title: Input_for_H3K9me3.0h.rep2-1


title: HP1b.48h.rep2-3

status: Public on Sep 19 2024

type: SRA

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

library_source: genomic

data_processing:
Index creation: mouse mm10 and drosophila dm6 assemblies were merged to create a hybrid genome, and a bowtie2 index for the hybrid genome was generated using bowtie2-build -f.
Alignment: FASTQs were aligned to the hybrid genome with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
Library repeat merge: reads from three sequencing runs of the same sample (technical repeats) were merged using samtools merge.
Replicate merge: bam files of the three biological replicates of each sample were merged using samtools merge.
Scalar calculation: the percentage of drosophila reads in each ChIP sample was used to calculate the scalars for library size adjustment. RPM was used for input samples.
Track creation: bigWig files were created using deeptools bamCompare (log2(ChIP/Input) and scaled based on the ratio of the spike-in reads).
Domain calling: merged BAM files were converted into bed files using bedtools bamtoBed and then processed with RSEG v0.4.8 rseg-diff -i 20 -v -mode 2 -d deadzones-k36-mm10.bed with deadzones downloaded from the RSEG website and lifted from mm9 to mm10 over using UCSC Genome Browser's liftOver tool.
Assembly: GRCm38 / mm10
Supplementary files format and content: BigWig files ending in *.merged.multimap.bw reflect the pool of three biological replicates with input subtraction and spike-in adjustment.
Supplementary files format and content: The table H3K9me3.DomainsByDecayRate.mm10.txt has a list of ~43k H3K9me3 domains identified at t=0hrs, with column 4 describing the decay kinetics (fast, intermediate, slow, residual).

molecule: genomic DNA

organism: Mus musculus

source_name: dTKO

growth_protocol: Mouse ESCs are maintained in LIF/FCS medium (DMEM-high glucose, 15% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-mercaptoethanol, 1,000 IU ESGRO) on 0.1% gelatin treated plates.

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde at room temperature for 10 mins, and quenched with 0.125 mM Glycine at room temperature for 5 minutes. The cells were then washed 3 times with ice cold DPBS and incubated with seven ml swelling buffer (25mM HEPES-KCl, pH7.2, 1.5 mM MgCl2, 20mM KCl, 0.1% NP-40) per 15cm dish incubated for 10 minutes at 4 °C. The cells were scrapped off the plates, collected and pelleted in 15 ml falcon tubes and immediately snap frozen in the liquid nitrogen, and stored in -80 °C freezer. On the day of sonication, the crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then resuspended in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) for 10 minutes on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were then resuspended in lysis buffer 3 and sonicated with Covaris with (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 15 minutes. The sonicated chromatin was centrifuging at 20,000g for 20 minutes and the soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest of the chromatin was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation. For H3K9me3 and HP1β ChIP-seq, 20 μg of chromatin was combined with 1.5 μg of Drosophila spike-in chromatin and incubated with 10 μl of Protein A/G dynabeads pre-coated with 0.5 μg of H3K9me3 (abcam, ab8898) or 1ug of HP1β antibody (Cell Signaling Technology, 8676) and 0.5 μg of drosophila spike-in antibody on a rotating wheel at 4 °C overnight. The chromatin-antibody-dynabeads slurry was then washed 5 times with The RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted with elution buffer by incubating at 65 C for 20 minutes and de-crosslinked at 65 °C over night, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA was used for each library and amplified with 11 PCR cycles and the library DNA was purified with Ampure XP beads and the distribution of the DNA fragments of the libraries was analyzed using High Sensitivity DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For the degradation timecourse, the auxin and dTAG13 were added to the medium at the final concentration of 100 μg/ml and 0.5 μM, respectively.

tag: cell line

value: dTKO

tag: cell type

value: ES cells

tag: genotype

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

tag: treatment

value: + auxin + dTAG13

tag: chip antibody

value: Cell Signaling Technology 8676

tag: time (hours post treatment)

tag: replicate


title: HP1b.48h.rep3-2


title: HK_20190108_Bud_tree565

city: Fukuoka

first: Atsuko

last: Miyawaki-Kuwakado

address: 744 Motooka, Nishi-ku

department: Department of Biology, Faculty of Science

country: Japan

institute: Kyushu University

library_source: transcriptomic

data_processing:
The quantification of expression was conducted as follows.
First, quality filtering was performed using the fastp v0.20.0 with default options (Chen et al., 2018).
Second, RNA-seq reads were mapped to the reference genome (Shirasawa et al., 2019) using STAR v1.5.2 (Dobin et al., 2013).
Third, RNA-seq reads were quantified using StringTie v1.3.5 (Pertea et al., 2015).
Assembly: Cerasus x yedoensis Somei-Yoshino Genome v1.0  (Shirasawa et al., 2019, https://www.rosaceae.org/species/cerasus_x_yedoensis/genome_v1.0)
Supplementary files format and content: tab-limited text files includes TPM values of all genes for each sample
Supplementary files format and content: tab-limited text files includes TPM values of the extracted genes whose expression levels across samples satisfy sum of TPM > 1.

molecule: total RNA

organism: Prunus yedoensis

source_name: Bud

growth_protocol: Samples were taken from the sun-exposed crown (approximately 2–3 m from the ground) using long pruning shears from 11:30 to 12:30 h.

extract_protocol:
Total RNA of leaf sample was extracted in accordance with the method described in a previous study. Total RNA of bud sample was extracted using the PureLink™ Plant RNA Reagent (Thermo Fisher Scientific, Waltham, MA, USA, DNase-processed using the TURBO DNA-free kit™ (Thermo Fisher Scientific, Waltham, MA, USA) according to their protocols, and purified using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to its RNA cleanup protocol.
Five to six micrograms of RNA extracted from the leaves of each sample were sent to Hokkaido System Science Co., Ltd., where a cDNA library was prepared with a NovaSeq 6000 S4 Reagent Kit, and 151 base paired-end transcriptome sequencing of each sample was conducted using an Illumina NovaSeq6000 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: For each sample, 0.2–0.4 g of tissue was preserved in a 2 ml microtube containing 1.5 ml of RNA-stabilizing reagent (RNAlater; Thermo Fisher Scientific, Waltham, MA, USA) immediately after harvesting. The samples were transferred to the laboratory within 3 hr after sampling, stored at 4 Celsius overnight and then stored at -80 Celsius until RNA extraction. During transport to the laboratory, the samples were kept in a cooler box with ice to maintain a low temperature.

tag: tissue

value: Bud

tag: variety

value: Somei-yoshino

tag: year of_sampling

tag: day of_sampling

tag: site of_sampling

value: Hokkaido

tag: tree id

value: Hokkaido Tree565


title: Input_for_H3K9me3.0h.rep2-2


title: HP1b.48h.rep3-1


title: HK_20181108_Bud_tree565


title: HK_20181011_Bud_tree565


title: HP1b.48h.rep1-3


title: HK_20180709_Bud_tree565


title: HK_20180907_Bud_tree565


title: HP1b.48h.rep2-2


title: HP1b.48h.rep1-2


title: HP1b.48h.rep1-1


title: HK_20180604_Bud_tree565


title: HK_20180709_Leaf_tree564

source_name: Leaf

value: Leaf

value: Hokkaido Tree564


title: HK_20180813_Leaf_tree564


title: HK_20180907_Leaf_tree564


title: HP1b.3h.rep3-3


title: HP1b.3h.rep3-2


title: HK_20180813_Bud_tree565


title: HP1b.3h.rep3-1


title: HK_20190408_Bud_tree564


title: HP1b.3h.rep2-3


title: HK_20180604_Leaf_tree564


title: HK_20190307_Bud_tree564


title: HK_20181203_Bud_tree564


title: HP1b.3h.rep1-1


title: HP1b.3h.rep2-2


title: HK_20190108_Bud_tree564


title: HP1b.48h.rep2-1


title: HK_20181011_Bud_tree564


title: HP1b.24h.rep3-2


title: HP1b.24h.rep3-1


title: HK_20181108_Bud_tree564


title: HP1b.3h.rep2-1


title: HP1b.3h.rep1-2


title: HK_20180907_Bud_tree564


title: TK_20180905_Leaf_tree104

value: Tsukuba

value: Tsukuba Tree104


title: HP1b.24h.rep1-3


title: HP1b.24h.rep3-3


title: TK_20180807_Leaf_tree104


title: HK_20180813_Bud_tree564


title: HP1b.3h.rep1-3


title: HP1b.24h.rep1-2


title: HP1b.24h.rep2-3


title: HP1b.24h.rep2-2


title: HK_20180709_Bud_tree564


title: HK_20190207_Bud_tree564


title: HP1b.24h.rep1-1


title: HK_20180604_Bud_tree564


title: HP1b.1h.rep3-3


title: HP1b.24h.rep2-1


title: HP1b.1h.rep3-2


title: TK_20180705_Leaf_tree104


title: HP1b.1h.rep3-1


title: TK_20190404_Bud_tree104


title: TK_20190214_Bud_tree104


title: TK_20190110_Bud_tree104


title: HP1b.1h.rep2-2


title: TK_20181116_Bud_tree104


title: TK_20180606_Leaf_tree104


title: TK_20190306_Bud_tree104


title: HP1b.1h.rep2-3


title: TK_20180905_Bud_tree104


title: HP1b.1h.rep1-1


title: TK_20181007_Bud_tree104


title: TK_20180705_Bud_tree104


title: HP1b.12h.rep3-3


title: TK_20180905_Leaf_tree92

value: Tsukuba Tree92


title: HP1b.12h.rep3-1


title: HP1b.1h.rep1-2


title: HP1b.12h.rep2-3


title: TK_20180807_Bud_tree104


title: HP1b.12h.rep2-2


title: HP1b.1h.rep1-3


title: TK_20180807_Leaf_tree92


title: TK_20180606_Leaf_tree92


title: TK_20180606_Bud_tree104


title: TK_20190404_Bud_tree92


title: TK_20180705_Leaf_tree92


title: TK_20181207_Bud_tree104


title: HP1b.12h.rep2-1


title: HP1b.12h.rep1-1


title: HP1b.1h.rep2-1


title: HP1b.12h.rep1-2


title: HP1b.0h.rep3-2


title: HP1b.0h.rep3-1


title: TK_20190214_Bud_tree92


title: TK_20190306_Bud_tree92


title: HP1b.12h.rep3-2


title: TK_20190110_Bud_tree92


title: TK_20181207_Bud_tree92


title: HP1b.0h.rep3-3


title: TK_20181007_Bud_tree92


title: TK_20180705_Bud_tree92


title: HP1b.0h.rep2-2


title: H3K9me3.48h.rep3-3

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-48h.merged.multimap.bw

value: Abcam ab8898


title: FK_20180801_Leaf_tree3

value: Fukuoka

value: Fukuoka Tree3


title: H3K9me3.48h.rep3-2

value: dTKO


title: TK_20180807_Bud_tree92


title: HP1b.12h.rep1-3

value: ES cells


title: TK_20180905_Bud_tree92


title: FK_20180704_Leaf_tree3


title: FK_20180829_Leaf_tree3


title: HP1b.0h.rep1-1

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: Input_for_HP1b.3h.rep2-3

value: + auxin + dTAG13


title: dLGN Nr2f1-control 3

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
Sequence reads were mapped with STAR against the mouse genome (mm10). Read counts and subsequent measures (TPM) were computed with Rsem on the RefSeq gene annotation, version April 2019, retrieved from the UCSC Genome Browser Database .
Assembly: mm10
Supplementary files format and content: counts_sox2.txt: tab separated text file with counts obtained from the Sox2 control and mutant samples.
Supplementary files format and content: counts_nr2f1.txt: tab separated text file with counts obtained from the Nr2f1 control and mutant samples.

source_name: visual thalamus (dLGN)

extract_protocol:
RNeasy Micro Kit (QIAGEN), see paper for details
Nugen Universal + mRNAseq kit

value: visual thalamus (dLGN)

value: dLGN postnatal day 0

value: Nr2f1 flox/flox;Ror-alphaCre;  no Cre


title: TK_20180606_Bud_tree92

value: Bud

value: Somei-yoshino


title: TK_20181116_Bud_tree92


title: HP1b.0h.rep2-3

value: Cell Signaling Technology 8676


title: FK_20190214_Bud_tree3


title: H3K9me3.48h.rep2-2


title: FK_20181219_Bud_tree3


title: FK_20190117_Bud_tree3


title: HP1b.0h.rep2-1


title: dLGN Nr2f1-control 1


title: H3K9me3.48h.rep2-3


title: HP1b.0h.rep1-3


title: HP1b.0h.rep1-2


title: FK_20180607_Leaf_tree3

value: Leaf


title: FK_20181024_Bud_tree3


title: dLGN Nr2f1-mutant 3

value: Nr2f1 flox/flox;Ror-alphaCre


title: FK_20181122_Bud_tree3


title: H3K9me3.48h.rep3-1


title: H3K9me3.48h.rep1-3


title: FK_20180926_Bud_tree3


title: dLGN Nr2f1-mutant 2


title: FK_20190313_Bud_tree3


title: FK_20180704_Bud_tree3


title: H3K9me3.48h.rep1-2


title: FK_20180801_Bud_tree3


title: dLGN Nr2f1-mutant 1


title: FK_20180607_Bud_tree3


title: dLGN Nr2f1-control 2


title: H3K9me3.48h.rep1-1


title: FK_20180801_Leaf_tree2

value: Fukuoka Tree2


title: dLGN Sox2-control 3

value: Sox2flox/flox or Sox2flox/+; no Cre


title: FK_20190313_Bud_tree2


title: dLGN Sox2-control 2


title: FK_20180607_Leaf_tree2


title: H3K9me3.3h.rep3-2

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-3h.merged.multimap.bw

value: Abcam ab8898


title: FK_20180704_Leaf_tree2

value: Fukuoka


title: dLGN Sox2-control 1


title: FK_20190214_Bud_tree2


title: H3K9me3.3h.rep3-3


title: H3K9me3.48h.rep2-1


title: FK_20180829_Bud_tree3

value: Fukuoka Tree3


title: dLGN Sox2-mutant 2


title: FK_20190117_Bud_tree2


title: FK_20181122_Bud_tree2


title: FK_20181024_Bud_tree2


title: dLGN Sox2-mutant 3


title: FK_20180829_Bud_tree2


title: FK_20180926_Bud_tree2


title: FK_20181219_Bud_tree2


title: H3K9me3.3h.rep2-2

value: dTKO


title: H3K9me3.3h.rep2-1

value: ES cells


title: FK_20180801_Bud_tree2


title: dLGN Sox2-mutant 1


title: H3K9me3.3h.rep2-3

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: H3K9me3.3h.rep3-1

value: + auxin + dTAG13


title: FK_20180704_Bud_tree2


title: FK_20180829_Leaf_tree2


title: T2AB R2, Hi-C

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz

data_processing:
MicroC reads were aligned to the hg38 using bwa mem (v0.7.17). The PCR duplicates were filtered out using pairtools (v0.3.0) and contact maps were generated using cooler (v0.8.6).
Assembly: hg38
Supplementary files format and content: Content: Hi-C maps. Format: ".hic"

organism: Homo sapiens

growth_protocol: HCT116, cultured in RPMI 1640 supplemented with 10% fetal bovine serum, L-glutamine, penicillin, and streptomycin. HEK293T cells were grown in DMEM (Gibco 41965062) supplemented with 10 % FBS, 100 U/mL penicillin/streptomycin and 2 mM L-glutamine. All the cells were cultured at 37°C under a humidified incubator with 5 % CO2. Cells were regularly tested for mycoplasma infection with a PCR-based method.

extract_protocol:
cells were washed twice with PBS and digested with Trypsin–EDTA 0.05% (Gibco) for 10 min at 37 °C. A 40-µm cell strainer was used to obtain single cells. The cell suspension was pelleted at 300g for 5 min and resuspended with cold 10% FCS. Subsequently, the cells were fixed by adding an equal volume of 4% formaldehyde (Sigma-Aldrich). The suspension was mixed for 10 min while shaking at room temperature in 50 ml tubes. Exactly after 10 min the fixation was quenched with 500 µl 1.425 M glycine (Merck) on ice. The suspension was pelleted at 400g for 8 min and resuspended in cold lysis buffer (50 mM Tris, pH 7.5; 150 mM NaCl; 5 mM EDTA; 0.5% NP-40; 1.15% Triton X-100; protease inhibitors (Roche)). Next we followed Hi-C protocol.
Universal sequencing adaptor were added using the NEBnext Ultra DNA Library Kit (NEB) according to the supplier’s recommendation. The PCR cycle number was adjusted to 4–12 based on the initial DNA concentration. The final libraries were purified using AMPure Beads (Beckman Coulter) and samples were sequenced with Ilumina Hi-Seq technology according to the standard protocols.

treatment_protocol: The degradation of TOP2A in HCT116 TOP2A-mAID and HCT116 TOP2A-mAID-TOP2B-/- cells was achieved by adding 500uM of Indole-3-acetic acid (Auxin, #REF) in the cell culture medium at 60-70% cell confluency. Cells were harvested for the experiments after 6 hours or 8 hours (for the cells arrested in G1 and G2) of treatment

value: human colorectal carcinoma

value: Both endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID). TOP2B knockout.

value: auxin (6h)


title: RNA CD14+ cells, TNFa, donor 5

city: Chicago

first: Eunsil

last: Hahm

address: 735 W Harrison St. , 753

institute: Rush University Medical Center

data_processing:
RNA-seq was completed by Psomagen and raw read files were analzyed in house. FASTQC files containing quality reads were aligned to the reference genome (GRCh38) using STAR (v2.7.11b) with default parameters.
Gene-level counts were obtained as output. Differential expression analysis was performed using edgeR (v3.28.0). Lowly expressed genes were filtered out, retaining genes with at least five count per million (CPM) for all samples cumulatively.
Normalization of the library sizes was conducted using the edgeR default of TMM (Trimmed Mean of M-values) method. Differential expression was determined using the exact test for differences between two groups, with a likelihood ratio test and a p-value < 0.05 considered significant.
Assembly: GRCh38
Supplementary files format and content: text file of count matrix, includes raw counts for each sample

source_name: Bone marrow HSPC

growth_protocol: Isolated CD34+ HSPCs were cultured in myeloid expansion medium (Stem Cell Technologies). Briefly, cells were cultured for 10-14 days in StemSpan SFEM II cell media (Stem Cell Technologies) containing myeloid expansion supplement I (Stem Cell Technologies) and II (Stem Cell Technologies) following manufacturer’s instructions.

extract_protocol:
RNA extraction following TruSeq Stranded Total RNA porotocol
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: To mimic the inflammatory conditions seen in the BM of patients with CKD, TNFα (10ng/ml) was added to the supplement medium at day 0. At days, 5, 7, and 10 fresh media with or without TNFα was added if cells reached the desired cell density.

value: Bone marrow HSPC

value: isolated CD34+ cells

value: CD14+ cells at day 10

value: TNFa


title: FK_20180607_Bud_tree2

value: Bud

value: Somei-yoshino


title: H3K9me3.3h.rep1-3


title: RNA CD14+ cells, TNFa, donor 3


title: H3K9me3.3h.rep1-2


title: T2B R2, Hi-C

value: no


title: T2A R2, Hi-C

value: Both endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID).


title: RNA CD14+ cells, untreated, donor 9

value: Untreated


title: H3K9me3.3h.rep1-1

value: Abcam ab8898


title: H3K9me3.24h.rep3-3

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-24h.merged.multimap.bw

value: dTKO


title: RNA CD14+ cells, untreated, donor 5


title: RNA CD14+ cells, untreated, donor 8


title: T2AB R1, Hi-C


title: H3K9me3.24h.rep3-2

value: ES cells


title: CD14+ cells, TNFa, donor 5

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program
Assembly: GRCh38
Supplementary files format and content: For each sample; bigWig files for peak metrics, signal map, and histogram densities.

extract_protocol:
Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif cat# 53150). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the iSeq (Illumina), and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the iSeq (Illumina), and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).


title: CD14+ cells, TNFa, donor 9


title: CD14+ cells, TNFa, donor 3


title: CD14+ cells, untreated, donor 5


title: CD14+ cells, untreated, donor 9


title: T2A R1, Hi-C


title: WT R1, Hi-C


title: H3K9me3.24h.rep2-3

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: BJ.TFEB_TFE3_DKO.C64.plus.cGAMP brep3

city: Pittsburgh

first: Jay Xiaojun

last: Tan

state: Pennsylvania

address: Bridgeside Point 1, 4th Floor, 100 Technology Drive

institute: Aging Institute, University of Pittsburgh

description: .tabular can be input into 3D RNA-seq and .csv is gene expression quantification

data_processing:
Trim Galore! done through "usegalaxy.org"
Salmon quant  done through "usegalaxy.org"
Reference transcriptome was "refMrna.fa.gz" from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/"
Reference genome was "hg38.fa.gz" from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/"
TPMs generated using the 3D RNA-seq online app "https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/"
hg38.refGene.gtf.gz was the GTF file use for 3D RNA-seq from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/"
Assembly: hg38
Supplementary files format and content: .tabular files that can be used with the aforementioned 3D RNA-seq
Supplementary files format and content: .csv file with gene expression quantification for all samples

molecule: polyA RNA

growth_protocol: BJ-5ta cells were grown at 37°C in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 8% fetal bovine serum (Invitrogen), penicillin (100 U/mL), and streptomycin (100 mg/mL) (Gibco), InvivoGen plasmocin (2.5 μg/mL) in a humidified 5% CO2 atmosphere.

extract_protocol:
PureLink RNA Mini Kit (Thermo Fisher Scientific, ref 12183018A)
NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: For cGAMP treatment, a mild digitonin buffer was used for cGAMP delivery into the cells. Specifically, cells were cultured until 90% confluent. Then, the media were transferred to new plates or dishes. Cells were incubated with pre-warmed digitonin buffer (50 mM HEPES-KOH, pH 7.2, 100 mM KCl, 3 mM MgCl2, 0.1 mM DTT, 85 mM Sucrose, 0.2% BSA, 1 mM ATP, 10 μg/mL digitonin) containing 1 μM 2’3’-cGAMP or the buffer alone as negative control. After 10 min treatment, the digitonin buffer was aspirated, and the original media added back. Incubation was carried out for the specified duration in the incubator.

value: TFEB_TFE3 DKO

value: Digitonin buffer + 1 μM cGAMP 10 min, incubate for 12 h


title: H3K9me3.24h.rep3-1

value: + auxin + dTAG13


title: WT R2, Hi-C

value: human colorectal carcinoma


title: CD14+ cells, untreated, donor 3

value: Bone marrow HSPC


title: H3K9me3.24h.rep2-2


title: BJ.TFEB_TFE3_DKO.C64.plus.cGAMP brep2


title: RNA CD14+ cells, TNFa, donor 9

value: isolated CD34+ cells


title: H3K9me3.24h.rep2-1


title: BJ.TFEB_TFE3_DKO.C64.minus.cGAMP brep3

value: Digitonin buffer 10 min, incubate for 12 h


title: BJ.TFEB_TFE3_DKO.C64.minus.cGAMP brep2


title: BJ.TFEB_TFE3_DKO.C64.plus.cGAMP brep1


title: BJ.TFEB_TFE3_DKO.C64.minus.cGAMP brep1


title: H3K9me3.24h.rep1-2


title: T2B R1, Hi-C

value: Both endogenous TOP2A alleles were tagged with the mini auxin-inducible degron protein domain (mAID). TOP2B knockout.


title: WT G1, Hi-C

value: palbociclib


title: BJ.TFEB_TFE3_DKO.C51.plus.cGAMP brep2


title: BJ.TFEB_TFE3_DKO.C51.plus.cGAMP brep3


title: T2AB G2, Hi-C

value: RO3306, auxin (8h)


title: BJ.TFEB_TFE3_DKO.C51.plus.cGAMP brep1


title: H3K9me3.24h.rep1-1


title: BJ.TFEB_TFE3_DKO.C51.minus.cGAMP brep3


title: WT G2, Hi-C


title: H3K9me3.1h.rep3-3

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-1h.merged.multimap.bw


title: BJ.TFEB_TFE3_DKO.C51.minus.cGAMP brep1


title: ip_tige3

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was performed with FastQC v0.11.5.
Adapters were filtered with eautils v1.2.2.18.
Splice-aware alignment was performed with STAR against the human hg19 human genome assembly. The number of allowed mismatches was 2. Reads that mapped to more than one site of the reference genome were discarded. The minimal score of alignment quality to be included in count analysis was 10.
Resulting Sequence Alignment/Map (SAM) and binary SAM alignment files were handled with Samtools v0.1.19.24.
Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Assembly: hg19 human genome assembly
Supplementary files format and content: HTSeq count files

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientific) and subjected to DNase treatment (Invitrogen) according to manufacturer’s instructions.
Samples were prepared for sequencing using TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions.

value: melanoma cell line

tag: fraction

value: IP

value: tigecycline


title: H3K9me3.1h.rep3-2

value: Abcam ab8898


title: BJ.plus.cGAMP brep3

value: wildtype


title: BJ.minus.cGAMP brep3


title: BJ.plus.cGAMP brep2


title: input_pbs3

value: input

value: PBS


title: input_tige3


title: H3K9me3.1h.rep3-1

value: dTKO

value: ES cells

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: BJ.plus.cGAMP brep1

value: Digitonin buffer + 1 μM cGAMP 10 min, incubate for 12 h


title: BJ.minus.cGAMP brep2


title: BJ.minus.cGAMP brep1


title: T2AB G1, Hi-C

value: human colorectal carcinoma

value: palbociclib, auxin (8h)


title: ISX9 (treated)_mRNA

city: Bloomington

first: Ahmed

middle: H

last: Ghobashi

state: IN

institute: Indiana University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment and gene-expression quantification of HT29 cells scRNA-seq and scATAC-seq data was performed using the CellRanger-arc Count pipeline (version 2.0.2, 10X Genomics
For scRNA-seq, cells were filtered to include only cells with no more than 25% mitochondrial gene. For scATAC-seq, data was processed using the standard Signac workflow53. Cells with fewer than 300 or more than 100,000 ATAC fragments were filtered, as were cells with nucleosomal enrichment > 1.5 or transcriptional start site enrichment < 1. Peaks within each dataset were identified using MACS2. Genomic blacklist regions were removed using subsetByOverlaps
Assembly: hg38
Supplementary files format and content: RDS file

source_name: HT29 cells

extract_protocol: Approximately 10,000 cells per sample were sequenced via the 10X Genomics Chromium System using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit A at the Indiana University School of Medicine (IUSM) Center for Medical Genomics core. The libraries were sequenced at the IUSM Center for Medical Genomics using a NovaSeq 600 with approximately 375 million ATAC read pairs and 500 million Gene Expression read pairs per sample.

value: HT29 cells

value: colon cancer

tag: library type

value: mRNA


title: H3K9me3.1h.rep2-2

value: + auxin + dTAG13


title: control_ATAC

description: 10x Genomics

library_source: genomic single cell

value: ATAC

value: DMSO


title: H3K9me3.1h.rep2-1


title: ip_tige2

value: melanoma cell line

value: IP

value: tigecycline


title: ISX9 (treated)_ATAC

description: 10x Genomics


title: control_mRNA

description: 10x Genomics


title: BJ.TFEB_TFE3_DKO.C51.minus.cGAMP brep2

value: TFEB_TFE3 DKO

value: Digitonin buffer 10 min, incubate for 12 h


title: WT replicate 4 in G2

extract_protocol:
Cells were trypsinized and washed once with PBS, followed by fixation with formaldehyde for MicroC.
Micro-C experiments in G1- or G2-arrested WT and TOP2DKO HCT116 cells were performed in collaboration with Dovetail Genomics as previously described (Zhang et al., 2023). Briefly, at least 2 libraries per condition/genotype were generated using ~1 million cells and pooled together for shallow sequencing. Those libraries that passed standard QC criteria (i.e., long-/short-range interaction ratio, PCR duplication levels) were pooled and paired-end sequenced on a NovaSeq6000 platform (Illumina) to >600 million read pairs per replicate

treatment_protocol: HCT116 TOP2A mAID and HCT116 TOP2A mAID/TOP2B -/- were synchronized in G1 by treating the cells with 2uM Palbociclib (Selleck Chemicals Cat #S1116) or G2 by treating with 10uM of RO-3306 for a total of 28 hours (Cat# S7747). TOP2A degradation was achieved by treating HCT116 TOP2A mAID/TOP2B -/- cells with 500μM of indole-3-acetic acid (IAA, Auxin Sigma-Aldrich Cat# I5148-2G) for 8 hours.

value: wildtype


title: H3K9me3.1h.rep1-3

value: dTKO

value: ES cells

value: Abcam ab8898


title: ip_pbs2

value: PBS


title: input_pbs2

value: input


title: WT replicate 2 in G2

value: human colorectal carcinoma


title: H3K9me3.1h.rep1-2

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: H3K9me3.1h.rep2-3


title: H3K9me3.1h.rep1-1


title: TOPA/B DKO replicate 4 in G2

value: TOP2A + TOP2B double knockout


title: WT replicate 1 in G2


title: ip_tige1


title: ip_pbs1


title: TOPA/B DKO replicate 3 in G2


title: H3K9me3.12h.rep3-3

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-12h.merged.multimap.bw

value: + auxin + dTAG13


title: TOPA/B DKO replicate 2 in G2


title: input_tige1


title: TOPA/B DKO replicate 1 in G2


title: WT replicate 4 in G1


title: H3K9me3.12h.rep3-2


title: input_tige2


title: WT replicate 2 in G1


title: WT replicate 1 in G1


title: input_pbs1


title: H3K9me3.12h.rep3-1


title: WT replicate 3 in G2


title: TOPA/B DKO replicate 4 in G1


title: cranial NCCs, DMSO

city: Aurora

first: Stanley

middle: Michinobu

last: Kanai

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

description: 10X Genomics

data_processing:
Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics). Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Facial mesenchyme

extract_protocol:
Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in (Barske et al., 2016; Askary et al., 2017; Mitchell et al., 2021) with some modifications. In brief, 140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase (Roche, cat. 10165921001), then 70 embryos were treated with 100 uM YM-254890 (Adipogen, cat. AG-CN2-0509-M001) or DMSO (control) from 16-36 hpf. At 36 hpf, 10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos, the heads were severed, pooled, and deyolked by gentle pipetting in Ca2+-free Ringer’s solution (116 mM NaCl, 2.9 mM KCl, 5 mM HEPES, pH 7.0). The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold-activated protease from Bacillus licheniformis (Sigma Aldrich, cat. P5380) in dissociation buffer (10 mg/ml Bacillus licheniformis protease, 125 U/ml DNAse, 2.5 mM EDTA, PBS), followed by enzyme neutralization with stop solution (30% fetal bovine serum, 0.8 mM CaCl2, in PBS). Cells were then centrifuged (400xg), resuspended in cell suspension buffer [1% fetal bovine serum, 0.8 mM CaCl2, Leibovitz’s L-15 Medium (Gibco, cat. 21083-027)], filtered through a 70 uM strainer (PluriSelect, cat. 43-10040-40), centrifuged (400xg) again and resuspended in sorting buffer (1% fetal bovine serum, 1 mM EDTA, 25 mM HEPES). EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 (Beckman Coulter). A total of 72,000 and 86,000 double positive cells were purified for DMSO and YM-treated samples, respectively. Cells were once again centrifuged (400xg) and resuspended in cell suspension buffer. After confirming cell viability with trypan blue (Gibco, cat. 15250-061), 8000 cells for each condition were submitted to the Genomics and Microarray Core (CU AMC) for single cell RNA-sequencing.
Library was prepared according to manufacturer's protocol (3' NextGEM V3.1, 10X Genomics)

treatment_protocol: Dechorionated zebrafish embryos were treated with 100uM YM-254890 or 10%v/v DMSO (vehicle control) from 16-36 hours post fertilization.

value: Facial mesenchyme

tag: age

value: 36 hpf

value: Cranial neural crest cells


title: TOPA/B DKO replicate 3 in G1


title: cranial NCCs, YM

description: 10X Genomics

value: YM


title: TOPA/B DKO replicate 2 in G1


title: Lung fibroblast, Control [NSCLC-S3-WT]

city: Shenzhen

first: Yang

last: Gao

address: Guangqiao Road, Guangming District

country: China

institute: Shenzhen Bay Laboratory

data_processing:
RNA sequencing data was aligned with STAR using genome reference hg38 and annotation downloaded from NCI GDC (Genomic Data Commons).
Gene-specific read counts were calculated using featureCounts with parameters '-M -O–fraction -Q 30'.
Assembly: hg38
Supplementary files format and content: RNA-seq_counts.csv.gz: raw counts for each Sample in csv format

source_name: Lung

extract_protocol:
Tissues were cut into sections of 0.1 grams and then placed into 5 mL microtubes. Sections were minced with scissors and enzymatically digested with MACS Tumor Dissociation Kit (Miltenyi Biotec) for 30 min on a rotor at 37°C, according to the manufacturer's instructions. Digestion was suspended by adding 8 mL fibroblast medium, containing DMEM/F12 medium (Gibco) and 10% fetal bovine serum (Gibco). Then the half-dissociated cells were centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in fibroblast mediums. Cells were seeded on plastic dishes in a humidified in 1.5% O2 and 5% CO2 incubator. Four days later, human-derived primary fibroblasts were obtained and blocked with Fc Receptor Blocking Solution (Biolegend). Subsequently, cell surface staining was conducted in PBS supplemented with 2% FBS using antibody cocktails (EPCAM, CD31, CD45) for 30 min at 4°C. After washing twice with PBS containing 2% FBS, the cells were sorted on the BD FACS AriaSORP. 2x10^4 fibroblasts were seeded in a 24-well plate, rested overnight and then stimulated with TNFa, IL1a, IL6, LIF, CXCL12, SPP1 or DMSO control. RNA was extracted according to the manufacture's instructions using the RNeasy Mini Kit (QIAGEN).
Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme).

value: Lung

tag: disease state

value: Adjacent normal

value: Untreated


title: Lung fibroblast, TNFa [NSCLC-S3-TNFa]

value: TNFa


title: H3K9me3.12h.rep2-2

tag: cell line

value: dTKO


title: TOPA/B DKO replicate 1 in G1

tag: cell type


title: H3K9me3.12h.rep2-3

value: ES cells

tag: genotype


title: PASMC Ferroptotic Media 4

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

institute: University of Minnesota

data_processing:
CLC Genomics Workbench
Assembly: Sequence reads were trimmed for quality and mapped to human genome. Read count extraction and normalization were performed
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Pulmonary Artery Smooth Muscle Cells (PASMC)

extract_protocol:
RNA was harvested from cells using
RNA libraries from RNA-seq were prepared by the University of Minnesota Genomics center.

treatment_protocol: spent media from control or ferroptotic endothelial cells

value: WT

tag: treatment

value: Ferroptotic Media

tag: time

value: 48 hours


title: Lung fibroblast, IL6 [NSCLC-S3-IL6]


title: Lung fibroblast, IL1a [NSCLC-S3-IL1a]


title: H3K9me3.12h.rep1-2

tag: chip antibody

value: Abcam ab8898

tag: time (hours post treatment)


title: Lung fibroblast, LIF [NSCLC-S3-LIF]

tag: tissue

value: LIF


title: Lung fibroblast, CXCL12 [NSCLC-S3-CXCL12]


title: Lung fibroblast, Control [NSCLC-S2-WT]


title: PASMC Ferroptotic Media 2

value: Pulmonary Artery Smooth Muscle Cells (PASMC)


title: H3K9me3.12h.rep1-1

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

value: + auxin + dTAG13

tag: replicate


title: H3K9me3.12h.rep1-3


title: PASMC Ferroptotic Media 1


title: Lung fibroblast, SPP1 [NSCLC-S2-SPP1]


title: Lung fibroblast, TNFa [NSCLC-S2-TNFa]


title: PASMC Control Media 4

value: Control Media


title: H3K9me3.0h.rep3-3

description:
H3K9me3.DomainsByDecayRate.mm10.txt
H3K9me3-B4d3-0h.merged.multimap.bw


title: PASMC Control Media 3


title: Lung fibroblast, LIF [NSCLC-S2-LIF]


title: H3K9me3.12h.rep2-1


title: PASMC Ferroptotic Media 3


title: Lung fibroblast, IL6 [NSCLC-S2-IL6]


title: Lung fibroblast, CXCL12 [NSCLC-S2-CXCL12]


title: H3K9me3.0h.rep3-2


title: Lung fibroblast, IL1a [NSCLC-S2-IL1a]


title: Lung fibroblast, Control [NSCLC-S1-WT]


title: PASMC Control Media 1


title: Lung fibroblast, TNFa [NSCLC-S1-TNFa]


title: H3K9me3.0h.rep2-3


title: Lung fibroblast, SPP1 [NSCLC-S3-SPP1]


title: Lung fibroblast, SPP1 [NSCLC-S1-SPP1]


title: Lung fibroblast, LIF [NSCLC-S1-LIF]


title: H3K9me3.0h.rep2-2


title: MB051_Xeno_inp

city: Toronto

first: Michael

middle: D

last: Taylor

state: ON

address: 686 Bay St.

country: Canada

institute: Hospital for Sick Children

data_processing:
ChIP-Seq - alignment with bowtie2, peakcalling with MACS2. Differential peak analysis with DESeq2
counts were collected by bedtools multicov
Assembly: hg19
Supplementary files format and content: Raw counts for each sample for each gene or ChIP-Seq peak
Supplementary files format and content: narrowpeak outputs from MACS2

extract_protocol:
ChIP-Seq libraries were generated with home made reagents
NEB Ultra DNA library prep kit was used for ChIP-Seq (NEB7645) library prep

value: Group 3 medulloblastoma patient derived xenograft

value: GFP-Luc-tagged

value: gDNA (DNA)


title: MB051_Xeno_27me3

value: enrichment of gDNA for 27me3 (enriched gDNA)


title: Lung fibroblast, IL6 [NSCLC-S1-IL6]

value: Lung

value: Adjacent normal


title: Lung fibroblast, IL1a [NSCLC-S1-IL1a]


title: Lung fibroblast, CXCL12 [NSCLC-S1-CXCL12]


title: Colon fibroblast, Control [CRC-S6-WT]

source_name: Colon

value: Colon

value: Untreated


title: MB051_Xeno_27Ac

value: enrichment of gDNA for 27ac (enriched gDNA)


title: H3K9me3.0h.rep1-3

value: dTKO

value: ES cells


title: H3K9me3.0h.rep2-1

value: Abcam ab8898


title: Colon fibroblast, SPP1 [CRC-S6-SPP1]


title: MB051_ZIC_1/4_3_RNA

data_processing:
RNA-Seq - alignment with STAR, differential expression analysis with DESeq2
Counts were collected with htseq for RNA-Seq
Assembly: hg19
Supplementary files format and content: Raw counts for each sample for each gene

extract_protocol:
Rneasy purification kit for extraction of RNA.
NEB Ultra II Directional mRNA kit
Poly A enriched, strand specific library prep for RNA-Seq.

value: GFP-Luc-tagged, BFP tagged, ZIC1/4 overexpression

value: whole transcriptome


title: ip_pbs3

value: melanoma cell line

value: IP

value: PBS


title: PASMC Control Media 2

value: Pulmonary Artery Smooth Muscle Cells (PASMC)

value: WT

value: Control Media

value: 48 hours


title: Colon fibroblast, TNFa [CRC-S6-TNFa]

value: TNFa


title: H3K9me3.0h.rep3-1

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

value: + auxin + dTAG13


title: MB051_ZIC_1/4_2_RNA

value: Group 3 medulloblastoma patient derived xenograft


title: H3K9me3.0h.rep1-1


title: Colon fibroblast, IL6 [CRC-S6-IL6]

value: Colon

value: Adjacent normal


title: MB051_ZIC_1/4_1_RNA


title: Colon fibroblast, LIF [CRC-S6-LIF]

value: LIF


title: Colon fibroblast, IL1a [CRC-S6-IL1a]


title: Colon fibroblast, CXCL12 [CRC-S6-CXCL12]


title: WT replicate 3 in G1

value: human colorectal carcinoma

value: wildtype


title: MB051_BFP_3_RNA

value: GFP-Luc-tagged, BFP tagged

value: whole transcriptome


title: Colon fibroblast, TNFa [CRC-S5-TNFa]


title: HSC5 cells, sgWDR77#2, biol rep 3

city: Cold Spring Harbor

first: Heng

last: Liang

state: NY

address: 1 BUNGTOWN RD, MILLS LAB

institute: Cold Spring Harbor Laboratory

data_processing:
STAR mapping
HTSeq-Counts
DEseq2
GSEA, GO, KEGG
Assembly: hg38
Supplementary files format and content: Counts generated via HTSeq-Counts

source_name: Human skin squamous cell carcinoma

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit
Libraries were constructed following the Illumina TruSeq Stranded mRNA (LT) Protocol

value: Human skin squamous cell carcinoma

value: Cancer cell line

value: WDR77 Knockout

value: Neomycin


title: H3K9me3.0h.rep1-2

value: dTKO

value: ES cells

value: Abcam ab8898


title: HSC5 cells, sgWDR77#2, biol rep 2


title: Colon fibroblast, Control [CRC-S5-WT]

value: Untreated


title: Colon fibroblast, LIF [CRC-S5-LIF]


title: HSC5 cells, sgWDR77#2, biol rep 1


title: MB051_BFP_1_RNA


title: Colon fibroblast, SPP1 [CRC-S5-SPP1]


title: Colon fibroblast, IL1a [CRC-S5-IL1a]


title: Colon fibroblast, IL6 [CRC-S5-IL6]


title: Colon fibroblast, CXCL12 [CRC-S5-CXCL12]


title: HSC5 cells, sgWDR77#1, biol rep 3


title: Colon fibroblast, Control [CRC-S4-WT]


title: HSC5 cells, sgWDR77#1, biol rep 2


title: MCF7-HG (2)

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

data_processing:
The paired-end RNA-seq reads were aligned against the human genome assembly GRCh38 using STAR  version 2.4.2a using default settings. Data from separate lanes were first merged. All samples passed quality checks at default settings.
To quantify transcriptome features we used Ensembl genome annotation version 90 and for gene level quantification we used HTseq  version 0.11.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

growth_protocol: MCF7 human BC cells (ER+, PR+, HER2-) were cultured in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 units/ml penicillin and 100 units/ml streptomycin, containing 25mM glucose (HG). Cultures were maintained in a humidified atmosphere of 95% air and 5% CO2 at 37°C. Human adipose tissue samples were obtained from mammary adipose biopsies of healthy woman undergoing surgical mammary reduction, free of neoplastic, metabolic or endocrine diseases. Informed consent was obtained before the surgical procedure approved by the ethical committee of the University of Naples “Federico II”. Adipose derived Mesenchymal Stem Cells (Ad-MSCs) were isolated from the Stromal Vascular Fraction as described in Ambrosio et al. (2017) and cultured in DMEM, supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 100 units/ml penicillin and 100 units/ml streptomycin (HG).  Media, sera and antibiotics for cell culture were from Lonza (Basel, Switzerland). Adipocyte differentiation of Ad-MSCs was obtained by the alternation (every three days, two times) of an Adipocyte differentiation Induction Mix (AIM) - containing 850 nM Insulin, 10 μM Dexamethasone, 0.5 mM 3-IsoButyl-1-MethylXanthine, 33 μM Biotin, 17 μM Pantothenate and 1 μM Rosiglitazone - and an Adipocyte differentiation Maintaining Mix (AMM) consisting of 850 nM Insulin and 1 μM Rosiglitazone. Then, the cells were stimulated (every two days, two times) with  1 μM Rosiglitazone. All the process was carried out in complete culture medium (HG). Adipocyte differentiation of Ad-MSCs was reached in 17 days. Lipid accumulation was determined by Oil red O staining (Aprile et al, 2018) and assessed by optical density determination at 510 nm using a microplate reader. All the chemicals for adipocyte differentiation were from Sigma-Aldrich (St Louis, MO, USA).

extract_protocol:
Total RNA was isolated from cells using TRIzol solution (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions. All RNA samples were quantified by measuring the absorbance at 260nm and 280nm (NanoDrop spectrophotometer, Life Technologies, Carlsbad, CA, USA). The integrity of RNA samples was further analyzed by using the digital electrophoresis system Experion with the “RNA StdSens Kit” (Biorad, Hercules, CA, USA), following the manufacturer's instructions. The run and result analysis were performed by the Experion software. RNA samples with a RNA Quality Indicator (RQI) value ≥ 9 were considered good for the further analysis.
Paired-end cDNA libraries were prepared for sequencing on the Illumina Hi-Seq 2500 platform, available at IGA Technology Service (Udine, Italy).

treatment_protocol: Adipocyte differentiation of Ad-MSCs was carried out in the bottom chamber of a transwell culture system (0.4 μm pore size, Costar, Cambridge, MA, USA). At the 15th days of the adipogenic  process, MCF7 cells were seeded in the upper chamber shifting - or not - both cancer cells and adipocytes  from 25mM to 5.5mM glucose (HG->LG). After 4 days, the cells were used to obtain RNA samples. Three independent experiments have been performed.

value: 25mM glucose


title: ADIPO [+MCF7] HG->LG (1)

value: adipocytes

value: 25mM glucose at day 0, 5.5mM glucose at day 15


title: Colon fibroblast, TNFa [CRC-S4-TNFa]

value: Colon

value: Adjacent normal

value: TNFa


title: HSC5 cells, sgWDR77#1, biol rep 1


title: Colon fibroblast, LIF [CRC-S4-LIF]

value: LIF


title: Colon fibroblast, SPP1 [CRC-S4-SPP1]


title: ADIPO [+MCF7] HG (1)


title: Colon fibroblast, IL6 [CRC-S4-IL6]


title: HSC5 cells, sgPRMT5#2, biol rep 3

value: PRMT5 Knockout


title: Colon fibroblast, IL1a [CRC-S4-IL1a]


title: MB051_BFP_2_RNA

value: Group 3 medulloblastoma patient derived xenograft

value: GFP-Luc-tagged, BFP tagged

value: whole transcriptome


title: HSC5 cells, sgPRMT5#2, biol rep 2

value: Human skin squamous cell carcinoma

value: Cancer cell line


title: Colon fibroblast, CXCL12 [CRC-S4-CXCL12]


title: MCF7 [+ADIPO] HG (1)


title: HEK293T transfected with dCasRx and nontargeting gRNA, replicate 2

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

data_processing:
For alternative splicing analysis, raw reads were aligned using the vast-tools pipeline, version 2.5.1 (https://github.com/vastgroup/vast-tools), to the hg38 VastDB library. Exons were filtered for coverage and junction balance, requiring a vast-tools quality score of SOK/OK/LOW and a balance score of OK/B1/B2/Bl/Bn in all samples. Exons were considered significantly changing if the absolute change in PSI was greater than 15 and the expected minimum change (MV) was greater or equal to 0.1 at p > 0.95 according to vast-tools diff module.
For gene expression analysis, raw reads were aligned to the hg38 genome using STAR v.2.7.10, and read counts per gene were computed using --quantMode GeneCounts, with the Ensembl hg38 GTF annotations (release 109). edgeR was used to calculate RPKM values, normalize counts using the TMM method, and calculate differential expression for all protein-coding genes using the quasi-likelihood F test. Genes were considered differentially expressed if they showed greater than two-fold change (log2fc > 1) at FDR < 0.05 and were expressed at a minimum of 2 RPKM in at least one condition.
Assembly: hg38
Supplementary files format and content: vast_tools_inclusion_table.tab is in tab-delimited format and contains vast-tools output showing the percent spliced in (PSI) values and quality scores for each splicing events across samples, see https://github.com/vastgroup/vast-tools . star_counts.csv is in comma-separated values format and contains gene counts for each sample.

growth_protocol: HEK293T cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) with on-column DNase treatment as recommended by the manufacturer.
500ng of total RNA was used for generation of polyA+ libraries with the NEB Next Ultra II Directional kit. Sequencing was performed by the Donnelly Sequencing Centre using a Nova-Seq 6000 instrument and S1 flow cell to an average depth of 50 million paired-end 150nt reads.

treatment_protocol: 25,000-30,000 HEK293T cells were seeded in 96 well plates the day before to reach a confluency of ~80% at transfection. 200ng of dCasRx, RBFOX1N-dCasRx-C, or dCasRx-RBM25 expression vector was co-transfected with 200ng gRNA expression vector using X-tremeGENE 9 (Roche) at a 3:1 ratio to DNA. RNA was harvested 48 hours post-transfection.

value: Human embryonic kidney

value: dCasRx with nontargeting gRNA


title: HSC5 cells, sgPRMT5#1, biol rep 3

value: Neomycin


title: HSC5 cells, sgPRMT5#2, biol rep 1


title: HEK293T transfected with dCasRx and nontargeting gRNA, replicate 1


title: HEK293T transfected with RBFOX1N-dCasRx-C and MAPT-targeting gRNA, replicate 2

value: RBFOX1N-dCasRx-C with MAPT-targeting gRNA


title: HEK293T transfected with RBFOX1N-dCasRx-C and MAPT-targeting gRNA, replicate 1


title: HSC5 cells, sgPRMT5#1, biol rep 2


title: ADIPO-HG (1)

source_name: adipocytes

value: 25mM glucose


title: HEK293T transfected with dCasRx-RBM25 and CD46-targeting gRNA, replicate 2

value: dCasRx-RBM25 with CD46-targeting gRNA


title: HEK293T transfected with RBFOX1N-dCasRx-C and nontargeting gRNA, replicate 1

value: RBFOX1N-dCasRx-C with nontargeting gRNA


title: ADIPO [+MCF7] HG->LG (3)

value: adipocytes

value: 25mM glucose at day 0, 5.5mM glucose at day 15


title: ADIPO [+MCF7] HG (3)


title: HSC5 cells, sgNeg, biol rep 3

value: WT


title: H3K9me3.24h.rep1-3

data_processing:
Index creation: mouse mm10 and drosophila dm6 assemblies were merged to create a hybrid genome, and a bowtie2 index for the hybrid genome was generated using bowtie2-build -f.
Alignment: FASTQs were aligned to the hybrid genome with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
Library repeat merge: reads from three sequencing runs of the same sample (technical repeats) were merged using samtools merge.
Replicate merge: bam files of the three biological replicates of each sample were merged using samtools merge.
Scalar calculation: the percentage of drosophila reads in each ChIP sample was used to calculate the scalars for library size adjustment. RPM was used for input samples.
Track creation: bigWig files were created using deeptools bamCompare (log2(ChIP/Input) and scaled based on the ratio of the spike-in reads).
Domain calling: merged BAM files were converted into bed files using bedtools bamtoBed and then processed with RSEG v0.4.8 rseg-diff -i 20 -v -mode 2 -d deadzones-k36-mm10.bed with deadzones downloaded from the RSEG website and lifted from mm9 to mm10 over using UCSC Genome Browser's liftOver tool.
Assembly: GRCm38 / mm10
Supplementary files format and content: BigWig files ending in *.merged.multimap.bw reflect the pool of three biological replicates with input subtraction and spike-in adjustment.
Supplementary files format and content: The table H3K9me3.DomainsByDecayRate.mm10.txt has a list of ~43k H3K9me3 domains identified at t=0hrs, with column 4 describing the decay kinetics (fast, intermediate, slow, residual).

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde at room temperature for 10 mins, and quenched with 0.125 mM Glycine at room temperature for 5 minutes. The cells were then washed 3 times with ice cold DPBS and incubated with seven ml swelling buffer (25mM HEPES-KCl, pH7.2, 1.5 mM MgCl2, 20mM KCl, 0.1% NP-40) per 15cm dish incubated for 10 minutes at 4 °C. The cells were scrapped off the plates, collected and pelleted in 15 ml falcon tubes and immediately snap frozen in the liquid nitrogen, and stored in -80 °C freezer. On the day of sonication, the crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then resuspended in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) for 10 minutes on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were then resuspended in lysis buffer 3 and sonicated with Covaris with (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 15 minutes. The sonicated chromatin was centrifuging at 20,000g for 20 minutes and the soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest of the chromatin was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation. For H3K9me3 and HP1β ChIP-seq, 20 μg of chromatin was combined with 1.5 μg of Drosophila spike-in chromatin and incubated with 10 μl of Protein A/G dynabeads pre-coated with 0.5 μg of H3K9me3 (abcam, ab8898) or 1ug of HP1β antibody (Cell Signaling Technology, 8676) and 0.5 μg of drosophila spike-in antibody on a rotating wheel at 4 °C overnight. The chromatin-antibody-dynabeads slurry was then washed 5 times with The RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted with elution buffer by incubating at 65 C for 20 minutes and de-crosslinked at 65 °C over night, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA was used for each library and amplified with 11 PCR cycles and the library DNA was purified with Ampure XP beads and the distribution of the DNA fragments of the libraries was analyzed using High Sensitivity DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

value: dTKO

value: ES cells

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

value: + auxin + dTAG13

value: Abcam ab8898


title: HEK293T transfected with dCasRx-RBM25 and nontargeting gRNA, replicate 2

value: dCasRx-RBM25 with nontargeting gRNA


title: HEK293T transfected with dCasRx-RBM25 and MAPT-targeting gRNA, replicate 2

value: dCasRx-RBM25 with MAPT-targeting gRNA


title: HSC5 cells, sgPRMT5#1, biol rep 1

value: Human skin squamous cell carcinoma

value: Cancer cell line

value: PRMT5 Knockout


title: HSC5 cells, sgNeg, biol rep 2

value: Neomycin


title: HEK293T transfected with dCasRx-RBM25 and CD46-targeting gRNA, replicate 1

value: Human embryonic kidney


title: MCF7 [+ADIPO] HG->LG (1)


title: MCF7 [+ADIPO] HG->LG (3)


title: HEK293T transfected with dCasRx-RBM25 and MAPT-targeting gRNA, replicate 1


title: HSC5 cells, sgNeg, biol rep 1


title: MCF7 [+ADIPO] HG (3)

value: 25mM glucose


title: ADIPO-HG->LG (3)


title: MNV_12hpi_mCD300lf-hCaco2, replicate 1, scRNAseq

city: Bethesda

first: Yuki

last: Matsushima

state: Maryland

address: Building 50, MSC 8026, 50 South Drive

department: LID/DIR/NIAID

institute: National Institutes of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Combined reference genomes of human (hg38), murine norovirus (GenBank No. NC_008311) and mCD300lf ORF (GenBank No. NM_001169153)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human Caco2 cells expressing mCD300lf

extract_protocol:
MNV was infected at MOI 5 titrated by RAW264.7 cells for 1 hour in a CO2 incubator at 37 C°. The UV-inactivated MNV was also inoculated on the cells for negative control on the infection. For mock controls, the MEM supplemented with GlutaMax and 20% FBS without the virus were added on the cells. The inoculums were removed from the infected cells and they were washed with PBS(-). The media were added on the infected cells and they were incubated with a CO2 incubator at 37 C° for 3 hour, 7 hours or 11 hours. The cells were detached by 0.25% Trypsin-EDTA and centrifugated with 250xg for 5 min. The cell pellets were resuspended with 1.5 mL of the media and the cells were passed through Flowmi cell strainers. The filtered cells were quantified by Acridine Orange/Propidium Iodide Stain and then the Luna fx7 cell counter. The cells were further washed with PBS(-) including 0.04% BSA for 2 times after centrifugation with 150xg for 3 min. The cell pellets were resuspended with 500uL of the PBS(-) including 0.04% BSA and quantified by the Luna fx7 cell counter again. The cells were diluted to 1,000 cells per microliter with the PBS(-) including 0.04% BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, mCD300lf-hCaco2 cells were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The polyA RNA from the cell lysate contained in single GEMs 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 appropriate 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: human Caco2 cells expressing mCD300lf

value: MNV infection


title: HEK293T transfected with dCasRx-RBM25 and nontargeting gRNA, replicate 1


title: ADIPO-HG->LG (1)

value: adipocytes

value: 25mM glucose at day 0, 5.5mM glucose at day 15


title: STAT3 CUTandRUN_ISX9_R4

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.12.1)
CUT&RUN sequences were aligned to the hg38 reference genome using Bowtie2 (v2.5.1). Peaks were called with MACS (v2.2.7.1).
Assembly: hg38
Supplementary files format and content: NarrowPeak(called peaks)
Library strategy: CUT&RUN

growth_protocol: HT29 cells were maintained in McCoy 5A media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&RUN was performed  using a commercial kit's protocol (EpiCypher CUTANA pAG-MNase for ChIC/CUT&RUN, 15-1116)
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) as per the manufacturer's protocol

value: Primary colorectal cancer cells

tag: antibody


title: HEK293T transfected with RBFOX1N-dCasRx-C and nontargeting gRNA, replicate 2

value: RBFOX1N-dCasRx-C with nontargeting gRNA


title: MCF7 HG->LG (1)


title: MNV_8hpi_mCD300lf-hCaco2, replicate 2, scRNAseq

description: 10x Genomics


title: MNV_8hpi_mCD300lf-hCaco2, replicate 1, scRNAseq

description: 10x Genomics


title: MNV_12hpi_mCD300lf-hCaco2, replicate 2, scRNAseq

description: 10x Genomics


title: MNV_4hpi_mCD300lf-hCaco2, replicate 2, scRNAseq

description: 10x Genomics


title: STAT3 CUTandRUN_ISX9_R3


title: ADIPO-HG (3)


title: MNV_4hpi_mCD300lf-hCaco2, replicate 1, scRNAseq

description: 10x Genomics


title: STAT3 CUTandRUN_ISX9_R2


title: UV_MNV_12hpi_mCD300lf-hCaco2, replicate 2, scRNAseq

description: 10x Genomics

value: UV_MNV infection


title: UV_MNV_12hpi_mCD300lf-hCaco2, replicate 1, scRNAseq

description: 10x Genomics


title: MCF7 HG->LG (3)


title: MCF7-HG (3)


title: STAT3 CUTandRUN_ISX9_R1


title: Mock_12hpi_mCD300lf-hCaco2, scRNAseq

description: 10x Genomics

value: Mock


title: IgG CUTandRUN_R2

value: IgG


title: ADIPO [+MCF7] HG->LG (2)


title: Mock_0hpi_mCD300lf-hCaco2, scRNAseq

description: 10x Genomics


title: IgG CUTandRUN_R1


title: cocul_e53_nas_E, replicate 2

city: Neuherberg

first: Sebastiano

last: Di Bucchianico

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

description:
cocul_e53_nas_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx

data_processing:
fastq files were generated by the usage bcl2fastq-v2.20.0.422 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the Homo sapians genome build GRCm38 using STAR (2.7.3a)
Reads were counted using Ensembl annotations (release 99), using HTSeq-counts (version 0.11.2).
Normalization and differential expression analysis were performed using DESeq2 (1.26.0)
Assembly: GRCm38
Supplementary files format and content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary files format and content: Excel file includes the normalized counts (DESeq Normalization)

growth_protocol: A549 and EA.hy926 cells were maintained in DMEM/F12 supplemented with 5 % fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5 % CO2 at 37 °C

extract_protocol:
RNA was harvested using RNA Plus mini plus (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
Inhouse polyA based RNA seq

treatment_protocol: A coculture model system (A549 cells at the apical side of the transwell and EA.hy926 cells at the basolateral side), which were grown at the air-liquid interphase in DMEM/F12 media supplemented with antiobiotics and 15 mM HEPES, were expsoed for 4 h to either fresh SPs (1mg/ml) or SOANAP-SP (4mg/ml naphtahlene mixed with 1 mg/ml SPs and athmopsherical aged) or SOAβPIN-SP (4mg/ml β-pinene mixed with 1 mg/ml SPs and athmopsherical aged). As a control the coculture model was exposed to clean air (CA).

value: somatic hybrid cell of a HUVE cell with an A549/8 cell

value: 4 h exposure to SPs


title: cocul_e53_CA_E, replicate 4

description:
cocul_e53_CA_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx

value: 4 h exposure to CA


title: cocul_e52_nas_E, replciate 1

description:
cocul_e52_nas_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: FLAG-CoREST2_CUTandRUN_Native(CoREST2 KD)

value: FLAG(control for native)


title: cocul_e46_NAP_E, replicate 3

description:
cocul_e46_NAP_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx

value: 4 h exposure to SOANAP-SP


title: FLAG-CoREST2_CUTandRUN_native

value: FLAG


title: MCF7 [+ADIPO] HG->LG (2)


title: MCF7 [+ADIPO] HG (2)


title: cocul_e49_NAP_E, replicate 4

description:
cocul_e49_NAP_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: FLAG-CoREST2_CUTandRUN_Fixed


title: SLC13A3 KO, replicate 2, scRNAseq

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

description:
10X Genomics
SLC13A3KO_WT_Seurat_Object.rds

data_processing:
BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files, and the Cell Ranger Pipeline (10X Genomics) was used to align reads and generate count matrices.
Assembly: mm10
Supplementary files format and content: SLC13A3KO_WT_Seurat_Object.rds

source_name: tumor B16F10

extract_protocol:
Samples were fixed and dissociated using the Miltenyi Octo MACS according to 10X Demonstrated Protocol #CG000553. Dissociated cells were counted on Luna Fx7 (Logos Biosystems).
Probes were hybridized, and samples were pooled and processed according to manufacturer instructions for 10X Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (PN 1000568). Final library quality was assessed using the Lab Chip GXII HT (PerkinElmer), and libraries were quantified by Qubit (Thermo Fisher).

value: tumor B16F10

tag: strain

value: SLC13A3 KO


title: FLAG-CoREST2_CUTandRUN_Fixed(CoREST2 KD)

value: FLAG(control for fixed)


title: cocul_e44_NAP_E, replicate 2

description:
cocul_e44_NAP_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: cocul_e42_NAP_E, replicate 1

description:
cocul_e42_NAP_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: ADIPO-HG (2)

value: 25mM glucose


title: SLC13A3 KO, replicate 1, scRNAseq


title: STAT3 CUTandRUN_DMSO_R3


title: Mock_8hpi_mCD300lf-hCaco2, scRNAseq

description: 10x Genomics

value: human Caco2 cells expressing mCD300lf


title: cocul_e56_nas_E, replciate 3

description:
cocul_e56_nas_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: ADIPO [+MCF7] HG (2)

value: adipocytes


title: cocul_e42_CA_E, replicate 3

description:
cocul_e42_CA_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: MCF7 HG->LG (2)

value: 25mM glucose at day 0, 5.5mM glucose at day 15


title: Mock_4hpi_mCD300lf-hCaco2, scRNAseq

description: 10x Genomics


title: MCF7-HG (1)


title: WT, replicate 2, scRNAseq

value: WT


title: STAT3 CUTandRUN_DMSO_R1

value: Primary colorectal cancer cells


title: WT, replicate 1, scRNAseq


title: cocul_e38_CA_E, replicate 2

description:
cocul_e38_CA_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: SLC13A3 KO, replicate 3, scRNAseq


title: ADIPO-HG->LG (2)


title: 73-U

city: Linköping

first: CecilIa

last: Gunnarsson

address: Linköping University Hospital

country: Sweden

institute: Linköping University Hospital

data_processing:
STAR (mapping)
nuDup (de-duplication algorithm for UMI provided by library manuyfacturer)
feautureCounts (counts)
DeSeq2 (statistics)
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: resected aortic coarctation

extract_protocol:
Samples were stored in DNA/RNA Shield (Zymo) , lysed using ZR BashingBead Lysis Tubes (Zymo) on a TissueLyser (Qiagen) set to 25Hz for 10 minutes and RNA was isolated using Quick-RNA Microprep kit (Zymo)
Ovation SoLo RNA-Seq System (Tecan)

value: resected aortic coarctation

tag: patient biobank_id

tag: patient sex

value: male

tag: patient age_(days)

tag: bav/tav

value: bav

tag: biopsy location

value: proximal

tag: biopsy group

value: proximal/distal

tag: age group


title: Sirt7-/-_Pax5K198R_2

city: Badalona

first: Alejandro

last: Vaquero

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

data_processing:
FastQ files were quality-checked using FastQC
Raw counts were obtained by performing Salmon "quant" pseudoalignment (mm10 reference mouse genome, with fragment-level GC bias correction (--gcBias), eight threads (-p 8) and selective alignment enabled (--validateMappings)
The quant.sf files were used to import transcript-level quantification data into Summarized Experiment using Tximeta
Counts were normalized by DESeq2's median of ratios methods
genome build/assembly: mm10
processed data files format and content: A .txt file containing the normalized counts for each sample

source_name: In vitro cultured primary bone marrow pro-B cells

growth_protocol: Pro-B cells were plated onto a layer of mitomycin C-inactivated OP9 feeder cells and grown on Opti-MEM supplemented with 10% heat-inactivated fetal bovine serum, 25 mM HEPES, 50 µg/mL Gentamicin and 50 µM β-mercaptoethanol in the presence of 10 ng/mL IL-7, 10 ng/mL SCF and 10 ng/mL FTL3-L

extract_protocol:
RNA was extracted from frozen cell pellets using the Maxwell RSC simplyRNA Tissue Kit
mRNA was enriched using oligo dT beads and fragmented. First strand cDNA was synthesized using random primers, and second strand cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of the 3' adenylated cDNA fragments. U-labeled second-strand template was digested with UDG and amplified by PCR. After QC, library was circularized and amplified to make DNA nanoball before sequencing.

treatment_protocol: Not appliable

tag: cell type


title: Sirt7-/-_Pax5K198R_1

value: In vitro cultured primary bone marrow pro-B cells

tag: genotype


title: cocul_e37_PIN_E, replicate 3

description:
cocul_e37_PIN_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx

tag: cell line

value: somatic hybrid cell of a HUVE cell with an A549/8 cell

tag: treatment

value: 4 h exposure to SOAβPIN-SP


title: CKO2-cKO.Input

city: Shanghai

first: Domgmin

last: Yin

state: Shanghai

address: No.3663, Zhongshan North Road

institute: Shanghai Key Laboratory of Brain Functional Genomics

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30 and FastQC. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes
Assembly: mm10
Supplementary files format and content: The excle contains the identified ac4C modification site information

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® ac4C RIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.

value: Hippocampus


title: CKO2-cKO.IP


title: 73-F

value: coarctation


title: cocul_e35_PIN_E, replicate 2

description:
cocul_e35_PIN_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: Sirt7-/-_Pax5Wt_1


title: WT, replicate 3, scRNAseq

value: tumor B16F10


title: CKO2-C.IP


title: Sirt7-/-_Pax5Wt_2


title: cocul_e34_PIN_E, replicate 1

description:
cocul_e34_PIN_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: Sirt7-/-_EV_2

value: EV


title: 73-D

value: ductus


title: STAT3 CUTandRUN_DMSO_R2


title: cocul_e24_CA_E, replicate 1

description:
cocul_e24_CA_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx

value: 4 h exposure to CA


title: cocul_e38_PIN_E, replicate 4

description:
cocul_e38_PIN_E
processed1_raw_counts_E.xlsx
processed2_normalized_counts_E.xlsx


title: CKO1-cKO.IP


title: 72-U


title: 72-N

value: distal


title: CKO2-C.Input


title: CKO1-cKO.Input


title: Sirt7-/-_EV_1


title: 72-F


title: cocul_e53_CA_A, replicate 4

description:
cocul_e53_CA_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: lung carcinoma epithelial cells


title: cocul_e49_NAP_A, replicate 4

description:
cocul_e49_NAP_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: 4 h exposure to SOANAP-SP


title: CKO1-C.IP


title: WT_EV_2

value: Wt


title: 73-N

value: resected aortic coarctation

value: male


title: cocul_e46_NAP_A, replicate 3

description:
cocul_e46_NAP_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: 71-U

value: female

value: tav

value: proximal


title: CKO1-C.Input


title: ChIP_Pax5_K198R_2

data_processing:
FastQ files were quality-checked using FastQC
FastQ files were aligned onto a reference mouse genome (mm10) using Bowtie2 to generate SAM files
SAM files were conerted to BAM files using SAMTools, skipping alignments with MAPQ smaller than 37
BAM files were sorted and filtered using Sambamba, eliminating unmapped and duplicated reads.
Index BAI files were generated using SAMTools "index"
BigWig files were created using deepTools "bamCoverage"
Peak calling was performed using MACS2
genome build/assembly: mm10
processed data files format and content: A ChIP-Seq .bigwig file for each sample
processed data files format and content: A .narrowPeak file for each sample containing the significant peaks for each ChIP sample

extract_protocol:
For anti-Pax5 ChIP-Seq, sheared DNA was washed after the ChIP, crosslink was reversed and DNA was purified using NucleoSpin Gel and PCR Clean-up columns.
IP-DNA and Input-DNA were 3' end repaired and adaptor-ligated before PCR amplification, purificaiton and sequencing.

value: In vitro cultured primary bone marrow pro-B cells


title: cocul_e44_NAP_A, replicate 2

description:
cocul_e44_NAP_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: cocul_e42_NAP_A, replicate 1

description:
cocul_e42_NAP_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: 70-N

value: bav

value: proximal/distal


title: ChIP_Pax5_K198R_1


title: cocul_e42_CA_A, replicate 3

description:
cocul_e42_CA_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: ChIP_Pax5_K198Q_1


title: cocul_e38_PIN_A, replicate 4

description:
cocul_e38_PIN_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: 4 h exposure to SOAβPIN-SP


title: 70-D


title: Hashtag sequencing library of 20200901

city: New York

first: Xueqian

last: Zhuang

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

description:
20200901_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version 5.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v 1.6.0) / AnnData (v. 0.7.5, Python) or Seurat (v 3.0.2, R) ecosystems.
Assembly: GRCm38/mm10
Supplementary files format and content: .txt matrix file

source_name: lung

growth_protocol: Cells were isolated from animals. No additional growth is involved.

extract_protocol:
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).

treatment_protocol: Aged (> 2 years old) and young (12-16 weeks old) Kras LSL-G12D/+; Trp53 fl/fl (KP) mouse models with or without reporter alleles were infected by adenoviral Cre recombinase and tumor cells at different tumor development were isolated for single-cell mRNA sequencing

value: lung

value: Primary lung AT2 cells

value: Normal cells


title: 70-F

value: coarctation


title: Hashtag sequencing library of 20200826

description:
20200826_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: Normal young and aged AT2, replicate 4

description:
20200901
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: ChIP_Pax5_Wt_2


title: 69-F


title: WT_EV_1

value: EV


title: ChIP_Pax5_K198Q_2


title: cocul_e38_CA_A, replicate 2

description:
cocul_e38_CA_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: lung carcinoma epithelial cells

value: 4 h exposure to CA


title: 68-U


title: Input_Pax5_K198R_2


title: Hashtag sequencing library of 2020-11-20_A_Y_LUAD

description:
2020-11-20_A_Y_LUAD_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary tumor cells

value: Tumor cells


title: Normal young and aged AT2, replicate 3

description:
20200826
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: cocul_e35_PIN_A, replicate 2

description:
cocul_e35_PIN_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: 68-N

value: resected aortic coarctation

value: male

value: distal


title: ChIP_Pax5_Wt_1


title: Input_Pax5_K198R_1


title: Lung tumor cells isolated from aged and young KP mice 17-18 weeks post tumor-initiation, replicate 2

description:
2020-11-20_A_Y_LUAD
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: Hashtag sequencing library of XZ-1601_20220302

description:
XZ-1601_20220302_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: 71-F

value: female

value: tav


title: cocul_e34_PIN_A, replicate 1

description:
cocul_e34_PIN_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: Lung tumor cells isolated from aged and young KP mice 8 weeks post tumor-initiation

description:
XZ-1601_20220302
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: cocul_e37_PIN_A, replicate 3

description:
cocul_e37_PIN_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: Input_Pax5_K198Q_2

value: In vitro cultured primary bone marrow pro-B cells


title: cocul_e24_CA_A, replicate 1

description:
cocul_e24_CA_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: 66-U

value: bav

value: proximal

value: proximal/distal


title: Hashtag sequencing library of XZ-1450_20211210

description:
XZ-1450_20211210_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: lung


title: Cocul_e56_nas_A, replicate 3

description:
Cocul_e56_nas_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: 4 h exposure to SPs


title: 68-F

value: coarctation


title: Input_Pax5_Wt_2


title: 66-F


title: Lung tumor cells isolated from aged and young KP mice 4 weeks post tumor-initiation

description:
XZ-1450_20211210
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: 66-N


title: Input_Pax5_K198Q_1


title: Cocul_e52_nas_A, replicate 1

description:
Cocul_e52_nas_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx


title: D283_ZIC1NF_WT2_IP

description:
none
D283_ZIC1NF_WT_G4M_merged_peaks_bam_counts.txt

data_processing:
ChIP-Seq - alignment with bowtie2, peakcalling with MACS2. Differential peak analysis with DESeq2
counts were collected by bedtools multicov
Assembly: hg19
Supplementary files format and content: Raw counts for each sample for each gene or ChIP-Seq peak
Supplementary files format and content: narrowpeak + broadpeak outputs from MACS2 for BT2019051

value: FLAG (Sigma, F1804)

value: Group 3 medulloblastoma

value: WT

value: WT ZIC1 overexpression


title: 66-D

value: ductus


title: 65-U

value: resected aortic coarctation


title: Pax5_K198R_2_RNA

description:
KO_R_REP2
Normalized_counts_RNA_seq_Pax5

data_processing:
RNA-Seq: FastQ files were quality-checked using FastQC
RNA-Seq: raw counts were obtained by performing Salmon "quant" pseudoalignment (mm10 reference mouse genome, with fragment-level GC bias correction (--gcBias), eight threads (-p 8) and selective alignment enabled (--validateMappings)
RNA-Seq: The quant.sf files were used to import transcript-level quantification data into Summarized Experiment using Tximeta
RNA-Seq: Counts were normalized by DESeq2's median of ratios methods
ChIP-Seq: FastQ files were quality-checked using FastQC
ChIP-Seq: FastQ files were aligned onto a reference mouse genome (mm10) using Bowtie2 to generate SAM files
ChIP-Seq: SAM files were conerted to BAM files using SAMTools, skipping alignments with MAPQ smaller than 37
ChIP-Seq: BAM files were sorted and filtered using Sambamba, eliminating unmapped and duplicated reads.
ChIP-Seq: Index BAI files were generated using SAMTools "index"
ChIP_Seq: BigWig files were created using deepTools "bamCoverage"
Assembly: mm10
Supplementary files format and content: A ChIP-Seq .bigwig file for each sample
Supplementary files format and content: Two RNA-Seq DESeq2-normalized count files (.txt), one per experiment, containing the normalized counts for each RNA sample

growth_protocol: Pro-B cells were plated onto a layer of mitomycin C-inactivated OP9 feeder cells and grown on Opti-MEM supplemented with 10% heat-inactivated fetal bovine serum,  25 mM HEPES, 50 µg/mL Gentamicin and 50 µM β-mercaptoethanol in the presence of 10 ng/mL IL-7, 10 ng/mL SCF and 10 ng/mL FTL3-L

extract_protocol:
RNA was extracted from frozen cell pellets using the Maxwell RSC simplyRNA Tissue Kit; For anti-Pax5 ChIP-Seq, sheared DNA was washed after the ChIP, crosslink was reversed and DNA was purified using NucleoSpin Gel and PCR Clean-up columns.
For RNA-Seq, mRNA was enriched using oligo dT beads and fragmented. First strand cDNA was synthesized using random primers, and second strand cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of the 3' adenylated cDNA fragments. U-labeled second-strand template was digested with UDG and amplified by PCR. After QC, library was circularized and amplified to make DNA nanoball before sequencing. For ChIP-Seq, IP-DNA and Input-DNA were 3' end repaired and adaptor-ligated before PCR amplification, purificaiton and sequencing.


title: Hashtag sequencing library of XZ-1344_20211018

description:
XZ-1344_20211018_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary tumor cells

value: Tumor cells


title: Pax5_K198R_1_RNA

description:
KO_R_REP1
Normalized_counts_RNA_seq_Pax5


title: Input_Pax5_Wt_1


title: D283_ZIC1NF_WT1_IP


title: Lung tumor cells isolated from aged and young KP mice 12 weeks post tumor-initiation, replicate 1

description:
XZ-1344_20211018
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: Pax5_K198Q_2_RNA

description:
KO_Q_REP2
Normalized_counts_RNA_seq_Pax5


title: D283_ZIC1NF_301_IP

value: Group 4 medullo mutant ZIC1 overexpression


title: 65-F

value: female

value: tav


title: Hashtag sequencing library of 071320_A_YLUAD

description:
071320_A_YLUAD_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: Lung tumor cells isolated from aged and young KP mice 19-20 weeks post tumor-initiation, replicate 2

description:
071320_A_YLUAD
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: Cocul_e53_nas_A, replicate 2

description:
Cocul_e53_nas_A
processed1_raw_counts_A.xlsx
processed2_normalized_counts_A.xlsx

value: lung carcinoma epithelial cells


title: Hashtag sequencing library of XZ-1344_20211019

description:
XZ-1345_20211019_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: 59-N

value: bav


title: D425_WT2_ZIC1_mut_constructs_RNA

description: D283_D425_ZIC1_mutant_constructs_RNA-Seq_htseq_counts.txt

data_processing:
RNA-Seq - alignment with STAR, differential expression analysis with DESeq2
Counts were collected with htseq for RNA-Seq
Assembly: hg19 for human, mm10 for mouse
Supplementary files format and content: Raw counts for each sample for each gene

extract_protocol:
Rneasy purification kit for extraction of RNA.
NEB Ultra DNA library prep kit for ChIP-Seq (NEB7645), NEB Ultra II Directional mRNA kit for RNA-Seq

value: empty vector overexpression


title: Lung tumor cells isolated from aged and young KP mice 12 weeks post tumor-initiation, replicate 2

description:
XZ-1345_20211019
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: lung


title: Pax5_Wt_2_RNA

description:
KO_P_REP2
Normalized_counts_RNA_seq_Pax5

value: In vitro cultured primary bone marrow pro-B cells


title: 59-F

value: coarctation


title: Hashtag sequencing library of 071020_A_YLUAD

description:
071020_A_YLUAD_HTO
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: D425_WT1_ZIC1_mut_constructs_RNA


title: Pax5_EV_2_RNA

description:
KO_REP2
Normalized_counts_RNA_seq_Pax5

value: EV


title: 57-N

value: proximal/distal


title: Lung tumor cells isolated from aged and young KP mice 19-20 weeks post tumor-initiation, replicate 1

description:
071020_A_YLUAD
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: 65-N

value: distal


title: D425_S403F_ZIC1_mut_constructs_RNA

value: Group 3 medulloblastoma

value: WT

value: SHH medullo mutant ZIC1 overexpression


title: Normal young AT2 cells, replicate 2

description:
Sample6_Y07_YoungHealthy
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary lung AT2 cells

value: Normal cells


title: Lung tumor cells isolated from aged KP mice 17-18 weeks post tumor-initiation, replicate 1

description:
Sample5_SM8822_AgedTumor
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary tumor cells

value: Tumor cells


title: D425_S399F_ZIC1_mut_constructs_RNA


title: D283_ZIC1NF_294_IP

description:
none
D283_ZIC1NF_WT_G4M_merged_peaks_bam_counts.txt

extract_protocol:
ChIP-Seq libraries were generated with home made reagents
NEB Ultra DNA library prep kit was used for ChIP-Seq (NEB7645) library prep

value: FLAG (Sigma, F1804)

value: Group 4 medullo mutant ZIC1 overexpression


title: 65-D

value: resected aortic coarctation

value: female

value: tav

value: ductus


title: D425_RNA_ZIC1_4_3

description: D425_BFP_vs_ZIC1_4_RNA_Seq_htseq_counts.txt

value: GFP-Luc-tagged

value: WT ZIC1 and ZIC4 overexpression


title: Sirt7-/-_preB_2

description:
KO.8_PreB
Normalized_counts_RNA_seq_Sirt7

source_name: Sorted bone marrow pre-B cells

value: Sorted bone marrow pre-B cells


title: 53-N

value: proximal/distal


title: Pax5_K198Q_1_RNA

description:
KO_Q_REP1
Normalized_counts_RNA_seq_Pax5

value: In vitro cultured primary bone marrow pro-B cells


title: Normal aged AT2 cell, replicate 2

description:
Sample4_KW1537_AgedHealthy
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: lung


title: Sirt7-/-_proB_2

description:
KO.8_ProB
Normalized_counts_RNA_seq_Sirt7


title: 53-F

value: coarctation


title: Pax5_Wt_1_RNA

description:
KO_P_REP1
Normalized_counts_RNA_seq_Pax5


title: D425_RNA_ZIC1_4_2

value: Group 3 medulloblastoma


title: Normal aged AT2 cell, replicate 1

description:
Sample3_KW1536_AgedHealthy
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary lung AT2 cells

value: Normal cells


title: Wt_preB_2

description:
WT.18_PreB
Normalized_counts_RNA_seq_Sirt7

value: Wt


title: 52-N

value: male

value: bav


title: D425_RNA_ZIC1_4_1


title: Wt_proB_2

description:
WT.18_ProB
Normalized_counts_RNA_seq_Sirt7


title: Normal young AT2 cells, replicate 1

description:
Sample2_GH2333_YoungHealthy
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5


title: 57-F

value: resected aortic coarctation


title: 52-F


title: Pax5_EV_1_RNA

description:
KO_REP1
Normalized_counts_RNA_seq_Pax5

value: EV


title: Lung tumor cells isolated from young KP mice 17-18 weeks post tumor-initiation, replicate 1

description:
Sample1_GH1529_YoungTumor
202111251525_LUAD_aging_raw.h5
202111251525_X_LUAD_aging_pp.h5
202111251525_Xs_LUAD_aging_KP_tumor_subsampled.h5
202111251525_Xs_LUAD_aging_all.h5

value: Primary tumor cells

value: Tumor cells


title: Sirt7-/-_proB_1

description:
KO.11_ProB
Normalized_counts_RNA_seq_Sirt7

source_name: Sorted bone marrow pro-B cells

value: Sorted bone marrow pro-B cells


title: Sirt7-/-_preB_1

description:
KO.11_PreB
Normalized_counts_RNA_seq_Sirt7


title: D425_RNA_BFP1

value: GFP-Luc-tagged

value: empty vector overexpression


title: 47-F


title: D425_RNA_BFP2


title: 42-N

value: female

value: tav

value: proximal/distal


title: D425_R294C_ZIC1_mut_constructs_RNA

description: D283_D425_ZIC1_mutant_constructs_RNA-Seq_htseq_counts.txt

value: WT

value: Group 4 medullo mutant ZIC1 overexpression


title: D425_P301S_ZIC1_mut_constructs_RNA

value: Group 3 medulloblastoma


title: Wt_preB_1

description:
WT.10_PreB
Normalized_counts_RNA_seq_Sirt7


title: WT & Adgrg6 mutant

city: Los Angeles

first: Zhaoyang

last: Liu

state: California

address: 2250 Alcazar Street, CSA 103

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description: FFPE Spatial Transcriptomic sequencing

data_processing:
Raw sequencing data were processed uwing the 10x Genomic Space Ranger pipeline to generate FASTQ files
Sequencing were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Note that the locations WT and Adgrg6 mutant tissue sections in the Spatial Transcriptomics chamber (10X visium) are indicated in the "WT_and_Adgrg6_tissue_spatial_location.png"
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiduvials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spot
Supplementary files format and content: tissue_hires_image.png: high resolution image
Supplementary files format and content: tissue_lowres_image.png: low resolution image
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: WT_and_Adgrg6_tissue_spatial_location.png: HE image indicating WT and Adgrg6 mutant tissue sections in the Spatial Transcriptomics chamber (10X visium)
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Library strategy: Spatial Transcriptomics

source_name: hindlimb

extract_protocol:
Hindlimbs of P20 Col2Cre; Adgrg6f/f mutants and Cre (-) littermate (wild-type) controls were harvested and immediately fixed in 10% neutral-buffered formalin at 4°C for 16 hours with gentle rocking. Samples were thoroughly washed with Milli-Q water (10min x 3 times and 5min x 3 times) at 4°C, and decalcified with Formic Acid Bone Decalcifier (Immunocal, StatLab UN3412) for 16 hours at 4°C with gentle rocking. After decalcification, samples were thoroughly washed with Milli-Q water (10min x 3 times and 5min x 3 times) at 4°C and stored in fresh-made 70% EtOH at 4°C for less than 12 hours. Tissues were processed with a paraffin processor with the following protocol: 45 min x3 with a gradient of EtOH (70%, 80%, 95%); 1h x3 with 100% EtOH; 1h x3 with Xylene; 1h x3 with wax. Samples were immediately embedded after processing. For this project, one control and one mutant knee joint were embedded into a single paraffin block to reduce the batch-to-batch discrepancy. To ensure even chilling and to preserve RNA integrity, the paraffin block was stored in a sealed tissue container at 4°C until needed. Tissue quality checks and gene expression assays were carried out according to the manufacturer’s protocol. RNA integrity was checked with DV200 evaluation using the Agilent RNA 6000 Pico Kit. This protocol generated a DV200 score >75%. A 5-micrometer tissue section was placed onto the capture area of the Visium gene expression slide (6.5mm x 6.5mm).
Libries were prepared following by the instruction of Visium Spatial Gene Expression Slides & Reagent Kit (10X Genomics)

value: hindlimb

value: WT & mutant