title: iBAT, Adrb1KO, KO, cold 4 days, Linpos, rep 1

city: Detroit

first: Rayanne

middle: B

last: Burl

address: 42 W. Warren Ave

institute: Wayne State University

description:
iBAT_Adrb1KO_KO_COLD_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger (v3.0.1) was used to perform sample demultiplexing, alignment, filtering, and UMI counting.
Count files were processed using SoupX (v1.0.1), an R package for the estimation and removal of cell-free mRNA contamination in single-cell data. For SoupX library cleanup, Fabp4 and Car3 were used as the non-expressed genes, as we expect the largest contribution of contamination to come from damaged mature BAs that have been excluded from these libraries, and clusters=FALSE.
Assembly: mm10
Supplementary files format and content: Processed data is provided as the filtered gene matrix files output from SoupX.

source_name: Interscapular brown adipose tissue

growth_protocol: All mice were housed at 24 degrees Celsius (+/- 2 degrees Celsius) with a 12:12 ligh-dark cycle in an AALAC approved animal facility.

extract_protocol:
Interscapular brown adipose tissues (iBAT) were surgically removed and processed for stromal vascular cell (SVC) isolation. Tissues of 3-4 mice were pooled after digestion. iBAT pads were washed with PBS, minced, and digested with 2 mg/mL type 2 collagenase (Worthington Biochemical Co.) in Hanks’ balanced salt’s solution (HBSS; Sigma-Aldrich) containing 4 mM sodium bicarbonate, 10 mM HEPES (pH 7.4, Gibco; Sigma-Aldrich) and 0.5% fatty acid free bovine serum albumin (FF-BSA; Gemini Bioproducts, West Sacramento, CA) for 30 minutes at 37°C. Ethylenediaminetetraacetic acid (EDTA) was added to a final concentration of 10 mM and samples were incubated for an additional 5 minutes to promote complete dissociation of SVCs. Digested cell samples from the same treatment group were combined and filtered through 100 μm and 40 μm sterile cell strainers. The samples were washed with PBS buffer containing 1 mM EDTA, 2.5 mM HEPES, and 10% heat-inactivated fetal bovine serum (FBS, Atlanta Biologicals Inc) (FACS buffer) and centrifuged at 500 x g for 10 minutes at 4°C. After removing the supernatant, pelleted stromal vascular cells were incubated in red blood cell lysis buffer containing 14 mM sodium bicarbonate, 0.154 M ammonium chloride, and 0.1 mM EDTA for 5 minutes at room temperature, then passed through a 100 μm sterile cell strainer. Cells were collected by centrifugation at 500 x g for 10 minutes at 4°C. Cellular debris was removed by density gradient centrifugation using Debris Removal Solution (Miltenyi Biotec). Cells recovered were resuspended in PBS containing 0.5% FF-BSA. iBAT SVCs were separated into lineage-marker positive (Lin+) and lineage-marker negative (Lin-) cell fractions using magnetic bead cell separation (MACS). SVCs were labeled using the mouse Lineage Cell Depletion kit (Miltenyi Biotec) according to the manufacturer’s instructions. This kit contains anti-CD5, anti-CD11b, anti-CD45R (B220), anti-Gr-1 (Ly-6G/C), anti-7-4, and anti-Ter-119 antibodies. Labeled samples were passed onto MS columns (Miltneyi Biotec) on the OctoMACS separator (Miltenyi Biotec); the flow through was collected as the Lin- cell fraction and bound Lin+ cells were eluted from the column. Samples were centrifuged at 500 x g for 10 minutes at 4°C and pelleted cells were resuspended in PBS with 0.04% FF-BSA. Cells were counted and diluted to a concentration of 1,000 cells/uL.
Single-cell libraries for all samples were prepared using the 10X Genomics Chromium Single Cell 3’ Reagent Kit v2, apart from ADRB1 KO and WT room temperature libraries which were prepared with Reagent Kit v3. Following MACS, single-cell suspensions were loaded onto the Single Cell Chip A. An estimated 10,000 cells were loaded per lane for an expected recovery of ~6,000 cells per library. The assembled chip was placed on a 10X Genomics Chromium Controller Instrument (10X Genomics) to generate single-cell gel beads in emulsion (GEMs). Single-cell RNA-seq libraries were prepared according to the manufacturer’s instructions. Libraries were quantified using the Kappa PCR kit (Kappa Biosystems) and sequenced with the Illumina NextSeq500 using high output 75-cycle kits with the following read length configuration: v2 libraries 26 bp read1, 8 bp I7 index, and 58 bp read2, v3 libraries 28 bp read1, 8 bp I7 index, and 56 bp read2.

treatment_protocol: For cold exposure experiments, mice were housed in a rodent incubator (Powers Scientific, Inc.) set to 6 degrees Celsius for up to five days or maintained at colony room temperature as controls. In the incubators, mice were housed individually with no nesting materials in static cages. For continuous ADRB3 stimulation, mice were subcutaneously implanted with micro-osmotic pumps (ALZET) containing the ADRB3 agonist CL316,243 (Sigma-Aldrich) which infused the animals at a rate of 0.75 nmol/hour for four days.

value: Interscapular brown adipose tissue

value: Adrb1 fl/fl; Pdgfra-CreER +/-

value: Female

value: 8-14 weeks

value: Lineage marker positive (immune)

value: Cold, 4 days


title: SI_bulk_mixed

status: Public on Aug 10 2022

type: SRA

city: Shanghai

first: seqcore

last: sii

address: Southern Chongqing Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
bulk.taxa.tsv
TS2010CLZM

library_source: transcriptomic

data_processing:
SpaceRanger 1.0.0
blastn 2.10.1+
phyloseq 1.32.0
Seurat 4.0.1
Assembly: mm10-3.0.0
Supplementary files format and content: rds was created from Seurat object in R
Supplementary files format and content: tsv was generated from blast output
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: mouse gut metagenome

source_name: small intestine

extract_protocol:
10x Genomics, Visium Spatial, Rev B for ST and TRIzol Reagent (#15596026, InvitrogenTM) for total RNA isolation extraction
The spatial gene libraries were constructed using Visium Spatial Library Construction kit (10X Genomics,PN-3000394). The cDNA was break into fragments of about 200-300bp, add poly(A) tails and connected the P7 adapter, 3’ end sequencing was performed using Illumina Novaseq 6000 sequencer with a sequencing depth of at least 100,000 reads per spot with pair-end 150 bp (PE150) reading strategy.

tag: tissue

value: small intestine

tag: Sex

value: male

tag: age

value: 6 weeks

tag: strain


title: LI_bulk_mixed

description:
bulk.taxa.tsv
TS2010CLZM

source_name: large intestine

value: large intestine


title: SMNB19_SES_1

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description: SES-transduced SNB19; SES-V5 Cut-n-Tag

library_source: genomic

data_processing:
Library strategy: CUT&TAG
ChIP-Seq/ATAC-Seq/Cut-n-Tag: Trimming and QC by Trimmomatic. Genome mapping by Bowtie2. Peak calling by MACS3. Coverage analysis by DeepTools.
RNA-Seq: Trimming and QC by Trimmomatic. Genome mapping and gene quantification by STAR. Differential analysis by DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 normalized counts, MACS3 peaks

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: SNB19 (human glioblastoma cell lines) were cultured in plastic-adherence condition in DMEM medium (Dulbecco’s Modified Eagle’s Medium - high glucose, Sigma-Aldrich) containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 1% Pen/Strept (Sigma-Aldrich), 2mM Glutamine (Sigma-Aldrich), 1% non-essential amino acids (MEM NEAA, ThermoFisher Scientific), 1% sodium pyruvate solution (Sigma-Aldrich) and passaged twice a week using Trypsin-EDTA solution (Sigma-Aldrich). Cortical neurons were coltured Neurobasal medium (Gibco), 2 % B27 (Thermo-fisher), 0.02 % Pen-strep and glutamin, 1.6 Glucose.

extract_protocol:
For RNA-seq RNA was extracted using the TRI Reagent isolation system (Sigma-Aldrich) according to the manufacturer’s instructions.RNA libraries were generated starting from 1 mg of total RNA (deriving from U87, SNB19 and murine hippocampi) which quality was assessed by using a TapeStation instrument (Agilent). ATAC-seq was performed using 50000 cells for each experimental condition (SNB19 infected with SOX2V5 or SESV5), 2 technical replicates each. Briefly, cells were detached, counted, collected, and then washed by performing a centrifuge at 500 rcf for 5’ at 4° in PBS. Subsequently cells were gently lysed by suspending them in 50 ul of ATAC-RSB (Corces et al., 2017) supplemented with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin for 5’ on ice. After the lysis cells were washed using 1ml of ATAC-RSB with Tween-20, but no NP-40 or digitonin. Transposition was then performed using Tn5 trasposase and buffer from Illumina (cod. 20034197). for meDiP 1μg of purified genomic DNA (gDNA) was used with qiAMP DNA mini kit (Qiagen, cat. 51304). In brief, for methylated DNA immune precipitation and purification MagMeDIPseq kit was used (Diagenode, cod. C02010040). First, gDNA was sonicated to obtain a fragment size between 150- 300 bp, then, it was de-naturated to ssDNA and immune-precipitated using α-metyl-cytosine antibody provided by the kit. The next day, immunoprecipitated DNA and Input were purified and eluted. Chromatins were isolated from SNB19. Cells were plated in adherent condition using Matrigel coated 15mm plates at a density of 6x10^6 per plate. When the plates reached 90% of confluence, cells were fixed adding formaldehyde directly to the cell culture media to reach a final concentration of 1%, then were incubated for 10 min at RT. The reaction was quenched adding glycine to a final concentration of 125 mM and incubated 5 min at RT. Medium was then removed and cells were washed 3 times with cold, sterile PBS + protease inhibitors, then cells were gently scraped and collected for centrifugation at 4°C for 50 at 1200 rpm. ChIP experiments were performed as previously described (Sessa et al. 2019). Briefly, collected cell pellets were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1% SDS, 10 mM EDTA pH 8, 1 mM phenylmethylsulfonyl fluoride (PMSF, Sigma # P7626), protease inhibitor cocktail (Roche #04693159001) and chromatin was sonicated with a Branson D250 sonifier (4 cycles of 30 s, 20% amplitude), to reach an average fragment size of 0.1–0.5 kb. Following quantification, 100 mg of sonicated chromatin were used in each immunoprecipitation and incubated O/N at 4° C with 4 mg of V5 antibody (mouse, 1:5, ThermoFisher Scientific, R96025).
RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol. ChIP-seq libraries were produced using 5 ng of each immunoprecipitated and purified DNA. End  repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with 0.15  U/ml T4 PNK (NEB #M0201L), 0.04 U/ml T4 POL (NEB #M0203L) and 0.1 mM dNTPs (NEB  #N0446S). A-base addition was performed by an incubation with 0.25 U/ml of Klenow fragment  (NEB # M0212L) and 167 mM dATP (NEB N0440S) for 30 min at 30°C. Adaptor ligation was  achieved by using the Quick ligation kit (NEB #M2200L) and performing an incubation of 15 min at  25°C. DNA fragments were finally amplified for 14 cycles, by using the PfuUltra II Fusion HS DNA  Pol kit (Agilent #600674). DNA purification steps after each enzymatic reaction were performed  using Agencourt AMPure XP SPRI beads (Beckman #A63882). MeDIP immunoprecipitated DNA and Input were purified and eluted. Library preparation was performed using NEBNext Ultra II kit for Illumina (cod. E7645), following  manufacturer instruction. ATAC-seq DNA After transposition was purified and libraries were amplified for the required amount of cycles  as previously described (Buenrostro et al., 2013).

treatment_protocol: Cells were infected with 10ul of mock (GFP), SOX2-V5 or SES-V5 in 6 well plate. Next day media was changed.

tag: cell line

tag: cell type

value: glioblastoma cells

tag: treatment

value: SES-transduced SNB19


title: MCAO-1

city: Nanjing

first: Ye

last: Hong

address: No.68, Changle Road, Nanjing, Jiangsu Province, China

department: Department of Neurology

institute: Nanjing First Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the Rat reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build:   rn6
Supplementary_files_format_and_content: The "miRNA_expression.txt" contains the values calculated by DEseq2 against the Count value and the 'miRNA_differential_expression.txt' contains all values greater than 200 and fold change >2, and P<0.05 between MCAO group and MCAO + rTMS group after counting the count value according to DEseq2 algorithm.

organism: Rattus norvegicus

source_name: peri-infarct cortex tissue

extract_protocol:
Total RNA was isolated from  tissues using the Magzol Reagent (Magen, China)according to the manufacturer's protocol.
Briefly, total RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext Multiplex Small RNA Library Prep Set for Illumina (Illumina, USA)

value: Sprague-Dawley

value: The right middle cerebral artery (MCA) was occluded for 90 min,cortex tissues were obtained at 7 days post reperfusion.

value: brain; peri-infarct cortex


title: MSC-M-

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

data_processing:
raw fastq data were trimed by trim_galore(version 0.6.0).
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by TPM(Transcripts Per Million)
Assembly: mm10
Supplementary files format and content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

organism: Mus musculus

source_name: human mesenchymal stem cells

growth_protocol: The human umbilical cord-derived MSCs used in this project were isolated from Wharton’s Jelly, a gelatinous tissue around umbilical vessels. The human umbilical cord was obtained from the healthy cesarean section fetus. The MSCs samples were donated from The Fifth Affiliated Hospital of Guangzhou Medical University. MSCs were cul-tured in a medium with Dulbecco's modified Eagle's medium (DMEM)/F12 and 10% fe-tal bovine serum (FBS) in a 37 °C 5% CO2 incubator.

extract_protocol:
TRIzol was used to extract the total RNA. HiScript II Reverse Transcriptase (Vazyme biotech R222-01) was used to reverse-transcribe cDNA from 2 μg of total RNA.
The VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina® (NR611-01/02) was used to prepare sequencing libraries, and the libraries were sequenced on an Illumina Novaseq platform, and 150 bp paired-end reads were generated.

value: human mesenchymal stem cells


title: iBAT, Adrb1KO, KO, cold 4 days, Linneg, rep 1

country: USA

description:
iBAT_Adrb1KO_KO_COLD_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

molecule: polyA RNA

value: Lineage marker negative (non-immune)


title: SESMeDIPSeq2S15

description: SES-transduced SNB19; MeDIP-Seq

data_processing:
ChIP-Seq/ATAC-Seq/Cut-n-Tag: Trimming and QC by Trimmomatic. Genome mapping by Bowtie2. Peak calling by MACS3. Coverage analysis by DeepTools.
RNA-Seq: Trimming and QC by Trimmomatic. Genome mapping and gene quantification by STAR. Differential analysis by DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: DESeq2 normalized counts, MACS3 peaks


title: iBAT, Adrb1KO, KO, room temperature, Linneg, rep 1

description:
iBAT_Adrb1KO_KO_RT_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v3; sequencing data from multiple lanes was concatenated for GEO upload.

value: Interscapular brown adipose tissue

value: Room temperature


title: LI_bulk3

description:
bulk.taxa.tsv
TS2010CLZM


title: iBAT, Adrb1KO, KO, room temperature, Linpos, rep 1

description:
iBAT_Adrb1KO_KO_RT_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v3; sequencing data from multiple lanes was concatenated for GEO upload.

value: Adrb1 fl/fl; Pdgfra-CreER +/-

value: Female


title: SESMeDIPSeq1S14

description: SES-transduced SNB19; MeDIP-Seq


title: LI_bulk2

description:
bulk.taxa.tsv
TS2010CLZM


title: LI_bulk1

description:
bulk.taxa.tsv
TS2010CLZM


title: JM21 plasma_Control Taqman OA

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

data_processing: text files were downloaded from the QuantStudio 12K Flex and were imported in R as data tables. Expression matrices in qPCRset format were created for every dataset using the HTqPCR R package

label: FAM

extract_protocol: Total RNA was extracted from 200 μl of plasma using the automatic nucleic acid extractor Maxwell 48 (Promega, Madison, WI, USA)

tag: gender

value: Male

tag: msc status

tag: disease state

value: heathy


title: iBAT, Adrb1KO, WT, cold 4 days, Linneg, rep 1

description:
iBAT_Adrb1KO_WT_COLD_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Adrb1 fl/fl; Pdgfra-CreER -/-

value: 8-14 weeks

value: Cold, 4 days


title: SESH3K9me3ChIPSeq1S10

description: SES-transduced SNB19; H3K9me3 ChIP-Seq


title: JM20 plasma_Control Taqman OA


title: iBAT, Adrb1KO, WT, cold 4 days, Linpos, rep 1

description:
iBAT_Adrb1KO_WT_COLD_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Lineage marker positive (immune)


title: SESV5ChIPSeq2S6

description: SES-transduced SNB19; SES-V5 ChIP-Seq

value: glioblastoma cells


title: iBAT, Adrb1KO, WT, room temperature, Linneg, rep 1

description:
iBAT_Adrb1KO_WT_RT_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v3; sequencing data from multiple lanes was concatenated for GEO upload.


title: SI_bulk3

description:
bulk.taxa.tsv
TS2010CLZM

value: small intestine

value: male

value: 6 weeks


title: JM19 plasma_NSCLC Taqman OA

value: NSCLC


title: SESV5ChIPSeq1S5

description: SES-transduced SNB19; SES-V5 ChIP-Seq

value: SES-transduced SNB19


title: JM18 plasma_Control Taqman OA


title: SI_bulk2

description:
bulk.taxa.tsv
TS2010CLZM


title: iBAT, Adrb1KO, WT, room temperature, Linpos, rep 1

description:
iBAT_Adrb1KO_WT_RT_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v3; sequencing data from multiple lanes was concatenated for GEO upload.


title: MockMeDIPSeq2S13

description: Mock-transduced SNB19; MeDIP-Seq

value: Mock-transduced SNB19


title: MockMeDIPSeq1S12

description: Mock-transduced SNB19; MeDIP-Seq


title: iBAT, C57, CL 4 days, Linpos, rep 2

description:
iBAT_C57_CL_Linpos_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Interscapular brown adipose tissue

value: CL, 4 days


title: SI_bulk1

description:
bulk.taxa.tsv
TS2010CLZM


title: JM17 plasma_NSCLC Taqman OA


title: SESH3K9me3ChIPSeq2S11

description: SES-transduced SNB19; H3K9me3 ChIP-Seq


title: MockH3K9me3ChIPSeq2S9

description: Mock-transduced SNB19; H3K9me3 ChIP-Seq


title: JM15 plasma_NSCLC Taqman OA


title: iBAT, C57, cold 4 days, Linneg, rep 2

description:
iBAT_C57_COLD_Linneg_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Lineage marker negative (non-immune)


title: iBAT, C57, cold 4 days, Linpos, rep 2

description:
iBAT_C57_COLD_Linpos_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.


title: MockH3K9me3ChIPSeq1S8

description: Mock-transduced SNB19; H3K9me3 ChIP-Seq


title: InputSOX2V5ChIPSeqS1

description: SOX2-transduced SNB19; Input

value: SOX2-transduced SNB19


title: JM13 plasma_NSCLC Taqman OA

value: Male


title: JM12 plasma_Control Taqman OA

value: heathy


title: InputSESV5ChIPSeqS2

description: SES-transduced SNB19; Input


title: Mut_lib_plasmid

city: Mainz

first: Peter

last: Baumann

address: Ackermannweg 4

country: Germany

institute: Johannes Gutenberg University of Mainz

description: plamid DNA

data_processing:
Library strategy: PCR amplicon seq
Trimmed reads with Trimmomatic 0.32 with parameters set to "ILLUMINACLIP:/home/dut/bin/trinityrnaseq-2.0.6/trinity-plugins/Trimmomatic/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36'" see https://github.com/baumannlab/Sp_Pan_rap1_select_detect/blob/master/rap1_analysis_notebook.ipynb for more detail
reference sequence used in alignment. See https://github.com/baumannlab/Sp_Pan_rap1_select_detect/blob/master/rap1_analysis_notebook.ipynb for more detail
Aligned reads with bwa "bwa mem -M -t 16 ../data/fasta/lili_PCR_for_NGS.fasta PATH_TO_TRIMMED_FASTQ" (see for more detail https://github.com/baumannlab/Sp_Pan_rap1_select_detect/blob/master/rap1_analysis_notebook.ipynb)
Converted alignements to table of nucleotide abundance (pysamstats) using this command "pysamstats -f %s --type variation --pad -D 100000000 --fields=chrom,pos,ref,reads_all,matches,mismatches,deletions,insertions,A,C,T,G,N" see https://github.com/baumannlab/Sp_Pan_rap1_select_detect/blob/master/rap1_analysis_notebook.ipynb for mor detail
Genome_build: lili_PCR_for_NGS.fasta
Supplementary_files_format_and_content: tsv files for each sample, count data

organism: Escherichia coli

source_name: unicellular organism

growth_protocol: Cells were cultured in EMM at 32 °C till 0.5-1 x10^7 cells/ml, arrested in EMM-nitrogen for 48 hours at 25 °C and then returned to growth in EMM at 32 °C till 0.5-1 x10^7 cells/ml for each round

extract_protocol:
For plasmid library from E.coli, use QIAfilter Plasmid Giga Kit (Qiagen) following manufacturer's manual. For DNA extracted from S.pombe, cells (~1.5x109)  were harvested and washed once with ddH2O and once with Z buffer (50 mM sodium citrate, 50 mM sodium phosphate dibasic, 40 mM EDTA at pH 7.8) followed by incubation in 2 mL of Z buffer plus 0.5 mg/mL Zymolase T100 (US Biological) and 2 mM dithiothreitol for 1 h at 37°C. Sodium dodecyl sulfate was then added to a final concentration of 2% (w/v), and incubation was continued for 10 min at 65°C. The volume was then increased to 10 mL with 5× TE (50 mM Tris-HCl at pH 8.0, 5 mM EDTA), and proteinase K (Sigma-Aldrich) was added to 50 μg/mL. After 1 h of incubation at 50°C, samples were precipitated with 3 mL of 5 M potassium acetate for 30 min on ice, and the precipitate was removed by two rounds of centrifugation at 3200g for 10 min. The supernatant was then mixed with 1 vol of 100% isopropanol. After 20 min on ice, DNA was collected by centrifugation at 10,500g for 10 min and resuspended in 5× TE with 50 μg/mL RNase A. After 1 h of incubation at 37°C, DNA was extracted twice with phenol:chloroform:isoamyl alcohol (25:24:1, equilibrated with 5× TE) and once with chloroform:isoamyl alcohol (24:1, equilibrated with 5× TE) and then precipitated for 1 h at −20°C following the addition of 2.5 vol of ethanol. DNA was collected by centrifugation at 16,000g for 10 min followed by one wash with 70% ethanol. DNA was solubilized in 1× TE buffer.
To amplify the mutated region for Illumina sequencing, PCR reactions (50 µl) containing 1 x Q5 reaction buffer (NEB), 200 µM dNTPs, 0.5 µM of Bloli6118 (TTCTTGATTGTAAAGTAAATTAC) and Bloli6119 (TAGAGAAATAGAATTTGGGC) , 1 U of Q5 Hot Start High-Fidelity DNA Polymerase (NEB) and 100ng genomic DNA from R0-R5 or 93pg of the original plasmid library isolated from bacteria were incubated at 98°C for 1min, followed by 18 cycles of 98°C for 10s, 56°C for 30s and 72°C for 30s with a final extension at 72°C for 2min. PCR products were gel purified with MinElute gel purification kit (Qiagen) and Illumina libraries were prepared with different indexes using Nextera XT Library Prep Kit (Illumina, FC-131-1096).

tag: genotype

value: TOP10 + Rap1_440-693 mutanenesis library


title: iBAT, C57, room temperature, Linneg, rep 2

description:
iBAT_C57_RT_Linneg_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: 8-14 weeks

value: Room temperature


title: JM16 plasma_Control Taqman OA


title: iBAT, C57, room temperature, Linpos, rep 2

description:
iBAT_C57_RT_Linpos_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Lineage marker positive (immune)


title: iBAT, C57, CL 4 days, Linneg, rep 2

description:
iBAT_C57_CL_Linneg_2
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.


title: JM14 plasma_Control Taqman OA


title: InputmockH3K9me3ChIPSeqS7

description: Mock-transduced SNB19; Input

value: glioblastoma cells


title: iBAT, C57, CL 4 days, Linpos, rep 1

description:
iBAT_C57_CL_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.


title: JM11 plasma_NSCLC Taqman OA

value: Female


title: SOX3

description: SOX2-transduced SNB19; ATAC-Seq


title: iBAT, C57, CL 4 days, Linneg, rep 1

description:
iBAT_C57_CL_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.


title: CD45+ E7.5 Myometrium, scRNAseq, HTO Replicate 2

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description:
10x Genomics
Hashtag-derived oligonucleotide (HTO)

data_processing:
Demultiplexing with cellranger v6.1.0 mkfastq, bcl2fastq v2.20.0.422
Barcode and UMI deconvolution, mapping with cellranger v6.1.0 count
Assembly: mm10
Supplementary files format and content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

source_name: E7.5 Myometrium

extract_protocol:
C57BL6 (Hashtag A0306) and Il33cit/cit (IL-33-deficient) (Hashtag A0309) dams were mated with C57BL6 studs. At E7.5, the decidua and myometrium were mechanically isolated and minced with scissors. Tissues were digested in RPMI-1640 + 1 mg/mL Collagenase A + 0.1 mg/mL DNase I in a shaker incubator at 250 rpm at 37ºC for 2x12 min (decidua) or 2x15 min (myometrium). After each cycle, tissues were mechanically dissociated by passage through 18G or 20G needle. Single cells suspension was filtered through 100 um strainer and washed with cold RPMI + 3% FBS. Red blood cell lysis was performed. Cells were enriched using anti-Podoplanin-Biotin antibody and Dead Cell Removal (Annexin V) kit, then stained separately with TotalSeq-A cell hashing  (BioLegend) antibodies. Cells were washed and re-suspended in RPMI + 10% FBS and stained with a DAPI. Live CD45.2+ cells were isolated by fluorescence-activated cell sorting (FACS) using a FACSAria II cell sorter. Sorted cells from decidua or myometrium were then pooled and resuspended for scRNA-seq analysis.
Cell number and viability were determined by a Propidium Iodide based fluorescence assay using Moxi GO II System, Orflo Prod#MXG102 (ORFLO Technologies, LLC). Cells hash tagged with TotalSeq-A antibodies were pooled and the GEMs (Gel Beads-in-Emulsion) were generated using the Chromium Single Cell 3ʹ Reagent Kits Next Gen v3.1 (10X Genomics, Pleasanton, CA) and by following the manufacturer’s protocol. Briefly, hash-tagged live cells in single cell suspension with a >90% viability were mixed with RT reagents and loaded onto Chromium Chip G along with Gel beads and Partitioning oil in the recommended order and then the chip was processed through 10X Chromium Controller for the generation of GEMs, followed by RT, Cleanup, and cDNA amplification. After the cDNA amplification, size selection was used to separate the cDNA molecules for 3’ Gexp (Gene Expression) library and HTO (Hash Tag Oligonuclotide) library construction. 3’ Gene expression libraries were prepared by following the Chromium NextGEM Single-Cell 3’ Reagent Kits v3.1 User Guide. HTO libraries were prepared using the TotalSeq-A antibodies and Cell Hashing with 10X Single Cell 3’ Reagent kit v3.1 (Dual Index) Protocol (BioLegend, San Diego, CA). Library quantity and quality control were performed using Qubit Fluorometer (London, England) and TapeStation (Agilent Technologies, Santa Clara CA). HTO and 3’Gexp libraries were mixed at the ratio of 1:5 and sequenced on Illumina NovaSeq 6000 system (Illumina, San Diego, CA), with a configuration of 28/90 bp as recommended by 10X Genomics.  The Chromium Single Cell Software is used to analyze and visualize single cell 3’ RNASeq data produced by the 10X Chromium Platform.  The 10X chromium software package includes Cell Ranger Pipelines and Loupe Cell Browser.  Cell Ranger pipelines use raw 10X single cell sequencing data from an Illumina sequencer and perform demultiplexing, unique barcode processing, and single cell 3’ gene counting. Loupe Cell Browser uses data output from the Cell Ranger pipelines for fast analysis of significant genes, cell types, and substructure using single cell data.
scRNA-seq with HTOs

value: E7.5 Myometrium

value: 8-12 weeks old

value: CD45.2+ cells

tag: strain/genotype

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI:C57BL6--/TotalSeq-A0306 ; Il33Deficient--/TotalSeq-A0312


title: JM10 plasma_Control rep2c Taqman OA


title: CD45+ E7.5 Decidua, scRNAseq, HTO Replicate 2

source_name: E7.5 Decidua

value: E7.5 Decidua

value: Anti CD45 + Anti MHC classI:C57BL6--/TotalSeq-A0306 ; Il33Deficient--/TotalSeq-A0311


title: JM09 plasma_NSCLC rep2b Taqman OA

value: NSCLC


title: JM08 plasma_Control rep2a Taqman OA


title: SOX1

description: SOX2-transduced SNB19; ATAC-Seq

value: SOX2-transduced SNB19


title: iBAT, C57, cold 4 days, Linneg, rep 1

description:
iBAT_C57_COLD_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Interscapular brown adipose tissue

value: Male

value: Lineage marker negative (non-immune)

value: Cold, 4 days


title: uveal melanoma OM431 cells-NC

first: hui

last: pan

address: Zhizaoju Road No.639, Huangpu District

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

description:
OM431-NC.CEL(normalized)
Gene expression data from human uveal melanoma cell line OM431-NC

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Prime view array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: human uveal melanoma cell line, OM431-NC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells are cultured with DMEM with 10%FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The medium was discarded. Cells were rinsed with PBS and placed on ice in the Trizol solution (Invitrogen).

value: NC


title: uveal melanoma OCM1a cells-NC

description:
OCM1A-NC.CEL(normalized)
Gene expression data from human uveal melanoma cell line OCM1A-NC

source_name: human uveal melanoma cell line, OCM1A-NC


title: SES3

description: SES-transduced SNB19; ATAC-Seq

value: SES-transduced SNB19


title: uveal melanoma OM431 cells-shMAT1

description:
OM431-shMAT1.CEL(normalized)
Gene expression data from human uveal melanoma cell line OM431-shMAT1

source_name: human uveal melanoma cell line OM431 with MAT1 knockdown


title: uveal melanoma OCM1a cells-shMAT1

description:
OCM1A-shMAT1.CEL(normalized)
Gene expression data from human uveal melanoma cell line OCM1A-shMAT1

source_name: human uveal melanoma cell line OCM1A with MAT1 knockdown


title: JM07 plasma_NSCLC Taqman OA


title: CD45+ E7.5 Decidua, scRNAseq, HTO Replicate 1

value: Anti CD45 + Anti MHC classI:C57BL6--/TotalSeq-A0306 ; Il33Deficient--/TotalSeq-A0309


title: SES1

description: SES-transduced SNB19; ATAC-Seq

value: glioblastoma cells


title: CD45+ E7.5 Myometrium, scRNAseq, Replicate 2

description:
10x Genomics
poly A RNA

value: E7.5 Myometrium

value: Female

value: mRNA


title: iBAT, C57, room temperature, Linneg, rep 1

description:
iBAT_C57_RT_Linneg_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: 8-14 weeks

value: Room temperature


title: CD45+ E7.5 Decidua, scRNAseq, Replicate 2

description:
10x Genomics
poly A RNA

value: E7.5 Decidua

value: 8-12 weeks old

value: CD45.2+ cells


title: JM05 plasma_NSCLC rep1b Taqman OA

value: NSCLC


title: JM06 plasma_Control rep1c Taqman OA

value: heathy


title: CD45+ E7.5 Myometrium, scRNAseq, HTO Replicate 1

value: HTO

value: Anti CD45 + Anti MHC classI:C57BL6--/TotalSeq-A0306 ; Il33Deficient--/TotalSeq-A0310


title: iBAT, C57, room temperature, Linpos, rep 1

description:
iBAT_C57_RT_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: Interscapular brown adipose tissue

value: Male

value: Lineage marker positive (immune)


title: CD45+ E7.5 Myometrium, scRNAseq, Replicate 1

description:
10x Genomics
poly A RNA


title: Cancer_neuron_rep4

city: montreal

first: sebastien

last: Talbot

state: quebec

address: 2900 Boulevard Edouard-Montpetit,

department: pharmacology

country: Canada

institute: university of Montreal

description: peformed by FULGENT (temple, CA)

data_processing:
Illumina sequencing was performed at the Fulgent Genetics (Temple City, CA). Reads were aligned to the Mouse mm10 reference genome using STAR v2.732.
Aligned reads were assigned to genic regions using featureCounts function from subread v1.6.4 33. Gene expression levels were represented by TPM (Transcripts Per Kilobase Million).
Hierarchical clustering was computed using heatmap.2 function (ward.D2 method) from gplots R package. Differential gene expression analysis was carried out by DeSeq2 v1.28.134.
Supplementary files format and content: Gene expression levels were represented by TPM (Transcripts Per Kilobase Million).

source_name: cell

extract_protocol:
1×104 naive TRPV1Cre::QuASR2fl/wt DRG neurons were co-cultured with 1 × 105 B16F10-mCherry-OVA overnight in T-cell media (supplemented with 0.05 ng/μL NGF (Life Technologies, #13257-019), 0.002 ng/μL GDNF (PeproTech, #450-51-10). One day after, 4 ×105 stimulated OVA-specific CD8+ T-cells under Tc1 condition were added to the co-culture. After 48h, the cells were detached and TRPV1 neurons (CD45- eGFP+ mCherry-), B16F10-mCherry-OVA (CD45- eGFP- mCherry+), and OVA-specific CD8+ T-cells (eGFP- mCherry- CD45+ CD3+ CD8+) were FACS-purified using a FACSAria IIu cell sorter (Becton Dickinson).
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.

value: cell

value: DRG neurons co-culture with B16F10-mCherry-OVA


title: Cancer_neuron_rep2

description: peformed by FULGENT (temple, CA)


title: Cancer_neuron_rep3

description: peformed by FULGENT (temple, CA)


title: JM03 plasma_NSCLC Taqman OA


title: CD45+ E7.5 Decidua, scRNAseq, Replicate 1

description:
10x Genomics
poly A RNA


title: Cit+ E7.5 Myometrium, scRNAseq

description:
10x Genomics
poly A RNA

extract_protocol:
The decidua and myometrium were mechanically isolated and minced with scissors. Tissues were digested in RPMI-1640 + 1 mg/mL Collagenase A + 0.1 mg/mL DNase I in a shaker incubator at 250 rpm at 37ºC for 2x12 min (decidua) or 2x15 min (myometrium). After each cycle, tissues were mechanically dissociated by passage through 18G or 20G needle. Single cells suspension was filtered through 100 um strainer and washed with cold RPMI + 3% FBS. Red blood cell lysis was performed. Cells were washed and resuspended in RPMI + 10% FBS and stained with DAPI. Live Citrine+ were sorted using a FACSAria II cell sorter according to the presence or absence of Citrine signal using a C57BL6 mouse as negative control. Citrine+ cells were washed in RPMI + 10% FBS and resuspended in PBS.
Cell number and viability were determined by a Propidium Iodide based fluorescence assay using Moxi GO II System, Orflo Prod#MXG102 (ORFLO Technologies, LLC). Single-cell partitioning and single-cell RNA-Seq libraries were generated using the 10X Chromium Controller and the Chromium Single-Cell 3′ Reagent v3 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol. Briefly, live cells in single cell suspension with a >90% viability were mixed with RT reagents and loaded onto chromium Chip B along with Gel beads and Partitioning oil in the recommended order and then the chip was processed through 10X Chromium Controller for the generation of Gel Beads-in-Emulsion (GEMs) and then the chip was processed through 10X Chromium Controller for the generation of GEMs, followed by RT, Cleanup, and cDNA amplification. After the cDNA amplification, size selection was used to separate the cDNA molecules for 3’ Gexp (Gene Expression) library. 3’ Gene expression libraries were prepared by following the Chromium NextGEM Single-Cell 3’ Reagent Kits v3 user guide. Library quantity and quality control were performed using Qubit Fluorometer (London, England) and TapeStation (Agilent Technologies, Santa Clara CA). Libraries were sequenced on Illumina NovaSeq 6000 system (Illumina, San Diego, CA), with a configuration of 28/90 bp as recommended by 10X Genomics.

value: E7.5 Myometrium

value: Citrine+ cells


title: JM04 plasma_Control rep1a Taqman OA

value: Female


title: Cancer_neuron_rep1

description: peformed by FULGENT (temple, CA)


title: JM02 plasma_Control Taqman OA


title: iBAT, C57, cold 4 days, Linpos, rep 1

description:
iBAT_C57_COLD_Linpos_1
10X Genomics Single Cell Gene Expression Kit, v2; sequencing data from multiple lanes was concatenated for GEO upload.

value: 8-14 weeks

value: Cold, 4 days


title: neuron_rep4

description: peformed by FULGENT (temple, CA)

value: DRG neurons alone


title: iBAT, cold, 5 days, rep 4

description:
COLD_5days_4
GCold_5days_Rep4

data_processing:
Sequencing reads were aligned to the mouse genome with STAR-2.6.1d.
HTseq (v0.11.2) was used to determine the read counts per gene based on Ensembl gene annotations from mouse Gencode release 38 (GRCm38.98).
Assembly: GRCm38.98
Supplementary files format and content: Processed data is provided as a raw count .csv file where the columns are the individual libraries.

growth_protocol: C57BL/6J mice (stock no. 000664) were purchased from the Jackson Laboratory. All mice were housed at 24 degrees Celsius (+/- 2 degrees Celsius) with a 12:12 ligh-dark cycle in an AALAC approved animal facility. Mice were fed a standard chow diet ad libitum (LabDiet 5L0D, PMI Nutrition International).

extract_protocol:
Mice were euthanized by CO2 asphyxiation and cervical dislocation. The interscapular brown adipose tissue (iBAT) was surgically removed and placed into PBS on ice. iBAT was trimmed to remove interscapular white adipose tissue and flash frozen with liquid nitrogen. One iBAT pad was added to QIAzol reagent (QIAGEN) and RNA was isolated following the standard protocol for the Direct-zol RNA Miniprep kit (Zymo Research). RNA quality was assessed using the Agilent 2200 TapeStation (Agilent Technologies).
Transcriptome profiles were generated using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) with 250 ng of total RNA. Libraries were sequenced on an Illumina NovaSeq 6000 using a SP 100 cycle NovaSeq flow cell with read length configuration 76 bp with dual indexing: 12 bp for i7 and i5 indexing.

treatment_protocol: For cold exposure experiments, mice were housed in a rodent incubator (Powers Scientific, Inc.) set to 6 degrees Celsius for up to five days or maintain at colony room temperature as controls. In the incubators, mice were housed individually with no nesting materials in static cages.

value: 9-10 weeks

value: cold, 5 days


title: neuron_rep3

description: peformed by FULGENT (temple, CA)


title: JM00 plasma_Control Taqman OA


title: JM01 plasma_NSCLC Taqman OA

value: NSCLC


title: iBAT, cold, 5 days, rep 5

description:
COLD_5days_5
GCold_5days_Rep5


title: JL99 plasma_NSCLC Taqman OA


title: RNA-seq_Ctrl_shEV_rep2

city: Beijing

first: lumeng

last: Jia

address: Yiheyuan

institute: Peking University

data_processing:
The adapter trimed Hi-C paired-end reads were aligned to the mm9 reference genome using HiC-Pro (Servant et al., 2015) (version 2.11.1, parameters: default settings).
The adapter-trimmed paired-end HiChIP reads were aligned to mm9 with HiC-Pro (Servant et al., 2015) version 2.11.1. HiChIP peaks and loops were called using Hichipper (Lareau and Aryee, 2018) version 0.7.7 with parameters ‘--min-dist 1000 --max-dist 100000000 --read-length 150’. All replicates were merged together and all reads were used to call peaks. To detect the differences between two conditions, the total valid pairs of each condition were subset to the same. All loops with FDR less than 0.01 were defined as significant loops.
ChIP-seq reads were aligned onto mm9 reference genome using Bowtie2 (version 2.2.5) with default parameters (Langmead and Salzberg, 2012). Reads with a mapq score less than 30 were filtered out by using Samtools (Li et al., 2009) (version 1.9). Duplicates were discarded from mapped reads with Picard MarkDuplicates (version 1.118, https://github.com/broadinstitute/picard). Peaks were called with MACS2 (Zhang et al., 2008) (version 2.1.2, with parameters: --nomodel --extsize 147) using IgG as control
Paird-end RNA-seq reads were aligned using STAR (Dobin et al., 2013) (version 2.6.1b, default parameters), and mm9 was used as reference genome. Gene-specific read counts were calculated using FeatureCounts (Liao et al., 2014) (version 1.6.0, parameters: ‘-p’). Differentially expressed genes were detected with R package EdgeR (Robinson et al., 2010) (version 3.16.5). FDR < 0.05 and fold change > 1.5 or < -1.5 were used as thresholds.
Genome_build: mm9
Supplementary_files_format_and_content: .mango filters of all replicates merged HiChIP putative interactions were generated using HiChIpper; .narrowPeaks files of ChIP-seq were generated using MACS2; .txt files of RNA-seq were generated from edgeR, which include the fold-change and P-value of all genes with RYBP knock out.

source_name: mouse embryonic stem cells

growth_protocol: R1 mouse embryonic stem cells were cultured in gelatin-coated dish with ESC medium, which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Thermo Fisher), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore). Cells were maintained at 37°C and 5% CO2. Medium was changed daily when cells were not passaged.  Then cells were infected with shRNA lentivirus that target Rybp (shRybp) or empty vector (shEV) for 96h, 2 ug/mL puromycin were added into medium for drug selection.

extract_protocol:
Total  RNA was extracted using Trizol
RNA libraries were prepared using standard Illumina protocols

treatment_protocol: 2 ug/mL puromycin for 72h

value: embryonic stem cells

tag: genotype/variation

value: shEV

tag: antibody


title: iBAT, cold, 5 days, rep 3

description:
COLD_5days_3
GCold_5days_Rep3


title: neuron_rep2

description: peformed by FULGENT (temple, CA)


title: Cit+ E7.5 Decidua, scRNAseq

description:
10x Genomics
poly A RNA

value: E7.5 Decidua

value: 8-12 weeks old

value: mRNA


title: iBAT, cold, 5 days, rep 2

description:
COLD_5days_2
GCold_5days_Rep2

value: Interscapular brown adipose tissue

value: Male


title: RNA-seq_Ctrl_shEV_rep1


title: neuron_rep1

description: peformed by FULGENT (temple, CA)

value: cell


title: DRG_rep4

description: peformed by FULGENT (temple, CA)

value: TRPV1+ nociceptor neurons

value: alone


title: RNA-seq_shRybp_rep2

value: shRybp


title: iBAT, cold, 5 days, rep 1

description:
COLD_5days_1
GCold_5days_Rep1


title: RNA-seq_shRybp_rep1


title: DRG_rep3

description: peformed by FULGENT (temple, CA)


title: iBAT, cold, 4 days, rep 5

description:
COLD_4days_5
FCold_4days_Rep5

value: cold, 4 days


title: ChIP-seq_Input

growth_protocol: R1 mouse embryonic stem cells were cultured in gelatin-coated dish with ESC medium, which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Thermo Fisher), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore). Cells were maintained at 37°C and 5% CO2. Medium was changed daily when cells were not passaged.

extract_protocol:
After formaldehyde crosslinking and sonication, each sample was inculcated with 10 ug anti-RYBP antibody coated beads (Thermo Fisher). Afetr washing, DNA was purified DNA for library construction.
ChIP libraries were prepared using standard Illumina protocols;

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes

value: wildtype

value: none (input)


title: iBAT, cold, 4 days, rep 4

description:
COLD_4days_4
FCold_4days_Rep4

value: 9-10 weeks


title: iBAT, cold, 4 days, rep 3

description:
COLD_4days_3
FCold_4days_Rep3


title: ChIP-seq_RYBP

value: anti-RYBP


title: Hi-C_Rybp-/-_rep2

growth_protocol: Mouse embryonic stem cells (Rybpfl/fl; Cre-ER TM;  ) were cultured on inactivated MEF with ESC medium, which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Thermo Fisher),   0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore).   Cells were maintained at 37°C and 5% CO2. Medium was changed daily when cells were not passaged.  For RYBP conditional deletion, Rybpfl/f mESCs were cultured in ESC medium with 0.5 μM 4-hydroxytamoxifen (4-OHT, Sigma) for 48 h. Rybpfl/fl mESCs cultured in ESC medium with methanol act as control.

extract_protocol: Five million cells were crosslinked with 1% formaldehyde for 10 min, then quenched with 0.125M glycine for 5 minutes. DNA was digested with MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides. After reversal of crosslinks, ligated DNA was purified and sheared to a length of 300-500 bp. After purification, DNA was prepared for sequencing.

treatment_protocol: 0.5 μM 4-hydroxytamoxifen or methanol  for 48 h

value: Rybp-/-


title: DRG_rep2

description: peformed by FULGENT (temple, CA)


title: DRG_CD8--DRG_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with OT1 CD8 T cells


title: DRG_rep1

description: peformed by FULGENT (temple, CA)


title: Hi-C_Rybp-/-_rep1

value: embryonic stem cells


title: iBAT, cold, 4 days, rep 1

description:
COLD_4days_1
FCold_4days_Rep1


title: iBAT, cold, 4 days, rep 2

description:
COLD_4days_2
FCold_4days_Rep2


title: iBAT, cold, 3 days, rep 5

description:
COLD_3days_5
ECold_3days_Rep5

value: cold, 3 days


title: Hi-C_Rybp+/+_rep2


title: DRG_CD8--DRG_rep3

description: peformed by FULGENT (temple, CA)


title: DRG_CD8--DRG_rep1

description: peformed by FULGENT (temple, CA)


title: iBAT, cold, 3 days, rep 4

description:
COLD_3days_4
ECold_3days_Rep4


title: DRG_B16_CD8--DRG_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with B16f10-mcherry-ova and OT1 CD8 T cells


title: CTCF_HiChIP_Rybp-/-_rep2

data_processing:
Library strategy: HiChIP
The adapter trimed Hi-C paired-end reads were aligned to the mm9 reference genome using HiC-Pro (Servant et al., 2015) (version 2.11.1, parameters: default settings).
The adapter-trimmed paired-end HiChIP reads were aligned to mm9 with HiC-Pro (Servant et al., 2015) version 2.11.1. HiChIP peaks and loops were called using Hichipper (Lareau and Aryee, 2018) version 0.7.7 with parameters ‘--min-dist 1000 --max-dist 100000000 --read-length 150’. All replicates were merged together and all reads were used to call peaks. To detect the differences between two conditions, the total valid pairs of each condition were subset to the same. All loops with FDR less than 0.01 were defined as significant loops.
ChIP-seq reads were aligned onto mm9 reference genome using Bowtie2 (version 2.2.5) with default parameters (Langmead and Salzberg, 2012). Reads with a mapq score less than 30 were filtered out by using Samtools (Li et al., 2009) (version 1.9). Duplicates were discarded from mapped reads with Picard MarkDuplicates (version 1.118, https://github.com/broadinstitute/picard). Peaks were called with MACS2 (Zhang et al., 2008) (version 2.1.2, with parameters: --nomodel --extsize 147) using IgG as control
Paird-end RNA-seq reads were aligned using STAR (Dobin et al., 2013) (version 2.6.1b, default parameters), and mm9 was used as reference genome. Gene-specific read counts were calculated using FeatureCounts (Liao et al., 2014) (version 1.6.0, parameters: ‘-p’). Differentially expressed genes were detected with R package EdgeR (Robinson et al., 2010) (version 3.16.5). FDR < 0.05 and fold change > 1.5 or < -1.5 were used as thresholds.
Genome_build: mm9
Supplementary_files_format_and_content: .mango filters of all replicates merged HiChIP putative interactions were generated using HiChIpper; .narrowPeaks files of ChIP-seq were generated using MACS2; .txt files of RNA-seq were generated from edgeR, which include the fold-change and P-value of all genes with RYBP knock out.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. Crosslinked cells were digested with MobI restriction enzyme. Nucleotides containing biotin-dATP (Thermo Fisher) were used to fill in the restriction fragment overhangs. Then DNA was captured with protein A beads. After elution, DNA was pulled down with Streptavidin T1 beads.
Following the manufacturer's protocol, the purified DNA was added with index for sequencing using TruePrepTM Index Kit V2 for Illumina® (Vazyme)

value: anti-CTCF


title: DRG_B16_CD8--DRG_rep3

description: peformed by FULGENT (temple, CA)


title: CTCF_HiChIP_Rybp-/-_rep1


title: iBAT, cold, 3 days, rep 3

description:
COLD_3days_3
ECold_3days_Rep3

value: Interscapular brown adipose tissue


title: iBAT, cold, 3 days, rep 2

description:
COLD_3days_2
ECold_3days_Rep2

value: Male


title: DRG_B16_CD8--DRG_rep2

description: peformed by FULGENT (temple, CA)

value: cell


title: CTCF_HiChIP_Rybp+/+_rep1


title: iBAT, cold, 3 days, rep 1

description:
COLD_3days_1
ECold_3days_Rep1


title: CTCF_HiChIP_Rybp+/+_rep2


title: CD8_rep4

description: peformed by FULGENT (temple, CA)

value: OT1 CD8_cytotoxic


title: iBAT, cold, 2 days, rep 4

description:
COLD_2days_4
DCold_2days_Rep4

value: cold, 2 days


title: RYBP_HiChIP_rep2

growth_protocol: R1 mouse embryonic stem cells were cultured in gelatin-coated dish with ESC medium,   which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Thermo Fisher),   0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore).   Cells were maintained at 37°C and 5% CO2. Medium was changed daily when cells were not passaged.

extract_protocol:
Crosslinked cells were digested with MobI restriction enzyme. Nucleotides containing biotin-dATP (Thermo Fisher) were used to fill in the restriction fragment overhangs. After sonication, anti-RYBP (Abcam) antibody was incubated with the sample overnight. Then DNA was captured with protein A beads. After elution, DNA was pulled down with Streptavidin T1 beads.
Following the manufacturer's protocol, the purified DNA was added with index for sequencing using TruePrepTM Index Kit V2 for Illumina® (Vazyme)

value: ls


title: iBAT, cold, 2 days, rep 5

description:
COLD_2days_5
DCold_2days_Rep5


title: CD8_rep3

description: peformed by FULGENT (temple, CA)

value: alone


title: iBAT, cold, 2 days, rep 3

description:
COLD_2days_3
DCold_2days_Rep3


title: CD8_rep1

description: peformed by FULGENT (temple, CA)


title: Hi-C_Rybp+/+_rep1

value: wildtype


title: RNAseq_PEACH_4

city: Cerdanyola del Vallès

first: Carlos

last: de Tomás

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: CRAG

description:
RNA-sequencing
Raw_TE_genes_read_counts_matrix.txt, rlog_values_TE_genes_matrix.txt

data_processing:
For WGBS, removal of adapter and low-quality sequences.
Trimmed almond and peach trimmed reads were aligned to the corresponding parental genomes. Reads from the hybrid were aligned independently to peach and to almond genomes.
Cytosine methylation was analysed using Bismark v.0.19.1 and SeqMonk software package v.1.4.1.
For RNAseq, we used the methology described in Vendrell-Mir et al., 2020, with minor modifications.
Assembly: Prunus dulcis Texas Genome v2.0 and Prunus persica Genome v2.0.a1 (GDR database)
Supplementary files format and content: Matrix table with read counts for every gene and TE per sample
Supplementary files format and content: Matrix table with rlog normalized expression values for every gene and TE per sample
Supplementary files format and content: Matrix table with mean TE methylation values (%), almond and hybrid using almond reference
Supplementary files format and content: Matrix table with mean TE methylation values (%), peach and hybrid using peach reference

organism: Prunus persica

source_name: Fully expanded leaves

growth_protocol: Field conditions, normally watered trees.

extract_protocol:
Genomic DNA was isolated using a sorbitol pre-wash (Inglis et al., 2018) followed by an adapted CTAB method (Doyle and Doyle, 1990). Total RNA was extrated using the Maxwell RSC Plant RNA Kit and the Maxwell RSC instrument (Promega Corporation, Madison, WI, USA).
Genomic DNA library preparation was carried out (Alioto et al., 2020), including two bisulfite conversion rounds. RNA libraries were prepared using TruSeq Stranded mRNA protocol and were sequenced on Illumina platform NewxSeq 500 (2x150 bp, Paired-end).

tag: cultivar

value: Early Gold

tag: recollection time

value: End of september


title: RNAseq_PEACH_3


title: B16_CD8--CD8_rep4

description: peformed by FULGENT (temple, CA)

tag: tissue

value: co-culture with B16f10-mcherry-ova


title: iBAT, cold, 2 days, rep 2

description:
COLD_2days_2
DCold_2days_Rep2

tag: Sex

tag: age

value: 9-10 weeks


title: iBAT, cold, 2 days, rep 1

description:
COLD_2days_1
DCold_2days_Rep1

tag: strain


title: SK-MEL-28-XL413 treated replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

description:
XL413 treated, 1 micromolar, 24 hours
SK28-trt-3

data_processing:
Illumina Hi-Seq 2500 platform was used for RNA-sequencing
Sequenced reads were trimmed using Trimmomatic version 0.33 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15; and then mapped to human reference genome version hg38 using HISAT2 version 2.1.0 with parameters --mp 6,2 --rdg 5,3--rfg 5,3
Transcriptome assembly and gene expression quantification were performed using StringTie version 1.3.3b with default parameters to calculate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample for each gene

source_name: SK-MEL-28 cell line

growth_protocol: A375 and SK-MEL-28 cells were grown in DMEM medium and RPMI medium respectively with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: A375 and SK-MEL-28 cells were treated with  CDC7 inhibitor (10 micomolar) XL413 for 48 hours,  were harvested and were used for preparing the total RNA and to perfrom RNA Seq.

tag: cell line


title: B16_CD8--CD8_rep3

description: peformed by FULGENT (temple, CA)

tag: cell type

tag: treatment


title: iBAT, cold, 1 day, rep 5

description:
COLD_1day_5
CCold_1day_Rep5

value: cold, 1 day


title: SK-MEL-28-XL413 treated replicate 2

description:
XL413 treated, 1 micromolar, 24 hours
SK28-trt-2


title: iBAT, cold, 1 day, rep 4

description:
COLD_1day_4
CCold_1day_Rep4


title: DRG_B16_CD8--DRG_rep1

description: peformed by FULGENT (temple, CA)

value: TRPV1+ nociceptor neurons


title: WGBS_PEACH_3

description:
Whole Genome Bisulphite Sequencing
PEACH_vs_HYBRID_methylation.txt


title: B16_CD8--CD8_rep2

description: peformed by FULGENT (temple, CA)


title: iBAT, cold, 1 day, rep 3

description:
COLD_1day_3
CCold_1day_Rep3


title: WGBS_PEACH_2


title: B16_CD8--CD8_rep1

description: peformed by FULGENT (temple, CA)


title: CD8_rep2

description: peformed by FULGENT (temple, CA)


title: RYBP_HiChIP_rep1

value: embryonic stem cells

value: anti-RYBP


title: DRG_CD8--CD8_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with TRPV1+ nociceptor neurons


title: SK-MEL-28-DMSO treated replicate 3

description:
DMSO treated, 24 hours
SK28-con-3

value: DMSO


title: SK-MEL-28-XL413 treated replicate 1

description:
XL413 treated, 1 micromolar, 24 hours
SK28-trt-1


title: DRG_CD8--CD8_rep3

description: peformed by FULGENT (temple, CA)


title: iBAT, cold, 1 day, rep 1

description:
COLD_1day_1
CCold_1day_Rep1

value: Interscapular brown adipose tissue

value: Male


title: iBAT, cold, 6 hours, rep 5

description:
COLD_6hr_5
BCold_6hr_Rep5

value: cold, 6 hours


title: SK-MEL-28-DMSO treated replicate 1

description:
DMSO treated, 24 hours
SK28-con-1


title: RNAseq_PEACH_1


title: A375-XL413 treated replicate 3

description:
XL413 treated, 1 micromolar, 24 hours
A37-trt-3

source_name: A375 cell line


title: srGAP1_1

city: New York

first: Jose Javier

last: Bravo-Cordero

state: NY

address: 1468 Madison Avenue

institute: Icahn School of Medicine

data_processing:
Raw reads were filtered and mapped with STAR software by Novogene.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with a RNeasy Mini Kit (Qiagen).
Novogene conducted the library preparation using an NEBNext® UltraTM RNA Library Prep Kit.

value: Human Breast Cancer

tag: tumor stage

value: Primary tumor from human xenograft


title: srGAP1_2


title: Ctrl_3


title: srGAP1_3


title: iBAT, cold, 6 hours, rep 4

description:
COLD_6hr_4
BCold_6hr_Rep4

source_name: Interscapular brown adipose tissue


title: Ctrl_2


title: DRG_CD8--CD8_rep1

description: peformed by FULGENT (temple, CA)

value: cell

value: OT1 CD8_cytotoxic


title: iBAT, cold, 6 hours, rep 3

description:
COLD_6hr_3
BCold_6hr_Rep3


title: A375-XL413 treated replicate 2

description:
XL413 treated, 1 micromolar, 24 hours
A37-trt-2


title: DRG_B16_CD8--CD8_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with TRPV1+ nociceptor neurons and B16f10-mcherry-ova


title: A375-XL413 treated replicate 1

description:
XL413 treated, 1 micromolar, 24 hours
A37-trt-1


title: iBAT, cold, 6 hours, rep 2

description:
COLD_6hr_2
BCold_6hr_Rep2


title: Ctrl_1


title: SK-MEL-28-DMSO treated replicate 2

description:
DMSO treated, 24 hours
SK28-con-2


title: iBAT, cold, 1 day, rep 2

description:
COLD_1day_2
CCold_1day_Rep2


title: DRG_B16_CD8--CD8_rep3

description: peformed by FULGENT (temple, CA)


title: A375-DMSO treated replicate 3

description:
DMSO treated, 24 hours
A37-con-3


title: iBAT, cold, 6 hours, rep 1

description:
COLD_6hr_1
BCold_6hr_Rep1


title: exp3_pb1_3h_inf

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

data_processing:
Processing is automated using the RNAsik pipeline (https://doi.org/10.5281/zenodo.1403976). The workflow is as follows:
Reads are aligned using the STAR aligner (version 2.7.1b)
Aligned reads are sorted with Samtools (version 1.9) and marked duplicate with Picard (2.20.2)
Finally, reads assigned to features using featureCounts from SubRead (version 2.0.0)
Assembly: Ensembl GRCh38
Supplementary files format and content: Tab delimited files including features ID's and feature information

growth_protocol: hPSC-maropahges were seeded in 24-well plate and grown in basl differentiation medium supplemented with 5 ng/ml M-CSF

extract_protocol:
RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico assay (Agilent Technologies). Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol.  Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2.5 reagents (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hPSC-derived macrophages were inoculated with M. abscessus-GFP at the multiplicity of infections (MOI) of 5. samples were collected the specified time points. Uninfected control samples were harvested in concert with those representing the 3-hour infection time point.

value: Macrophage

value: M. abscessus

tag: time point


title: exp3_pb1_24h_inf


title: iBAT, room temperature, rep 5

description:
RT_5
ART_Rep5

value: 9-10 weeks

value: room temperature control


title: A375-DMSO treated replicate 2

description:
DMSO treated, 24 hours
A37-con-2


title: DRG_B16_CD8--CD8_rep2

description: peformed by FULGENT (temple, CA)


title: B16_rep2

description: peformed by FULGENT (temple, CA)

value: alone


title: exp3_pb1_3h_un

value: Uninfected


title: DRG_CD8--CD8_rep2

description: peformed by FULGENT (temple, CA)


title: iBAT, room temperature, rep 3

description:
RT_3
ART_Rep3


title: A375-DMSO treated replicate 1

description:
DMSO treated, 24 hours
A37-con-1


title: iBAT, room temperature, rep 4

description:
RT_4
ART_Rep4


title: B16_CD8--B16_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with OT1 CD8 T cells


title: exp2_pb1_2d_inf


title: iBAT, room temperature, rep 2

description:
RT_2
ART_Rep2


title: exp2_pb1_3h_inf


title: C_R5

description: genomic and plasmid DNA

organism: Schizosaccharomyces pombe

tag: genotype

value: rap1delta + Rap1_440-693 mutanenesis library

tag: replicate

value: C

value: Round 5


title: B16_CD8--B16_rep1

description: peformed by FULGENT (temple, CA)


title: DRG_B16--B16_rep4

description: peformed by FULGENT (temple, CA)

value: co-culture with TRPV1+ nociceptor neurons


title: iBAT, room temperature, rep 1

description:
RT_1
ART_Rep1

value: Interscapular brown adipose tissue

value: Male


title: C_R3

description: genomic and plasmid DNA

value: Round 3


title: PD-brian, scRNAseq

city: 上海市

first: Junjie

last: Ma

address: 上海市徐汇区岳阳路320号

institute: SINH

description: 10x Genomics

data_processing:
We used Cell Ranger 5.0.1 (10×Genomics) to process raw sequencing data, and then Seurat v4.0 was applied for downstream analysis. Before we started downstream analysis, we focused on four filtering metrics to guarantee the reliability of our data.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tsv.gz and mtx.gz

extract_protocol:
Eight-week-old male MPTP-induced Parkinson model mice (on a C57BL/6J background, MPTP-PD) and recommended control (C57BL/6J, CN) were purchased from the Shanghai Model Organisms Center, Inc. The animals were anesthetized with 500 mg/kg tribromoethanol (Sigma, Saint Louis, USA) and were killed by cervical dislocation. After the animals were sacrificed, brain tissues (cerebral cortex, hippocampus, striatum and cerebellum) were isolated, quickly frozen in liquid nitrogen and stored in liquid nitrogen until library construction. Nuclei were isolated by adapting the published 10X Genomics® protocol for ‘Isolation of Nuclei for Single Cell RNA Sequencing’. In brief, the tissue was lysed in a chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0,1% NP-40). Then, the suspension was filtered and nuclei were pelleted by centrifugation. Nuclei pellets were then washed in ‘nuclei wash and resuspension buffer’ (1x PBS, 1% BSA, 0.2 U/μL RNase inhibitor, 2 mM DTT), filtered and pelleted again. Cell count was then performed to calculate the concentration of nuclear suspension.
Sorted nuclei were processed using the 10x Chromium Next GEM Single Cell 3’ Kit v3.1 to generate the cDNA libraries. The quality of cDNA was assessed using the Agilent 2100 Bioanalyzer System. Sequencing was performed on Illumina NovaSeq 6000-S2.

value: nuclei

value: 8 weeks old


title: exp2_pb1_3h_un


title: C_R2

description: genomic and plasmid DNA

value: Round 2


title: C_R4

description: genomic and plasmid DNA

value: Round 4


title: DRG_B16--B16_rep3

description: peformed by FULGENT (temple, CA)

value: cell


title: Cnzu, scRNAseq

address: 上海市徐汇区岳阳路320号

description: 10x Genomics

source_name: cerebral cortex, hippocampus, striatum and cerebellum


title: DRG_B16--B16_rep1

description: peformed by FULGENT (temple, CA)


title: exp1_pb1_24h_inf

value: Macrophage

value: M. abscessus


title: B16_rep1

description: peformed by FULGENT (temple, CA)

value: alone


title: B_R5

description: genomic and plasmid DNA

value: B


title: exp1_pb1_3h_inf


title: DRG_B16_CD8--B16_rep4

description: peformed by FULGENT (temple, CA)


title: hippocampus, Radiation 3

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: hippocampus

value: male

tag: time

value: 3 months after IR

value: radiation


title: exp2_pb1_24h_inf


title: DRG_B16_CD8--B16_rep2

description: peformed by FULGENT (temple, CA)

value: co-culture with TRPV1+ nociceptor neurons and OT1 CD8 T cells


title: B_R4

description: genomic and plasmid DNA

extract_protocol:
For plasmid library from E.coli, use QIAfilter Plasmid Giga Kit (Qiagen) following manufacturer's manual. For DNA extracted from S.pombe, cells (~1.5x109)  were harvested and washed once with ddH2O and once with Z buffer (50 mM sodium citrate, 50 mM sodium phosphate dibasic, 40 mM EDTA at pH 7.8) followed by incubation in 2 mL of Z buffer plus 0.5 mg/mL Zymolase T100 (US Biological) and 2 mM dithiothreitol for 1 h at 37°C. Sodium dodecyl sulfate was then added to a final concentration of 2% (w/v), and incubation was continued for 10 min at 65°C. The volume was then increased to 10 mL with 5× TE (50 mM Tris-HCl at pH 8.0, 5 mM EDTA), and proteinase K (Sigma-Aldrich) was added to 50 μg/mL. After 1 h of incubation at 50°C, samples were precipitated with 3 mL of 5 M potassium acetate for 30 min on ice, and the precipitate was removed by two rounds of centrifugation at 3200g for 10 min. The supernatant was then mixed with 1 vol of 100% isopropanol. After 20 min on ice, DNA was collected by centrifugation at 10,500g for 10 min and resuspended in 5× TE with 50 μg/mL RNase A. After 1 h of incubation at 37°C, DNA was extracted twice with phenol:chloroform:isoamyl alcohol (25:24:1, equilibrated with 5× TE) and once with chloroform:isoamyl alcohol (24:1, equilibrated with 5× TE) and then precipitated for 1 h at −20°C following the addition of 2.5 vol of ethanol. DNA was collected by centrifugation at 16,000g for 10 min followed by one wash with 70% ethanol. DNA was solubilized in 1× TE buffer.
To amplify the mutated region for Illumina sequencing, PCR reactions (50 µl) containing 1 x Q5 reaction buffer (NEB), 200 µM dNTPs, 0.5 µM of Bloli6118 (TTCTTGATTGTAAAGTAAATTAC) and Bloli6119 (TAGAGAAATAGAATTTGGGC) , 1 U of Q5 Hot Start High-Fidelity DNA Polymerase (NEB) and 100ng genomic DNA from R0-R5 or 93pg of the original plasmid library isolated from bacteria were incubated at 98°C for 1min, followed by 18 cycles of 98°C for 10s, 56°C for 30s and 72°C for 30s with a final extension at 72°C for 2min. PCR products were gel purified with MinElute gel purification kit (Qiagen) and Illumina libraries were prepared with different indexes using Nextera XT Library Prep Kit (Illumina, FC-131-1096).

value: rap1delta + Rap1_440-693 mutanenesis library


title: hippocampus, Radiation 2


title: B_R3

description: genomic and plasmid DNA


title: exp1_pb1_3h_un

value: Uninfected


title: DRG_B16_CD8--B16_rep1

description: peformed by FULGENT (temple, CA)


title: hippocampus, Radiation 1


title: exp1_pb1_2d_inf


title: hippocampus, control 3

value: sham


title: B_R2

description: genomic and plasmid DNA


title: C_R1

description: genomic and plasmid DNA

value: C

value: Round 1


title: hippocampus, control 2


title: A_R5

description: genomic and plasmid DNA

value: A

value: Round 5


title: ifn270720 4d h1

data_processing:
Processing is automated using the RNAsik pipeline (url). The workflow is as follows:
Reads are aligned using the STAR aligner (version 2.7.1b)
Aligned reads are sorted with Samtools (version 1.9) and marked duplicate with Picard (2.20.2)
Finally, reads assigned to features using featureCounts from SubRead (version 2.0.0)
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Tab delimited files including features IDs and feature information

source_name: Macrophages

growth_protocol: hPSC-macropahges were seeded in 24-well plate and grown in basl differentiation medium supplemented with 25 ng/ml M-CSF

extract_protocol:
RNA was isolated using the ISOLATEII RNA micro-Kit (Bioline, BIO-52075).
Library generation was prepared using the Ribo-Zero GOLD kit (Illumina)
Library sequenced on by the Illumina Novaseq-6000 system for 20 million reads per sample.

value: Human pluripotent stem cell derived macrophages

value: 4 days

tag: infection

value: Mycobacterium abscessus


title: ifn270720 4d pb1


title: hippocampus, control 1


title: LN_CD8_Ramp1 KO..B16_rep2

description: peformed by FULGENT (temple, CA)

data_processing:
Nextseq500 (0.5 Flowcell High Output; 200 M de fragments; 75 cycles Single-End read) sequencing was performed onsite at the IRIC (Institute for Research in Immunology and Cancer) genomic center. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M23, based on Ensembl 98) using STAR v2.5.1b32.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in TPM (Transcripts Per Kilobase Million) values, for these stranded RNA libraries. DESeq2 version 1.18.134 was then used to normalize gene readcounts. Sample clustering based on normalized log readcounts produces the following hierarchy of samples.
Supplementary files format and content: Individual cell data are shown as a log10 of (transcript per million x 1000).

source_name: Tumor

extract_protocol:
Total CD8+ T-cells were isolated from the spleen of wild-type (CD45.1+) or RAMP1-/- (CD45.2+) mice, expanded and amplified in vitro using a mouse T-cell Activation/Expansion Kit (Miltenyi cat #130-093-627). CD8+ cells from RAMP1-/- and RAMP1wt were injected separately or 1:1 mix through tail vein of Rag1-/- mice. One week after, the mice were inoculated with B16F10-OVA-mCherry cancer cells (5 × 105), and tumor growth was measured daily using a handheld digital caliper. On day 14, tumor and draining lymph node were harvested, and RAMP1-/- (CD45.2+) and RAMP1wt (CD45.1+) CD8+ T-cells were FACS-purified using a FACSAria IIu cell sorter (Becton Dickinson).
For FACS-purified cells, RAMP1-/- and RAMP1wt CD8+ T-cells RNA-seq libraries were constructed using KAPA Hyperprep RNA (1x75bp) following the manufacturer’s instructions.

value: Tumor


title: ifn270720 2d rm

value: 2 days


title: B_R1

description: genomic and plasmid DNA

source_name: unicellular organism

value: B


title: A_R3

description: genomic and plasmid DNA

value: Round 3


title: ifn270720 2d pb1


title: LN_CD8_Ramp1 KO..B16_rep1

description: peformed by FULGENT (temple, CA)


title: A_R2

description: genomic and plasmid DNA

value: Round 2


title: ifn270720 2d h1


title: ifn270720 4d rm


title: LN_CD8_Ramp1 WT..B16_rep1

description: peformed by FULGENT (temple, CA)

value: RAMP1wt (CD45.1+)


title: cortex, Radiation 2

source_name: cortex

value: cortex

value: male

value: 3 months after IR

value: radiation


title: C4

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

institute: Centro de Investigación Médica Aplicada

data_processing:
RNA-seq reads are trimmed using Trim Galore v0.4.4 using default parameters to remove the Nextera adapter sequence.
Mapping is performed using STAR (2.6) against the mouse NCBIM37 genome, guided by gene models from Ensembl annotation release 68
Quantification and generation of gene expression matrices were performed with the function featureCounts, implemented in the R package Rsubread
Aligned fragments are imported into RStudio and before statistical analysis, the function filterbyExpr, implemented in the R package edgeR was used to determine genes with enough counts for further analyse
Differential gene expression analysis is performed using the DESeq2 algorithm within R and RStudio
Assembly: NCBIM37 genome, guided by gene models from Ensembl annotation release 68
Supplementary files format and content: Matrix tumor extracts.xlsx

source_name: Tumor fragment from 129SV mice bearing F9 teratocarcinoma tumors

extract_protocol:
Total RNA from tumors was isolated using the MagMAX mirVana total RNA isolation Kit (Applied Biosystems). Following mechanical homogenization with an Ultra-turrax (T10 basis Ultra-Turrax, IKA), RNA was extracted according to the manufacturer's instructions and  stored at -80C until processed. RNA concentration was quantified using a Qubit 3.0 Fluorometer and its quality was examined in Agilent's 4200 TapeStation System
150ng of quality total RNA were used for the transcriptome interrogation using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s instructions (Illumina). Briefly, cytoplasmic and mitochondrial rRNAs as well as beta globin transcripts were depleted from the samples. The remaining RNA was fragmented and reverse-transcribed. A second strand cDNA synthesis step removed the RNA template while incorporating dUTP in place of dTTP in order to preserve strand specificity. Next, double-stranded cDNA was A-tailed, then ligated to Illumina anchors bearing T-overhangs. PCR-amplification of the library allowed the barcoding of the samples with 10bp dual indexes and the completion of Illumina sequences for cluster generation. Libraries were quantified with Qubit dsDNA HS Assay Kit and their profile was examined using Agilent’s HS D1000 ScreenTape Assay. Sequencing was carried out in an Illumina NextSeq2000 using paired-end, dual-index sequencing (Rd1: 59 cycles; i7: 10 cycles; i5: 10 cycles Rd2:59 cycles) at a depth of 50 million reads per sample.

treatment_protocol: 129Sv mice bearing tumors induced by subcutaneous administration of F9 tumor cell line (2×106 cells  per mouse), were trerated when tumors were around 5 mm in diameter, with a mixture of 1×107 CD4+ and 2×106 CD8+  EDA CAR-T cells or left untreated . At day 14 of treatment, mice were sacrificed and tumor were used for RNA extraction.

tag: gender

value: Female

value: Two months


title: LN_CD8_Ramp1 WT..B16_rep2

description: peformed by FULGENT (temple, CA)


title: C3


title: cortex, Radiation 3


title: cortex, Radiation 1


title: A_R4

description: genomic and plasmid DNA

value: rap1delta + Rap1_440-693 mutanenesis library

value: A

value: Round 4


title: cortex, control 3

value: sham


title: ifn270720 3h rm

value: Human pluripotent stem cell derived macrophages

value: 3 Hours

value: Mycobacterium abscessus


title: A_R1

description: genomic and plasmid DNA

value: Round 1


title: ifn270720 3h pb1


title: cortex, control 2


title: ABC_R0

description: genomic and plasmid DNA

value: Round 0


title: C2


title: C1


title: ifn270720 3h h1


title: RNAseq_HYBRID_3

organism: Prunus persica x Prunus dulcis

value: End of september


title: cortex, control 1


title: ifn270720 un 3h rm

value: no


title: RNAseq_HYBRID_2


title: EDACAR3

source_name: Tumor fragment from 129SV mice bearing F9 teratocarcinoma tumors and treated with EDA-CART

value: EDA-CART


title: RNAseq_HYBRID_1


title: ifn270720 un 3h pb1


title: ifn270720 un 3h h1


title: Adipose-F11 [G-L147]

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) using kallisto v0.46
Gene counts were tabulated with tximport.
Assembly: GRCm38.p6
Supplementary files format and content: *.txt files are tab-delimited text containing gene counts

source_name: adipose

extract_protocol:
Total RNA from mouse heart and white adipose samples  was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
Libraries were prepared using the Nugen Universal Plus mRNA kit (Tecan Genomics Inc, Redwood City, CA)
RNA-Seq: single and paired-end mode to a length of 2x50 base pairs using the Illumina NovaSeq S2 platform

treatment_protocol: Mice were injected with AAV8-GFP or AAV8-F11, and fed a HFD + l-NAME diet for 7 weeks.  Tissues were collected at 15 weeks of age.

value: adipose

value: M


title: WGBS_HYBRID_3

description:
Whole Genome Bisulphite Sequencing
ALMOND_vs_HYBRID_methylation.txt, PEACH_vs_HYBRID_methylation.txt


title: EDACAR1


title: WGBS_HYBRID_2


title: Adipose-F11 [G-L146]


title: Adipose-F11 [G-L148]


title: RNAseq_ALMOND_3

organism: Prunus dulcis

value: Texas


title: NELL1 KO rep #4

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

data_processing:
Illumina read samples at 2 x 75 bases
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq
The data were aligned to the GRCh38 reference genome using the CLCGenomicsServer with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 9.1.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored as NULL) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: GRCh38 reference genome
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples, contains NULLs.

source_name: 143B osteosarcoma cell line

growth_protocol: The cells were cultured Dulbecco's Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
RNA extraction was performed using TRIzol reagent according to the manufacturer’s instructions
Illumina TruSeq Stranded Total RNA using manufacturer's default parameters

treatment_protocol: The transient plasmid DNA transfection was performed using TransIT®-LT1 Transfection Reagent according to manufacture's protocol

value: 143B osteosarcoma cell line

value: 143B cells transfected with NELL1KO plasmid for 48 h

value: NELL1 knockout


title: Adipose-F11 [G-L144]


title: SuHDam1

city: Urbana

first: Xin

last: Li

state: IL

address: 601 S. Goodwin Avenue, B107 CLSL

department: CDB

institute: University of Illinois Urbana-Champaign

data_processing:
Library strategy: Dam-ID-seq
DamID-seq data was analyzed using the damidseq-pipeline(Marshall, O. J. & Brand, A. H. Bioinformatics 31, 3371-3373, doi:10.1093/bioinformatics/btv386 (2015)). Duplicate samples of Ey-Dam and Su(H)-Dam samples and Dam-only controls were aligned to the Drosophila reference genome UCSC dm6.
The main utility of the damid-seq pipeline was used to align reads to the genome using bowtie2, bin and count reads, normalize counts and generate log-2 ratio bedgraph files for each DamID-sample and its corresponding Dam-only control. . The provided gatc.track file was used for running the script.
Next, the findpeaks utility was used with an F.D.R. <0.01 to identify peaks.
We then used the provided peaks2genes utility to assign peaks to genes.
To assess the reproducibility of our data we also ran the findpeaks script using F.D.R <0.1 to discover peaks with weaker statistical confidence and used this as input for the I.D.R. Python package (https://github.com/nboley/idr). 984 of 1810 (54.4.%) Ey-Dam and 972 of 1996 (48.7%) of Su(H)-Dam peaks passed an I.D.R. threshold of 0.05. Lists of genes bound by both replicates of Ey-Dam and by Su(H)-Dam were used in BioVenn89 to visualize the overlap between these two lists and estimate overlap percentage.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: Ey_1-vs-Dam.gatc-FDR0.01.peaks.gff: gff file showing locations of peaks with FDR<0.01 for EyDam1
Supplementary_files_format_and_content: Ey_2-vs-Dam.gatc-FDR0.01.peaks.gff: gff file showing locations of peaks with FDR<0.01 for EyDam2
Supplementary_files_format_and_content: Ey_overlap_all_replicate_peaks.gff: gff file showing overlaps of FDR<0.01 peaks for two EyDam replicates
Supplementary_files_format_and_content: Ey_and_SuH_overlap_allpeaks.gff: gff file showing overlaps of Ey binding peaks and Su(H) bidnings peaks
Supplementary_files_format_and_content: SuH_1-vs-Dam.gatc-FDR0.01.peaks.gff: gff file showing locations of peaks with FDR<0.01 for SuHDam1
Supplementary_files_format_and_content: SuH_2-vs-Dam.gatc-FDR0.01.peaks.gff: gff file showing locations of peaks with FDR<0.01 for SuHDam2
Supplementary_files_format_and_content: SuH_overlap_all_replicate_peaks.gff: gff file showing overlaps of FDR<0.01 peaks for two SuHDam replicates

organism: Drosophila melanogaster

source_name: medulla neuroblasts from larval brain

growth_protocol: Mating crosses were incubated at 25 °C. Eggs laid within an 8-hour window were then shifted to 18°C for 3 days until they hatched.

extract_protocol:
fly brains were dissected in 1X PBS and genomic DNA was isolated using QIAamp DNA Micro kit (Qiagen). Genomic DNA was then digested with DpnI and purified using spin column purification (Qiagen PCR-purification kit). To the DpnI digested DNA, DamID-PCR adaptors were ligated. Subsequently the adaptor ligated DNA fragments were digested with DpnII. The DpnII digested genomic DNA fragments were then amplified by PCR to enrich for bound GATC fragments.
To make sequencing libraries the PCR enriched genomic DNA sample was sonicated using a Bioruptor bath sonicator (Diagenode), purified using AMPure XP beads, end-repaired and 3’-adenylated. Illumina sequencing indexes were then ligated to these fragments. Index-labeled DNA fragments were then further enriched by PCR amplification, checked for quality and fragment size distribution on an Agilent Bioanalyzer and by qPCR.

treatment_protocol: The expressions of the Dam-fusion proteins were then induced in larval brains by shifting the larvae to 29°C for 72 hours. Climbing third instar larvae were then dissected. Only the optic lobes were used for further sample preparation. For each sample around 100 brains were dissected.

value: Drosophila medulla neuroblasts

value: Induce at 29 C for 72 hours


title: SuHDam2


title: NELL1 KO rep #3


title: EyDam2


title: NELL1 KO rep #2


title: RNAseq_ALMOND_2


title: Adipose-F11 [G-L143]


title: Dam2


title: EyDam1


title: RNAseq_ALMOND_1


title: EDACAR2

value: Female

value: Two months


title: Adipose-F11 [G-L142]


title: Vector control rep #4

value: 143B cells transfected with vector plasmid for 48 h

value: control


title: WGBS_ALMOND_3

description:
Whole Genome Bisulphite Sequencing
ALMOND_vs_HYBRID_methylation.txt


title: Adipose-F11 [G-L141]


title: Adipose-F11 [G-L145]


title: Dam1


title: Vector control rep #3


title: Adipose-GFP [G-L140]


title: kidney, s200813M4

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

data_processing:
To generate gene expression profiles, raw reads of samples were processed to generate internal pipeline, poly-A tails and adapters were trimmed (fastp V1), and read two was aligned to GRCh38 in conjunction with ensemble version 02 gene annotation (fastp 2.5.3a and featureCounts 1.6.2). Reads that possessed the same UMI, gene, and barcode were grouped together to ascertain the number of UMIs per gene per cell.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: kidney

extract_protocol:
Single-cell suspensions were obtained by being placed in a 15ml centrifuge tube with a maintained constant agitation at 37°C for 15min and digested in 2ml GEXSCOPE Tissue Dissociation Solution (Singleron Biotechnologies). Then samples were filtered via a 40-mm sterile cell strainer (Corning) which removed cell debris and additional impurities, before being centrifuged at 1000 rpm (300 x g for 5 minutes) at 4°C. In addition, the cell pellets were re-suspended with the use of a 1ml phosphate buffer saline (PBS HyClone). Next came cell suspension incubation via using a 2ml GEXSCOPE Red Blood Cell Lysis Buffer (Singleron Biotechnologies) at 25°C for a total of 10 minutes to extract and discard the red blood cells. After which, the cells were centrifuged at 1000 rpm (300 x g for 5 min) and re-suspended in cold PBS for downstream analyses. Ultimately, quantification of cell yields was subsequently conducted by using the TC20 automated cell counter (Bio-Rad), and live cells were determined by trypan blue staining (Gibco). Once cell viability exceeded 85%, sample processing was conducted.
RNA-seq libraries were prepared by drawing upon the Singleron GEXSCOPE Single Cell RNA-seq Library Kit (Singleron Biotechnologies) which is comprised of   mRNA (UMI and mRNA trapping, cell lysis, reverse transcription mRNA into cDNA and amplification, labeling cells (barcode) and fragment cDNA. Individual libraries were diluted to 4 nM and pooled for sequencing. Pools were sequenced on an Illumina HiSeq X with 150 bp paired end reads.

value: kidney

value: male

tag: disease state

value: Hepatitis B Virus-Associated Membranous Nephropathy


title: Vector control rep #1


title: Adipose-GFP [G-L138]


title: F4_2

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq software was used to calculated the expression abundance of each gene and normalized to the expected number of fragments per kilobase of transcript sequence per million fragments mapped (FPKM).
Genome_build: The clean reads was mapped to the genome dataset of Zanthoxylum armatum obtained in FigShare database (https://doi.org/10.6084/m9.figshare.14400884.v1) (Wang et al., 2021c).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Zanthoxylum armatum

source_name: Zanthoxylum armatum_tissue

extract_protocol:
Total RNA from four vital periods was separately extracted using FastPure Plant Total RNA Isolation Kit (Vazyme, Nanjing, China). The quantity and purity of total RNA were investigated by agarose gel electrophoresis and Nanodrop 2100 (Agilent, USA).
The twenty-four cDNA libraries, including M1_1, M1_2, M1_3, M2_1, M2_2, M2_3, M3_1, M3_2, M3_3, M4_1, M4_2, M4_3, F1_1, F1_2, F1_3, F2_1, F2_2, F2_3, F3_1, F3_2, F3_3, F4_1, F4_2 and F4_3, were constructed and sequenced using Illumina HiSeq™ 4000 platform at Novegene Bioinformatics Technology Co. Ltd (Beijing, China).

tag: plant

value: Zanthoxylum armatum DC.

value: flower

tag: floral sex differentiation stage


title: F4_3

tag: tissue


title: Huh7_siNC

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deepTools.

source_name: Huh 7

growth_protocol: Huh 7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:24ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).   CUT&Tag was performed according to the recommended protocol of NovoNGS® CUT&Tag High‐Sensitivity Kit (Novoprotein, Jiangsu, China).  RNA samples were extracted using TRIzol reagent (Invitrogen, CA, USA).   0-8).
For the ChIPseq, input amounts of DNA was converted into high quality libraries for next-generation sequencing on the Illumina platform using the NEBNext Ultra II DNA Library Prep Kit. Bead based size selection was performed for final library size selection to obtain ChIP-seq libraries containing fragments of 250 bp to 500 bp.   For the RNA-seq, the sequencing library was prepared using an Illumina mRNA-seq sample preparation kit and was then subjected to paired-end sequencing on the Illumina HiSeq platform.   CUT&Tag was performed according to the manufacturer's protocol (Novoprotein, Shanghai, China). The DNA was mixed with a universal i5 and a uniquely barcoded i7 primer. The sample was placed in a Thermocycler for PCR, and post-PCR clean-up was performed by bead based size selection and cleanup.
CUT&Tag, ChIP-Seq and RNA-seq

treatment_protocol: To set up stable cell lines overexpressed or knockdown ARID3A, Huh7 cells were seeded in 6well plates at the cell density of 50%-70%. Lentiviruses were constructed and collected to infect them. Infected cells were sorted with puromycin 24 hours later. The transfection assay was done using RNAiMAX (Invitrogen) with 5μM siKDM3A or siNC according to the manufacturer's protocol. The infection or transfection efficiency were confirmed by qPCR or WB assays. Extraction steps were started at least 48 hours after infection or transfection.

value: HCC

tag: chip antibody

value: Huh 7 cells were transfected with siNC using Lipofectamine RNAiMAX.


title: Huh7_siKDM3A

value: Huh 7 cells were transfected with siKDM3A7 using Lipofectamine RNAiMAX.


title: F4_1


title: Huh7_sphere

value: Huh 7 cells were cultured in ultra-low-attachment plates


title: Adipose-GFP [G-L137]

value: adipose

tag: Sex

value: M


title: NELL1 KO rep #1

value: 143B osteosarcoma cell line

value: 143B cells transfected with NELL1KO plasmid for 48 h

value: NELL1 knockout


title: Adipose-GFP [G-L136]

tag: strain


title: F3_3


title: F3_2


title: Huh7_shARID3A

value: Huh7 cells were infected with shARID3A lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: Adipose-GFP [G-L135]


title: Vector control rep #2

tag: cell line

value: 143B cells transfected with vector plasmid for 48 h


title: F3_1


title: Adipose-GFP [G-L134]


title: WGBS_ALMOND_2

source_name: Fully expanded leaves

tag: cultivar

value: Texas

tag: recollection time

value: End of september


title: Adipose-GFP [G-L139]


title: Huh7_shNC

tag: cell type

tag: treatment

value: Huh7 cells were infected with shNC lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: Formerly obese_Tumor_Mouse_150

city: Chapel Hill

first: Stephen

middle: D

last: Hursting

state: North Carolina

address: 215B MHRC

institute: University of North Carolina - Chapel Hill

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix).

scan_protocol: Scanning of the Clariom S peg plate was carried out using the GeneTitan MC Instrument (Affymetrix).

data_processing: Transcriptome analysis console software (version 4.0; ThermoFisher Scientific)

label: Biotin

source_name: Azoxymethane-induced colon tumor

label_protocol: Total RNA was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Clariom S peg plate. The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA) was used to prepare the samples, following manufacturer’s instructions.

extract_protocol: Total RNA was isolated from colon tumor tissue via TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) according to manufacturer’s instructions.

treatment_protocol: See methods of corresponding paper for details.

value: colon tumor

value: Male

value: FVB/N

tag: diet

value: High-fat to low-fat diet switch

tag: sulindac treatment

value: No sulindac


title: F2_3

value: Zanthoxylum armatum DC.

value: flower


title: Formerly obese_Tumor_Mouse_152


title: Formerly obese_Tumor_Mouse_146


title: Adipose-GFP [G-L133]

value: adipose


title: F2_1


title: Huh7_2D

value: HCC

value: untreated


title: Heart-F11 [L40]

source_name: heart

value: heart

value: M


title: Heart-F11 [L39]


title: Huh7_oeARID3A

value: Huh7 cells were infected with oeARID3A lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: Formerly obese_Tumor_Mouse_140


title: Huh7_shA2_H3K9me2

value: H3K9me2, Active motif, 39239

value: Huh7 cells were infected with shA2 lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: F1_3


title: Heart-F11 [L38]


title: Formerly obese_Tumor_Mouse_134


title: Huh7_shA2_Input


title: F1_2


title: Huh7_shA1_H3K9me2

value: Huh7 cells were infected with shA1 lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: F1_1


title: Heart-F11 [L36]


title: F2_2


title: DIO_Sulindac_Tumor_Mouse_129

value: High-fat diet (60% kcal fat)

value: Sulindac


title: Heart-F11 [L35]


title: Heart-F11 [L33]


title: M4_3


title: Heart-F11 [L31]


title: Huh7_shNC_Input

value: Huh7 cells were infected with shNC lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: DIO_Sulindac_Tumor_Mouse_X

value: colon tumor

value: Male

value: FVB/N


title: M4_2

value: Zanthoxylum armatum DC.


title: Huh7_shNC_H3K9me2


title: M4_1

value: flower


title: DIO_Sulindac_Tumor_Mouse_131


title: DIO_Sulindac_Tumor_Mouse_114


title: Heart-GFP [L10]


title: Huh7_CEP131

value: CEP131 (AZI1), Abcam， ab99379


title: Huh7_shA1_Input

value: HCC


title: M3_3


title: DIO_Sulindac_Tumor_Mouse_124


title: Huh7_Flag_ARID3A

value: Flag, sigma, F1804

value: Huh7 cells were infected with Flag_ARID3A lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: Heart-GFP [L8]

value: heart

value: M


title: M3_2


title: DIO_Sulindac_Tumor_Mouse_125