title: JH35_WT_2466_2629199__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R02C01

value: tumors


title: LPS_1

status: Public on Apr 09 2025

type: SRA

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

country: China

institute: Northwestern Polytechnical University

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: BMDM

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the 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). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: tissue

value: BMDM

tag: cell line

tag: cell type

value: Bone marrow-derived macrophages

tag: genotype

value: WT

tag: treatment

value: LPS


title: WT-p18-PolII_rep2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

library_source: genomic

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

molecule: genomic DNA

source_name: Mammary gland

growth_protocol: Mouse mammary gland tissues were harvested at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 10min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-271542), STAT5B (ThermoFisher scientific, 13-5300), NFIB (Sigma-Aldrich, HPA003956), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 or Novaseq 6000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: strain

tag: Stage

value: day 18 of pregnancy (p18)

tag: chip-seq antibody

value: RNA polymerase II (Abcam, ab5408)


title: Infected Salivary Gland, time 08, LD, Sample 2

city: Berkeley

first: Filipa

last: Rijo-Ferreira

state: CA

address: Koshland Hall

institute: UC Berkeley

description: Library name: Sample 12

data_processing:
FASTQC
STAR
Cutadapt
Assembly: PlasmoDB-26_PbergheiANKA from plasmoDB.org and Anopheles-stephensi-SDA-500_AsteS1.6 from vectorbase.org
Supplementary files format and content: RPKMs for each organism and timepoint

molecule: polyA RNA

organism:
Plasmodium berghei
Anopheles stephensi

source_name: Salivary glands

extract_protocol:
RNA was extracted using Trizol LS reagent according to manufactor's instructions.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol:
[infection protocol]  Anopheles stephensi mosquitos were reared at 28°C and 80% humidity under a 12-h/ 12-h light/dark cycle and fed on 10% glucose (Sigma) and 0.2% 4-aminobenzoic acid (Millipore Sigma) in MilliQ water changed daily. Female Anopheles stephensi mosquitos 4-5 days old were allowed to bite two mice (BALB/c, male, 7-8 weeks of age) infected with Plasmodium berghei ANKA (GFPcon, 259cl2 for one hour). After the infectious bloodmeal, mosquitos were kept in 12h light/12h dark, at constant temperature of 20ºC. Mosquitos were fed by cotton pads soaked with 10% glucose (Sigma) and 0.2% 4-aminobenzoic acid (Millipore Sigma) in MilliQ water changed daily.
[collection protocol] Two independent experiments were done. On day 16 post-bloodmeal, mosquitos were divided into smaller cages holding ~30-40 mosquitos. On day 19, mosquitos were either maintained in the 12h light/dark schedule (LD) or kept in constant darkness (DD) for salivary gland collection that started on day 20 every 4h for 2 days (experiment 1) or on day 21 for 3 days (experiment 2). When combining both experiments, for each dataset (LD or DD) the first 48h (13 timepoints) have two independent experiments, each timepoint with a pool of salivary glands from ~20 mosquitos. The additional 24h (6 timepoints) have one replicate of pooled salivary glands (~20 mosquitos). Each dissected mosquito showed ~30-50,000 sporozoites/mosquito. Mosquito euthanasia was achieved by CO2 to avoid a putative cold shock response of gene expression. Dissections of salivary glands were performed in PBS with RNAse inhibitor (Invitrogen) (0.1U/μl) to avoid a nutrient rich environment that could reset the circadian rhythm of cells and each dissected tissue was snap frozen with a minimum volume of PBS. RNA was extracted from whole salivary glands using TRIzol LS according to manufacturer’s instructions (Life Technologies). Measurements were taken from the samples discussed in this paragraph.

value: Salivary glands

value: light/dark


title: WT-p18-PolII_rep1


title: PBS-1

city: Shanghai

first: Jia

middle: bing

last: Li

address: 197, Ruijin Er Street

institute: Shanghaijiaotong university

description: CDX model in C57 mice treated with PBS

data_processing:
The raw reads were initially processed using FastQC (v0.10.1) for quality control;
adapter sequences and poor-quality reads were removed using Cutadapt (v1.9.1)
Quality-filtered reads were then aligned to the Mus musculus genome (GRCm38) using HISAT2 (v2.0.1)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: tumor

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
Total RNA was isolated using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: condition

value: C57 mice control group

value: tumor

value: PBS


title: JH35_MUT_2361_2629204__mousemethylation

type: genomic

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R01C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data processing involved reading IDAT files using the minfi (v1.44) and sesame (v1.61) packages, with normalization steps including quality masking, inferring Infinium I channel, dye bias correction, and PooBah adjustment to generate beta values for methylation levels (betas_table.txt)

label: Cy5 and Cy3

source_name: tumor,mouse

label_protocol: Standard Illumina Protocol

growth_protocol: For Elp1HET or WT ;Ptch1gRNA MB models, GNPs were isolated from cerebella of P7 Elp1+/-;Cas9-eGFP mice (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J, JAX#024858) and cultured on Poly-D-Lysine coated dishes in Granule Cell Medium (GCM) (50 ml Neurobasal Medium containing 1x Penicillin/Streptomycin, 2 mM Glutamine, 4.5% D-(+)-Glucose, 1x SPITE Medium Supplement, 1x Oleic Acid Albumin/Linoleic Acid, 1x B27, 1x N-Acetyl Cysteine), and 1 μg/ml recombinant mouse Shh (PeproTech, Inc. Cat#100-45). Next day, the transduction was performed with lentivirus mix carrying guide RNA targeting Ptch1 (gRNA-31 GAGATCTCAGAGCGTGGCT and gRNA-41 GCATAGTGATATGGGTTTCG). After 24 h, the GNPs were harvested from the dishes and suspended in ice cold PBS.For Elp1WT or gRNA;Ptch1gRNA;p53NULL MB models, GNPs were isolated from cerebella of P7 p53NULL mice (B6.129S2-Trp53tm1Tyj/J, JAX#002101) and subjected to the same procedures as described above, except that the virus carrying guide RNA targeting Elp1 was also added for transduction to knockout both the alleles of Elp1 (gRNA-17 TATGACGTCCCCAGAGG).

extract_protocol: Genomic DNA was isolated from tissue samples using the AllPrep DNA/RNA Mini Kit (QIAGEN)

treatment_protocol: NSG mice were injected orthotopically with 1 million cells and monitored for signs of tumor growth with biweekly MRI imaging. Mice were observed daily and euthanized at the onset of signs of sickness including lethargy and neurological abnormalities.


title: PBS-2

description: CDX model in C57 mice treated with PBS


title: JH35_WT_2464_2629197__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R06C02


title: Infected Salivary Gland, time 08, DD, Sample 2

description: Library name: Sample 10

value: dark


title: Reg-3

description: tumor tissues from ATO-treated p53R282W/R282W mice  with T-lymphomas in tumor-regression status at  day 150 after birth

source_name: thymus

value: W/W mice R group

value: thymus

value: W/W

value: ATO


title: Infected Salivary Gland, time 08, LD, Sample 1

description: Library name: Sample 11


title: STAT5B-Y665F-p13-H3K27ac_rep3

value: day 13 of pregnancy (p13)

value: H3K27ac (Abcam, ab4729)


title: JH35_WT_2237_2629191__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R06C01

value: tumors


title: Infected Salivary Gland, time 08, DD, Sample 1

description: Library name: Sample 9

value: WT


title: Reg-2


title: STAT5B-Y665F-p13-STAT5B_rep2

value: Mammary gland

value: STAT5B (ThermoFisher scientific, 13-5300)


title: JH35_WT_2235_2629190__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R05C01


title: Infected Salivary Gland, time 04, DD, Sample 2

description: Library name: Sample 6


title: JH35_WT_2461_2629196__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R05C02


title: STAT5B-Y665F-p13-H3K27ac_rep2


title: Infected Salivary Gland, time 12, LD, Sample 1

description: Library name: Sample 15


title: JH35_WT_2234_2629189__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R04C01


title: Infected Salivary Gland, time 04, LD, Sample 2

description: Library name: Sample 8


title: Reg-1


title: STAT5B-Y665F-p13-PolII_rep2

value: RNA polymerase II (Abcam, ab5408)


title: Infected Salivary Gland, time 00, LD, Sample 2

description: Library name: Sample 4

value: Salivary glands


title: Infected Salivary Gland, time 04, LD, Sample 1

description: Library name: Sample 7

value: light/dark


title: NonReg-3

description: tumor tissues from ATO-treated p53R282W/R282W mice  with T-lymphomas in tumor-progression status at  day 150 after birth

value: W/W mice NR group


title: STAT5B-Y665F-p13-H3K27ac_rep1


title: ctl-3

description: tumor tissues from p53R282W/R282W mice with T-lymphomas at  day 150 after birth

value: W/W mice control group

value: water


title: JH35_WT_2452_2629195__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R04C02


title: Infected Salivary Gland, time 00, LD, Sample 1

description: Library name: Sample 3


title: STAT5B-Y665F-p13-PolII_rep1


title: STAT5B-Y665F-p13-STAT5B_rep1


title: STAT5B-Y665F-p13-NFIB_rep1

value: NFIB (Sigma-Aldrich, HPA003956)


title: JH35_WT_2241_2629192__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R01C02


title: JH35_WT_2465_2629198__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
207363410070_R01C01


title: NonReg-1


title: JH35_WT_2245_2629194__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R03C02


title: JH35_WT_2243_2629193__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206975990056_R02C02


title: Infected Salivary Gland, time 00, DD, Sample 2

description: Library name: Sample 2

value: dark


title: JH35W_2227_2580545__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R06C01


title: WT-p13-STAT5B_rep2


title: ctl-1

value: thymus


title: Infected Salivary Gland, time 04, DD, Sample 1

description: Library name: Sample 5


title: JH35M_2354_2580544__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R05C01


title: NonReg-2

value: W/W


title: Infected Salivary Gland, time 00, DD, Sample 1

description: Library name: Sample 1


title: Methylobacterium extorquens SLI 505 in 50 mM methanol, biological replicate C

first: N. Cecilia

last: Martinez-Gomez

address: 421 Koshland Hall

department: Plant and Microbial Biology

description:
Library name: M.ext_SLI505_MeOH_C
column name in both processed data files: 505_MeOH_C_expression

data_processing:
KBase was used to align 12 million 2 x 150 bp paired-end reads per sample via HISAT2 v2.1.0 to M. extorquens SLI 505 genome
Transcripts were assembled via StringTie v2.1.5 to generate FPKM values
DESeq2 v1.20.0 was used to generate gene counts and call differentially expressed genes
Assembly: M. extorquens SLI 50 genome is accessible via IMG Genome ID 2918966707. It is under the archived name Methylorubrum zatmanii SLI 505 with NCBI Assembly Accession version JALKFG000000000.1, whole genome-sequencing JALKFG010000001-JALKFG010000004
Supplementary files format and content: TSV file of FPKM values for all samples
Supplementary files format and content: CSV file of gene counts for all samples

organism: Methylorubrum extorquens

source_name: strain SLI 505

growth_protocol: 3 mL pre-cultures of M. extorquens SLI 505 in Methylobacterium PIPES (MP) minimal media with 15 mM succinate (Millipore Sigma) were grown overnight in 14-mL polystyrene round-bottom plastic culture tubes (Falcon) at 30°C and 200 rpm in an Innova S44i incubator shaker (Eppendorf). Pre-cultures were washed twice in MP by centrifugation at 2000 x g for 10 minutes and diluted into a desired volume of fresh media with indicated substrate in MP to an OD600 of 0.1.

extract_protocol:
40 mL of culture were harvested at mid-exponential phase (OD600 of 0.5-1 for all conditions) by centrifugation at 4°C at 2000 x g for 10 minutes. Total RNA was extracted using the Qiagen RNeasy Kit and quantified. rRNA depletion using the Ribo-Zero RNA Plus rRNA Depletion Kit (Illumina) was performed by SeqCoast Genomics.
Library preparation and Illumina Hi-Seq sequencing was performed by SeqCoast Genomics.

treatment_protocol: Pre-cultures of M. extorquens SLI 505 were grown and prepared as described above and used to inoculate triplicate 250-mL glass culture flasks containing 50 mL of MP supplemented with either 5 mM vanillic acid, 10 mM vanillic acid, 50 mM MeOH, or 10 mM acetate at an OD600 of 0.1.

value: strain SLI 505


title: MexTKO_OD3_3

city: Seattle

first: Andrew

last: Frando

state: WA

address: 1705 NE Pacific Street

department: Pulmonary, Critical Care, and Sleep Medicine

institute: University of Washington

description: Library name: MexTKO_OD3_3

data_processing:
Fastq.gz files were trimmed to remove adapters using Trimmomatic. Reads were mapped to transcriptome and genome using StrandNGS version 3.3.1 RNA alignment workflow using default parameters. Transcripts were quantified in StrandNGS 3.3.1 using the RNA-Seq workflow. Using the DESeq2 script function within StrandNGS, differential expression analysis was performed using the Benjamini-Hochberg adjustment for multiple comparisons and a false-discovery rate α = 0.05.
DESeq2 matrices for differential expression analyses compared transcript abundance for 2 strains at two different growth phases.
Assembly: NC_002516
Supplementary files format and content: Processed data files are in comma-separated values file that includes raw transcript counts, normalized transcript counts, and differential expression data with associated cold-changes and p-values.

molecule: cytoplasmic RNA

organism: Pseudomonas aeruginosa

source_name: Bacterial

growth_protocol: Pseudomonas aeruginosa strain PAO1 (WT, mexT knockout) were grown in LB supplemented with 50 mM MOPS.

extract_protocol:
Wild-type PAO1 and PAO1∆mexT cultures were started from single colonies in LB-MOPS in biological triplicate. Cultures were incubated for 18 hours at 37˚C with shaking. Cultures were back diluted to an OD600 of 0.1 until cultures doubled, and then cultures are diluted back to an OD600 of 0.05. At an OD600 of 1.0 and 2.0, a total of an OD600 of 2.0 was pelleted at 4000 RPM for 5 min. Supernatant was discarded and pellets were resuspended in 1 mL QIAzol containing lysis beads. Samples were lysed by bead-beating at maximum RPM for 1 min with chilling for 5 min. Bead-beating was repeated twice. Chloroform was added, shaken vigorously, and centrifuged for 15 min at 12,000 x g at 4˚C. 450 µL of the upper phase was combined with 675 µL of 100% ethanol. RNA was extracted using a RNeasy kit, and RNA was eluted using RNase-free water.
rRNA depletion, library generation, and >20 million 150-bp paired-end Illumina HiSeq reads were generated for each sample commercially (Genewiz; Azenta).

treatment_protocol: Bacteria were harvested at an OD600 of 1.0 and 2.0.

value: Bacterial

value: MexTKO


title: WT-p13-H3K27ac_rep2

value: day 13 of pregnancy (p13)

value: H3K27ac (Abcam, ab4729)


title: ctl-2


title: MexTKO_OD2_2

description: Library name: MexTKO_OD2_2


title: JH35W_2467_2580549__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R04C02

value: tumors


title: MexTKO_OD2_1

description: Library name: MexTKO_OD2_1


title: Methylobacterium extorquens SLI 505 in 50 mM methanol, biological replicate A

description:
Library name: M.ext_SLI505_MeOH_A
column name in both processed data files: 505_MeOH_A_expression


title: Methylobacterium extorquens SLI 505 in 10 mM acetate, biological replicate C

description:
Library name: M.ext_SLI505_Ace_C
column name in both processed data files: 505_Ace_C_expression


title: JH35M_2218_2580543__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R04C01


title: MexTKO_OD1_3

description: Library name: MexTKO_OD1_3


title: JH35M_2217_2580542__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R03C01


title: WT-p13-NFIB_rep2

value: Mammary gland

value: WT


title: JH35W_2236_2580548__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R03C02


title: MexTKO_OD1_1

description: Library name: MexTKO_OD1_1


title: Methylobacterium extorquens SLI 505 in 10 mM acetate, biological replicate B

description:
Library name: M.ext_SLI505_Ace_B
column name in both processed data files: 505_Ace_B_expression


title: WT-p13-NFIB_rep1


title: MexTKO_OD1_2

description: Library name: MexTKO_OD1_2


title: JH35W_2229_2580547__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R02C02


title: WT-p13-STAT5B_rep1

value: STAT5B (ThermoFisher scientific, 13-5300)


title: Methylobacterium extorquens SLI 505 in 10 mM acetate, biological replicate A

description:
Library name: M.ext_SLI505_Ace_A
column name in both processed data files: 505_Ace_A_expression


title: WT-p13-STAT5A_rep2

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: WT_OD3_3

description: Library name: WT_OD3_3


title: JH35M_2214_2580541__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R02C01


title: Methylobacterium extorquens SLI 505 in 10 mM vanilliic acid, biological replicate C

description:
Library name: M.ext_SLI505_10mMVA_C
column name in both processed data files: 505_10VA_C_expression


title: JH35W_2228_2580546__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R01C02


title: WT_OD2_1

description: Library name: WT_OD2_1


title: Methylobacterium extorquens SLI 505 in 10 mM vanilliic acid, biological replicate B

description:
Library name: M.ext_SLI505_10mMVA_B
column name in both processed data files: 505_10VA_B_expression


title: WT_OD2_2

description: Library name: WT_OD2_2


title: Methylobacterium extorquens SLI 505 in 5 mM vanilliic acid, biological replicate C

description:
Library name: M.ext_SLI505_5mMVA_C
column name in both processed data files: 505_5VA_C_expression


title: Methylobacterium extorquens SLI 505 in 5 mM vanilliic acid, biological replicate B

description:
Library name: M.ext_SLI505_5mMVA_B
column name in both processed data files: 505_5VA_B_expression


title: TBI_IMP_24h

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

library_source: transcriptomic single cell

data_processing:
FastQ data was proceed using CellRanger v6 to generate the attached expression matrix data
Assembly: GRCm39 (mm39)
Supplementary files format and content: Matrix dataset containing matrix, features, and barcodes files

source_name: Mouse cerebral cortex tissue

extract_protocol:
Dissected brain tissue was dissociated using papain tissue dissociation kit (Worthington) following manufacturer's protocols. Single cells were check for viability using LiveDead stain to ensure greater than 90% viability before proceeding to loading into GEMs via the 10x genomic Chromium controller.
scRNA-seq were prepared using 10x Genomics Chromium v3 Library Prep Kit following manufacturer's protocols.
10x genomic chromium 3' kit v3.1 library

value: Mouse cerebral cortex tissue

value: Controlled Cortical Impact TBI with IMP injection 2hrs post injury

tag: time

value: Tissue collected 24 hrs post injury


title: Methylobacterium extorquens SLI 505 in 50 mM methanol, biological replicate B

description:
Library name: M.ext_SLI505_MeOH_B
column name in both processed data files: 505_MeOH_B_expression


title: WT-p13-H3K27ac_rep1


title: WT-p13-STAT5A_rep1


title: JH35M_2207_2580540__mousemethylation

description:
genetically modified GNPs implantation into the mouse cerebellum
206796510111_R01C01


title: Methylobacterium extorquens SLI 505 in 10 mM vanilliic acid, biological replicate A

description:
Library name: M.ext_SLI505_10mMVA_A
column name in both processed data files: 505_10VA_A_expression


title: TBI_saline_24h

value: Controlled Cortical Impact TBI with saline injection 2hrs post injury


title: WT-p13-PolII_rep1

value: RNA polymerase II (Abcam, ab5408)


title: RNA-seq of C2C12 myotubes treated with dexamethasone (50 µM), replicate 3

city: Gangneung

first: Hye-Young

last: Youn

address: 679 Saimdang-Ro

country: South Korea

institute: KIST

description: Library name: C2C12_DEX_3

data_processing:
Adapter sequences and low-quality bases were trimmed using default parameters. Trimmed reads were aligned to the Mus musculus reference genome (GRCm39/mm39) using STAR aligner (v2.7.10a). Gene-level counts were generated using featureCounts with GENCODE M32 annotation.
Assembly: GRCm39 (GENCODE M32)
Supplementary files format and content: Tab-delimited text file containing raw gene-level read counts for each sample (e.g., counts.txt).

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated from C2C12 myotubes using the Hybrid-R™ RNA isolation kit (GeneAll, Korea).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA) following the manufacturer’s protocol.

value: Skeletal muscle

value: Myotube


title: ICO_coculture_day7_D2

city: Utrecht

first: Maya

last: Haaker

address: Yalelaan 2

country: Netherlands

institute: Utrecht University

data_processing:
library preparation following the protocol for Smart-seq2
amplification of cDNA using an Illumina Nextera XT kit
sequence depth of around 20 Mio reads per sample
The raw reads were first cleaned by removing adapter sequences and poly-x sequences, alignment against the Mouse reference genome (build GRCm39) and quantification of gene level expression was carried out using Kallisto (Version 0.46.1).
analysis of differentially expressed genes using software package DESeq2 (R version: 4.2.0, DESeq2 version: 1.36.0)
Assembly: Mouse reference genome (build GRCm39)
Supplementary files format and content: Count_QC-raw-count_tab.txt

source_name: Intrahepatic cholangiocyte organoids (ICO) co-culture in matrigel day 7

growth_protocol: Cells were grown in 50% DMEM with 5%FBS, 50% AdvDMEM/F12 supplemented with B27 and N2, N-Acetylcysteine, gastrin, EGF, FGF10, nicotinamide, HGF and RSPO3.

extract_protocol:
RNA was isolated using a RNeasy Micro Kit (Qiagen, Hilden, Germany) including an on-column DNase-I treatment to minimize DNA contamination.
The libraries were prepared following the protocol for Smart-seq2. Following reverse transcription, an Agilent 4200 TapeStation System was used to evaluate the quality of the cDNAs. Using an Illumina Nextera XT kit 1.0 ng of amplified cDNA from each sample was tagmented and amplified. The resulting libraries were pooled, double-sided size selected (0.5x followed by 0.8x ratio using Beckman Ampure XP beads) and quantified using an Agilent 4200 TapeStation System.

tag: replicate

value: ICO

value: CCM

tag: timepoint


title: Sbj2_19

type: protein

city: Siena

first: Viola

last: Viviani

address: Via Fiorentina, 1

country: Italy

institute: GSK

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit). The array was then incubated 1h a room temperature (RT) with mAbs diluted 0,5 ug/ml for anti-human IgG-specific analysis. After two washing with 0.1% Tween in PBS buffer (TPBS), arrays were incubated with an AlexaFluor 647-conjugated IgG anti-human (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before and washed once in PBS, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a InnoScan 710AL (Innopsys) and the 16-bit images were generated with Mapix software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).

label: AlexaFluor 647-conjugated anti-human IgG secondary antibody

molecule: protein

organism: Homo sapiens

source_name: recombinant HumAbs

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol:
Protein extracted from samples.
Briefly: bacterial pellets were either resuspended in equilibration buffer (50?mM NaH2PO4 and 300?mM NaCl, pH 8.0) before mechanical lysis by sonication or resolubilized in B-PER Bacterial Protein Extraction Reagent (B-PER, Thermo Fisher, 1?g/10?ml) or Cell-Lytic Express (Sigma-Aldrich). The unbroken cells and bacterial debris were removed by centrifugation and proteins were purified from the supernatant by IMAC (immobilized metal-ion-affinity chromatography) purification using cobalt-based chelating columns (Hitrap TALON Crude; Merck) according to the manufacturer?s instructions. Columns were washed with equilibration buffer, and proteins bound to the resin were then eluted with imidazole gradient (from 0?mM to 250?mM imidazole) in equilibration buffer. Samples were dialyzed in PBS. The recombinant PorA and PorB proteins were instead purified from inclusion bodies. PorA bacterial pellets were dissolved in Guanidine 6?M, 50?mM Tris-HCl, pH 8.5, whereas PorB bacterial pellets were lysed in 8?M Urea, 50?mM Tris-HCl, pH 8,0. The solubilized inclusion bodies were concentrated in an Amicon concentrator, 10?kDa cutoff (Millipore). Then samples were diluted into a refolding buffer (200?mM CAPS, 400?mM NaCl, 50?mM Tris-HCl, 0.3% Lauryl-N,N-dimethylamine-N-Oxide [LDAO], pH 11). The mixtures were stirred ON at 4?°C and the pH was adjusted to 8.0 with 1?N HCl. The refolded porins were loaded onto an IMAC column (HisTrap HP, GE Healthcare), washed with PBS?+?0,1% LDAO (PBSL) and eluted with PBSL containing 300?mM imidazole. The samples were concentrated with Amicon (10?kDa cutoff) and then loaded onto an S-300 Sephacryl column (GE Healthcare) and the protein was eluted in 0,1% PBSL.

treatment_protocol: Recombinant expressed monoclonal antibodies in mammalian cells

tag: subclass

value: PBMC


title: L1-2nd_IP-STAT5B

value: Lactation day 1 (L1)


title: RNA-seq of C2C12 myotubes treated with 10 µM THSG and dexamethasone (50 µM), replicate 2

description: Library name: C2C12_THSG10_2


title: WT_OD1_3

description: Library name: WT_OD1_3

value: Bacterial


title: WT_OD1_1

description: Library name: WT_OD1_1


title: Cre_plus_15W_2

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

department: Center for Cancer Research

institute: National Institutes of Health, National Cancer Institute

data_processing:
For RNA-seq data analysis, reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic 0.36 software before alignment with the reference genome (Mouse-mm10) and the annotated transcripts using STAR 2.5.1.
The mapping statistics were calculated using Picard 1.84 software.
Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
The gene expression quantification analysis was performed for all samples using STAR/RSEM 1.2.22 tools.
Differential gene expression was assessed with DESeq2 with the parameters P-adj 0.05 and log2 fold 1 (for 2-fold differentially expressed genes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Small Intestine

extract_protocol:
Using Rneasy Plus Mini Kit (#74136, Qiagen)
Illumina TruSeq Stranded mRNA Library Prep (#20020596, Illumina)

value: Small Intestine

value: Cre+

value: Wide-type mice fed chow diet

value: Rep 2


title: RNA-seq of C2C12 myotubes treated with dexamethasone (50 µM), replicate 1

description: Library name: C2C12_DEX_1


title: L1-1st_IP-STAT5A

value: Mammary gland

value: WT

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: RNA-seq of C2C12 myotubes treated with 10 µM THSG and dexamethasone (50 µM), replicate 1

description: Library name: C2C12_THSG10_1


title: Sbj1_20

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: WT_OD1_2

description: Library name: WT_OD1_2


title: Methylobacterium extorquens SLI 505 in 5 mM vanilliic acid, biological replicate A

description:
Library name: M.ext_SLI505_5mMVA_A
column name in both processed data files: 505_5VA_A_expression

value: strain SLI 505


title: Cre_plus_15W_3

value: Rep 3


title: RNA-seq of C2C12 myotubes treated with vehicle (control), replicate 3

description: Library name: C2C12_CON_3


title: Cre_plus_15W_1

value: Rep 1


title: HSC_coculture_day7_D3

source_name: Hepatic stellate cells (HSC) co-culture in matrigel day 7

value: HSC


title: TIL (cartridge 1)

city: Newcastle Upon Tyne

first: Jing Xuan

last: Lim

address: Framlington Place

department: Bioscience Institute

country: United Kingdom

institute: Newcastle University

description: BD Rhapsody

data_processing:
Fastq files were transferred to seven brdiges platform and files were checked for quality control and DBEC files were obtained through the BD Rhapsody Targeted Analysis Pipeline run. The DBEC files were imported to R using ReadMtx() function.
Assembly: mm10
Supplementary files format and content: Combined_Sample1_AbSeq_SMK_DBEC_MolsPerCell.csv: tables containing all cell labels of ≥10 reads
Supplementary files format and content: Sample1_AbSeq_SMK_Sample_Tag_Metrics.csv: assigned sample tag for each putative cell
Supplementary files format and content: Sample1_AbSeq_SMK_Sample_Tag_ReadsPerCell.csv: Reads per bioproduct per cell

source_name: Melanoma tumours

extract_protocol: As per manufacturer's instruction

value: Melanoma tumours

value: B16F10 cells

value: Immune cells

value: C57BL6 WT and PD1KO


title: HSC_coculture_day7_D2

value: CCM


title: RNA-seq of C2C12 myotubes treated with vehicle (control), replicate 2

description: Library name: C2C12_CON_2

value: Skeletal muscle

value: Myotube


title: ICO_coculture_day7_D3

value: ICO


title: RNA-seq of C2C12 myotubes treated with dexamethasone (50 µM), replicate 2

description: Library name: C2C12_DEX_2


title: RNA-seq of C2C12 myotubes treated with vehicle (control), replicate 1

description: Library name: C2C12_CON_1


title: HSC_coculture_day7_D1


title: ICO_coculture_day7_D1


title: RNA-seq of C2C12 myotubes treated with 10 µM THSG and dexamethasone (50 µM), replicate 3

description: Library name: C2C12_THSG10_3


title: Cre_minus_15W_3

value: Small Intestine

value: Cre-

value: knockout mice fed chow diet


title: E18p5_sample_3

city: Los Angeles

first: Jifan

last: Feng

address: 2250 Alcarza Street CSA 103

institute: University of Southern California

description: Library name: E18p5_scRNAseq_mouse_palate_3

data_processing:
Sequencing was performed using a NovaSeq 6000 (Illumina) or NovaSeq XPlus (Illumina), and the quality control, sequence alignment, and read counts were processed and quantified using Cell Ranger (v9.0.0) through the 10x Genomics Cloud Analysis platform (10x Genomics).
Assembly: Mouse GRCm39 (GENCODE vM33/Ensembl110 annotations)
Supplementary files format and content: Matrix table with raw gene counts for every gene
Supplementary files format and content: H5 files from 10X Cell Ranger pipeline containing matrix, features, and barcodes information.

source_name: Embryonic Palate

extract_protocol:
Maxillary tissues of the palatal region from E12.5, E13.5, E14.5, E15.5, and E18.5 embryos (3 biological replicates per stage) were dissected and dissociated using Multi Tissue Dissociation Kit 3 (130-110-204, Miltenyi Biotec) at 37°C and 600 rpm for 15-30 minutes in a thermomixer (Thermo Fisher Scientific, 2231000269).
The single-cell suspension was filtered using MACS® SmartStrainers (30 µm) (130-098-458 Miltenyi Biotec) and processed into a single-cell library using 10x Genomics Chromium single-cell 3’ v3 reagent kits (10x Genomics, PN-1000269) according to the manufacturer’s protocol.

value: Embryonic Palate

tag: age


title: ICO_monoculture_day7_E2

source_name: Intrahepatic cholangiocyte organoids (ICO) mono-culture in matrigel day 7

value: MCM


title: E18p5_sample_2

description: Library name: E18p5_scRNAseq_mouse_palate_2


title: ICO_monoculture_day7_E1


title: Cre_minus_15W_1


title: Sbj1_1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

value: PBMC


title: WT_BMDMs_Mock_2

type: RNA

city: Tainan

first: Yi

middle: Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: mRNA expression data from untreated WT BMDMs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: WT PLUS

source_name: BMDMs from WT mice

label_protocol: For fragmentation, the concentration of cRNA should be more than 0.8 μg/Μl. The result with cRNA fragmentation was checked by Agilent 2100 Bioanalyzer. The amount of ss-cDNA should be more than 5.5 μg.

growth_protocol: BMDMs were grown in DMEM medium with 10% FBS, 1% pen/strep, and 10 ng/ml macrophage colony-stimulating factor (M-CSF). BMDMs were allowed to differentiate for 7 days at 37oC with 5% CO2, and the medium was changed every 2 days during the ex vivo culture.

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

treatment_protocol: Cells were cultured in 10 cm plates and treated with or without LLC CM for 24 hours.

value: WT

value: pimary macrophages

value: untreated


title: E15p5_sample_3

description: Library name: E15p5_scRNAseq_mouse_palate_3


title: Cre_plus_11W_3

value: Cre+

value: Wide-type mice fed HFD for 4 weeks

value: Rep 3


title: WT_BMDMs_Mock_1


title: Cre_plus_11W_1

value: Rep 1


title: ICO_monoculture_day7_E3


title: WT_BMDMs_LLC 24h_1

description: mRNA expression data from LLC CM treated 24h WT BMDMs

source_name: LLC CM treatmnt 24h of BMDMs from WT mice

value: LLC CM treated


title: HSC_matrigelmonoculture_day7_C3

source_name: Hepatic stellate cells (HSC) mono-culture in matrigel day 7

value: HSC


title: Sbj1_11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Cre_minus_15W_2

value: Rep 2


title: E14p5_sample_3

description: Library name: E14p5_scRNAseq_mouse_palate_3


title: KO_BMDMs_LLC 24h_2

description: mRNA expression data from LLC CM treated 24h Rab37 KO BMDMs

source_name: LLC CM treatmnt 24h of BMDMs from Rab37 KO mice

value: Rab37 KO


title: Cre_minus_11W_2

value: Small Intestine

value: knockout mice fed HFD for 4 weeks


title: HSC_matrigelmonoculture_day7_C2


title: E15p5_sample_2

description: Library name: E15p5_scRNAseq_mouse_palate_2


title: HSC_matrigelmonoculture_day7_C1


title: E14p5_sample_2

description: Library name: E14p5_scRNAseq_mouse_palate_2


title: KO_BMDMs_LLC 24h_1


title: WT_BMDMs_LLC 24h_2


title: HSC_plasticmonoculture_day7_B3

source_name: Hepatic stellate cells (HSC) mono-culture on plastic day 7

value: MCP


title: Cre_minus_11W_1

value: Cre-


title: Cre_plus_11W_2


title: E13p5_sample_2

description: Library name: E13p5_scRNAseq_mouse_palate_2

value: Embryonic Palate


title: Cre_minus_11W_3


title: KO_BMDMs_Mock_2

description: mRNA expression data from untreated Rab37 KO BMDMs

source_name: BMDMs from Rab37 KO mice


title: Cre_plus_4W_3

value: wide-type mice fed HFD for 3 weeks


title: HSC_day0_A3

source_name: Hepatic stellate cells (HSC) direct after isolation day 0

value: non


title: HSC_plasticmonoculture_day7_B2


title: E13p5_sample_3

description: Library name: E13p5_scRNAseq_mouse_palate_3


title: E12p5_sample_2

description: Library name: E12p5_scRNAseq_mouse_palate_2


title: Cre_plus_4W_2


title: Mpdn4mt1-1 Sperm (4mC-TAB-seq)

city: Norwich

first: Xiaoqi

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

data_processing:
For ATAC-seq, ATAC and input reads were mapped to the Marchantia genome (v5.1) with bowtie (v2-2.3.4.1) (Langmead, and Salzberg, 2012). bigWig files were then created from these mapped reads using the command bamCompare.
For 4mC-AMD-seq, 4mC-TAB-seq and BS-seq, low-quality reads and potential adaptor sequence were first trimmed using TrimGalore version 0.4.2 with default parameters. DNA methylation analysis was performed by using miniature-sniffle-mapper (https://github.com/martinjvickers/miniaturesniffle-mapper), which is based on Bismark (Krueger and Andrews, 2011), but with the additional ability to map ambiguous reads.  Methylation data was mapped to the Marchantia chromosome assembly v5.1 (Montgomery et al., 2020) as well as to the pUC19 vector sequence and lambda cl857 genome where appropriate.
For SMRT-seq, subreads were mapped to the Marchantia (v5.1) genome using pbmm2 (v1.1.0). Base modifications were detected using ipdSummary (v2.0) with the following flags set (--identify 4mC --methylFraction). For 5mCG analysis, circular consensus reads were generated with ccs (v6.4) using the “—hifi-kinetics” option to generate consensus kinetics tags, and primrose (v1.3) was used to predict 5mC modification of each CG motif and generate base modification (“MM”) and base modification probability (“ML”) BAM tags. Pileup-based consensus methylation sites and probabilities were generated by the script “aligned_bam_to_cpg_scores.py” from pb-CpG-tools (v1.1.0) with the “-q 1 -m reference -p model -c 10” options.
Assembly: MpTak1v5.1
Supplementary files format and content: gff files (BS-seq, 4mC-AMD-seq, 4mC-TAB-seq, and SMRT seq), bigWig files and bam files (ATAC-seq)
Library strategy: 4mC-AMD-seq

organism: Marchantia polymorpha subsp. ruderalis

source_name: Sperm

growth_protocol: Plants were grown on plates containing 1/2× Gamborg’s B5 medium with 1% agar (Sigma) under constant light at 21 °C. Plants were transferred to jiffy pellets after 2 weeks on plates and placed in a growth chamber at 21 °C with 70% humidity under constant light with far-red irradiation for induction of sexual reproduction, as described previously (Chiyoda et al., 2008).

extract_protocol:
Sperm were isolated as described previously (Schmid et al., 2018). Sperm DNA was extracted as described (Healey et al., 2014).
ATAC-seq sperm libraries were constructed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits, catalogue number: 20034197, as described (Ding et al., 2021).
WT and Mpdn4mt1-1 mutant 4mC-AMD-seq sperm libraries were prepared with the ACCEL-NGS methyl seq DNA library kit (Qiagen, 59104) after treatment of sheared DNA with APOBEC (NEB #E7120S), following manufacturer’s instructions.
WT and Mpdn4mt1-1 mutant 4mC-TAB-seq sperm libraries were prepared with Ovation Ultralow Methyl-Seq Library Systems (Nugen, 0336) and EpiTect Bisulfite Kit (Qiagen, 59104) according to manufacturer’s instructions, with the incorporation of one round of bisulfite conversion. Prior to adaptor ligation, sheared DNA was treated with TET2 (NEB #E7120S) following manufacturer’s instructions.

treatment_protocol: No special treatment was given.

tag: 4mc/5mc spike_added

value: No

value: Sperm

value: Mpdn4mt1-1 double knockout

value: One BS treatment


title: Mpdn4mt1-2 knockout Sperm single BS treatment (Ovation BS seq)

data_processing:
For ATAC-seq, ATAC and input reads were mapped to the Marchantia genome (v5.1) with bowtie (v2-2.3.4.1) (Langmead, and Salzberg, 2012). bigWig files were then created from these mapped reads using the command bamCompare.
For 4mC-AMD-seq, 4mC-TAB-seq and BS-seq, low-quality reads and potential adaptor sequence were first trimmed using TrimGalore version 0.4.2 with default parameters. DNA methylation analysis was performed by using miniature-sniffle-mapper (https://github.com/martinjvickers/miniaturesniffle-mapper), which is based on Bismark (Krueger and Andrews, 2011), but with the additional ability to map ambiguous reads.  Methylation data was mapped to the Marchantia chromosome assembly v5.1 (Montgomery et al., 2020) as well as to the pUC19 vector sequence and lambda cl857 genome where appropriate.
For SMRT-seq, subreads were mapped to the Marchantia (v5.1) genome using pbmm2 (v1.1.0). Base modifications were detected using ipdSummary (v2.0) with the following flags set (--identify 4mC --methylFraction). For 5mCG analysis, circular consensus reads were generated with ccs (v6.4) using the “—hifi-kinetics” option to generate consensus kinetics tags, and primrose (v1.3) was used to predict 5mC modification of each CG motif and generate base modification (“MM”) and base modification probability (“ML”) BAM tags. Pileup-based consensus methylation sites and probabilities were generated by the script “aligned_bam_to_cpg_scores.py” from pb-CpG-tools (v1.1.0) with the “-q 1 -m reference -p model -c 10” options.
Assembly: MpTak1v5.1
Supplementary files format and content: gff files (BS-seq, 4mC-AMD-seq, 4mC-TAB-seq, and SMRT seq), bigWig files and bam files (ATAC-seq)

value: Yes

value: Mpdn4mt1-2 double knockout


title: HSC_plasticmonoculture_day7_B1


title: Mpdn4mt1-1 Sperm (4mC-AMD-seq)


title: RNC_WT-2

first: Sally

last: Shen

address: Meilong Road No.130

institute: East China University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in Cutadapter v4.3. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-Nor with low quality from raw data. At the same time,Q20, Q30 and GC content of the clean data were calculated by FastQC v0.11.9. All the downstream analyses were performed based on the clean data with high quality. Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using star v2.7.10b and paired-end clean reads were mapped to the reference genome. Quantification of gene expression level featureCounts (v2.0.3) was used to count the read numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Supplementary files format and content: RPKM values for each Sample

source_name: bacterial cells

growth_protocol: LB (Luria-Bertani) medium

extract_protocol:
Bacterial samples were treated with pre-chilled cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer): 20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200 mM KCl, 100 𝜇g/ml cycloheximide, and 2 mM dithiothreitol]. After a 30 min ice bath, cell lysates were collected and transferred to pre-chilled 1.5 mL tubes. After that, cell debris was removed by centrifuging at 4 °C for 10 min. Supernatants were transferred to the surface of sucrose buffer (30% sucrose in ribosome buffer), then ultracentrifuged at 4°C by T-865 fixed angle rotor (ThermoFisher, Germany) to pellet RNCs. Pellets were then resuspended with RB buffer.
Isolation of total RNA was carried out by the Trizol Reagent (Invitrogen, USA) according to the manufacturer's instructions. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following the manufacturer’s instructions.

value: bacterial cells

value: S1 overexpression


title: Cre_plus_4W_1

value: Cre+

value: Rep 1


title: HSC_day0_A2

value: HSC


title: Cre_minus_4W_2

value: Small Intestine

value: knockout mice fed HFD for 3 weeks

value: Rep 2


title: RNC_K247R-3

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S


title: Cre_minus_4W_3

value: Cre-

value: Rep 3


title: WT Sperm (4mC-AMD-seq)

value: WT


title: HSC_day0_A1

value: non


title: RNAseq_heart_homo_rep3

city: Guangzhou

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

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

data_processing:
Paired-end reads were handled with Trim Galore, and then mapped to mouse (mm10) genome using STAR aligner.
Transcript abundance was quantified using RSEM. Differentially expressed genes (DEGs) were determined using DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM values.

source_name: heart tissue from E18.5 mouse embryo

growth_protocol: Mice were housed in a specific pathogen–free (SPF) facility with a 12 h dark/12 h light cycle and provided with food and water ad libitum.

extract_protocol:
Total RNAs from each mouse tissue or cells were extracted, and were purified by two rounds of mRNA purification with mRNA capture beads to ensure removal of rRNA.
RNA-seq libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina according to the manufacturer's instructions.

treatment_protocol: CTCF-R567W mutation were generated by CRISPR/Cas9-mediated genome editing.

value: heart tissue from E18.5 mouse embryo

value: Ctcf homozygous


title: WT Sperm (4mC-TAB-seq)

value: No

value: Sperm

value: One BS treatment


title: RNC_WT-1

value: bacterial cells


title: RNC_K247R-2


title: RNC_WT-3

value: S1 overexpression


title: Cre_plus_3W_2

value: Cre+

value: Knockout mice fed HFD for 15 weeks


title: KO_BMDMs_Mock_1

value: Rab37 KO

value: pimary macrophages

value: untreated


title: RNAseq_heart_homo_rep1


title: Cre_plus_3W_3

value: Small Intestine


title: RNC_K247R-1


title: Mpdn4mt1-1 Sperm (ATAC-seq)

value: Mpdn4mt1-1 double knockout


title: WT Sperm (ATAC-seq)


title: RNC_K247Q-3


title: Cre_minus_3W_3

value: Cre-

value: Wide-type mice fed HFD for 15 weeks

value: Rep 3


title: Cre_minus_4W_1

value: knockout mice fed HFD for 3 weeks

value: Rep 1


title: Cre_plus_3W_1


title: RNAseq_heart_heter_rep3

value: heart tissue from E18.5 mouse embryo

value: Ctcf heterozygous


title: RNAseq_heart_heter_rep2


title: WT Sperm Input gDNA (ATAC-seq)

value: No

value: Sperm

value: WT


title: Cre_minus_3W_2

value: Rep 2


title: RNC_K247Q-1

value: bacterial cells


title: Mpdn4mt1-1 knockout Sperm rep2 (Picelli RNA seq)

description: Picelli RNA seq

data_processing:
For BS-seq, low-quality reads and potential adaptor sequence were first trimmed using TrimGalore version 0.4.2 with default parameters. DNA methylation analysis was performed by using miniature-sniffle-mapper (https://github.com/martinjvickers/miniaturesniffle-mapper), which is based on Bismark (Krueger and Andrews, 2011), but with the additional ability to map ambiguous reads.  Methylation data was mapped to the Marchantia chromosome assembly v5.1 (Montgomery et al., 2020) as well as to the pUC19 vector sequence and lambda cl857 genome where appropriate.
For RNA-seq, low-quality reads and potential adaptor sequence were first trimmed using  TrimGalore version 0.4.2 with default parameters. RNA-seq reads were processed into kallisto version 0.43.0 and sleuth package version 0.30.0.
For SMRT seq, subreads were mapped using pbmm2 (v1.1.0) and base modifications were detected using ipdSummary (v2.0)
Genome_build: MpTak1v5.1
Supplementary_files_format_and_content: gff files (BS-seq and SMRT seq). HDF5 binary file, plaintext files, json files (RNA-seq)

source_name: dn4mt knockout Sperm

growth_protocol: Plants were grown on plates containing 1/2× Gamborg’s B5 medium with 1% agar (Sigma) under constant light at 21 °C, and Tak-1 thallus tissue was collected from 2-week old plants. Plants were transferred to jiffy pellets after 2 weeks on plates and placed in a growth chamber at 21 °C with 70% humidity under constant light with far-red irradiation for induction of sexual reproduction, as described previously (Chiyoda et al., 2008). Fertilisation was performed as previously described (Schmid et al., 2018).

extract_protocol:
DNA and RNA were extracted simultaneously from the frozen antheridium halves and sperm using the DynabeadsTM mRNA DIRECTTM Micro Kit (Invitrogen).
RNA library preparation was simultaneously carried out from the same input as the bisulphite libraries.

tag: 4mc/5mc spike added


title: Cre_minus_3W_1


title: RNAseq_heart_heter_rep1


title: Mpdnmt3b knockdown Sperm (Smallwood BS seq)

description: Smallwood BS-seq

source_name: DNMT3a knockdown Sperm

extract_protocol:
Tak-1 thallus tissue was collected from 2-week old plants.Sperm were isolated and developing antheridia were manually dissected as described previously (Schmid et al., 2018; Higo et al., 2016). Embryos were dissected from fertilised gametophores 7 days following sperm application and the surrounding pseudoperianths were removed. DNA and RNA were extracted simultaneously from the frozen antheridium halves and sperm using the DynabeadsTM mRNA DIRECTTM Micro Kit (Invitrogen).  Thallus, sperm, and embryo DNA was extracted as described (Healey et al., 2014).
For the thallus, embryo and sperm, single-end bisulphite-sequencing libraries for Illumina sequencing were constructed with Ovation Ultralow Methyl-Seq Library Systems (Nugen, 0336) and EpiTect Fast Bisulphite Conversion (Qiagen, 59802) kits according to manufacturer’s instructions, with the incorporation of either one (WT and dn4mt mutant sperm) or two rounds (WT sperm, thallus, and embryo) of bisulphite conversion. For antheridia, WT sperm, and CMTa knockdown sperm, bisulphite sequencing library preparation was carried out as previously described (Picelli et al., 2014; Smallwood et al., 2014).

value: Mpdnmt3b knockdown


title: RNAseq_heart_homo_rep2

value: Ctcf homozygous


title: RNAseq_heart_wt_rep3

value: wild type


title: RNAseq_heart_wt_rep2


title: Cre_plus_Chow_3

source_name: Small Intestine

value: Small Intestine

value: Cre+

value: Wide-type mice fed HFD for 11 weeks


title: WT Sperm rep2 (Picelli RNA seq)

description: Picelli RNA seq

source_name: WT Sperm


title: Mpdn4mt1-1 knockout Sperm rep1 (Picelli RNA seq)

description: Picelli RNA seq

value: Mpdn4mt1-1 double knockout


title: RNAseq_heart_wt_rep1


title: RNA_WT-2

value: S1 overexpression


title: Cre_plus_Chow_1


title: RNA_WT-1


title: Cre_plus_Chow_2


title: 9099rh5

city: Nashville

first: Yinqiu

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

description: 10X genomics

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v7.0.1.
Assembly: mm10
Supplementary files format and content: Tap-seperated values files and matrix files

source_name: kidney

extract_protocol:
Cd45+ cells were isolated from kidney then submitted for processing using the 10X Genomics platform.
Libraries were prepared using P/N 1000121, 1000157, and 1000213 following the manufacturer's protocol.  The libraries were sequenced using the NovaSeq 6000 with 150 bp paired end reads.

value: kidney

value: CD11b-Cre:EGFRf/f (myeloid EGFR-/-)

value: aki 3days


title: RNA_K247R-3


title: RNC_K247Q-2


title: WT Late stage antheridia rep2 (Picelli RNA seq)

description: Picelli RNA seq

source_name: WT Late stage antheridia

value: Antheridia


title: WT Sperm rep1 (Picelli RNA seq)

description: Picelli RNA seq

value: No


title: WT Late stage antheridia rep1 (Picelli RNA seq)

description: Picelli RNA seq


title: Cre_minus_Chow_1

value: Cre-

value: knockout mice fed HFD for 11 weeks

value: Rep 1


title: WT Middle stage antheridia rep2 (Picelli RNA seq)

description: Picelli RNA seq

source_name: WT Middle stage antheridia

value: WT


title: RNA_WT-3

value: bacterial cells


title: RNA_K247Q-3


title: 8083rh1

description: 10X genomics

value: EGFRf/f (WT)


title: CB_MUT2_EXP5

description:
2451183_Elp1-P7_MUT2_072822_10xscRNA_S8
10x Genomics

data_processing:
barcoded processing, gene counting and aggregation were made using the STARsolo (v2.7.3a)
Assembly: mm10
Supplementary files format and content: Tab-separated files

source_name: cerebellum

extract_protocol:
Single cells from developing mouse cerebellar tissue were processed using the microfluidics-based 10x Chromium protocol, according to manufacturer instructions
mouse cerebellar tissue  were isolated and processed using the 10x Chromium technology

value: cerebellum

value: Elp1+/-16bp,  Elp1HET

value: dual index 10x


title: CB_MUT1_EXP5

description:
2451182_Elp1-P7_MUT1_072822_10xscRNA_S7
10x Genomics


title: RNA_K247R-2


title: WT Early stage antheridia rep1 (Picelli RNA seq)

description: Picelli RNA seq

source_name: WT Early stage antheridia


title: WT Early stage antheridia rep2 (Picelli RNA seq)

description: Picelli RNA seq


title: Cre_minus_Chow_2

value: Small Intestine

value: Rep 2


title: CB_WT2_EXP5

description:
2451181_Elp1-P7_WT2_072822_10xscRNA_S6
10x Genomics


title: WT Embryo two BS treatments (Ovation BS seq)

description: Ovation BS-seq

source_name: WT Embryo

value: Embryo

value: Two BS treatments


title: 9099rh4

description: 10X genomics

value: kidney

value: CD11b-Cre:EGFRf/f (myeloid EGFR-/-)

value: aki 1day


title: RNA_K247R-1


title: CB_WT1_EXP5

description:
2451180_Elp1-P7_WT1_072822_10xscRNA_S5
10x Genomics


title: 8260rh2

description: 10X genomics


title: CB_MUT_EXP4

description:
2432503_Elp1-P7_sample54redo_061622_10xsc_S11
10x Genomics


title: tumor_s_7246

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence, cleaned reads were mapped to mm10 using STAR
Assembly: mm10
Supplementary files format and content: Tab-separated ReadsPerGene.out.tab

source_name: tumor

extract_protocol:
GNPs were isolated, and cell pellet snap frozen in liquid N2 (LN2). The 1.5 ml Eppendorf tubes containing the GNP pellet was placed in the mortar super cooled under LN2. 150 ml of 1X polysome lysis buffer- pH 7.5 (10 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.5% (w/v) sodium deoxycholate, 1% (v/v) Nonidet-P40, 10 mM DTT, 100 µg/ml cycloheximide, 1 U/ml SUPERaseIn RNase Inhibitor, 1X protease inhibitor cocktail (EDTA-free) in RNAse-free deionized water). The frozen mix of cell pellet and lysis buffer was pulverized using a pre-chilled pestle. Eppendorf tubes were placed on ice to thaw and mixed with pipetting using a 200 ml tip. Samples were centrifuged at 2000×g for 5 min at 4°C to pellet nuclei and cell debris. Supernatant was transferred to a fresh tube and centrifuged at 12,000×g for 5 min at 4°C. 150 ml of the resulting supernatant was loaded onto the top of a 10-50% sucrose gradient in 4 ml Polypropylene ultracentrifuge tubes (Cat# 344062, Beckman Coulter, Inc) . The tubes were centrifuged in a SW60Ti rotor at 246,606×g (38,000 RPM) for 125 min with low acceleration and brakes off. All tubing was washed with RNase-free H2O at 3 ml/min using a clean ultracentrifuge tube. The BioComp™ Piston Gradient Fractionator was used to fractionate and record absorbance of the samples, setting the baseline absorbance by 60% sucrose. The first material to come out was free RNA and protein, followed by the 40S, 60S, 80S monosome, and increasing polysome peaks. Fractions were collected into microcentrifuge tubes as they exit the reader for use in downstream applications. Once the last of the sample was collected, several additional milliliters of 60% sucrose were flown through the tubing to clean it out and set the baseline again for next sample. RNA was extracted separately from monosomic, disomic and polysomic fractions using TRIzol™ Reagent (Life Technologies) and processed for RNA-sequencing.
RNA libraries for RNA-seq were prepared following manufacturer's protocols

value: tumor


title: WT Middle stage antheridia rep1 (Picelli RNA seq)

description: Picelli RNA seq

value: No

value: Antheridia


title: tumor_s_7762


title: Sbj3_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

source_name: recombinant HumAbs


title: Sbj3_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: RNA_K247Q-2


title: tumor_s_7765


title: Mpdn4mt1-1 knockout Sperm single BS treatment (Ovation BS seq)

description: Ovation BS-seq

value: Yes

value: Sperm

value: Mpdn4mt1-1 double knockout

value: One BS treatment


title: tumor_s_7248


title: RNA_K247Q-1

value: bacterial cells


title: CB_WT_EXP4

description:
2432502_Elp1-P7_sample56_061622_10xsc_S10
10x Genomics

value: cerebellum

value: WT


title: tumor_s_7763


title: Sbj3_mAb12

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: CB_MUT_EXP3

description:
2303680_Elp1_P7_pooled_Mut_S2
10x Genomics

value: Elp1+/-16bp,  Elp1HET

value: single index 10x


title: WT Sperm two BS treatments (Ovation BS seq)

description: Ovation BS-seq


title: tumor_s_4790


title: tumor_s_7247


title: WT Thallus two BS treatments (Ovation BS seq)

description: Ovation BS-seq

source_name: WT Thallus

value: Thallus


title: tumor_s_7756


title: Sbj3_mAb10

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj3_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj3_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: WT Sperm single BS treatment (Ovation BS seq)

description: Ovation BS-seq


title: tumor_s_7758


title: WT Sperm (Smallwood BS seq)

description: Smallwood BS-seq


title: Mpcmta knockdown Sperm (Smallwood BS seq)

description: Smallwood BS-seq

source_name: CMTa knockdown Sperm

value: Mpcmta knockdown


title: WT Late stage antheridia rep2 (Smallwood BS seq)

description: Smallwood BS-seq


title: Sbj2_mAb20

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_s_7760


title: tumor_s_7757


title: CB_WT_EXP2

description:
2291571_Elp1_P7_1_S1
10x Genomics


title: WT Late stage antheridia rep1 (Smallwood BS seq)

description: Smallwood BS-seq


title: tumor_s_4784


title: CB_WT_EXP1

description:
2270182_Elp1_P7_1_S1
10x Genomics


title: scRNA_TrackerSeq_e16.5_barcode_pt2

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute for Biological Intelligence

description:
lineage barcode RNA
10x Genomics
Sample15_16_17_18.Rdata

library_source: other

data_processing:
Transcriptomic dataset:Sequencing reads in FASTQ files were aligned to a reference genome(mm10) and umi counts were calculated using 10x Genomics Cell ranger software.Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome
Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Assembly: mm10-2.1.0
Supplementary files format and content: Processed_Transcript: Rdata file with genes and counts
Supplementary files format and content: Processed_LBC TRACKERseq: Rdata file with columns for "CBC" and "Lineage-Barcode"

molecule: other

source_name: forebrain

extract_protocol:
Embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custumed primers with standard Illumina adapters.

value: forebrain

tag: developmental stage

value: wild type

value: TrackerSeq labelling


title: WT Middle stage antheridia rep2 (Smallwood BS seq)

description: Smallwood BS-seq

tag: tissue


title: tumor_s_4781

value: tumor


title: CB_WT_EXP3

description:
2303679_Elp1_P7_pooled_WT_S1
10x Genomics


title: CB_MUT_EXP2

description:
2291572_Elp1_P7_2_S2
10x Genomics


title: Sbj2_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_s_4789


title: scRNA_TrackerSeq_e16.5_transcriptome_pt2

description:
10x Genomics
Sample15_16_17_18.Rdata


title: WT Early stage antheridia rep2 (Smallwood BS seq)

description: Smallwood BS-seq

value: No


title: Sbj2_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb17

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: WT Middle stage antheridia rep1 (Smallwood BS seq)

description: Smallwood BS-seq

value: Antheridia


title: Col_RNA_rep5

city: Cambridge

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

data_processing:
The raw reads were first filtered with fastp (version 0.22.0) for low-quality reads, then mapped against the reference genome (TAIR10) using hisat2 (version 5.4.0). The transcriptome was quantified using a subread software, and the GTF file annotated by araport11 was used as the annotation file. We used DEseq2 to analyze differential expression.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: The arabidopsis seeds were germinated and grew on soil under LD conditions (16 h light and 8 h dark at 22 °C)

extract_protocol:
The total RNA from 28-day-old plants was exracted using TRIzol (Invitrogen). The supernatant containing total RNA was further purified using AxyPrep Multisource Total RNA (Axygen) kit.
We sent RNA samples from five biological replicates to BGI genomics (https://www.bgi.com) for sequencing.

value: seedling


title: scRNA_TrackerSeq_e16.5_barcode_pt1


title: tumor_s_4788

address: 262 Danny Thomas Place


title: tumor_s_4786


title: Sbj2_mAb10

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_s_4787


title: WT Early stage antheridia rep1 (Smallwood BS seq)

description: Smallwood BS-seq


title: scRNA_TrackerSeq_e16.5_transcriptome_pt1

description:
10x Genomics
Sample15_16_17_18.Rdata


title: Sbj2_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb12

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: CB_MUT_EXP1

description:
2270183_Elp1_P7_2_S2
10x Genomics


title: scRNA_FlashTag_e16.5+6h_replicate2

description: 10x Genomics

source_name: ganglionic eminence

value: ganglionic eminence

value: FlashTag labelling


title: tumor_s_4937


title: scRNA_FlashTag_e12.5+6h_replicate2

description: 10x Genomics


title: scRNA_FlashTag_e12.5+96h_replicate1

description: 10x Genomics

source_name: cortex, striatum

value: cortex, striatum


title: tumor_s_4938


title: Col_RNA_rep4


title: tumor_s_4936


title: scRNA_Reference_e16.5_replicate2

description: 10x Genomics

source_name: ganglionic eminence, cortex, striatum

value: ganglionic eminence, cortex, striatum


title: Sbj2_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Col_RNA_rep3


title: tumor_s_4785


title: Sbj1_mAb23

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_s_4783


title: scRNA_Reference_e12.5_replicate2

description: 10x Genomics


title: al7m_RNA_rep4


title: tumor_s_4782


title: Sbj2_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35_2475


title: Col_RNA_rep2


title: e16_to_e12_replicate3

description:
SMART-Seq v4
Sample 35

data_processing:
Galaxy web platform was used for analysis of the data.
Paired end reads were trimmed with Trimmomatic tool and quality control was performed with FastQC.
Reads were mapped to the mouse reference genome using HISAT2 algorithm
Number of reads per annotated genes were counted using featureCounts
Assembly: mm10
Supplementary files format and content: Transcript Counts: Rdata

extract_protocol: Total RNA sequencing libraries were prepared using the SMART-Seq® Stranded Kit (634442, Takara), according to standard manufacturer’s protocol (Low-input Workflow, PCR 1: 5 cycles and PCR 2: 12-15 cycles). The library quality was checked by Qubit™ Flex Fluorometer (Q33327, Thermo Fisher Scientific) and 4200 TapeStation System (G2991BA, Agilent).


title: al7m_RNA_rep1


title: al7m_RNA_rep5


title: tumor_JH35_2351


title: H28 Renilla knockout cells, (H28 Ren KO), replicate 2

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

description:
Library name: Sample 12
H28_counts.txt
EN00006885_H28_Ren_2_1

data_processing:
RNA-seq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for all samples

growth_protocol: Knockout cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Nucleospin RNA mini kit (MN).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero H/M/R Kit by Macrogen company

tag: cell line

value: malignant pleural mesothelioma

value: Renilla control


title: Sbj1_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data  was performed using in-house developed R scripts. For each protein the fluorescence intensity data of the replicates was subtracted by local background values surrounding each spot and averaged, hence resulting in a single data point per sample named Mean Fluorescence Intensity (MFI).

extract_protocol:
Protein extracted from samples.
Briefly: bacterial pellets were either resuspended in equilibration buffer (50?mM NaH2PO4 and 300?mM NaCl, pH 8.0) before mechanical lysis by sonication or resolubilized in B-PER Bacterial Protein Extraction Reagent (B-PER, Thermo Fisher, 1?g/10?ml) or Cell-Lytic Express (Sigma-Aldrich). The unbroken cells and bacterial debris were removed by centrifugation and proteins were purified from the supernatant by IMAC (immobilized metal-ion-affinity chromatography) purification using cobalt-based chelating columns (Hitrap TALON Crude; Merck) according to the manufacturer?s instructions. Columns were washed with equilibration buffer, and proteins bound to the resin were then eluted with imidazole gradient (from 0?mM to 250?mM imidazole) in equilibration buffer. Samples were dialyzed in PBS. The recombinant PorA and PorB proteins were instead purified from inclusion bodies. PorA bacterial pellets were dissolved in Guanidine 6?M, 50?mM Tris-HCl, pH 8.5, whereas PorB bacterial pellets were lysed in 8?M Urea, 50?mM Tris-HCl, pH 8,0. The solubilized inclusion bodies were concentrated in an Amicon concentrator, 10?kDa cutoff (Millipore). Then samples were diluted into a refolding buffer (200?mM CAPS, 400?mM NaCl, 50?mM Tris-HCl, 0.3% Lauryl-N,N-dimethylamine-N-Oxide [LDAO], pH 11). The mixtures were stirred ON at 4?°C and the pH was adjusted to 8.0 with 1?N HCl. The refolded porins were loaded onto an IMAC column (HisTrap HP, GE Healthcare), washed with PBS?+?0,1% LDAO (PBSL) and eluted with PBSL containing 300?mM imidazole. The samples were concentrated with Amicon (10?kDa cutoff) and then loaded onto an S-300 Sephacryl column (GE Healthcare) and the protein was eluted in 0,1% PBSL.


title: Sbj1_mAb21

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: al7m_RNA_rep3


title: Sbj2_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb12

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: H2452 Renilla knockout cells, (H2452 Ren KO), replicate 2

description:
Library name: Sample 10
H2452_counts.txt
EN00006885_H2452_Ren_2_1

tag: cell type


title: scRNA_Reference_e14.5

description: 10x Genomics

tag: genotype


title: tumor_JH35_2237

first: Paul

institute: St. Jude Children's Research Hospital


title: Sbj1_mAb10

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: H2452 Renilla knockout cells, (H2452 Ren KO), replicate 1

description:
Library name: Sample 9
H2452_counts.txt
EN00006885_H2452_Ren_1_1


title: Sbj1_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: al7m_RNA_rep2


title: tumor_JH35_2452


title: Sbj1_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35_2465


title: tumor_JH35_2458


title: Sbj1_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: e16_to_e12_replicate2

description:
SMART-Seq v4
Sample 34

tag: treatment


title: e16_to_e12_replicate1

description:
SMART-Seq v4
Sample 33


title: H28 BUB1 knockout cells, (H28 BUB1 KO), replicate 2

description:
Library name: Sample 6
H28_counts.txt
EN00006885_H28_g5_2_1

value: BUB1 KO


title: H28 Renilla knockout cells, (H28 Ren KO), replicate 1

description:
Library name: Sample 11
H28_counts.txt
EN00006885_H28_Ren_1_1


title: e12_to_e16_replicate5

description:
SMART-Seq v4
Sample 28


title: tumor_JH35_2243


title: e12_to_e16_replicate4

description:
SMART-Seq v4
Sample 27


title: Sbj1_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35_2209


title: e12_to_e16_replicate3

description:
SMART-Seq v4
Sample 26


title: e16_to_e16_replicate4

description:
SMART-Seq v4
Sample 32


title: tumor_JH35_2456


title: e16_to_e16_replicate3

description:
SMART-Seq v4
Sample 31


title: e16_to_e12_replicate4

description:
SMART-Seq v4
Sample 36


title: e16_to_e16_replicate2

description:
SMART-Seq v4
Sample 30


title: H2052 Renilla knockout cells, (H2052 Ren KO), replicate 2

description:
Library name: Sample 8
H2052_counts.txt
EN00006885_H2052_Ren_2_1


title: e12_to_e16_replicate2

description:
SMART-Seq v4
Sample 25


title: e16_to_e16_replicate1

description:
SMART-Seq v4
Sample 29


title: Sbj1_mAb7

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35_2461


title: tumor_JH35_2453


title: H2052 Renilla knockout cells, (H2052 Ren KO), replicate 1

description:
Library name: Sample 7
H2052_counts.txt
EN00006885-H2052_Ren_1_1


title: H2052 BUB1 knockout cells, (H2052 BUB1 KO), replicate 2

description:
Library name: Sample 2
H2052_counts.txt
EN00006885_H2052_g5_2_1


title: tumor_JH35_2217


title: e12_to_e12_replicate5

description:
SMART-Seq v4
Sample 23


title: H28 BUB1 knockout cells, (H28 BUB1 KO), replicate 1

description:
Library name: Sample 5
H28_counts.txt
EN00006885_H28_g5_1_1


title: Cre_minus_Chow_3

data_processing:
For RNA-seq data analysis, reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic 0.36 software before alignment with the reference genome (Mouse-mm10) and the annotated transcripts using STAR 2.5.1.
The mapping statistics were calculated using Picard 1.84 software.
Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
The gene expression quantification analysis was performed for all samples using STAR/RSEM 1.2.22 tools.
Differential gene expression was assessed with DESeq2 with the parameters P-adj 0.05 and log2 fold 1 (for 2-fold differentially expressed genes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Small Intestine

extract_protocol:
Using Rneasy Plus Mini Kit (#74136, Qiagen)
Illumina TruSeq Stranded mRNA Library Prep (#20020596, Illumina)

value: Small Intestine

value: Cre-

value: knockout mice fed HFD for 11 weeks

value: Rep 3


title: H2052 BUB1 knockout cells, (H2052 BUB1 KO), replicate 1

description:
Library name: Sample 1
H2052_counts.txt
EN00006885_H2052_g5_1_1


title: tumor_JH35_2361


title: Sbj1_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj3_mAb9

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: H2452 BUB1 knockout cells, (H2452 BUB1 KO), replicate 2

description:
Library name: Sample 4
H2452_counts.txt
EN00006885_H2452_g3_2_1


title: tumor_JH35_2470


title: e12_to_e12_replicate2

description:
SMART-Seq v4
Sample 20

value: wild type


title: Sbj3_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: MHH-CALL-2, 1:10000 DMSO, rep 2

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

institute: University Hospital Düsseldorf

description:
Library name: Unknown_CF408-001T0038
M2

data_processing:
Analysis of fastq files was performed by using the nf-core/rnaseq pipeline (https://nf-co.re/rnaseq/3.15.1/).
Assembly: hg38
Supplementary files format and content: text file includes TPM values for each sample

source_name: MHH-CALL-2 (DSMZ, #ACC 341)

growth_protocol: BCP-ALL cells were maintained at 37 °C and 5% CO2 in RPMI GlutaMAX (Thermo Fisher Scientific) with 20% fetal bovine serum (Biowest).

extract_protocol:
BCP-ALL cells were lysed using RLT buffer (Qiagen) and RNA was isolated with the RNeasy Mini kit with on-column DNA digestion (Qiagen).
RNA concentration was detected with Nanodrop2000 (Thermo Fisher Scientific) and the integrity was confirmed with Agient2100 (Perkin Elmer LabChip GX). VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 was used to construct the mRNA library in strict accordance with the protocol provided by Vazyme. Quality control, library preparation and sequencing were performed by Biomarker Technologies (BMK) GmbH (Münster, Germany).

treatment_protocol: 1 x 10^6 BCP-ALL cells were treated with 1 µM Quisinostat or a 1:10000 dilution of DMSO for 24 hours.

value: MHH-CALL-2 (DSMZ, #ACC 341)

value: B cell precursor leukemia

value: human hyperdiploid karyotype with 13% polyploidy

tag: Sex

value: female


title: H2452 BUB1 knockout cells, (H2452 BUB1 KO), replicate 1

description:
Library name: Sample 3
H2452_counts.txt
EN00006885_H2452_g3_1_1


title: MHH-CALL-2, 1:10000 DMSO, rep 3

description:
Library name: Unknown_CF408-001T0039
M3


title: tumor_JH35_2365

city: Memphis

last: Northcott

value: tumor


title: Sbj1_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: e12_to_e12_replicate4

description:
SMART-Seq v4
Sample 22

value: ganglionic eminence


title: Sbj3_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: MHH-CALL-2, 1:10000 DMSO, rep 1

description:
Library name: Unknown_CF408-001T0037
M1


title: Sbj1_mAb2

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: e12_to_e12_replicate3

description:
SMART-Seq v4
Sample 21

value: FlashTag labelling


title: MHH-CALL-2, 1 µM Quisinostat, rep 3

description:
Library name: Unknown_CF408-001T0036
L3


title: tumor_JH35_2245


title: tumor_JH35_2466


title: tumor_JH35_2241


title: e12_to_e16_replicate1

description:
SMART-Seq v4
Sample 24


title: tumor_JH35_2464


title: e12_to_e12_replicate1

description:
SMART-Seq v4
Sample 19


title: Sbj3_mAb4

description:
FS00007535 Area1.txt
MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb24

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj3_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35_2235


title: helpless P14 TE (d7), replicate #2

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger pipeline v 5.0.0 (https://www.10xgenomics.com/support/software/cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Analyzed dataset using Scanpy in H5AD format

source_name: spleen

extract_protocol:
Helped and helpless spleens were harvested  processed according to standard prodecures and live P14 cells were FACS-purified on a Cytek Aurora CS sorter based on congenic marker expression.
Libraries were prepared according to manufacturer's instructions using the 5’ gene expression (5’ GEX) v2 kit (10x Genomics).

value: spleen

tag: host age

value: ~7 weeks

tag: host &_donor_gender

value: male

tag: strain

value: TCRtg P14 TE (day 7 post LCMV)

value: GK1.5 (CD4+ T cell depletion) & LCMV infection


title: tumor_JH35_2234


title: REH, 1:10000 DMSO, rep 2

description:
Library name: Unknown_CF408-001T0032
K2

source_name: REH (DSMZ, #ACC 22)

value: REH (DSMZ, #ACC 22)

value: human pseudodiploid karyotype, ETV6::RUNX1 fusion gene


title: Sbj3_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35W_2467


title: helpless P14 TE (d7), replicate #1


title: Sbj1_mAb22

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: REH, 1:10000 DMSO, rep 1

description:
Library name: Unknown_CF408-001T0031
K1


title: helpless P14 TE (d7), replicate #3


title: Sbj3_mAb5

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: MHH-CALL-2, 1 µM Quisinostat, rep 1

description:
Library name: Unknown_CF408-001T0034
L1


title: helped P14 TE (d7), replicate #4

value: isotype control & LCMV infection


title: helpless P14 TE (d7), replicate #4


title: REH, 1 µM Quisinostat, rep 3

description:
Library name: Unknown_CF408-001T0030
J3


title: Sbj3_mAb8

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb15

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: REH, 1:10000 DMSO, rep 3

description:
Library name: Unknown_CF408-001T0033
K3


title: tumor_JH35W_2236


title: helped P14 TE (d7), replicate #1


title: MHH-CALL-2, 1 µM Quisinostat, rep 2

description:
Library name: Unknown_CF408-001T0035
L2


title: tumor_JH35W_2227


title: REH, 1 µM Quisinostat, rep 1

description:
Library name: Unknown_CF408-001T0028
J1


title: Sbj2_mAb16

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj2_mAb14

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: REH, 1 µM Quisinostat, rep 2

description:
Library name: Unknown_CF408-001T0029
J2


title: tumor_JH35M_2354


title: L-OHP+FUC 3

city: Nanjing

first: Wentao

last: Liu

state: Jiangsu Province

address: No.101 Longmian Avenue, Jiangning District, Nanjing

department: Department of Pharmacology

institute: Nanjing medical university

data_processing:
Illumina bcl2fastq 2.0 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 HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: BMDM

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from BMDM using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: The BMDM were extracted by isolating the tibia and femurs of the mice after their necks were removed. The cells within the tibia and femurs were blown into DMEM medium (10% FBS+10% L929 culture medium +1% penicillin-streptomycin solution,100×) . After they were cultured for 7 days, trypsin was used to digest them followed by centrifugation, suspension, and seeding onto a focus dish. Fucoidan (250μg/ml) was administered prior to treating with L-OHP for 12 hours. Then L-OHP (5μM) was used to stimulate BMDM cells for 12h.

value: BMDM

value: Pretreatment of BMDM with Fucoidan (250μg/ml) for 12h in advance, followed by L-OHP (5μM) stimulation given for 12h


title: SUP-B15, 1:10000 DMSO, rep 3

description:
Library name: Unknown_CF408-001T0027
I3

source_name: SUP-B15 (DSMZ, #ACC 389)

value: SUP-B15 (DSMZ, #ACC 389)

value: human pseudodiploid karyotype, BCR::ABL1 fusion gene


title: L-OHP+FUC 2


title: L-OHP+FUC 1


title: SUP-B15, 1:10000 DMSO, rep 1

description:
Library name: Unknown_CF408-001T0025
I1

value: B cell precursor leukemia


title: SUP-B15, 1:10000 DMSO, rep 2

description:
Library name: Unknown_CF408-001T0026
I2


title: L-OHP 3

value: L-OHP (5μM) was used to stimulate BMDM cells for 12h


title: tumor_JH35M_2214

value: tumor


title: Sbj2_mAb6

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: helped P14 TE (d7), replicate #3


title: tumor_JH35M_2207


title: Sbj2_mAb4

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: helped P14 TE (d7), replicate #2


title: L-OHP 2


title: SUP-B15, 1 µM Quisinostat, rep 2

description:
Library name: Unknown_CF408-001T0023
H2


title: tumor_JH35W_2228


title: Sbj1_mAb17

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Sbj1_mAb3

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: L-OHP 1


title: Sbj2_mAb19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35M_2217


title: 80S_MUT_Rep5

source_name: cerebellum

value: cerebellum

tag: fraction

value: GNP

value: Elp1+/-16bp,  Elp1HET


title: Polysome_MUT_Rep5

value: Polysome


title: si-NC rep2

first: Zhichun

last: Jin

address: 140hanzhong road

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9).
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: BMDMs

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the 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). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: BMDMs


title: Sbj1_mAb20

address: Via Fiorentina, 1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: Total_RNA_MUT_Rep5

value: Total


title: Di-trisome_MUT_Rep5

value: Di-trisome


title: Sbj2_mAb13

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: tumor_JH35W_2229

source_name: tumor


title: RS4;11, 1:10000 DMSO, rep 2

description:
Library name: Unknown_CF408-001T0020
G2

value: human hyperdiploid karyotype, KMT2A::AFF1 fusion gene

value: female


title: si-NC rep1


title: SUP-B15, 1 µM Quisinostat, rep 1

description:
Library name: Unknown_CF408-001T0022
H1

value: male


title: SUP-B15, 1 µM Quisinostat, rep 3

description:
Library name: Unknown_CF408-001T0024
H3


title: Sbj1_mAb18

description: MENB NEXT GEN-001 (V114_01) 205285/ETR

source_name: recombinant HumAbs


title: Sbj1_mAb19

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: RS4;11, 1:10000 DMSO, rep 1

description:
Library name: Unknown_CF408-001T0019
G1


title: RS4; 11, 1 µM Quisinostat, rep 2

description:
Library name: Unknown_CF408-001T0017
F2


title: Sbj1_mAb11

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: 80S_MUT_Rep4


title: Polysome_MUT_Rep4


title: si-ATF6 rep3


title: si-ATF6 rep1


title: RS4; 11, 1 µM Quisinostat, rep 1

description:
Library name: Unknown_CF408-001T0016
F1


title: si-ATF6 rep2


title: Sbj1_mAb1

description: MENB NEXT GEN-001 (V114_01) 205285/ETR


title: X817o

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw data were transformed into methylation estimates (beta values) by normalization with the SeSAMe R package. Beta values were derived from the ratio of the fluorescence intensity of a methylated probe for a specific CpG to the total probe intensity (the sum of the signal from both the methylated and unmethylated probes plus a constant). These values fell in the range from zero to one, where zero indicated no methylation. A beta value was generated for each probe of the array for every animal and was supported by a detection p-value corresponding to the confidence in the normalized beta value.

label: Cy3 and Cy5

source_name: skeletal muscle

label_protocol: Standard Illumina protocol

extract_protocol: DNA from QUAD of young and old control and Nampt KO mice was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Germany)

value: skeletal muscle

value: ko


title: Di-trisome_MUT_Rep4


title: X815o

value: wt


title: si-NC rep3


title: Polysome_MUT_Rep3