title: siKMT2C#2-3

first: Jianpo

last: Lian

address: Huangpu

institute: Tongji hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: VCaP cell line

growth_protocol: Human prostate cancer cells VCaP were cultured in DMEM medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Then total RNA was extracted from VCaP cells using Trizol (Invitrogen, CA, USA) according to the manufacturer’s protocol for RNA sequencing (RNA-seq).
RNA library were prepared for sequencing using standard Illumina protocols

treatment_protocol: VCaP cells  were cultured in 6-well plates and transfected with siRNA for 4 days

value: VCaP

value: Prostate cancer cell

value: transfection with KMT2C siRNA#2 for 4 days

value: KMT2C deficiency


title: A-81

status: Public on Feb 12 2025

type: SRA

city: Shanghai

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
Differentially expressed genes were identified using the DESeq2 R package, with those exhibiting a P-value of less than 0.05 considered significant. Gene ontology and pathway enrichment analysis were performed using the clusterProfiler R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: mES cells

growth_protocol: Mouse ES cells were maintained on 0.1% gelatin-coated plate and cultured in DMEM supplemented with 15% FBS (GIBCO), 2 mM L-glutamine, 0.1 mM non-essential amino acids (GIBCO), 1 mM sodium pyruvate (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), 1x Pen/Strep, 3 μM CHIR99021, 1 μM PD0325901, and 1000 U/ml mouse LIF (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted from mES cells using the RNAsimple Total RNA Kit (TIANGEN).
The raw paired-end FASTQ files were analyzed following the standard protocol as previously described

treatment_protocol: no

tag: cell line

value: mES cells

tag: cell type

tag: genotype

value: Tet1KO Tet2 N1300T

tag: treatment

value: no


title: RPMI8226, C, R1 RNA-seq

city: Pamplona

first: Nahia

last: Gomez-Echarte

address: Avenida Pio XII, 55

country: Spain

institute: CIMA

description:
RNAseq
RPMI8226_Ctrol_Rep1

data_processing:
The reads were aligned to the human genome hg38 (GRCh38.p13) for all the samples.
RNA-seq: differential gene expression analysis was performed using DESeq2 package in R Studio.
ATAC-seq and ChIP-seq: After low quality and duplicated reads removal, peaks were determined using MACS2 (q-value 0.01, and p-value 0.001 for ATAC-seq and 10-9 for ChIP-seq) and sample specific regions and constant rows were removed. Then, paired wise analysis comparing the control samples with the treated ones in each cell line per separate.
Assembly: GRCh38.p13
Supplementary files format and content: RNA-seq: Text file containing raw counts of all samples included in the study.
Supplementary files format and content: ATAC-seq and ChIP-seq: excel file with chromosome regions and LFC for each MM cell line compared to the matched control (CellLine_JQ1 vs CellLine_Ctrol)

organism: Homo sapiens

growth_protocol: MM cell lines were maintained in RPMI-1640 medium containing L-Glutamine supplemented with 1% of penicillin-treptomycin, 2% HEPES Buffer and 20% of Fetal Bovine Serum.

extract_protocol:
RNA was isolated with the MagMAX mirVana total RNA Isolation kit (applied biosystems). ChIP-seq and ATAC-seq protocols were performed as described in Ordoñez, R et al (Genome Res, 2020).
RNA-seq library was prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina). Libraries for ChIP-seq and ATAC-seq were performed as described in Ordoñez, R et al (Genome Res, 2020).

treatment_protocol: JQ1 (Selleck, S7110) resuspended in DMSO was added to cell plates resulting in a final concentration of 1µM. For the negative control of the experiments, DMSO was diluted in PBS in the same way as for the compounds in order to reach equal volumes of DMSO in all conditions.

value: Multiple Myeloma

value: WT

value: DMSO


title: siKMT2C#2-2


title: A-49


title: Control-2, Replicate3, RNA-seq

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Control-2_Rep3
Mm_bulk.counts.xls

data_processing:
Demultiplexing, barcode processing, alignment, gene counting, and the generation of raw count matrix were performed by the Cell Ranger toolkit (version 3.1.0)
Assembly: GRCh38, mm10
Supplementary files format and content: Excel file, and matrix files enclosed in RDS

source_name: Breast

extract_protocol:
Tumor biopsy samples were first stored in RNAlater RNA stabilization reagent (QIAGEN) after collection and kept on ice to avoid RNA degradation. Samples were then collected in the RPMI-1640 medium (Gibco), and enzymatically digested with gentle MACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37 °C according to the manufacturer’s protocol. The dissociated cells were next passed through a 40-μm cell-strainer (BD) in the RPMI-1640 medium (Invitrogen) with 10% FBS until uniform cell suspensions were obtained. Subsequently, the suspended cells were passed through cell strainers and centrifuged at 400 g for 10 min. Red blood cells were removed via the same procedure described above. After washing twice with 1x PBS (Invitrogen), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit from 10x Genomics, following the manufacturer’s instructions; Bulk RNA-seq libraries were constructed in Sequanta Technologies Co., Ltd at Shanghai.

tag: tissue

value: Breast

value: Total cells

tag: group

value: Post-treatment

value: Control


title: Control-2, Replicate2, RNA-seq

description:
Control-2_Rep2
Mm_bulk.counts.xls


title: KMS-12, JQ1, R1 RNA-seq

description:
RNAseq
KMS12_JQ1_Rep1

value: 1microM JQ1 for 72h


title: C48/80, Replicate1, RNA-seq

description:
C48/80_Rep1
Mm_bulk.counts.xls

value: Compound 48/80


title: A-41

value: Tet1 Tet2 DKO


title: Anti-PD-L1, Replicate3, RNA-seq

description:
Anti-PD-L1_Rep3
Mm_bulk.counts.xls

value: Anti-PD-L1 antibody


title: opt-hACE2_infected_rep3

city: Guangzhou

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
To analyze the transcriptome changes, raw reads were first trimmed to remove the adapter contamination, and then aligned to the mouse mm10 and SARS-CoV-2 (NC_045512.2) genome reference using STAR (2.7.10a) with default settings.
FeatureCounts (2.0.1) was used for read assignment with the following parameters, -T 5 -g gene_name -p. DEseq2 was used for data normalization, differential expression analysis, and data visualization.
Genes with P-value <0.05 and |log2(fold change)| >1 were considered as differentially expressed genes and used for GO analysis.
Assembly: mm10
Supplementary files format and content: normalized read count using Deseq2 in csv format

molecule: polyA RNA

source_name: lung

extract_protocol:
RNA was isolated from homogenized lung tissue using TRizol with standard protocol
For ployA based mRNA-seq, 1 μg total RNAs were used for library construction. mRNA was enriched and purified using Library Preparation VAHTSTM mRNA Capture Beads (Vazyme, NR401-01). Next, purified mRNAs were fragmented, followed by cDNA synthesis, second-strand synthesis, end repair, adaptor ligation and amplification using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-01) and VAHTS DNA Clean Beads.
Libraries were sequenced for on average 20 million pair-end reads.

treatment_protocol: Balb/c mice with different genetic backgrounds (WPRE-hACE2, hACE2/β-globin, and opt-hACE2) were treated with tribromoethanol (Avertin, 250mg/kg) and intranasally infected with either 1 x 105 TCID50 SARS-CoV-2 in 50 μL DMEM  or DMEM only per mouse

value: lung

value: mix cell types from lung

value: infected by SARS-CoV-2


title: siKMT2C#1-2

value: VCaP

value: Prostate cancer cell

value: transfection with KMT2C siRNA#1 for 4 days

value: KMT2C deficiency


title: KMS-11, JQ1, R1 RNA-seq

description:
RNAseq
KMS11_JQ1_Rep1

value: Multiple Myeloma

value: WT


title: siKMT2C#1-1


title: KMS-11, C, R1 RNA-seq

description:
RNAseq
KMS11_Ctrol_Rep1

value: DMSO


title: Anti-PD-L1, Replicate2, RNA-seq

description:
Anti-PD-L1_Rep2
Mm_bulk.counts.xls

value: Breast

value: Total cells


title: Nab-PTX, Replicate3, RNA-seq

description:
Nab-PTX_Rep3
Mm_bulk.counts.xls

value: Post-treatment

value: Nab-paclitaxel


title: opt-hACE2_infected_rep2


title: opt-hACE2_infected_rep1


title: CTRL-2

value: transfection with Control siRNA for 4 days

value: KMT2C normal


title: opt-hACE2_mock_rep3


title: opt-hACE2_mock_rep2


title: BCG/Ad, 4w postchallenge-2

city: Cheongju-si, Chungcheongbuk-do

first: Jin-Seung

last: Yun

address: 212, Osongsaengmyoung 2-ro, Osong-eup, Heungdeok-gu

country: South Korea

institute: Korea National Institute of Health

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Whole blood

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: Whole blood


title: Nab-PTX, Replicate2, RNA-seq

description:
Nab-PTX_Rep2
Mm_bulk.counts.xls


title: Anti-PD-L1, Replicate1, RNA-seq

description:
Anti-PD-L1_Rep1
Mm_bulk.counts.xls

value: Anti-PD-L1 antibody


title: CTRL-1


title: BCG/Ad, 4w postchallenge-3


title: CTRL-3


title: opt-hACE2_mock_rep4

value: lung

value: mix cell types from lung


title: Control-1, Replicate3, RNA-seq

description:
Control-1_Rep3
Mm_bulk.counts.xls

value: Control


title: KMS-12, C, R1 RNA-seq

description:
RNAseq
KMS12_Ctrol_Rep1


title: siKMT2C#1-3

value: VCaP

value: Prostate cancer cell


title: Control-2, Replicate1, RNA-seq

description:
Control-2_Rep1
Mm_bulk.counts.xls


title: Nab-PTX, Replicate1, RNA-seq

description:
Nab-PTX_Rep1
Mm_bulk.counts.xls


title: BCG/Ad, 4w postchallenge-1


title: 972: DMSO Cyto Rep 3

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapters using trimmomatic v0.39
The SlamDunk pipeline v0.2.4 was used to align reads to a joint human genome (GRCh37.73) and Drosophila genome (Dm3), and the 3’ UTR of gene, and call T to C conversions and count the numbers of total and TC converted reads.
HiSAT2 was used to align reads to a joint human (GRCh37.73), Drosophila (Dm3) and ERCC genome and htseq was used to assign reads to genes, to calculate the size factors for spike-in normalisation.
The DESeq2 package in R was used to normalise the T to C converted read counts using the size factors calculated from the total ERCC read counts.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: ERCC normalised Total and TC counts

source_name: Breast; Mammary gland

extract_protocol:
Cells were trypsinised, washed with cold PBS, counted, and 10% Drosophila S2 cells spiked in prior to permeabilisation. Cells were permeabilised (1mg/ml Digitonin (SKU0215948050, MP Biomedicals), 100mM NaCl, 10mM Tris pH 8.0, 1:100 protease Inhibitor (Complete Mini EDTA-free, 4693159001 Sigma), 1:1000 RNase OUT (10-777-019, Invitrogen) for 10 min on ice. After centrifugation at 1000g for 3 min, the supernatant (cytoplasmic fraction) was set aside and the pelleted nuclei were resuspended in RLT buffer (Qiagen) and put through a QIAshredder column (Qiagen). Both cytoplasmic and nuclear fractions were then diluted 1:3 with RLT buffer (Qiagen), and ethanol added to a final concentration of 30%. RNA was recovered using a RNeasy mini spin column (Qiagen).carboxyamidomethylation of 4sU was performed using freshly prepared iodacetamide as described (Herzog et al Nature Methods 2017 PMID: 28945705). ERCC RNA (4456740, Ambion; 2l per 2g RNA) was spiked in according the manufacturer’s instructions. RNA was cleaned up using MinElute RNeasy kit (Qiagen).
Libraries were prepared using QuantaSeq 3′ mRNA Library Prep kit (Lexogen). Libraries were sequenced on a Novaseq with 100bp single-end reads.

treatment_protocol: Drug added for 3 hours. 0.1 mM 4-thiouridine (4sU, Sigma-Aldrich) was added to the medium of drug-treated cells 60 min prior to harvesting.

tag: cellular fraction

value: Cyto

tag: replicate


title: hACE2/β-globin_infected_rep4

value: infected by SARS-CoV-2


title: Control-1, Replicate2, RNA-seq

description:
Control-1_Rep2
Mm_bulk.counts.xls


title: BCG, 4w postchallenge-1


title: siKMT2C#2-1

value: transfection with KMT2C siRNA#2 for 4 days

value: KMT2C deficiency


title: BCG, 4w postchallenge-3


title: opt-hACE2_mock_rep1


title: hACE2/β-globin_infected_rep2


title: cko3, thalamic tissues, 4month

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road268

institute: zhejiang university

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: GRCm38
Supplementary files format and content: tab-delimited xls files include FPKM and counts for each Sample

source_name: thalamic tissues

extract_protocol:
Tissure were homogenized in TRIzol reagent (Thermo Fisher Scientific) to extract total RNA and was purified with chloroform following the manufacturer’s protocol. The concentration of RNA was quantified using a NanoDrop
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp.
we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: thalamic tissues

value: Mettl3 loxp/loxp, camk2alpha_cre

tag: age

value: 4 months


title: BCG, 4w postchallenge-2


title: hACE2/β-globin_infected_rep1


title: Control-1, Replicate1, RNA-seq

description:
Control-1_Rep1
Mm_bulk.counts.xls

value: Breast

value: Total cells

value: Post-treatment


title: BCG/Ad, 1w postchallenge-2

value: Whole blood


title: cko2, thalamic tissues, 4month


title: hACE2/β-globin_infected_rep3


title: cko1, thalamic tissues, 4month


title: BCG/Ad, 1w postchallenge-3


title: hACE2/β-globin_mock_rep2


title: hACE2/β-globin_mock_rep1


title: BCG, 1w postchallenge-3


title: 973: JQ1 Cyto Rep 3


title: BCG/Ad, 1w postchallenge-1


title: BCG, 1w postchallenge-2


title: 955: IBET151-VHL Nuc Rep 3

value: Nuc


title: WPRE-hACE2_infected_rep5

value: lung


title: ctrl2, thalamic tissues, 4month

value: Mettl3 loxp/loxp


title: BCG, 1w postchallenge-1


title: ctrl1, thalamic tissues, 4month


title: BCG/Ad, Prechallenge-3


title: ctrl3, thalamic tissues, 4month


title: 964: JQ1 Nuc Rep 3


title: 961: IBET151-VHL Cyto Rep 3


title: 953: JQ1-VHL Nuc Rep 3


title: WPRE-hACE2_infected_rep4

value: mix cell types from lung


title: WPRE-hACE2_infected_rep3


title: 960: IBET151 Cyto Rep 2


title: 959: JQ1-VHL Cyto Rep 3


title: 963: DMSO Nuc Rep 3

value: DMSO


title: BCG, Prechallenge-3


title: WPRE-hACE2_infected_rep1


title: 948: IBET151 Cyto Rep 1


title: 947: JQ1-VHL Cyto Rep 2


title: BCG/Ad, Prechallenge-1


title: cko2, thalamic tissues, 2month

value: 2 months


title: WPRE-hACE2_mock_rep3


title: cko1, thalamic tissues, 2month


title: BCG, Prechallenge-2


title: ctrl3, thalamic tissues, 2month


title: 954: IBET151 Nuc Rep 2


title: WPRE-hACE2_mock_rep2


title: ctrl2, thalamic tissues, 2month


title: 949: IBET151-VHL Cyto Rep 2

value: Cyto


title: cko3, thalamic tissues, 2month


title: 946: JQ1 Cyto Rep 2


title: WPRE-hACE2_infected_rep2

value: infected by SARS-CoV-2


title: WPRE-hACE2_mock_rep1


title: ctrl1, thalamic tissues, 2month


title: 945: DMSO Cyto Rep 2


title: 943: IBET151-VHL Nuc Rep 2


title: TR3, replicate C, EC3 Embryonal carcinoma cells differentiated with thioridazine

city: Ithaca

first: Michelle

last: Liu

state: NY

address: 618 Tower Road

country: USA

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: Genome_build: mm10 (Ensembl gene annotation)
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts output from STAR (--quantMode GeneCounts)

growth_protocol: Spontenous malignant teratocarcinomas were isolated and disaggregated with 2 mg/mL Collagenase A (Roche) in serum-free DMEM (Corning) with penicillin, streptomycin, and gentamycin at 37C for approximately 1 hour with shaking. Cells were then passed through a 40 µM filter to remove large clumps, pelleted at 1.5 x g for 5 minutes, resuspended in DMEM containing 10% FBS (Sigma) with 1x LIF (ORF Genetics) and 10 μM ROCKi (Selleckchem) and plated at various densities into 10-cm tissue culture plates. Cultures were passed at confluence until embryonal carcinoma colonies were visually observed, followed by subsequent passages to propagate each cell line. EC cell lines were maintained in EC medium (DMEM + 15% heat-inactivated Bovine Growth Serum (Hyclone) + 2% L-glutamine (Corning) + 1% non-essential amino acids (Corning) + 1% Pen/Strep (Corning) + β-mercaptoethanol + 1x LIF). Media was replaced daily, and cells were passaged by trypsinization 1:10 every other day.

extract_protocol:
Total RNA was extracted from cells using RNA Stat-60 according to the manufacturer’s protocol, with the addition of GlycoBlue Coprecipitant (Invitrogen) immediately prior to isopropanol precipitation. RNA sample quality was determined by spectrophotometry (Nanodrop) to determine concentration and chemical purity and with a Fragment Analyzer (Advanced Analytical) to determine RNA integrity.
Directional RNA-seq libraries were prepared from 1ug total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: To induce differentiation, cells were incubated with thioridazine hydrochloride (Sigma) (10 μM for TR14 and 20 μM for TR11) in media without LIF, for up to 2 weeks or until EC colonies were no longer observed, at which point the cultures were maintained in EC media without LIF.

value: Pten-/- Kras+/G12D Stra8-CreTg OCT4-gfpTg

value: Thioridazine


title: BCG, Prechallenge-1


title: TR3, replicate B, EC3 Embryonal carcinoma cells differentiated with thioridazine


title: F16m IUGR-RC

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Raw sequencing files were demultiplexed using in house python script.
Quality of Raw-seq data were reviewed using FastQC. Single end reads from individual libraries were aligned to the rat reference genome (rn6) using STAR aligner (Dobin, Davis et al., 2013).
From each library,  raw counts were obtained from uniquely aligned reads for all the Rattus norvegicus genes (rn6; ucsc genome annotation) using the featureCounts tools from the Subread package
Differential expression analysis was performed using DESEq2 package  (absolute log2FC >= 1 and q <0.05)
Assembly: rn6
Supplementary files format and content: tab-delimited text files includes raw readcounts for each samples
Supplementary files format and content: comma separated .csv files as output of DESEq2 analysis

organism: Rattus norvegicus

source_name: Mouse Liver

growth_protocol: Pregnant Sprague-Dawley rats (Charles River Laboratories, Hollister, CA) were housed in individual cages at 21-23C within 12h light/dark cycles.

extract_protocol:
Liver samples were collected from adult offspring (Day 180) and total RNA was extracted for transcriptomic profile using Zymo Direct-zol RNA miniprep kit (#R2050; Zymo research, Irvine, CA, USA) following manufacturer’s instructions.
mRNA seq libraries were prepared with Kapa Stranded RNA sequencing kit with Ribo-erase (# KK8483; Kapa Biosystem, Cape Town, South Africa) following manufacturer’s protocol. . Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 4000.

treatment_protocol: At gestational day 11  dams were randomized to either continue regular chow (CON group) or on a Western diet ad libitum (HFhf group)along with 25% fructose in their drinking water.The pregnant dams in the IUGR group were 50% calorie restricted beginning from gestation day (G) 10 in their access to regular chow diet until the birth of their pups.after birth, the maternal diet was switched to either regular chow accessed ad libitum forming the IUGR-RC (regular chow) group, or a HFhf diet creating the IUGR-HFhf group

value: Mouse Liver

tag: Sex

value: Female

tag: time

tag: study group

value: IUGR-RC


title: macrophages, L_plus_Ska.7

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the mouse genome (mm10) using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on GENCODE vM25 annotations was determined using stringtie (v2.0) with the default parameter settings.
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated for representing the expression of each gene.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene TPM for every gene and every sample

source_name: Male Abelson murine leukemia virus-induced tumors

growth_protocol: 6×10^5 RAW264.7 cells were seeded onto one plate and cultured in DMEM with 10% FBS and 1% P/S.

extract_protocol:
Total RNA was isolated using RNA-Quick Purification Kit (ES Science)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: 24 h later, cells were divided into three groups and treated with: DMSO, DMSO+LPS, and LPS+Skatole respectively for 24 h.

value: macrophages

value: WT

value: LPS+Skatole


title: TR3, replicate A, EC3 Embryonal carcinoma cells differentiated with thioridazine


title: F15m, IUGR-RC


title: macrophages, L_plus_Ska.6

value: Male Abelson murine leukemia virus-induced tumors


title: 941: JQ1-VHL Nuc Rep 2

value: Nuc


title: F13m, IUGR-RC


title: macrophages, L_plus_Ska.5


title: EC3, replicate C, Embryonal carcinoma cells derived from a murine malignant teratocarcinoma

value: embryonal carcinoma

value: Untreated


title: F11m, IUGR-RC


title: macrophages, D_plus_L.7

value: DMSO+LPS


title: 940: JQ1 Nuc Rep 2


title: EC3, replicate B, Embryonal carcinoma cells derived from a murine malignant teratocarcinoma


title: 939: DMSO Nuc Rep 2

value: DMSO


title: macrophages, D_plus_L.5


title: T94m, HFhf

value: HFhf


title: macrophages, D_plus_L.6


title: T96m, HFhf


title: 937: IBET151-VHL Cyto Rep 1

value: Cyto


title: EC3, replicate A, Embryonal carcinoma cells derived from a murine malignant teratocarcinoma


title: 936: JQ1-VHL Cyto Rep 1


title: T71m, HFhf


title: Cold exposed, brown adipose tissue, mouse 6

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
The STAR aligner v. 2.5.3a was used to align RNA-seq read against the mm10 mouse  genome assembly and GENCODE vM15 mouse transcripts
The software program featureCounts v. 1.5.3 was used to summarize reads onto genes.
Testing for differential expression was performed using edgeR using the quasi-likelihood  framework with a fitted model of the form ~ 0 + group where group encoded both tissue and temperature. Contrasts were constructed as described in the edgeR manual
Gene Ontology and Reactome  enrichments were found using the gseGO from the  clusterProfiler package, and gsePathway from the ReactomePA package. Only gene ontologies with between 10 and 500 genes were investigated.
Genes were marked as potentially secreted if they were present in one or more of the  MDSEC, SignalP, Phobius & SPOCTOPUS list from the Human Protein Atlas
Assembly: mm10
Supplementary files format and content: comma-separated file (.csv). Gene-by-sample matrix containing gene (row) expression count per sample (column)

source_name: brown adipose tissue

extract_protocol:
RNA was isolated from mature adipocytes using a combined method of trizol-CHCl3  (Sigma, Cat. C2432) and RNeasy Mini Kit (Qiagen, Cat. 74104) and RNA quality was assessed using an RNA 6000 Nano Kit (Agilent Technologies).
mRNA was fragmented and cleaned using RNA Clean XP beads (Beckman Coulter)  and cDNA was generated using a SuperScript III Reverse Transcriptase (Life Technologies, Cat. 18080044), followed by A-tailing and adapter ligation steps performed following the instructions of the manufacturer. The resulting double-stranded DNA (dsDNA) fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat. A63880) and concentration was determined with specific adapters using a Qubit dsDNA High-Sensitivity Kit (Invitrogen, Cat. Q32851).

value: brown adipose tissue

value: Cold exposed


title: macrophages, D.7


title: 942: IBET151 Nuc Rep 1


title: Cold exposed, brown adipose tissue, mouse 5


title: 934: JQ1 Cyto Rep 1


title: Cold exposed, visceral fat, mouse 6

source_name: visceral fat

value: visceral fat


title: T70m,HFhf

value: Mouse Liver


title: T91m, IUGR-HFhf

value: Female

value: IUGR-HFhf


title: Cold exposed, subcutaneous fat, mouse 6

source_name: subcutaneous fat

value: subcutaneous fat


title: macrophages, D.6

value: macrophages

value: WT


title: macrophages, D.5

value: Male Abelson murine leukemia virus-induced tumors


title: 933: DMSO Cyto Rep 1


title: 931: IBET151-VHL Nuc Rep 1

value: Nuc


title: T90m, IUGR-HFhf


title: Cold exposed, visceral fat, mouse 5


title: P48-3

first: Yun

address: Panjiayuan Street

institute: Institute of Laboratory Animals Science,CAMS & PUMC

data_processing:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments,Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer.
PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer.
PCR products were purified(AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an lllumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system(Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained

value: macrophage

value: PVM infected

tag: time (hours)


title: 929: JQ1-VHL Nuc Rep 1


title: 928: JQ1 Nuc Rep 1


title: P48-1


title: 927: DMSO Nuc Rep 1


title: P48-2


title: T67m, IUGR-HFhf


title: BCG/Ad, Prechallenge-2

value: Whole blood


title: Cold exposed, brown adipose tissue, mouse 4


title: T66m ,IUGR-HFhf


title: Cold exposed, visceral fat, mouse 4


title: T86m, CON

value: CON


title: P24-3


title: Cold exposed, subcutaneous fat, mouse 4


title: T85m, CON


title: Lung_Fasting [DRS]

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
lung.mouse.isoforms.gtf
lung.mouse.isoforms.bed
lung.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

data_processing:
The ONT Guppy workflow (version 2.1.0) was used for basecalling the DRS data with the parameters "--flowcell FLO-MIN106 --kit SQK-RNA002 -x cuda:all --records_per_fastq 0" being employed
The FASTQ files were aligned to the  GRCm38 mouse genome reference respectively using minimap2/2.17, with the parameters "-ax splice -uf -k14" being employed.
The FLAIR pipeline (https://github.com/BrooksLabUCSC/flair) with some modifications was employed to identify the isoform from the aligned reads.
The nanopore reads were quantified to DRS annotation using FLAIR quantify by default parameters. Only alignments with quality scores of 1 or greater were counted.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample; isoform structure  files (GTF and BED files);isoform sequence  files (FASTA files)
Library strategy: direct RNA sequencing

source_name: Lung

extract_protocol:
The 75 ug of fresh Trizol isolated RNAs were adjusted to a volume of 100 μL with nuclease-free water. The polyadenylated RNAs were selected using the Dynabeads™ mRNA Purification Kit (Invitrogen, Cat. 61006) following the manufacturer's instructions.
The 500 ng of fresh isolated polyadenylated RNAs were used for nanopore direct RNA sequencing (DRS) generally following the Oxford Nanopore Technologies (ONT) SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. Libraries were loaded onto ONT R9.4 flow cells (Oxford Nanopore Technologies) and were sequenced using the GridION platform, with the standard MinKNOW/19.12.5 protocol script being used.

tag: strain

value: Lung

value: Male

value: Fasting


title: P24-2


title: T63m, CON


title: Lung_Fed [DRS]

value: Fed


title: P24-1


title: F9m, IUGR-RC

value: IUGR-RC


title: Cold exposed, brown adipose tissue, mouse 3

value: brown adipose tissue

value: Cold exposed


title: Kidney_Fasting [DRS]

description:
kidney.mouse.isoforms.gtf
kidney.mouse.isoforms.bed
kidney.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

source_name: Kidney

value: Kidney


title: P12-3


title: Cold exposed, visceral fat, mouse 3

value: visceral fat


title: Kidney_Fed [DRS]


title: Cold exposed, subcutaneous fat, mouse 5

value: subcutaneous fat


title: F7m, IUGR-RC

value: Mouse Liver

value: Female


title: P12-2

value: WT


title: Cold exposed, subcutaneous fat, mouse 3


title: Spleen_Fasting [DRS]

description:
spleen.mouse.isoforms.gtf
spleen.mouse.isoforms.bed
spleen.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

source_name: Spleen

value: Spleen


title: F2m, IUGR-RC


title: P12-1

value: macrophage

value: PVM infected


title: Cold exposed, brown adipose tissue, mouse 2


title: Cold exposed, visceral fat, mouse 2


title: Spleen_Fed [DRS]


title: Heart_Fasting [DRS]

description:
heart.mouse.isoforms.gtf
heart.mouse.isoforms.bed
heart.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

source_name: Heart

value: Heart


title: T83m, HFhf

value: HFhf


title: P6-2


title: T60m, HFhf


title: P6-1


title: T80m, IUGR-HFhf

value: IUGR-HFhf


title: T59m, HFhf


title: Cold exposed, brown adipose tissue, mouse 1


title: Heart_Fed [DRS]

value: Male


title: Brown_Adipose_Fasting [DRS]

description:
B_A.mouse.isoforms.gtf
B_A.mouse.isoforms.bed
B_A.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

value: Fasting


title: P3-3


title: P3-2


title: P3-1


title: T79m, IUGR-HFhf


title: Brown_Adipose_Fed [DRS]

value: Fed


title: Cold exposed, visceral fat, mouse 1


title: Cold exposed, subcutaneous fat, mouse 2


title: Cold exposed, subcutaneous fat, mouse 1


title: T55m, IUGR-HFhf


title: White_Adipose_Fasting [DRS]

description:
W_A.mouse.isoforms.gtf
W_A.mouse.isoforms.bed
W_A.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt


title: Thermo neutral, visceral fat, mouse 5

value: Thermo neutral


title: H48-2

value: MHV infected


title: H48-3


title: H48-1


title: P6-3


title: Thermo neutral, brown adipose tissue, mouse 5

value: brown adipose tissue


title: Liver_Fasting [DRS]

description:
liver.mouse.isoforms.gtf
liver.mouse.isoforms.bed
liver.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

source_name: Liver

value: Liver


title: T75m, CON

value: CON


title: Muscle_Fasting [DRS]

description:
muscle.mouse.isoforms.gtf
muscle.mouse.isoforms.bed
muscle.mouse.isoforms.fa
comprehensive.isoforms.gtf
comprehensive.isoforms.bed
comprehensive.isoforms.fa
Nanopore.raw_counts.txt

source_name: Muscle

value: Muscle


title: H24-3


title: Liver_Fed [DRS]


title: T49m, CON

value: Mouse Liver

value: Female


title: T73m, CON


title: Thermo neutral, subcutaneous fat, mouse 5

value: subcutaneous fat

value: WT


title: Thermo neutral, visceral fat, mouse 4

value: visceral fat


title: H24-2

value: macrophage


title: T54m, IUGR-HFhf


title: Brn1-HA ChIP, Lrs4-KR4A no tension, IP

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
Library name: 34393IP_S6
Reads mapped to sacCer3 only/calibrated to s.pombe

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt v1.18 (MAPQ 10, min. length 65)
To obtain reads mapping only to S.cerevisiae Sc3;
ChIP-Seq reads were first mapped with MiniMap2 v2.20 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools v1.11
Unmapped pombe reads were then mapped to Sc3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.30.0
chrMito was excluded with samtools
To obtain reads mapping only to S.Pombe;
Reads were also mapped to Sc3
Unmapped Sc3 reads were filtered using samtools
Unmapped Sc3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Assembly: S.cerevisiae Sc3 + s.pombe ASM294v2.22
Supplementary files format and content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig v377 (RPM normalization)
Supplementary files format and content: To obtain calibrated bigWigs; samtools flagstat was used to count reads mapping to Sc3 and pombe only for each sample,the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (Sc3)), calibrated Sc3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Whole organism

growth_protocol: Cells were diluted to OD(600)=0.2 and  metaphase arrest by nocodazole for 3hours

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Roche 12CA5 anti-HA antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were adde d using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells were fixed in 1% formaldehyde for 30 minutes before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: chip antibody

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA

tag: cell cycle_stage

value: Metaphase

tag: tension/no tension

value: No tension (Nocodazole treatment)

value: Whole organism


title: White_Adipose_Fed [DRS]

value: Male

value: Fed


title: M14m, IUGR-RC

value: IUGR-RC


title: H24-1

tag: cell line

value: MHV infected


title: Thermo neutral, brown adipose tissue, mouse 4

value: brown adipose tissue

value: Thermo neutral


title: M13m, IUGR-RC


title: Thermo neutral, visceral fat, mouse 3


title: Thermo neutral, subcutaneous fat, mouse 6


title: Brn1-HA ChIP, Lrs4-KR4A no tension, Input

description:
Library name: 34393INPUT_S5
Reads mapped to sacCer3 only


title: Brn1-HA ChIP, Lrs4-L322E no tension, IP

description:
Library name: 34392IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Lrs4(L322E)::URA3 BRN1-6HA::TRP


title: Muscle_Fed [DRS]

value: Muscle


title: Thermo neutral, subcutaneous fat, mouse 4


title: H12-3

tag: cell type


title: T48m, HFhf

value: Mouse Liver

value: HFhf


title: Thermo neutral, subcutaneous fat, mouse 2

value: subcutaneous fat

tag: genotype

value: WT


title: M10m, IUGR-RC

tag: treatment


title: Brn1-HA ChIP, Lrs4-L322E no tension, Input

description:
Library name: 34392INPUT_S3
Reads mapped to sacCer3 only

tag: tissue


title: T45m, HFhf


title: Thermo neutral, visceral fat, mouse 2

value: visceral fat


title: Brn1-HA ChIP, no tension, IP

description:
Library name: 5708IP_S2
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA


title: H6-3

value: macrophage


title: Brn1-HA ChIP, no tension, Input

description:
Library name: 5708INPUT_S1
Reads mapped to sacCer3 only

value: Metaphase

value: No tension (Nocodazole treatment)


title: M12m, IUGR-RC

value: Male


title: Thermo neutral, brown adipose tissue, mouse 1


title: H12-2


title: H6-2


title: Thermo neutral, visceral fat, mouse 1


title: H6-1


title: H3-3


title: Brn1-HA ChIP, ΔLrs4 no tension, IP

description:
Library name: 9766IP_S6
Reads mapped to sacCer3 only/calibrated to s.pombe

value: lrs4delta::Kan BRN1-6HA::TRP

value: Whole organism


title: H12-1

value: MHV infected


title: Brn1-HA ChIP, Lrs4-L322A no tension, Input

description:
Library name: 34391INPUT_S3
Reads mapped to sacCer3 only

value: Lrs4(L322A)::URA3 BRN1-6HA::TRP


title: T21m, HFhf


title: H3-1


title: T23m, HFhf


title: Brn1-HA ChIP, ΔLrs4 no tension, Input

description:
Library name: 9766INPUT_S5
Reads mapped to sacCer3 only


title: MON-79-NI-01

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

institute: Technical University of Denmark

description: single cell RNA sequencing analysis of infected or bystander (noninfected) monocytes during M. marinum infection

library_source: transcriptomic single cell

data_processing:
Demultipexing and alignment of reads with CellRanger v2.1.1 for replicates 01 and v3.1.0 for replicates 02. Data is paired and pooled on 4 lanes.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Assembly: mm10 (replicates 01) and mm10-2.1.0 (replicates 02)
Supplementary files format and content: tsv.gz & mtx.gz

source_name: Monocytes

growth_protocol: Bacteria (WT, dRD1 and EspK::tn M. marinum) were inoculated from frozen stocks and grown at 30°C in 7H9 culture medium until late log phase.

extract_protocol:
Two independent experiments were performed. For each experiment 14 to 15 tails (i.e. infected tissue) per group were collected, pooled and digested at two weeks post infection. Cell surface markers were stained with antibodies. Live infected monocytes (CD45+Ly6G+CD11b+Wasabi+) or live uninfected monocytes (CD45+Ly6G+CD11b+Wasabi-) were sorted by FACS in PBS supplemented with 1% BSA using a FACS ARIA Fusion (BD Biosciences).
Single cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223). Library quality control and quantification were performed using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems, KK4873) and the 2100 Bioanalyzer equipped with a High Sensitivity DNA kit (Agilent, 5067-4626).

treatment_protocol: C57Bl/6JRj female 8 weeks old mice were infected via tail vein injections with 5 x 10^7 bacteria per mouse, in a total volume of 200 µL.

tag: group

value: Not infected

value: EspK::tn M. marinum M-strain


title: C48-3

value: natural culture


title: MON-WT-NI-01

value: Wild-type M. marinum M-strain


title: T42m, IUGR-HFhf

value: Mouse Liver

value: IUGR-HFhf


title: C48-1

value: WT


title: Brn1-HA ChIP, Lrs4-L322A no tension, IP

description:
Library name: 34391IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe


title: siRBFox2_rep1

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Briefly, the adapter and low-quality sequences were trimmed from 3’ to 5’ ends by Trimmomatic and the reads shorter than 36 bp were discarded
Subsequently, the preprocessed reads were aligned to the mouse genome (hg19) using STAR. The aligned reads were then converted to bam format using samtools.
The aligned RNA-Seq reads were accepted  and assembled into a parsimonious set of transcripts.  These transcripts were then estimated the relative abundances by Cufflinks.
Assembly: hg19
Supplementary files format and content: bedGraph

growth_protocol: Human leukemia K562 cells (CCL-243) were obtained from ATCC and maintained at 37°C under 5% CO2 in RPMI-1640 medium (Thermo Fisher Scientific, 22400089) with 10% fetal bovine serum, 100 units/ml of penicillin, and 100μg of streptomycin. All cell lines were tested as negative for mycoplasma contamination.

extract_protocol:
total RNAs were subject to polyA selection (Ambion, 61006) followed by library preparation using NEBNext Ultra II RNA Library Preparation Kit (NEB, E7770S).
Libraries were paired-end sequenced with read lengths of 150 bp on Illumina HiSeq X Ten or Nova-seq instruments.

treatment_protocol: For transfection, siRNA against RBFox2 or control oligos were obtained from Shanghai GenePharma Corp., China. Transfections of K562 cells were conducted with Amaxa Cell Line Nucleofector Kit V (Lonza, Basel, Switzerland). Briefly, K562 cells were grown for 24h and resuspended in 100μl Nucleofector Solution V. siRNA oligos targeting RBFox2 or control oligos were used at a concentration of 300nM and the transfection was completed with Lonza Nucleofector™ using program T-016. Cells were harvested 48h after transfection.

value: RBFox2 KD


title: MON-79-INF-01

value: Infected


title: siRBFox2_rep2


title: Brn1-HA ChIP, ΔLrs4 no tension, IP

description:
Library name: 9766IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA


title: siNC_rep2

value: ctrl


title: T39m, CON

value: CON


title: T17m, IUGR-HFhf

value: Male


title: Brn1-HA ChIP, Lrs4-WT no tension, Input

description:
Library name: 34390INPUT_S1
Reads mapped to sacCer3 only

value: Metaphase

value: No tension (Nocodazole treatment)

value: Lrs4::URA3 BRN1-6HA::TRP


title: T13m, CON


title: T41m, IUGR-HFhf


title: C48-2

value: macrophage


title: C24-2


title: Brn1-HA ChIP, Lrs4-L322E no tension, IP

description:
Library name: 33967IP_S2
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Whole organism


title: MON-DEL-NI-01

value: Not infected

value: dRD1 M. marinum M-strain


title: T40m, CON


title: T20m, IUGR-HFhf


title: M8m, IUGR-RC

value: IUGR-RC


title: M7m, IUGR-RC

value: Mouse Liver


title: Brn1-HA ChIP, ΔLrs4 no tension, Input

description:
Library name: 9766INPUT_S3
Reads mapped to sacCer3 only

value: lrs4delta::Kan BRN1-6HA::TRP


title: C24-3

value: WT

value: natural culture


title: siNC_rep1


title: MON-DEL-INF-01

value: Infected


description:
Library name: 33967INPUT_S1
Reads mapped to sacCer3 only

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA


title: Brn1-HA ChIP, Lrs4-WT no tension, IP

description:
Library name: 34390IP_S2
Reads mapped to sacCer3 only/calibrated to s.pombe


title: C24-1


title: Blastocyst

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

description:
Library name: Sample 2
10x Genomics

data_processing:
To analyze 10X Genomics single-cell data, the base call files (BCL) were transferred to FASTQ files by using CellRanger (v.7.1.0) mkfastq with default parameters, followed by aligning to the most recent bovine reference genome downloaded from Ensembl database (UCD1.2.109), then the doublets were detected and removed from single cells by using Scrublet (0.2.3) with default parameters. The generated count matrices from all the samples were integrated by R package Seurat (4.3.0) utilizing canonical correlation analysis (CCA) with default parameters (https://satijalab.org/seurat/articles/get_ started.html). The data was scaled for linear dimension reduction and non-linear reduction using principal component analysis (PCA) and UMAP, respectively. The following clustering and visualization were performed by using the Seurat standard workflow with the parameters ‘‘dim = 1:10’’ in ‘‘FindNeighbors’’ function and ‘‘resolution =0.5’’ in ‘‘FindClusters’’ function. The function ‘‘FindAllMarkers’’ in Seurat was used to identify differentially expressed genes in each defined cluster. The cutoff value to define the differentially expressed genes was p.adjust value <0.05, and fold change >0.25. The UMAP plots and bubble plots with marker genes were generated using ‘‘CellDimPlot’’ and ‘‘GroupHeatmap’’ functions in R package SCP (0.4.0) (https://github.com/zhanghao-njmu/SCP), respectively. Gene ontology (GO) and pathway analysis was performed using R package clusterProfiler (4.6.1).
Assembly: ARS-UCD1.3
Supplementary files format and content: feature_bc_matrix folder, containing barcodes.tsv, features.tsv, matrix.mtx files

organism: Bos taurus

source_name: blastocyst

growth_protocol: For 3L-blastoid formation, bEPSCs, bTSCs, and bXENs were dissociated into single cells by treating with TrypLE for 3min, 15min, and 7min, respectively, followed by neutralizing with the same volume of their culture medium. After centrifugation at 300 x g for 5min, cells were resuspended in their normal culture media with ROCK inhibitor. Single-cell dissociation was made by gentle but constant pipetting until no visible cell clumps exist. To deplete iMEF cells, cells of three cell lines were filtered through passing 40mm cell strainers (Corning) separately and placed in precoated 6 well plates (Corning) with 0.1% gelatin and incubated for 35 minutes at 37ºC. Cells were then collected and stained with 1x trypan blue and manually counted in a Neubauer chamber. Current protocol is optimized for 8 bEPSCs, 8 bXENML and 16 bTSCs per well in a 1200 well Aggrewell 400 microwell culture plate (Stemcell technologies) for 9,600, 9,600, and 19,200 of each cell type per well. Each well was precoated with 500ml of Anti-Adherence Rinsing Solution (Stemcell technologies) and spun for 5 minutes at 1500 g. Wells were rinsed with 1ml of PBS just before aggregation. The cells for one well were mixed and centrifuged at 300 x g for 5min, followed by resuspension with 1mL ACL medium (DMEM: F12 (Gibco) and Neurobasal medium (Gibco) (1:1), 1x N2-supplement (Gibco), 1x B27-supplement (Gibco), 1x NEAA (Gibco), 1x GlutaMAX (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 0.5x ITS-X, 20ng/ml LIF, 10ng/ml ActivinA, 1mM Chir99021, supplemented with 1x CEPT cocktail (50 nM chroman-1 [C, Tocris], 5 mM emricasan [E, Selleckchem], 0.7 mM trans-ISRIB [T, Tocris], and 1 x polyamine supplement [P, Thermo])). To ensure even distribution of the cells within each microwell, cells were gently mixed by pipetting with a P200 pipette. The plate was first placed in incubator for 8min to allow the cells to settle down, then centrifuged at 700 x g for 3 minutes and put back to incubator. Half of the medium was changed daily, the blastoids showed up from day 2 and could be collected on day 3 or day4.

extract_protocol:
The snRNA-seq libraries from frozen blastoids and day8 blastocysts were prepared using Chromium Nuclei Isolation Kit (10x Genomics,PN-1000493) with minor modifications from the manufacturer’s instructions. In brief, frozen blastoids and day8 blastocysts were transferred to pre-chilled sample dissociation tube and were dissociated with pestle within lysis buffer, then the tube was incubated on ice for 7min. Then the dissociated tissue was pipetted onto assembled nuclei isolation column and centrifuged 16,000 x rcf for 20 sec. After being washed with debris removal buffer and wash buffer, the nuclei pellet was resuspended in 50ul resuspension buffer and performed cell counting.
Nucleus were loaded into a 10x Genomics Chromium Chip following manufacturer instruction (10x Genomics, Chromium Next GEM Single Cel 3’ Reagent Kit v3.1 Dual Index) and sequenced with an Illumina Novaseq 6000 System (Novogene).

value: blastocyst

value: embryo


title: M6m, IUGR-RC

value: Male


title: Brn1-HA ChIP, Lrs4-L322A no tension, IP

description:
Library name: 33966IP_S4
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Metaphase


title: 3L_Blastoid

description:
Library name: Sample 1
10x Genomics

source_name: stem cells

value: stem cells


title: M5m, IUGR-RC


description:
Library name: 33966INPUT_S3
Reads mapped to sacCer3 only

value: No tension (Nocodazole treatment)


title: C12-3

value: macrophage


title: CCl43

city: Guiyang city

first: Tao

last: Huang

address: No.252 Shuangjiang Road

institute: the Affiliated Hospital of Guizhou Medical University

data_processing:
featureCounts software
Assembly: HISAT2 software
Supplementary files format and content: excel file include raw count for each file

source_name: liver

extract_protocol:
RNA was harvest using Rneasy mini plus kt (Qiagen). 1.3ug 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 folllwing manufacturer's protocols

value: liver


title: Brn1-HA ChIP, Lrs4-WT no tension, IP

description:
Library name: 33965IP_S2
Reads mapped to sacCer3 only/calibrated to s.pombe

value: Lrs4-6HIS-3FLAG::URA3 BRN1-6HA::TRP

value: Whole organism


title: C12-2


title: CCl42


title: Brn1-HA ChIP, Lrs4-WT no tension, Input

description:
Library name: 33965INPUT_S1
Reads mapped to sacCer3 only


title: C12-1


title: C6-3


title: control3

value: oil


title: T10m, HFhf

value: Mouse Liver

value: HFhf


title: T32m ,IUGR-HFhf

value: IUGR-HFhf


title: control2

value: WT


title: T12m, HFhf


title: C6-1

value: natural culture


title: Brn1-HA ChIP, ΔSgo1 no tension, IP

description: Reads mapped to sacCer3 only/calibrated to s.pombe

source_name: Saccharomyces cerevisiae/Schizosaccharomyces pombe (S. pombe is for calibration)

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Roche 12CA5 anti-HA antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA


title: C6-2


title: CCl41


title: C3-3


title: T9m ,HFhf

source_name: Mouse Liver


title: control1


title: Brn1-HA ChIP, ΔSgo1 no tension, Input

description: Reads mapped to sacCer3 only


title: H3-2

value: MHV infected


title: C3-2


title: Brn1-HA ChIP, Sgo1-2E no tension, IP


title: T28m ,CON

value: CON


title: C3-1


title: Vehicle-treated, rep 4

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Sequencing data were processed using the Nextflow rnaseq v.3.14.0 pipeline, the mouse mm10 reference genome, and the STAR-RSEM gene quantification method. RNA-seq counts were analyzed for differential expression using the edgeR v.4.2.0 R package.
Assembly: mm10
Supplementary files format and content: text, counts

source_name: spinal cord

extract_protocol:
RNA was purified from lumbar spinal cord samples (see above) using RNeasy mini kit (Qiagen).
Total RNA (5 µg) was used for mRNA library construction following instructions of Illumina RNA sample kit. All libraries were sequenced on an Illumina HiSeq 2500 platform.

value: spinal cord

value: Vehicle


title: Vehicle-treated, rep 5


title: Brn1-HA ChIP, Sgo1-2E no tension, Input

description: Reads mapped to sacCer3 only

value: Metaphase


title: Vehicle-treated, rep 3


title: Sample2KO-Alung

city: Los Angeles

first: Xiuju

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using Cell Ranger software v3.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Freshly harvested lungs from C57BL/6J mice were enzymatically dissociated with 5mg/ml Dispase in PBS/2%FBS in room temperature for 1 hour, tissues were minced, then were incubated on the shaker (100rpm) with 50 µg/ml DNase I for 30 min. Cell suspension was washed and filtered with 70 µm strainers. Cells were labeled with VE-cadherin-PE and CD45-FTIC antibodies, VE-cadherin+ and CD45- cells were sorted by fluorescence-activated cell sorting (FACS) for scRNA-seq analysis.
scRNA libraries were constructed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics).

value: Lung endothelial cells

value: Lung

value: 10-12 weeks old


title: Sample1WT-Alung

description: 10x Genomics


title: Vehicle-treated, rep 2


title: T3m ,CON

value: Male


title: T2m ,CON


title: 11145-AC-16-BDL

city: Ann Arbor

first: Ashley

last: Calder

state: Michigan

address: 109 Zina Pitcher Place

department: Internal Medicine

institute: University of Michigan

description:
Sample 16
BDL_48h_BD_F_s16

data_processing:
Salmon was used to count the trimmed data against the transcriptome defined in Gencode vM33.
Assembly: GRCm39
Supplementary files format and content: Excel file of raw counts data.

source_name: Extrahepatic bile duct

extract_protocol:
RNA was harvested from the extrahepatic bile duct using a Qiagen Rneasy Micro Kit with a Dnase treatment.
Libraries were prepped using the SMART-Seq mRNA kit according to the manufacturer's protocol

value: Extrahepatic bile duct

value: Whole tissue

value: Bile duct ligated (BDL)


title: Vehicle-treated, rep 1


title: Brn1-HA ChIP, Ycg1-4A no tension, Input

description: Reads mapped to sacCer3 only

value: No tension (Nocodazole treatment)


title: Brn1-HA ChIP, Sgo1-2A no tension, IP


title: MON-79-NI-02

value: Not infected

value: EspK::tn M. marinum M-strain


title: T7m, IUGR-HFhf

value: Mouse Liver

value: IUGR-HFhf


title: 11145-AC-15-BDL

description:
Sample 15
BDL_48h_BD_F_s15


title: Brn1-HA ChIP, Sgo1-WT no tension, Input

description: Reads mapped to sacCer3 only


title: 11145-AC-14-BDL

description:
Sample 14
BDL_48h_BD_M_s14


title: Paclitaxel-treated, rep 4

value: Paclitaxel


title: MON-79-INF-02

value: Infected


title: MON-DEL-NI-02

value: Not Infected

value: dRD1 M. marinum M-strain


title: T5m ,IUGR-HFhf


title: Brn1-HA ChIP, Sgo1-2A no tension, Input

description: Reads mapped to sacCer3 only

value: Metaphase


title: Paclitaxel-treated, rep 5

value: spinal cord


title: Sgo1-FLAG ChIP, Ycg1-4A no tension, IP

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt v1.18 (MAPQ 10, min. length 65)
To obtain reads mapping only to S.cerevisiae Sc3;
ChIP-Seq reads were first mapped with MiniMap2 v2.20 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools v1.11
Unmapped pombe reads were then mapped to Sc3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.30.0
chrMito was excluded with samtools
To obtain reads mapping only to S.Pombe;
Reads were also mapped to Sc3
Unmapped Sc3 reads were filtered using samtools
Unmapped Sc3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Assembly: S.cerevisiae Sc3 + S.pombe ASM294v2.22
Supplementary files format and content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig v377 (RPM normalization)
Supplementary files format and content: To obtain calibrated bigWigs; samtools flagstat was used to count reads mapping to Sc3 and pombe only for each sample,the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (Sc3)), calibrated Sc3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 30 seconds three times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating in a Bioruptor (Diagenode) for two times 30 cycles at 30sec on/off intervals at "High" setting. The supernatant was subject to IP with Sigma M2 anti-FLAG antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

value: Mouse monoclonal M2 anti-FLAG (Sigma) against Sgo1-6HIS-3FLAG/Rad21-6HIS-3FLAG


title: 11145-AC-13-BDL

description:
Sample 13
BDL_48h_BD_M_s13


title: Paclitaxel-treated, rep 3


title: 11145-AC-19-Sham

description:
Sample 19
Sham_48h_BD_M_s19

value: Sham


title: MON-DEL-INF-02


title: Sgo1-FLAG ChIP, Ycg1-4A no tension, Input

description: Reads mapped to sacCer3 only


title: Paclitaxel-treated, rep 2


title: MON-WT-NI-02

value: Wild-type M. marinum M-strain


title: Brn1-HA ChIP, Sgo1-WT no tension, IP

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA


title: 11145-AC-17-Sham

description:
Sample 17
Sham_48h_BD_F_s17

value: Extrahepatic bile duct

value: Whole tissue


title: TAX-R3

city: San Francisco

first: Jonathan

middle: Michael

last: Budzik

address: 513 Parnassus Ave.

department: Medicine

institute: UC San Francisco

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus and mycobacterium tuberculosis reference genomes available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison.
Assembly: Mycobacterium tuerculosis str Erdman ATCC 35801  Genome assembly: ASM35020v1; Mus musculus GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample
Supplementary files format and content: tab-delimited text file containing differential gene expression analysis for mouse mRNA
Supplementary files format and content: tab-delimited text file containing differential gene expression analysis for tuberculosis mRNA

source_name: primary alveolar macrophage

growth_protocol: Alveolar macrophages were maintained in RPMI-1640 medium supplemented with 10% (v/v) FBS, 2 mM GlutaMAX, and 10 mM HEPES.

extract_protocol:
The monolayers were washed with PBS and macrophages lysed in Trizol reagent.  Mtb was centrifuged, the supernatant containing host RNA was removed, and the Mtb pellet was resuspended in fresh Trizol and 0.1 mm zirconia/silica beads. Mtb was mechanically disrupted with the Mini Bead-Beater Plus (Biospec Products). 70% of the sample containing host RNA was pooled with the sample containing Mtb RNA, the samples were treated with chloroform, and RNA was purified with the Trizol Plus RNA purification kit (Ambion). Purified total RNA was treated with DNAseI (ThermoFisher) and dried by rotary evaporation in RNA stabilization tubes (Azenta Life Sciences).
Sample QC, dual rRNA depletion for bacteria and mouse, library preparation, Illumina sequencing (2x150 bp; 30M reads per sample), and differential gene expression analysis were performed by Azenta Life Sciences US, Inc. ERCC RNA Spike-In Mix kit (cat. 4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. rRNA depletion was performed using QIAGEN FastSelect rRNA Bacteria + HMR Kit or HMR/Bacteria (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Alveolar macrophages were infected with Mtb Erdman strain in RPMI-1640 medium supplemented with 10% horse serum at a multiplicity of infection of 2 by 'spinfection' for 10 minutes at 162 g. The media was replaced with fresh RPMI-1640 medium supplemented with 10% (v/v) FBS, 2 mM GlutaMAX, and 10 mM HEPES.  The samples were incubated in 5% CO2, 37 degrees C, for 36 hours.

value: primary alveolar macrophage

value: M. tuberculosis-infected


title: Paclitaxel-treated, rep 1


title: ARP1 cells, PNPO-OE

city: Jiangsu Nanjing

first: Deng

middle: Zhen

last: Dong

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

growth_protocol: ARP1 and H929 multiple myeloma cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096).
RNA libraries for RNA-seq were prepared using MJzol animal RNA Extraction Kit following manufacturer's protocols.

treatment_protocol: ARP1 and H929 pTSB-EV and PNPO-OE multiple myeloma cells

value: multiple myeloma

value: PNPO-OE


title: Sgo1-FLAG ChIP, Sgo1-2A no tension, Input

description: Reads mapped to sacCer3 only

value: No tension (Nocodazole treatment)


title: 11145-AC-18-Sham

description:
Sample 18
Sham_48h_BD_M_s18


title: H929 cells, PNPO-OE


title: MON-WT-INF-02


title: TAX-R2


title: Control

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

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

source_name: mouse corpus cavernous tissue

growth_protocol: Tissue was harvest after normal and DM mice treatment with MT-100 1 weeks

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

value: mouse corpus cavernous tissue

value: Control


title: Sgo1-FLAG ChIP, Sgo1-2E no tension, IP


title: H929 cells, EV

value: EV


title: DM+MT-100


title: TAX-R1


title: Sgo1-FLAG ChIP, Sgo1-2A no tension, IP


title: DM+NC

value: DM+NC

value: NC


title: placenta, obese dam ID=94E, female fetus

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

institute: Wake Forest School of Medicine

data_processing:
Sequence reads were demultiplexed using Illumina CASAVA v1.8 .
RNA-Seq data analysis was performed in Partek Flow.
Sequence reads with Phred scores ≥ Q30 were aligned against the mouse reference genome (GRCm38/mm10) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm, and transcript counts were normalized by the Trimmed mean of M-values method.
Assembly: mm10
Supplementary files format and content: Matrix table of transcript counts before normalization for 20 samples.
Supplementary files format and content: Matrix table of transcript counts after normalization for 20 samples.

source_name: placenta

extract_protocol:
Tissue samples were flash frozen in liquid nitrogen immediately after collection and stored at -80oC. Total RNA was extracted from tissue samples using the Direct-zol RNA MiniPrep kit (Zymo Research).
RNA-Seq libraries were prepared using 1 mg of total RNA according to the Illumina TruSeq Stranded Total RNA protocol, and quantified using KAPA Library Quantification kit.

treatment_protocol:
Obese dams were fed a high fat (41 kcal% fat) and high sugar (20% sucrose solution) diet during pregnancy. Control dams were fed a diet with 10.6 kcal% fat.
Placenta samples were collected on embryonic day 18.5.

value: placenta

tag: fetus sex

value: female

value: obese dam

tag: dam id


title: Sgo1-FLAG ChIP, Sgo1-WT no tension, IP

value: Mouse monoclonal M2 anti-FLAG (Sigma) against Sgo1-6HIS-3FLAG/Rad21-6HIS-3FLAG

value: Metaphase


title: ARP1 cells, EV


title: WT-4

value: wild-type


title: Sgo1-FLAG ChIP, Sgo1-2E no tension, Input

description: Reads mapped to sacCer3 only


title: Positive-lbrain-scRNA

city: Wuxi

first: Wei

last: Tian

address: Zhongshan Road

institute: Wuxi No.2 People's Hospital

data_processing:
Quality control
Raw files were demultiplexed and mapped to the reference genome GRCm38 using the Cell Ranger Single Cell v2.0 software (10X Genomics).
Assembly: GRCm38 using Ensemble v.92 gene annotation
Supplementary files format and content: expression matrix file using RNA raw count

source_name: brain tissue

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

value: Balb/c

value: without 4T1 metastasis

tag: molecular typing

value: TNBC


title: WT-R2

value: primary alveolar macrophage

value: M. tuberculosis-infected


title: placenta, obese dam ID=52C, male fetus

value: male


title: Control-brain-scRNA

value: with 4T1 metastasis


title: treat, replicate3, scRNAseq

city: hefei

first: Dongjin

last: zhao

state: anhui

address: 117 Meishan Road, Hefei City, Anhui Province, China

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: DNB C4

data_processing:
We used the official software cell ranger v2.1.1 (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) provided by 10X Genomics to generate expression matrix, feature, barcode files
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
A total of 5ml peripheral blood was collected from each sample, and peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation with Ficoll-Paque plus (17144003, Cytiva). After washing twice in PBS, PBMCs were preserved in serum-free cell lyophilization solution (abs9417, absin) and were stored in liquid nitrogen at −196°C until thawing.
After PBMC resuscitation,  incubation, centrifuge, wash, and resuspend with an appropriate volume of resuspended buffer and filter through 40 µm cell sieve. The single-cell suspension, oil, beads are added into C4 scRNA slide and instrument in order. Cell lysis and magnetic bead capture mRNA are performed in droplets. Prepare reagents for emulsion breakage in advance, vacuum pump is used for emulsion breakage. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, reverse transcription is conducted. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, cDNA second strand is synthesised. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, cDNA and oligo products were amplified. The purification was conducted separately. The cDNA and oligo products are subjected to quality detection of their concentration and the size distribution of the fragments. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, Oligo products are subjected to amplification, index ligation and purification for further circularization. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand. Finally, the products are purified. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to adaptor ligation. Finally, the products are purified. The PCR reaction system is configured. After reacting at the suitable temperature for a fixed period of time, amplification is processed via PCR. The products are then purified. The corresponding library quality control protocol will be selected depending upon product requirements.  cDNA and Oligo products are respectively denatured into single stranded. The reaction system and program for circularization are respectively configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.

value: blood

value: pbmc

tag: disease state


title: WT-R1


title: treat, replicate2, scRNAseq

description: DNB C4


title: alpha cells, Nkx2.2-alphaKO, 3

city: Aurora

first: Lori

last: Sussel

state: Colorado

address: 1775 Aurora ct.

institute: CU Anschutz

description: ribo depleted low input RNA-seq

data_processing:
Fastqc for quality control
bbduk for adapter trimming
STAR for alignment
featurecounts for counts table
DESeq2 for DE analysis
Assembly: mm10
Supplementary files format and content: raw counts table in .txt format

source_name: pancreatic islets

extract_protocol:
FACS purified alpha cells using tomato fluorescence expression, RNA extracted using a Qiagen RNEasy Micro kit
Takara Bio SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

value: pancreatic islets

value: alpha cells


title: placenta, obese dam ID=48H, male fetus

value: placenta


title: Sgo1-FLAG ChIP, Sgo1-WT no tension, Input

description: Reads mapped to sacCer3 only

value: No tension (Nocodazole treatment)


title: alpha cells, Nkx2.2-alphaKO, 1

description: ribo depleted low input RNA-seq


title: placenta, obese dam ID=48F,female fetus

value: female

value: obese dam


title: placenta, obese dam ID=384F, male fetus


title: alpha cells, Gcg-iCre control, 4

description: ribo depleted low input RNA-seq


title: WT_Male_Dust_81123_1

type: RNA

city: Fort Collins

first: Tara

last: Nordgren

state: CO

address: 1380 Centre Ave.

department: Environmental and Radiological Health Sciences

institute: Colorado State University

hyb_protocol: The custom code set (XT_PGX_MmV2_Myeloid) was hybridized with 100 ng RNA during an overnight incubation at 65 ºC before acquisition.

scan_protocol: Hybridized samples were processed and aquired on the NanoString nCounter® FLEX Analysis System.

data_processing: Each nCounter® XT panel included 15 housekeeping genes, 6 positive control probes, and 8 negative control probes. All samples that passed QC flags were combined and normalized using nSolver 4.0 (NanoString Technologies, Seattle, WA, United States) with recommended software parameters. Seven  housekeeping genes (Alas1, Edc3, Pol1rb1, Rpl19, Sap130, Sdha) were utilized for count normalization based on lack of differential expression between experimental groups of genotype, sex, and exposure.

source_name: Left Lung

label_protocol: Extract was labeled by 1. Date of extraction 2. Genotype 3. Sex 4. Exposure 5. replicate.

growth_protocol: Organs were extracted from isoflourane euthanised mice and stored in RNA Later at -80 until RNA extraction.

extract_protocol: Mice were euthanized via isoflourane overdose, cervically dislocated, and diaphram punctured. Bronchoalveolar lavage fluid was collected from the whole lung before tie off and extraction of the left lobe for storage in RNA later until RNA extraction.

treatment_protocol: Lungs were exposed to 14 instillations of organic dust extract or PBS vehichle control.

value: Left Lung

value: WT

tag: Sex

value: Male

tag: exposure

value: Dust


title: WT_Female_Saline_81123_1

value: Female

value: Saline


title: Mod, replicate2, scRNAseq

description: DNB C4


title: Mod, replicate1, scRNAseq

description: DNB C4


title: placenta, obese dam ID=384A, female fetus


title: WT_Female_Dust_81123_1


title: placenta, obese dam ID=94B, male fetus


title: WT_Female_Saline_81123_2


title: WT_Male_Saline_81123_1


title: alpha cells, Gcg-iCre control, 3

description: ribo depleted low input RNA-seq


title: Con, replicate3, scRNAseq

description: DNB C4

value: control


title: Fat-1_Male_Dust_81123_1


title: alpha cells, Gcg-iCre control, 2

description: ribo depleted low input RNA-seq


title: placenta, obese dam ID=21D, male fetus

value: male


title: alpha cells, Gcg-iCre control, 1

description: ribo depleted low input RNA-seq


title: placenta, obese dam ID=21G, female fetus


title: placenta, control dam ID=57A, male fetus

value: control dam


title: placenta, obese dam ID=52A, female fetus


title: alpha cells, Nkx2.2-alphaKO, 2

description: ribo depleted low input RNA-seq


title: Brn1-HA ChIP, Ycg1-4A no tension, IP

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt v1.18 (MAPQ 10, min. length 65)
To obtain reads mapping only to S.cerevisiae Sc3;
ChIP-Seq reads were first mapped with MiniMap2 v2.20 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools v1.11
Unmapped pombe reads were then mapped to Sc3
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads) using bedtools v2.30.0
chrMito was excluded with samtools
To obtain reads mapping only to S.Pombe;
Reads were also mapped to Sc3
Unmapped Sc3 reads were filtered using samtools
Unmapped Sc3 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Assembly: S.cerevisiae Sc3 + s.pombe ASM294v2.22
Supplementary files format and content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig v377 (RPM normalization)
Supplementary files format and content: To obtain calibrated bigWigs; samtools flagstat was used to count reads mapping to Sc3 and pombe only for each sample,the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (Sc3)), calibrated Sc3 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

value: Mouse monoclonal 12CA5 anti-HA (Roche) against Brn1-6HA/Rad21-6HA

value: Metaphase


title: Con, replicate2, scRNAseq

description: DNB C4

value: blood

value: pbmc


title: Mod, replicate3, scRNAseq

description: DNB C4


title: alphaTC, Klf4-KD, NKX2.2 ChIP, 1

data_processing:
Fastqc for quality control
bbduk for adapter trimming
Bowtie2 for alignment
MACS2 for peakcalling
Csaw was used for differential binding analysis
Assembly: mm10
Supplementary files format and content: .csv file containing the csaw differential binding results for all genomic intervals used in the analysis

extract_protocol:
Cell signaling simpleChIP enzymatic shearing kit was used to perform this ChIP
Tecan Ovation Ultralow System V2

treatment_protocol: RNAiMax Lipofectamine was used in this 48 hour reverse transfection

value: alpha cells

value: Klf4-KD siRNA transfection


title: WT_Female_Dust_81123_3


title: WT_Male_Dust_81023_3


title: Fat-1_Female_Dust_81123_1


title: Fat-1_Female_Saline_81123_1


title: Con, replicate1, scRNAseq

description: DNB C4


title: Fat-1_Male_Saline_81123_1


title: placenta, control dam ID=45E, male fetus

value: placenta


title: placenta, control dam ID=57C, female fetus

value: female


title: alphaTC, Klf4-KD, NKX2.2 ChIP, 2


title: WT_Female_Dust_81023_1

value: Left Lung


title: Homo sapiens, T1R Cells, sh2 IL-6 knock down, biol rep1

city: Yancheng

first: XINYI

last: ZHANG

address: Renmin Road No.66

institute: Yancheng First People's Hospital

description:
Library name: T1R-sh2-1
Column name gene_count.txt: read_count_T882sh2_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.22.0 (the default parameters) Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: hg38
Supplementary files format and content: Tab separated table count values of genes for each sample

growth_protocol: GIST-T1R and GIST-882R（derived from the sensitive parental cell lines GIST-T1 and GIST-882, respectively, which were provided by the Laboratory of Nanjing Medical University） were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA, USA), penicillin (100U/mL; Invitrogen) and streptomycin (100 U/mL; Invitrogen). Cells were kept in a humidified incubator at 37°C with an atmosphere of 5% CO2. Lentiviral particles were generated in 293T cells using DMEM medium and were cotransfected with the packaging vectors psPAX2 and pMDG.2 (Addgene) through a standard calcium phosphate transfection method.

extract_protocol:
RNA was harvested using TRIzol reagent (Takara). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).Sequencing Platform:BGISEQ,Sequencing length:SE50

value: experiment


title: Homo sapiens, T1R Cells, sh1 IL-6 knock down, biol rep2

description:
Library name: T1R-sh1-2
Column name gene_count.txt: read_count_T882sh1_2


title: alphaTC, scramble, NKX2.2 ChIP, 3

value: WT

value: siScramble transfection


title: Homo sapiens, T1R Cells, control blank, biol rep2

description:
Library name: T1R-NC-2
Column name gene_count.txt: read_count_T882nc_2

value: Control blank


title: placenta, control dam ID=51C, male fetus


title: placenta, control dam ID=51B, female fetus


title: alphaTC, scramble, NKX2.2 ChIP, 2


title: alphaTC, scramble, NKX2.2 ChIP, 1


title: Homo sapiens, 882R Cells, sh2 IL-6 knock down, biol rep2

description:
Library name: 882R-sh2-2
Column name gene_count.txt: read_count_R882sh2_2


title: placenta, control dam ID=41G, male fetus


title: alphaTC, scramble, NKX2.2 ChIP, 4


title: placenta, control dam ID=41I, female fetus


title: Homo sapiens, 882R Cells, sh2 IL-6 knock down, biol rep1

description:
Library name: 882R-sh2-1
Column name gene_count.txt: read_count_R882sh2_1


title: WT_Female_Dust_81123_2

value: Female

value: Dust


title: WT_Female_Dust_81023_2


title: alphaTC, Klf4-KD, Input, 2


title: Homo sapiens, T1R Cells, sh1 IL-6 knock down, biol rep1

description:
Library name: T1R-sh1-1
Column name gene_count.txt: read_count_T882sh1_1


title: alphaTC, Klf4-KD, NKX2.2 ChIP, 3


title: alphaTC, Klf4-KD, Input, 1


title: WT_Male_Saline_81023_1

value: Male

value: Saline


title: Fat-1_Male_Saline_81023_1


title: Fat-1_Male_Dust_81023_2


title: JQ1-VHL BRD4 ChIP

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (GRCh37) and Drosophila genome () with BWA-mem
Peak calling was performed with MACS2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks called by MACS2

source_name: Breast; Mammary gland

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 15 min at RT, and crosslinking was quenched by addition of 0.125 M glycine. Cells were scraped from flasks and lysed in 500ul 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0 and protease inhibitors per 107 cells. Crosslinked Drosophila S2 cells were spiked in at 20% and lysates were sonicated in a Covaris ultrasonicator for 40 min (30 sec on/off cycles) to achieve a mean DNA fragment size of ~500 bp. Immunoprecipitation with anti-RNA polymerase II (05-623, Millipore) or anti-BRD4 (13440, Cell Signaling) was performed overnight at 4 °C in modified RIPA buffer (10 mM Tris-HCl pH 8.0, 90 mM NaCl, 1% Triton X-100 and 0.1% deoxycholate). Protein A or G magnetic beads (Life Technologies) were used to bind the antibody and associated chromatin. Reverse crosslinking of DNA was followed by DNA purification using the QIAquick PCR purification kit (Qiagen).
Sequencing libraries were prepared from eluted DNA using ThruPLEX DNA-seq kit (Rubicon). Libraries were size-selected between 200–500 bp and sequenced on a NextSeq500 with 75-bp single-end reads.

treatment_protocol: 10-20 x10^6 cells treated for 3 hours with drug

value: BRD4 Cell Signalling E2A7X#13440S


title: Homo sapiens, T1R Cells, sh2 IL-6 knock down, biol rep2

description:
Library name: T1R-sh2-2
Column name gene_count.txt: read_count_T882sh2_2


title: Homo sapiens, 882R Cells, control blank, biol rep2

description:
Library name: 882R-NC-2
Column name gene_count.txt: read_count_R882nc_2


title: WT_Male_Dust_81023_1


title: DMSO BRD4 ChIP

value: DMSO


title: placenta, control dam ID=45A, female fetus

value: control dam


title: Homo sapiens, T1R Cells, control blank, biol rep1

description:
Library name: T1R-NC-1
Column name gene_count.txt: read_count_T882nc_1


title: placenta, control dam ID=27A, female fetus


title: WT_Male_Dust_81023_2


title: alphaTC, Klf4-KD, Input, 3


title: placenta, control dam ID=27C, male fetus

value: male


title: alphaTC, scramble, Input, 3

value: alpha cells


title: WT_Female_Saline_81023_2


title: Homo sapiens, 882R Cells, control blank, biol rep1

description:
Library name: 882R-NC-1
Column name gene_count.txt: read_count_R882nc_1


title: Homo sapiens, 882R Cells, sh1 IL-6 knock down, biol rep2

description:
Library name: 882R-sh1-2
Column name gene_count.txt: read_count_R882sh1_2


title: DMSO Pol II ChIP

value: Pol II Millipore 05-623


title: alphaTC, scramble, Input, 2


title: Homo sapiens, 882R Cells, sh1 IL-6 knock down, biol rep1

description:
Library name: 882R-sh1-1
Column name gene_count.txt: read_count_R882sh1_1


title: alphaTC, scramble, Input, 4


title: Mouse M4 founder tag sequencing, day 13 post C1498-FLARE injection

city: Lebanon

first: Rachel

middle: Danielle

last: Saxe

state: New Hampshire

address: 1 Medical Center Dr

institute: Dartmouth Cancer Center

description: Library name: sample8_M4_d13_ftag

data_processing:
Basecalling with BCL2fastq or BCL Convert
Assembly: mm10
Supplementary files format and content: FLARE lineage tracing barcode pipeline output with aligned reads and edit patterns (.stats files)

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood and Tissue kit
Libraries were constructed with custom targeted PCR primers

value: AML, PBMC

tag: genetic modification

value: FLARE lineage recording


title: TM2

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: hg38
Supplementary files format and content: xlsx files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: Human liver cancer cells

value: TM


title: islets, Klf4-alphaKO, 3

extract_protocol:
Total RNA from isolated islets was extracted using a Qiagen Rneasy Mini Kit
Tecan Universal Plus mRNA-seq library preparation kit with NuQuant

value: pancreatic islets


title: Fat-1_Female_Dust_81023_1

value: Left Lung


title: OE_2_KB17

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

description: SPOCK2 overexpression

data_processing:
RNA-seq raw paired-end reads were trimmed with fastp (Chen S., et al., 2018). Trimmed reads were aligned to Ensembl GRCh38 human genome with STAR (v2.7) (Dobin, A., et al. 2013) and counts were obtained using featureCounts v1.6.3 (Liao, Y., et al. 2014) . RNA-seq raw sequence reads analysis was performed using iDEP9.4 interactive platform) (Ge, S. X., et al. 2018). All aligned reads were normalized using DESeq2 package (Love M. I., et al., 2014).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: normalized counts txt file

source_name: Pancreas

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium containing 1g/L glucose (DMEM; Corning) supplemented with 2% BSA fraction V fatty acid free (Millipore), 50 μM 2-mercaptoethanol (Thermo Fisher Scientific), 10 mM nicotinamide (Sigma Aldrich), 5.5 μg/ml transferrin (Sigma Aldrich), 6.7 ng/ml selenite (Sigma Aldrich), 100 U/ml penicillin, and 100 μg/ml streptomycin on Geltrex (200 μg/ml) and fibronectin (4 μg/ml; Sigma Aldrich)-coated cell culture plates. Every 2 weeks cells were tested for mycoplasma presence. The cells were seeded at the density of 8x105 cells/cm² and were passaged every 7 days using Trypsin (GIBCO). The media was usually changed every 2-3 days. The cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted and purified using Trizol as previously described (Varshney et al., 2017).
RNAseq was performed according to the TruSeq RNA Library Prep Kit protocol

value: human pancreatic beta cell line

tag: genotype/variation

value: SPOCK2 OE


title: WT_Female_Saline_81023_1

value: WT

value: Female


title: islets, Klf4-alphaKO, 2


title: Mouse M2 founder tag sequencing, day 13 post C1498-FLARE injection

description: Library name: sample6_M2_d13_ftag


title: JQ1-VHL Pol II ChIP

tag: chip antibody


title: GIPZ_2_KB5

description: GIPZ control done with shRNA plazmid

value: GIPZ control


title: SPOCK2_KO_beta

data_processing:
The raw scRNA-seq data were processed with bcl2fastq v2.20 to demultiplex samples and convert .bcl files to .fastq format. For initial data processing and some basic analyses 10xGenomics Cell Ranger pipelines and Seurat R package were used.
Assembly: hg38
Supplementary files format and content: tap-separated values files and matrix files

source_name: cell line

extract_protocol:
hPSC derived WT and SPOCK2 KO beta-cell spheroids, were dispersed with Tripsin, washed with 0.1% saponin – 1% BSA – PBS, filtered through 30 μm mesh filter. Afterwards cells were counted using Countess and adjusted to 700-1,200 cells/μl.
The scRNA-seq was performed with 10xGenomics platform and Illumina according to the manufacturer's protocol. Libraires were pair-end sequenced with depth of 40,000 reads per cell.

value: cell line

value: hPSC derived pancreatic beta cells

value: early beta cells, stage 7, day 21

value: SPOCK2 KO


title: WT_1_KB2

description: wild type


title: Fat-1_Female_Dust_81023_2

value: Dust


title: alphaTC, scramble, Input, 1

value: alpha cells

value: siScramble transfection


title: islets, Gcg-iCre control, 2


title: WT_2_KB3

description: wild type


title: TM3

institute: The First Affiliated Hospital of Anhui Medical University

value: liver


title: Mouse M3 founder tag sequencing, day 13 post C1498-FLARE injection

description: Library name: sample7_M3_d13_ftag

value: AML, PBMC

value: FLARE lineage recording