title: ACPFC10_2xLPS_2

description: 3' Quant seq with UMI tags

value: frontal cortex


title: AP_031_from_anterior_to_posterior

status: Public on Sep 25 2024

type: SRA

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

country: Japan

institute: Aoyama Gakuinn University

description:
DjTomoAP80-31
Lasy-Seq ver. 1.1
AP80.csv

library_source: transcriptomic

data_processing:
The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v2.20.0. The demultiplexing option (--barcode-mismatches) was set to default (value : 0).
Read 1 reads were processed with fastp (version 0.21.0) using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to a D. japonica reference sequences, using BWA mem (version 0.7.17-r1188) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0).
D. japonica reference transcriptome sequences deposited in http://www.planarian.jp/download.html

molecule: polyA RNA

organism: Dugesia japonica

source_name: whole

extract_protocol: Lasy-Seq version 1.1 (Kashima et al., Frontiers in bioinformatics, 2021)

treatment_protocol: Direct-TRI (Ujibe et al., bio-protocol, 2021)

tag: tissue

value: whole

tag: strain

value: AF


title: C2C12 cells, CBD 2

city: Liverpool

first: Daniel

middle: John

last: Owens

address: Byrom Street

department: Research Institute for Sport and Exercise Science

country: United Kingdom

institute: Liverpool John Moores University

data_processing:
Partek® Flow® Genomic Analysis Software
Pre-alignment QA/QC was performed on all reads prior to read trimming. STAR alignment 4.4.1d was used to align trimmed reads to the Mus musculus genome
Aligned reads were then quantified to the Ensembl transcriptome annotation model associated with Mus musculus mm39 genome.
Filtered raw counts were used for normalisation and differential analysis with DESeq2
Assembly: Mus musculus mm39 genome
Supplementary files format and content: Matrix table, raw counts (quantification)
Supplementary files format and content: Matrix table, normalized counts (normalization)

molecule: total RNA

organism: Mus musculus

growth_protocol: C2C12 murine myoblasts were cultured on gelatin (0.2%) coated 6-well culture plates in humidified 5% CO2 at 37°C in growth media comprising DMEM, 10% FBS, 10% NBCS and 1% of a pen-strep solution. Upon reaching ~80% confluence, monolayers were washed twice with pre-warmed PBS and switched to low serum differentiation media (DM), DMEM, 2% HS and 1% pen-strep. Every 48h thereafter, DM was removed from monolayers via aspiration and was replaced with fresh media. Cells were terminally differentiated by day-8 of low serum DM exposure

extract_protocol:
Following a 24-hour treatment with CBD/sCBD/vehicle control, terminally differentiated C2C12 monolayers were lysed with buffer RLT from the Qiagen RNeasy kit (Qiagen Ltd). RNA was then extracted from cell lysates using the RNeasy kit with proteinase K digestion, as per the manufacturer’s guidelines. Eluted RNA was stored at -80oC until required for determination of total RNA and library processing.
Libraries were constructed from 100 ng of total RNA with Poly-A tail enrichment of mRNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with Agencourt AMPureXP Sample Purification Beads (Beckman Coulter. Wycombe, UK) as per manufacturers guidelines, by Bart's and the London Genome Centre at Queen Mary, University of London.

treatment_protocol: We terminally differentiated C2C12 myotubes as described above. On day 8 of differentiation, DM was removed and swapped with DM containing vehicle (DMSO), CBD (10 µM) and sCBD (10 µM). Myotubes were then cultured in the respective treatments for 24 hours before being harvested for RNA extraction. Duplicate wells for each treatment were used and the experiment repeated three times to generate an n=6 samples per treatment.

tag: cell line

tag: cell type

value: Myotube

tag: genotype

value: WT

tag: treatment

value: CBD 10 uM


title: C2C12 cells, Control 5

value: Control (vehicle DMSO)


title: ACPFC11_2xLPS_3

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

description: 3' Quant seq with UMI tags

data_processing:
Raw sequencing reads were assessed for quality control using FastQC and multiqc umi indexes were added using umi2index (Lexogen) and then trimmed to remove adapter contamination, polyA read through and low-quality reads using BBDuk.
All samples were then re-assessed for quality using FastQC and multiqc.
Samples were aligned to the mouse genome (mm10) using STAR
Aligned bam files were then filtered for only unique UMIs using collapse_UMI_bam (Lexogen).
Filtered bam files were sorted and indexed using samtools.
Reads per gene were then counted using feature counts at the gene id levels with -s 1 desginated for stranded RNAseq.
Counts were then read into R for statistical analysis using EdgeR and LimmaVoom.
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts counts table in .txt

source_name: frontal cortex tissue

extract_protocol:
On the fourth day, all animals were immediately euthanized 3 hours post-injection. Mice were then transcardially perfused with PBS (1 mL/g of body weight). RNA was extracted from whole tissue from hippocampus, striatum and front cortex using the RNA/DNA Miniprep Plus Zymo Kit (Cat D7003) with on column DNase digestion as described in the kit manual. RNA quality was assessed by bioanalyzer and all samples had RNA Integrity Numbers >7.
QuantSeq 3’mRNA sequencing FWD (RNAseq) libraries (Lexogen, Cat No 015) were prepared as stated in the Lexogen manual using 75ng of total input RNA per sample and 17 cycles of PCR amplification. All samples were prepared with incorporation of Unique Molecular Identifiers as part of the second strand synthesis step (Lexogen, Cat No 081) and sample unique, dual index barcodes. All samples were then pooled, exonuclease VII treated and sequenced across two lanes of a HiSeq4000 to generate Single End 100 base pair reads.
Pooled samples were exonuclease VII treated and sequenced on the HiSeq4000 to generate Single End 100 base pair reads.

treatment_protocol: 10 week old male mice were injected intraperitoneally with low-dose lipopolysaccharide (LPS, Sigma) at a daily dose of 500 ug/kg bodyweight or an equal volume of vehicle PBS. Each mouse was given a total of four injections spaced 24 hours apart. Animals received either four LPS injections on four consecutive days (4xLPS), a single vehicle injection followed by three LPS injections on the following three days (3xLPS), two vehicle injections on two consecutive days followed by two LPS injections on the following two days (2xLPS), three vehicle injections on three consecutive days followed by a single LPS injection on the fourth day (1xLPS), or four vehicle injections (PBS control).

tag: hemisphere

value: left

tag: Sex

value: M

tag: age in weeks


title: ACPFC1_PBS_1

description: 3' Quant seq with UMI tags

value: PBS


title: AP_029_from_anterior_to_posterior

description:
DjTomoAP80-29
Lasy-Seq ver. 1.1
AP80.csv


title: AP_030_from_anterior_to_posterior

description:
DjTomoAP80-30
Lasy-Seq ver. 1.1
AP80.csv


title: ACHC40_4xLPS_4

description: 3' Quant seq with UMI tags

source_name: hippocampal tissue

value: hippocampal

value: right


title: C2C12 cells, Control 3


title: ACHC39_4xLPS_3

description: 3' Quant seq with UMI tags


title: ACHC38_4xLPS_2

description: 3' Quant seq with UMI tags


title: C2C12 cells, Control 2


title: C2C12 cells, Control 4


title: C2C12 cells, Control 1


title: AP_026_from_anterior_to_posterior

description:
DjTomoAP80-26
Lasy-Seq ver. 1.1
AP80.csv


title: AP_027_from_anterior_to_posterior

description:
DjTomoAP80-27
Lasy-Seq ver. 1.1
AP80.csv


title: AP_028_from_anterior_to_posterior

description:
DjTomoAP80-28
Lasy-Seq ver. 1.1
AP80.csv


title: ACHC36_3xLPS_4

description: 3' Quant seq with UMI tags


title: ACHC34_3xLPS_2

description: 3' Quant seq with UMI tags


title: AP_024_from_anterior_to_posterior

description:
DjTomoAP80-24
Lasy-Seq ver. 1.1
AP80.csv


title: Foxc1 Mutant1

city: Aurora

first: Christina

last: Como

state: CO

country: USA

institute: University of Colorado

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw data was processed using 10x Genomics Space Ranger pipeline to generate fastq files
Sequences were aligned to the mm10 genome
Spot selection for forebrain spots were selected using Space Ranger
Data was imported into Seurat objects
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Fresh frozen tissue were frozen in OCT and sectioned on a cryostat at 10 microns
Spatial transcriptomic sequencing libraries were processed per the 10 Visium manufacturer's prototcol

value: Brain

value: Foxc1 KO


title: Foxc1 Mutant2


title: AP_025_from_anterior_to_posterior

description:
DjTomoAP80-25
Lasy-Seq ver. 1.1
AP80.csv


title: Control2

value: Foxc1 WT


title: AP_023_from_anterior_to_posterior

description:
DjTomoAP80-23
Lasy-Seq ver. 1.1
AP80.csv


title: AP_022_from_anterior_to_posterior

description:
DjTomoAP80-22
Lasy-Seq ver. 1.1
AP80.csv


title: ACHC33_3xLPS_1

description: 3' Quant seq with UMI tags


title: Control1


title: ACHC32_2xLPS_4

description: 3' Quant seq with UMI tags


title: K27ac_cKO_cDC1_3

city: Grand Rapids

first: Connie

middle: M

last: Krawczyk

state: MI

address: 333 Bostwick Ave

department: Metabolism and Nutritional Programming

institute: Van Andel Institute

library_source: genomic

data_processing:
Reads were trimmed using TrimGalore v0.6.0 with default parameters and aligned to the mm10 genome and decoy sequences, including viral sequences and cfMeDIP-seq spike-in sequences using bwa mem v0.7.17. PCR duplicates were marked using SAMBLASTER v0.1.24. Only high-confidence and properly-paired alignments were retained using samtools view with parameters, “-q 30 -f 2 -F 2828” (v1.9). Bigwig files for visualization was produced using DeepTools v3.4.3; bamCoverage was run with the parameters, “--binSize 10 --extendReads --normalizeUsing ‘CPM’ --samFlagExclude 1024 --samFlagInclude 64”.
Assembly: mm10
Supplementary files format and content: Bigwig, normalized coverage
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Spleen

growth_protocol: Dendritic cells sorted from mouse spleens

extract_protocol:
CUT&RUN:  Unfixed cells (15K) were bound to concanavalin A-coated magnetic beads for 15 min at room temperature, permeabilized with 0.05% digitonin and incubated with primary antibodies overnight at 4°C. After addition of pA-MNase and digestion, bound complexes were released for DNA extraction.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina using Multiplex Oligos for Illumina dual index primer pair barcodes purchased from NEB. 6ng of DNA was used for library construction. Libraries were amplified using 12 cycles on the thermocycler. Post-amplification libraries were size selected using 200-600 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agient High Sensitivity DNA Kit.

value: Spleen

value: KO

value: naïve


title: ACHC37_4xLPS_1

description: 3' Quant seq with UMI tags


title: AP_021_from_anterior_to_posterior

description:
DjTomoAP80-21
Lasy-Seq ver. 1.1
AP80.csv

value: whole


title: AP_020_from_anterior_to_posterior

description:
DjTomoAP80-20
Lasy-Seq ver. 1.1
AP80.csv

value: AF


title: ACHC30_2xLPS_2

description: 3' Quant seq with UMI tags


title: ACHC35_3xLPS_3

description: 3' Quant seq with UMI tags


title: Progenitors, Control, Isotype, rep3

data_processing:
NF-Core CUT&RUN pipeline was ran with default parameters, normalized to spike-in DNA
Peaks were called using Seacr in relaxed mode and normalization set to 'norm'
Replicate threshold for consensus peaks were set to 3
Assembly: mm10
Supplementary files format and content: bigWig, bedgraph files (except for inputs)
Library strategy: CUT&RUN

source_name: Cortex

extract_protocol:
Progenitor cells were isolated using a Prom1+ magnetic bead labeling and then CUT&RUN experiment was followed according to protocol from Epicypher, but with 0.05% digitonin.
Libraries were constructed using the Epicypher CUT&RUN library prep kit

value: Cortex

tag: antibody

value: IgG (Epicypher 13-0042)

value: Prom1+ neural progenitors


title: K27ac_WT_cDC1_3

value: WT


title: ACHC28_1xLPS_4

description: 3' Quant seq with UMI tags


title: AP_019_from_anterior_to_posterior

description:
DjTomoAP80-19
Lasy-Seq ver. 1.1
AP80.csv


title: Progenitors, Foxc1 Mutant, Isotype, rep1


title: AP_018_from_anterior_to_posterior

description:
DjTomoAP80-18
Lasy-Seq ver. 1.1
AP80.csv


title: K27ac_cKO_cDC1_2


title: K27ac_WT_cDC1_1


title: ACHC27_1xLPS_3

description: 3' Quant seq with UMI tags

value: left


title: AP_017_from_anterior_to_posterior

description:
DjTomoAP80-17
Lasy-Seq ver. 1.1
AP80.csv


title: K27ac_cKO_cDC1_1


title: Progenitors, Foxc1 Mutant, Isotype, rep2


title: AP_016_from_anterior_to_posterior

description:
DjTomoAP80-16
Lasy-Seq ver. 1.1
AP80.csv


title: Progenitors, Foxc1 Mutant, Myctag, rep3

value: MycTag (CST 2276)


title: ACHC26_1xLPS_2

description: 3' Quant seq with UMI tags

value: M


title: K4me3_cKO_cDC1_3


title: AP_015_from_anterior_to_posterior

description:
DjTomoAP80-15
Lasy-Seq ver. 1.1
AP80.csv


title: Progenitors, Foxc1 Mutant, Myctag, rep2


title: K27ac_WT_cDC1_2


title: K4me3_cKO_cDC1_2


title: AP_014_from_anterior_to_posterior

description:
DjTomoAP80-14
Lasy-Seq ver. 1.1
AP80.csv


title: Progenitors, Foxc1 Mutant, Myctag, rep1


title: Progenitors, Control, Isotype, rep2


title: ACHC24_PBS_4

description: 3' Quant seq with UMI tags

value: hippocampal

value: PBS


title: K4me3_WT_cDC1_3


title: Progenitors, Control, Isotype, rep1


title: K4me3_WT_cDC1_2


title: AP_012_from_anterior_to_posterior

description:
DjTomoAP80-12
Lasy-Seq ver. 1.1
AP80.csv


title: ACHC23_PBS_3

description: 3' Quant seq with UMI tags


title: ACHC31_2xLPS_3

description: 3' Quant seq with UMI tags


title: K4me3_WT_cDC1_1


title: ACHC21_PBS_1

description: 3' Quant seq with UMI tags


title: ACHC22_PBS_2

description: 3' Quant seq with UMI tags

value: right


title: Progenitors, Control, Myctag, rep1


title: AP_010_from_anterior_to_posterior

description:
DjTomoAP80-10
Lasy-Seq ver. 1.1
AP80.csv


title: APP_BRICHOS_3

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Sample quality was assessed using FastQC (v0.11.8).
Reads were aligned to a reference built from Ensembl GRCm38 genome sequences using STAR (v2.6.1d).
Counts for each gene were obtained using featureCounts (v1.5.1) using the GRCm38.101 GTF file from Ensembl.
Bioconductor package DESEq2 was used for count normalization and sample group comparisons, generating log2 fold changes, Wald test p-values and p-value adjustments for multiple testing (Benjamini-Hochberg method).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited matrix of raw counts for all samples

source_name: brain

growth_protocol: The cortical tissue was minced and incubated in papain enzyme solution at +37°C for 40 min to digest the connective tissue. A single cell pellet was collected by density gradient centrifugation. The cells were filtered through 70 mm cell strainers, incubated with magnetic beads conjugated with anti-CD11b antibodies and the CD11b-positive microglia were isolated. The microglial cells were suspended in RNAlater solution (Thermo Fisher, Catalog No. AM7020) and stored at -80°C until used.

extract_protocol:
Papain dissociation kits (Worthington, Catalog. No. LK003178) along with magnetic cell isolation were used to isolate CD11b-positive microglia from cerebral cortex samples.
Libraries were prepared according to the Illumina Stranded mRNA Prep Ligation protocol.

treatment_protocol: Forty male AppNL-G-F and forty WT mice were randomly selected and equally divided into 4 groups each. The mice were treated for 12 weeks with i.v. injections of PBS (vehicle) or rh Bri2 BRICHOS R221E (10 mg/kg, n = 10/group) twice a week (total of 24 injections) starting from the age of 9 months. After twelve weeks of treatment, and another four weeks without treatment as used in previous studies the mice were anaesthetized and perfused intracardially with physiological saline. The brains were dissected out and divided into hemispheres.Frozen in dry ice and stored at −80 °C.

value: brain

value: microglial

value: App NL-G-F

value: rh Bri2 BRICHOS


title: K4me3_cKO_cDC1_1

value: Spleen

value: KO

value: naïve


title: primary neuron, OGD/R,-3

city: NanJing

first: Jiang

middle: Dong

last: ya

state: 江苏省

address: 12 Xuefu Road, Nanjing, Jiangsu, China

country: China

institute: NanJing university

data_processing:
The clean reads were mapped to the reference genome using HISAT22.
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4.
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: report_Filtered_data_stat

organism: Rattus norvegicus

growth_protocol: Primary neuron was mentained in 1% Glutamax/2% B27 in neurobasal medium (Gibco, 17504-044, USA) in cell incubator with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions

treatment_protocol: Primary rat cortical neurons were separated from postnatal 0-day SD rat.

value: primary neuron

value: OGD/R


title: primary neuron, OGD/R,-2


title: AP_009_from_anterior_to_posterior

description:
DjTomoAP80-9
Lasy-Seq ver. 1.1
AP80.csv

value: whole

value: AF


title: APP_BRICHOS_1


title: KO_cDC2A_12

data_processing:
Reads were aligned to the mm10 genome and ERCC sequences using Takara’s CogentAP v1.5, specifying the ‘Strnd_UMI’ kit configuration.
Assembly: mm10
Supplementary files format and content: csv, UMI counts from CogentAP workflow

source_name: spleen

extract_protocol:
10K cells were sorted into 1.5ml tubes containing buffer RL from the Norgen Biotek Single Cell RNA Purification Kit. This kit was used to isolate RNA from the sorted cells, included DNAse I treatment on the column. Protocol was followed as written. RNA was eluted into 10ul of elution buffer and quants were done using HS RNA qubit.
Library construction was done using 5ug of RNA in the Takara SMARTer Stranded Total RNA-seq v3 Pico Input kit as written.

treatment_protocol: Mice were infected with LCMV-Armstrong 20hrs prior to splenocyte harvest

value: spleen

value: 20hr LCMV


title: primary neuron, OGD/R,-1

value: WT


title: Progenitors, Control, Myctag, rep2

value: Cortex

value: MycTag (CST 2276)

value: Prom1+ neural progenitors


title: APP_Veh_3

value: brain

value: PBS


title: ACHC29_2xLPS_1

description: 3' Quant seq with UMI tags

value: hippocampal

value: left

value: M


title: primary neuron, Control,-3

value: control


title: AP_008_from_anterior_to_posterior

description:
DjTomoAP80-8
Lasy-Seq ver. 1.1
AP80.csv


title: KO_cDC1_12

value: KO


title: AP_013_from_anterior_to_posterior

description:
DjTomoAP80-13
Lasy-Seq ver. 1.1
AP80.csv


title: ACHC25_1xLPS_1

description: 3' Quant seq with UMI tags


title: AP_007_from_anterior_to_posterior

description:
DjTomoAP80-7
Lasy-Seq ver. 1.1
AP80.csv


title: KO_pDC_Ly6c_pos_12

value: pDC Ly6c+


title: primary neuron, Control,-2

value: primary neuron


title: primary neuron, Control,-1


title: APP_Veh_1

value: microglial

value: App NL-G-F


title: APP_Veh_2


title: KO_cDC2B_12

value: spleen


title: KO_pDC_Ly6c_neg_12

value: pDC Ly6c-

value: 20hr LCMV


title: APP_BRICHOS_2

value: rh Bri2 BRICHOS


title: AP_004_from_anterior_to_posterior

description:
DjTomoAP80-4
Lasy-Seq ver. 1.1
AP80.csv

value: whole

value: AF


title: shFTO_rep2_ip [S4_IP]

city: Guangzhou

first: Zhixiang

last: Zuo

address: No. 651 Dongfeng Dong road

department: Cancer Center

institute: Sun Yat-sen University

data_processing:
*library strategy: MeRIP-seq
Fastp were employed to perform quality control and preprocessing of raw sequencing reads. Clean reads were aligned to the Rn6 genome using STAR. FeatureCounts was performed to quantify the expression of genes. MACS2 and MetPeak were used to identify m6A enriched peaks.
Assembly: Rn6
Supplementary files format and content: tab-delimited file includes gene raw counts and modification peaks for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, USA) following the manufacturer's procedure.
Cleaved RNA fragments were incubated for 2 h at 4℃ with m6A-specific antibody (Synaptic Systems, cat.202003, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).

value: shFTO


title: WT_BRICHOS_3

value: brain

value: WT


title: KO_cDC2A_11


title: WT_BRICHOS_2


title: AP_003_from_anterior_to_posterior

description:
DjTomoAP80-3
Lasy-Seq ver. 1.1
AP80.csv


title: WT_BRICHOS_1


title: KO_cDC1_11


title: shFTO_rep1_ip [S3_IP]


title: WT_Veh_3

value: PBS


title: control_rep2_ip [S2_IP]


title: AP_005_from_anterior_to_posterior

description:
DjTomoAP80-5
Lasy-Seq ver. 1.1
AP80.csv


title: AP_006_from_anterior_to_posterior

description:
DjTomoAP80-6
Lasy-Seq ver. 1.1
AP80.csv


title: AP_001_from_anterior_to_posterior

description:
DjTomoAP80-1
Lasy-Seq ver. 1.1
AP80.csv


title: control_rep1_ip [S1_IP]


title: KO_pDC_Ly6c_neg_11


title: KO_cDC2B_11


title: shFTO_rep2_input [S4_input]


title: WT_cDC2B_10


title: shFTO_rep1_input [S3_input]


title: WT_cDC2A_10


title: preT_Input5

city: Nanjing

first: Tingting

last: Gu

state: Jiangsu

address: 1 Weigang

department: Horticulture

institute: Nanjing Agricultural University

description: Corresponding input for 'preT_H3K9me2_2' and 'preT_H3K36me3_2'

data_processing:
Clean reads were aligned to Fragaria vesca genome v6.0 using bowtie2 v2.3.4.3
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Bed files were generated by  'chromHMM' with 'LearnModel' with combination of relevance classes into eight states.
Assembly: Fragaria vesca genome v6.0
Supplementary files format and content: Bigwig files, enriched value (log2(fold-change))
Supplementary files format and content: Bed files, genomic occurrence of the strawberry fruit eight-state model.

organism: Fragaria vesca

source_name: receptacle

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and purified by RaPure Plant DNA mini Kit(Magen, D3187).
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

value: receptacle

tag: chip antibody

value: no antibody

value: not applicable


title: Progenitors, Control, Myctag, rep3

value: Cortex

value: MycTag (CST 2276)

value: Prom1+ neural progenitors


title: control_rep2_input [S2_input]

value: control


title: CSF_OlinkTarget96_CaseT

type: protein

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: SAMPLE T

hyb_protocol: Hybridizations were performed by Olink Proteomics Headquarters as per protocol

scan_protocol: Scans were performed by Olink Proteomics Headquarters as per protocol

data_processing: Data were analyzed with Prism version 10.0.2 and Olink Statistical Analysis App (2023)

label: Olink probes (2 per analyte)

molecule: protein

organism: Homo sapiens

source_name: 35 year old female with Progressive MS

label_protocol: As per Olink manufacturer's protocol

extract_protocol: CSF collected via LP was centrifuged to pellet out cells. Supernatant was collected was stored at -80C and thawed for use in this assay. Samples were plated in a 96-well as per Olink protocol and sent to Olink headquarters for assay completion.

tag: disease

value: Multiple Sclerosis (DMT Naive)

value: Archive CSF

value: female

tag: plate


title: WT_cDC1_10

value: spleen

value: 20hr LCMV


title: CSF_OlinkTarget96_CaseR

description: SAMPLE R

source_name: 65 year old male with Progressive MS

value: male


title: preT_H3K36me3_rep2

description: H3K36me3 ChIP-seq in preT fruits, replicate 2,  'preT_Input_5'' as input

value: H3K36me3(Abcam, ab9050)


title: AP_002_from_anterior_to_posterior

description:
DjTomoAP80-2
Lasy-Seq ver. 1.1
AP80.csv

value: whole

value: AF


title: control_rep1_input [S1_input]


title: KO_pDC_Ly6c_pos_11

value: pDC Ly6c+

value: KO


title: WT_Veh_2

value: brain

value: microglial

value: WT

value: PBS


title: preT_H3K9me2_rep2

description: H3K9me2 ChIP-seq in preT fruits, replicate 2,  'preT_Input_5' as input

value: receptacle

value: H3K9me2(Abcam, ab1220)

value: not applicable


title: WT_pDC_Ly6c_pos_10


title: CSF_OlinkTarget96_CaseQ

description: SAMPLE Q

source_name: 61 year old male with Progressive MS

value: Multiple Sclerosis (DMT Naive)

value: Archive CSF


title: AP_011_from_anterior_to_posterior

description:
DjTomoAP80-11
Lasy-Seq ver. 1.1
AP80.csv


title: WT_cDC2B_9

value: spleen


title: CSF_OlinkTarget96_CaseS

description: SAMPLE S

source_name: 44 year old female with Progressive MS

value: female


title: FTOOE_rep3

data_processing:
Fastp were employed to perform quality control and preprocessing of raw sequencing reads. Clean reads were aligned to the Rn6 genome using STAR. FeatureCounts was performed to quantify the expression of genes.
Assembly: Rn6
Supplementary files format and content: tab-delimited file includes raw counts for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, USA) following the manufacturer's procedure.
Cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). At last, we performed sequencing using Illumina NovaSeq6000 PE150 (LC-Bio Technology Co., Ltd., Hangzhou, China).

value: FTOOE


title: WT_cDC2A_9

value: 20hr LCMV


title: WT_Veh_1


title: FTOOE_rep2


title: preT_Input_rep3

description: Corresponding input for 'preT_H3K4me1_rep1' and 'preT_H3K36me3_rep1'

data_processing:
Clean reads were aligned to Fragaria vesca genome v4.0 using bowtie2 v2.3.4.3
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Bed files were generated by  'chromHMM' with 'LearnModel' with combination of relevance classes into eight states.
Assembly: Fragaria vesca genome v4.0
Supplementary files format and content: Bigwig files, enriched value (log2(fold-change))
Supplementary files format and content: Bed files, genomic occurrence of the strawberry fruit eight-state model.

value: no antibody


title: preT_Input_rep4

description: Corresponding input for 'preT_H3K4me1_rep2' and 'preT_H3K9me2_rep1'


title: FTOOE_rep1


title: preT_Input_rep2

description: Corresponding input for 'preT_H3K4me3_rep2' , 'preT_H3K9/K14ac_rep2',  'preT_H3K27me3_rep2' and 'preT_H3K27ac_rep2'


title: CSF_OlinkTarget96_CaseP

description: SAMPLE P

source_name: 46 year old female with Progressive MS


title: OENC_rep3

value: OENC


title: WT_pDC_Ly6c_pos_9

value: pDC Ly6c+


title: WT_cDC1_9


title: OENC_rep2


title: CSF_OlinkTarget96_CaseO

description: SAMPLE O

source_name: 34 year old female with tumefactive MS


title: WT_cDC2B_8


title: CSF_OlinkTarget96_CaseM

description: SAMPLE M

source_name: 41 year old female with RRMS


title: CSF_OlinkTarget96_CaseN

description: SAMPLE N

source_name: 47 year old female with Tumefactive MS


title: CSF_OlinkTarget96_CaseL

description: SAMPLE L

source_name: 26 year old female with RRMS


title: preT_H3K27ac_rep2

description: H3K27ac ChIP-seq in preT fruits, replicate 2,  'preT_Input_rep2' as input

value: H3K27ac(Abcam, ab4729)


title: WT_cDC2A_8


title: CSF_OlinkTarget96_CaseK

description: SAMPLE K

source_name: 26 year old male with RRMS

value: male


title: shFTO-3_rep3


title: OENC_rep1


title: preT_H3K27ac_rep1

description: H3K27ac ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep1' as input


title: WT_cDC1_8


title: preT_H3K27me3_rep1

description: H3K27me3 ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep1' as input


title: preT_H3K27me3_rep2

description: H3K27me3 ChIP-seq in preT fruits, replicate 2,  'preT_Input_rep2' as input


title: shFTO-3_rep1


title: WT_pDC_Ly6c_pos_8


title: preT_H3K9/K14ac_rep2

description: H3K9/K14ac ChIP-seq in preT fruits, replicate 2,  'preT_Input_rep2' as input


title: KO_cDC2B_7

value: KO


title: CSF_OlinkTarget96_CaseI

description: SAMPLE I

source_name: 39 year old female with RRMS


title: CSF_OlinkTarget96_CaseJ

description: SAMPLE J

source_name: 28 year old male with RRMS


title: preT_Input_rep1

description: Corresponding input for 'preT_H3K4me3_rep1' , 'preT_H3K9/K14ac_rep1',  'preT_H3K27me3_rep1' and 'preT_H3K27ac_rep1'

value: WT


title: shFTO-2_rep3


title: preT_H3K9/K14ac_rep1

description: H3K9/K14acChIP-seq in preT fruits, replicate 1,  'preT_Input_rep1' as input


title: KO_cDC2A_7


title: preT_H3K9me2_rep1

description: H3K9me2 ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep4' as input


title: KO_cDC1_7


title: CSF_OlinkTarget96_CaseG

description: SAMPLE G

source_name: 49 year old male with RRMS


title: shFTO-2_rep1


title: CSF_OlinkTarget96_CaseF

description: SAMPLE F

source_name: 65 year old female with RRMS


title: KO_pDC_Ly6c_neg_7

value: pDC Ly6c-


title: CSF_OlinkTarget96_CaseH

description: SAMPLE H

source_name: 25 year old female with RRMS


title: preT_H3K4me3_rep2

description: H3K4me3 ChIP-seq in preT fruits, replicate 2,  'preT_Input_rep2' as input

value: receptacle

value: H3K4me3(Abcam, ab8580)


title: shFTO-3_rep2


title: shCtrl_rep3

value: shCtrl


title: preT_H3K4me3_rep1

description: H3K4me3 ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep1' as input

value: not applicable


title: KO_pDC_Ly6c_pos_7

source_name: spleen


title: shCtrl_rep2


title: KO_cDC2B_6

value: PBS


title: CSF_OlinkTarget96_CaseC

description: SAMPLE C

value: Multiple Sclerosis (DMT Naive)

value: Archive CSF


title: preT_H3K36me3_rep1

description: H3K36me3 ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep3'' as input

source_name: receptacle

value: H3K36me3(Abcam, ab9050)


title: shCtrl_rep1


title: shFTO-2_rep2


title: preT_H3K4me1_rep2

description: H3K4me1 ChIP-seq in preT fruits, replicate 2,  'preT_Input_rep4' as input

value: H3K4me1(Abcam, ab8895)


title: KO_pDC_Ly6c_neg_6

value: spleen


title: Fannyhessea vaginae single biofilms_biol rep3 (br3)

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description: Fvaginae_Single vs Mixed biofilms_RPKM

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (v 2.17.1.14) starting from raw sequencing reads. The quality of individual sequences was evaluated using FastQC software after adapter trimming with cutadapt software (v 1.18).
Adapter trimmed data was further analysed by CLC Genomics Workbench v 21.99.
Sequence data were trimmed for low quality using CLC Genomics Workbench (parameter - quality limit: 0.05 and Maximum number of ambiguities allowed: 2).
Trimmed sequences read were mapped to either G. vaginalis NCTC 10287, F. vaginae FDAARGOS_934 or P. bivia DSM 20514 using CLC Genomics Workbench (parameters-Mismatch cost: 2, insertion cost; deletion cost: 3; length fraction 0.8, similarity fraction: 0.8 and maximum number of hits for a read: 10).
Differential expression analysis was performed using CLC Genomics Workbench, upon normalisation to RPKM. Baggerley statistical test was used to identify significant alterations in gene transcription. Only alterations with fold-changes > 2 and a false discovery rate (FDR)-adjusted P value < 0.05 were used for further bioinformatics analyses.
Assembly: G. vaginalis NCTC 10287 (NZ_LR134385.1), F. vaginae FDAARGOS_934 (CP065631.1) and P. bivia DSM 20514 (scaffolds NZ_JH660658.1; NZ_JH660659.1; NZ_JH660660.1)
Supplementary files format and content: The tab-delimited text file present RPKM values of either G.vaginalis, F. vaginae or P. bivia of the three replicas performed, for both single (S) and multispecies/mixed (M) biofilms.

organism: Fannyhessea vaginae

source_name: Fannyhessea vaginae (Fv)

growth_protocol: Single and triple-species biofilms of G. vaginalis, F. vaginae and P. bivia were formed on 24-well culture plates (Orange Scientific). First, an inoculum of each species was prepared in NYCIII medium [0.24% (w/v) HEPES (VWR), 1.5% (w/v) proteose peptone (Liofilchem), 0.38% (w/v) yeast extract (Liofilchem), 0.5% (w/v) NaCl (VWR), 0.5% (w/v) glucose (Fisher Scientific), and 10% (v/v) of inactivated horse serum (Sigma)] and incubated at 37˚C under anaerobic conditions for 24 h. Bacterial concentration was then adjusted to 1x107 CFU/mL and 1 mL of suspension was dispensed into 24-well plates. The plates were incubated for 48 h at 37˚C under anaerobic conditions. After 48 h, the medium was removed, and the biofilms were washed once with 1x phosphate-buffered saline (PBS) solution (Fisher Scientific). Biofilms were then detached from the bottom of the plate in RNA Protect bacteria reagent (QIAGEN), which was diluted 2:1 in PBS; and 12 biofilms (i.e. biofilms from 12 wells) were combined to obtain samples with enough RNA for further analysis. Finally, samples were centrifuged at 5000 xg for 10 min at room temperature.

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (QIAGEN), according to the manufacturer's instructions with some brief modifications. First, cells were suspended in 600 μL of the lysis buffer RLT and the volume was transferred into a tube with 0.1 mm zirconium beads (Merck). Cells were lysed using the BeadBug 6 Microtube Homogenizer (Benchmark Scientific) at maximum speed for 35s. The cycle was repeated four times and the samples were kept on ice for 5 min between cycles. Then, the samples were centrifuged, and the supernatant was recovered into a new tube. Ethanol [70% (Thermo Fisher Scientific)] was added, in the same proportion (vol: vol), to the supernatant and the solution was transferred to an RNeasy Mini spin column. RNA was then eluted in RNase-free water (GRISP) and treated with Turbo DNase (Invitrogen) to degrade genomic DNA following the manufacturer's instructions for rigorous protocol. RNA quality was assessed using an Agilent 2100 Fragment Analyzer system (Agilent) and only samples with RNA quality indicators above 7 were used.
RNA-seq libraries were prepared by Lexogen (outsourced) using Lexogen’s CORALLTM Total RNA-seq kit with 100 ng of total RNA. Before RNA-seq, rRNA was removed using the RiboCop for Bacteria (Mixed Bacterial Samples META) rRNA Depletion kit (Lexogen). Sequencing libraries were evaluated for quality on a Fragment Analyzer System (Agilent) and quantified with QubitTM dsDNA HS Assay Kit (Invitrogen). Data were generated using Illumina NextSeq2000 Sequencing from single-end reads (SR100).

value: ATCC BAA-55


title: preT_H3K4me1_rep1

description: H3K4me1 ChIP-seq in preT fruits, replicate 1,  'preT_Input_rep3' as input


title: CSF_OlinkTarget96_CaseB

description: SAMPLE B

source_name: 64 year old female with RRMs

value: female


title: Red_Input_rep6

description: Corresponding input for 'Red_H3K27me3_rep2'

value: no antibody


title: CSF_OlinkTarget96_CaseA

description: SAMPLE A

source_name: 32 year old female with RRMS


title: KO_pDC_Ly6c_pos_6

value: pDC Ly6c+


title: Fannyhessea vaginae single biofilms_biol rep2 (br2)

description: Fvaginae_Single vs Mixed biofilms_RPKM


title: Red_Input_rep5

description: Corresponding input for 'Red_H3K9me2_rep1'


title: Fannyhessea vaginae single biofilms_biol rep1 (br1)

description: Fvaginae_Single vs Mixed biofilms_RPKM


title: CSF_OlinkTarget96_CaseE

description: SAMPLE E


title: KO_cDC2A_5

value: KO


title: KO_cDC2B_5


title: CSF_OlinkTarget96_CaseD

description: SAMPLE D

source_name: 51 year old female with RRMS


title: Control lung paracancer tissue [ANT Sup]

type: RNA

city: Nanning

first: Aruo

address: No.22 Shuangyong Road, Qingxiu District

institute: Guangxi Medical University

description: ANT(Sup,Normalized)

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10× Blocking Agent and 1 μL of 25× Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2× Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m7G-circRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Scanned on Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: lung cancer  para-tissue

label_protocol: The “IP” RNAs and “Sup” RNAs digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched “IP” RNAs and “Sup” RNAs were then added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, the total RNAs were immunoprecipitated with anti-m7G antibody (MBL, RN017M).

value: lung cancer  para-tissue

tag: molecule subtype

value: circRNA


title: Lung cancer tissue [LCA Sup]

description: LCA(Sup,Normalized)

source_name: lung cancer tissue

value: lung cancer tissue


title: Red_Input_rep4

description: Corresponding input for 'Red_H3K4me3_rep2' ,  'Red_H3K9K14ac_rep2' and 'Red_H3K27ac_rep2'

value: receptacle

value: WT


title: KO_pDC_Ly6c_neg_5

value: pDC Ly6c-


title: Lung cancer tissue [LCA anti-m7G IP]

description: LCA(IP,Normalized)

source_name: Cancerous tissue

value: Cancerous tissue

value: anti-m7G antibody (MBL, RN017M)


title: SLC6A8-KO_week5_rep3

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
read trimming (Galaxy Version 4.8+galaxy1): options: g- GTGGAAAGGACGTGTCACCG…GTTTAAGAGCTA --overlap 10 --discard_untrimmed
gRNA mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw gRNA count table
Library strategy: Amplicon-Seq

source_name: cell line

growth_protocol: HCT116 (RRID:CVCL_0291) cells and HCT116 KO clones were cultivated in RPMI 1640 (R8758 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco).

extract_protocol:
Genomic DNA was purified using QIAamp DNA Mini columns (Qiagen)
gDNA was digested overnight with 20U PacI (NEB) and double size-selected to enrich the sgRNA containing fragments (380 bp). Briefly, 0.7 x vol AmpliClean magnetic beads (Nimagen) were added to the sample to bind large gDNA fragments; the cleared supernatant was added to fresh beads (0.6 x volume of the original gDNA sample) to bind the smaller fragments. After size selection, sgRNA sequences were amplified in  with Q5 Polymerase (NEB) using the program recommended by the manufacturer (28 cycles, 65°C annealing temperature). PCR products were further double size-selected to remove residual large gDNA fragments as described above. Purified PCR products were used in barcoding PCRs to add Illumina adapters and indices for pooled sequencing. A detailed protocol can be found on Addgene (https://www.addgene.org/pooled-library/human-transporters/).

treatment_protocol: Cells were transduced with lentiviral particles containing KO library in triplicates and selected with blasticidin to remove non-transduced cells. After 13 days of selection, each replicatewas independently was passaged in standard growth media for a total of five weeks. Samples were harvested for NGS analysis 3 to 7 weeks after transduction.

value: Colorectal carcinoma cell line

tag: inserted grna_(ko_clones_only)

value: GGAAACGGAAGTAGTAGG

tag: screening library

value: Human Transporter KO (Addgene  #213695)


title: KO_cDC1_5

value: spleen

value: PBS


title: Control lung paracancer tissue [ANT anti-m7G IP]

description: ANT(IP,Normalized)

source_name: Paracancer tissue

value: Paracancer tissue


title: Red_Input_rep3

description: Corresponding input for 'Red_H3K4me3_rep1' , 'Red_H3K9me2_rep2', 'Red_H3K9K14ac_rep1', 'Red_H3K27me3_rep1' and 'Red_H3K27ac_rep1'

value: not applicable

value: no antibody


title: Red_Input_rep2

description: Corresponding input for 'Red_H3K4me1_rep2' and 'Red_H3K36me3_rep2'


title: KO_cDC1_6

value: KO


title: Red_Input_rep1

description: Corresponding input for 'Red_H3K4me1_rep1' and 'Red_H3K36me3_rep1'


title: SLC6A8-KO_week5_rep1


title: KO_pDC_Ly6c_pos_5

value: pDC Ly6c+


title: Red_H3K27ac_rep2

description: H3K27ac ChIP-seq in red fruits, replicate 2,  'Red_Input_rep4' as input

value: H3K27ac(Abcam, ab4729)


title: SLC6A8-KO_week2_rep3


title: WT_cDC2B_4


title: SLC6A8-KO_week5_rep2


title: Red_H3K27ac_rep1

description: H3K27ac ChIP-seq in red fruits, replicate 1,  'Red_Input_rep3' as input


title: WT_cDC2A_4


title: SLC6A8-KO_week2_rep2


title: Red_H3K27me3_rep2

description: H3K27me3 ChIP-seq in red fruits, replicate 2,  'Red_Input_rep6' as input


title: SLC25A37-KO_week5_rep3

value: CTGGATTCATTACCGCATCG


title: WT_pDC_Ly6c_neg_4


title: SLC25A37-KO_week5_rep2


title: Red_H3K9/K14ac_rep2

description: H3K9/K14ac ChIP-seq in red fruits, replicate 2,  'Red_Input_rep4' as input

value: receptacle


title: SLC25A37-KO_week5_rep1


title: Red_H3K27me3_rep1

description: H3K27me3 ChIP-seq in red fruits, replicate 1,  'Red_Input_rep3' as input

value: WT


title: WT_pDC_Ly6c_pos_4


title: WT_cDC2B_3


title: Red_H3K9/K14ac_rep1

description: H3K9/K14ac ChIP-seq in red fruits, replicate 1,  'Red_Input_rep3' as input


title: WT_cDC1_4


title: WT_cDC2A_3


title: SLC25A37-KO_week2_rep3


title: Red_H3K9me2_rep2

description: H3K9me2 ChIP-seq in red fruits, replicate 2,  'Red_Input_rep3' as input

value: H3K9me2(Abcam, ab1220)


title: medium cultured with hPL-MSCs_C alone

city: Seoul

first: Sun Jeong

last: Kim

address: 701, Yeongdong-daero, Gangnam-gu

country: South Korea

institute: ENCell Co. Ltd.

hyb_protocol: Drying the glass slide, Blocking and Incubations. Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer I and 1X wash buffer II and de-ionized water. Detection Buffer including Cy3-Streptavidin was treated for 2hr at room temperature in dark. And slide was washed with 1X wash buffer I, II and DW.

scan_protocol: Scanned on an GenePix 4100 scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction.

label: biotin

source_name: placenta-derived human mesenchymal stem cell

label_protocol: Sample was labeled according to the protocol in the kit manual from Raybiotech.

growth_protocol: hWJ-MSCs and hPL-MSCs were maintained in MEM-a supplemented with 10% fetal bovine serum (FBS) and 0.5% gentamicin in humidifed atmosphere with 5% CO2 at 37℃. C2C12 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 0.5% gentamicin in humidifed atmosphere with 5% CO2 at 37℃.

extract_protocol: The secreted proteins in the conditioned media collected from hMSCs alone culture, C2C12 alone culture, and co-culture of hMSCs and C2C12 cells

treatment_protocol: We collected the conditioned media from the following groups to perform the array: C2C12 alone, hWJ-MSCs alone (A, B, C), hPL-MSCs alone (A, B, C), and C2C12 cells co-cultured with hWJ-MSCs (A, B, C), or hPL-MSCs (A, B, C).

value: medium cultured with hPL-MSCs_C alone


title: medium co-cultured with C2C12 and hWJ-MSCs_B

organism:
Homo sapiens
Mus musculus

source_name: mouse myoblast cell line, Wharton’s jelly-derived human mesenchymal stem cell


title: medium cultured with hWJ-MSCs_C alone

source_name: Wharton’s jelly-derived human mesenchymal stem cell

value: medium cultured with hWJ-MSCs_C alone


title: medium co-cultured with C2C12 and hWJ-MSCs_A


title: medium cultured with hPL-MSCs_B alone

value: medium cultured with hPL-MSCs_B alone


title: medium co-cultured with C2C12 and hPL-MSCs_C

source_name: mouse myoblast cell line, placenta-derived human mesenchymal stem cell


title: medium cultured with hPL-MSCs_A alone

value: medium cultured with hPL-MSCs_A alone


title: SLC6A8-KO_week2_rep1

value: Colorectal carcinoma cell line

value: GGAAACGGAAGTAGTAGG

value: Human Transporter KO (Addgene  #213695)


title: medium co-cultured with C2C12 and hPL-MSCs_A


title: medium co-cultured with C2C12 and hWJ-MSCs_C


title: medium co-cultured with C2C12 and hPL-MSCs_B


title: SLC25A37-KO_week2_rep2


title: WT_cDC1_3

value: spleen

value: PBS


title: WT_pDC_Ly6c_pos_3


title: Red_H3K9me2_rep1

description: H3K9me2 ChIP-seq in red fruits, replicate 1,  'Red_Input_rep5' as input

value: not applicable


title: Red_H3K4me3_rep2

description: H3K4me3 ChIP-seq in red fruits, replicate 2,  'Red_Input_rep4' as input

value: H3K4me3(Abcam, ab8580)


title: medium cultured with hWJ-MSCs_B alone

value: medium cultured with hWJ-MSCs_B alone


title: SLC25A37-KO_week2_rep1


title: SLC25A28-KO_week5_rep2

value: GTACACAGTCTGTCACCCGG


title: medium cultured with hWJ-MSCs_A alone

value: medium cultured with hWJ-MSCs_A alone


title: medium cultured with C2C12 alone

source_name: mouse myoblast cell line

value: medium cultured with C2C12 alone


title: Red_H3K36me3_rep2

description: H3K36me3 ChIP-seq in red fruits, replicate 2,  'Red_Input_rep2' as input

value: receptacle

value: WT

value: H3K36me3(Abcam, ab9050)


title: WT_cDC2B_2


title: Red_H3K4me3_rep1

description: H3K4me3 ChIP-seq in red fruits, replicate 1,  'Red_Input_rep3' as input


title: SLC25A28-KO_week5_rep3


title: WT_cDC2A_2


title: SLC25A28-KO_week5_rep1


title: H358_NT_MRTX849_BI3406_72h_2_rep1

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

institute: Boehringer-Ingelheim

data_processing:
Sequencing libraries were quantified by real-time PCR using KAPA Library Quantification Kit for NGS (Roche) and assessed for size distribution on a Fragment Analyzer (Agilent) to confirm absence of adapter dimers and unligated library molecules. Sequencing libraries were pooled at <40-plex and sequenced on a NovaSeq 6000 (Illumina) using a 200 cycle SBS kit (Illumina) with paired-end reads at 101 bp length targeting >60 million reads per sample.
Quality control was performed on samples using FASTQC (v.0.11.5), multiqc (v.1.12), picardmetrics(v0.2.4), and bioconductor-dupRadar (v1.0.0) at respective steps. Single-end reads were mapped against Homo sapiens genome (GRCh38) using the STAR (v2.5.2b) aligner. Samples were quantified with the transcript abundances using featureCount (v1.5.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

source_name: lung

growth_protocol: H23 andH358 cells were seeded in 6-well micropatterned Aggrewell 400 low-attachment plates (StemCell) at 3.5 × 106cells/well in 4 mL of medium

extract_protocol:
RNA was isolated using an RNeasy spin column (Qiagen) according to the manufacturer’s instructions. After elution, RNA was quantified with the Quant-iT Ribogreen RNA Kit according to the manufacturer’s instructions (Invitrogen). All samples were normalized to 20 ng/μL, aliquoted and frozen at −80°C
For each sample, a total RNA input of 200 ng was used for library preparation using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina) and IDT for Illumina RNA UD Indexes Set A, Ligation (96 Indexes, 96 Samples).

value: lung

value: cancer cell line


title: H358_NT_MRTX849_BI3406_72h_2_rep2


title: WT_cDC1_2

source_name: spleen


title: WT_pDC_Ly6c_neg_2

value: pDC Ly6c-


title: SLC25A28-KO_week2_rep3

value: Colorectal carcinoma cell line


title: SLC25A28-KO_week2_rep2


title: H358_NT_MRTX849_BI3406_6h_2_rep2


title: SLC25A28-KO_week2_rep1


title: H358_NT_MRTX849_BI3406_72h_1_rep2


title: Red_H3K4me1_rep1

description: H3K4me1 ChIP-seq in red fruits, replicate 1,  'Red_Input_rep1' as input

source_name: receptacle

value: H3K4me1(Abcam, ab8895)


title: Red_H3K36me3_rep1

description: H3K36me3 ChIP-seq in red fruits, replicate 1,  'Red_Input_rep1' as input


title: Red_H3K4me1_rep2

description: H3K4me1 ChIP-seq in red fruits, replicate 2,  'Red_Input_rep2' as input


title: H358_NT_MRTX849_BI3406_72h_1_rep1


title: WT_pDC_Ly6c_pos_2

value: pDC Ly6c+


title: Red_sRNA_rep1

description: sRNA in the red-stage fruits

data_processing:
Clean reads were aligned to Fragaria vesca genome v4.0 using bowtie with dedault parameters
phasiRNA (21 nt and 24 nt) were extracted using 'sRNAminer'
Bigwig files were generated by UCSC tool "bedGraphToBigWig" using dedault parameters
Assembly: Fragaria vesca genome v4.0
Supplementary files format and content: bigwig files, enrichment of small RNAs.

extract_protocol:
The total RNA was extracted from the fruit tissue by ethanol precipitation and the CTAB-PBIOZOL reagent
After extraction, the total RNA was qualified and quantified using a Nano Drop (NanoDrop, Madison, USA) and Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA). The library was prepared with 1 µg of total RNA for each sample.


title: H358_NT_MRTX849_BI3406_6h_2_rep1


title: H358_NT_MRTX849_BI3406_6h_1_rep2


title: SLC16A3-KO_week5_rep3

value: AGTGTGTGCGTGAACCGCTT

value: Human Transporter KO (Addgene  #213695)


title: SLC16A3-KO_week5_rep2


title: KO_cDC2A_1

value: spleen

value: KO

value: PBS


title: preT_sRNA_rep1

description: sRNA in the preT-stage fruits


title: SLC16A3-KO_week5_rep1


title: KO_cDC1_1


title: H358_NT_MRTX849_72h_2_rep2


title: KO_pDC_Ly6c_neg_1


title: 8220 cells, shFUS, biol rep3

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

country: Spain

institute: Biogipuzkoa Health Research Institute

data_processing:
RNA-seq reads were quasi-mapped to the reference transcriptome hg38 and the abundance of each transcript was quantified using Salmon v.1.5.2. with default options for paired-end reads (Patro et al. 2017).
Output quants files were processed in R Studio v.4.0.4.
Tximport package was used for non-normalized gene-level counts estimation from transcript-level counts using the “bias corrected counts without an offset” method (Soneson, Love, and Robinson 2015).
The differential expression modelling and analysis were performed using the R package DEseq2 (Love, Huber, and Anders 2014).
Assembly: hg38
Supplementary files format and content: DEGs_LFC_adjp.xlsx contains Differentialy Expressed Genes with log2FC and statistics
Supplementary files format and content: Normalized_counts_shRNA_shTDP-43_shFUS.xlsx contains the abundance measurements for every sample (data prior to differential expression analysis)

growth_protocol: Skeletal Growth Medium (SGM, PromoCell) supplemented with 10% FBS, 1% Glutamax and 1% gentamicin.

extract_protocol:
Total RNA was extracted from independent experiments using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions, including DNase I treatment.
Libraries of Stranded Full-length Total RNA were prepared using Illumina Ribo-Zero Plus rRNA depletion kit

value: Inmortalized myoblasts

value: FUS knockdown


title: H358_NT_MRTX849_BI3406_6h_1_rep1


title: 8220 cells, shFUS, biol rep2


title: SLC16A3-KO_week2_rep3


title: KO_cDC2B_1


title: KO_pDC_Ly6c_pos_1


title: 8220 cells, shFUS, biol rep1


title: SLC16A3-KO_week2_rep2


title: H358_NT_MRTX849_72h_2_rep1


title: Y1.7_RTT_ROSA26

first: Anais

last: Elewaut

address: Vienna Biocenter 1

institute: IMP

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Three independent cellplex multiplexing libraries with equal pooling ratios of all samples were generated, and independently analyzed using cellranger multi (version 6.1.1). Filtered count matrices for all samples were merged in Seurat v4.3.0, and cells were quality filtered  retaining cells with more than 1000 detected genes and less than 15 percent of mitochondrial and less than 40 percent of ribosomal RNAs reads.
Assembly: mm10
Supplementary files format and content: Cellranger output files

source_name: Melanoma tumor

extract_protocol:
To be updated
Individual samples were CMO labelled, pooled and loaded three times on a Chromium chip. Gene expression (GEX) libraries were constructed according to manufacturer’s protocol using the 10x Genomics 3' CellPlex multiplex kit.

treatment_protocol: Tumors were isolated, cut into pieces, and digested for approximately 1.5 h at 37°C with collagenase A (1 mg/ml, Roche) and DNAse (20mg/ml, Worthington) in RPMI-1640 media. Digested tumors were strained through a 70um filter and resuspended in FACS buffer (0.5% BSA, 2mM EDTA). FC-block with anti-CD16/32 (clone 93, BioLegend) was performed for 10 min at 4°C to avoid unspecific antibody binding and staining was performed for 30 min at 4°C degrees. Samples were stained for CD45+ cells and live dead exclusion was performed by staining with the fixable viability dye eF780 (1:1000, eBioscience). For each condition 1 tumor was used.

value: Melanoma tumor

value: CD45+ Immune cell


title: 8220 cells, shTDP-43, biol rep3

value: TARDBP knockdown


title: H358_NT_MRTX849_72h_1_rep2

value: WT


title: H358_NT_MRTX849_72h_1_rep1

value: lung


title: Y1.7_RTT_PTGS12KO

description: 10x Genomics


title: 8220 cells, shTDP-43, biol rep1


title: Y1.7_RTT

description: 10x Genomics


title: SLC16A1-KO_week5_rep2

value: ACAGACGTATAGTTGCTGTA


title: 8220 cells, shTDP-43, biol rep2


title: H358_NT_MRTX849_6h_2_rep2

value: cancer cell line


title: Y1.7_NTT

description: 10x Genomics


title: 8220 cells, shControl, biol rep3


title: H358_NT_MRTX849_6h_2_rep1


title: C3H10T1-2_NSD123_SETD2_QKO_ATACseq_rep2

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

data_processing:
Raw ChIP-Seq reads were aligned to a combined reference of mm10 and dm6 genome assembly using BWA version 0.7.17 with default parameters. Afterwards, they were filtered using a cut-off of MAPQ < 3 using Samtools v.1.18.
Raw ATAC-Seq reads were trimmed and filtered for quality using Trimmomatic v0.39. Trimmed reads were mapped to the mm10 genome assembly using Bowtie2 v2.5.1, and non-uniquely mapping reads were removed. Afterwards, the reads were adjusted by shifting all positive-strand reads 4 bp downstream and all negative-strand reads 5 bp upstream to the center of the reads on the transposase binding event.
For H3K36me2 NSD1/2/3-SETD2-QKO and NSD1/2/3-SETD2-ASH1L-QuiKO replicates, samclip v.0.2 (samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam) was used to filter contaminated sequences prior to alignment.
ENCODE blacklisted regions were excluded from all analyses.
For ATAC-Seq samples, peak calling was performed on each replicate using MACS2 v2.2.6 with ‘-extsize 200 -shift -100 -nomodel’ parameters. To find a set of reproducible peaks across ATAC-Seq replicates, the irreproducible discovery rate (IDR) was calculated and peaks with an IDR greater than 0.05 across every pair of replicates were excluded.
bigWig files were generated using deepTools v3.5.3 bamCoverage with parameters '-b ${samp}.sorted.bam -o ${samp}.cpm.bw -p $nprocs --normalizeUsing CPM --centerReads -e 200'.
Replicates were merged using the deepTools v3.5.3 bigwigCompare tool. The initial merging step employed these parameters: '-b1 rep1 -b2 rep2 $outdir --operation mean -bs 200 -o $merged.step1.cpm.bw' while the final merging step utilized the following parameters: '-b1 $merged.step1.cpm.bw -b2 rep3 $outdir --operation mean -bs 200 -o $merged.final.cpm.bw.'
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax.

extract_protocol:
Approximately 20 million mMSC cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification of total levels of histone marks. The ChIP reactions were performed using the Diagenode SX-8G IP-Star Compact and Diagenode automated iDeal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hrs, followed by a 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq Kit for Histones). Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
ChIP-seq library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001). ChIP libraries were sequenced using the Illumina HiSeq 4000 at 50 bp single reads or NovaSeq 6000 at 100 bp single reads. ATAC-seq library preparation was performed according to the Omni-ATAC protocol. 50,000 C3H10T1/2 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 rcf for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 uL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O ) (Illumina Tagment DNA Enzyme and Buffer Small Kit, 20034197). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with DNA Clean and Concentrator 5 columns (Zymo Research). Illumina Nextera DNA Unique Dual Indexes Set C (Illumina, 20027215) were added and amplified (12 cycles) using NEBNext 2x MasterMix. Sequencing of the ATAC-Seq libraries was performed on the Illumina NovaSeq 6000 system using 100-bp paired-end sequencing.

value: Mouse mesechymal stem cells

value: NSD1/2/3 SETD2 quadruple knock-out


title: SLC16A1-KO_week5_rep1

value: Colorectal carcinoma cell line


title: 8220 cells, shControl, biol rep2


title: SLC16A1-KO_week2_rep3


title: H358_NT_MRTX849_6h_1_rep2


title: 8220 cells, shControl, biol rep1


title: H358_NT_MRTX849_6h_1_rep1


title: SLC16A1-KO_week2_rep2


title: C3H10T1-2_NSD123_SETD2_QKO_ATACseq_rep1


title: H358_NT_BI3406_6h_2_rep2


title: Poly(I:C) treated MuTuDC1940 replicate 3

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

data_processing:
Raw Illumina BCL files were converted to FASTQ files using bcl2fastq v2.20.0.422
RNASeq reads were pseudomapped to murine NCBI RefSeq transcript models using Kallisto 0.42.4 (Bray et al., 2016).
Assembly: GRCm38
Supplementary files format and content: tab-delimited FPKM for all samples, RefSeq transcript IDs as keys in first column

extract_protocol:
RNA was isolated from the MuTuDC1940 cells using the GeneJet RNA purification kit. Quality control of the preparation was performed by TapeStation RNAScreen Tape.
NEBNext Ultra II Directional RNA Library Prep: poly(A) capture

value: dendiritic cells

value: Activator/adjuvant poly(I:C)


title: SLC16A3-KO_week2_rep1

value: AGTGTGTGCGTGAACCGCTT

value: Human Transporter KO (Addgene  #213695)


title: SLC16A1-KO_week2_rep1


title: SLC16A1-KO_week5_rep3


title: SLC16A13-KO_week5_rep3

value: TTTGACCTTCGCTCCGACCC


title: H358_NT_BI3406_6h_2_rep1


title: Poly(I:C) treated MuTuDC1940 replicate 1


title: Y3.3_RTT/108157

description: 10x Genomics

data_processing:
ScRNAseq reads were processed with cellranger v6.1.1 (10X Genomics), using the prebuild 10X refdata-gex-mm10-2020-A.
Assembly: mm10
Supplementary files format and content: Cellranger output files

extract_protocol:
Tumors were isolated, cut into pieces, and digested for approximately 1.5 h at 37°C with collagenase A (1 mg/ml, Roche) and DNAse (20mg/ml, Worthington) in RPMI-1640 media. Digested tumors were strained through a 70um filter and resuspended in FACS buffer (0.5% BSA, 2mM EDTA). FC-block with anti-CD16/32 (clone 93, BioLegend) was performed for 10 min at 4°C to avoid unspecific antibody binding and staining was performed for 30 min at 4°C degrees. Samples were stained for CD45+ cells and live dead exclusion was performed by staining with the fixable viability dye eF780 (1:1000, eBioscience). Dissociated cell concentration after FACS was measured using NucleoCounter NC250 (Chemometec) following the manufacturer's instructions.
Library was constructed according to manufacturer’s protocol using the Chromium Next GEM Single cell 3’ kit, 10x Genomics


title: C3H10T1-2_NSD12_SETD2_TKO_ATACseq_rep1

value: NSD1/2 SETD2 triple knock-out


title: Y3.3_NTT/108155

description: 10x Genomics


title: H358_NT_BI3406_6h_1_rep2


title: SLC16A13-KO_week5_rep1


title: SLC16A13-KO_week5_rep2


title: Untreated MuTuDC1940 replicate 3

value: Untreated


title: H358_NT_BI3406_6h_1_rep1


title: H358_NT_6h_2_rep2

value: Vehicle


title: Y1.7_RTT_COX2i/S231731_229119

description: 10x Genomics

data_processing:
scRNAseq data was aligned and quantified using Cellranger (version 7.1.0) using references: refdata-gex-mm10-2020A and the Chromium_Mouse_Transcriptome_probe_Set_v1.0.1_mm10-2020-A.csv. Barcodes are provided as a separate (barcodes.csv) file.
Assembly: mm10
Supplementary files format and content: Cellranger output files

extract_protocol:
Dissociated cell concentration after FACS was measured using NucleoCounter NC250 (Chemometec) following the manufacturer's instructions. One million cells were fixed 22 hours at 4°C, quenched and long term stored at -80°C according to 10X genomic Fixation of Cells & Nuclei for Chromium Fixed RNA profiling (CG000478) using Chromium Next GEM Single Cell Fixed RNA Sample preparation kit (PN-1000414, 10X Genomics). 250,000 cells per sample were used for probe hybridization using the Chromium Fixed RNA Kit, Mouse Transcriptome, 4rxn x 4BC (PN-1000496, 10X Genomics), pooled equally and washed following the Pooled Wash Workflow as described in the Chromium Fixed RNA Profiling Reagent kit protocol (CG000527, 10X Genomics).
Library was constructed according to manufacturer’s protocol using the Chromium Fixed RNA profiling (10x Genomics)

treatment_protocol: Tumors were isolated, cut into pieces, and digested for approximately 1.5 h at 37°C with collagenase A (1 mg/ml, Roche) and DNAse (20mg/ml, Worthington) in RPMI-1640 media. Digested tumors were strained through a 70um filter and resuspended in FACS buffer (0.5% BSA, 2mM EDTA). FC-block with anti-CD16/32 (clone 93, BioLegend) was performed for 10 min at 4°C to avoid unspecific antibody binding and staining was performed for 30 min at 4°C degrees. Samples were stained for CD45+ cells and live dead exclusion was performed by staining with the fixable viability dye eF780 (1:1000, eBioscience). For each condition, 3 individual tumors were pooled before the FACS.

value: Melanoma tumor

value: CD45+ Immune cell

value: Celecoxib (COX2i)


title: SLC16A13-KO_week2_rep3


title: C3H10T1-2_NSD12_SETD2_TKO_ATACseq_rep2


title: Untreated MuTuDC1940 replicate 2


title: Y1.7_RTT_COX2i_Aza/S231731_229120

description: 10x Genomics

value: Celecoxib (COX2i) + 5-Azacytidine


title: H358_NT_6h_2_rep1

value: lung

value: WT


title: Y1.7_RTT_IRF3.7_OE/S231731_229118

description: 10x Genomics


title: SLC16A13-KO_week2_rep1


title: H358_NT_6h_1_rep2

value: cancer cell line


title: Poly(I:C) treated MuTuDC1940 replicate 2


title: WT_week7_rep3

value: HCT116 (RRID:CVCL_0291)


title: H358_NT_6h_1_rep1


title: 4T1, Leflu, rep 3

city: Ottawa

first: Julie

last: St-Pierre

address: 451 Smyth Rd

institute: University of Ottawa

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed sequences were aligned to the reference mouse genome version GRCm38
Gene expressions were computed using RSEM in order to obtain normalized gene level expression for these stranded RNA libraries
Assembly: mm10
Supplementary files format and content: comma-separated values file containing RSEM counts for each sample

extract_protocol:
RNA was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher). DNA was removed using an on-column DNAse protocol.
Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) with a poly-A selection (Thermo Scientific).

value: Mammary carcinoma

value: Leflu


title: 4T1, DMSO, rep 3

value: DMSO


title: CKO-Rep3

city: shanghai

first: bao

last: wang

address: jin zun road

institute: shanghai jiao tong university school of medicine

data_processing:
The sequencing data were aligned to the mouse reference genome (mm10) using the STAR aligner (version 2.7.3a). All mapped reads were subsequently counted using HTSeq (version 0.12.4).
Assembly: mm10

source_name: Naive CD4+ T cells

extract_protocol: RNA-seq libraries were constructed by Anoroad (Beijing, China) using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-01/02) according to the manufacturer’s instructions.

treatment_protocol: Mice spleen were harvested and CD4+ naive T cells were enriched by magnetic beads. Cells were activated using CD3/CD28 antibody for 24 hours followed by RNA-sequencing.

value: Naive CD4+ T cells

value: Satb1 conditional knockout


title: 4T1, Leflu, rep 2


title: AIG Patient 3

city: St. Louis

first: Richard

last: DiPaolo

state: MO

address: 1100 S Grand Ave

institute: Saint Louis Univeristy

description: 10x Genomics

data_processing:
Raw data were processed using cellranger-6. Conditional repeats were combined using cellranger aggr. Analysis was conducted in R using Seurat. Each dataset was filtered to exclude cells with low gene expression (<500/cell), high gene counts (outliers), and high percent mitochondrial transcript load (>25%/cell). Per species, datasets were merged, normalized, scaled, and dimensionally reduced. Layers were joined and clusters were generated using a resolution of 0.8 for mouse and 1.2 for human datasets. Cluster identities were established by attaining global distinguishing genes per cluster and relating them to known profiles for gastric epithelial cells.
Signature scores were calculated using AddModuleScore. Scores were generated for each cell based on overall average gene expression across signature transcripts. Signature scores were normalized by subtracting average expression of randomly selected control genes, resulting in a relative per-cell signature score. Signatures were either extracted from the Molecular Signatures Database or generated from known metaplasia- and cancer-associated transcripts (Supplementals Tables 2 and 3) or from cluster defining transcripts within the original dataset (Supplemental Tables 4 and 5). Epithelial cell label transfers were created by transferring cluster labels from the Hp tumor biopsies onto the metaplastic subclusters using the Satija Lab reference-mapping approach.
See full code for reproducing figures on our GitHub repository: github.com/hoftsg/Hoft_et_al_2024.git.
Assembly: Mus musculus - mm10-2020-A, Homo sapiens - GRCh38-2020-A
Supplementary files format and content: All samples include files processed on cellranger 6. Replicates were aggregated together prior to processing. Each sample includes a filtered feature, barcode, and matrix file.

source_name: Corpus

extract_protocol:
Corpus tissues were obtained from 2-7 mice per group and 3 AIG patients. Tissues were rinsed in PBS and placed in a 50mL conical with 10mL gland digest buffer: Advanced DMEM (Thermo Fisher), 20mM HEPES (Thermo Fisher), 0.2% BSA (MilliporeSigma, Burlington, MA), 50μg/mL gentamicin (MilliporeSigma), 1% penicillin/streptomycin (MilliporeSigma), DNaseI (100U/mL; MilliporeSigma). 1mg/mL collagenase 1A (MilliporeSigma) was added to each tube prior to 37C incubation with constant shaking for 20-45 minutes. Samples were then checked for presence of gastric glands, rinsed, and spun down (50RCF for 10 minutes). Samples were resuspended in 1mL/stomach prewarmed Trypsin-EDTA (MilliporeSigma) and incubated for ~25 minutes at 37C, agitating every 5-10 minutes. Digestion was considered complete when single cells were observed. Cells were then washed twice with DMEM plus 10% fetal bovine serum. Cells were filtered twice, counted, and resuspended to a final cell concentration of ~1,000 cells/uL. Viability of each sample was confirmed to be greater than 70% by trypan blue staining (Thermo Fisher).
Library construction of mouse tissues was performed at Saint Louis University and construction of AIG human libraries was performed at the Washington University in Saint Louis Genome Technology Access Center. To generate libraries, the Chromium Controller (10X Genomics, Pleasanton, CA) was used following manufacturer protocols. Libraries were prepared using the Chromium Next GEM Single Cell 5' Kit v2 (1000263, 10X Genomics). Each library was generated to have a maximum recovery of 10,000 cells. PCR reactions were conducted in the T100 Thermal Cycler (BioRad, Hercules, CA). Final quality control was performed on the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA) and libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA).

value: Corpus

value: autoimmune gastritis (AIG)


title: 4T1, DMSO, rep 2


title: AIG Patient 2

description: 10x Genomics


title: WT_week7_rep1

value: Colorectal carcinoma cell line

value: Human Transporter KO (Addgene  #213695)


title: CKO-Rep2


title: CKO-Rep1


title: WT_week7_rep2


title: 4T1, Leflu, rep 1


title: SLC16A13-KO_week2_rep2

value: TTTGACCTTCGCTCCGACCC


title: WT_week6_rep3


title: Untreated MuTuDC1940 replicate 1

value: dendiritic cells

value: Untreated


title: AIG Patient 1

description: 10x Genomics


title: CON-Rep3


title: Y1.7_RTT_mCherry_CTRL/S231731_229117

description: 10x Genomics

value: Melanoma tumor

value: CD45+ Immune cell


title: 4T1, DMSO, rep 1

value: WT


title: CON-Rep2


title: Sort 15B, Placebo

city: New Haven

first: Ana

last: Lledo Delgado

state: CONNECTICUT

address: 300 George St

department: Immunobiology

institute: Yale University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v3.1
Hashtag 1; Baseline. Hashtag 2; 3 months. Hashtag 3: 18 months Hashtag 4: Baseline. Hashtag 5: 3months. Hashtag 6: 18 months
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: PBMCs

extract_protocol:
PBMCs (25 x 105 cells) per patient and visit were reconstituted with wash buffer and incubated with Human TrueStain Fc Blocker (Biolegend) 10 minutes. TotalSeq antibodies were applied without washing the cells and were incubated at 4 °C for 30 min. After 3 rounds of washing, samples were pooled into one tube based on cell counts, and super-loaded onto the 10× Chromium Chip.
The loaded Chip was generated and processed by YCGA (Yale Center for Genome Analysis).The cDNA samples were used to construct 2 types of cDNA libraries, according to the steps outlined in the user guide: gene expression libraries and cell surface hashtag libraries. cDNA libraries were then sequenced on an Illumina Novaseq 6000 platform.

value: PBMCs

value: EBV Negative

value: Placebo


title: 4T1, Mff KO, clone 2, rep 3

value: Mammary carcinoma

value: Mff KO


title: 4T1, Mff KO, clone 1, rep 3


title: WT_week6_rep2

value: HCT116 (RRID:CVCL_0291)


title: WT_week5_rep3


title: 4T1, Fis1 KO, clone 2, rep 3

value: Fis1 KO


title: Sort14B, Teplizumab

description: 10x Genomics

value: Teplizumab


title: Fenofibrate4

city: Gwangju

first: JiWon

last: Park

address: 123, Cheomdangwagi-ro, Buk-gu

department: Biomedical Science and Technology

institute: Gwangju Institute of Science Technology

data_processing:
adaptor sequence and raw qaulity reads were trimmed thorugh cutadptor v.2.10 followed by aligning to the GRCm38.101 genome using STAR v.2.7.3 and then duplicated reads were removed by Mark duplicates v2.23.3. Processed reads mapped into the mouse genome, were counted by HT-seq count v.0.6.1.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text files

source_name: db/db,Fenofibrate, 8week

growth_protocol: Male C57BLKS/J-Lepr (db/db) mice were donated by Jackson Laboratories for this investigation (Shizuoka Laboratory Center, SLC). Mice were fed a standard chow diet and given unlimited access to water while being housed in a 12-hour light-dark cycle at room temperature (22°C).

extract_protocol:
RNA was harvested using trizol. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using llumina Stranded mRNA Prep kit following manufacturer's protocols.

treatment_protocol: Fenofibrate (#F6020) and corn oil (#C8267). Mice were conditioned at 5 weeks of age and treated between 6 and 18 weeks of age. Fenofibrate was given at a dose of 100 mg/kg/day

value: heart

value: C57BLKS/J-Lepr (db/db)

value: Fenofibrate 100mg/kg/day


title: Sort 14A, Teplizumab

description: 10x Genomics

value: EBV Positive


title: WT_week5_rep2

value: Colorectal carcinoma cell line

value: Human Transporter KO (Addgene  #213695)


title: Fenofibrate3


title: WT_week5_rep1


title: 4T1, Drp1 KO, clone 2, rep 3

value: Drp1 KO


title: Fenofibrate2


title: Sort 13B, Placebo

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software v3.1
Hashtag 1; Baseline. Hashtag 2; 3 months. Hashtag 3: 18 months Hashtag 4: Baseline. Hashtag 5: 3months. Hashtag 6: 18 months
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files
Library strategy: CITE-seq


title: Sort 13A, Teplizumab

description: 10x Genomics


title: WT_week3_rep3


title: 4T1, Drp1 KO, clone 1, rep 3


title: Sort 15A, Teplizumab

description: 10x Genomics


title: Sort 12B, Placebo

description: 10x Genomics


title: Fenofibrate1


title: WT_week3_rep2


title: WT_week6_rep1


title: WT_week3_rep1


title: Sort 12A, Teplizumab

description: 10x Genomics


title: 4T1, Mff KO, clone 2, rep 2


title: 4T1, parental, rep 3


title: CON-Rep1

value: Naive CD4+ T cells


title: Sort 10B, Placebo

description: 10x Genomics


title: 4T1, Mff KO, clone 1, rep 2


title: Control1

source_name: db/db, Corn oil, 8week

value: Corn oil


title: Sort 10A, Placebo

description: 10x Genomics

value: PBMCs


title: Control2


title: HiC data for COLO320-DM cell line, Replicate 1.

city: Stanford

first: Matthew

middle: G

last: Jones

state: MA

address: 500 Main Street (Building 76)

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Paired-end HiC reads were aligned to hg19 genome with the HiC- Pro pipeline ( Servant, Varoquaux et al. 2015 PMID: 26619908). Pipeline was set to default and set to assign reads to DpnII restriction fragments and filter for valid pairs. The data was then binned to generate raw contact maps which then underwent ICE normalization to remove biases.
Assembly: hg19
Supplementary files format and content: Contact matrices for HiC data.

growth_protocol: COLO320-DM cells were maintained in RPMI; Life Technologies, Cat# 11875-119 supplemented with 10% fetal bovine serum (FBS; Hyclone, Cat# SH30396.03) and 1% penicillin-streptomycin (pen-strep; Thermo Fisher, Cat# 15140-122).

extract_protocol:
Hi-C libraries were generated as described previously  following a standard protocol  (Rao, Huntley et al. 2014 PMID: 25497547)
Hi-C libraries were generated as described previously  following a standard protocol  (Rao, Huntley et al. 2014 PMID: 25497547)

treatment_protocol: Ten million cells were fixed in 1% formaldehyde in aliquots of one million cells each for 10 minutes at room temperature and combined after fixation.


title: HiC data for COLO320-DM cell line, Replicate 2.


title: 4T1, Fis1 KO, clone 1, rep 3


title: 4T1, Fis1 KO, clone 2, rep 2


title: Sort 9B, Placebo

description: 10x Genomics

value: EBV Negative


title: 4T1, Fis1 KO, clone 1, rep 2


title: Zebrafish, usp39, 4

city: Frankfurt

first: Cristian

last: Prieto-Garcia

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute of Biochemistry II

data_processing:
BCL convert, v4.0.3
Sequence reads were trimmed for adaptor sequences/low-quality sequences using Trimmomatic, v0.40-rc1, parameters ILLUMINACLIP: TruSeq3-SE.fa:2:30:10; CROP:111; HEADCROP:12
GENCODE annotation was used to map reads to the zebrafish genome (version Danio_rerio.GRCz11.110) with STAR, v2.7.11a, parameters: --runMode alignReads: --outSAMtype BAM SortedByCoordinate;
Count reads into exons was determined by using the htseq-count, v1.99.2
Differential gene expression analysis was done with DESeq2, v1.42.1
Assembly: Danio_rerio.GRCz11.110
Supplementary files format and content: tab-delminted text file includes raw count for each Sample

organism: Danio rerio

source_name: whole organism

extract_protocol:
Samples were homogenized in 200 µl RNAzol® RT (Sigma-Aldrich) in gentleMACS™ M Tubes using gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec), program RNA_02.01. RNA was extracted following the RNAzol® RT extraction protocol.
Ribosomal RNA was depleted from 1.0 µg total RNA using RiboCop rRNA Depletion Kit for Human/Mouse/Rat (Lexogen) following the manufacturer’s instructions. Sequencing libraries were generated using the CORALL RNA-Seq kits (Lexogen) following the manufacturer’s instructions.

value: whole organism

value: AB line

value: ups39 CRISPR/Cas9 KO


title: HS+TSA 0.05µM_day2_rep3

city: Wageningen

first: Anneke

last: Horstman

state: Nederland

address: Droevendaalsesteeg,

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research

data_processing:
Before mapping of the reads to the Brassica napus genome, raw reads were trimmed by removing adapter sequences.
The reads were aligned to the B. napus genome (version 4.1; http::/brassicadb.org) using Tophat2 with zero mismatches allowed
Count tables were generated using HTSeq-count
Assembly: B. napus genome (version 4.1; http::/brassicadb.org)
Supplementary files format and content: Joint_count_table.xlsx: raw counts generated with HTSeq-count

organism: Brassica napus

source_name: microspores + pollen + embryogenic cells

growth_protocol: Microspore isolation was performed according to the protocol described by (Custers, 2003).

extract_protocol:
Each sample (400,000 - 1,000,000 microspores) was disrupted with stainless steel beads and RNA was using the InviTrap Spin Plant RNA Mini Kit (Stratec).
DNAse-treated RNA was used as template for RNA-seq library preparation (TruSeq RNA Library Prep Kit).

treatment_protocol: To induce microspore embryogenesis, the microspores in culture were treated with heat stress (at 33 °C) and the histone deacetylase inhibitor (HDACi) trichostatin A (TSA) at a concentration of 0.05µM for 24-hrs. To induce pollen development, microspores were treated with DMSO (as a control for TSA) and cultured at 25 °C. After 24-hrs, TSA (or DMSO) was removed by centrifugation and the cultures were refreshed with new NLN-13 medium. All cultures were then moved to 25 °C for 1 additional day, and collected at day 2.

value: late unicellular microspores

value: heat shock + TSA 0.05µM


title: Control4


title: HS+TSA 0.05µM_day2_rep2

value: microspores + pollen + embryogenic cells


title: Control3

value: heart


title: Sort 8B, Teplizumab

description: 10x Genomics

value: Teplizumab


title: HS+TSA 0.05µM_day2_rep1


title: Zebrafish, usp39, 2


title: Sort 8A, Teplizumab,

description: 10x Genomics


title: 4T1, Drp1 KO, clone 1, rep 2

value: Mammary carcinoma


title: Zebrafish, usp39, 1


title: Pollen_day2_rep3

source_name: microspores + pollen

value: microspores + pollen

value: untreated


title: 4T1, parental, rep 2

value: WT


title: Pollen_day2_rep2


title: Zebrafish, gfp, 4


title: 4T1, Mff KO, clone 2, rep 1

value: Mff KO


title: Zebrafish, gfp, 3


title: 4T1, Mff KO, clone 1, rep 1


title: Pollen_day2_rep1


title: Donor 16, PAK1

city: Duarte

first: Debbie

last: Thurmond

state: CA

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

institute: City of Hope

data_processing:
RNA-seq raw fastq reads were aligned to the human hg19 genome using TopHat2.
Gene counts were obtained using htseq-count, with UCSC known gene annotations (TxDb.Hsapiens.UCSC.hg19.knownGene), and converted into counts per million (CPM) using edgeR.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with columns containing raw gene counts from each sample.

source_name: Pancreatic islets

extract_protocol:
RNA extraction was performed using QIAGEN RNase kit.
250ng of total RNA from each samples was used for sequencing library preperation with KAPA mRNA Hyperp Kit according to user manual. The library QC was checked with Agilent bioanalyzer DNA high sensitivity chip, and qubit was used for library quantification. The final libries were sequenced on Illumina Hiseq2500 wtih single read mode of 51 cyles, plus 7 cycles of index sequencing with V4 kit.

value: Pancreatic islets

tag: individual

value: Donor 16

tag: disease state

value: Type 2 diabetes


title: Sort 9A, Placebo

description: 10x Genomics

tag: tissue

value: PBMCs

value: EBV Positive

value: Placebo


title: Zebrafish, gfp, 2

value: whole organism

tag: strain

value: AB line


title: 4T1, Fis1 KO, clone 2, rep 1

tag: cell line

tag: cell type

value: Fis1 KO


title: 4T1, Drp1 KO, clone 2, rep 2

tag: genotype

value: Drp1 KO


title: Zebrafish, usp39, 3

value: ups39 CRISPR/Cas9 KO


title: Donor 16, Ctrl

value: Ctrl


title: 4T1, Fis1 KO, clone 1, rep 1

value: Mammary carcinoma


title: Zebrafish, gfp, 1


title: Donor 15, PAK1

value: Donor 15

value: ND


title: TLu10_2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural 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 mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: testis

extract_protocol:
testis were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: testis

tag: age

value: 8 weeks


title: Donor 15, Ctrl

value: Pancreatic islets


title: 4T1, Drp1 KO, clone 2, rep 1


title: 4T1, Drp1 KO, clone 1, rep 1


title: MSCs, three-dimensional, scRNA-Seq

city: Shenzhen

first: Ruiqing

last: Lu

state: Guangdong

address: Taoyuan Street, Nanshan District

institute: Tsinghua University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.  In barcodes.tsv.gz, barcode-1 corresponds to 2D and  barcode-2 corresponds to 3D.

source_name: Placenta

growth_protocol: Cells were cultured in monolayers in Dulbecco's modified Eagle's medium (DMEM; Corning) supplemented with 10% fetal bovine serum (FBS) at 37°C and 5% CO2, and subcultured when reaching 85% confluence. MSC in total passage 5-6 were subjected to 3D spheroid culture for 60 h in a culture spinner

extract_protocol:
To obtain single cells, the 2D and 3D cell were digested with 0.05% trypsin containing 0.53 mM EDTA for 3-5 min. Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
Library was performed according to the manufacture's instructions (Chromium Single Cell 3ʹ Reagent Kits v3.1. 10x Genomics). Briefly, MSCs were resuspended in the master mix loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Appropriated sized fragments were selected with SPRlselect reagent for subsequent library construction. P5 and P7 primers, and TruSeq Read2 (read2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Placenta

value: Primary cell

value: Mesenchymal stem cells

value: Wild type

tag: treatment

value: Three-dimensional spherical culture


title: TLu10_1


title: Donor 14, PAK1

value: Donor 14

value: Type 2 diabetes


title: Donor 13, PAK1

value: Donor 13


title: Tcon_3

description: Control


title: GPR64_Control

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Muscle

growth_protocol: A673 cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum. 10 microgram/ml insulin, and 55 microM beta-mercaptoethanol. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Invitrogen).
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: A673 cells were transfected with either scrambled-siRNA or SMPD1-siRNAs or GPR64-siRNA for 48 hours. Transfection was carried out  using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol.

value: Muscle

value: A673 cell line

value: Ewing Sarcxoma

value: scrambled-siRNA control


title: MSCs, two-dimensional, scRNA-Seq

value: Two-dimensional adhesion culture


title: 4T1, parental, rep 1

value: Mammary carcinoma

value: WT


title: Donor 14, Ctrl

value: Ctrl


title: Tcon_2

description: Control

value: ICR

value: testis

value: 8 weeks


title: GPR64_siRNA

value: GPR64 knockdown


title: Donor 13, Ctrl

value: Pancreatic islets


title: Tcon_1

description: Control


title: p74-myc-PAK1

data_processing:
The 75-nt single-end (SE75) sequence reads were mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings). Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
The tags were extended in silico (using Active Motif software) at their 3 ́- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. The fragment density was determined in 32-nt bins along the genome and stored in bigWig (.bw) files.
Peaks were called using MACS2.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: Excel file with peak intensities and genomic annotations.

extract_protocol:
Cells were treated with 1% paraformadehyde at room temperature for 20 mins. Quenched cell lysate was sonicated to generate DNA fragments using Bioruptor (Diagenode).
Genomic DNA was prepared by treating aliquots of chromatin with Rnase, proteinase K and heat (overnight, 65 degrees C), followed by SPR1 bead clean up and quantified using a CLARIOstar microplate reader. An aliquot of chromatin was precleared with protein agarose beads. Genomic DNA regions of interest were isolated using antibody against myc-tag. Illumina sequencing libraries were prepared from the input DNA using standard enzymatic steps of end-polishing, dA-addition, and adapter ligation using an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: Human EndoC-H1 cells

value: MygTag antibody (Abcam, Cat# ab9132, Lot# GR3235624-5)


title: TBLu10_3


title: Donor10, PAK1

value: ND


title: p84-myc-PAK1


title: TBLu10_2


title: Donor9, PAK1


title: TLu10_3


title: TBLu10_1


title: Donor9, Ctrl


title: Donor8, Ctrl


title: TB_2

description: busulfan


title: Donor8, PAK1


title: TB_1

description: busulfan


title: Donor5, PAK1

value: Type 2 diabetes


title: Donor4, PAK1


title: Donor5, Ctrl


title: SLu10_2

extract_protocol:
spleen were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen


title: Donor4, Ctrl


title: Donor10, Ctrl


title: SLu10_1


title: Scon_3

description: Control


title: Donor3, PAK1


title: RWPE1_shcontrol

city: Sacramento

first: yatian

last: yang

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

value: normal prostate cell

value: shctrl

tag: time

value: 48 hours


title: Scon_2

description: Control


title: RWPE1_shNR1D1


title: UCB CD34+ cells_7-day expanded without SR1_Rep3

city: Pretoria

first: Juanita

last: Mellet

state: Gauteng

address: 5 Bophelo road

department: Immunology

country: South Africa

institute: University of Pretoria

hyb_protocol: Following fragmentation, cRNA were hybridized for 17 hours in an Affymetrix GeneChip® Hybridization Oven-645 at 45⁰C rotating at 60 rpm to the Affymetrix GeneChip® Human Gene 2.0 ST arrays. The hybridized chips were washed and stained in an Affymetrix GeneChip® Fluidics Station-450Dx.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip® Scanner-7G.

data_processing: The CEL files were imported into Affymetrix Transcriptome Analysis Console™ (TAC) Software 4.0 to perform background correction, summarization, normalization and calculation of expression values using default analysis settings.

label: Biotin

source_name: Umbilical cord blood CD34+ cells, expanded for 7 days without SR1

label_protocol: Biotinylated cRNA were prepared according to the manufacturer’s manual.

growth_protocol: StemSpan animal component free (ACF) medium supplemented with 2% penicillin (100 units/mL), streptomycin (0.1 mg/mL) and recombinant human growth factors, each at 100 ng/mL: Stem cell factor (SCF), thrombopoietin (TPO), FMS-like tyrosine kinase 3 ligand (FLT3L), granulocyte colony stimulating factor (G-CSF) and interleukin 3 (IL-3). Cultures were maintained at 37⁰C and 5% CO2 in a humidified atmosphere for 7 days.

extract_protocol: The Qiagen RNeasy Micro Plus kit was used to perform RNA extractions according to the manufacturer’s instructions.

treatment_protocol: SR1 was dissolved in dimethyl sulfoxide (DMSO) and further dilutions were made using StemSpan ACF to achieve a final concentrations of 1 µM.

value: Umbilical cord blood

value: CD34+ cells

tag: time point

value: 7 days

value: no


title: UCB CD34+ cells_7-day expanded with SR1_Rep2

source_name: Umbilical cord blood CD34+ cells, expanded for 7 days with SR1

value: yes


title: Scon_1

description: Control

source_name: spleen

value: ICR


title: TB_3

description: busulfan

value: testis

value: 8 weeks