title: SkinUnk_tdNeg_rep1

city: Goettingen

first: Nadine

last: Brandes

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

country: Germany

institute: University Medical Center Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422. The sequencing quality was asserted using FastQC. FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)(version 0.11.5).
Sequences were aligned to the reference genome Mus musculus (mm10 version 96, https://www.ensembl.org/Mus_musculus/Info/Index) using the STAR aligner
Read counting was performed using featureCounts  Read counts were analyzed in the R/Bioconductor environment (version 3.4.4, www.bioconductor.org) using the DESeq2 package version 1.18.1. Candidate genes were filtered using an absolute log2 fold-change >1 and FDR-corrected p-value <0.05. Genes were annotated using the Mus Musculus gene version 96 Gene transfer format (GTF) file.
Genome_build: mm10
Supplementary_files_format_and_content: text file includes gene expression for each sample
Supplementary_files_format_and_content: gene counts

source_name: Dorsal skin

extract_protocol:
Epidermal cells were isolated with thermolysin from dorskal skin and sorted by FACS. RNA was harvested using Trizol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® RNA Sample Preparation v2 kit.

value: CD4Cre R26-tdT (C57Bl6/N)

value: 29 weeks

tag: Sex

value: male

tag: # of mice pooled

tag: sorted population


title: SUDHL1_RG1_H3K4me3_ChIPseq

status: Public on Apr 21 2022

type: SRA

city: Guangzhou

first: Wenchao

last: Wu

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District,

country: China

institute: Sun Yat-sen University Cancer Center

description: Len-regrown1 H3K4me3 ChIPseq

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to human reference genome using BWA (v0.7.12).
Peak detection was performed with MACS2 (v2.1.0)
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files for each sample

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Chromatin immunoprecipitation (ChIP) was performed on SU-DHL-1 parental, SU-DHL-1 lenalidomide-regrown cells, SU-DHL-1 cells with JUN-KO, Karpas 299, SMZ-1, and SUP-M2 cells (2x10^7).

extract_protocol:
The crosslinking was reversed overnight at 65 °C. Input and ChIPed DNA was cleaned up and submitted to Novogene (Sacramento, CA) for libraries construction and sequencing.
Immunoprecipitated DNA sample quality was assessed by DNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 DNA HS assay (ThermoFisher, Massachusetts, USA). The KAPA HyperPrep kit (Roche, Indianapolis, USA) was used for library preparation and indexing was performed using Illumina 8-nt dual-indices. Final libraries were quantified by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and run on TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA) to evaluate the quality of the purified libraries. Final library size was approximately 300 bp. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 80M PE reads per sample (40M in each direction).

treatment_protocol: The ChIP assay was performed with EZ-ChIP kit (Cell Signaling Technology, #9003) following the manufacturer’s instruction. Briefly, cells were fixed in 1% formaldehyde at room temperature for 10 min, quenched with 0.125 M glycine for 5 min at room temperature, washed with ice-cold PBS. The cells were lysed in ice-cold 1 x Buffer A + DTT + Protease Inhibitor Cocktail (PIC) for 10 min and resuspend in 2 ml 1 x Buffer B + DTT. The chromatin was digested by 2 µl of Micrococcal Nuclease for 20 min at 37°C with frequent mixing. The digestion was stopped by adding 20 µl 0.5M EDTA. Nuclei were lysed by sonication (Qsonica) in 1 x ChIP Buffer + PIC with 3 sets of 20% power of pulses for 15 sec and pause for 15 sec in between. The lysates were then centrifuged for 10 min at 4 °C, supernatants collected and diluted with 4 volume of 1 x ChIP Buffer + PIC. A small portion (2%) of the digested chromatin was set aside as input sample and stored at -20°C. For immunoprecipitation (IP) reaction, 10 µg of ChIP-Grade antibody was added to IP samples and incubate end over end overnight at 4°C. The following day, ChIP-Grade Protein G Magnetic Beads were added to IP reaction and incubated end over end at 4°C for 2 h. Beads were washed with low-salt buffer, high-salt buffer, and LiCl buffer. DNA was then eluted in elution buffer.

tag: tissue

value: lymph node

tag: cell type

value: ALK+ ALCL

tag: cell line

tag: chip antibody

value: Anti-H3K4me3, Cell Signaling Technology, #9751


title: SUDHL1_P_H3K4me3_ChIPseq

description: SUDHL1 parental H3K4me3 ChIPseq


title: SkinUnk_tdPos_rep3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

value: 32 weeks


title: SkinUnk_tdPos_rep2


title: SUDHL1_RG2_Input_ChIPseq

description: Len-regrown2 Input for ChIPseq

value: none (input)


title: SUDHL1_RG3_Input_ChIPseq

description: Len-regrown3 Input for ChIPseq


title: SkinUnk_tdPos_rep1


title: SUDHL1_RG1_Input_ChIPseq

description: Len-regrown1 Input for ChIPseq


title: SkinStem_tdNeg_rep3


title: SUDHL1_P_Input_ChIPseq

description: SUDHL1 parental Input for ChIPseq


title: SUDHL1_RG2_H3K27ac_ChIPseq

description: Len-regrown2 H3K27ac ChIPseq

value: Anti-H3K27ac, Cell Signaling Technology, #8173


title: SkinUnk_tdNeg_rep2


title: SkinStem_tdNeg_rep2


title: KIJK_CSNK2B_OE2_RNAseq

description:
KIJK transduced with CSNK2B overexpression vector
KIJK_CSNK2B_OE_RNAseq_counts.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the human reference genome using STAR (v2.6.1d) with mismatch = 2.
Differential expression between experimental criteria was determined using raw counts and normalization procedures within the DESeq2 (v1.20.0, padj<0.05) and EdgeR (v3.24.3, padj<0.005 and |log2(FoldChange)| > 1) package in R.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include read counts per gene for all samples

source_name: KI-JK

growth_protocol: RNA-seq was performed in KIJK cells overexpressed with CSNK2B or empty vector control. Cells were cultured in RPMI1640 + 20%FBS media.

extract_protocol:
Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: KIJK cells were transduced with CSNK2B overexpression vector or empty control vector.

value: pleural effusion

value: KI-JK


title: SkinStem_tdNeg_rep1


title: SUDHL1_RG2_H3K4me3_ChIPseq

description: Len-regrown2 H3K4me3 ChIPseq


title: HeLa-TFEB-Flag-siRNA-Control-3

city: Bethesda

first: Jose

last: Martina

state: Maryland

address: 50 South Dr., Building 50, Room 3533

department: NHLBI, CDBC

country: USA

institute: NIH

description: 3_4427NIH_HeLa-siRNA-Control-3_RNASeq_hs_i16

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all samples.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

source_name: HeLa-TFEB-Flag

growth_protocol: HeLa cells stably expressing TFEB-Flag were grown in DMEM, high glucose, GlutaMAX, sodium pyruvate (Gibco, 10569044) supplemented with 10% fetal bovine serum (Invitrogen, 21041-025), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 2114).

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 100 nM of either siRNA-Control or siRNA-FACT for 72h. Then, cells were incubated with 50 μM sodium arsenite for additional 6h.

tag: cell line background

value: HeLa

value: Epithelial cells

tag: disease

value: Adenocarcinoma

tag: treatment

value: Treated with 50 μM sodium arsenite for 6h

tag: sirna treatment

value: Treated with 100 nM siRNA-Control for 72h


title: KIJK_CSNK2B_OE3_RNAseq


title: KIJK_CSNK2B_CON2_RNAseq

description:
KIJK transduced with Empty vector control
KIJK_CSNK2B_OE_RNAseq_counts.txt


title: Sample 2_HeLa-TFEB-Flag-siRNA-Control

data_processing:
Basecalls performed using Illumina bcl2fastq2 version 2.20
ChIP-seq reads were aligned to the human GRCh38/hg38 genome assembly using Burrows-Wheeler Aligner algorithm with default settings.
Data were filtered as follows: Duplicate reads were removed, and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7 [2]. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: hg38
Supplementary_files_format_and_content: bigWIG files were generated using wigToBigWig version 4 software

growth_protocol: HeLa cells (CCL-2, ATCC) and HeLa cells stably expressing TFEB-Flag were grown in DMEM, high glucose, GlutaMAX, sodium pyruvate (Gibco, 10569044) supplemented with 10% fetal bovine serum (Invitrogen, 21041-025), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 2114).

extract_protocol:
Chromatin was isolated from cells by adding lysis buffer (1% SDS, 10 mM EDTA and 50mM Tris-HCl, pH 8.1 containing protease inhibitors), followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Genomic DNA regions of interest were isolated using monoclonal antibody against Flag.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara) following the manufacturer's protocol. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end) following the manufacturer's protocols.

treatment_protocol: Cells were left untreated or treated with 100 nM of either siRNA-Control or siRNA-FACT for 72h. Then, cells were incubated with 50 μM sodium arsenite for additional 6h.

value: Mouse anti-Flag (clone M2, Sigma-Aldrich, Cat# F1804)

value: Untreated


title: Sample 4_HeLa-TFEB-Flag-siRNA-FACT

description: 3_07KX_010CNIH_HeLa-siRNA-FACT_FLAG_hs_i77

value: Treated with 100 nM siRNA-FACT for 72h


title: KIJK_CSNK2B_CON3_RNAseq


title: Sample 1_HeLa-WT

source_name: HeLa-WT


title: SUDHL1_RG_LEN3_DGEseq

description:
lenalidomide regrown line#3 treated with Lenalidomide
SUDHL1_LEN-treatment_DGEseq_counts.txt

data_processing:
Library strategy: 3'DGE-seq
FastQC was used to perform a basic quality control on the resulting reads for 3'DGE-seq data.
Reads were aligned to the human genome hg19 with BOWTIE (v2.2.3).
Differential expression between experimental criteria was determined using raw counts and normalization procedures within the DESeq2 package in R based on a negative binomial distribution. Prior to testing rows that had no counts or only a single count across all samples were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read counts per gene for all samples

growth_protocol: 3'DGE-seq was performed in SUDHL1 parental and lenalidomide-regrown cells, both of which lines were cultured in RPMI1640 + 10%FBS media.

treatment_protocol: Both SUDHL1 parental or len-regrown cells were treated with DMSO or 2.5uM lenaliodmide for 18 h.


title: KIJK_CSNK2B_CON1_RNAseq


title: SUDHL1_CSNK2B_OE3_RNAseq

description:
SUDHL1 transduced with CSNK2B overexpression vector
SUDHL1_CSNK2B_OE_RNAseq_counts.txt

growth_protocol: RNA-seq was performed in SUDHL1 cells overexpressed with CSNK2B or empty vector control. Cells were cultured in RPMI1640 + 10%FBS media.

treatment_protocol: SUDHL1 parental cells were transduced with CSNK2B overexpression vector or empty control vector.


title: SkinStem_tdPos_rep2

value: CD4Cre R26-tdT (C57Bl6/N)

value: male


title: SUDHL1_RG_LEN2_DGEseq

description:
lenalidomide regrown line#2 treated with Lenalidomide
SUDHL1_LEN-treatment_DGEseq_counts.txt

value: lymph node

value: ALK+ ALCL


title: SkinStem_tdPos_rep1

value: 29 weeks


title: SUDHL1_CSNK2B_OE1_RNAseq


title: SUDHL1_RG_LEN1_DGEseq

description:
lenalidomide regrown line#1 treated with Lenalidomide
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: NHBE-4_submerged: NHBE submerged rep 4

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
trim reads for quality with trim galore (-q 20)
quasi mapping with salmon (--numBootstraps 30)
DEG at gene level with R tximport and DESeq2 packages compare control to EMT samples; and compare 2D to 3D samples
Genome_build: hg38
Supplementary_files_format_and_content: EMT_vs_ctrl_gene_res_exp_TPM_ann.xlsx contains TPM and counts for the samples and p-values and statistics comparing untreated vs samples treated with EMT
Supplementary_files_format_and_content: submerged_vs_ALI_gene_res_exp_TPM_ann.xlsx contains TPM and counts for the samples and p-values and statistics comparing submerged vs ALI cultures

molecule: polyA RNA

source_name: healthy submerged HBECs

growth_protocol: HBECs were expanded and differentiated according to manufacturer protocols [Clonetics™B-ALI™ air-liquid interface cultures]. Briefly, 1x106 HBECs were seeded into T-75 flask containing 25 ml of pre-warmed B-ALI™ growth medium and were grown as submerged cultures. For ALI cultures, 80% confluent submerged cultures were harvested and seeded [50,000 cells per 24-well insert] into the apical chamber of inserts [pre-coated with collagen solution 30μg/ml] in 100 μl of B-ALI™ growth medium; the basal chambers of the inserts were cell free and immersed in 500 μl of B-ALI™ growth medium. After 3 days, B-ALI™ growth medium from the apical and basal chambers were removed and 500 μl B-ALI™ differentiation medium was added to the basal chamber only (air-lift). Upon airlifting, media was replaced every other day with 500 μl B-ALI™ differentiation medium only to the basal chamber until the cultures reached full differentiation [day 25]

extract_protocol:
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol (Qiagen) according to the manufacturer’s instructions. Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.
PolyA enriched RNA was sequenced on llumina HiSeq 2500 using TruSeq SBS Kit v4 reagents
non stranded
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol (Qiagen) according to the manufacturer’s instructions. Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.

treatment_protocol: On day 25, the basal chamber of fully differentiated ALI cultures were supplemented with 1X of StemXVivo EMT Inducing Media (R&D; CCM017). Medium was replaced every other day with 500 μl B-ALI™ Differentiation Medium containing 1X of StemXVivo EMT Inducing Media only to the basal chamber until the cultures reached day 30.

value: primary bronchial epithelial cells

tag: disease state

value: healthy

value: submerged cultures


title: SUDHL1_CSNK2B_CON2_RNAseq

description:
SUDHL1 transduced with Empty vector control
SUDHL1_CSNK2B_OE_RNAseq_counts.txt


title: SUDHL1_CSNK2B_OE2_RNAseq


title: SUDHL1_CSNK2B_CON1_RNAseq


title: SUDHL1_CSNK2B_CON3_RNAseq


title: KIJK_CSNK2B_OE1_RNAseq

value: pleural effusion

value: KI-JK


title: SUDHL1_RG_DMSO2_DGEseq

description:
lenalidomide regrown line#2 treated with DMSO
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: SUDHL1_RG_ZFP91_KO2_RNAseq

description:
lenalidomide regrown line#2 with dox-induced ZFP91-KO
SUDHL1_ZFP91_KO_RNAseq_counts.txt

growth_protocol: RNA-seq was performed in SUDHL1 parental and lenalidomide-regrown cells, both of which lines were cultured in RPMI1640 + 10%FBS media.

extract_protocol:
After dox-induced ZFP91 knockout, cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SUDHL1 parental or len-regrown cells with Cas9 expression were transduced with inducible sgRNA vector targeting ZFP91. For treatment of cells to induce expression of sgRNA, doxycycline (1ug/ml) was added to culture media for 96 hours.


title: NHBE-2_submerged: NHBE submerged rep 2


title: SUDHL1_RG_ZFP91_KO3_RNAseq

description:
lenalidomide regrown line#3 with dox-induced ZFP91-KO
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: NHBE-3_submerged: NHBE submerged rep 3


title: SUDHL1_P_ZFP91_KO3_RNAseq

description:
parental with dox-induced ZFP91-KO
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: NHBE-1_submerged: NHBE submerged rep 1


title: SUDHL1_RG_ZFP91_WT3_RNAseq

description:
lenalidomide regrown line#3 without dox ZFP91-WT
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: SUDHL1_P_LEN3_DGEseq

description:
parental treated with Lenalidomide
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: Sample 3_HeLa-TFEB-Flag-siRNA-Control

description: 2_07KW_010CNIH_HeLa-siRNA-Control_FLAG_hs_i76

value: HeLa

value: Epithelial cells


title: SUDHL1_P_ZFP91_KO2_RNAseq


title: SUDHL1_RG_ZFP91_WT2_RNAseq

description:
lenalidomide regrown line#2 without dox ZFP91-WT
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: SUDHL1_P_LEN2_DGEseq


title: DHBE-6_submerged: DHBE submerged rep 2

source_name: diseased submerged HBECs

value: diseased


title: SUDHL1_P_ZFP91_KO1_RNAseq


title: SUDHL1_P_ZFP91_WT3_RNAseq

description:
parental without dox ZFP91-WT
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: DHBE-7_submerged: DHBE submerged rep 3


title: SUDHL1_RG_DMSO3_DGEseq

description:
lenalidomide regrown line#3 treated with DMSO
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: SUDHL1_P_LEN1_DGEseq


title: SUDHL1_P_ZFP91_WT1_RNAseq


title: SUDHL1_RG3_PROseq

description:
lenalidomide regrown line#3
SUDHL1_PROseq_counts.txt

data_processing:
Library strategy: PRO-seq
PRO-seq reads were trimmed to 40bp and subsequently trimmed via cutadapt v1.14 to remove adapters: --match-read-wildcards -m 20 -q 10
PRO-seq Read 1 was aligned (single-end) using bowtie v1.2.2: -v 2 -p 6 --best --un
PRO-seq Read 2 and RNA-seq data were used to identify active, dominant TSS-to-TES windows (1 per gene). featureCounts v1.6.2 quantified raw counts within these windows per sample: -s 2 -Q 10
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include read counts per gene for all samples

growth_protocol: PRO-seq was performed in SUDHL1 parental and lenalidomide-regrown cells, both of which lines were cultured in RPMI1640 + 10%FBS media.

extract_protocol:
Cells were washed once in ice-cold 1x PBS and resuspended in Wash Buffer at the density of 5x10^6 cells/mL. Once filtered to ensure single-cell suspension, 9x volume of Permeabilization Buffer (10mM Tris-HCl pH 8, 10mM KCl, 250mM Sucrose, 5mM MgCl2, 1mM EDTA, 0.5mM DTT, 10% Glycerol, 0.05% Igepal CA-630) was gently added. The cells were incubated on ice for 3 minutes and then recovered by centrifugation and washed in Freezing Buffer (50mM Tris-HCl pH 8.3, 40% Glycerol, 5mM MgCl2. 0.5mM DTT, 2µL/mL RNase Inhibitor). Permeabilized cells were resuspended in Freezing Buffer at a density of 1x10^6 cells/100µL, flash frozen, and stored at -80°C until library preparation.
PRO-seq libraries were generated as previously described (DOI: 10.1016/j.molcel.2019.10.034).

treatment_protocol: Three independent pools of lenalidomide-resistant SU-DHL-1 cells were generated by long-term culture in the presence of increasing concentrations of lenalidomide. Cells were stably resistant to lenalidomide and withdrown from drugs for at least 2 months.


title: DHBE-5_submerged: DHBE submerged rep 1


title: SUDHL1_RG2_PROseq

description:
lenalidomide regrown line#2
SUDHL1_PROseq_counts.txt


title: SUDHL1_RG1_PROseq

description:
lenalidomide regrown line#1
SUDHL1_PROseq_counts.txt


title: SUDHL1_P_DMSO1_DGEseq

description:
parental treated with DMSO
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: SUDHL1_P3_PROseq

description:
SUDHL1 parental
SUDHL1_PROseq_counts.txt


title: NHBE-4_ALI: NHBE ALI rep 4

source_name: healthy HBECs ALI cultures

value: ALI cultures


title: SUDHL1_RG_ZFP91_WT1_RNAseq

description:
lenalidomide regrown line#1 without dox ZFP91-WT
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: SUDHL1_RG_ZFP91_KO1_RNAseq

description:
lenalidomide regrown line#1 with dox-induced ZFP91-KO
SUDHL1_ZFP91_KO_RNAseq_counts.txt


title: NHBE-3_ALI: NHBE ALI rep 3


title: Patient 5 - Plate 2

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
CEL-seq libraries were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Read 1 contains UMI (first 6 bp) followed by 8 bp barcode. The remainder of R1 is not used. R2 contains the biological read.
The file readme_demultiplexing_Cel-seq2_data.pdf includes the cell barcode sequence for each numerical cell ID.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the number of sections/primers, separated by an underscore.
*ReadCounts.tsv = raw mapped read count
*BarcodeCounts.tsv = UMI corrected version raw counts
*TranscriptCounts.tsv = poisson counting statistics corrected version of Barcode counts. This is the file we use as input for downstream analysis since it comes closest to the real situation in the cell.

source_name: Heart. Left Ventricle. Myectomy

extract_protocol:
Myectomy samples were obtained directly after surgery, minced and enzymatically digested, then single-cell sorted into 384-well plates containing a lysis buffer. Once filled, plates were flash frozen on dry ice.
RNA libraries were prepared according to SORT-Seq

tag: patient diagnosis

value: hypertrophic cardiomyopathy

tag: patient id

value: heart

tag: heart region

value: Left ventricle


title: SUDHL1_P2_PROseq


title: SUDHL1_P_ZFP91_WT2_RNAseq


title: Patient 5 - Plate 1


title: FTAZ:PCBM, HC2

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

description: DNBSEQ Technology Platform

data_processing:
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to RefSeq GCF_000188115.4 annotations using featureCounts and read abundances quantified at the gene-level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: RefSeq GCF_000188115.4
Supplementary files format and content: Text files with counts for each sample by gene

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: growth chamber under ceramic metal halide + incandescent bulbs

extract_protocol:
PureLink RNA Mini on-column kit with TRIzol with on-column DNAse treatment
mRNA library was prepped by BGI Genomics Co., Ltd. with polyA selection by an oligo dT library
All 31 samples were multiplexed, pooled and loaded together onto a DNBSEQ Technology Platform

treatment_protocol: OSC filter vs spectrally neutral control

value: leaf

tag: genotype

value: wildtype

tag: cultivar

value: Moneymaker

tag: intensity experiment

value: Height Controlled (HC)

tag: osc filter


title: SUDHL1_P1_PROseq

tag: tissue

value: lymph node

tag: cell type

value: ALK+ ALCL


title: FTAZ:PCBM, HC3

description: DNBSEQ Technology Platform


title: NHBE-2_ALI: NHBE ALI rep 2

value: primary bronchial epithelial cells

value: healthy


title: FTAZ:PCBM, HC4

description: DNBSEQ Technology Platform


title: SUDHL1_P_DMSO3_DGEseq

tag: cell line

tag: chip antibody


title: Patient 4 - Plate 1

data_processing:
CEL-seq libraries were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Read 1 contains UMI (first 6 bp) followed by 8 bp barcode. The remainder of R1 is not used. R2 contains the biological read.
The file readme_demultiplexing_Cel-seq2_data.pdf includes the cell barcode sequence for each numerical cell ID.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated data file for each sequencing library. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the number of sections/primers, separated by an underscore.
*ReadCounts.tsv = raw mapped read count
*BarcodeCounts.tsv  = UMI corrected version raw counts
*TranscriptCounts.tsv =  poisson counting statistics corrected version of Barcode counts. This is the file we use as input for downstream analysis since it comes closest to the real situation in the cell.


title: SUDHL1_RG_DMSO1_DGEseq

description:
lenalidomide regrown line#1 treated with DMSO
SUDHL1_LEN-treatment_DGEseq_counts.txt


title: Patient 4 - Plate 2


title: DHBE-8_submerged: DHBE submerged rep 4

value: submerged cultures


title: FTAZ:PCBM, HC1

description: DNBSEQ Technology Platform


title: DHBE-8_ALI: DHBE ALI rep 4

source_name: diseased HBECs ALI cultures


title: Embryonic Fibroblasts 4h IFNA rep2

city: Boulder

first: Edward

middle: B

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Raw sequences were quality and adapter trimmed using BBDuk v38.05 with arguments "-Xmx4g ktrim=r k=31 mink=11 hdist=1 tpe tbo qtrim=r trimq=10  ref=/opt/bbmap/38.05/resources/adapters.fa".
Sequences were mapped to the myoLuc2_HiC.fa (www.dnazoo.org) using a 2pass mapping strategy in STAR (v2.7.3a). The annotation file available on DNAzoo, here referred to as “functional annotation” (www.dropbox.com/sh/xt300ht42mihjov/AADoENW7RTvR3jTh1a8qUOmRa) was used as reference for the mapping process.
Aligned files were then analyzed for gene and transposable element expression using TETranscripts (v2.1.4). The same gene annotation file used for read mapping and our custom TE annotation derived from RepeatMasker were used as reference files.
Pairwise differential expression analysis of both transposable elements and genes were performed independently for the 24hrs and the 4hrs datasets using DESeq2 (v1.32.0)
Assembly: myoLuc2_HiC
Supplementary files format and content: CPM normalized signal tracks in UCSC bigwig format

organism: Myotis lucifugus

source_name: Embryonic Fibroblasts

growth_protocol: Myotis lucifugus embryonic fibroblast cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in DMEM (cat #10566016, ThermoFisher) supplemented with 10%FBS, 5% MEM nonessential amino acids, 1% PenStrep, and 1% sodium pyruvate.

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Libraries were generated with 200ng or 500ng RNA using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to the manufacturer's instructions. Briefly, single-indexed adapters (KAPA #KK8700) or unique dual-indexed adapters (KAPA #KK8727) were added to each sample at a final concentration of 78 nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups. Purified, adapter-ligated samples were amplified for 10 (500ng input RNA) or 12 (200ng input RNA) cycles according to the manufacturer's instructions and purified using a 1.0X KAPA Pure Bead cleanup.

treatment_protocol: Cells were seeded in 6 well plates (200,000 cells per well).After 24hrs culturing media was replaced with fresh media containing either 1000U/mL universal IFNA (PBL Assay Science #11200) or equal volume of DPBS. Cells were treated for 24hrs or 4hrs.

value: embryonic fibroblast

tag: timepoint


title: Embryonic Fibroblasts 4h IFNA rep1


title: FTAZ:IT-M, HC4

description: DNBSEQ Technology Platform


title: Embryonic Fibroblasts 4h IFNA rep3


title: NHBE-1_ALI: NHBE ALI rep 1


title: FTAZ:IT-M, HC3

description: DNBSEQ Technology Platform


title: EMT7: DHBE EMT rep 4

source_name: diseased HBECs ALI cultures treated with EMT

extract_protocol:
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol (Qiagen) according to the manufacturer’s instructions. Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.
PolyA enriched RNA was sequenced on llumina HiSeq 2500 using TruSeq SBS Kit v3-HS reagents
stranded
Total RNA was extracted using RLT buffer supplemented with Beta-mercaptoethanol (Qiagen) according to the manufacturer’s instructions. Isolated RNA was quantified by spectrophotometry, and RNA concentrations were normalized.

value: ALI cultures treated with EMT


title: Control, HC4

description: DNBSEQ Technology Platform

value: Control


title: DHBE-7_ALI: DHBE ALI rep 3

value: diseased


title: DHBE-6_ALI: DHBE ALI rep 2

value: ALI cultures


title: EMT4: NHBE EMT rep 4

source_name: healthy HBECs ALI cultures treated with EMT


title: Patient 3 - Plate 4

value: hypertrophic cardiomyopathy


title: DHBE-5_ALI: DHBE ALI rep 1


title: Patient 3 - Plate 3

value: heart


title: Patient 2- Plate 4

value: Left ventricle


title: FTAZ:IT-M, HC2

description: DNBSEQ Technology Platform

value: leaf


title: Embryonic Fibroblasts 4h UT rep3

value: wildtype


title: FTAZ:IT-M, HC1

description: DNBSEQ Technology Platform

value: Moneymaker


title: Patient 3 - Plate 2


title: Control, HC1

description: DNBSEQ Technology Platform

value: Height Controlled (HC)


title: EMT5: DHBE EMT rep 3


title: EMT2: NHBE EMT rep 3


title: Embryonic Fibroblasts 24h IFNA rep2


title: Control, HC3

description: DNBSEQ Technology Platform


title: Embryonic Fibroblasts 4h UT rep1


title: Patient 3 - Plate 1


title: Patient 2- Plate 1


title: Embryonic Fibroblasts 24h IFNA rep1


title: PTB7-Th:IEICO-4F, HC4

description: DNBSEQ Technology Platform


title: Embryonic Fibroblasts 24h IFNA rep3


title: Embryonic Fibroblasts 24h UT rep2


title: Patient 2- Plate 3


title: PTB7-Th:IEICO-4F, HC1

description: DNBSEQ Technology Platform


title: Control, HC2

description: DNBSEQ Technology Platform


title: Patient 2- Plate 2


title: Embryonic Fibroblasts 4h UT rep2


title: Embryonic Fibroblasts 24h UT rep3


title: EMT1: NHBE EMT rep 2


title: EMT6: DHBE EMT rep 2


title: PTB7-Th:IEICO-4F, HC3

description: DNBSEQ Technology Platform


title: Patient 1 - Plate 4


title: Patient 1 - Plate 1


title: EMT8: DHBE EMT rep 1


title: Embryonic Fibroblasts 24h UT rep1


title: SUDHL1_P_DMSO2_DGEseq

value: lymph node


title: EMT3: NHBE EMT rep 1


title: C4: NHBE control rep 4

source_name: healthy untreated HBECs ALI cultures

value: untreated ALI cultures


title: Patient 1 - Plate 3


title: SkinStem_tdPos_rep3

tag: strain

value: CD4Cre R26-tdT (C57Bl6/N)

tag: age

value: 32 weeks

tag: Sex

value: male

tag: # of mice pooled

tag: sorted population


title: myoLuc_IFNa_4h_RPB1_R1

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 using options ‘ktrim=r k=34 mink=11 hdist=1 tpe tbo qtrim=r trimq=10’. Trimmed reads were aligned to the myoLuc2_HiC assembly using BWA-MEM v0.7.15, and only uniquely mapping reads with a minimum MAPQ of 10 were retained. Fragments aligning to the mitochondrial genome (HiC_scaffold_93) were removed. Peak calling was performed using alignment files with MACS2 v2.1.1 in a two-step process where separate sets of peaks were called with 1) single-end options ‘--format BAM --shift=-75 --extsize=150’ and 2) paired-end option ‘--format BAMPE’. For both modes only peaks with a p-value < 0.01 were retained. Independently, peaks were called from IgG control libraries using MACS2 v2.1.1 with paired-end option ‘--format BAMPE’ and subtracted from pulldown peak files. Bigwig files were prepared from the MACS2 normalized bedgraph files using bedGraphToBigWig v4.
Assembly: myoLuc2_HiC
Supplementary files format and content: Normalized signal tracks corresponding to read coverage per 1 million fragments in UCSC bigwig format

growth_protocol: Myotis lucifugus embryonic fibroblast cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in DMEM (cat #10566016, ThermoFisher) supplemented with 10% FBS, 5% MEM nonessential amino acids, 100 U/mL penicillin-streptomycin, and 1 mM sodium pyruvate.

extract_protocol:
CUT&RUN pulldowns were generated using a protocol from Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). All buffers were prepared according to the “High Ca2+/Low Salt” section of the protocol using 0.04% digitonin. 500,000 viable cells were used for each pulldown. The following antibodies were used: rabbit anti-mouse IgG (1:100, Abcam #ab46540), rabbit anti-H3K27ac (1:100, Millipore #MABE647), rabbit anti-pPOLR2A-Ser5 (Cell Signaling #13523S), rabbit anti-STAT1 (1:100, Cohesion Biosciences #3322), rabbit anti-pSTAT1-Ser727 (1:100, Active Motif #39634). pAG-MNase was added to each sample following primary antibody incubation at a final concentration of 700 ng/mL. Chromatin digestion, release, and extraction was carried out according to Meers et al. 2019 (PMID: 31232687, https://dx.doi.org/10.17504/protocols.io.zcpf2vn). Pulldown success was determined by Qubit dsDNA High Sensitivity (Life Technologies #Q32851) and TapeStation 4200 HSD5000 (Agilent #50675588) before proceeding with library preparation.
Libraries were generated using a modified protocol for use with the KAPA HyperPrep Kit (Roche #KK8502). Briefly, the full volume of each pulldown (~30 uL) was diluted to 50 uL in nuclease-free water, and libraries were generated following the manufacturer’s protocol with the following modifications. Freshly diluted 0.200 uM single-index adapters were added to each library at a low concentration (9 nM) to minimize adapter dimer formation. Adapter-ligated libraries underwent a double-sided 1.0X/1.2X cleanup using KAPA Pure Beads (Roche #07983280001). Purified, adapter-ligated libraries were amplified using the following PCR cycling conditions: 45 s at 98°C, 15x(15 s at 98°C, 10 s at 60°C), 60 s at 72°C. Amplified libraries underwent a double-sided 1.1/1.2X cleanup. The final libraries were quantified using Qubit dsDNA High Sensitivity and TapeStation 4200 HSD5000. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 (Novogene) as 150bp paired-end reads.
CUT&RUN

treatment_protocol: For CUT&RUN, cells were seeded in 15cm plates (2,000,000 cells per dish). After 48hrs culturing media was replaced with fresh media containing either 1000U/mL universal IFNA (PBL Assay Science #11200) or equal volume of DPBS. Cells were treated for 4hrs.

value: embryonic fibroblast

tag: antibody

value: Rabbit anti-pPOL2RA-Ser5 (Cell Signaling #13523S)

tag: treatment

value: IFNa


title: sifra_sicjun_OLAP_2_S11

city: Stockholm

first: Dandan

last: Song

address: Tomtebodavägen 23

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: transfected with Fosl1 and cJUN on-target siRNA and treated with olaparib for 48 h

data_processing: Basecall files were converted and demultiplexed to fastq files with bcl2fastq v2.20.0.422

source_name: Breast cancer cell line

growth_protocol: BT549 cell line is cultured with RPMI with 10%FBS and 1%P/S

extract_protocol:
Total RNA was extracted use RNeasy Plus Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sample1-6 were transfected with Non-targeting siRNA pool (D-001810-10-05), sample7-12 were transfected with siRNA Human FOSL1 ON-TARGET plus SMART pool (L-004341-00), Human c-Jun ON-TARGET plus SMART pool (L-003268-0-0010), sample 1-3, 7-9 were treated with DMSO for 48 h, sample 4-6, 10-12 were treated with PARP inhibitors olaparib (S1060, Selleck Chemicals).

tag: transfection

value: Fosl1 and cJUN on-target siRNA

value: olaparib for 48 h


title: myoLuc_IFNa_4h_STAT1_R1

value: Rabbit anti-STAT1 (Cohesion Biosciences #3322)


title: FTAZ:PCBM, PC4

description: DNBSEQ Technology Platform

tag: genotype

value: PPFD Controlled (PC)


title: myoLuc_IFNa_4h_STAT1_R2


title: C8: DHBE control rep 4

source_name: diseased untreated HBECs ALI cultures

value: primary bronchial epithelial cells

tag: disease state

value: diseased


title: sifra_sicjun_OLAP_1_S10


title: Patient 1 - Plate 2

tag: patient diagnosis

value: hypertrophic cardiomyopathy

tag: patient id

value: heart

tag: heart region

value: Left ventricle


title: C3: NHBE control rep 2

tag: cell type

value: healthy


title: myoLuc_IFNa_4h_pSTAT1_R2

value: Rabbit anti-pSTAT1-Ser727 (Active Motif #39634)


title: C5: DHBE control rep 3

value: untreated ALI cultures


title: sifra_sicjun_OLAP_3_S12


title: myoLuc_IFNa_4h_RPB1_R2


title: PTB7-Th:IEICO-4F, PC4

description: DNBSEQ Technology Platform

tag: tissue

value: leaf

value: wildtype

tag: cultivar

value: Moneymaker

tag: intensity experiment

tag: osc filter


title: FTAZ:PCBM, PC3

description: DNBSEQ Technology Platform


title: C2: NHBE control rep 3


title: FTAZ:PCBM, PC1

description: DNBSEQ Technology Platform


title: FTAZ:PCBM, PC2

description: DNBSEQ Technology Platform


title: C1: NHBE control rep 1


title: myoLuc_IFNa_4h_pSTAT1_R1

value: embryonic fibroblast

tag: timepoint


title: myoLuc_IFNa_4h_IgG_R1

value: Rabbit anti-mouse IgG (Abcam #ab46540)

value: IFNa


title: PTB7-Th:IEICO-4F, PC1

description: DNBSEQ Technology Platform


title: PTB7-Th:IEICO-4F, PC3

description: DNBSEQ Technology Platform


title: myoLuc_IFNa_4h_H3K27me3_R1

value: Rabbit anti-H3K27me3 (Cell Signaling #9733)


title: C6: DHBE control rep 2


title: sifra_sicjun_DMSO_3_S9

description: transfected with Fosl1 and cJUN on-target siRNA and treated with DMSO for 48 h

tag: strain

value: Fosl1 and cJUN on-target siRNA

value: DMSO for 48 h


title: PTB7-Th:IEICO-4F, PC2

description: DNBSEQ Technology Platform

value: PPFD Controlled (PC)


title: sifra_sicjun_DMSO_2_S8


title: sictrl_OLAP_3_S6

description: transfected with non-target siRNA and treated with olaparib for 48 h

value: non-target siRNA

value: olaparib for 48 h


title: Control, PC3

description: DNBSEQ Technology Platform

value: Control


title: sictrl_OLAP_2_S5


title: myoLuc_IFNa_4h_H3K27ac_R2

value: Rabbit anti-H3K27ac EMD (Millipore #MABE647)


title: Control, PC2

description: DNBSEQ Technology Platform


title: LYK4 OE SA187 NaCl replicate 3

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were trimmed using Trimmomatic 0.36 to remove all low quality reads / base pairs.
Trimmed reads were aligned to the TAIR10 genome using Tohat V2.1.1
Normalization was done by DESeq2
Differential expression between two samples / condition is calculated using DESeq2
Outputs were visualized using cummerbund, Venny etc.,
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel, Normalized Count values

organism: Arabidopsis thaliana

source_name: entire plantlet

growth_protocol: Sterilized seeds were sown on ½ MS plates containing or not SA187 (2x10^5 CFUs/mL). The seeds were stratified for 2 days at 4°C in the dark and then the plates were placed vertically to grow for 5 days.

extract_protocol: Total RNA extractions were performed using the NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's recommendations

treatment_protocol: Five  day-old seedlings were transferred onto ½ MS plates with or without 100 mM NaCl and let to grow for 14 days before to be rapidly frozen in liquid nitrogen.

value: whole plant

value: LYK4 OE

tag: growth medium

value: 1/2 MS + 100mM NaCl


title: sifra_sicjun_DMSO_1_S7


title: myoLuc_IFNa_4h_H3K27ac_R1


title: myoLuc_0h_STAT1_R2

value: Rabbit anti-STAT1 (Cohesion Biosciences #3322)

value: untreated


title: C7: DHBE control rep 1

value: primary bronchial epithelial cells

value: diseased

value: untreated ALI cultures


title: sictrl_OLAP_1_S4


title: LYK4 OE SA187 NaCl replicate 2


title: Control, PC1

description: DNBSEQ Technology Platform

value: leaf

value: wildtype

value: Moneymaker


title: FTAZ:IT-M, PC4

description: DNBSEQ Technology Platform


title: sictrl_DMSO_2_S2

description: transfected with non-target siRNA and treated with DMSO for 48 h

value: DMSO for 48 h


title: sictrl_DMSO_3_S3


title: lyk4 SA187 NaCl replicate 3


title: myoLuc_0h_STAT1_R1

value: embryonic fibroblast


title: lyk4 SA187 NaCl replicate 2


title: myoLuc_0h_RPB1_R2

value: Rabbit anti-pPOL2RA-Ser5 (Cell Signaling #13523S)


title: Control, PC4

description: DNBSEQ Technology Platform

value: PPFD Controlled (PC)


title: lyk4 SA187 NaCl replicate 1


title: myoLuc_0h_RPB1_R1


title: FTAZ:IT-M, PC3

description: DNBSEQ Technology Platform


title: FTAZ:IT-M, PC2

description: DNBSEQ Technology Platform


title: myoLuc_0h_pSTAT1_R2

value: Rabbit anti-pSTAT1-Ser727 (Active Motif #39634)


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 17]

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: Sample 17

data_processing:
Sequences were trimmed by Cutadapt to remove the Nextera transposase adaptor (Martin 2011).
The trimmed sequences were aligned with BWA to mouse mm10. Peaks were called using MACS14 with default parameters (Zhang et al. 2008).
Differentially bound peaks were called using DiffBind (Stark and Brown 2011; Ross-Innes et al. 2012).
Peaks were annotated by CHIPseeker (Yu et al. 2015).
Peak heatmaps and average profile of peaks were visualized using CHIPseeker.
Assembly: mm10 (GRCm38)
Supplementary files format and content: DiffPeaks_KOvsWT.post.csv: Comma-separated text file includes peaks.
Supplementary files format and content: DiffPeaks_KOvsWT.pre.csv: Comma-separated text file includes peaks.
Supplementary files format and content: DiffPeaks_postvspre.KO.csv: Comma-separated text file includes peaks.
Supplementary files format and content: DiffPeaks_postvspre.WT.csv: Comma-separated text file includes peaks.

source_name: pancreatic islets

extract_protocol:
40,000 isolated islet cells in single cell suspension were used to prepare crude nuclei, which were immediately used for the transposition reaction following a published protocol (Buenrostro et al. 2015).
Transposition reaction using Nextera Tn5 transposase (Nextera Tn5 Transposase, Illumina #FC-121-1030) was incubated at 37 °C for 30 min with gentle shaking. DNA was eluted using Qiagen MinElute PCR Purification kit and transposed DNA fragments were amplified using Nextera PCR Primer 1 and Primer 2 (containing barcode). Thermal cycle settings were as follows: 1 cycle of 72°C for 5 min, 98°C for 30 sec, 5 cycles of 98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min. 5-6 additional cycles were used as determined for each sample with a qPCR reaction to avoid artifacts due to over-amplification. Amplified library was purified using Qiagen MinElute PCR Purification kit. Amplified libraries were size selected using Ampure XP beads and quality was analyzed using Bioanalyzer High Sensitivity DNA kit. Indexed libraries were multiplexed in a single flow cell and underwent 75 base pair single-end sequencing on an Illumina NextSeq500 using the High Output kit v2 (75 cycles).

treatment_protocol: Islets were freshly isolated from 4 control and 3 Arid1a βKO mice pre-PPx and 4 control and 4 Arid1a βKO mice 6 days post-PPx, all males. Mice were given 1 g/L dox in the drinking water for two weeks. PPx was performed one week after dox withdrawal. Animals were sacrificed and islets were isolated 6 days after the PPx.

value: pancreatic islets

tag: age

value: 3 months

value: Arid1a betaKO

tag: Sex

value: male

value: pancreatectomy

tag: time point

value: 6 days post-PPx


title: WT SA187 NaCl replicate 3

value: whole plant

value: WT

value: 1/2 MS + 100mM NaCl

tag: treatment


title: CUT&RUN H2AK119ub1  Ly49G2 negative NK cells

city: Berkeley

first: Djem

middle: Ulian

last: Kissiov

state: CA

address: 485 Weill Hall

department: MCB

institute: UC Berkeley

data_processing:
Library strategy: CUT&RUN
Raw data were assessed using FastQC
fastq files were aligned to the mm10 reference genome using bowtie2 with the --sensitive parameter
Mitochondrial reads were removed using samtools
PCR duplicate reads were revoed using Picard
Reads mapping to blacklisted regions (ENCODE mm10 database) were removed using bedtools.
Data were normalized to signal per million reads (SPRM) when calling narrow peaks with macs2.
The resulting bedgraph files were converted to bigwigs using the bedGraphToBigWig program from UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
SNPs between the C57BL/6 and BALB/c genomes were sourced from the Wellcome Sanger Institute Mouse Genomes Project dbSNP (v142)
Delineation of allele-informative reads
SNPs annotated by the database were replaced by an ‘N’ in the mm10 reference genome using SNPsplit (Babraham Institute)
ATAC-seq datasets were aligned to the N-masked reference genome.
Allele-informative reads were flagged with SNPsplit, and processed and normalized as the rest of the files
Genome_build: mm10/N-masked
Supplementary_files_format_and_content: bigwig

source_name: IL-2 expanded NK cells

growth_protocol: Primary fresh splenic NK cells were isolated from single cell splenocyte suspensions by FACS sorting the indicated NK cell populations. CUT&RUN experiments were performed using splenocyte cultures in 1000U/mL IL-2 + 5% FCS RPMI-1640 cultures. Crude splenocytes were cultured in IL-2 containing medium for 48 hours, then the indicated NK cell populations were FACS sorted and further cultured in IL-2 containing medium for 7-10 days. IL-2 cultures were maintained at a density of ~1 million cells per mL.

extract_protocol:
The ATAC-seq Tn5 transposase reaction was performed on a crude Igepal CA-630 nuclear prep from ~50,000 NK cells. CUT&RUN experiments were performed on ConA-bead immobilized cells permeabilized with a 0.05% Digitonin solution.
ATAC-seq libraries were constructed using Nextera compatible primers. CUT&RUN libraries were constructed using the New England Biolabs Ultra II DNA library prep kit for Illumina

value: IL-2 expanded NK cells

value: (B6 x BALB/c)F1 hybrid

tag: allelic expression status

value: Ly49G2 negative

tag: genome alig

tag: antibody

value: anti-H2AUb1 (D27C4)


title: FTAZ:IT-M, PC1

description: DNBSEQ Technology Platform

value: leaf

tag: genotype

value: wildtype

value: Moneymaker


title: LYK4 OE SA187 NaCl replicate 1

value: LYK4 OE


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 16]

description: Sample 16

value: pancreatic islets


title: SBW25, Malathion, Replicate 3, 70 minutes

city: Santa Barbara

first: Aqib

last: Hasnain

state: California

address: UCEN Road

institute: University of California Santa Barbara

data_processing:
Reads were first trimmed of adapter sequences and low quality reads using Trimmomatic
Trimmed reads were mapped to the reference transcriptome using Kallisto
Read counts and normalized counts are Kallisto outputs
Assembly: GCA_000009225.1
Supplementary files format and content: tab delimited text files containing read counts, normalized counts (TPM), gene length,  effective gene length, and gene target ID

organism: Pseudomonas fluorescens

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA (DNA free) was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

tag: cell line

tag: time

value: 70 minutes

value: Malathion


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 18]

description: Sample 18

tag: tissue

value: 3 months

value: control

value: male


title: WT SA187 NaCl replicate 2

value: whole plant


title: myoLuc_0h_H3K27me3_R1

tag: cell type

value: embryonic fibroblast

value: Rabbit anti-H3K27me3 (Cell Signaling #9733)

value: untreated


title: myoLuc_0h_IgG_R1

value: Rabbit anti-mouse IgG (Abcam #ab46540)


title: myoLuc_0h_H3K27ac_R1

value: Rabbit anti-H3K27ac EMD (Millipore #MABE647)


title: LYK4 OE mock NaCl replicate 3

value: 1/2 MS + 100mM NaCl

value: mock


title: SBW25, Control, Replicate 1, 70 minutes

value: WT

value: Control


title: sictrl_DMSO_1_S1

tag: transfection

value: non-target siRNA

value: DMSO for 48 h


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 12]

description: Sample 12

value: pancreatic islets

value: pancreatectomy

value: 6 days post-PPx


title: lyk4 mock NaCl replicate 3


title: myoLuc_0h_pSTAT1_R1

value: Rabbit anti-pSTAT1-Ser727 (Active Motif #39634)


title: LYK4 OE mock NaCl replicate 2

value: LYK4 OE


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 13]

description: Sample 13

value: 3 months

value: control

value: male


title: LYK4 OE mock NaCl replicate 1

value: whole plant


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 14]

description: Sample 14

value: Arid1a betaKO


title: SBW25, Malathion, Replicate 3, 60 minutes

value: 60 minutes

value: Malathion


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 7]

description: Sample 7

value: baseline


title: SBW25, Control, Replicate 3, 60 minutes

value: WT


title: SBW25, Control, Replicate 3, 70 minutes

value: 70 minutes

value: Control


title: WT SA187 NaCl replicate 1

value: 1/2 MS + 100mM NaCl


title: WT mock NaCl replicate 3

value: mock


title: SBW25, Control, Replicate 1, 60 minutes


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 10]

description: Sample 10

value: pancreatic islets

value: pancreatectomy


title: myoLuc_0h_H3K27ac_R2

value: embryonic fibroblast

value: Rabbit anti-H3K27ac EMD (Millipore #MABE647)

value: untreated


title: TLR2/4 ligand treatment

city: Los Angeles

first: Ichiro

last: Nishimura

department: Dentistry

institute: UCLA

library_source: transcriptomic single cell

data_processing: The Cell Ranger output of single cell RNA sequencing data were analyzed using R-program (Seurat, https://satijalab.org/seurat/).

source_name: Palatal gingiva

extract_protocol:
At 4 days after the TLR9 ligand or TLR2/4 ligand treatment of the mice, the gingival tissue from the palate was harvested (n=4). Gingival tissues were cut into 1-mm pieces and placed in digestion buffer containing 1 mg/ml collagenase II (Life Technologies, Grand Island, NY), 10 units/ml DNase I (Sigma-Aldrich) and 1% bovine serum albumin (BSA; Sigma-Aldrich) in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) for 20 min at 37°C on a 150 rpm shaker. The tissues were passed through a 70µm cell strainer. The collected cells were pelleted at 1,500 rpm for 10 min at 4°C and resuspended in phosphate buffered saline (PBS; Life Technologies) that was supplemented with 0.04% BSA (Cell suspension A).  The remaining tissues were further incubated in 0.25% trypsin (Life Technologies) and 10 units/ml DNase I for 30 min at 37 ℃ on a 150 rpm shaker.
The combined trypsin-released cells and collagenase II-released cells were counted and the equal number of cells (2,000~3,000) from each animal were combined in the group for single cell RNA sequencing (10X Genomics, San Francisco, CA).

treatment_protocol: Three µl of 1 µg/ml of TLR9 ligand (InvivoGen, San Diego, CA) or TLR2/4 ligand (InvivoGen) were topically applied to the palate of female C57Bl6/J mice, and the palate were covered by an oral appliance. After 1 hour of covering the palate, the oral appliances were removed.

value: Gingiva

value: 8-12 weeks old


title: SBW25, Malathion, Replicate 1, 60 minutes


title: lyk4 mock NaCl replicate 1

value: whole plant


title: WT mock NaCl replicate 2


title: SBW25, Malathion, Replicate 1, 70 minutes


title: lyk4 mock NaCl replicate 2


title: SBW25, Malathion, Replicate 1, 50 minutes

value: 50 minutes


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 4]

description: Sample 4

value: 3 months

value: Arid1a betaKO

value: male


title: S110010

type: RNA

city: Lisboa

first: Mariana

middle: Batista

last: Santos

address: Av Brasilia

department: Champalimaud Physiology and Cancer Programme

country: Portugal

institute: Champalimaud Foundation

description: XP_4 vs ctrl_4 (dye-swap)

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

label_protocol: Adjust RNA volume to 3 µL with DEPC-water and add 1 µL 3'-SMART CDS Primer IIA (10 µM) and 1 µL SMART IIA chimeric oligo (10 µM). Incubate at 70 °C for 5 minutes, then snap cool on ice. Add 2 µl 5x First Strand Buffer (Invitrogen), 0.5 µL 0.1M DTT (Invitrogen), 0.5 µL 10 mM dNTP mix and 1 µl 200 U/µL Superscript III (Invitrogen). Incubate at 46 °C for 1.5 hours, then cool on ice (store samples at 4 °C or -20 °C). To determine the optimal number of cycles required for generating products in exponential phase, 2 µL of the PCR products from a parallel run are visualised at every second cycle from cycle 18 to 26 on 1% agarose gel using one reaction of each sample type. To 5 µL of the first-strand reaction (include negative and positive controls) add 5 µL 10x Advantage II PCR buffer (Clontech), 1 µL 10 mM dNTP mix, 2 µL 20 µM 5' PCR Primer II, 1 µL 50x Advantage II Polymerase Mix (Clontech) and adjust volume to 50 µL with DEPC-water. Run PCR program: step 1: 95 °C - 1 min, step 2: 95 °C - 5 sec, step 3: 65 °C - 5 sec, step 4: 68 °C - 6 min, cycle from step 2 for 27 more times. Run PCR aliquots on 1% agarose gel and select cycle number below saturation. Then perform amplification using the optimal number of XX cycles on the remaining 5 µL of the first-strand reaction. Purify PCR products using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).  SMART II A chimeric primer: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CGC-888-3'  (8 = riboG)  3' SMART CDS Primer IIA: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-VN-3' (V = G+A+C, N = A+C+G+T)  5' PCR Primer II: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GT-3' In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen Dual Colour Kit) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen Dual Colour Kit). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen Dual Colour Kit), 8 Nuclease-free Water (Nimblegen Dual Colour Kit) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen Dual Colour Kit), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen Dual Colour Kit). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat.

extract_protocol: Homogenise tissue in 150-200 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes 4 °C to pellet debris and transfer supernatant to a prespun 1.5 ml Phase Lock Gel heavy tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds. Centrifuge at 13,000 rpm for 5 minutes. Remove upper phase to a new RNase-free tube, being careful not to touch the gel. Add 0.4 µl GeneElute Linear Polyacrylamide (Sigma) (25 µg / µl stock diluted 1:10 in DEPC MilliQ water) and 0.8 volumes of isopropanol, invert and then incubate for 1 hour at -20 °C. Pellet the RNA by centrifugation at 13,000 rpm for 30 minutes. Discard the supernatant and wash the RNA pellet with 500 µl 70% ethanol/DEPC MilliQ water. Air-dry the pellet. Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 5 µl. Verify quality of RNA on a 0.8 % agarose gel stained with SYBR-gold (Molecular Probes).

treatment_protocol: The medulla of the adult optic lobe was injured with a sterile small metal filament (∅ 0,1mm or 0,2mm, Fine Science Tools) via a puncture through the eye.

value: brain

value: injured

value: control


title: S110009

description: XP_3 vs ctrl_3


title: S110004

description: XP_2 vs ctrl_2 (dye-swap)


title: LYK4 OE SA187 MS replicate 3

value: LYK4 OE


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 8]

description: Sample 8

value: baseline


title: SBW25, Malathion, Replicate 3, 50 minutes

value: WT

value: Malathion


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA; TRE-Cre (Arid1a βKO) [Sample 5]

description: Sample 5

value: pancreatic islets


title: TLR9 ligand treatment


title: Post-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 11]

description: Sample 11

value: pancreatectomy

value: 6 days post-PPx


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 6]

description: Sample 6


title: WT mock NaCl replicate 1

value: 1/2 MS + 100mM NaCl

value: mock


title: SBW25, Control, Replicate 1, 50 minutes

value: Control


title: Early periodontitis [Ligature_Day1]

extract_protocol:
At 1 days after ligature placement, the gingival tissue from the ligature side of the palate was harvested (n=4). Gingival tissues were cut into 1-mm pieces and placed in digestion buffer containing 1 mg/ml collagenase II (Life Technologies, Grand Island, NY), 10 units/ml DNase I (Sigma-Aldrich) and 1% bovine serum albumin (BSA; Sigma-Aldrich) in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) for 20 min at 37°C on a 150 rpm shaker. The tissues were passed through a 70µm cell strainer. The collected cells were pelleted at 1,500 rpm for 10 min at 4°C and resuspended in phosphate buffered saline (PBS; Life Technologies) that was supplemented with 0.04% BSA (Cell suspension A).  The remaining tissues were further incubated in 0.25% trypsin (Life Technologies) and 10 units/ml DNase I for 30 min at 37 ℃ on a 150 rpm shaker.
The combined trypsin-released cells and collagenase II-released cells were counted and the equal number of cells (2,000~3,000) from each animal were combined in the group for single cell RNA sequencing (10X Genomics, San Francisco, CA).

treatment_protocol: A silk thread (ligature) was gently tied around the left maxillary second molar of female C57BL6/J wild type mice.

value: Gingiva

value: 8-12 weeks old


title: S110002

description: XP_1 vs ctrl_1


title: PKO_PHT_89

city: la jolla

first: Siting

state: california

address: 9500 Gilman Drive, University of California San Diego

department: Medicine

institute: UCSD

data_processing:
The sequencing reads longer than 36nt are kept are downstream analysis.
Then, the reads were mapped to assembly of the mouse genome (mm10) using STAR (2.5.3a).
The differential expressed genes were identified by using DESeq2 (v1.12.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: nuclear RNA

source_name: Ptpmt1 cardiomyocytes-specific Knockout and Hri nockout mouse line

extract_protocol: RNA libraries for RNA-seq were prepared using  KAPA RNA Hyper+RiboErase HMR Library Prep Kit following manufacturer's protocols.

value: cardiomyocytes

value: Ptpmt1 cardiomyocytes-specific Knockout only


title: lyk4 SA187 MS replicate 3

value: whole plant


title: DKO_PHT_90

value: Ptpmt1 cardiomyocytes-specific Knockout and Hri Knockout


title: LYK4 OE SA187 MS replicate 2


title: lyk4 SA187 MS replicate 2


title: Arid1a FL/FL; UbcCreERT2 - PPx [Sample 8]

description: Sample 8

data_processing:
Adaptors and low quality sequences (Phred<20) were removed by trimming raw sequencing reads using galore package.
The sequence reads were aligned to the GRCm38/mm10 with HiSAT2 (Kim et al. 2015).
After duplicate removal by SAMtools (Li et al. 2009), read counts were generated for the annotated genes based on GENCODE V20, using featureCounts (Harrow et al. 2012; Liao et al. 2014).
Differential gene expression analysis was performed on edgeR, using FDR < 0.05 as cutoff (McCarthy et al. 2012; Robinson et al. 2010).
Heatmaps to visualize the data were generated by using GENE-E (Robinson et al. 2010).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Normalized_read_counts.xlsx: Excel file includes normalized read counts.

extract_protocol:
RNA was isolated using TRIzol reagent.
RNA-seq libraries were prepared using Ovation RNA-Seq Systems 1-16 (Nugen).
Indexed libraries were multiplexed in a single flow cell and underwent 75 base pair single-end sequencing on an Illumina NextSeq500 using the High Output kit v2 (75 cycles) at the Children’s Research Institute Sequencing Facility.

treatment_protocol: Islets were isolated from 2 Arid1aFl/Fl and 5 Ubc-CreER; Arid1aFl/Fl mice for no-PPx and 2 Arid1aFl/Fl and 2 Ubiquitin-CreER; Arid1aFl/Fl mice 6 days post-PPx, all males. Deletion was induced in 45-60 day old mice by administration of 10 mg tamoxifen per day for two consecutive days by oral gavage. Two weeks after tamoxifen, PPx was performed and post-PPx islets were isolated 6 days after the surgery.

value: 3 months

value: Arid1a KO

value: male


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 2]

description: Sample 2

value: control

value: baseline


title: Arid1a FL/FL; UbcCreERT2 - PPx [Sample 7]

description: Sample 7

value: pancreatic islets


title: SBW25, Control, Replicate 3, 50 minutes

value: 50 minutes

value: WT


title: LYK4 OE SA187 MS replicate 1

value: LYK4 OE


title: PKO_PHT_39


title: lyk4 SA187 MS replicate 1


title: SBW25, Malathion, Replicate 3, 40 minutes

value: 40 minutes

value: Malathion


title: Arid1a FL/FL - PPx [Sample 6]

description: Sample 6

value: pancreatectomy

value: 6 days post-PPx


title: Pre-PPx: Arid1aFl/Fl; MIP-rtTA control  [Sample 3]

description: Sample 3


title: HKO_PHT_83

value: cardiomyocytes

value: Hri cardiomyocytes-specific Knockout only


title: SBW25, Control, Replicate 3, 40 minutes

value: Control


title: SBW25, Malathion, Replicate 1, 40 minutes


title: SBW25, Malathion, Replicate 1, 30 minutes

value: 30 minutes


title: SBW25, Control, Replicate 1, 40 minutes


title: WT SA187 MS replicate 3

value: whole plant


title: PKO_PHT_28

value: Ptpmt1 cardiomyocytes-specific Knockout only


title: HKO_PHT_71


title: SBW25, Malathion, Replicate 3, 30 minutes


title: WT SA187 MS replicate 2


title: DKO_PHT_67

value: Ptpmt1 cardiomyocytes-specific Knockout and Hri Knockout


title: Arid1a FL/FL; UbcCreERT2 - no PPx [Sample 14]

description: Sample 14

value: 3 months

value: Arid1a KO

value: male


title: Arid1a FL/FL; UbcCreERT2 - no PPx [Sample 16]

description: Sample 16

value: pancreatic islets

value: baseline


title: WT_PHT_78


title: LYK4 OE mock MS replicate 3

value: LYK4 OE

value: mock


title: Arid1a FL/FL - PPx [Sample 5]

description: Sample 5

value: control


title: PTe173 (cKO)

source_name: Ptpmt1 cardiomyocytes-specific Knockout mouse line

value: Ptpmt1 cardiomyocytes-specific Knockout


title: SBW25, Control, Replicate 1, 30 minutes

value: WT


title: WT_PHT_64

value: cardiomyocytes


title: LYK4 OE mock MS replicate 2


title: SBW25, Malathion, Replicate 3, 20 minutes

value: 20 minutes

value: Malathion


title: PTe167 (cKO)


title: SBW25, Malathion, Replicate 1, 20 minutes


title: WT SA187 MS replicate 1


title: Arid1a FL/FL; UbcCreERT2 - no PPx [Sample 12]

description: Sample 12


title: Arid1a FL/FL; UbcCreERT2 - no PPx [Sample 13]

description: Sample 13


title: Arid1a FL/FL - no PPx [Sample 11]

description: Sample 11


title: PTe143 (cKO)


title: Arid1a FL/FL; UbcCreERT2 - no PPx [Sample 15]

description: Sample 15


title: LYK4 OE mock MS replicate 1


title: PTe171 (Ctrl)

value: Control


title: lyk4 mock MS replicate 3

value: whole plant


title: PTe170 (Ctrl)


title: ATAC-seq Ly49G2 both alleles NK cells

description:
processed data file (B6 genome-aligned): Ly49G2-DP_genome1.final.bw
processed data file (BALB genome-aligned): Ly49G2-DP_genome2.final.bw

data_processing:
Raw data were assessed using FastQC
fastq files were aligned to the mm10 reference genome using bowtie2 with the --sensitive parameter
Mitochondrial reads were removed using samtools
PCR duplicate reads were revoed using Picard
Reads mapping to blacklisted regions (ENCODE mm10 database) were removed using bedtools.
Data were normalized to signal per million reads (SPRM) when calling narrow peaks with macs2.
The resulting bedgraph files were converted to bigwigs using the bedGraphToBigWig program from UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
SNPs between the C57BL/6 and BALB/c genomes were sourced from the Wellcome Sanger Institute Mouse Genomes Project dbSNP (v142)
Delineation of allele-informative reads
SNPs annotated by the database were replaced by an ‘N’ in the mm10 reference genome using SNPsplit (Babraham Institute)
ATAC-seq datasets were aligned to the N-masked reference genome.
Allele-informative reads were flagged with SNPsplit, and processed and normalized as the rest of the files
Genome_build: mm10/N-masked
Supplementary_files_format_and_content: bigwig

source_name: Primary splenic NK cells

value: Primary splenic NK cells

value: (B6 x BALB/c)F1 hybrid

value: Ly49G2 both alleles


title: SBW25, Control, Replicate 3, 20 minutes


title: SBW25, Control, Replicate 3, 30 minutes

value: 30 minutes


title: SBW25, Malathion, Replicate 1, 10 minutes

value: 10 minutes


title: Arid1a FL/FL - no PPx [Sample 9]

description: Sample 9

value: pancreatic islets

value: 3 months

value: male


title: WT mock MS replicate 2

value: mock


title: lyk4 mock MS replicate 1


title: WT mock MS replicate 1


title: SBW25, Control, Replicate 1, 10 minutes


title: ATAC-seq Ly49G2 negative NK cells

description:
processed data file (B6 genome-aligned): Ly49G2-DN_genome1.final.bw
processed data file (BALB genome-aligned): Ly49G2-DN_genome2.final.bw

value: Ly49G2 negative


title: 72 Hippocampus, 22M

first: Qi

last: Shang

state: Guangzhou

address: No.16, Airport road, BaiYun Road, Guangzhou City,

institute: Guangzhou University of Chinese Medicine

data_processing:
For read alignment, the software Hisat2 was used.
For read quantification/FPKM calculation, the software Ballgown was used.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Excel file with  FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
The total RNA was extracted from young (3M) and aging (22M) hippocampus samples in mice by using Trizol reagents (Invitrogen). The extracted total RNA samples were subjected to agarose electrophoresis and Nanodrop for quality inspection and quantification.1-2g total RNA was selected from each sample for sequencing library construction.
Oligo magnetic beads were used to enrich the mRNA, and the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used to construct the library

value: Hippocampus

value: Male

value: aged


title: SBW25, Control, Replicate 1, 20 minutes

value: 20 minutes

value: WT


title: J15 Hippocampus, 3M

value: Young


title: WT mock MS replicate 3

value: whole plant


title: PTe146 (Ctrl)

value: cardiomyocytes

value: Control


title: ATAC-seq Ly49G2 B6 allele only NK cells

description:
processed data file (B6 genome-aligned): Ly49G2-B6_genome1.final.bw
processed data file (BALB genome-aligned): Ly49G2-B6_genome2.final.bw

value: Primary splenic NK cells

value: (B6 x BALB/c)F1 hybrid

value: Ly49G2 B6 allele only


title: SBW25, Malathion, Replicate 3, 10 minutes

value: 10 minutes

value: Malathion


title: lyk4 mock MS replicate 2


title: ATAC-seq Ly49G2 BALB allele only NK cells

description:
processed data file (B6 genome-aligned): Ly49G2-BALB_genome1.final.bw
processed data file (BALB genome-aligned): Ly49G2-BALB_genome2.final.bw

value: Ly49G2 BALB allele only


title: Q001S0001B0003R1N

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description: Hordeum vulgare L. (Barley) + Blumeria graminis f. sp. hordei (Bgh)

data_processing:
Library strategy: Amplicon-seq
Adapter Trimming - Each sample was processed using Trimmomatic to trim off adapters. Fastqc analysis revealed that most of the reads are of high quality. Hence, no quality trimming was performed.
Alignment - Reads from each sample were aligned to the genome of barley, Blumeria and vector sequences using STAR (dobin et. Al 2013).
Fusion read recognition - Custom python scripts were used to recognize fusion reads based on the partial alignment to the genomes and vector sequences. Vector portions were trimmed off from fusion reads.
Differential expression analysis - Salmon (Patro 2017) was used to obtain gene counts. Samples were size normalized and differential expression analysis was carried out using DESeq2 (Love 2014).
In-frame fusion reads  - Fusion reads expressed in-frame with the protein were recognized by translating the entire sequence and comparing with the protein.
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew.

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: Yeast were grown at 28C shaking at 225rpm. Cells were subcultured once they reached saturation (OD600 >2.5).

extract_protocol:
Yeast cells were treated with lyticase to digest cell walls and Y2H plasmids were extracted using alkaline lysis and precipitation.
Libraries were constructed using the Nugen Ultralow System V2 with Custom AnyDeplete to reduce the abundance of an amplicon common to all libraries using the manufacturer's instructions.

treatment_protocol: Yeast were incubated in SC-Leu-Trp (no selection) or SC-Leu-Trp-His (reporter selection) liquid media. Two rounds of growth selection were performed.

tag: plant genotype

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

tag: fungal isolate

value: Bgh isolate 5874 (AVRa6)

value: Non-selected

tag: replication


title: 78 Hippocampus, 22M

tag: strain

value: Hippocampus

value: Male


title: SBW25, Control, Replicate 3, 0 minutes

value: 0 minutes


title: J13 Hippocampus, 3M

value: WT

tag: age


title: Q001S0001B0003R3S

value: Selected


title: 76 Hippocampus, 22M

tag: Sex

value: aged


title: Lenti-X 293T,FAIRE-input

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

data_processing:
FAIRE-seq NGS reads were aligned to the human genome(hg38) using Bowtie with default settings, and only the unique mapped reads were used for follow-up analysis.Narrow peaks were generated by MACS2 (v2.1.1) with p-value = 0.00001. Bigwig files were created using deepTools "bamCoverage".
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Lenti-X 293T

growth_protocol: Lenti-X 293T cells were cultured in Dulbecco’s Modified Eagle’s Medium  containing 1% penicillin/streptomycin and 10% (v/v) FBS. The cells were grown at 37°C with 5% CO2,

extract_protocol:
Briefly, cells were fixed with 1% formaldehyde for 10 minutes, and the residual formaldehyde was quenched with 0.125M glycine. The cell pellet from each 10cm cell culture dish was collected and washed once with cold 1× PBS buffer and lyzed in 1 ml Hypotonic lysis buffer containing Protease Inhibitor (MCE, Cat#HY-K0010). The nuclei were pelleted by a 12000rpm centrifuge at 4°C and washed once with cold 1x PBS buffer. The pellet was then resuspended in 0.1% SDS lysis buffer and incubated for 60 minutes at 4°C. Chromatin was sonicated to a fragment size of 200-300bp using Bioruptor (Bioruptor pico). The chromatin lysate was cleared by centrifugation at 12000 rpm for 5 minutes at 4°C. For each FAIRE reaction, 100 μl chromatin lysate was supplied with 400 μl 1× TE buffer (pH = 8.0) and subjected to twice phenol/chloroform/isoamyl alcohol (25:24:1) extraction, and then chloroform/isoamyl alcohol extraction. The DNA-containing water layer was transferred to a new 1.5 ml tube and supplied with 1/10 volume of 3M sodium acetate, two volumes of 100% ethanol, and 1 μl of 20 mg/ml glycogen (Thermo Fisher Scientific, Cat# R0551). After incubating at -80°C for 2 h, the DNA was precipitated by centrifugation and washed once with 70% ethanol. Subsequently, the DNA was resuspended in 10 mM Tris-HCl (pH=7.4) and reverse cross-linked through overnight incubation at 64°C in the presence of Proteinase K and 0.3M NaCl. Thereafter, RNaseA (Thermo Fisher Scientific) was supplied to remove the trace amount of RNA with incubation at 37°C for 30 min. The DNA was purified with VAHTS DNA Clean Beads (Vazyme, Cat#N411-01) and subjected to both qPCR assay and FAIRE-seq analysis.
100 ng FAIRE DNA/Input DNA was employed for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina

value: Lenti-X 293T

value: Human embryonic kidney


title: acj66_adPN_1

city: Stanford

first: Qijing

last: Xie

address: Bass Biology Building, Room 334

department: Department of Biology

institute: Howard Hughes Medical Institute

description: acj6 mutant adPN transcriptome

data_processing:
de-mutiplexd (bcl2fastq 2.19.0.316)
alignment (STAR 2.5.4)
gene count (HTseq 0.11.2, default settings except ‘‘-m  536 intersection-strict’)
Assembly: Dmel r6.10
Supplementary files format and content: .tab count table

source_name: neuron

extract_protocol: Modified SMART-seq2 (Li et al. 2017)

value: acj6 mutant

tag: Stage

value: 36-40 hr after puparium formation

value: adPN


title: Q001S0001B0003R3N

tag: treatment


title: SBW25, Control, Replicate 3, 10 minutes

value: 10 minutes

value: Control


title: Q001S0001B0003R1S


title: RENCA SDHB KO rep 2

city: New Haven

first: Ranjit

last: Bindra

state: CT

address: 15 York Street

department: Therapeutic Radiology

institute: Yale University

data_processing:
RNA-seq reads were aligned using the nf-core pipeline.
The nf-core pipeline aligned reads to the mm10 genome using the Hisat2 aligner
read counts were generated using the featureCounts v2.0.3
DESeq2 v1.30.1 R Bioconductor package was used to identify differentially expressed genes (DEGs) using the alternative shrinkage estimator ashr to control for false discovery rates (FDR), and effect sizes.
Assembly: mm10
Supplementary files format and content: comma-delimited values file containing read counts of FH1 KO samples and parental samples
Supplementary files format and content: comma-delimited values file containing read counts of SDHB KO samples and parental samples

source_name: kidney

growth_protocol: The RENCA, RENCA Fh1-KO, RENCA Sdhb-KO cells were cultured in a humidified atmosphere at 37 °C in RPMI1640 medium with 10% fetal bovine serum and non-essential amino acids (0.1mM extra), sodium pyruvate (1mM extra), L-glutamine (2 mM extra).

extract_protocol:
RNA from Renca Parental, Sdhb-KO and Fh1-KO was isolated using RNeasy microcolumns (Qiagen) and quantified using NanoDrop
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: No Treatment

value: kidney

value: RENCA

value: epithelial cell

value: SDHB KO


title: WT_adPN_3

description: wild-type adPN transcriptome

value: wild-type


title: RENCA SDHB KO rep 1


title: SBW25, Malathion, Replicate 1, 90 minutes

value: 90 minutes

value: Malathion


title: Q001S0001B0003R2N

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)

value: Non-selected


title: RENCA FH KO rep 2

value: FH1 KO


title: Sample Q001S0002B0015R2N


title: SBW25, Control, Replicate 3, 90 minutes

value: WT


title: RENCA FH KO rep 1


title: SBW25, Malathion, Replicate 1, 0 minutes

value: 0 minutes


title: Lenti-X 293T,FAIRE-rep2

value: Lenti-X 293T

value: Human embryonic kidney


title: J11 Hippocampus, 3M

city: Guangzhou

value: Hippocampus

value: Male

value: Young


title: SBW25, Control, Replicate 1, 0 minutes

value: Control


title: SBW25, Malathion, Replicate 3, 0 minutes


title: Q001S0001B0003R2S

value: Selected


title: SBW25, Malathion, Replicate 3, 90 minutes


title: Lenti-X 293T,FAIRE-rep1


title: Sample Q001S0002B0015R3N


title: acj66_adPN_2

description: acj6 mutant adPN transcriptome

value: acj6 mutant

value: 36-40 hr after puparium formation

value: adPN


title: SBW25, Malathion, Replicate 3, 80 minutes

value: 80 minutes

value: Malathion


title: acj66_adPN_3

description: acj6 mutant adPN transcriptome


title: WT_adPN_2

description: wild-type adPN transcriptome

value: wild-type


title: RENCA Parental rep 1

value: kidney

value: RENCA

value: epithelial cell

value: parental


title: Mouse duodenum encasing to a 4 mm punch section of human skin (sample HM-1 in the manuscript)

city: Madison

first: Zijian

last: Ni

address: 425 Henry Mall

institute: University of Wisconsin-Madison

description: Chimera composed of mouse duodenum as "sausage" casing to a 4 mm punch section of human skin (sample MS-1 in the manuscript)

data_processing:
bcl2fastq v2.20.0.422 was used for basecalling and demultiplexing.
Tissues were manually aligned using Loupe Browser v4.2.0.
Raw fastq files were aligned and quantified using Space Ranger v1.2.2 under default settings. The Visium slide ID is V10F06-009. The capture areas for 1_S1, 2_S2, 3_S3 are A1, B1, C1.
Genome_build: GRCh38+mm10
Supplementary_files_format_and_content: tar.gz: A tarball for each sample containing all outputs from Space Ranger pipeline, except for BAM file.

organism:
Homo sapiens
Mus musculus

source_name: Mouse duodenum and human skin

extract_protocol:
Moue tissues and human skin were harvested on the same day and manually prepared into chimera tissue blocks on ice, then flash frozen in OCT histology media. Spatial transcriptomics was performed using standard 10x protocol for the Visium Spatial Gene Expression kit (Cat no. PN-1000-187) with permeabilization time of 12 min.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: Mouse duodenum and human skin

value: 10 week old mouse and 52 year old human

value: wild type


title: WT_adPN_1

description: wild-type adPN transcriptome


title: SBW25, Control, Replicate 1, 90 minutes

value: 90 minutes

value: WT


title: SRSF2f/f/Myf5-Cre/tdT

city: s

first: ruochen

last: guo

address: 320 Yueyang RD.

institute: Shanghai Institute of Nutrition and Health

description: one sample from murine embryo

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat (version 3.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: cell barcode files
Supplementary_files_format_and_content: gene files
Supplementary_files_format_and_content: gene-barcode counts

source_name: tdtomato+ cells

extract_protocol:
SRSF2f/f/Myf5-Cre/tdT and SRSF2f/w/Myf5-Cre/tdT embryos were collected. To generate single cells, embryonic trunks and limbs were incubated in collagenase-type XI and dispase II and then sorted with a tdTomato+ gating strategy on a Beckman moflo Astrios EQ. The cells were resuspended in 20% FBS/PBS buffer before 10× Genomics library preparation
RNA libraries were prepared with Chromium Single cell 3'Reagent v3.1 Kits according to the manufacturer's protocol.

tag: tag

value: developmental stage

value: embryo

value: genotype


title: SRSF2f/w/Myf5-Cre/tdT

description: one sample from murine embryo


title: Sample Q001S0002B0015R1N

value: CI 16151 (Resistant progenitor), m19089 (resistant bln1 mutant), m18982 (susceptible mla6 mutant), m19028 (susceptible mla6 + bln1 double mutant), m11526 (susceptible rar3 mutant)

value: Bgh isolate 5874 (AVRa6)

value: Non-selected


title: Sample Q001S0002B0015R2S

value: Selected


title: RENCA Parental rep 2


title: SBW25, Control, Replicate 3, 80 minutes

value: 80 minutes

value: Control


title: Mouse heart encasing a 4-mm section of human skin (sample HM-3 in the manuscript)

description: Chimera of mouse heart encasing a 4-mm section of human skin (sample MS-3 in the manuscript)

source_name: Mouse heart and human skin

value: Mouse heart and human skin


title: Sample Q001S0002B0015R1S


title: SBW25, Control, Replicate 1, 80 minutes


title: Mouse colon encasing to a 4 mm punch section of human skin (sample HM-2 in the manuscript)

description: Chimera composed of mouse colon as "sausage" casing to a 4 mm punch section of human skin (sample MS-2 in the manuscript)

source_name: Mouse colon and human skin

value: Mouse colon and human skin


title: Sample Q001S0002B0015R3S


title: SBW25, Malathion, Replicate 1, 80 minutes

value: Malathion


title: STRS_3D

status: Public on Apr 20 2022

city: New York

first: David

middle: William

last: McKellar

state: NY

address: 101 6th Ave

institute: New York Genome Center

description: Two tibialis anterior sections (uninjured and notexin-2dpi) processed with in situ polyadenylation and Visium (spTotal, w/ Protector Rnase Inhibitor)

data_processing:
3' polyA trimming with cutadapt v3.4
3' polyG trimming and 5' TSO trimming (CCCATGTACTCTGCGTTGATACCACTGCTT) with cutadapt v3.4
Alignment and quantitation with STAR v2.7.10a; used GRCm39 reference with GENCODE M28 annotations or the same reference appended with the Reovirus Type 1-Lang sequence/annotations
Pseudoalignment with  kallisto v0.48.0 and quantitation with bustools v0.41.0; used GRCm39 reference with GENCODE M28 annotations or the same reference appended with the Reovirus Type 1-Lang sequence/annotations
Assembly: GRCm39 (GENCODE M28 annotaitons)
Supplementary files format and content: Count matrices were uploaded in matrix market (.mtx) with the spot barcodes and feature names in separate tab-delimited .txt files (count matrices from the Reovirus-appended reference have "REO" in the filename)
Supplementary files format and content: Stitched and shading-corrected H&E images are uploaded as .tif files
Supplementary files format and content: Tissue section coordinates are uploaded as .json files, manually selected using the Loupe Browser software from 10x Genomics

source_name: muscle

extract_protocol:
In situ polyadenylation (yeast poly(A) polymerase) followed by Visium Spatial Gene Expression v1
Spatial Total RNA-sequencing

value: muscle

value: female

value: Notexin (uninjured & 2dpi)

tag: injury


title: STRS_3B_xGen

description: Vis_yPAP_3B, final seuqencing library enriched for Reovirus-derived transcripts using the xGen pulldown workflow

tag: genotype

value: Oral infection with Reovirus Type 1-Lang, 7dpi (final library processed to enrich for Reovirus-derived transcripts)


title: STRS_3B

description: One heart section (infection with T1L-Reovirus, collected 7dpi) processed with in situ polyadenylation and Visium (spTotal, w/ Protector Rnase Inhibitor)

value: Oral infection with Reovirus Type 1-Lang, 7dpi


title: P14_Vgat_Esr1_con_male_b

city: Cold Spring Harbor

first: Melody

last: Wu

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Reads were demultiplexed and aligned to the reference genome using cellranger (v6.0.0) count
Gene expression matrices were constructed using cellranger (v6.0.0) software
Predicted doublets and low-quality nuclei were removed using Seurat (v4.0.3)
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Matrix.mtx file contains the gene x cell matrix for all samples. Barcode suffix indicates sample ID: 1 = Esr1_con_male_a, 2 = Esr1_con_male_b, 3 = Esr1_con_female_a, 4 = Esr1_con_female_b, 5 = Esr1_KO_male_a, 6 = Esr1_KO_male_b.
Supplementary_files_format_and_content: Features.tsv file contains the genes (matches row names of matrix file).
Supplementary_files_format_and_content: Barcodes.tsv file contains the cell barcodes (matches column names of matrix file).

source_name: Bed nucleus of the stria terminalis, posterior

growth_protocol: P14 Vgat-Cre; Esr1-lox; Sun1-GFP-lox female and male mice

extract_protocol:
Flash-frozen tissue samples (n=3 group) were removed from -80degC and maintained on dry ice. With the tissue still frozen, Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, 1 U/ul Protector RNase inhibitor, pH 7.8) was added to the tube, and the tissue was immediately transferred to a glass homogenizer. The tissue was homogenized 15x with a loose pestle. 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer. The nuclei were diluted 2:1 with cold, supplemented homogenization buffer and immediately used for sorting. 80,000-90,000 GFP+ nuclei were collected into 100 μl of cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2), supplemented with 1% sterile-filtered BSA, and 1 U/μl Protector RNase inhibitor, in a 0.5 ml DNA lo-bind tube pre-coated with 30% BSA. After collection, nuclei were pelleted with 2 rounds of gentle centrifugation (200 x g for 1 min) in a swinging-bucket centrifuge at 4degC. After the second round, the supernatant was carefully removed, leaving ~40 μl in the tube. The nuclei were gently resuspended in this remaining volume and immediately used for the 10X Genomics Single Cell 3’ Gene Expression kit v3, following the manufacturer’s instructions.
10X Genomics Single Cell 3’ Gene Expression kit v3

value: BNSTp

value: Male

tag: molecule subtype

value: Single-nucleus RNA


title: P14_Vgat_Esr1_con_male_a


title: P14_Vgat_Esr1_KO_male_a

value: KO


title: STRS_3C

description: Two tibialis anterior sections (notexin-5dpi and notexin-7dpi) processed with in situ polyadenylation and Visium (spTotal, w/ Protector Rnase Inhibitor)

value: Notexin (5dpi & 7dpi)


title: P14_Vgat_Esr1_KO_male_b


title: P14_Vgat_Esr1_con_female_b

value: Female


title: VAF6 rep1

city: Shanghai

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: TXT file contains counts for each sample

organism: Sus scrofa

source_name: Visceral fat

growth_protocol: Male Bama pigs with similar genetic backgrounds, produced by one sire, were born and raised under the same environmental and nutritional conditions and housed at Taizhou experimental miniature pig breeding case managed by Taihe Biotechnology Co. LTD in Taizhou, Jiangsu Province, China.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were fasted 24-h prior to slaughter. Fasting blood samples were collected. Then animals were euthanized by intravenous injection of pentobarbital sodium (150mg/kg). The adipose tissues were sampled immediately after death. All animals were humanely treated to ameliorate suffering.

value: Visceral fat

tag: origin

value: Visceral fat tissues adjacent to kidney deposition

value: 6 mo


title: VAF3 rep2

tag: tissue

value: 3 mo


title: STRS_3A

description: One heart section(mock-infection) processed with in situ polyadenylation and Visium (spTotal, w/ Protector Rnase Inhibitor)

value: male

value: Mock/saline injection


title: VAF1 rep3

value: 1 mo


title: VAF1 rep2


title: VAF6 rep2


title: P14_Vgat_Esr1_con_female_a

value: Control


title: SAF6 rep3

source_name: Subcutaneous fat

value: Subcutaneous fat

value: subcutaneous fat tissues on the back between the third and fourth last ribs


title: SAF6 rep1


title: SAF3 rep2


title: SAF3 rep3


title: VAF3 rep3


title: SAF1 rep2


title: SAF1 rep3


title: VAF1 rep1


title: VAF6 rep3


title: VAF3 rep1


title: DT3_ALBI_Sp_V

city: Boston

first: Flaminia

last: Catteruccia

state: MA

address: 655 huntington ave

institute: Harvard University

data_processing:
Alignment: hisat2/2.0.5. Parameters: -q -x --threads 4
Mapping quality filter: samtools/1.3.1. Parameters: view -bS -q 30
Sort mapped reads: samtools/1.3.1. Parameter: sort
Read count: htseq/0.9.1. Parameters: --stranded=no  --mode=union --quiet  -a 30
Assembly: Anopheles gambiae PEST AgamP4.12; Anopheles albimanus STECLA AalbS2.4
Supplementary files format and content: Processed data files format: Plain text file.  Content: Read counts

organism: Anopheles albimanus

source_name: Anopheles albimanus Virgin spermatheca rep D 24 hr

extract_protocol:
Total RNA was extracted with TRI reagent (Thermo Fisher Scientific, MA) from pools of 10–12  tissues following the manufacturer’s instructions. RNA was treated with TURBO DNase (Thermo Fisher Scientific, MA), and purified with Qiagen RNeasy MinElute Cleanup Kit.
Illumina TruSeq Stranded mRNA kit

value: spermatheca

tag: mating status

value: Virgin

tag: replicate

value: D

tag: time point

value: 24 hr post-mating or time-matching virgins


title: SAF1 rep1


title: BT3_ALBI_Sp_V

source_name: Anopheles albimanus Virgin spermatheca rep B 24 hr

value: B


title: BT3_ALBI_RB_V

source_name: Anopheles albimanus Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 24 hr


title: BT3_ALBI_Sp_M

source_name: Anopheles albimanus Mated spermatheca rep B 24 hr

value: Mated


title: DT3_ALBI_RB_V

source_name: Anopheles albimanus Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 24 hr

value: Female


title: AT3_ALBI_Sp_V

source_name: Anopheles albimanus Virgin spermatheca rep A 24 hr

value: A


title: DT3_ALBI_Sp_M

source_name: Anopheles albimanus Mated spermatheca rep D 24 hr


title: BCD-T3_RBv_Albi

source_name: Anopheles albimanus Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [BCD] combined 24 hr

value: Male

value: [BCD] combined


title: CT3_ALBI_RB_V

source_name: Anopheles albimanus Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 24 hr

value: C


title: DT3_ALBI_RB_M

source_name: Anopheles albimanus Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 24 hr


title: CT3_ALBI_RB_M

source_name: Anopheles albimanus Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 24 hr


title: SAF6 rep2

value: 6 mo


title: SAF3 rep1

value: 3 mo


title: AT3_ALBI_Sp_M

source_name: Anopheles albimanus Mated spermatheca rep A 24 hr


title: BT3_MAG-V_Albi

source_name: Anopheles albimanus Virgin Male accessor glands rep B 24 hr

value: Male accessor glands


title: DT3_MAG-V_Albi

source_name: Anopheles albimanus Virgin Male accessor glands rep D 24 hr


title: ACD-T3_RBm_Albi

source_name: Anopheles albimanus Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [ACD] combined 24 hr

value: [ACD] combined


title: CT3_MAG-M_Albi

source_name: Anopheles albimanus Mated Male accessor glands rep C 24 hr


title: DT3_MAG-M_Albi

source_name: Anopheles albimanus Mated Male accessor glands rep D 24 hr


title: CT3_MAG-V_Albi

source_name: Anopheles albimanus Virgin Male accessor glands rep C 24 hr


title: CT3_ALBI_H_V

source_name: Anopheles albimanus Virgin Head rep C 24 hr

value: Head


title: BT3_ALBI_H_V

source_name: Anopheles albimanus Virgin Head rep B 24 hr


title: AT3_MAG-M_Albi

source_name: Anopheles albimanus Mated Male accessor glands rep A 24 hr


title: DT3_ALBI_H_M

source_name: Anopheles albimanus Mated Head rep D 24 hr


title: BT3_ALBI_H_M

source_name: Anopheles albimanus Mated Head rep B 24 hr


title: CT3_ALBI_H_M

source_name: Anopheles albimanus Mated Head rep C 24 hr