cortex


title: Sample_141ctx

value: Cortex


title: Sample_138ctx


title: Riboseq_V11A_water_Rep1

description: Ribosomal footprint RNA


title: r15058, Group_2, D14

value: Unvaccinated


title: r16003, Group_2, D14


title: Sample_138pl


title: P12_ATAC-seq_Ino80WT_rep3

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were trimmed using Trim Galore and aligned to mm10 using BWA. Duplicates were marked by Picard.
BigWig files were created from merged replicates scaled to 1 million mapped reads using BEDTools.
Assembly: mm10
Supplementary files format and content: Bigwig files for genomic tracks.

organism: Mus musculus

source_name: spermatogenic cells from Testes

extract_protocol:
Seminiferous tubules from P12 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for ATAC-seq library preparation by Omni-ATAC protocol (Corces et al., 2017).
Libraries were generated by following Omni-ATAC protocol (Corces et al., 2017)

tag: age

tag: strain

value: Mixed background

value: Spermatogenic cells

value: Testis


title: s40_cortex_NNN_F3

description: small RNA


title: r18067, Group_2, D3


title: Riboseq_G3BP1_water_Rep2

description: Ribosomal footprint RNA

tag: cell line


title: Riboseq_KO_water_Rep1

description: Ribosomal footprint RNA

tag: genotype

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: Riboseq_G3BP1_water_Rep1

description: Ribosomal footprint RNA

tag: treatment


title: s38_placenta_NNN_F3

description: small RNA

source_name: placenta

value: placenta


title: RNAseq_V11A_Tg_Rep2

data_processing:
FASTQ files were converted to FASTA format. Reads were aligned with bowtie2 2.4.1 and filtered against a collection of repeat RNAs like tRNA, rRNA, snRNA, scRNA, srpRNA, among others (RMSK). Filtered reads were mapped to the hg38 version of the human genome using STAR 2.7.5a with --sjdbOverhang set to 99. Quality control of mapped reads was performed with MultiQC tool (doi: 10.1093/bioinformatics/btw354).
We used bamCoverage from deeptools to convert RNA-seq pre-processed .bam files to .bigwig files. Raw counts of sequencing reads from exons were stored in a .csv file.
Assembly: hg38
Supplementary files format and content: Coverage tracks were stored in .bw files.
Supplementary files format and content: Raw counts of sequencing reads from exons were stored in .csv files.

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B V11A

value: Thapsigargin for 2 hours


title: s41_cortex_NNN_F3

description: small RNA


title: KneeOA_ObeseBMI14 (ST)

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

description: fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using 10X Genomics Space Ranger pipeline to make FASTQ files
Reads were aligned to human genome and transcriptome (vGrCh38) to gene expression count using Space Ranger's default parameters.
Normalization and deconvolution using snRNA-seq data was performed with help of Seurat (v5.0.1) R package and integration of all sequenced samples was performed using Harmony (v0.1.1) R package.
Assembly: GrCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: matrix of gene expression counts
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Infrapatellar Fat Pad

extract_protocol:
Fresh frozen human fat pad samples were embedded in Optimal Cutting Temperature (OCT) medium and frozen in liquid nitrogen. The frozen tissue block was cut into 10 μM sections in a cryostat. RNA was isolated using the Qiagen RNeasy Mini kit per manufacturer’s recommendations. RNA quality control was performed with the Agilent Bioanalyzer using the RNA 6000 Nano Kit.
Spatial sequencing libraries were constructed using the 10X Genomics Visium CytAssist Spatial Gene Expression Reagent Kits. Library quality was assessed on a high sensitivity DNA chip on the Bioanalyzer. Sequencing libraries were volumetrically pooled and sequenced on an Illumina NovaSeq sequencer for 150 paired end read-cycles at the Princess Margaret Genomics Cancer Centre (Toronto, ON, Canada).

value: Infrapatellar Fat Pad

tag: condition

value: OA

tag: procedure

value: Total Knee Replacement

tag: bmi

tag: bmi category

value: Obese


title: r17103, Group_2, D3

value: Whole blood PAXgene

tag: animal id

value: male

tag: time

tag: outcome

tag: num challenges

tag: final virus_dose


title: Riboseq_KO_water_Rep2

description: Ribosomal footprint RNA

tag: tissue

value: Bone

value: epithelial

value: water for 2 hours


title: r08014, Group_1, D14

value: Vaccinated


title: s39_placenta_NNN_F3

description: small RNA


title: s37_placenta_NNN_F3

description: small RNA


title: r15058, Group_2, D10

value: Unvaccinated


title: RNAseq_G3BP2B_Tg_Rep2

tag: cell type

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B WT


title: P12_ATAC-seq_Ino80WT_rep2

value: Mixed background

value: Spermatogenic cells

value: Testis


title: r16003, Group_2, D10

tag: Sex

value: female


title: KneeOA_ObeseBMI13 (ST)

tag: age


title: r08014, Group_1, D10


title: s36_cortex_S_F1

description: small RNA

value: cortex


title: RNAseq_G3BP2B_Tg_Rep1

value: Thapsigargin for 2 hours


title: KneeOA_ObeseBMI12 (ST)

value: Infrapatellar Fat Pad

value: OA


title: r17103, Group_2, D0


title: RNAseq_KO_Tg_Rep2

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: s35_cortex_S_F1

description: small RNA


title: KneeOA_ObeseBMI9 (ST)

value: Total Knee Replacement

value: Obese


title: r15058, Group_2, D7

value: Whole blood PAXgene

value: male


title: KneeOA_ObeseBMI8 (ST)


title: RNAseq_V11A_Tg_Rep1

value: Bone

value: epithelial

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B V11A


title: KneeOA_ObeseBMI10 (ST)


title: s31_cortex_N _F1

description: small RNA

value: N _F1


title: RNAseq_V11A_DMSO_Rep2

value: DMSO for 2 hours


title: r16003, Group_2, D7

value: Unvaccinated


title: r08014, Group_1, D7

value: Vaccinated


title: KneeOA_NormalBMI7 (ST)

value: female

value: Normal


title: KneeOA_NormalBMI5 (ST)


title: r16003, Group_2, D3


title: RNAseq_V11A_DMSO_Rep1


title: r15058, Group_2, D3


title: RNAseq_G3BP2B_DMSO_Rep2

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP2B WT


title: KneeOA_NormalBMI4 (ST)

value: Infrapatellar Fat Pad


title: s30_placenta_S_F1

description: small RNA

value: placenta


title: r18067, Group_2, D0


title: s29_placenta_S_F1

description: small RNA


title: s33_cortex_N _F1

description: small RNA

value: cortex


title: KneeOA_NormalBMI3 (ST)

value: OA

value: Total Knee Replacement


title: s32_cortex_N _F1

description: small RNA


title: RNAseq_KO_DMSO_Rep2

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: RNAseq_G3BP2B_DMSO_Rep1


title: r08014, Group_1, D3

value: Whole blood PAXgene

value: male


title: KneeOA_NormalBMI2 (ST)


title: RNAseq_KO_Tg_Rep1

value: Bone

value: epithelial

value: Thapsigargin for 2 hours


title: P12_ATAC-seq_Ino80WT_rep1

tag: strain

value: Mixed background

value: Spermatogenic cells

value: Testis


title: r16003, Group_2, D0

value: female

value: Unvaccinated


title: CNA KnC3HDZ_8m Input

city: Philadelphia

first: Aman

last: Husbands

email: aman.husbands@gmail.com, ayh@upenn.edu

state: Pennsylvania

address: 103B Caroline Lynch Bldg, 433 S University Ave

institute: University of Pennsylvania

description: 24hrs post induction

data_processing:
Sequences were trimmed with trimmomatic using an initial ILLUMINA CLIP for TruSeq3 singled ended adaptors, and performing sliding window trimming averaging across 4 bp with an average score of 20.
Reads were aligned to the TAIR10 genome using Bowtie2
Peaks were called using MACS2
Differential binding was determined using DiffBind
Assembly: TAIR10
Supplementary files format and content: bigwig, bed file in narrowPeak format (Except input samples)

organism: Arabidopsis thaliana

source_name: 10 day seedling

growth_protocol: seedlings were grown at 22°C under long-day conditions on soil or 1% agarose Murashige and Skoog medium plates (pH 5.7).

extract_protocol:
Seedlings were fixed with 2% formaldehyde for 30 minutes. After quencing, cell lysis, and nuclei isolation, chromatin was sonicated using a Covaris E220
NEBNext Ultra II DNA Library kit

treatment_protocol: Inductions were performed by spraying 9 day old T2 seedlings on agarose plates 10 times with a 50uM β-Estradiol, 1% DMSO, and 0.005% Silwet L-77 solution

value: 10 day seedling

tag: cell line

value: whole seedling

tag: chip antibody


title: r15058, Group_2, D0

tag: genotype

tag: treatment


title: s26_placenta_N _F1

description: small RNA

value: placenta

value: N _F1


title: RNAseq_KO_DMSO_Rep1

value: DMSO for 2 hours


title: RNAseq_V11A_NaAs_Rep2

description: instrument model: NovaSeq X

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 V11A

value: Arsenite for 2 hours


title: s25_placenta_N _F1

description: small RNA


title: KneeOA_NormalBMI1 (ST)

value: Infrapatellar Fat Pad

tag: condition

value: OA

tag: procedure

value: Total Knee Replacement

value: Normal


title: CNA KnC3HDZ_8m FLAG biol rep 2

description: 24hrs post induction

value: FLAG (Sigma-Aldritch, #F1804)


title: s28_placenta_S_F1

description: small RNA


title: IFNaR-/- PD-1

city: Daejeon

first: Juhee

last: Lim

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description: IFNaR KO_PD1

library_source: transcriptomic single cell

data_processing:
The Cell Ranger package (10x Genomics) was used to perform single-cell data processing and to read alignments and feature-barcode matrices generation.
Assembly: mm10-202-A, GRCm38-alts-ensemnl-5.0.0
Supplementary files format and content: features, barcode, matrix

source_name: Brain

extract_protocol:
Brains were harvested and single cells were obtained using a Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Brain cells were separated from debris using Percoll (GE Healthcare Life Sciences) density gradient centrifugation and were treated with ammonium-chloride-potassium lysis buffer to eliminate red blood cells. Cell suspensions were pooled and blocked with anti-CD16/CD32 (clone 2.4G2). Cells were stained with PE anti-mouse CD45.2 (eBioscience) antibody and 7-AAD (BioLegend) at 4°C for 30 min. After washing with DPBS containing 1% FBS, CD45.2+7-AAD- live lung immune cells were isolated using a BD FACSAria II (BD Biosciences). For sorting of CD45.2+ TILs in brains of anti-PD1 treated WT and IFNaR-/- mice, CD3+ and CD3- cells were mixed ina 1:1 ratio and sorted using BD FACSAria II (BD Biosciences).
Sorted cells were counted and resuspended to perform library preparation using Chromium Next GEM Single Cell 5' v2 (Dual Index) kits (10x Genomics) and Chromium Next GEM Single Cell VDJ library v2 kits (10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced using a HiSeq X ten (Illumina) platform for 10,000 cells.

value: Brain

tag: disease state

value: GBM

value: immune cells

value: IFNaR-/-


title: RNAseq_V11A_NaAs_Rep1

description: instrument model: NovaSeq X

source_name: Bone

value: Bone

value: epithelial


title: s24_cortex_SSS_F3

description: small RNA

value: cortex


title: CNA KnC3HDZ_8m FLAG biol rep 1

description: 24hrs post induction

value: 10 day seedling

value: whole seedling


title: s23_cortex_SSS_F3

description: small RNA


title: RNAseq_G3BP1_NaAs_Rep2

description: instrument model: NovaSeq X

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 WT


title: s27_placenta_N _F1

description: small RNA

value: placenta

value: N _F1


title: WT PD-1

value: WT


title: CNA KnC3HDZ Input

description: 24hrs post induction


title: RNAseq_KO_NaAs_Rep2

description: instrument model: NovaSeq X

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)

value: Arsenite for 2 hours


title: s22_cortex_SSS_F3

description: small RNA


title: s21_cortex_SNN_F3

description: small RNA


title: RNAseq_G3BP1_NaAs_Rep1

description: instrument model: NovaSeq X


title: WT D20


title: IFNaR-/- D20

description: IFNaR KO_D20


title: r08014, Group_1, D0

source_name: Whole blood PAXgene

value: Whole blood PAXgene

tag: animal id

value: male

value: Vaccinated


title: CNA KnC3HDZ FLAG biol rep 1

description: 24hrs post induction

value: FLAG (Sigma-Aldritch, #F1804)


title: s050547

city: Guangzhou

first: manman

last: cui

address: Baiyun District

institute: Southern Medical University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
UMI-tools was applied to extract and add 8bp cell barcode sequence and unique molecular identifiers (UMIs) to read name of sequencing read pairs.
Template Switch Oligo (TSO) sequence and ployA tail sequence were trimmed in read1 and removed low-quality bases using costumed script and seqtk tool.
The clean read1 reads were aligned to mm10 reference genome by STAR.
Genomic features were added to reads by featureCounts of subread to count uniquely aligned reads of genes.
Assembly: "count" tool was used to obtain UMI counts.
Supplementary files format and content: mm10
Supplementary files format and content: A comma-separated values (csv) file include UMI counts for each single cell RNA sample

source_name: Female fetal ovaries

growth_protocol: Mice were housed in a light and temperature-controlled room (light: 12 h dark and 12 h light cycles; temperature: 24 ± 0.5 °C) with ad libitum access to food and water. Then, 6~7-week-old female mice were mated with 8-week-old male mice (2:1) overnight and the vaginal plug was checked the next morning.

extract_protocol:
Single cells were randomly picked into precooled lysate by mouth. After shaking for 1min, the lysates were incubated at 72℃ for 3min to release RNA and initial denaturation.
Herein, STRT-seq (modified single-cell tagged reverse transcription protocol) was applied. Firstly, single cells are picked into a PCR tube containing lysates, oligo(dT) primers, and barcode primers. After reverse transcription and cDNA amplification, the single cells labelled with different barcodes were pooled together for subsequent library construction. Additional amplifying for pooled cDNAs were performed by biotin-indexed primers, following shearing to about 300bp by sonication Then, Dynabeads® MyOne™ Streptavidin C1 beads were used to enrich for the 3’ terminal of cDNAs. Finally, the library was constructed by Kapa Hyper Prep Kit and sequenced on illumina Hiseq X Ten for 150bp pair-end reads.

treatment_protocol: Crossed female mice were checked and the day of vaginal plug appearance was defined as E0.5. At the concerned days of gestation (E11.5-18.5), gonads of BVSC transgene mice were dissected and confirmed under the fluorescent microscope. Female gonads were identified by PCR without Sry gene at E11.5 and by dispersive morphology from E12.5 on. For each stage, the gonads pooled from several embryos were digested using 0.05% Trypsin at 37 °C with pipetting at intervals, neutralized with 10% FBS in DMEM, and then filtered through 40 mm cell strainers to obtain single cell suspension for fluorescence-activated cell sorting (FACS).

value: Female fetal ovaries

value: BVSC (Blimp1-mVenus and Stella-ECFP) transgenic mice

value: Trypsin digestion


title: s19_cortex_SNN_F3

description: small RNA


title: RNAseq_KO_NaAs_Rep1

description: instrument model: NovaSeq X

value: Bone

value: epithelial


title: CNA PpHOX32 Input

description: 24hrs post induction

value: 10 day seedling


title: Sample_261pl

value: Placenta


title: s050545

description: polyA RNA


title: CNA PpHOX32 FLAG biol rep 2

description: 24hrs post induction

value: whole seedling


title: s18_placenta_SSS_F3

description: small RNA

value: placenta


title: CNA KnC3HDZ FLAG biol rep 2

description: 24hrs post induction


title: s050544

description: polyA RNA


title: RNAseq_G3BP1_water_Rep2

description: instrument model: NovaSeq X

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 WT

value: water for 2 hours


title: CNA PpHOX32 FLAG biol rep 1

description: 24hrs post induction


title: s17_placenta_SSS_F3

description: small RNA


title: s20_cortex_SNN_F3

description: small RNA

value: cortex


title: CNA SmHOX32 FLAG biol rep 2

description: 24hrs post induction


title: s050540

description: polyA RNA


title: s16_placenta_SSS_F3

description: small RNA


title: RNAseq_KO_water_Rep2

description: instrument model: NovaSeq X

value: G3BP1/2 KO, G3BP deletions by CRISPR Cas9 machinery (doi:10.1083/jcb.201508028)


title: s14_placenta_SNN_F3

description: small RNA


title: s15_placenta_SNN_F3

description: small RNA


title: CNA SmHOX32 Input

description: 24hrs post induction


title: RNAseq_G3BP1_water_Rep1

description: instrument model: NovaSeq X


title: RNAseq_V11A_water_Rep1

description: instrument model: NovaSeq X

value: G3BP1/2 KO cells stably expressing transgenic mEGFP-G3BP1 V11A


title: s13_placenta_SNN_F3

description: small RNA


title: PHB Sddelta Input

description: 24hrs post induction


title: RNAseq_KO_water_Rep1

description: instrument model: NovaSeq X


title: s050538

description: polyA RNA


title: PHB Sddelta FLAG biol rep 3

description: 24hrs post induction


title: TKO-sh2-3

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 transcriptome with STAR, and gene expression was quantified with RSEM.
Differential gene expression analysis was performed with DESeq2.
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Pseudo-counts for all genes in all samples

growth_protocol: Advanced RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% pen/strep in humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was subnitted to the core for the construction of sequencing libraries.
Illumina RNA-seq library prep (Poly A)

treatment_protocol: Cells were transduced with Lentiviral vectors expressing scrambled (shSc) or AK2 (shAK2) shRNA for 72 hrs

value: AK2 Knockdown

tag: biorep


title: s050541

description: polyA RNA


title: CNA SmHOX32 FLAG biol rep 1

description: 24hrs post induction


title: s050534

description: polyA RNA


title: s12_cortex_SS_F2

description: small RNA


title: TKO-sh2-1


title: TKO-sh2-2


title: s11_cortex_SS_F2

description: small RNA


title: s050535

description: polyA RNA


title: s050537

description: polyA RNA


title: TKO-Ctrl-3

value: Scrambled Control


title: PHB Sddelta FLAG biol rep 2

description: 24hrs post induction

value: FLAG (Sigma-Aldritch, #F1804)


title: PHB Sddelta FLAG biol rep 1

description: 24hrs post induction


title: s10_cortex_SS_F2

description: small RNA


title: CNA Sddelta Input

description: 24hrs post induction


title: s050531

description: polyA RNA

value: Female fetal ovaries


title: TKO-Ctrl-2


title: s050529

description: polyA RNA

value: BVSC (Blimp1-mVenus and Stella-ECFP) transgenic mice


title: RNAseq_V11A_water_Rep2

description: instrument model: NovaSeq X


title: s9_cortex_SN_F2

description: small RNA


title: s050528

description: polyA RNA

value: Trypsin digestion


title: CNA Sddelta FLAG biol rep 3

description: 24hrs post induction


title: NTKO-sh2-3


title: s7_cortex_SN_F2

description: small RNA


title: CNA Sddelta FLAG biol rep 2

description: 24hrs post induction


title: NTKO-sh2-2


title: CNA Sddelta FLAG biol rep 1

description: 24hrs post induction


title: s050525

description: polyA RNA


title: s6_placenta_SS_F2

description: small RNA


title: s8_cortex_SN_F2

description: small RNA


title: Col-0 Input

description: 24hrs post induction


title: s050532

description: polyA RNA


title: s050523

description: polyA RNA


title: NTKO-sh2-1


title: s5_placenta_SS_F2

description: small RNA


title: Col-0 FLAG biol rep 2

description: 24hrs post induction


title: NTKO-Ctrl-3


title: s4_placenta_SS_F2

description: small RNA


title: s050522

description: polyA RNA


title: NTKO-Ctrl-2


title: PHB Input

description: 24hrs post induction


title: s050520

description: polyA RNA


title: TKO-Ctrl-1


title: NTKO-Ctrl-1


title: s2_placenta_SN_F2

description: small RNA


title: s3_placenta_SN_F2

description: small RNA


title: PHB FLAG biol rep 3

description: 24hrs post induction


title: s050518

description: polyA RNA


title: TKO-5D-2

data_processing:
library strategy: Amplicon seq
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the Brunello library using Bowtie2.
Quantifcation of sgRNA hits was performed with custom scripts.
Assembly: GRCh38
Supplementary files format and content: Counts of hits to each guide RNA in each sample

extract_protocol:
Genomic DNA was extracted using Blood and Cell Culture DNA Maxi Kit (Qiagen) from cell samples collected at Day 5 and Day 23 (NTKO) or Day 25 (TKO)
PCR using primers with Illumina adapters and multiplexing barcodes

treatment_protocol: Cells weere transduced with the Brunello Library and selected in puromycing for 5 days

tag: timepoint

value: Day 5 Post Transduction


title: TKO-5D-1


title: PHB FLAG biol rep 2

description: 24hrs post induction


title: s050516

description: polyA RNA


title: PHB FLAG biol rep 1

description: 24hrs post induction


title: s050526

description: polyA RNA


title: TKO-25D-2

value: Day 25 Post transduction


title: TKO-25D-1


title: Col-0 FLAG biol rep 1

description: 24hrs post induction

value: 10 day seedling


title: s030711

description: polyA RNA


title: s030712

description: polyA RNA


title: s030708

description: polyA RNA


title: CNA Input

description: 24hrs post induction


title: regenerating hepatocytes, CRISPRi-Neurl1b, mouse2

city: Rochester

first: Dingzi

last: Yin

address: 222 3rd Ave SW

institute: Mayo Clinic

data_processing:
The abundance of transcripts was analyzed by using kallisto
Assembly: mm39
Supplementary files format and content: tab de-limited text file include TPM from each sample

source_name: Liver

growth_protocol: Fah–/–;dCas9+ mice were maintained on 7.5 μg/mL nitisinone until injection of the transposon plasmids

extract_protocol:
400mg liver sample were lysated, ribosome were pulled down with anti-GFP. RNA was extracted from the pulled down product
mRNA was enriched with NEBNext Poly(A) mRNA Magnetic isolation module (E7490). The sequencing libraries were prepared with NEBNext Ultra RNA Library Prep Kit.

treatment_protocol: 10 µg CRISPRi plasmid pkt2-fah-GFPL10a-CRISPRi-Nontargeting or pkt2-fah-GFPL10a-CRISPRi-Neurl1b were mixed with 1x1011 AAV8.TBG.PI.Cre.rBG virus in lactated Lactated Ringer’s solution and hydrodynamically injected through the tail vein at a volume of 1/10 each mouse’s body weight. Nitisinone was withheld immediately after injection. The livers were collected 4 weeks later.

value: Liver

value: hepatocytes

value: regenerating hepatocytes


title: regenerating hepatocytes, CRISPRi-Neurl1b, mouse3


title: regenerating hepatocytes, CRISPRi-nontargeting control,mouse3

value: CRISPRi-nontargeting control


title: CNA FLAG biol rep 3

description: 24hrs post induction

value: whole seedling


title: regenerating hepatocytes, CRISPRi-Neurl1b, mouse1


title: NTKO-5D-2


title: s1_placenta_SN_F2

description: small RNA

value: placenta


title: CNA FLAG biol rep 2

description: 24hrs post induction


title: s030705

description: polyA RNA


title: CNA FLAG biol rep 1

description: 24hrs post induction


title: NTKO-23D-2

value: Day 23 Post transduction


title: s030704

description: polyA RNA


title: regenerating hepatocytes, CRISPRi-nontargeting control,mouse2


title: regenerating hepatocytes, CRISPRi-nontargeting control,mouse1


title: NTKO-23D-1


title: HeLa_nuclear_RNA

status: Public on Oct 06 2024

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: RNA-seq

data_processing:
For circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 (version 2.3.2) were mapped to the reference genome (human: hg38; muose: mm10) by bowtie2 followed by samtools (version 2.3.2) to generate sorted BAM files. The unmapped sequences were obtained by samtools and anchor sequences were extracted from both ends of the sequence. The circRNA were predicted by find_circ (v1.2) after anchor sequences were aligned to the genome.
Assembly: hg38, mm10
Supplementary files format and content: bed files include count values for each Sample

molecule: nuclear RNA

source_name: HeLa

extract_protocol:
The isolated nuclei were lysed in TRizol (Life Technologies). RNA were extracted by using TRizol reagent according to the manufacturer’s instructions.
For RNA-seq, the RNA extracted from nuclei were digested by RNase R. The library construction was conducted as followed: First, RNAs were concentrated. Second, 100 ng of RNA was fragmented at high temperature, followed by the addition of a 5' adaptor. Subsequently, reverse transcription was performed using a 3' adaptor with random hexamers to obtain library cDNA. This was followed by PCR and fragment size selection. After quantification and quality control of the constructed library, sequencing was performed on the HiSeq X10 sequencing platform.

value: HeLa

value: WT


title: ush,ush-GFP,embryonic,Exp1,Input1

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

data_processing:
alignment with BWA Version: 0.7.17-r1188
peak calling with SPP Version 1.15.5
Irreproducible Discovery Rate (IDR) Version 2.0.4.2
Signal tracks using macs2 version 2.2.4 for read pileup
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, html

organism: Drosophila melanogaster

source_name: ush-GFP

extract_protocol:
Fly growth was performed as described previously for the modENCODE and modERN projects Kudron et al., 2018(PMID: 29284660). Transgenic flies were expanded in vials and bottles containing standard Drosophila media at ~22℃ and larvae, white pre-pupae(WPP) and adults were collected from these expansion vials. Pupae were obtained by collecting WPP and incubating for 1-2 days at ~22℃. For embryonic collections, 0-8 day old adult flies were moved to embryo cages capped with apple juice plates. After a 24 hour hours, apple juice plates were replaced at appropriate intervals, restricting the collected embryos to their desired developmental stages. For late embryonic stages, collection plates were removed and embryos were grown at room temperature until the desired stage was reached prior to chromatin collection.    Chromatin was collected and ChIP was performed using the goat anti-GFP as described previously Kudron et al., 2018 (PMID: 29284660).  However, later experiments were performed using Ab290 (Abcam) and denoted as such in Kudron et al., 2024;
Library preparation during the modENCODE and early stages of the modERN project were performed as previously described in Zhong et al. 2010 (PMID: 20174564); Niu et al. 2011 (PMID: 21177963); Kasper et al. 2014(PMID: 25373775); and Kudron et al., 2018(PMID: 29284660). More recently, chromatin has been prepared for sequencing using the following methods at the Yale Center for Genome Analysis (Kudron et al., 2024 Supplemental_File_S1). ChIP and input control samples (genomic DNA from the same sample) for two technical replicates for worm and three for fly were used for library construction using approximately 5-10ng of DNA after the samples were end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles) (KAPA Biosystems, Part#KK8504).  Indexed libraries were quantified by qPCR (KAPA Biosystems, Part#KK4854) and inserts were distributed by size using the Caliper LabChip GX system.  Samples that had a concentration of ≥0.5 ng/ul were used for sequencing.  Samples were normalized to 10 nM and sequenced using 100bp paired-end sequencing on an Illumina HiSeq NovaSeq Sequencer achieving > 5 million reads passing filter clusters.  A positive control provided by Illumina is spiked into every lane at a concentration of 0.3% to monitor quality in real time. Sequencing data that passed internal quality controls at YCGA were transferred to the Waterston Lab for downstream processing.

value: ush-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=ush-GFP.FPTB}VK00031

tag: genetic modification

value: site-specific recombination

tag: developmental stage

value: embryonic


title: s030714

description: polyA RNA

tag: tissue

value: Female fetal ovaries

value: BVSC (Blimp1-mVenus and Stella-ECFP) transgenic mice

value: Trypsin digestion


title: ush,ush-GFP,embryonic,Exp1,ChIP2


title: ush,ush-GFP,embryonic,Exp1,ChIP3


title: ush,ush-GFP,embryonic,Exp1,ChIP1


title: TfAP-2,TfAP-2-GFP,embryonic,Exp1,Input1


title: TfAP-2,TfAP-2-GFP,embryonic,Exp1,ChIP2


title: Skin-TMA

type: RNA

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

hyb_protocol: TMA was sectioned at 5um tickness and placed on Xenium slide following 10x Genomics Demonstrated Protocol CG000578; deparaffainized and decrosslinked according to 10x Genomics Demonstrated Protocol CG000580; probe hybridization, ligataion, and rolling circle amplification subject to 10x Genomics User Guide CG000582; and run through the Xenium Analyzer following the 10x Genomics User Guide CG000584. Custom probes were generated to supplement the predesigned multi-tissue atlasing panel (cat 1000627) using the Xenium Cloud Panel Designer tool.  The custom gene panel is included in the data files.

scan_protocol: Xenium In Situ Analyzer

data_processing: Data processed using Xenium Ranger software

label: Xenium Mouse Multi Tissue Atlassing Probeset + Custom 100 Gene Add-on

source_name: dorsal cutaneous skin wound

label_protocol: Xenium Mouse Multi-tissue Atlasing Probeset + 100 Custom Target Add-on panel

extract_protocol: Wound samples were harvested at the indicated timepoints post wounding. Following animal euthanasia via CO2, wounds were immediately excised with a 3mm margin, briefly immersed in sterile saline prior to fixation in 4% paraformaldehyde for 4-8 hours. Samples were then transferred to 70% ethanol solution and paraffin embedded prior to sectioning at 8um section size on a microtome.  For Xenium, sample cores were harvested from paraffin blocks from unwounded skin and wounds 6 days post injury (both treated with 6 doses of tamoxifen) collected from p21-Cre/+tdT/+ animals, and sample cores were embedded within a tissue microarray prior to sectioning at 5um onto Xenium slides (10x Genomics).

value: tamoxifen, 6 doses


title: NTKO-5D-1

value: Day 5 Post Transduction


title: SoxN,SoxN-GFP,embryonic,Exp1,ChIP2

source_name: SoxN-GFP

value: SoxN-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=SoxN-GFP.FPTB}VK00031


title: term,term-GFP,embryonic,Exp1,ChIP2

source_name: term-GFP

value: term-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=term-GFP.FPTB}VK00037


title: term,term-GFP,embryonic,Exp1,Input1


title: SoxN,SoxN-GFP,embryonic,Exp1,Input1


title: slp1,slp1-GFP,embryonic,Exp1,Input1

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=slp1-GFP.FPTB}VK00031


title: term,term-GFP,embryonic,Exp1,ChIP1


title: TfAP-2,TfAP-2-GFP,embryonic,Exp1,ChIP1


title: SoxN,SoxN-GFP,embryonic,Exp1,ChIP1


title: slp1,slp1-GFP,embryonic,Exp1,ChIP2


title: slp1,slp1-GFP,embryonic,Exp1,ChIP1


title: Sidpn,Sidpn-GFP,embryonic,Exp1,ChIP3

source_name: Sidpn-GFP

value: Sidpn-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=Sidpn-GFP.FPTB}VK00033


title: Sidpn,Sidpn-GFP,embryonic,Exp1,ChIP2


title: Sidpn,Sidpn-GFP,embryonic,Exp1,ChIP1


title: scro,scro-GFP,embryonic,Exp1,ChIP2

source_name: scro-GFP

value: scro-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=scro-GFP.FPTB}VK00037


title: scro,scro-GFP,embryonic,Exp1,ChIP1


title: RunxB,RunxB-GFP,embryonic,Exp1,ChIP2

source_name: RunxB-GFP

value: RunxB-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=RunxB-GFP.FPTB}VK00037


title: RunxB,RunxB-GFP,embryonic,Exp1,Input1

value: site-specific recombination

value: embryonic


title: Sidpn,Sidpn-GFP,embryonic,Exp1,Input1


title: scro,scro-GFP,embryonic,Exp1,Input1


title: pdm2,pdm2-GFP,embryonic,Exp1,ChIP2

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=pdm2-GFP.FPTB}VK00033/TM6C, Sb[1]


title: pdm2,pdm2-GFP,embryonic,Exp1,Input1


title: 293T_nuclear_RNA

description: RNA-seq

value: WT


title: RunxB,RunxB-GFP,embryonic,Exp1,ChIP1


title: nub,nub-GFP,embryonic,Exp1,ChIP1

source_name: nub-GFP

value: nub-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=nub-GFP.FPTB}VK00031/TM6B, Tb[1]


title: nub,nub-GFP,embryonic,Exp1,Input1


title: pdm2,pdm2-GFP,embryonic,Exp1,ChIP1


title: nub,nub-GFP,embryonic,Exp1,ChIP3


title: mid,mid-GFP,embryonic,Exp1,ChIP4

source_name: mid-GFP

value: mid-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=mid-GFP.FPTB}VK00031


title: mid,mid-GFP,embryonic,Exp1,ChIP2


title: Mes2,Mes2-GFP,embryonic,Exp1,Input1

value: y[1] w[*]; P{y[+t7.7] w[+mC]=Mes2-GFP.FPTB}attP40/CyO


title: Mef2,Mef2-GFP,embryonic,Exp1,ChIP3

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=Mef2-GFP.FPTB}VK00031/TM6B, Tb[1]


title: Mes2,Mes2-GFP,embryonic,Exp1,ChIP2


title: mid,mid-GFP,embryonic,Exp1,ChIP1


title: mid,mid-GFP,embryonic,Exp1,Input1


title: l(1)sc,l(1)sc-GFP,embryonic,Exp1,Input1


title: l(1)sc,l(1)sc-GFP,embryonic,Exp1,ChIP4


title: Mef2,Mef2-GFP,embryonic,Exp1,Input1


title: Mes2,Mes2-GFP,embryonic,Exp1,ChIP1


title: l(1)sc,l(1)sc-GFP,embryonic,Exp1,ChIP3


title: Mef2,Mef2-GFP,embryonic,Exp1,ChIP1


title: l(1)sc,l(1)sc-GFP,embryonic,Exp1,ChIP1


title: l(1)sc,l(1)sc-GFP,embryonic,Exp1,ChIP2


title: Kr-h1,Kr-h1-GFP,embryonic,Exp1,ChIP2

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=Kr-h1-GFP.FPTB}VK00031/TM6B, Tb[1]


title: Kr-h1,Kr-h1-GFP,embryonic,Exp1,ChIP3


title: nub,nub-GFP,embryonic,Exp1,ChIP2


title: Kr-h1,Kr-h1-GFP,embryonic,Exp1,ChIP1


title: HGTX,HGTX-GFP,embryonic,Exp1,ChIP4

source_name: HGTX-GFP

value: HGTX-GFP

value: y[1] w[*]; P{y[+t7.7] w[+mC]=HGTX-GFP.FPTB}attP40


title: HGTX,HGTX-GFP,embryonic,Exp1,Input1


title: HGTX,HGTX-GFP,embryonic,Exp1,ChIP3


title: mid,mid-GFP,embryonic,Exp1,ChIP3


title: Mef2,Mef2-GFP,embryonic,Exp1,ChIP2


title: HGTX,HGTX-GFP,embryonic,Exp1,ChIP1


title: FoxK,FoxK-GFP,embryonic,Exp1,ChIP2

source_name: FoxK-GFP

value: FoxK-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=FoxK-GFP.FPTB}VK00037


title: FoxK,FoxK-GFP,embryonic,Exp1,Input1


title: fd19B,fd19B-GFP,embryonic,Exp1,ChIP3

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=fd19B-GFP.FPTB}VK00033


title: FoxK,FoxK-GFP,embryonic,Exp1,ChIP1


title: fd19B,fd19B-GFP,embryonic,Exp1,Input1


title: HGTX,HGTX-GFP,embryonic,Exp1,ChIP2


title: fd19B,fd19B-GFP,embryonic,Exp1,ChIP2


title: erm,erm-GFP,embryonic,Exp1,Input1

source_name: erm-GFP

value: erm-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=erm-GFP.FPTB}VK00031


title: fd19B,fd19B-GFP,embryonic,Exp1,ChIP1

value: site-specific recombination

value: embryonic


title: erm,erm-GFP,embryonic,Exp1,ChIP3


title: erm,erm-GFP,embryonic,Exp1,ChIP2


title: dve,dve-GFP,embryonic,Exp1,Input1

source_name: dve-GFP

value: dve-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=dve-GFP.FPTB}VK00031


title: erm,erm-GFP,embryonic,Exp1,ChIP4


title: dve,dve-GFP,embryonic,Exp1,ChIP2


title: dve,dve-GFP,embryonic,Exp1,ChIP1


title: drm,drm-GFP,embryonic,Exp1,Input1

source_name: drm-GFP

value: drm-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=drm-GFP.FPTB}VK00031


title: Kr-h1,Kr-h1-GFP,embryonic,Exp1,Input1


title: dve,dve-GFP,embryonic,Exp1,ChIP3


title: erm,erm-GFP,embryonic,Exp1,ChIP1


title: drm,drm-GFP,embryonic,Exp1,ChIP1


title: drm,drm-GFP,embryonic,Exp1,ChIP2


title: CG7691,CG7691-GFP,prepupa,Exp1,Input1

value: prepupa


title: CG7691,CG7691-GFP,prepupa,Exp1,ChIP1


title: CG4936,CG4936-GFP,embryonic,Exp1,Input1


title: CG4936,CG4936-GFP,embryonic,Exp1,ChIP3


title: CG7691,CG7691-GFP,prepupa,Exp1,ChIP2


title: CG4936,CG4936-GFP,embryonic,Exp1,ChIP2


title: CG4936,CG4936-GFP,embryonic,Exp1,ChIP1


title: CG42741,CG42741-GFP,embryonic,Exp1,ChIP3


title: CG42741,CG42741-GFP,embryonic,Exp1,ChIP1


title: CG15436,CG15436-GFP,embryonic,Exp1,ChIP3

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=Paris-GFP.FPTB}VK00033


title: CG15436,CG15436-GFP,embryonic,Exp1,Input1


title: CG42741,CG42741-GFP,embryonic,Exp1,Input1


title: CG15436,CG15436-GFP,embryonic,Exp1,ChIP1


title: CG15436,CG15436-GFP,embryonic,Exp1,ChIP2


title: drm,drm-GFP,embryonic,Exp1,ChIP3


title: CG11966,CG11966-GFP,embryonic,Exp1,ChIP2


title: CG11906,CG11906-GFP,embryonic,Exp1,Input1


title: CG13897,CG13897-GFP,embryonic,Exp1,Input1


title: CG11906,CG11906-GFP,embryonic,Exp1,ChIP4


title: CG11906,CG11906-GFP,embryonic,Exp1,ChIP3


title: CG11906,CG11906-GFP,embryonic,Exp1,ChIP1


title: CG10949,CG10949-GFP,embryonic,Exp1,Input1


title: CG10949,CG10949-GFP,embryonic,Exp1,ChIP2


title: CG10949,CG10949-GFP,embryonic,Exp1,ChIP1


title: Cf2,Cf2-GFP,embryonic,Exp1,Input1

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=Cf2-GFP.FPTB}VK00031


title: Cf2,Cf2-GFP,embryonic,Exp1,ChIP2


title: CG15436,CG15436-GFP,embryonic,Exp1,ChIP4


title: CG42741,CG42741-GFP,embryonic,Exp1,ChIP2


title: bs,bs-GFP,embryonic,Exp1,Input1

source_name: bs-GFP

value: bs-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=bs-GFP.FPTB}VK00031


title: CG42741,CG42741-GFP,embryonic,Exp1,ChIP4


title: CG13897,CG13897-GFP,embryonic,Exp1,ChIP1


title: bs,bs-GFP,embryonic,Exp1,ChIP2


title: bin,bin-GFP,embryonic,Exp1,Input1

source_name: bin-GFP

value: bin-GFP

value: y[1] w[*]; PBac{y[+mDint2] w[+mC]=bin-GFP.FPTB}VK00037


title: bin,bin-GFP,embryonic,Exp1,ChIP2


title: bs,bs-GFP,embryonic,Exp1,ChIP1


title: CG13897,CG13897-GFP,embryonic,Exp1,ChIP2


title: CG11966,CG11966-GFP,embryonic,Exp1,Input1


title: Cf2,Cf2-GFP,embryonic,Exp1,ChIP1


title: bin,bin-GFP,embryonic,Exp1,ChIP1


title: bap,bap-GFP,embryonic,Exp1,ChIP2

source_name: bap-GFP

value: bap-GFP


title: CG11966,CG11966-GFP,embryonic,Exp1,ChIP1


title: bap,bap-GFP,embryonic,Exp1,Input1


title: bap,bap-GFP,embryonic,Exp1,ChIP1


title: apt,apt-GFP,embryonic,Exp1,Input1

source_name: apt-GFP

value: apt-GFP


title: apt,apt-GFP,embryonic,Exp1,ChIP1


title: apt,apt-GFP,embryonic,Exp1,ChIP2


title: Mouse, Plcb3_KO, Ileum, H2O, rep1

first: Ikuo

last: Takazawa

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Ileum from Plcb3_KO without DSS

hyb_protocol: Standard hybridization

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The gene expression profiles were assessed using a microarray technology with   Agilent Sure Print G3 Mouse GE 8x60K Ver 3.0 according to the manufacturer’s instruction.   gMedian fluorescence of probes from individual samples were normalized by agilp package.

source_name: Ileum

label_protocol: Standard labeling

extract_protocol: RNAs were extracted from isolated intestinal epithelial cells, whole jejunum or ileum   using Rneasy (QIAGEN) and on column Dnase kit (QIAGEN) following manufacturer's instruction. RNA integrity was assessed by 0.8 % agarose gel electrophoresis and Bioanalyzer (Agilent)

treatment_protocol: 3 % (w/v) DSS was added or not to drinking water and mice were treated ad libitum for 5 days.


title: Mouse, WT, Ileum, DSS, rep1

description: Ileum from WT with DSS

value: WT

value: DSS


title: Mouse, Plcb3_KO, Ileum, DSS, rep2

description: Ileum from Plcb3_KO with DSS


title: Mouse, Plcb3_KO, Jejunum, H2O, rep1

description: Jejunum from Plcb3_KO without DSS

source_name: Jejunum


title: Mouse, Plcb3_KO, Ileum, DSS, rep1

description: Ileum from Plcb3_KO with DSS


title: Mouse, Plcb3_KO, Ileum, H2O, rep2

description: Ileum from Plcb3_KO without DSS


title: Mouse, WT, Ileum, H2O, rep2

description: Ileum from WT without DSS


title: Mouse, Plcb3_KO, Jejunum, DSS, rep2

description: Jejunum from Plcb3_KO with DSS


title: Mouse, WT, Jejunum, DSS, rep1

description: Jejunum from WT with DSS


title: Mouse, WT, Ileum, DSS, rep2

description: Ileum from WT with DSS


title: Mouse, Plcb3_KO, Jejunum, H2O, rep2

description: Jejunum from Plcb3_KO without DSS


title: Mouse, WT, Ileum, H2O, rep1

description: Ileum from WT without DSS


title: Mouse, WT, Jejunum, H2O, rep2

description: Jejunum from WT without DSS


title: Mouse, Plcb3_deltaIEC, IEC, H2O, rep3

description: IEC from Plcb3_deltaIEC without DSS

source_name: intestinal epithelial cells


title: Mouse, Plcb3_deltaIEC, IEC, DSS, rep1

description: IEC from Plcb3_deltaIEC with DSS


title: Mouse, Plcb3_deltaIEC, IEC, DSS, rep2

description: IEC from Plcb3_deltaIEC with DSS


title: Mouse, Plcb3_deltaIEC, IEC, H2O, rep1

description: IEC from Plcb3_deltaIEC without DSS


title: Mouse, WT, Jejunum, DSS, rep2

description: Jejunum from WT with DSS


title: Mouse, Plcb3_Flox, IEC, DSS, rep3

description: IEC from Flox control with DSS


title: Mouse, Plcb3_deltaIEC, IEC, H2O, rep2

description: IEC from Plcb3_deltaIEC without DSS


title: Mouse, Plcb3_Flox, IEC, DSS, rep1

description: IEC from Flox control with DSS


title: Mouse, Plcb3_Flox, IEC, H2O, rep2

description: IEC from Flox control without DSS


title: Mouse, WT, Jejunum, H2O, rep1

description: Jejunum from WT without DSS


title: Mouse, Plcb3_Flox, IEC, H2O, rep3

description: IEC from Flox control without DSS


title: Mouse, Plcb3_Flox, IEC, DSS, rep2

description: IEC from Flox control with DSS


title: Mouse, Plcb3_KO, IEC, DSS, rep3

description: IEC from Plcb3_KO with DSS


title: Mouse, Plcb3_Flox, IEC, H2O, rep1

description: IEC from Flox control without DSS


title: Mouse, Plcb3_KO, Jejunum, DSS, rep1

description: Jejunum from Plcb3_KO with DSS


title: Mouse, Plcb3_deltaIEC, IEC, DSS, rep3

description: IEC from Plcb3_deltaIEC with DSS


title: Donor_3_ZNF791

city: Baltimore

first: Josh

last: Weinstock

state: MD

address: 3100 Wyman Park Dr

institute: Johns Hopkins University

data_processing:
Adapters were trimmed from fastq files with cutadapt. Low-quality bases from reads were trimmed using the Phred algorithm implemented in seqtk. Reads were aligned with STAR and mapped to GRCh38. Gene counts from deduplicated reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: dedup_counts.txt stores gene counts from deduplicated reads

source_name: CD4 T cells

growth_protocol: Primary CD25-CD4+ effector T cells were isolated from fresh Human Peripheral Blood Leukopaks (STEMCELL Technologies, #70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). Peripheral blood mononuclear cells (PBMCs) were washed twice with a 1X volume of EasySep buffer (DPBS, 2% fetal Bovine Serum (FBS), 1mM pH 8.0 EDTA). The washed PBMCs were resuspended at 200E6 cells/mL in EasySep buffer and isolated with the EasySep™ Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, #18063), according to the manufacturer’s protocol. Cells were seeded at 1x106 cells/mL in complete RPMI-1640 supplemented with 10% FCS, 2 mM L-Glutamine (Fisher Scientific #25030081), 10 mM HEPES (Sigma, #H0887-100ML), 1X MEM Non-essential Amino Acids (Fisher, #11140050), 1 mM Sodium Pyruvate (Fisher Scientific #11360070), 100 U/mL Penicillin-Streptomycin (Sigma, #P4333-100ML), and 50 U/mL IL-2 (Amerisource Bergen, #10101641) and stimulated with 6.25 uL/mL ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, #10990). Following activation and electroporation, cells were split 1:2 every other day to maintain an approximate density of 1x106 cells/mL.

extract_protocol:
8 days after T cell isolation and activation, the cells were pelleted and resuspended at 1×106cells per 300 ul of RNA lysis buffer (Zymo, #R1060–1-100). Cells were pipette mixed and frozen at −80 until RNA isolation was performed. RNA was isolated using the Zymo-Quick RNA micro prep kit (#R1051) according to the manufacturer’s protocol with the following modifications: After thawing the samples, each tube was vortexed vigorously to ensure complete lysis prior to loading into the extraction columns. In lieu of the kit provided DNAse, RNA was eluted from the isolation column after the recommended washes and digested with Turbo-DNAse (Fisher Scientific, AM2238) at 37 C for 20 minutes. Following digestion, RNA was purified using the RNA Clean & Concentrator-5 kit (Zymo, #R1016) according to the manufacturer’s protocol. The resulting purified RNA was submitted to the UC Davis DNA Technologies and Expression Analysis Core to generate 3′ Tag-seq libraries with unique molecular indices (UMIs).
Barcoded sequencing libraries were prepared using the QuantSeq FWD kit (Lexogen) for multiplexed sequencing on an Hiseq 4000 (Illumina).

treatment_protocol: Custom crRNAs (Dharmacon) and Dharmacon Edit-R CRISPR-Cas9 Synthetic tracrRNA (Dharmacon, #U-002005-20) were resuspended in Nuclease Free Duplex Buffer (IDT, #11-01-03-01) at 160uM stock concentration. In a 96 well plate, each crRNA was combined with tracrRNA at a 1:1 molar ratio and incubated at 37°C for 30 minutes. Single-stranded donor oligonucleotides (ssODN; sequence: TTAGCTCTGTTTACGTCCCAGCGGGCATGAGAGTAACAAGAGGGTGTGGTAATATTACGGTACCGAGCACTATCGATACAATATGTGTCATACGGACACG, 100uM stock) was added to the complex at a 1:1 molar ratio and incubated at 37°C for 5 minutes. Finally, Cas9 protein (MacroLab, Berkeley, 40 µM stock) was added at a 1:2 molar ratio and incubated at 37°C for 15 minutes. The resulting RNPs were frozen at -80°C until the day of electroporation. 48 hours following effector T cell activation, the cells were pelleted at 100x g for 10 minutes and resuspended in room temperature Lonza P3 buffer (Lonza, catalog no. V4XP-3032) at 1.5x106 cells per 20 ul P3. The cells were combined with 5 ul aliquots of the thawed RNPs, transferred to a 96-well electroporation cuvette plate (Lonza, #VVPA-1002) and nucleofected with pulse code EH-115. Immediately following electroporation, the cells were gently resuspended in 90 ul warmed complete RPMI with IL-2 and incubated at 37 C for 15 minutes. After recovery, the cells were cultured in 96 well plates at 1x106 cells/mL for the duration of the experiment. To prevent edge effects, the guides were randomly distributed across each plate and the first and last column of each plate was excluded, being filled instead with PBS to prevent evaporation.

tag: cell type

value: CD4 T cells


title: Donor_3_AAVS1_1_2


title: Donor_3_ZKSCAN1


title: Donor_3_NFKB1


title: Donor_3_ZNF329


title: Donor_3_STAT1


title: Donor_3_AAVS1_3_2


title: Donor_3_STAT2


title: Donor_3_NFE2L3


title: Donor_3_RBCK1


title: Donor_3_KLF9


title: Mouse, Plcb3_KO, IEC, DSS, rep2

city: La Jolla

description: IEC from Plcb3_KO with DSS


title: Mouse, WT, IEC, DSS, rep2

description: IEC from WT with DSS


title: Mouse, WT, IEC, DSS, rep3

description: IEC from WT with DSS


title: Mouse, Plcb3_KO, IEC, H2O, rep3

description: IEC from Plcb3_KO without DSS


title: Mouse, WT, IEC, DSS, rep1

description: IEC from WT with DSS


title: Donor_3_LCOR


title: Mouse, WT, IEC, H2O, rep3

description: IEC from WT without DSS


title: Mouse, WT, IEC, H2O, rep2

description: IEC from WT without DSS


title: Mouse, Plcb3_KO, IEC, H2O, rep1

description: IEC from Plcb3_KO without DSS


title: Mouse, Plcb3_KO, IEC, DSS, rep1

description: IEC from Plcb3_KO with DSS


title: Donor_3_ZNF331


title: Mouse, WT, IEC, H2O, rep1

description: IEC from WT without DSS


title: Mouse, Plcb3_KO, IEC, H2O, rep2

description: IEC from Plcb3_KO without DSS


title: Donor_3_TP53


title: Donor_3_AAVS1_7_2


title: Donor_3_ZBTB14


title: Donor_3_ZNF655


title: Donor_3_AKAP8


title: Donor_3_POU2F1


title: Donor_3_RFX5


title: Donor_3_BACH2


title: Donor_3_AAVS1_5_2


title: Donor_3_SREBF1


title: Donor_3_AAVS1_8_2


title: Donor_3_IRF8


title: Donor_3_ZNF341


title: Donor_3_YBX3


title: Donor_3_FOXP3


title: Donor_3_NFKB2


title: Donor_3_AAVS1_6_2


title: Donor_3_SP110


title: Donor_3_TCF3


title: Donor_3_SETDB1


title: Donor_3_GFI1


title: Donor_3_TTF1


title: Donor_3_NFE2L2


title: Donor_3_BPTF


title: Donor_3_AAVS1_2_2


title: Donor_3_EGR3


title: Donor_3_IRF7


title: Donor_3_SON


title: Donor_3_AAVS1_4_2


title: Donor_3_ZBTB24


title: Donor_3_STAT3


title: Donor_3_ELK4


title: Donor_3_RORC


title: Donor_3_ZNF708


title: Donor_3_ATMIN


title: Donor_3_RELB


title: Donor_3_AAVS1_12_2


title: Donor_3_AAVS1_11_2


title: Donor_3_DR1


title: Donor_3_BCL11B


title: Donor_3_ZFP3


title: Donor_3_REL


title: Donor_3_IRF9


title: Donor_3_ZNF575


title: Donor_3_CLOCK


title: Donor_3_AAVS1_10_2


title: Donor_3_EPAS1


title: Donor_3_HIVEP3


title: Donor_3_NFAT5


title: Donor_3_MYSM1


title: CG11906,CG11906-GFP,embryonic,Exp1,ChIP2

value: site-specific recombination

value: embryonic


title: Donor_3_TET2


title: Donor_3_TBX21


title: Donor_3_YBX1


title: Donor_3_AAVS1_9_2


title: Donor_3_ARID5A


title: Donor_3_IRF3


title: Donor_3_IKZF1


title: Donor_2_AAVS1_1_2


title: Donor_3_AIRE


title: Donor_2_NFKB1


title: Donor_2_ZNF791


title: Donor_2_ZKSCAN1


title: Donor_2_TP53


title: Donor_2_AAVS1_3_2


title: Donor_2_STAT1


title: Donor_2_STAT2


title: Donor_2_RBCK1


title: Donor_2_ZNF329


title: Donor_2_AAVS1_5_2


title: Donor_2_NFE2L3


title: Donor_2_KLF9


title: Donor_2_SREBF1


title: Donor_2_IRF8


title: Donor_2_BACH2


title: Donor_3_ZNF319


title: Donor_2_AKAP8


title: Donor_2_POU2F1


title: Donor_2_RELB


title: Donor_2_NFKB2


title: Donor_2_AAVS1_6_2


title: Donor_2_ZNF331


title: Donor_2_RFX5


title: Donor_2_SP110


title: Donor_2_ZBTB14


title: Donor_2_FOXP3


title: Donor_2_ZNF655


title: Donor_2_SETDB1


title: Donor_2_AAVS1_8_2


title: Donor_2_AAVS1_7_2


title: Donor_2_ZNF341


title: Donor_2_TCF3


title: Donor_2_TTF1


title: Donor_2_EGR3


title: Donor_2_AAVS1_2_2


title: Donor_2_SON


title: Donor_2_BPTF


title: Donor_2_NFE2L2


title: Donor_2_IRF7


title: Donor_2_LCOR


title: Donor_2_AAVS1_4_2


title: Donor_2_ZBTB24


title: Donor_2_ELK4


title: Donor_2_RORC


title: Donor_2_ZFP3


title: Donor_2_ZNF708


title: Donor_2_STAT3


title: Donor_2_AAVS1_12_2


title: Donor_2_REL


title: Donor_2_ATMIN


title: Donor_2_YBX3


title: Donor_2_IKZF1


title: Donor_2_ZNF575


title: Donor_2_IRF9


title: Donor_2_GFI1


title: Donor_2_BCL11B


title: Donor_2_DR1


title: Donor_2_MYSM1


title: Donor_2_HIVEP3


title: Donor_2_NFAT5


title: Donor_2_CLOCK


title: Donor_2_TET2


title: Donor_2_AAVS1_9_2


title: Donor_2_ZNF319


title: Donor_2_IRF3


title: Donor_2_ARID5A


title: Donor_2_AIRE


title: Donor_1_AAVS1_1_2


title: Donor_1_ZNF791


title: Donor_1_TP53


title: Donor_1_AAVS1_3_2


title: Donor_1_NFKB1


title: Donor_1_ZKSCAN1


title: Donor_1_KLF9


title: Donor_2_EPAS1


title: Donor_2_AAVS1_10_2


title: Donor_1_ZNF329


title: Donor_1_STAT1


title: Donor_1_NFE2L3


title: Donor_1_SREBF1


title: Donor_1_STAT2


title: Donor_1_IRF8


title: Donor_2_YBX1


title: Donor_1_AAVS1_5_2


title: Donor_1_AAVS1_6_2


title: Donor_1_LCOR


title: Donor_1_BACH2


title: Donor_2_TBX21


title: Donor_1_POU2F1


title: Donor_1_SP110


title: Donor_1_AKAP8


title: Donor_1_ZNF331


title: Donor_1_RELB


title: Donor_1_ZBTB14


title: Donor_1_NFKB2


title: Donor_1_RFX5


title: Donor_1_AAVS1_7_2


title: Donor_1_RBCK1


title: Donor_1_SETDB1


title: Donor_1_ZNF655


title: Donor_1_YBX3


title: Donor_1_ZNF341


title: Donor_1_TCF3


title: Donor_1_GFI1


title: Donor_1_EGR3


title: Donor_1_TTF1


title: Donor_1_AAVS1_2_2


title: Donor_1_AAVS1_4_2


title: Donor_1_IRF7


title: Donor_1_BPTF


title: Donor_1_SON


title: Donor_1_ATMIN


title: Donor_1_RORC


title: Donor_1_ELK4


title: Donor_1_ZBTB24


title: Donor_1_NFE2L2


title: Donor_1_ZFP3


title: Donor_1_AAVS1_12_2


title: Donor_1_ZNF708


title: Donor_1_STAT3


title: Donor_1_ZNF575


title: Donor_1_FOXP3


title: Donor_1_REL


title: Donor_1_IKZF1


title: Donor_1_DR1


title: Donor_1_IRF9


title: Donor_1_BCL11B


title: Donor_1_AAVS1_10_2


title: Donor_1_MYSM1


title: Donor_1_TET2


title: Donor_1_EPAS1


title: Donor_1_YBX1


title: Donor_1_NFAT5


title: Donor_1_AAVS1_9_2


title: Donor_1_AAVS1_11_2


title: Donor_1_TBX21


title: Donor_1_ZNF319


title: CMT93, Control, rep3

data_processing:
Basecalling was performed with GenerateFASTQ:1.1.0.64 through Illumina BaseSpace platform
Sequenced reads were mapped to GrCM38/mm10 using Bowtie2: 2.3.4.1 through Galaxy (usegalaxy.org).
BAM files from triplicated samples for each replicate were merged by sam_merge2:1.2.0
Peakcalls were performed with macs2_callpeak: 2.2.7.1 with the setting lower mfold: 5, upper mfold 10000
Differential accessibility analysis was performd using diffbind: 2.10.0
BAM files were converted to Bigwig files by deeptools_bam_coverage: 3.5.4
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak in bed format
Supplementary files format and content: diffbind

growth_protocol: PLC-β3 KO or control CMT-93 cell were cultured in DMEM supplemented with 10% FBS  and antibiotics at 37C with 5% CO2

extract_protocol:
Subconfluent Plcb3-deficient (clones 3P11, 3P13 and 2P9) or control (clones Scr1, Scr2 and Scr4) CMT_x0002_93 cells were dissociated with Trypsin/EDTA (in 1x PBS pH 7.4) and the numbers of cells were counted.  Cells were resuspended with PBS at 1x106/ml and 5x104 cells were aliquoted and centrifuged at 2000 rpm  (500 rcf) for 5 min. Supernatant was removed and cells were resuspended with 50 μl of cold lysis buffer  (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) in 1.5 ml Eppendorf tubes.  Tubes were vortexed for 1 min and centrifuged at 2000 rpm (500 rcf) for 10 min at 4℃.  Supernatant was carefully removed and pellets were resuspended with 20 μl of Tagment DNA (TD)  buffer (Illumina) and 3 μl of QXT transposase were added to the samples on ice. Samples were incubated  at 37℃ for 60 min, then placed on ice for 1 min to cool. 2 μl of 1% SDS (final concentration is 0.1%) was  added and incubated at RT for 2 min to stop reactions. 30 μl of AMpure beads (Fisher Scientific, Cat #  NC9959336) was added to each sample, pipetted 10 times to mix, then, incubated for 5 min at RT.  Samples were placed on the magnetic stand for 2 min, then, supernatant was removed. Samples were  washed with 200 μl of freshly prepared 80% ethanol twice, then, air dried for 10 min after complete  removal of the residual ethanol. Pellets were resuspended with 11 μl of nuclease free water and incubated  for 2 min. Samples were placed on the magnet and incubated for 2 min. 10 μl of samples were transferred  to new tubes.
10 μl of samples were mixed with Kapa-Hifi 2x master mix (Fisher Scientific, Cat #  NC0295239) 25 μl, H2O 13 μl, QXT custom 5XX primer 1 μl and QXT custom 7XX primer 1 μl. PCR  reaction was conducted with following protocol (1: 68℃ for 2 min, 2: 98℃ for 2 min, 3: 98℃ for 30 sec,  4: 57℃ for 30 sec, 5: 72℃ for 1 min, 6: Repeat steps 3 to 5 (12 cycles in total), 7: 72℃ 5 min, 8: 4℃ hold). 20 μl of AMpure beads was added to the samples, incubated for 5 min, placed on magnet, then,  supernatants were transferred to other tubes. 30 μl of AMpure beads were added to the samples, incubated  for 5 min, placed on magnet, washed twice, eluted with 13 μl of nuclease free water. Quality of library  was checked by Tapestation HS 1000 (Agilent) and the amount of usable library was further quantified by  qPCR. Samples were pooled for sequencing with HiSeq (Illumina).

value: rectum polypoid carcinoma


title: Donor_1_IRF3


title: Donor_1_AIRE


title: CMT93, Plcb3_KO, rep2


title: CMT93, Plcb3_KO, rep3


title: CMT93, Control, rep2


title: CMT93, Plcb3_KO, rep1


title: CMT93, Control, rep1


title: Donor_1_CLOCK


title: s387_SerF09-combine_ctrl_39_b

city: Durham

first: Aashutosh

last: Vihani

address: 264 CARL Building

institute: Duke University

data_processing:
Library strategy: pS6-IP-Seq
STAR alignment
RSEM read quantification
Genome_build: modified GENCODE M25
Supplementary_files_format_and_content: expected_count, TPM, FPKM

source_name: Whole olfactory mucosa

extract_protocol:
Antibody: Cell Signaling D68F8
Qiagen RNeasy Mini Kit #74104
Library construction protocol: Illumina Nexterra XT DNA Library Preparation Kit #15032354

tag: group

value: control

tag: odor

tag: concentration

tag: differential expression number

tag: trial

value: b


title: s386_SerF08-combine_1p_heptanoicAcid_39_a

tag: strain

value: experimental

value: heptanoicAcid

value: a


title: s390_SerF12-combine_1p_heptanoicAcid_39_b


title: s388_SerF10-combine_1p_ethylTiglate_39_b

value: ethylTiglate


title: s384_SerF06-combine_1p_ethylTiglate_39_a


title: s391_SerJ1-12072017_ctrl_39_c

value: c


title: s392_SerJ2-12072017_1p_ethylTiglate_39_c


title: Donor_1_HIVEP3


title: s394_SerJ4-12072017_1p_heptanoicAcid_39_c


title: Donor_1_ARID5A


title: s383_SerF05-combine_ctrl_39_a


title: s380_SerF02-combine_1p_geraniol_38_c

value: geraniol


title: s381_SerF03-combine_1p_bIonone_38_c

value: bIonone


title: s379_SerF01-combine_ctrl_38_c


title: s378_SerJ12-12072017_1p_dimethylsulfide_38_b

value: dimethylsulfide


title: s376_SerJ10-12072017_1p_geraniol_38_b


title: s377_SerJ11-12072017_1p_bIonone_38_b


title: s375_SerJ9-12072017_ctrl_38_b


title: s373_SerJ7-12072017_1p_bIonone_38_a


title: s372_SerJ6-12072017_1p_geraniol_38_a


title: s367_SerH06-combine_1p_propionicAcid_37_b

value: propionicAcid


title: s365_SerH04-combine_ctrl_37_b


title: s366_SerH05-combine_1p_pLimonene_37_b

value: pLimonene


title: s368_SerH07-combine_ctrl_37_c


title: s371_SerJ5-12072017_ctrl_38_a


title: s374_SerJ8-12072017_1p_dimethylsulfide_38_a


title: s370_SerH09-combine_1p_propionicAcid_37_c


title: s361_SerG12-L001-R1-001_10p_tmt_36_c

value: tmt


title: s382_SerF04-combine_1p_dimethylsulfide_38_c


title: s359_SerG10-L001-R1-001_p01_tmt_36_c


title: s356_SerG7-L001-R1-001_p1_tmt_36_b


title: s357_SerG8-L001-R1-001_10p_tmt_36_b


title: s363_SerH02-combine_1p_pLimonene_37_a


title: s360_SerG11-L001-R1-001_p1_tmt_36_c


title: s354_SerG5-L001-R1-001_ctrl_36_b


title: s355_SerG6-L001-R1-001_p01_tmt_36_b


title: s364_SerH03-combine_1p_propionicAcid_37_a


title: s353_SerG4-L001-R1-001_10p_tmt_36_a


title: s352_SerG3-L001-R1-001_p1_tmt_36_a


title: s348_SerH11-combine_1p_methylSalicylate_10_b

value: methylSalicylate


title: s369_SerH08-combine_1p_pLimonene_37_c


title: s347_SerH10-combine_ctrl_10_b


title: s344_SerE10-L001-R1-001_ctrl_10_a


title: s350_SerG1-L001-R1-001_ctrl_36_a


title: s345_SerE11-L001-R1-001_1p_methylSalicylate_10_a


title: s342_SerE8-L001-R1-001_p01_acetophenone_35_c

value: acetophenone


title: s358_SerG9-L001-R1-001_ctrl_36_c


title: s362_SerH01-combine_ctrl_37_a


title: s343_SerE9-L001-R1-001_p1_acetophenone_35_c


title: s340_SerE6-L001-R1-001_p1_acetophenone_35_b


title: s341_SerE7-L001-R1-001_ctrl_35_c


title: s337_SerE3-L001-R1-001_p1_acetophenone_35_a