title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad004

status: Public on Sep 17 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G11_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G10_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F8_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G2_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F7_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F7_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F7_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F7_ad002


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F5_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F6_ad002


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F3_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F2_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F2_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F2_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F5_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F2_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F11_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F11_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F11_ad008


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F11_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F1_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F1_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F1_ad006


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F1_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad001


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_F11_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E9_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad010


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F1_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F10_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E8_ad004


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E7_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E6_ad001


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E4_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E4_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E5_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E2_ad010


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E2_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E2_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E2_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E10_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E10_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_F9_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E11_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E10_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E10_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E10_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E1_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E1_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E1_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_E1_ad008


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_E1_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D9_ad008


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_D8_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D8_ad010


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_D9_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D9_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad012


title: Pm_mantle_a

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

library_source: transcriptomic

data_processing:
Initial trimming of poor quality sequence and residual Illumina adaptors with TrimGalore v0.6 at default parameters.
Reads were mapped using STAR 2.7 with the --quantMode GeneCounts option to a genome library of xPecMax.fa (produced using --sjdbOverhang 149)
Genome_build: GCA_902652985.1
Supplementary_files_format_and_content: Tab-delimtied STAR output of read counts

molecule: total RNA

organism: Pecten maximus

source_name: mantle tissue of the King Scallop

extract_protocol:
Cells were disrupted manually with a pestle in liquid nitrogen before RNA extraction using RNeasy universal kit (Qiagen).
Libraries were made at the Wellcome Sanger Institute. These were made according to their autoRNA library preparation process, with poly(A) pulldown, fragmentation, 1st and 2nd strand synthesis, end prep and ligation using the NEB Ultra II RNA custom kit (New England Biolabs, Massachusetts, United States) on an Agilent Bravo WS automation system (Agilent, California, United States). 14 rounds of PCR were used in library construction.

tag: tissue

value: mantle


title: Pm_mantle_b


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad010


title: Repolarization: 72h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

city: Bellevue

first: Serena

last: Liu

state: Washington

department: Genome Sciences

institute: University of Washington

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M2_0

data_processing:
For bulk RNA-seq, demultiplexed reads were aligned to the mouse (mm10) reference genome using Tophat v2.0.14 with default settngs; aligned reads were quantified using Cuffquant v2.2.2, and a normalized gene expression matrix was generated using Cuffnorm v2.2.2.
For single-cell RNA-seq data, expression matrix files and BAM files were generated using cellranger (10X genomics) version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.
For bulk ATAC-seq, demultiplexed reads were aligned to the mouse (mm10) reference genome using Tophat v2.0.14 with default settings; PCR duplicates were removed using Samtools v1.9, and data from all alignment files were merged into a single file for peak calling using MACS v2.1.0 (parameters: --nomodel --keep-dup-all --extsize 200 --shift -100 -B --SPMR --call-summits) to generate a master list of peaks observed in the experiment. A peak count matrix was calculated by using Bedtools v2.28.0 to compute the intersection between each sample's aligned reads and the master list of peaks.
Genome_build: mm10
Supplementary_files_format_and_content: For bulk RNA-seq, an expression matrix (csv format) containing FPKM data for all conditions across all replicates is provided. For 10X single cell RNA-seq, three files are provided for each sample: 1) matrix files containing the UMI expression data, 2) tsv file containing gene metadata, 3) tsv file containng barcode (i.e. cell) metadata. For bulk ATAC-seq, a count matrix (tsv format) containing peak counts for all samples and replicates measured is provided.

source_name: bone-marrow derived macrophages (BMDMs) from 6-10 week old C57BL/6J mice

growth_protocol: C57BL/6J (6-10 weeks) mice were killed by cervical dislocation, and bone marrow cells were harvested by flushing femure bones with RPMI-1640. Bone marrow cells were plated at a concentration of 6 x 10^6 cells per 3 cm petri dish, then cultured in a base media of RPMI-1640 with 20% horse serum, 100 U/mL penicillin, 100 μg/mL streptomycin, and 20 ng/mL macrohpage colony stimulating factor (MCSF).

extract_protocol:
For bulk RNA-seq, trizol followed by phenol extraction of bulk RNA. For single-cell RNA-seq, 10X Genomics single cell gene expression protocol following manufacturer recommendations. For bulk ATAC-seq, nuclei extraction and DNA tagmentation was performed as described in Buenrostro et al. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods 10, 1213-18.
For bulk RNA-seq, libraries were prepared using the Illumina TruSeq kit, following manufacturer recommendations. For single-cell RNA-seq, 10X Genomics single cell gene expression protocol following manufacturer recommendations. For bulk ATAC-seq, library prep was performed as described in Buenrostro et al. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods 10, 1213-18.

treatment_protocol: On day 7 of culture, cells were stimulated with 100 ng/mL LPS and 25 ng/mL interferon-γ (IFN-γ) or 25 ng/mL interleukin-4 (IL-4) to induce polarization to M1 or M2 states, respectively, or maintained in base media as a control (M0). For repolarization, BMDMs were primed with LPS + IFN-γ or IL-4 for 24h, washed with PBS, then either treated with the opposing stimulus, maintained in the original stimulus, or returned to base media. Samples were collected for bulk RNA-seq analysis 1h, 2h, 4h, 6h, 12h, and 24h post-treatment for polarization, and 1h, 2h, 4h, 6h, 12h, 24h, and 72h post-treatment for repolarization. Three biological replicates were collected for the full set of polarization and repolarization conditions. For single-cell RNA-seq, a single biological replicate was collected in which cells were harvested and cultured as described above for a subset of polarization conditions: 0h M0, 6h M0, 6h M1, 6h M2, 24h M0, 24h M1, 24h M2. For bulk ATAC-seq, cells were also harvested and cultured as described above for three biological replicates of the following conditions: 0h M0, 24h M1, 72h M1→M0.

tag: cell type

value: Bone-marrow derived macrophages (BMDMs)

tag: cytokines added

value: LPS + IFN-gamma, PBS wash, then IL-4


title: Repolarization: 72h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M1_0

value: IL-4, PBS wash, then LPS + IFN-gamma


title: Repolarization: 72h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M1_2


title: Repolarization: 72h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M1_1


title: Repolarization: 72h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D5_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D4_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D12_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D2_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad010


title: Repolarization: 72h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D3_ad007


title: Repolarization: 72h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M2_2

value: IL-4, PBS wash, then IL-4


title: Repolarization: 72h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M0_0

value: LPS + IFN-gamma, PBS wash, then none


title: Repolarization: 72h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M0_2

value: IL-4, PBS wash, then none


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad007


title: Repolarization: 72h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M1_2

value: LPS + IFN-gamma, PBS wash, then LPS + IFN-gamma


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad006


title: Repolarization: 72h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M0_0


title: Repolarization: 72h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M0_2


title: Repolarization: 72h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad012


title: Repolarization: 72h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 4

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M0_3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad012


title: Repolarization: 72h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M0_1


title: Repolarization: 72h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M2_0


title: Repolarization: 72h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M0_0


title: Repolarization: 72h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M2_1


title: Repolarization: 72h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M2_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad006


title: Repolarization: 24h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M1_1


title: Repolarization: 72h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad004


title: Repolarization: 72h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M1_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D11_ad007


title: Repolarization: 24h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad001


title: Repolarization: 72h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_72h_M0_2


title: Repolarization: 24h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M2_0


title: Repolarization: 24h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C9_ad008


title: Repolarization: 24h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M1_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D10_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C9_ad007


title: Repolarization: 24h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M2_2


title: Repolarization: 24h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C9_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_D1_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad012


title: Repolarization: 24h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M0_0


title: Repolarization: 24h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C9_ad012


title: Repolarization: 24h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M0_0


title: Repolarization: 24h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M0_1


title: Repolarization: 24h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C9_ad004


title: Repolarization: 24h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad006


title: Repolarization: 24h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M1_2


title: Repolarization: 24h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad010


title: leufree_21d

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Reads were quality and adapter trimmed with TrimGalore! and aligned to the mouse genome with bowtie2.
Reads mapping to mtDNA were removed. Concordant, uniquely mapping read pairs were used to determine genome coverage with bamCoverage feature in Deeptools, with binsize 10 and RPGC normalization.
Peaks were called with MACS2 and motif analysis was performed with Homer.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of genomic alignments

source_name: KRPC pancreatic adenocarcinoma cells

extract_protocol:
Nuclei from 50,000 cells were used in transposition reactions using the Nextera DNA Library Prep Kit (Buenrostro et al, 2013). DNA was purified using the Qiagen MinElute kit.
Libraries were amplified with indexed primers using NEBNext High-Fidelity PCR master mix and quantified by qPCR using KAPA Illumina Standards.

tag: time point

tag: medium

value: leucine-free DME/F12 + 3percent  BSA


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad004


title: leufree_16h


title: Repolarization: 24h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M0_1


title: Repolarization: 24h unpolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M0_0


title: Repolarization: 24h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C8_ad010


title: comp_16h

value: complete DME/F12 + 3percent  BSA


title: Repolarization: 24h M2→M2-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M2_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad004


title: Repolarization: 12h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad012


title: Repolarization: 12h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad010


title: Repolarization: 24h M1→M1-polarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_24h_M1_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad007


title: leufreeBSA_21d_rep1

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Reads were quality and adapter trimmed with TrimGalore!
Trimmed reads were aligned to the mouse genome with Tophat2.
Concordant read pairs that aligned to gene features were counted with htseq-count.
Normalization and differential expression analysis was performed with the edgeR package.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited txt file of gene counts per million reads

molecule: polyA RNA

extract_protocol:
Total RNA was extracted with Trizol reagent and precipitated with isopropanol
Libraries were prepared from polyA-enriched RNA with NEBNext Ultra RNA library prep kit


title: compBSA_21d_rep2


title: Repolarization: 12h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad002


title: comp_21d


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C6_ad001


title: compBSA_21d_rep1


title: Repolarization: 12h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M2_1


title: leufreeBSA_16h_rep2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C7_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad010


title: Repolarization: 12h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M1_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad008


title: leufreeBSA_21d_rep2


title: leufreeBSA_16h_rep1


title: Repolarization: 12h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M0_1


title: Repolarization: 12h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M0_0


title: Repolarization: 12h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M2_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad006


title: leufree_16h_rep2

value: leucine-free DME/F12


title: leufree_16h_rep1


title: Repolarization: 12h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad012


title: compBSA_16h_rep2


title: Repolarization: 12h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad008


title: Repolarization: 12h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C5_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad010


title: compBSA_16h_rep1


title: comp_16h_rep2

value: complete DME/F12


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad002


title: Repolarization: 6h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M1_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad012


title: comp_16h_rep1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C4_ad006


title: Repolarization: 6h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad010


title: Repolarization: 12h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_12h_M1_M0_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad008


title: Repolarization: 6h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad007


title: Repolarization: 6h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M2_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C3_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad010


title: Repolarization: 6h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad001


title: Repolarization: 6h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M2_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C12_ad006


title: Repolarization: 6h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C2_ad004


title: Repolarization: 6h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad012


title: Repolarization: 6h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M2_M0_0


title: Repolarization: 6h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad007


title: Repolarization: 6h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad004


title: Repolarization: 6h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_6h_M1_M0_0


title: Repolarization: 4h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 4

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M1_3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C11_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad006


title: Gastrocnemius_24m_rep1

type: RNA

city: Lausanne

first: Xu

last: Wang

address: EPFL SV IBI-SV NCEM AI 1148 (Bâtiment AI) Station 15

department: School of Life Sciences

country: Switzerland

institute: École polytechnique fédérale de Lausanne

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Microarray data was normalized with RMA-sketch method and analyzed using the Affymetrix Expression and Transcriptome analysis consoles.

label: biotin

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Female C57BL/6J mice were group housed and received standard chow (#2018, containing 18% protein, 50% carbohydrate and 6.0% fat; Harlan Laboratories, Madison, WI, USA).

extract_protocol: Tissues were frozen in liquid nitrogen for biochemical and molecular analyses. Total RNA was isolated using Trizol (Life Technologies) and purified using the RNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s instructions. It was then assessed for degradation using an Advanced Analytical Agilent Fragment Analyzer.

treatment_protocol: After reaching the age of 24 (~6 month) or 103 weeks (~24 month), mice were sacrificed after overnight fasting.

value: female

value: 24 month

value: Gastrocnemius


title: Gastrocnemius_24m_rep3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad004

value: DG


title: Gastrocnemius_24m_rep2


title: Gastrocnemius_6m_rep4

value: 6 month


title: Gastrocnemius_24m_rep4


title: Repolarization: 4h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M1_0


title: Gastrocnemius_6m_rep3


title: Repolarization: 4h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M1_1


title: Gastrocnemius_6m_rep1


title: Gastrocnemius_6m_rep2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad012

value: male


title: Heart_24m_rep2

value: Heart


title: Heart_6m_rep4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad010


title: Heart_24m_rep3


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad010


title: Repolarization: 4h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M2_2

value: Bone-marrow derived macrophages (BMDMs)

value: LPS + IFN-gamma, PBS wash, then IL-4


title: Heart_24m_rep4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad007


title: Heart_6m_rep3


title: Repolarization: 4h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M1_2

value: IL-4, PBS wash, then LPS + IFN-gamma


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C10_ad007


title: Erythrocyte population

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

country: China

institute: Institute of Hematology and Blood Diseases Hospital

data_processing:
Raw reads of  Smart-seq2 were first split based on the cell-specific barcode sequences attached in read2. And UMI sequence in read2 was integrated into the paired read1 by Python scripts. Then, the template switch oligo (TSO) sequence, the polyA tail sequence and the low-quality reads (N>10%) were discarded for each separated single cell using Cutadapt.
The clean reads were aligned to human reference genome (hg38 from Ensembl) by Hisat2 (version 2.0.3-beta), followed by calculating uniquely mapped reads through htseq-count (version 0.9.1) based on the genome annotation file from Ensembl (hg38). Finally, the total number of different UMIs for each gene was quantified as the read count of that gene.
Genome_build: hg38
Supplementary_files_format_and_content: .csv (UMI matrix of single cells)

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
Samples were incubated on ice for 30 mins in the dark and washed with PBS + 2% FBS (Gibco), cell suspension of which were added with DAPI (1 ug/ml, Sigma-Aldrich) to deplete dead cells for FACS.
Smart-seq2

treatment_protocol: All samples were freshly prepared and immediately stained with human antibodies.

tag: developmental stage

value: adult

value: bone marrow

tag: cell population

value: Erythrocyte


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad004


title: Repolarization: 4h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M2_1


title: Neutrophil population

value: Neutrophil


title: Repolarization: 4h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M2_0


title: Monocyte population

value: Monocyte


title: Repolarization: 4h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M0_2

value: IL-4, PBS wash, then none


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_C1_ad001


title: Repolarization: 4h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M0_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad007


title: Repolarization: 4h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M0_2

value: LPS + IFN-gamma, PBS wash, then none


title: Heart_24m_rep1

value: female


title: T cell population

source_name: bone marrow and peripheral blood

value: bone marrow and peripheral blood

value: T


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad012

value: DG


title: Heart_6m_rep1

value: 6 month


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad002

value: male


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad001


title: NK cell population

value: NK


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad008


title: B cell population

value: B


title: Heart_6m_rep2

value: Heart


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad004


title: A549 cells, con3

city: Los Angeles

first: Xinshu

last: Xiao

address: 610 Charles E. Young Drive S

institute: University of California, Los Angeles

data_processing:
Trim reads with cutadapt (v 1.12). cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 35 -o ${outR1} -p ${outR2} ${inputR1} ${inputR2}
Combine reads across lanes for each sample
Align reads with HISAT2 (v 2.0.5). hisat2 -q --phred33 --no-softclip --add-chrname --no-unal --reorder --no-discordant --no-mixed --un-conc-gz ${unaligned} -x ${genome_snp_tran} -1 ${fastq1} -2 ${fastq2} -S ${sam}
Run htseq-count (v 0.6.0) and calculate TPM (transcripts per million).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited format includes gene expression values, calculated as TPM, for each ADAR KD and control condition

source_name: A549 cells

growth_protocol: A549 cells were maintained in DMEM with 10% FBS and Antibiotic-Antimycotic reagent (Gibco).

extract_protocol:
Cells were lysed using TRIzol (Thermo Fisher Scientific). Total RNA was isolated using Direct-zol RNA Miniprep Plus kit (Zymo Research) following the manufacturer’s protocol.
RNA sequencing libraries were generated using NEBNext Ultra II Directional RNA library Prep kit and NEBNext multiplex oligos for Illumina according to the manufacturer’s instructions (New England Biolabs, E7760S).

treatment_protocol: siRNAs were introduced at the final concentration of 22nM using lipofectamine RNAiMAX (Invitrogen), according to the manufacturer’s protocol. For individual ADAR1 or ADAR2 knockdown, 11nM siRNA of ADAR1 or ADAR2 were mixed with 11nM control siRNAs. For double knockdown of ADAR1 and ADAR2, 11nM siRNA of ADAR1 and 11nM siRNA of ADAR2 were mixed.

tag: cell line

tag: sirna transfection

value: control siRNA


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B8_ad006


title: A549 cells, con2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad012


title: Repolarization: 4h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M1_M0_0

value: Bone-marrow derived macrophages (BMDMs)


title: A549 cells, A2si3

value: siRNA of ADAR2


title: Repolarization: 4h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_4h_M2_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B9_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad007


title: Repolarization: 2h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M1_1

value: IL-4, PBS wash, then LPS + IFN-gamma


title: A549 cells, A2si2


title: Repolarization: 2h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M1_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad002


title: Repolarization: 2h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M2_2

value: LPS + IFN-gamma, PBS wash, then IL-4


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B7_ad004


title: A549 cells, A2si1


title: A549 cells, A1si3

value: siRNA of ADAR1


title: Repolarization: 2h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M2_1


title: A549 cells, con1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad012


title: Repolarization: 2h M1→M2-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M2_0


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad008


title: A549 cells, A1si1


title: Repolarization: 2h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M0_2

value: IL-4, PBS wash, then none


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad007


title: A549 cells, A1si2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad006


title: Repolarization: 2h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M0_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B6_ad002


title: Repolarization: 2h M2→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M2_M0_0


title: Repolarization: 2h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M0_1

value: LPS + IFN-gamma, PBS wash, then none


title: Repolarization: 2h M1→M0-depolarized mouse BMDMs, bulk RNA-seq, biological replicate 3

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_2h_M1_M0_2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad008


title: A549 cells, A12si3

value: siRNA of ADAR1 and siRNA of ADAR2


title: A549 cells, A12si1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B5_ad001


title: A549 cells, A12si2


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B4_ad010


title: CS17_DL_3

city: Edinburgh

first: Edie

last: Crosse

address: 5 Little France Road

department: Centre for Regenerative Medicine

institute: University of Edinburgh

description:
Total RNA (ribosome depleted)
CS17_Raw_Counts.txt

data_processing:
Adapter trimming Flexbar/2.5
Alignment STAR/2.5.1b
Gene counts with bedtools multicov, gtf = Homo_sapiens.GRCh38.86.gtf.gz
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: .txt, raw read count matrices are provided with ENSEMBL_ID row names, sample column names

source_name: Embryo dorsal aorta

extract_protocol:
Human embryos embedded in OCT were sectioned in a caudal-to-rostral direction using a cryotome FSE cryostat (Thermo Scientific).  Sections were stained using a rapid Haematoxylin and Eosin staining protocol - 3 minutes (min) in 70% ethanol, 1 min H2O, 4 min Mayer’s Haematoxylin Solution (Sigma-Aldrich), 2 min tap H2O, 15 seconds Eosin Y (Sigma-Aldrich), 1 min 70% ethanol, 1 min 90% ethanol, 3 mins 100% ethanol. All H2O was treated with diethyl pyrocarbonate (DEPC) and all reagents were pre-cooled in ice except 100% ethanol which was room temperature. The laser capture microscope used was the PALM microbeam (Zeiss). The microscope and surrounding area were sprayed down with RNaseAWAY ® (Sigma-Aldrich). Sections were viewed and microdissected in brightfield using a 10X objective. The microdissected regions were collected into the caps of AdhesiveCap 500 opaque (Zeiss) 500µl PCR tubes. 15µl lysis buffer (0.2% Triton X-100 (Sigma-Aldrich), 2U/µl RNase inhibitor (Takara), Phosphate Buffer Solution (PBS, (Nichterwitz et al., 2016)) was added directly on top of the dissected tissue in the tube caps and the tubes closes in an inverted position. PicoPure RNA Isolation Kit was used to extract RNA for samples 1-12. Samples 13-30 were directly amplified from lysed material
SMARTer® Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian kit (Takara) for samples 1-12, LCM-Seq (Picelli et al., 2014) for samples 13-30.

tag: embryo

value: dorsal aorta

tag: subdomain

value: Dorsal-lateral ([DL])


title: CS17_D_3

value: Dorsal ([D])


title: CS17_VL_3

value: Ventro-lateral ([VL])


title: Repolarization: 1h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 2

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M1_1


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B4_ad004

value: DG

value: male


title: Repolarization: 1h M2→M1-repolarized mouse BMDMs, bulk RNA-seq, biological replicate 1

description:
Data collected from murine bone marrow-derived macrophages cultured in vitro with different combinations of cytokines to stimulate polarization or repolarization into either M1 or M2 states, with unpolarized (M0) as the control state. Bulk RNA-seq was performed on samples at multiple timepoints following both polarization and repolarization, for three biological replicates. Bulk RNA was phenol-extracted, and libraries were prepared using the Illumina TruSeq kit according to manufacturer instructions.
log10_polRP_all_samples_fpkmMatrix.csv
RP_1h_M2_M1_0


title: CS17_V_3

value: Ventral ([V])


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B4_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B4_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_B3_ad010