title: A, scRNAseq

description: 10x Genomics

data_processing:
Sequenced FASTQ files were aligned, filtered, barcoded, and UMI counted using Cell Ranger Chromium Single Cell RNA-seq version 6.0.1, by 10X Genomics with Cell Ranger, mm10 (version 2020-A) as the mouse genome reference.
Assembly: mm10
Supplementary files format and content: cell ranger filtered tab-separated values files and matrix files

source_name: Epithelial intestinal tumoroids

extract_protocol:
Matrigel domes containing the indicated organoid lines were collected and washed with cold cell recovery solution, then incubated in TryPLE  for 10 mins at 37C. Next, they were dissociated to single cells with gentle tritruation. Cells were stained and counted with Trypan blue to estimate the live/dead ratio.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, organoids dissociated to single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Epithelial intestinal tumoroids

value: A


title: WT, scRNAseq

status: Public on Oct 17 2024

type: SRA

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

source_name: Epithelial intestinal organoids

tag: tissue

value: Epithelial intestinal organoids

tag: genotype

value: WT


title: WT/A-YAPsh1-3

library_source: transcriptomic

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: mm10 (GRCm38 GENCODE release M25)
Supplementary files format and content: .csv, salmon counts and median-ratios-normalized salmon counts for all samples

molecule: total RNA

source_name: WT/A

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacturer's protocol.

tag: cell line

value: WT/A

tag: cell type

value: Epithelial inestinal tumoroids

value: A (Apc flox/flox+OHT)

tag: treatment

value: Yap_shRNA1 + OHT


title: WT/A-YAPsh1-1


title: APC Rep1 (rxri_rnaseq)

source_name: A tumoroids

extract_protocol:
RNA was extracted  using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using Netflex Rapid Directional RNAseq Kit (Perkin Elmer) following manufacturer's protocol.

value: DMSO

tag: time

value: passage 7


title: Tibia, Model, M2

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

country: China

institute: Nanjing University of Chinese medicine

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs) .
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Rattus norvegicus

source_name: tibia

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min. G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3. I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
1. Purify and Fragment mRNA a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly. b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperature for 5 min. c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. f. Add 50 μL of Elution Buffer in each well and mix thoroughly. g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature. h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min. i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly. m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge. 2. Synthesize First Strand cDNA a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly. b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C. 3. Synthesize Second Strand cDNA a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well. b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. The mixture was incubated at 16°C for 60 min. 3.1 Purification a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard all of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 15 μL the supernatant from each well into the new PCR plate. 4. Adenylate 3’Ends a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well. b. Add 12.5 μL A-Tailing Mix and mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 5. Ligate Adapters a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well. b. Add 2.5 μL Ligation Mix. c. Add 2.5 μL RNA Adapter Index and mix thoroughly. d. The mixture was incubated at 30°C for 10 min. e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly. 5.1 Purification a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 79.5 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 50 μL the supernatant from each well into the new PCR plate. j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. k. Place it on the magnetic stand at room temperature for 15 min. l. Remove and discard 95 μL of the supernatant from each well. m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer and mix thoroughly. q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. r. Transfer 20 μL the supernatant from each well into the new PCR plate. 6. Enrich DNA Fragments a. Add 5 μL PCR Primer Cocktail. b. Add 25 μL PCR Master Mix and mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15 cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C. 7. Purification a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 95 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 30 μL the supernatant from each well into the new PCR plate. 8. Validate library a. Load 1 μL sample on an Agilent 2100 Bioanalyzer. b. Check the size and purity of the library.

value: tibia

tag: strain

value: Sprague Dawley

tag: Sex

value: male

value: Model


title: APC Rep3 (rxri_rnaseq)

value: passage 9


title: WT/A-Scr4

value: control ShRNA + OHT


title: RXRi Rep3 (rxri_rnaseq)

source_name: RXRi organoids

value: WT (RXRi)


title: APC Rep2 (rxri_rnaseq)

value: Epithelial intestinal tumoroids

value: passage 8


title: WT/A-Scr3


title: WT/A-Scr2


title: ohev3

city: Toronto

first: Fabian

last: Doktor

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

data_processing:
fastq files were obtained from NovaSeq S4, aligned to the rat genome (rattus norvegicus, rn7), and analyzed using bioconductor R (DESeq2)
Assembly: rattus norvegicus rn7
Supplementary files format and content: feature count of each gene by sample

source_name: hypoplastic lung

extract_protocol:
Frozen lungs were stored in -80C until RNA extraction, which occurred on the same day for all libraries. Lungs were homogenized using a mortar/pestle into a fine powder, then RNEasy plus microkit was used according to manufacturer's instructions.
Ribo-Zero Plus rRNA Depletion Kit was used for library preparation following supplier recommended protocols
Total RNA subjected to ribosomal RNA-depletion using the Ribo-Zero Plus rRNA Depletion Kit

value: hypoplastic lung

value: Sprague-Dawley

value: AFSC-EV


title: Tibia, Model, M1


title: ohev2


title: WT Rep1 (rxri_rnaseq)

source_name: wild type organoids (WT)

value: Epithelial intestinal organoids

value: WT


title: WT/A-Scr1

value: WT/A

value: Epithelial inestinal tumoroids

value: A (Apc flox/flox+OHT)


title: Vehicle 3

city: Tampa

first: Ana

middle: P

last: Da Silva Gomes

state: Florida

address: 12902 Magnolia Drive

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center

data_processing:
Raw data cleanedby removing reads containing adapters or ploy-N and low quality reads using Novogene in-houseperlscripts.
Index of the reference genome was built using Hisat2 v2.0.5
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCountsv1.5.0-p3 was used to count the reads numbers mapped to each gene
FPKM was calculated based on gene length and reads count mapped to this gene.
Assembly: GRCm39/mm39
Supplementary files format and content: tab delimited text file including raw counts for each sample
Supplementary files format and content: tab delimited text file including FPKM values for each sample

source_name: CD8 T cells

growth_protocol: Mouse CD8+ T cells were cultured in RPMI-1640 media supplemented with 10% FBS, 1% penicillin/streptomycin, 50 μM β-mercaptoethanol, 1 mM sodium pyruvate, and 1% MEM nonessential amino acids in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and contaminant DNA was digested on column with RNase-free DNase (Qiagen)
Libraries were preapared using NEB ultra kit following it's instructions

treatment_protocol: Cells were treated with water or 5 mM methylmalonic acid (Sigma) for three days

value: CD8 T cells

value: Water


title: RXRi Rep1 (rxri_rnaseq)

value: passage 7


title: WT Rep2 (rxri_rnaseq)

value: DMSO


title: A-Rep2 (rxri_atacseq)

library_source: genomic

data_processing:
Quality control has been performed using FastQC (v0.11.8). Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using Bowtie2 (v2.1.0). Unaligned reads and reads mapped to mitochondrial were removed. PCR duplications was removed using Picard (v2.2.4)
post-filtering bam files were merged together using samtools (v1.11) and peaks were called using macs (v 2.1.0) on merged bam file.
Quantification of reads in peaks region was performed using bedtools (v2.29.2)
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: mm10 (GRCm38 GENCODE release M25)
Supplementary files format and content: .csv, atac_raw_counts.csv contain bedtool multicov counts with peak coordinates, and atac_counts_normalized_MR contains median-ratio normalized counts without low-count peaks

molecule: genomic DNA

extract_protocol:
Dissociated organoids/tumroids were collected in nuclear extraction buffer, then treated with Tn5 transposase before purfying the DNA using Qiagen MinElute PCR Purification Kit.
Following transpostion, library fragments were amplified using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2.

value: A


title: AKSP, scRNAseq

description: 10x Genomics

value: AKSP


title: oh3


title: wRXR-Rep3 (rxri_atacseq)

value: WT (RXRi)

value: passage 9


title: A-Rep1 (rxri_atacseq)

value: Epithelial intestinal tumoroids


title: oh2

value: hypoplastic lung


title: RXRi Rep2 (rxri_rnaseq)

value: passage 8


title: wRXR-Rep2 (rxri_atacseq)


title: WT-Scr3

source_name: WT

value: WT/APC flox/flox)

value: control ShRNA


title: wRXR-Rep1 (rxri_atacseq)

value: Epithelial intestinal organoids


title: oh1

value: Sprague-Dawley


title: WT-Scr2

value: WT

value: Epithelial inestinal tumoroids


title: WT-Rep1 (rxri_atacseq)


title: WT-Rep2 (rxri_atacseq)


title: ohev1

value: AFSC-EV


title: cont3

source_name: control lung

value: control lung


title: WT-Scr1


title: AKSP Rep3 (crc_rnaseq)

source_name: AKSP tumoroids

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using Netflex Rapid Directional RNAseq Kit (Perkin Elmer) following manufacturer's protocol.


title: WT Rep3 (rxri_rnaseq)


title: AKSP Rep2 (crc_rnaseq)


title: WT_RXROE+OHT_rep4

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit . 1 ug of total RNA was used for library prepration.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®  following manufacturer's protocol.

value: WT/A

value: A (Apc flox/flox+OHT)_RXROE

value: RXRa Overexpression


title: AKSP Rep1 (crc_rnaseq)


title: cont1


title: cont2


title: APC Rep2 (crc_rnaseq)

value: A


title: WT_RXROE+OHT_rep3


title: APC Rep3 (crc_rnaseq)


title: APC Rep1 (crc_rnaseq)


title: WT-Scr4


title: WT_RXROE+OHT_rep2


title: WT Rep2 (crc_rnaseq)


title: tpst seedlings, 1 uM PSK 5 hours, day 7, replicate 2

city: Chicago

first: Dian

last: Liu

state: IL

address: 929 East 57th Street GCIS W519P

department: Department of Molecular Genetics and Cell Biology

institute: The University of Chicago

data_processing:
Raw data of FASTQ format were processed through fastp.
Clean datawas obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were mapped to the reference genome using HISAT2 (2.0.5).
FeatureCounts (1.5.0-p3) was used to count the read numbers mapped of each gene.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: xlsx file includes raw counts of each sample.
Supplementary files format and content: xlsx file includes FPKM of each sample.

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis thaliana Col-0 ecotype and tpst mutant were grew in liquid 1/2 MS basal medium with 1% sucrose for 7 days at 22 °C 16 h light / 8 h dark long day growth room.

extract_protocol:
Total RNA was extreated from separated shoot tissue and root tissue using Rneasy Plant Mini Kit (Qiagen). 1 ug total RNA per sample was used to construct sequencing libraries.
Sequencing libraries were generated using NEBNexxt Ultra RNA Library Prep Kit for Illumina following manufacturer's recommendations.

treatment_protocol: PSK solutions were added to the growth medium to achieve a final PSK concentration of 100 nM or 1 uM.

value: Seedling

value: tpst

tag: age

value: 1 uM PSK

value: 5 hours


title: WT Rep1 (crc_rnaseq)


title: WT_EV+OHT_rep4

value: A (Apc flox/flox+OHT)_EV

value: Empty vector


title: tpst seedlings, 1 uM PSK 5 hours, day 7, replicate 1


title: AKSP Rep1 (crc_atacseq)

value: Epithelial intestinal tumoroids


title: AKSP Rep2 (crc_atacseq)


title: tpst seedlings, 100 nM PSK 5 hours, day 7, replicate 3

value: 100 nM PSK


title: APC Rep2 (crc_atacseq)


title: WT_EV+OHT_rep3


title: WT_EV+OHT_rep2


title: APC Rep1 (crc_atacseq)


title: RXR-OE_rep3

value: AKSP tumoroids


title: tpst seedlings, 100 nM PSK 5 hours, day 7, replicate 2


title: VAKPS_FOLFIRI_3

source_name: VAKPS tumoroids

value: VAKPS tumoroids

value: FOLFIRI


title: tpst seedlings, 100 nM PSK 5 hours, day 7, replicate 1


title: VAKPS_FOLFIRI_2

value: Epithelial inestinal tumoroids


title: WT Rep2 (crc_atacseq)

value: Epithelial intestinal organoids

value: WT


title: VAKPS_FOLFIRI_1


title: RXR-OE_rep2


title: WT Rep3 (crc_rnaseq)


title: VAKPS_DMSO_2

value: DMSO


title: RXR-OE_rep1

value: RXRa Overexpression


title: tpst seedlings, 1 uM PSK 5 hours, day 7, replicate 3


title: tpst seedlings, none treatment, day 7, replicate 3


title: tpst seedlings, none treatment, day 7, replicate 2


title: VAKPS_DMSO_3


title: VAKPS_DMSO_1


title: EV_rep3


title: VAKSP GFP_Neg_rep4

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Sample normalization was carried out using the median-ratio normalization method from DESeq2 R package (v1.30.1)
Assembly: mm10 (GRCm38 GENCODE release M25)
Supplementary files format and content: .csv, salmon counts and normalized salmon counts for all samples

tag: gfp status


title: tpst seedlings, none treatment, day 7, replicate 1


title: VAKSP GFP_Neg_rep3


title: EV_rep2


title: VAKSP GFP_Neg_rep1


title: WT Rep1 (crc_atacseq)


title: EV_rep1


title: VAKSP GFP_high_rep4


title: Col-0 seedlings, none treatment, day 7, replicate 3


title: VAKSP GFP_high_rep1


title: VAKSP GFP_high_rep3


title: Col-0 seedlings, none treatment, day 7, replicate 2


title: Ana_HF_Setdb1_cKO

city: Houston

first: Yejing

last: Ge

state: Texas

department: Cancer Biology

institute: The University of Texas, MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0.
Data normalization, unsupervised cell clustering and differential expression were carried out using the Seurat R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

growth_protocol: We used mice during anagen stage (around postnatal 30 days)

extract_protocol:
Following euthanasia, back skin at anagen stage was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spin down at 400g for 10 min at 4°C, and washed once with cold PBS containing 2% FBS(-). Freshly isolated cells were incubated with DAPI and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI- to isolate live cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, live cells seperated from mouse back skin were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: male

value: skin

value: anagen hair follicle cells

tag: sort markers

value: DAPI-


title: Col-0 seedlings, none treatment, day 7, replicate 1

value: Seedling


title: WGBS_Ana_HF_Setdb1_cKO_rep2

data_processing:
The Illumina adapters and low-complexity adapters were removed from the reads by Trim Galore! (version 0.4.1), cutadapt (version 1.7.1) and an in-house bash script. Then the reads (277-315 million pairs of reads per sample) were mapped to the mouse genome mm10 by the bisulfite converted read mapper Bismark (version v0.16.3) and Bowtie2 (version 2.1.0). 69-71% pairs of reads were uniquely mapped to the mouse genome. After deduplication by the deduplicate_bismark script from Bismark, 149-175 million uniquely mapped pairs of reads were used in the final analysis.
The methylation percentages for the CpG sites were calculated by the bismark_methylation_extractor script from Bismark and an in-house Perl script. Then the methylation percentages for the CpG sites with read coverage ≥ 10 (about 16.5-17.8 million CpG sites) were written in wiggle format and displayed using Integrative Genomics Viewer (IGV). The differential methylation on CpG sites was statistically assessed by R/Bioconductor package methylKit (version 0.9.5). The CpG sites with read coverage ≥ 10 in all the samples (about 14 million CpG sites) were qualified for the test and the cutoffs used to call differential CpG sites is methylation difference >= 25% and Q-value <= 0.01.
Assembly: mm10
Supplementary files format and content: bed file containing detected CpGs with coverage >= 10 in the library

growth_protocol: We used mice during anagen (around postnatal 30 days) for all samples.

extract_protocol:
FACS-sorted cells were subjected to genomic DNA extraction with Qiagen DNeasy Blood & Tissue Kit (Cat# 69504) following the manufacturer’s instructions.
The genomic DNA spiked with lambda DNA were fragmented to 200-400bp. The DNA fragments were bisulfite treated to generate single strand DNA. During the bisulfite conversion, unmethylated cytosine were converted into uracil, while methylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis, size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Following euthanasia, back skin at anagen stage was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spin down at 400g for 10 min at 4°C, and washed once with cold PBS containing 2% FBS(-). Freshly isolated cells were incubated with conjugated antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD31-CD140A-CD45-ITGA6+ to isolate epithelial cells, and further separated into epidermal (Sca1+) and hair follicle (Sca1-) cells.

value: DAPI-, CD31-, CD140A-, CD45-, ITGA6+, Scar-


title: Caco2 del Int11 cl.6 +15.6 kb [AH1289]

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: 4C-seq library with the CFTR +15.6 kb region as the viewpoint

data_processing:
Library strategy: 4C-Seq
Libraries (AH974, 1001, 1000, 1002, 1064, 1065, 1066, and 1097) were sequenced on Illumina HiSeq4000 machine, while rest were sequenced on Nextseq550 machine.
Data were analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367 for domainograms. For bigwig tracks, 4C-seq was quantified and mapped using the pipe4C processing pipeline. Raw reads were aligned to the hg19 genome using Bowtie2 v4.8.3 and sorted using SAMtools v1.3.
Genome_build: hg19
Supplementary_files_format_and_content: Aligned 4C-seq of each clone and viewpoint in bigWig format

organism: Homo sapiens

source_name: Human colon

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Nuclei were made as per the above Methods papers with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per the above papers  PMID: 22609568 or PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above papers, PMID: 22609568 or PMID: 31351925 for corresponding samples as listed in the treatment protocol section.

value: Colon adenocarcinoma cells

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 WT cl # 6

tag: growth media

value: DMEM + 10percent FBS


title: Ana_HF_Setdb1_Het

description: 10x Genomics


title: Caco2 del Int1 Int11 cl. D58 +15.6 kb [AH1294]

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 del int1 cl.1 clone # D58


title: tpst roots, 10 nM PSK 11 days, day 11, replicate 3

data_processing:
Raw data of FASTQ format were processed through fastp.
Clean datawas obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were mapped to the reference genome using HISAT2 (2.0.5).
FeatureCounts (1.5.0-p3) was used to count the read numbers mapped of each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: xlsx file includes raw counts of each sample.
Supplementary files format and content: xlsx file includes FPKM of each sample.

source_name: Root

growth_protocol: Arabidopsis thaliana Col-0 ecotype and tpst mutant were grew in liquid 1/2 MS basal medium with 1% sucrose for 11 days at 22 °C 16 h light / 8 h dark long day growth room.

treatment_protocol: Growth medium were replaced with medium containing 10 nM PSK for 30 minutes, 2 hours, 5 hours and 11 days.

value: Root

value: tpst

value: 10 nM PSK

value: 11 days


title: Ana_HF_Setdb1_cKO_rep3

description: "AF5" column in two processed data files

data_processing:
Raw sequencing 150-bp paired-end reads were aligned to the mus musculus reference genome (version mm10 from Genome Reference Consortium GRCm38) using tophat/2.1.1 aligner.
Aligned reads were counted using subread/2.0.3 for mouse genes (parameters: featureCounts -B -C -p) and transposons (parameters: featureCounts -B -C -p --primary)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: For sample 1-5, we used mice during anagen (around postnatal 30 days); for sample 6-10, we used aged mice (24mon) or young mice (2mon) one week post-depilation

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Kit (Zymo, R2051).
Use NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit NEB #E7760) for library preparation.

value: female


title: tpst roots, 10 nM PSK 11 days, day 11, replicate 2


title: WGBS_Ana_HF_Setdb1_cKO_rep1


title: WGBS_Ana_HF_Setdb1_Het_rep2


title: tpst roots, 10 nM PSK 11 days, day 11, replicate 1


title: WGBS_Ana_HF_Setdb1_Het_rep1


title: Ana_HF_Setdb1_cKO_rep1

description: "AF3" column in two processed data files


title: Caco2 del Int1 cl.1 +15.6 kb [AH1284]

value: CRISPR/Cas9 mediated deletion of int1 CRE from the CFTR locus in Caco2 clone # 1


title: Caco2 WT NC siRNA KD CFTR -80.1 kb [AH1300]

description: 4C-seq library with the CFTR -80.1 kb region as the viewpoint

value: NC siRNA (Ambion) siRNA depletion in Caco2 WT cells


title: Caco2 WT NC siRNA KD CFTR promoter [AH1299]

description: 4C-seq library with the CFTR promoter region as the viewpoint


title: Caco2 WT CFTR +15.6 kb [AH1278]

value: Wild type


title: tpst roots, 10 nM PSK 5 hours, day 11, replicate 3

value: 5 hours


title: Ana_HF_Setdb1_Het_rep1

description: "AF1" column in two processed data files

value: skin

value: anagen hair follicle cells


title: tpst roots, 10 nM PSK 5 hours, day 11, replicate 2


title: ChIP_Ana_HF_KO_H3K9me3_rep2

data_processing:
Raw sequencing 150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 1 (MACS1) or Model based Analysis of Chip-seq 2 (MACS2) pipeline.
Assembly: mm10
Supplementary files format and content: bed or broadPeak files include peak informations for each Sample (except for control sample)

growth_protocol: MIK were cultured in media containing DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycinat at 37C at 5% CO2. Hair follicle cells are from P30 anagen C57BL/6J mice cultured in a specific pathogen-free barrier facility on a standard light-dark cycle.

extract_protocol:
MIK cells or Freshly FACS-sorted cells were fixed with 1% formaldehyde for 10 minutes. For IgG and H3K9me3 ChIP, after quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator; for Setdb1 ChIP, use CST SimpleChIP protocol following manufacture recommendation.
The DNA extract was incubated overnight at 4°C with primary antibody. 10 μl of Dynal Protein G magnetic beadswas added to each sample the following day, incubated at 4°C for 2-4 h, followed by washes for several times. Bound complexes were treated with 5ul Tn5 transposase at 37°C for 5min, eluted and crosslinking was reversed by 6-10h incubation at 65°C, cleaned up with MinElute PCR Purification Kit and PCR-amplified for 10-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads and submitted to Novogene for library quality control (QC)

tag: chip antibody


title: Caco2 WT CDX2 siRNA KD CFTR -80.1 kb [AH1296]

value: CDX2 siRNA depletion in Caco2 WT cells


title: ChIP_Ana_HF_KO_H3K9me3_rep1

value: DAPI-, CD31-, CD140A-, CD45-, ITGA6+, Scar-


title: ChIP_Ana_HF_Het_H3K9me3_rep2


title: ChIP_Ana_HF_Het_H3K9me3_rep1


title: Caco2 WT FOXA1/A2 siRNA KD CFTR -80.1 kb [AH1243]

value: Colon adenocarcinoma cells

value: FOXA1/FOXA2 siRNA depletion in Caco2 WT cells


title: tpst roots, 10 nM PSK 2 hours, day 11, replicate 3

value: 2 hours


title: Caco2 WT CDX2 siRNA KD CFTR promoter [AH1295]

value: DMEM + 10percent FBS


title: Ana_HF_Setdb1_cKO_rep2

description: "AF4" column in two processed data files


title: ChIP_MIK_Setdb1

value: immortalized keratinocytes

value: wild type


title: ChIP_Ana_HF_Setdb1


title: tpst roots, 10 nM PSK 2 hours, day 11, replicate 2

value: Root

value: tpst

value: 10 nM PSK


title: Ana_HF_Setdb1_Het_rep2

description: "AF2" column in two processed data files

value: female


title: Caco2 WT NC siRNA KD CFTR -80.1 kb [AH1241]

value: NC siRNA (Santacruz) siRNA depletion in Caco2 WT cells


title: ChIP_MIK_IgG_Ctrl

value: IgG


title: ATAC_Ana_HF_Setdb1_cKO_rep2

data_processing:
Raw sequencing 150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 2 (MACS2) pipeline with the parameter --nomodel.
Assembly: mm10
Supplementary files format and content: narrowPeak files include peak informations for each Sample

growth_protocol: For sample 1-4, we used mice during anagen (around postnatal 30 days); for sample 5-10, we used aged mice (24mon) or young mice (2mon) one week post-depilation

extract_protocol:
Freshly FACS-sorted cells were subjected to tagmentation reactions with 10ul Tn5 transposase (Illumina Cat#20034198) and cleaned up with MinElute PCR Purification Kit (Qiagen Cat#28004)
DNA fragments were PCR-amplified for 8-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads (Fisher Cat#NC9959336) and run on D1000 High Sensitivity Tape Station (Agilent Cat# 5067-5584) for quality control (QC) prior to sequencing.

value: approximately postnatal day 30


title: tpst roots, 10 nM PSK 30 minutes, day 11, replicate 3

value: 30 minutes


title: Caco2 WT FOXA1/A2 siRNA KD CFTR +15.6 kb [AH1227]


title: ATAC_Ana_HF_Setdb1_cKO_rep1

value: skin

value: anagen hair follicle cells


title: ATAC_Ana_HF_Setdb1_Het_rep2

value: DAPI-, CD31-, CD140A-, CD45-, ITGA6+, Scar-


title: tpst roots, 10 nM PSK 30 minutes, day 11, replicate 2


title: tpst roots, 10 nM PSK 2 hours, day 11, replicate 1


title: Caco2 WT FOXA1/A2 siRNA KD CFTR int11 [AH1226]

description: 4C-seq library with the CFTR int11 region as the viewpoint

value: Colon adenocarcinoma cells


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); negative control input

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: W126 Millennium Science Road

institute: The Pennsylvania State University

data_processing:
Raw sequencing reads were trimmed (Trimmomatic v0.32.3) to remove Illumina adaptor sequences and low-quality reads below 30 Phred (Paired-end options - "PE ILLUMINACLIP:TrueSeq3-PE:2:30:10 SLIDINGWINDOW:4:30"). FastQC (v0.11.9) was used to check the quality after trimming. The output file format being FASTQ.
Processed reads were then mapped to the P. falciparum genome (PlasmoDB.org; Plasmodium falciparum 3D7 strain; version 3; release 52) using BWA-MEM (v0.7.17.2) simple Illumina mode. Multiple mapped reads filtered out using SamTools (v1.1.2) with option "-q 1" (MAPQ=1). The output file format being BAM.
Aligned BAM files were displayed using DeepTools BAMCompare (v3.3.2.0.0) with options "--binSize 20 --scaleFactorsMethod readCount --operation log2 --pseudocount 1 --smoothLength 60". The output file format being BIGWIG.
Assembly: Plasmodium falciparum genome (strain 3D7; version 3; release 52)
Supplementary files format and content: BIGWIG: DeepTools BAMCompare output files for Log2(IP/Input) sample display

organism: Plasmodium falciparum

source_name: 3D7 strain background

growth_protocol: Wild type and PfSNF2L+3xHA modified parasites (3D7 strain) were cultured under standard P. falciparum culturing conditions (5% O2, 7% CO2, 37°C, RPMI 1640 media with 0.5% AlbumaxII and hypoaxanthine). No additional drug selection added to PfSNF2L+3xHA modified parasites after transfection.

extract_protocol:
PfSNF2L ChIP-seq was performed similarly to previously published ChIP-seq experiments in Plasmodium falciparum (Josling et al. 2020, Singh et al. 2021, Russell et al. 2022). ChIP experiments were performed on PfSNF2L+HA parasites at four timepoints (10/22/34/46 hpi) in duplicate with an additional no-epitope control on WT 3D7 parasites. In brief, the protocol includes five steps: (1) Treated with 1% formaldehyde to crosslink the suspended PfSNF2L+HA parasite cultures at 37°C for 10 minutes; (2) Collected parasite nuclei using prechilled glass dounce homogenizer for 200 strokes per 10^9 rings and 100 strokes per 10^9 trophozoites/schizonts; (3) Lysed parasite nuclei and mechanically sheared chromatin until sufficiently sheared using Covaris Focus-Ultrasonicator M220 (5% duty cycle, 75 W peak incident power, 200 cycles per burst, 7°C, for 5 minutes). (4) We collected 10% of each sample for the nonimmunoprecipitated “input” control and then immunoprecipitated the remaining 90% of each sample. The remaining 90% of each sample was immunoprecipitated with 1:1000 anti-HA antibody (0.5 mg/mL Roche Rat Anti-HA High Affinity [11867423001]) overnight at 4°C with rotation. (5) DNA was purified after reverse crosslinking using a MinElute column (Qiagen) as directed and quantified by a Qubit fluorometer (Invitrogen).
The PfSNF2L ChIP-seq libraries were performed similarly to previously published ChIP-seq experiments in Plasmodium falciparum (Josling et al. 2020, Singh et al. 2021, Russell et al. 2022). DNA sequencing libraries were prepared for high-throughput Illumina sequencing on the NextSeq 2000 with the P1 150 x 150 paired-end mode. The library prep underwent 12 rounds of amplification using KAPA HiFi polymerase. Completed libraries were quantified using the Qubit fluorometer (Invitrogen) for high-sensitivity DNA and library sequence length by the Agilent TapeStation 4150.

treatment_protocol: At least 10^9 parasites (at early ring, late ring, trophozoite, and schizont) synchronized more than one cycle prior.

value: 3D7 strain background

value: Schizont Stage (46hpi) Parasitized Erythrocyte Cells

value: 3xHA-tagged PfSNF2L (C-terminal) in 3D7 strain background

value: No Treatment


title: ATAC_Ana_HF_Setdb1_Het_rep1


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); negative control IP


title: tpst roots, 10 nM PSK 5 hours, day 11, replicate 1

value: 5 hours


title: tpst roots, 10 nM PSK 30 minutes, day 11, replicate 1

value: Root


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); replicate 2 IP


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); replicate 2 input


title: Caco2 WT NC siRNA KD CFTR int11 [AH1224]

value: DMEM + 10percent FBS


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); replicate 1 IP


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 46hpi (hours post invasion); replicate 1 input


title: Caco2 WT NC siRNA KD CFTR promoter [AH1380]

value: NC siRNA (Ambion) siRNA depletion in Caco2 WT cells


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); negative control IP

value: Trophozoite Stage (34hpi) Parasitized Erythrocyte Cells


title: tpst roots, none treatment, day 11, replicate 2

value: tpst


title: Caco2 WT GATA6 siRNA KD CFTR promoter [AH1376]

value: GATA6 siRNA depletion in Caco2 WT cells


title: Caco2 WT NC siRNA KD CFTR int11 [AH1379]


title: Col-0 roots, none treatment, day 11, replicate 3


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); replicate 2 IP


title: tpst roots, none treatment, day 11, replicate 1


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); negative control IP

value: Late Ring Stage (22hpi) Parasitized Erythrocyte Cells


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); replicate 2 input


title: Caco2 WT GATA6 siRNA KD CFTR int11 [AH1375]


title: Col-0 roots, none treatment, day 11, replicate 2


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); negative control input


title: Caco2 del. Int1 cl.1 CFTR int11 [AH1365]

value: CRISPR/Cas9 mediated deletion of int1 CRE from the CFTR locus in Caco2 clone # 1


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); replicate 1 input


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); replicate 2 input


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); replicate 2 IP


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); replicate 1 IP


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 22hpi (hours post invasion); replicate 1 input


title: tpst roots, none treatment, day 11, replicate 3


title: Caco2 WT CFTR int11 [AH1387]

value: Wild type


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); negative control input


title: tpst shoots, 10 nM PSK 11 days, day 11, replicate 3

source_name: Shoot

value: Shoot

value: 10 nM PSK

value: 11 days


title: Caco2 del. -80.1 kb CFTR -20.9 kb [AH1167]

description: 4C-seq library with the CFTR -20.9 kb region as the viewpoint

value: Colon adenocarcinoma cells

value: CRISPR/Cas9 mediated deletion of -80.1 kb CRE from the CFTR locus in Caco2 WT cl # 101


title: tpst shoots, 10 nM PSK 11 days, day 11, replicate 2


title: Caco2 WT NC siRNA KD CFTR +15.6 kb [AH1225]

value: NC siRNA (Santacruz) siRNA depletion in Caco2 WT cells


title: tpst shoots, 10 nM PSK 11 days, day 11, replicate 1


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); replicate 1 input

value: 3D7 strain background

value: Early Ring Stage (10hpi) Parasitized Erythrocyte Cells

value: 3xHA-tagged PfSNF2L (C-terminal) in 3D7 strain background

value: No Treatment


title: Caco2 del. Int11 cl. 6 CFTR +48.9 kb [AH1286]

description: 4C-seq library with the CFTR +48.9 kb region as the viewpoint

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 WT cl # 6

value: DMEM + 10percent FBS


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); replicate 2 input


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 34hpi (hours post invasion); replicate 1 IP

value: Trophozoite Stage (34hpi) Parasitized Erythrocyte Cells


title: tpst shoots, 10 nM PSK 5 hours, day 11, replicate 2

value: tpst

value: 5 hours


title: Col-0 roots, none treatment, day 11, replicate 1

value: Root


title: tpst shoots, 10 nM PSK 5 hours, day 11, replicate 3


title: Caco2 del. Int11 cl. 6 CFTR -20.9 kb [AH1287]


title: tpst shoots, 10 nM PSK 5 hours, day 11, replicate 1


title: Caco2 del. Int11 cl. 6 CFTR promoter [AH1290]

description: 4C-seq library with the CFTR promoter as the viewpoint


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); negative control IP


title: 3D7, nontreated, 35hpi, Rep2, RNA

city: Regensburg

first: Simon

last: Holzinger

address: Universitätsstraße 31

country: Germany

institute: University of Regensburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Reads were trimmed with trimmomatic v0.39 and "ILLUMINACLIP:<ADAPTERS>:2:30:10", "MAXINFO:30:0.2" and "MINLEN:35" options
Alignment was done with STAR v2.7.4a using "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 5 --alignIntronMax 1000 --alignMatesGapMax 1000000 --outMultimapperOrder Random"
Rsubread/FeatureCounts v2.12.2 was used to calculate read counts in a strand specific way, counting multimapping reads as fractional counts.
Assembly: P. falciparum 3D7 genome v3.0, plasmoDB release 52

growth_protocol: P. falciparum clone 3D7 was cultured according to standard procedures in RPMI 1640 with Albumax®. For synchronization, schizonts were purified on a bed of 70% Percoll®, incubated with new red blood cells for 1-2 h, before leftover schizonts were removed with Percoll and subsequent sorbitol treatment.

extract_protocol:
Total RNA from infected red blood cells containing highly synchronized parasites was isolated at the indicated timepoint using Whole Blood Quick RNA kit (Zymo Research) according to the manufacturer’s protocol.
300 ng total RNA were used as input for Illumina Stranded mRNA Prep Ligation (Illumina).

treatment_protocol: For KO induction, synchronous parasites were treated with 100 nM rapamycin for 4 h (DMSO treatment as control), washed and returned to culture.    For drug treatment, parasites were cultured after synchronization in media supplemented with 1 µM drug until RNA isolation.

value: wild type

tag: harvesting time

value: 35 hpi

value: non treated


title: 3D7, nontreated, 35hpi, Rep1, RNA


title: Caco2 del. Int1_Int11 cl. D58 CFTR -80.1 kb [AH1291]

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 del int1 cl.1 clone # D58


title: 3D7, nontreated, 35hpi, Rep3, RNA


title: 3D7, drugtreated, 35hpi, Rep3, RNA

value: drug treated


title: 3D7, drugtreated, 35hpi, Rep2, RNA


title: 3D7, drugtreated, 35hpi, Rep1, RNA


title: 3D7, nontreated, 25hpi, Rep3, RNA

value: 25 hpi


title: tpst shoots, 10 nM PSK 2 hours, day 11, replicate 3

value: Shoot

value: 10 nM PSK

value: 2 hours


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); negative control input

value: 3D7 strain background

value: Early Ring Stage (10hpi) Parasitized Erythrocyte Cells

value: 3xHA-tagged PfSNF2L (C-terminal) in 3D7 strain background


title: Caco2 del. -80.1 kb CFTR promoter [AH1166]

value: Colon adenocarcinoma cells

value: CRISPR/Cas9 mediated deletion of -80.1 kb CRE from the CFTR locus in Caco2 WT cl # 101

value: DMEM + 10percent FBS


title: tpst shoots, 10 nM PSK 2 hours, day 11, replicate 2

value: tpst


title: 3D7, nontreated, 25hpi, Rep2, RNA


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); replicate 2 IP

value: No Treatment


title: Caco2 del. Int1_Int11 cl. D58 CFTR +48.9 kb [AH1293]

description: 4C-seq library with the +48.9 kb as the viewpoint


title: Caco2 del. Int11 cl. 6 CFTR -80.1 kb [AH1288]

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 WT cl # 6


title: tpst shoots, 10 nM PSK 2 hours, day 11, replicate 1


title: 3D7, nontreated, 25hpi, Rep1, RNA

value: wild type


title: 3D7, drugtreated, 25hpi, Rep2, RNA


title: 3D7, drugtreated, 25hpi, Rep3, RNA


title: Caco2 del. Int1_Int11 cl. D58 CFTR -20.9 kb [AH1292]


title: tpst shoots, 10 nM PSK 30 minutes, day 11, replicate 3

value: 30 minutes


title: 3D7, drugtreated, 25hpi, Rep1, RNA


title: Caco2 del. Int1_Int11 cl. D58 CFTR promoter [AH1285]

value: CRISPR/Cas9 mediated deletion of int11 CRE from the CFTR locus in Caco2 del int1 cl.1 clone # D58


title: 3D7, nontreated, 20hpi, Rep3, RNA

value: 20 hpi

value: non treated


title: 3D7, nontreated, 20hpi, Rep2, RNA


title: 3D7, nontreated, 20hpi, Rep1, RNA


title: Caco2 del. Int1 cl.1 CFTR -80.1 kb [AH1282]

value: CRISPR/Cas9 mediated deletion of int1 CRE from the CFTR locus in Caco2 clone # 1


title: tpst shoots, 10 nM PSK 30 minutes, day 11, replicate 1

value: Shoot

value: 10 nM PSK


title: 3D7, drugtreated, 20hpi, Rep2, RNA

value: drug treated


title: Caco2 del. Int1 cl.1 CFTR -20.9 kb [AH1281]


title: Caco2 del. Int1 cl.1 CFTR +48.9 kb [AH1280]

description: 4C-seq library with the CFTR +48.9 region as viewpoint


title: 3D7, drugtreated, 20hpi, Rep1, RNA


title: tpst shoots, none treatment, day 11, replicate 3


title: Caco2 del. Int1 cl.1 CFTR promoter [AH1279]


title: tpst shoots, none treatment, day 11, replicate 1


title: 3D7, drugtreated, 20hpi, Rep3, RNA


title: tpst shoots, none treatment, day 11, replicate 2


title: Caco2 WT CFTR +48.9 kb [AH1199]

value: Wild type


title: iKO, induction24, 84hpi, Rep3, RNA

tag: ko induction_time

value: 84 hpi

value: conditional KO induced


title: iKO, induction24, 84hpi, Rep2, RNA


title: noKO, induction24, 84hpi, Rep3, RNA

value: not induced


title: noKO, induction24, 84hpi, Rep1, RNA


title: noKO, induction24, 84hpi, Rep2, RNA


title: Caco2 WT CFTR -80.1 kb [AH1196]

value: Colon adenocarcinoma cells

value: DMEM + 10percent FBS


title: tpst shoots, 10 nM PSK 30 minutes, day 11, replicate 2

value: tpst


title: iKO, induction24, 74hpi, Rep3, RNA

value: 74 hpi


title: iKO, induction24, 74hpi, Rep2, RNA


title: Col-0 shoots, none treatment, day 11, replicate 2


title: Caco2 WT CFTR -20.9 kb [AH1197]


title: iKO, induction24, 74hpi, Rep1, RNA


title: Col-0 shoots, none treatment, day 11, replicate 1


title: noKO, induction24, 74hpi, Rep3, RNA


title: noKO, induction24, 74hpi, Rep1, RNA


title: iKO, induction24, 84hpi, Rep1, RNA


title: noKO, induction24, 74hpi, Rep2, RNA


title: iKO, induction24, 69hpi, Rep3, RNA

value: 69 hpi


title: iKO, induction24, 69hpi, Rep2, RNA


title: Caco2 WT CFTR promoter [AH1198]

source_name: Human Colon


title: 13t2

city: Paris

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

country: France

institute: UPMC

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver

growth_protocol: Liver and aortas were obtained from atherosclerosis-prone Ldlr-/- or Apoe-/- mice backcrossed with or without Gls2-/-.

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and amount was assessed by Nanodrop (Ozyme)
Library construction were conducted by BGI Hong Kong Company Limited using a DNBseqTM platform

treatment_protocol: Atherosclerosis-prone Ldlr-/- and Apoe-/- mice were backrossed with or without Gls2-/- mice. Then, hyperlipidemia was induced in these mice by feeding them with an atherogenic diet (Western diet, TD88137, Ssniff) for 12 weeks. Livers were obtained from all four genotypes and aortas were collected from Western died-fed Ldlr-/- and Ldlr-/-Gls2-/- mice.

value: liver

tag: condition

value: Apoe-/-

value: 12 weeks Western diet


title: 16t2


title: iKO, induction24, 69hpi, Rep1, RNA


title: noKO, induction24, 69hpi, Rep2, RNA


title: KO2

city: South San Francisco

first: Xin

last: Luo

state: CA

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

data_processing:
RNA-Seq reads were aligned to human genome GRCh38 (GENCODE V24) using OSA aligner63 of the OmicSoft Array Suite
Gene level expression was quantified by RSEM and normalized as Fragments Per Kilobase per Million mapped reads (FPKM)
Downstream plotting and analyses were done using packages in R
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file include raw counts for each sample
Supplementary files format and content: Tab-delimited file include normaized FPKM value for each sample

source_name: skin equivalent culture

growth_protocol: NHEKs were maintained in medium with 10μM Y-27632. NHEK was added on top of the collagen bed-NHDF in each well and  NHEK complete medium was added outside of the trans-well. On day 4, the trans-wells were air lifted by removing NHEK medium and 500μl of the differentiation medium (Millipore Sigma, SCM310) was added outside of the trans well. The differential medium was replaced every two days and the skin culture was harvested after 9 days in air-lift culture.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: NHEKs were transfected with Cas9-gRNA ribonucleoprotein complexes targeting coding regions of the NLRP10.

value: skin equivalent culture

value: NHEK

value: differentiated into stratified epidermal layer

value: NLRP-10 KO


title: WT3

value: WT


title: noKO, induction24, 69hpi, Rep1, RNA


title: 11t2


title: 07wt2


title: KO1


title: WT2


title: iKO, induction0, 60hpi, Rep1, RNA

value: 60 hpi


title: iKO, induction0, 60hpi, Rep2, RNA


title: noKO, induction0, 60hpi, Rep3, RNA


title: 06wt2


title: WT1


title: iKO, induction0, 60hpi, Rep3, RNA


title: 01wt2


title: KO3


title: 11t1

value: Ldlr-/-


title: noKO, induction24, 69hpi, Rep3, RNA


title: noKO, induction0, 60hpi, Rep1, RNA


title: 3-Glucose-VACV-untreated - rep3

city: Dallas

first: Dustin

last: Hancks

address: 5323 Harry Hines Blvd MC 9093

institute: UT Southwestern Medical Center

description:
raw_counts.xlsx
TPM_values.csv

data_processing:
Fastq files were aligned to version 38 of the human reference genome GRCh38 using STAR aligner v.2.5.2b  post removal of possible adapter sequences and poor quality nucleotides using Trimmomatic v.0.36
BAM files from alignments were summarized and unique gene hit counts were calculated using featureCounts algorithms from Subread package v1.5.2
Differential expression analysis by comparison of gene expression between the groups of samples was performed using DESeq2  and Wald test to generate p-values and log2 fold changes (p-values <0.05 and absolute log2 foldchange >1)
Differential expressed genes further filtered with abosulte log2fold change of >2 or < -2 and an adjusted p-value of ≤ 0.01
Ingenuity Pathway Analysis was performed on selected genes using Qiagen IPA software
Assembly: GRCh38
Supplementary files format and content: Matrix table(CSV file) with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table (CSV file) with TPM counts for every gene and every sample

extract_protocol:
Total RNA was extracted from cells with mirVana (ThermoFisher) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using Ultra II RNA Library Prep Kit for IIIumina (NEB) following the manufacturer's protocols.

value: lung adenocarcinoma

value: wildtype

value: untreated/ vaccinia virus infection

value: Samples were harvested 48hrs post-Mock treatment/ 24hrs post-infection (vaccinia virus)


title: 10t1


title: Col-0 shoots, none treatment, day 11, replicate 3

value: Shoot


title: 3-Glucose-VACV-IFNgamma - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: iKO, induction0, 50hpi, Rep1, RNA

value: 50 hpi

value: conditional KO induced


title: iKO, induction0, 50hpi, Rep2, RNA


title: noKO, induction0, 50hpi, Rep2, RNA

value: not induced


title: noKO, induction0, 50hpi, Rep1, RNA


title: 3-Glucose-VACV-IFNalpha - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha/ vaccinia virus infection


title: 3-Glucose-uninfected-untreated - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: untreated

value: Samples were harvested 48hrs post-Mock treatment


title: 09t1

value: liver

value: 12 weeks Western diet


title: noKO, induction0, 50hpi, Rep3, RNA


title: 08t1


title: iKO, induction0, 45hpi, Rep2, RNA

value: 45 hpi


title: 3-Glucose-uninfected-IFNgamma - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma

value: Samples were harvested 48hrs post-IFN treatment


title: iKO, induction0, 45hpi, Rep3, RNA


title: 3-Glucose-uninfected-IFNalpha - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: wildtype

value: IFNalpha


title: 3-Galactose-VACV-untreated - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: untreated/ vaccinia virus infection

value: Samples were harvested 48hrs post-Mock treatment/ 24hrs post-infection (vaccinia virus)


title: iKO, induction0, 45hpi, Rep1, RNA


title: noKO, induction0, 45hpi, Rep3, RNA


title: noKO, induction0, 60hpi, Rep2, RNA

value: 60 hpi


title: 05wt1

value: Ldlr-/-

value: WT


title: noKO, induction0, 45hpi, Rep2, RNA

value: not induced


title: iKO, induction0, 50hpi, Rep3, RNA

value: 50 hpi

value: conditional KO induced


title: noKO, induction0, 45hpi, Rep1, RNA


title: 02wt1


title: iKO, induction0, 40hpi, Rep1, RNA

value: 40 hpi


title: 03wt1

value: liver


title: 3-Galactose-VACV-IFNalpha - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: 3-Galactose-VACV-IFNgamma - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma/ vaccinia virus infection


title: iKO, induction0, 40hpi, Rep3, RNA


title: iKO, induction0, 40hpi, Rep2, RNA


title: noKO, induction0, 40hpi, Rep3, RNA


title: KO14

source_name: aorta

value: aorta

value: 12 weeks Western diet


title: noKO, induction0, 40hpi, Rep2, RNA


title: 3-Galactose-uninfected-untreated - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: wildtype

value: untreated

value: Samples were harvested 48hrs post-Mock treatment


title: noKO, induction0, 40hpi, Rep1, RNA


title: iKO, induction0, 35hpi, Rep2, RNA

value: 35 hpi


title: 3-Galactose-uninfected-IFNgamma - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma

value: Samples were harvested 48hrs post-IFN treatment


title: 04wt1

value: Ldlr-/-

value: WT


title: KO10


title: iKO, induction0, 35hpi, Rep3, RNA

value: conditional KO induced


title: KO11


title: KO9


title: noKO, induction0, 35hpi, Rep3, RNA

value: not induced


title: noKO, induction0, 35hpi, Rep1, RNA


title: 3-Galactose-uninfected-IFNalpha - rep3

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha


title: KO7


title: 2-Glucose-VACV-untreated - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: untreated/ vaccinia virus infection

value: Samples were harvested 48hrs post-Mock treatment/ 24hrs post-infection (vaccinia virus)


title: noKO, induction0, 35hpi, Rep2, RNA


title: 2-Glucose-VACV-IFNgamma - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: iKO, induction0, 30hpi, Rep3, RNA

value: 30 hpi


title: iKO, induction0, 30hpi, Rep2, RNA


title: iKO, induction0, 30hpi, Rep1, RNA


title: noKO, induction0, 30hpi, Rep3, RNA


title: noKO, induction0, 30hpi, Rep2, RNA


title: 2-Glucose-VACV-IFNalpha - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: IFNalpha/ vaccinia virus infection


title: Ctrl05

value: aorta

value: 12 weeks Western diet


title: Ctrl04


title: noKO, induction0, 30hpi, Rep1, RNA


title: iKO, induction0, 35hpi, Rep1, RNA

value: 35 hpi


title: 2-Glucose-uninfected-IFNgamma - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: wildtype

value: IFNgamma


title: iKO, induction0, 25hpi, Rep2, RNA

value: 25 hpi


title: iKO, induction0, 25hpi, Rep3, RNA


title: iKO, induction0, 25hpi, Rep1, RNA


title: 2-Glucose-uninfected-IFNalpha - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: Samples were harvested 48hrs post-IFN treatment


title: Ctrl01

value: Ldlr-/-

value: WT


title: 2-Galactose-VACV-untreated - rep2

description:
raw_counts.xlsx
TPM_values.csv


title: noKO, induction0, 25hpi, Rep2, RNA

value: not induced


title: 2-Galactose-VACV-IFNgamma - rep2

description:
raw_counts.xlsx
TPM_values.csv


title: DONglu2

source_name: MOVAS

growth_protocol: Immortalized smooth muscle cell line MOVAS and modulation of glutamine and glutamate metabolism.

treatment_protocol: Immortalized smooth muscle cell line MOVAS (ATCC CRL-2797) were cultured at 37°C and 5% CO2 in standatd growth media consisting of Dulbecco’s Modified Eagle’s Medium (DMEM, Corning), 100 U/ml of penicillin/streptomycin (Corning), 10% Fetal Bovine Serum (Corning) and 0.2mg/mL geneticin (G418, VWR Life Science). Cells used at 60-70% confluency were treated for 24 hours with glutaminase inhibitors (50mM DON, Sigma-SML0601) and supplemented or not with 2mM glutamate (Gibco-35050061)

value: MOVAS

value: 50mM DON (Sigma-SML0601); 2mM glutamate (Gibco-35050061)


title: noKO, induction0, 25hpi, Rep1, RNA


title: DONglu3


title: iKO, induction0, 20hpi, Rep1, RNA

value: 20 hpi

value: conditional KO induced


title: iKO, induction0, 20hpi, Rep3, RNA


title: 2-Glucose-uninfected-untreated - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: untreated

value: Samples were harvested 48hrs post-Mock treatment


title: noKO, induction0, 20hpi, Rep3, RNA


title: noKO, induction0, 20hpi, Rep1, RNA


title: 2-Galactose-uninfected-untreated - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma


title: DONglu1


title: 2-Galactose-VACV-IFNalpha - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: DON3

value: 50mM DON (Sigma-SML0601)


title: Ctrl03

value: aorta

value: 12 weeks Western diet


title: iKO, induction0, 15hpi, Rep3, RNA

value: 15 hpi


title: Ctrl02


title: 2-Galactose-uninfected-IFNgamma - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: wildtype

value: IFNgamma

value: Samples were harvested 48hrs post-IFN treatment


title: iKO, induction0, 15hpi, Rep1, RNA


title: 2-Galactose-uninfected-IFNalpha - rep2

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha


title: DON2

value: MOVAS


title: DON1


title: noKO, induction0, 15hpi, Rep2, RNA

value: not induced


title: noKO, induction0, 15hpi, Rep3, RNA


title: iKO, induction0, 15hpi, Rep2, RNA


title: iKO, induction0, 20hpi, Rep2, RNA

value: 20 hpi


title: noKO, induction0, 25hpi, Rep3, RNA

value: 25 hpi


title: noKO, induction0, 15hpi, Rep1, RNA


title: iKO, induction0, 10hpi, Rep3, RNA

value: 10 hpi

value: conditional KO induced


title: 1-Glucose-VACV-untreated - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: untreated/ vaccinia virus infection

value: Samples were harvested 48hrs post-Mock treatment/ 24hrs post-infection (vaccinia virus)


title: Ctrl2


title: iKO, induction0, 10hpi, Rep2, RNA


title: Ctrl3


title: iKO, induction0, 10hpi, Rep1, RNA


title: noKO, induction0, 20hpi, Rep2, RNA


title: 1-Glucose-VACV-IFNalpha - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: noKO, induction0, 10hpi, Rep3, RNA


title: Ctrl1


title: 1-Glucose-uninfected-untreated - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: untreated

value: Samples were harvested 48hrs post-Mock treatment


title: noKO, induction0, 10hpi, Rep2, RNA


title: noKO, induction0, 10hpi, Rep1, RNA


title: Aorta from Ldlr-/-AAV-Gls2shRNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
10x Genomics
Ldlr-/-Gls2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Whole aortas from 3 to 4 animals were flushed, dissociated with a scalpel and dounce homogenization was performed in 1mL chilled lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1mM DTT, 0.4U/mL RNase inhibitor (LifeTechnologies-N8080119) and 0.4U/mL Riboblock (FisherScientific-EO0381)) according to 10X Genomics protocol. Single nuclei suspension was recovevered after centrifugation (500 g for 5min at 4°C) in 250μl of chilled lysis buffer and mixed 1:1 with density gradient medium (40mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH7.4 in OptiPrep (Sigma-D1556)). Enrichment of nuclei fraction was achieved by cushioned-density gradient centrifugation with a 29% Optiprep density gradient medium (129mM sucrose, 77.5mM KCl, 15.5mM MgCl2, 31mM Tris-HCl pH7.4 in OptiPrep (Sigma-D1556)) and centrifugation at 13,500 g for 20min at 4°C. Nuclei pellet was resuspended in 30μl wash buffer (PBS containing 1% BSA and 0.4U/mL RNase inhibitors) and directly processed to 10x Genomics protocol
Library was performed according to the manufacter’s instructions (chromium Single-Cell 3' v3.1 kit, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: aorta

value: aorta cells

value: Ldlr-/-


title: 1-Glucose-uninfected-IFNgamma - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: wildtype

value: IFNgamma

value: Samples were harvested 48hrs post-IFN treatment


title: iKO, induction0, 5hpi, Rep3, RNA

value: 5 hpi


title: iKO, induction0, 5hpi, Rep2, RNA


title: Aorta from Ldlr-/- AAV-scrambled shRNA (control)

description:
10x Genomics
Control

value: AAV-scrambled shRNA


title: 1-Glucose-uninfected-IFNalpha - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha


title: noKO, induction0, 5hpi, Rep3, RNA

value: not induced


title: Pool S4_Gdnf-treated orgnaoids_2

city: Helsinki

first: Toni

last: Lemmetyinen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Quality library metrics were assed using multiqc tool (https://multiqc.info/).  Fastq files were aligned to the mouse reference genome (GRCm38) using STAR-aligner (v2.7.8a).Samples were demultiplex and count matrix of unique molecular identifier (UMI) counts was created using the CreateDGEMatrix command from the suite of tools BRB-seqToolsv1.4 (https://github.com/DeplanckeLab/BRB-seqTools). Barcode and treatment information is in the metadata files.
Differential expression analysis was performed with Deseq2 package following the pipeline
Assembly: GRCm38
Supplementary files format and content: Multiplex data

source_name: Gdnf-treated orgnaoids

growth_protocol: Intestinal crypts were mixed with ENR media containing 50 ng/ml of EGF (PMG8041, Gibco), 100 ng/ml of Noggin (250-38, Peprotech), 250 ng/ml of R-spondin 1 (3474-RS, R&D systems), 1 µM of n-acetylcysteine (A-5131, Sigma) and 10 µM of Y-27632 (Y0503, Sigma) which was used in culture media only for the first two days.  Crypts in ENR media were mixed in 1:3 ratio with Matrigel (356231, Corning) before plating 20 µl domes to 48-well plates. Organoids were cultured for 4 days prior to the RNA isolation. Culture media was changed after 2 days.

extract_protocol:
Organoids in Matrigel were lyzed and RNA was extracted with Nucleospin RNA II isolation kit (Macherey-Nagel).
3’UTR RNAseq ”Bulkseq” is based upon Dropseq method for single-cell sequencing (Macosko et al. 2015) Saavalainen group at the University of Helsinki then developed methodology for sequencing from total RNA (Freitag et al. 2020). Method involves priming mRNA with an oligo dT primer which also contains a 12 bp “Cell barcode” and an 8 bp UMI sequence which can be used to remove PCR duplicates during data analysis. Single-stranded cDNA is then converted to ds cDNA using the template switch effect and double-stranded cDNA product is then amplified with PCR and another set of primers (SMART PCR primer). The number of PCR cycles used (9-20x) depends upon the quality and starting amount of RNA. Samples are then pooled together and PCR sequencing pools are made with Nextera i7 primers and the Dropseq P5 primer. Sequencing is then performed on the NextSeq High Output 75 cycle flow cell on the NextSeq 500 to produce (Read 1: 20 bp, Index 1 (i7): 6 bp and Read 2 (61 bp). Ret+ and Ret- cells were mixed with lysis buffer (3% triton X-100, 100 mM DTT, RNAse inhibitor, H2O) and mixed.  Indexing Oligobeads were added to cell lysis mix and after 5 min incubation beads were pelleted with magnet and washed 2 times with 6X SSC and once with 1X Maxima RT Buffer. Bead mixture was combined with RT mix (1 x Maxima RT buffer, Maxima H- RTase, RNase inhibitor, 10 mM dNTPs and 50 µM Template Switch Oligo (5M Betaine)). Samples were incubated for 30 minutes at 22°C and 90 minutes at 52°C. After incubation beads were washed with TE-SDS and TE-Tween.   The constructed cDNA was amplified by PCR. The PCR products were pooled together in sets containing different Indexing Oligos and purified with Agencourt AMPure XP Beads according to the manufacturer’s instructions. The 3’-end cDNA fragments were prepared for sequencing using the Nextera XT (Illumina) tagmentation reaction. The reaction was performed according to manufacturer’s instruction, with the exception of the P5 SMART primer that was used instead of S5xx Nextera primer. Each set of samples, that was pooled after the PCR reaction, was tagmented with a different Nextera N7xx index. Subsequently, the samples were PCR amplified and purified twice using Agencourt AMPure Beads. The libraries were sequenced on an Illumina NextSeq 500, with a custom primer producing read 1 of 21 bp and read 2 of 62 bp.

treatment_protocol: For Gdnf-treated sample also 500ng/ml of Gdnf and Gfra1 was added.

value: small intestine

value: epithelial cells

value: epithelial crypt cells

value: WT


title: noKO, induction0, 5hpi, Rep2, RNA


title: Pool S3_Gdnf-treated orgnaoids


title: 1-Galactose-VACV-IFNgamma - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: IFNgamma/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: 3D7, iKO, induction24, 69hpi, Rep2, Mnase

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Sequencing adapters were trimmed using skewer v0.2.2 and mapped
Reads were mapped to P. falciparum 3D7 genome v3.0 using Bowtie2 v2.3.5 with “--very-sensitive --no-discordant --no-mixed --no-unal“ options.
Mapped fragments were filtered with deeptools v3.5.0 for a mapping quality of at least 20, a fragment size between 75 -175 bp and proper read pairs.
The remaining fragments were used for nucleosome calling with DANPOS v3 using the flags "-m 1 -c 51137214 --extend 73 -a 1 -jd 100 -e 1 -z 20 -s 1"
Assembly: P. falciparum 3D7 genome v3.0, plasmoDB release 52
Supplementary files format and content: bigwig files of pooled, normalized and smoothed nucleosome coverage

extract_protocol:
Parasites were crosslinked for 15 min in 1 % formaldehyde and stopped with 0.125M glycine. Erythrocytes were lysed with 0.1 % saponin and nuclei were isolated as in Josling et al. 2015. Nuclei were resuspended in 75 µl 50 mM Tris pH7.4/4 mM MgCl2/1 mM CaCl2/0.075 % NP40/1 mM DTT, PIC with 0.75 U Micrococcal nuclease (Worthington Biochemicals Corporation) and 50 U Exonuclease III (NEB). Each sample was aliquoted in 3 x 25 µl and incubated for 2.5 / 10 min at 37 °C under agitation (low/high digestion), before the reaction was stopped by adding 25 µl 2 % Triton X100/0.6 % SDS/300 mM NaCl/6 mM EDTA/PIC. and placed at 4 °C. Decrosslinking was performed at 45 °C overnight after adjusting to 1 % SDS/0.1 M NaHCO3/0.5 M NaCl. Proteins were digested by addition of 40 µg of Proteinase K (Zymo Research) and incubation for 1 h at 55 °C. Subsequently, DNA was isolated using EXTRACTME DNA clean-up kit and Micro Spin columns (Blirt) as manufacturer recommends. For low digested samples, DNA fragments >700 bp were removed using SPRI beads, no size-selection step was applied for high digested samples.
1 ng of high/low digested samples was used as input for NEBNext Ultra II DNA library prep kit (NEB), according to manufacturer’s protocol.

treatment_protocol: For KO induction, synchronous parasites were treated with 100 nM rapamycin for 4 h (DMSO treatment as control), washed and returned to culture.

value: 69 hpi

value: conditional KO induced


title: noKO, induction0, 0hpi, Rep3, RNA

value: 0 hpi


title: 1-Glucose-VACV-IFNgamma - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: wildtype


title: noKO, induction0, 0hpi, Rep2, RNA


title: Pool S1_Sorted Ret+ and Ret- cells

source_name: Sorted Ret+ and Ret- cells


title: 1-Galactose-VACV-IFNalpha - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha/ vaccinia virus infection


title: iKO, induction0, 5hpi, Rep1, RNA


title: noKO, induction0, 0hpi, Rep1, RNA


title: 1-Galactose-uninfected-untreated - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: untreated

value: Samples were harvested 48hrs post-Mock treatment


title: 3D7, noKO, induction24, 69hpi, Rep2, Mnase


title: 3D7, noKO, induction24, 69hpi, Rep1, Mnase


title: 3D7, iKO, induction24, 69hpi, Rep1, Mnase


title: 1-Galactose-uninfected-IFNgamma - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: IFNgamma

value: Samples were harvested 48hrs post-IFN treatment


title: miR223, D14 endometriosis lesion, rep4

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Illumina RNA sequencing data was processed using an in-house RNA-seq workflow. Quality control was carried out using FastQC [98], followed by quality and adapter trimming using AdapterRemoval2 [99], aligned to the GENCODE mm10 (GRCm38.p4) mouse reference genome using HISAT2 [100] and quantified to mm10 annotation using featureCounts [101, 102].
Additional sample quality control and normalisation were performed using the R Statistical Software Suite, and differential expression analyses carried out using R packages limma [103, 104] and edgeR [105] on a total of 36 biological samples, comprising 12 samples each from C57Bl/6 mice, miR-155-/- mice and miR-223-/- mice (Refer to Figure S1 and S2).
Significance was inferred from adjusting raw p values (p) using the Benjamini Hochberg false discovery rate method [106] to yield a false discovery rate (FDR) with ≤ 0.05 being the chosen cut-off. Using the limma::treat function, significance was determined based on a null hypothesis of log2FC (log2Fold Change) ≥ ±1
The Ingenuity Pathway Analysis software (IPA 2023; QIAGEN Inc.) was used to identify enriched cellular and molecular functions amongst differentially expressed genes, identify upstream regulators of genes, and to further classify these genes into functionally related groups.
NOTE: One sample pair was lost due to a data atsorage failure (KS_Kav_35_R2)
Assembly: GRCm38.p4
Supplementary files format and content: tsv gene counts

source_name: endometriosis lesion

extract_protocol:
Total RNA was extracted from snap-frozen samples using Qiagen miRNeasy RNA extraction and purification kit, followed by Dnase treatment using TURBO DNA-free kit
Libraries for a total of 36 samples (4 biological samples from each timepoint per genotype) were made from approximately 1ug total RNA. The mRNA sequencing library was prepared using Illumina’s TruSeq RNA Sample Preparation Kit for PolyA+ selection.

value: endometriosis lesion


title: miR223, D14 endometriosis lesion, rep3


title: 1-Galactose-uninfected-IFNalpha - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: IFNalpha


title: 3D7, iKO, induction0, 45hpi, Rep1, Mnase

value: 45 hpi


title: 3D7, iKO, induction0, 45hpi, Rep3, Mnase


title: miR223, D14 endometriosis lesion, rep2


title: Caco2 WT -20.9 kb [AH1066]

value: Colon adenocarcinoma cells

value: Wild type

value: DMEM + 10percent FBS


title: 3D7, noKO, induction0, 45hpi, Rep3, Mnase

value: not induced


title: 1-Galactose-VACV-untreated - rep1

description:
raw_counts.xlsx
TPM_values.csv

value: lung adenocarcinoma

value: untreated/ vaccinia virus infection

value: Samples were harvested 48hrs post-IFN treatment/ 24hrs post-infection (vaccinia virus)


title: 3D7, noKO, induction0, 45hpi, Rep2, Mnase


title: miR223, D14 endometriosis lesion, rep1


title: Pool S2_Sorted Ret+ and Ret- cells_2

value: small intestine

value: epithelial cells

value: epithelial crypt cells

value: WT


title: 3D7, iKO, induction0, 45hpi, Rep2, Mnase

value: conditional KO induced


title: 3D7, noKO, induction0, 45hpi, Rep1, Mnase


title: Caco2 WT -80.1 kb [AH1065]


title: miR223, D7 endometriosis lesion, rep3


title: Caco2 WT CFTR promoter [AH1064]


title: scRNA_ATR_inhibitor_rep2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.0.
Data normalization, unsupervised cell clustering and differential expression were carried out using the Seurat R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Mice were maintained on a mixed C57BL/6J background in a specific pathogen-free barrier facility on a standard light-dark cycle, housed in groups, and monitored for health status every other day.

extract_protocol:
Cells were isolated from anagen mice (around 3 months old). Following euthanasia, back skin was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Single-cell suspensions were incubated with the appropriate antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD45-CD31-CD140A-ITGA6+ to isolate epithelial cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, epithelial cells seperated from mouse back skin were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skin

value: Male

value: skin epithelia

value: Setdb1 fl/fl; K14Cre +/-

value: Ceralasertib (AZD6738)


title: scRNA_Vehicle_Ctrl_rep1

value: Female

value: vehicle Ctrl


title: scRNA_ATR_inhibitor_rep1


title: Caco2 del. +15.6 kb cl. 23 CFTR -80.1 kb [AH1097]

value: Colon adenocarcinoma cells

value: CRISPR/Cas9 mediated deletion of +15.6 kb CRE from the CFTR locus in Caco2 WT cl # 23

value: DMEM + 10percent FBS


title: miR223, D7 endometriosis lesion, rep4

value: endometriosis lesion


title: ATRi_Treatment_rep2

description: "R27" column in two processed data files

data_processing:
Raw 150-bp pair-end reads were aligned to the mus musculus reference genome mm10 (GRCm38) using STAR (v2.7.2b) with default setting.
FeatureCounts (v. 2.0.3) was then used to quantify gene or transponson expression by counting fragments overlapped with Ensemble genes and transponsons in RepeatMasker or gEVE database, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
Total RNA was extracted from back skin epithelium using Direct-zol RNA Miniprep Kit (Zymo, R2051).
Use NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit NEB #E7760) for library preparation.

treatment_protocol: For antiviral treatment, Tenofovir disoproxil fumarate (Fisher Scientific AC461250010, 100 mg/kg) was dissolved in DMSO and Emtricitabine (Fisher Scientific AC462070010, 60 mg/kg) were dissolved in water and administered via oral gavage daily starting postnatal two weeks until analysis. For ATRi treatment, Ceralasertib (AZD6738, Selleckchem S7693, 50 mg/kg) was dissolved in DMSO and administered with vehicle (5% DMSO, 40% propylene glycol, and 50% dH2O) via oral gavage daily upon anagen entry until analysis.


title: scRNA_Vehicle_Ctrl_rep2


title: ATRi_Treatment_rep1

description: "R25" column in two processed data files


title: miR223, D7 endometriosis lesion, rep2


title: Caco2 del. +15.6 kb cl. 23 CFTR +48.9 kb [AH1002]


title: ATRi_Ctrl_rep1

description: "R24" column in two processed data files


title: ATRi_Ctrl_rep2

description: "R26" column in two processed data files


title: Caco2 del. +15.6 kb cl. 23 CFTR -80.1 kb [AH1000]


title: NRTI_Treatment_rep2

description: "R23" column in two processed data files

value: Emtricitabine + Tenofovir disoproxil fumarate


title: miR223, decidualized endometrium, rep4

source_name: decidualized endometrium

value: decidualized endometrium


title: miR223, D7 endometriosis lesion, rep1


title: NRTI_Treatment_rep1

description: "R21" column in two processed data files


title: NRTI_Ctrl_rep1

description: "R20" column in two processed data files


title: Caco2 del. +15.6 kb cl. 23 CFTR -20.9 kb [AH1001]


title: miR223, decidualized endometrium, rep3


title: Setdb1/Tet3_dKO_rep1

description: "R12" column in two processed data files

value: P30 skin epithelia

value: Setdb1 fl/fl; Tet3 fl/fl; K14Cre +/-


title: Setdb1/Tet3_dKO_rep2

description: "R30" column in two processed data files


title: Tet3_sKO_rep1

description: "R10" column in two processed data files

value: Setdb1 fl/+; Tet3 fl/fl; K14Cre +/-


title: Setdb1_sKO_rep2

description: "R31" column in two processed data files

value: Setdb1 fl/fl; Tet3 fl/+; K14Cre +/-


title: miR223, decidualized endometrium, rep1


title: miR155, D14 endometriosis lesion, rep4

value: B6.Cg-Mir155 tm1Rsky /J


title: Setdb1_sKO_rep1

description: "R11" column in two processed data files

value: skin

value: Setdb1 fl/fl; Tet3 +/+; K14Cre +/-


title: DAPT+sErbB4- 2

city: Bethesda

first: David

middle: A

last: Talmage

state: MD

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

data_processing:
QC inspection using FastQC, MultiQC, and Fastx_Screen
Adaptor sequences clipped, low quality and/or nucleotide biased positions in sequences were trimmed using Trimmomatic and QC was repeated
Alignment to ref. genome using HISAT2 and QC of alignment using RSeqC
Transcript assembly using StringTie, QC using gffcompare
Gene and isoform level enumeration using IsoformSwitchAnalyzeR
within sample normalization (cpm), cross-sample normalization CyclicLowess, PCA for outlier detection
Sequence batch correction using Limma, filter and floor values to 2.25
ANOVA for differential gene expression
Assembly: mm10
Supplementary files format and content: Gene level enumeration text file

source_name: Brain

growth_protocol: See Manuscript for details on culture conditions

extract_protocol:
Qiagen RNeasy micro kit
NEBNext Library Prep Kit

value: Hippocampus

value: Neuronal culture

value: WT

value: DAPT 20uM + sErbB4 20nM


title: Setdb1/Tet3_Ctrl_rep2

description: "R13" column in two processed data files

value: Setdb1 fl/+; Tet3 +/+; K14Cre +/-


title: DAPT+sErbB4- 3


title: ChIP-seq on PfSNF2L in a PfSNF2L+3xHA parasite line at 10hpi (hours post invasion); replicate 1 IP

value: 3D7 strain background

value: Early Ring Stage (10hpi) Parasitized Erythrocyte Cells

value: 3xHA-tagged PfSNF2L (C-terminal) in 3D7 strain background

value: No Treatment


title: DAPT+sErbB4- 1


title: miR155, D14 endometriosis lesion, rep3

value: endometriosis lesion


title: hMedIP_P0_Dnmt1cKO_hMeDIP_rep2_input

description: hMeDIP

data_processing:
Raw sequencing150-bp paired-end reads were aligned to mus musculus genome mm10 using STAR.
Reads mapped to a single genomic location were kept for peak identification using the Model based Analysis of Chip-seq 1 (MACS1) or Model based Analysis of Chip-seq 2 (MACS2) pipeline.
Assembly: mm10
Supplementary files format and content: bed or broadPeak files include peak informations for each Sample (except for control sample)
Library strategy: hMeDIP

growth_protocol: C57BL/6J mice cultured in a specific pathogen-free barrier facility on a standard light-dark cycle.

extract_protocol:
Freshly FACS-sorted cells were fixed with 1% formaldehyde for 10 minutes. For IgG and H3K9me3 ChIP, after quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator; for Setdb1 ChIP, use CST SimpleChIP protocol following manufacture recommendation.
For ChIPseq, the DNA extract was incubated overnight at 4°C with primary antibody. 10 μl of Dynal Protein G magnetic beadswas added to each sample the following day, incubated at 4°C for 2-4 h, followed by washes for several times. Bound complexes were treated with 5ul Tn5 transposase at 37°C for 5min, eluted and crosslinking was reversed by 6-10h incubation at 65°C, cleaned up with MinElute PCR Purification Kit and PCR-amplified for 10-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads and submitted to Novogene for library quality control (QC). For hMeDIP, fragmented DNA was used for end-repair, A-tailing and ligation of adapters using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).  10% of the ligated material was saved as input reference and the remaining material was immunoprecipitated using Diagenode’s hMeDIP kit (Diagenode, Denville, NJ). Final libraries from input and 5hmC-immunoprecipitate were obtained by PCR amplification using barcoded primers, followed by clean-up using magnetic beads.

treatment_protocol: For hair follicle cell isolation from P30 mice, back skin at anagen stage was removed and submerged in 0.25% collagenase/HBSS (Gibco) containing DNase I for 1hr at 37°C. Release cells were scraped off, resuspended in cold PBS, and the remaining skin was then incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37C, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spin down at 400g for 10 min at 4°C, and washed once with cold PBS containing 2% FBS(-). Freshly isolated cells were incubated with conjugated antibodies and sorted using a 70-μm nozzle on a BD FACSAria equipped with FACSDiva software (BD Biosciences), gating on DAPI-CD31-CD140A-CD45-ITGA6+ to isolate epithelial cells, and further separated into epidermal (Sca1+) and hair follicle (Sca1-) cells. For epithelia cells islolation from P0 mice, back skin was dissected and submerged dermis side down on 2.5 U/mL Dispase (Gibco) in PBS overnight at 4°C. The epidermis was then peeled off and incubated with 0.25% trypsin-EDTA (Gibco) for 10 min at 37°C, minced, neutralized by cold PBS containing 2% calcium-chelated fetal bovine serum FBS(-), and filtered through a 40-μm cell strainer. Cells were spun down at 300 g for 10 min at 4°C and washed once with cold PBS containing 2% FBS(-).

value: P0 skin epithelia


title: DAPT3

value: DAPT 20uM


title: hMedIP_P0_Dnmt1cKO_hMeDIP_rep2

description: hMeDIP


title: NRTI_Ctrl_rep2

description: "R22" column in two processed data files

value: skin epithelia

value: Setdb1 fl/fl; K14Cre +/-

value: vehicle Ctrl


title: miR155, D14 endometriosis lesion, rep2

value: B6.Cg-Mir155 tm1Rsky /J


title: Setdb1/Tet3_Ctrl_rep1

description: "R9" column in two processed data files

value: skin

value: P30 skin epithelia

value: Setdb1 fl/+; Tet3 fl/+; K14Cre +/-


title: hMedIP_P0_Dnmt1cKO_hMeDIP_rep1_input

description: hMeDIP


title: DAPT2

value: Hippocampus

value: Neuronal culture

value: WT


title: miR155, D14 endometriosis lesion, rep1


title: donor1, CD8+ T cell, 2-week CMV stimulated, Dextramer, V(D)J

city: Philadelphia

first: Siwei

address: 3401 Civic Center Blvd.

institute: Children’s Hospital of Philadelphia

description: 10X Single Cell V(D)J Library

data_processing:
The barcoded processing, V(D)J clonotye analysis from 10X Single Cell V(D)J libraries were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/pipelines-overview)
Assembly: GRCh38
Supplementary files format and content: csv files contain single-cell V(D)J clonotype annotations
Library strategy: TCR-seq

source_name: Blood

extract_protocol:
After the cell sorting in Dextramer staining, collected T cell suspension was transferred to laminar wash plate (~80μl in each well) and incubated at room temperature for 30min, followed by washing 5 times with DPBS in Laminar Wash HT2000. Then, the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits were used to resuspend T cells into a proper concentration to achieve targeted cell recovery and prepare the V(D)J library for single-cell TCR sequencing.
Followed the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits

treatment_protocol: These PBMCs went through a conventional long-term 2-week antigen-stimulation, instead of the two-day antigen-stimulation before the Dextramer staining in all other parts of this study.

value: Blood

value: CD8+ T cell


title: hMedIP_P0_Dnmt1cKO_hMeDIP_rep1

description: hMeDIP


title: miR223, decidualized endometrium, rep2

value: decidualized endometrium


title: Caco2 del. +15.6 kb cl. 23 CFTR promoter [AH974]

description: 4C-seq library with the CFTR promoter as the viewpoint

data_processing:
Library strategy: 4C-Seq
Libraries (AH974, 1001, 1000, 1002, 1064, 1065, 1066, and 1097) were sequenced on Illumina HiSeq4000 machine, while rest were sequenced on Nextseq550 machine.
Data were analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367 for domainograms. For bigwig tracks, 4C-seq was quantified and mapped using the pipe4C processing pipeline. Raw reads were aligned to the hg19 genome using Bowtie2 v4.8.3 and sorted using SAMtools v1.3.
Genome_build: hg19
Supplementary_files_format_and_content: Aligned 4C-seq of each clone and viewpoint in bigWig format

extract_protocol:
Nuclei were made as per the above Methods papers with corresponding samples as listed in the treatment protocol section.
All libraries were constructed as per the above papers  PMID: 22609568 or PMID: 31351925 with the samples corresponding to the Methods papers as listed in the treatment protocol section.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above papers, PMID: 22609568 or PMID: 31351925 for corresponding samples as listed in the treatment protocol section.

value: Colon adenocarcinoma cells

value: CRISPR/Cas9 mediated deletion of +15.6 kb CRE from the CFTR locus in Caco2 WT cl # 23

value: DMEM + 10percent FBS


title: DAPT1

value: DAPT 20uM


title: miR155, D7 endometriosis lesion, rep4

value: endometriosis lesion