title: A20-104 A31A20-104 A31_ROI019PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F09.dcc


title: A20-104 A31A20-104 A31_ROI017PanCK+

status: Public on Nov 14 2020

type: SRA

city: Seattle

first: Jason

middle: W

last: Reeves

state: WA

address: 530 Fairview Blvd

department: R&D

country: USA

institute: Nanostring

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F06.dcc

library_source: transcriptomic

data_processing:
Library strategy: GeoMx Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx COVID19 Immune Response Atlas v1 Platform file & GeoMx_COVID19_v1.0.pkc file
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

molecule: total RNA

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: FFPE Rapid Autopsy Tissue

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: case number

value: Case 8

tag: patient id

tag: roi number

tag: segment type

tag: tissue substructure

value: Alveoli

tag: sars-cov-2 rna ish

value: Positive

tag: patient viral load

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: note


title: A20-104 A31A20-104 A31_ROI015geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F04.dcc

value: Geometric

value: Negative


title: A20-104 A31A20-104 A31_ROI014geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F03.dcc


title: A20-104 A31A20-104 A31_ROI016geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F05.dcc


title: A20-104 A31A20-104 A31_ROI011geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E12.dcc


title: A20-104 A31A20-104 A31_ROI009geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E10.dcc


title: A20-104 A31A20-104 A31_ROI034PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-H10.dcc

value: Bronchial


title: A20-104 A31A20-104 A31_ROI013geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-F02.dcc


title: A20-104 A31A20-104 A31_ROI008geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E09.dcc


title: A20-104 A31A20-104 A31_ROI007geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E08.dcc


title: A20-104 A31A20-104 A31_ROI004geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E05.dcc


title: A20-104 A31A20-104 A31_ROI006geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E07.dcc


title: A20-104 A31A20-104 A31_ROI010geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E11.dcc


title: A20-104 A31A20-104 A31_ROI005geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E06.dcc


title: A20-104 A31A20-104 A31_ROI002geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E03.dcc


title: A20-102 A40A20-102 A40_ROI032PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E01.dcc

value: Case 7


title: A20-102 A40A20-102 A40_ROI031PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D10.dcc


title: A20-102 A40A20-102 A40_ROI032PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D12.dcc


title: A20-104 A31A20-104 A31_ROI003geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E04.dcc


title: A20-102 A40A20-102 A40_ROI030PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D09.dcc


title: A20-102 A40A20-102 A40_ROI031PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D11.dcc


title: A20-102 A40A20-102 A40_ROI029PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D07.dcc


title: A20-102 A40A20-102 A40_ROI028PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D05.dcc


title: A20-102 A40A20-102 A40_ROI029PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D06.dcc


title: A20-102 A40A20-102 A40_ROI027PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D03.dcc


title: A20-102 A40A20-102 A40_ROI027PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D02.dcc


title: A20-102 A40A20-102 A40_ROI026PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C12.dcc


title: A20-102 A40A20-102 A40_ROI025PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C10.dcc


title: A20-102 A40A20-102 A40_ROI024PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C09.dcc


title: A20-102 A40A20-102 A40_ROI024PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C08.dcc


title: A20-102 A40A20-102 A40_ROI022PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C05.dcc


title: A20-102 A40A20-102 A40_ROI023PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C07.dcc


title: A20-104 A31A20-104 A31_ROI001geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-E02.dcc


title: A20-102 A40A20-102 A40_ROI022PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C04.dcc


title: A20-102 A40A20-102 A40_ROI023PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C06.dcc


title: A20-102 A40A20-102 A40_ROI021PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C03.dcc


title: A20-102 A40A20-102 A40_ROI020PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B12.dcc


title: A20-102 A40A20-102 A40_ROI019PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B11.dcc


title: A20-102 A40A20-102 A40_ROI018PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B09.dcc


title: A20-102 A40A20-102 A40_ROI020PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C01.dcc


title: A20-102 A40A20-102 A40_ROI018PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B08.dcc


title: A20-102 A40A20-102 A40_ROI021PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C02.dcc


title: A20-102 A40A20-102 A40_ROI019PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B10.dcc


title: A20-102 A40A20-102 A40_ROI017PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B06.dcc


title: A20-102 A40A20-102 A40_ROI017PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B07.dcc


title: A20-102 A40A20-102 A40_ROI030PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D08.dcc


title: A20-102 A40A20-102 A40_ROI028PanCK+

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D04.dcc


title: A20-102 A40A20-102 A40_ROI015geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B04.dcc


title: A20-102 A40A20-102 A40_ROI026PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-D01.dcc


title: A20-102 A40A20-102 A40_ROI014geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B03.dcc


title: A20-102 A40A20-102 A40_ROI025PanCK-

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-C11.dcc


title: A20-102 A40A20-102 A40_ROI012geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B01.dcc


title: A20-102 A40A20-102 A40_ROI013geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B02.dcc


title: A20-102 A40A20-102 A40_ROI011geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A12.dcc


title: A20-102 A40A20-102 A40_ROI009geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A10.dcc


title: A20-102 A40A20-102 A40_ROI007geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A08.dcc


title: A20-102 A40A20-102 A40_ROI006geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A07.dcc


title: A20-102 A40A20-102 A40_ROI004geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A05.dcc


title: A20-102 A40A20-102 A40_ROI005geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A06.dcc


title: A20-102 A40A20-102 A40_ROI003geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A04.dcc


title: A20-102 A40A20-102 A40_ROI002geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A03.dcc


title: A20-102 A40A20-102 A40_ROI001geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A02.dcc


title: A20-102 A40A20-102 A40_ROI016geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-B05.dcc


title: 32-7weeks-after-transection-whole-nose-larvae

city: Göttingen

first: Carsten

last: Lueder

address: Kreuzbergring 57

country: Germany

institute: Institut für Medizinische Mikrobiologie

data_processing:
Basecall was performed using bcl2fastq v2.17.1.14
Sequenced reads were aligned to reference genome Xenopus laevis  using STAR aligner  version 2.5
Raw counts were calculated using featureCounts from subread package version 1.5.0
Transcripts Per Million (TPM) were calculated as proposed by Wagner et al 2012.
Genome_build: 9.1
Supplementary_files_format_and_content: tab-delimited text files including  TPM for each Sample; normalised text file and raw data txt files

organism: Xenopus laevis

source_name: premetamorphosis

extract_protocol: none provided by the submitter

tag: tissue

value: nose


title: A20-102 A40A20-102 A40_ROI010geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A11.dcc

tag: case number


title: 36-aminoacid-exposure-200M-5h-wholenoselarvae


title: 43-aminoacid-exposure-1000-M5h-whole-nose-larvae


title: 41-aminoacid-exposure-1000-M5h-wholenoselarvae


title: 33-7weeks-after-transection-whole-nose-larvae


title: 34-7weeks-after-transection-whole-nose-larvae


title: 49-7weeks-after-transection-whole-bulb-larvae

value: bulb


title: 23-1week-after-transection-whole-bulb-larvae


title: 31-2days-after-transection-whole-bulb-larvae


title: 20-1week-after-transection-whole-nose-larvae

source_name: week after transection


title: 37-aminoacid-exposure-200-M5h-whole-nose-larvae


title: A20-102 A40A20-102 A40_ROI008geometric

description:
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation
DSP-1001250365000-A09.dcc

tag: patient id


title: 42-aminoacid-exposure-1000-M5h-wholenoselarvae


title: 35-aminoacid-exposure-200-M5h-whole-nose-larvae


title: 30-2-days-after-transection-whole-bulb-larvae


title: 22-1week-after-transection-whole-nose-larvae


title: 24-1weekafter-transection-whole-bulb-arvae


title: 21-1week-after-transection-whole-nose-larvae


title: 47-7weeks-after-transection-whole-bulb-larvae


title: 29-2days-after-transection-wholebulb-larvae


title: 48-7weeks-after-transection-whole-bulb-larvae


title: 27-2days-after-transection-whole-nose-larvae


title: 28-2-days-after-transection-whole-nose-larvae


title: 26-2days-after-transection-whole-nose-larvae


title: 62-whole-bulb-larvae

source_name: premetamorphotic bulb


title: 25-1-week-after-transection-whole-bulb-larvae


title: 16-VNO-larvae

source_name: part of the premetamorphotic accessory olfactory subsystem

value: olfactory lobe


title: 61-whole-bulb-larvae


title: 12-VNO-larvae


title: 60-whole-bulb-larvae


title: 15-principal-cavity-larvae

source_name: Main epithelium of the premetamorphotic nose


title: 11-principal-cavity-larvae


title: 9-whole-nose-larvae

source_name: Whole nose of larvae premetamorphosis


title: 14-VNO-larvae


title: 13-principal-cavity-larvae


title: 8-whole-nose-larvae


title: DEN/HFD CTL 1 [148]

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description:
57-years-old Japanese male
148_FNUSA_S17

data_processing:
Reads trimmed using Trimmomatic
Reads aligned with STAR (ver. 2.7.0e)
Reads counted with htseq-count
Normalization and comparisons performed using DESeq2
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text files include variance-stabilized transformed values for each sample

organism: Mus musculus

source_name: C57BL6J - diethylnitrosamine+high fat diet

growth_protocol: C57BL6J mice 2 weeks old were divided in two groups, one received an injection of low dose of a carcinogen (25 mg/kg diethynitrosamine, DEN) and the second only the vehicle. Mice treated with DEN were fed till the six week with chow diet and for the next 32 weeks with high fat diet (HFD, 60% energy from lard) in order to establish a progressive NAFLD model (Park et al Cell. 2010 PMID:20141834), while the other continued with the chow diet.

extract_protocol:
Total RNA was extracted from control and MCOPPB-treated mice liver using TRIzol Reagent (ThermoFisher Scientific, Waltham, USA).
Indexed libraries were prepared from 250 ng purified RNA using a NEB Next Ultra II Directional RNA Library Prep Kit (Illumina, UK), according to the manufacturer's instructions. The libraries were pooled in equimolar amounts, subjected to cluster generation and sequenced on an Illumina MiSeq System (Illumina) in a 1x75 format. Quality control was performed by FastQC and MultiQC.

treatment_protocol: For each diet model, mice were divided in further two groups,one wich was  administered i.p. with MCOPPB (5 mg/kg) for five consecutive days followed by two days wash-out per cycle, for three consecutive cycles (21 days in total), while the other group received a saline solution injection as control.

tag: strain

value: C57BL6J - mice

value: Liver

tag: age

value: 9.5 months-old mice male

tag: rin


title: DEN/HFD + MCOPPB 2 [145]

description:
57-years-old Japanese male
145_FNUSA_S11


title: DEN/HFD + MCOPPB 1 [144]

description:
57-years-old Japanese male
144_FNUSA_S10


title: CTL mice 3 [50]

description:
57-years-old Japanese male
50_FNUSA_S7

source_name: C57BL6J - mice chow diet


title: DEN/HFD CTL 2 [150]

description:
57-years-old Japanese male
150_FNUSA_S13


title: MCOPPB treated-mice 5 [46]

description:
57-years-old Japanese male
46_FNUSA_S8


title: CTL mice 2 [49]

description:
57-years-old Japanese male
49_FNUSA_S6


title: MCOPPB treated-mice 4 [45]

description:
57-years-old Japanese male
45_FNUSA_S4


title: CTL mice 1 [48]

description:
57-years-old Japanese male
48_FNUSA_S5


title: DEN/HFD + MCOPPB 3 [146]

description:
57-years-old Japanese male
146_FNUSA_S12


title: MCOPPB treated-mice 3 [43]

description:
57-years-old Japanese male
43_FNUSA_S3


title: 2-whole-nose-stage-66

source_name: Whole nose of adult animals postmetamorphosis


title: DEN/HFD CTL 4 [153]

description:
57-years-old Japanese male
153_FNUSA_S16


title: MCOPPB treated-mice 2 [42]

description:
57-years-old Japanese male
42_FNUSA_S2


title: 3-whole-nose-stage-66


title: DEN/HFD CTL 3 [151]

description:
57-years-old Japanese male
151_FNUSA_S14


title: 7-whole-nose-larvae


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: SSp

tag: target

value: SC

tag: gender

value: male


title: 1-whole-nose-stage66


title: Distal colon from Spry2-f/f mice - S7

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Statistical tests for differential expression were performed using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

source_name: Full-thickness distal colon

growth_protocol: Homozygous "floxed" Spry2 (Spry2-f/f) were bred to Vil1::Cre mice to generate Vil1::Cre;Spry2-f/f mice harboring an intestinal epithelial-specific deletion of Spry2 (Sprouty2) and littermate "wildtype-like" Spry2-f/f controls. Animals were reared to 6 wks of age and euthanized and their distal colons dissected for RNA isolation and analysis.

extract_protocol:
Distal colonic homogenate was collected from 8 week old mice. RNA was prepared using OMEGA Bio-tek EZNA on-column isolation kit.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit and sequenced to obtain paired-end reads.

tag: litter

value: A

tag: Sex

value: F

tag: genotype

value: WT


title: Distal colon from Spry2-f/f mice - S10

value: B


title: Distal colon from Spry2-f/f mice - S9

value: M


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD004

value: MOp


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S5

value: KO


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S11


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S4


title: Distal colon from Spry2-f/f mice - S2


title: MCOPPB treated-mice 1 [41]

description:
57-years-old Japanese male
41_FNUSA_S1


title: Distal colon from Spry2-f/f mice - S3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD008


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD006


title: NCI-H1299 DICER1 KO #1

type: RNA

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D SG13054284) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: NCI-H1299 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the miRNA Complete Labeling and hyb Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RPMI-1640 supplemented with 10% fetal calf serum, penicillin (100 units/ml), and streptomycin (100 μg/ml)

extract_protocol: Total RNA was prepared using the miRNeasy mini kit (Qiagen)

tag: cell line

tag: cell type

value: Human non-small cell lung cancer


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD010

value: female


title: Normal NCI-H1299

hyb_protocol: miRNA Complete Labeling and hyb Kit (Agilent)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD002


title: NCI-H1299 DICER1 KO #2


title: Distal colon from Vil1::Cre;Spry2-f/f mice - S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D3_AD001


title: Distal colon from Spry2-f/f mice - S13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD007


title: pAL1B5_pre_VZV6hour

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

description:
gene_count_matrix.csv
pAL1B5V6_S5

data_processing:
RNA-seq data was aligned to GRCh38 genome assembly using hisat2 using the parameters --known-splicesite-infile and --dta
Samtools was used to select for reads paired mates.
Gene level count was generated using Stringtie.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: skin biopsy

extract_protocol:
Skin biopsy specimens were collected from the injection site after injection with VZV antigen (6 or 72 hours) or normal saline (6 hours). Normal (uninjected) skin from the same site was collected as a control. Frozen tissue was homogenized, and total RNA was extracted from bulk tissue homogenates by using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Kappa Hyperprep kit (Roche Diagnostics)

value: skin

tag: losmapimod status

value: pre

tag: treatment

value: 6 hours after varicella zoster virus antigen challenge


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD010


title: pAL1B7_pre_normalskin

description:
gene_count_matrix.csv
pAL1B7N_S9

value: Normal skin


title: pAL1B6_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B6D2_S4

value: 2 days after varicella zoster virus antigen challenge


title: pAL1B7_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B7V6_S11


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD012

value: brain

value: SSp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD008

value: SC

value: male


title: pAL1B3_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B3V6_S1


title: pAL1B3_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B3D2_S2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD002


title: pAL1B31_pre_normalskin

description:
gene_count_matrix.csv
pAL1B31N_S1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD006


title: pAL1B7_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B7D2_S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD004


title: pAL1B6_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B6V6_S3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD002


title: AL1B6_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495945
gene_count_matrix.csv
pAL1B6S6_S2

value: 6 hours after saline injection


title: pAL1B6_pre_normalskin

description:
gene_count_matrix.csv
pAL1B6N_S1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D1_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD004


title: pAL1B31_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B31V6_S3


title: pAL1B5_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B5D2_S6


title: AL1B31_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495944
gene_count_matrix.csv
pAL1B31S6_S2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD012


title: AL1B7_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495946
gene_count_matrix.csv
pAL1B7S6_S10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D2_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD006


title: pAL1B31_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B31D2_S4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD008


title: pAL1B30_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B30V6_S11


title: pAL1B26_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B26V6_S3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD007


title: pAL1B30_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B30D2_S12


title: AL1B30_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495943
gene_count_matrix.csv
pAL1B30S6_S10


title: pAL1B30_pre_normalskin

description:
gene_count_matrix.csv
pAL1B30N_S9


title: pAL1B26_pre_normalskin

description:
gene_count_matrix.csv
pAL1B26N_S1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD001


title: pAL1B29_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B29V6_S11


title: pAL1B26_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B26D2_S4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D12_AD001


title: pAL1B29_pre_normalskin

description:
gene_count_matrix.csv
pAL1B29N_S9


title: AL1B25_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495940
gene_count_matrix.csv
pAL1B25S6_S10


title: AL1B29_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495942
gene_count_matrix.csv
pAL1B29S6_S10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD008


title: pAL1B25_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B25V6_S11


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D11_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD012


title: AL1B24_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495939
gene_count_matrix.csv
pAL1B24S6_S2


title: pAL1B25_pre_normalskin

description:
gene_count_matrix.csv
pAL1B25N_S9


title: AL1B26_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495941
gene_count_matrix.csv
pAL1B26S6_S2


title: pAL1B24_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B24D2_S4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_D10_AD004


title: pAL1B29_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B29D2_S12


title: pAL1B23_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B23V6_S11


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD006


title: pAL1B25_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B25D2_S12


title: pAL1B24_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B24V6_S3


title: pAL1B24_pre_normalskin

description:
gene_count_matrix.csv
pAL1B24N_S1


title: pAL1B23_pre_normalskin

description:
gene_count_matrix.csv
pAL1B23N_S9


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD008


title: pAL1B23_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B23D2_S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD012


title: AL1B23_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495938
gene_count_matrix.csv
pAL1B23S6_S10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C9_AD001


title: pAL1B22_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B22V6_S3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD010


title: pAL1B22_pre_normalskin

description:
gene_count_matrix.csv
pAL1B22N_S1


title: AL1B22_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495937
gene_count_matrix.csv
pAL1B22S6_S2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD007


title: pAL1B22_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B22D2_S4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD004


title: pAL1B19_pre_normalskin

description:
gene_count_matrix.csv
pAL1B19N_S9


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD002


title: AL1B19_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495936
gene_count_matrix.csv
pAL1B19S6_S10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD012


title: pAL1B18_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B18V6_S3


title: AL1B18_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495935
gene_count_matrix.csv
pAL1B18S6_S2


title: pAL1B18_pre_normalskin

description:
gene_count_matrix.csv
pAL1B18N_S1


title: pAL1B18_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B18D2_S4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD006


title: pAL1B16_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B16D2_S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD004


title: pAL1B13_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B13V6_S3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD002


title: AL1B15_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495934
gene_count_matrix.csv
pAL1B15S6_S9


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD012


title: pAL1B19_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B19V6_S11


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD010


title: pAL1B13_pre_normalskin

description:
gene_count_matrix.csv
pAL1B13N_S1


title: pAL1B12_pre_VZV6hour

description:
gene_count_matrix.csv
pAL1B12V6_S11


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD008


title: pAL1B19_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B19D2_S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD006


title: AL1B12_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495932
gene_count_matrix.csv
pAL1B12S6_S10


title: pAL1B12_pre_normalskin

description:
gene_count_matrix.csv
pAL1B12N_S9


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD004


title: pAL1B12_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B12D2_S12


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD001


title: AL1B7_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495931
gene_count_matrix.csv
AL1B7S6_S14

value: post


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD012


title: AL1B7_post_normalskin

description:
gene_count_matrix.csv
AL1B7N_S13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C6_AD002


title: AL1B13_pre_saline6hr_reanalyzed

description:
re-analysis of GSM3495933
gene_count_matrix.csv
pAL1B13S6_S2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD010


title: AL1B7_post_VZV6hour

description:
gene_count_matrix.csv
AL1B7V6_S15


title: AL1B6_post_VZV6hour

description:
gene_count_matrix.csv
AL1B6V6_S7


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD007


title: AL1B6_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495930
gene_count_matrix.csv
AL1B6S6_S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD006


title: pAL1B13_pre_VZVday2

description:
gene_count_matrix.csv
pAL1B13D2_S4


title: AL1B6_post_VZVday2

description:
gene_count_matrix.csv
AL1B6D2_S8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD002


title: AL1B6_post_normalskin

description:
gene_count_matrix.csv
AL1B6N_S5


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD008


title: AL1B5_post_VZV6hour

description:
gene_count_matrix.csv
AL1B5V6_S7


title: AL1B3_post_VZV6hour

description:
gene_count_matrix.csv
AL1B3V6_S3


title: AL1B5_post_VZVday2

description:
gene_count_matrix.csv
AL1B5D2_S8


title: AL1B3_post_VZVday2

description:
gene_count_matrix.csv
AL1B3D2_S4


title: AL1B31_post_VZV6hour

description:
gene_count_matrix.csv
AL1B31V6_S7


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD007


title: AL1B31_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495929
gene_count_matrix.csv
AL1B31S6_S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD004


title: AL1B7_post_VZVday2

description:
gene_count_matrix.csv
AL1B7D2_S16


title: AL1B31_post_normalskin

description:
gene_count_matrix.csv
AL1B31N_S5


title: AL1B31_post_VZVday2

description:
gene_count_matrix.csv
AL1B31D2_S8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD001


title: AL1B30_post_VZV6hour

description:
gene_count_matrix.csv
AL1B30V6_S15


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C4_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD010


title: AL1B30_post_normalskin

description:
gene_count_matrix.csv
AL1B30N_S13


title: AL1B30_post_VZVday2

description:
gene_count_matrix.csv
AL1B30D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD002


title: AL1B29_post_VZV6hour

description:
gene_count_matrix.csv
AL1B29V6_S15


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD006


title: AL1B29_post_normalskin

description:
gene_count_matrix.csv
AL1B29N_S13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C3_AD001


title: AL1B29_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495927
gene_count_matrix.csv
AL1B29S6_S14


title: AL1B29_post_VZVday2

description:
gene_count_matrix.csv
AL1B29D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD012


title: AL1B26_post_normalskin

description:
gene_count_matrix.csv
AL1B26N_S5


title: AL1B26_post_VZV6hour

description:
gene_count_matrix.csv
AL1B26V6_S7


title: AL1B26_post_VZVday2

description:
gene_count_matrix.csv
AL1B26D2_S8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD007


title: AL1B26_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495926
gene_count_matrix.csv
AL1B26S6_S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD008


title: AL1B25_post_VZV6hour

description:
gene_count_matrix.csv
AL1B25V6_S15


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD004


title: AL1B25_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495925
gene_count_matrix.csv
AL1B25S6_S14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C2_AD001


title: AL1B25_post_normalskin

description:
gene_count_matrix.csv
AL1B25N_S13


title: AL1B25_post_VZVday2

description:
gene_count_matrix.csv
AL1B25D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD012


title: AL1B24_post_VZV6hour

description:
gene_count_matrix.csv
AL1B24V6_S7


title: AL1B30_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495928
gene_count_matrix.csv
AL1B30S6_S14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD008


title: AL1B24_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495924
gene_count_matrix.csv
AL1B24S6_S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD010


title: AL1B24_post_normalskin

description:
gene_count_matrix.csv
AL1B24N_S5


title: AL1B23_post_VZV6hour

description:
gene_count_matrix.csv
AL1B23V6_S15


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C12_AD001


title: AL1B23_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495923
gene_count_matrix.csv
AL1B23S6_S14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD010


title: AL1B22_post_VZV6hour

description:
gene_count_matrix.csv
AL1B22V6_S7


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD007


title: AL1B22_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495922
gene_count_matrix.csv
AL1B22S6_S6


title: AL1B23_post_normalskin

description:
gene_count_matrix.csv
AL1B23N_S13


title: AL1B23_post_VZVday2

description:
gene_count_matrix.csv
AL1B23D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD010


title: AL1B22_post_VZVday2

description:
gene_count_matrix.csv
AL1B22D2_S8


title: Tumor conditioned HRH1-/- macrophage rep2

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
fastq files were mapped to mm10 using STAR2 and raw read counts obtained using htseq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample
tab-delimited text files include FPKM values for each gene and each sample

source_name: bone marrow derived macrophage

growth_protocol: Bone marrow cells were collected from femurs obtained from 8-week old C57BL/6  mice. After red blood cell lysis, bone marrow cells were seeded at a density of 5×10exp6 cells/150×15 mm Petri dish and cultured at 37°C in complete Dulbecco modified Eagle medium (DMEM) containing 20% L929 cell-conditioned medium, providing macrophage colony-stimulating factor. Macrophages were ready for use on day 7 following a fresh medium change on day 4.

extract_protocol:
RNA from macrophages was harvested using Trizol reagent. After removing DNA by DNase, RNA was further purified using RNeasy MinElute Cleanup Kit (Qiagen). 1 ug of total RNA from each sample (total 3 groups, duplicate samples for each group) were sent to UT health sequencing core for library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages derived from wild type and HRH1-/- bone marrow cells were cultured with DMEM medium or conditioned medium from EO771 cells for two days.

value: bone marrow derived macrophage

value: tumor conditioned medium from EO771


title: Tumor conditioned wild type macrophage rep2

value: wild type


title: Tumor conditioned HRH1-/- macrophage rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD008


title: AL1B22_post_normalskin

description:
gene_count_matrix.csv
AL1B22N_S5


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD012


title: AL1B24_post_VZVday2

description:
gene_count_matrix.csv
AL1B24D2_S8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD007


title: AL1B19_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495921
gene_count_matrix.csv
AL1B19S6_S14


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD001

value: MOp


title: Naïve wild type macrophage rep 2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C11_AD012


title: Tumor conditioned wild type macrophage rep1


title: AL1B19_post_normalskin

description:
gene_count_matrix.csv
AL1B19N_S13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD012


title: AL1B19_post_VZV6hour

description:
gene_count_matrix.csv
AL1B19V6_S15


title: AL1B19_post_VZVday2

description:
gene_count_matrix.csv
AL1B19D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD006


title: AL1B18_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495920
gene_count_matrix.csv
AL1B18S6_S6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_C10_AD004


title: AL1B18_post_normalskin

description:
gene_count_matrix.csv
AL1B18N_S5


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD004


title: LAB_LAB_24

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

data_processing:
Fastq files pseudo aligned using kallisto to get transcript-level quantifications
Gencode version 34 transcriptome with GRCh38 genome used in quantifications.
Transcript-level abundances aggregated to gene-level abundances using R package tximport with lengthScaledTPM option
Gene-level abundances filtered using filterByExpr function of edgeR package; filtered abundances rounded to integer counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited files include kallisto generated transcript-level fractional counts and TPMs per sample
Supplementary_files_format_and_content: Matrix table with filtered gene-level counts per sample

molecule: polyA RNA

source_name: Left Atria

extract_protocol:
Human left atrial tissue was obtained from a 75-year-old deceased white male organ donor who died of stroke. The brain dead donor had a medical history of atrial fibrillation, hypertension, pneumonia, and hypercholesteremia, with a body mass index of 24.4. The heart and lungs were clinically rejected because of poor organ function. The pulmonary artery was perfused with 4 liter of Perfadex (XVIVO Perfusion Inc., Englewood, CO) prior to explant and stored on ice for 5 hours. The heart and lung block was procured in the same manner as our clinical transplant team. The left atrium was photographed, cut into regional fragments, labeled, and snap frozen in liquid nitrogen and stored at -80°C until RNA extraction. Tissue was homogenized in one mL of TRIzol® (Invitrogen) with sterile Omni Tip Disposable Generator Probes.  RNA was isolated from the homogenate following the TRIzol method by the manufacturer's protocol.  The RNA pellet was dried and re-suspended in 80 µl of RNase-free water; the concentration was determined by Nanodrop spectrometry (OD260 nm) and stored at -80°C.
Library generation for RNA-sequencing was done at the University of Chicago Genomics Facility using standard Illumina protocols.

tag: donor age

tag: donor sex

value: Male

tag: donor race

value: White

tag: bmi

tag: donor disease

value: Atrial Fibrillation,Hypertension,Stroke

value: left atria

tag: tissue region

value: Left Atrial Body


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B9_AD001

tag: strain

tag: age

tag: tissue


title: LAB_LAB_25


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD012

tag: source

tag: target

tag: gender

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD007


title: LAB_LAB_22


title: LAB_LAB_23


title: AL1B16_post_normalskin

description:
gene_count_matrix.csv
AL1B16N_S13

value: skin

value: Normal skin


title: AL1B18_post_VZVday2

description:
gene_count_matrix.csv
AL1B18D2_S8

value: 2 days after varicella zoster virus antigen challenge


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD006

value: brain

value: SSp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD001

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD002


title: PV_RIPV_21

value: Right Inferior Pulmonary Vein


title: Naïve wild type macrophage rep 1

tag: genotype

value: bone marrow derived macrophage


title: PV_RIPV_20


title: AL1B16_post_VZVday2

description:
gene_count_matrix.csv
AL1B16D2_S14

value: post


title: AL1B15_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495919
gene_count_matrix.csv
AL1B15S6_S11

value: 6 hours after saline injection


title: AL1B18_post_VZV6hour

description:
gene_count_matrix.csv
AL1B18V6_S7

value: 6 hours after varicella zoster virus antigen challenge


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD012

value: SC


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD010


title: LAB_LAB_19

value: Male

value: White


title: AL1B15_post_normalskin

description:
gene_count_matrix.csv
AL1B15N_S10


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B8_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD006

value: MOp


title: LAB_LAB_18

value: Atrial Fibrillation,Hypertension,Stroke

value: left atria

value: Left Atrial Body


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD001


title: PV_RSPV_16

value: Right Superior Pulmonary Vein


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B7_AD002


title: AL1B13_post_normalskin

description:
gene_count_matrix.csv
AL1B13N_S5

value: skin

value: Normal skin


title: AL1B13_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495918
gene_count_matrix.csv
AL1B13S6_S6


title: PV_RIPV_17


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD010

value: brain

value: SSp

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD012


title: PV_RSPV_15


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD007

value: male


title: PV_RSPV_14


title: AL1B13_post_VZVday2

description:
gene_count_matrix.csv
AL1B13D2_S8

value: post

value: 2 days after varicella zoster virus antigen challenge


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD008


title: AL1B12_post_VZV6hour

description:
gene_count_matrix.csv
AL1B12V6_S15

value: 6 hours after varicella zoster virus antigen challenge


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD006


title: AL1B12_post_saline6hr_reanalyzed

description:
re-analysis of GSM3495917
gene_count_matrix.csv
AL1B12S6_S14

value: 6 hours after saline injection


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD002


title: PV_RSPV_12

value: Male


title: AL1B12_post_normalskin

description:
gene_count_matrix.csv
AL1B12N_S13


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD012

value: SC


title: AL1B13_post_VZV6hour

description:
gene_count_matrix.csv
AL1B13V6_S7


title: PV_LIPV_11

value: White

value: Left Inferior Pulmonary Vein


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD008


title: AL1B12_post_VZVday2

description:
gene_count_matrix.csv
AL1B12D2_S16


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD006

value: MOp


title: PV_LIPV_10

value: Atrial Fibrillation,Hypertension,Stroke

value: left atria


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD004


title: LAB_LAB_9

value: Left Atrial Body


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD012


title: LAB_LAB_8


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B6_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD010


title: PV_RSPV_13

value: Right Superior Pulmonary Vein


title: PV_LSPV_7

value: Left Superior Pulmonary Vein


title: Y5

city: Tampere

first: Arttu

last: Autio

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
Raw reads were trimmed using TrimGalore v. 0.4.4.
Trimmed reads were aligned to human genome reference using Hisat2 v. 2.0.0.
Non-unique mappings filtered out with SAMtools v. 1.4.
HTSeq was used to obtain the read counts for all transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: CSV, raw read counts

source_name: plasma

extract_protocol:
Samples were thawed at room temperature and filtered with 0.8 μm Millex AA syringe filters (Merck Millipore) to exclude larger particles, such as remaining platelets, while retaining exosomes and MVs. Total RNAs were extracted from 0.3 ml of plasma with miRNasy micro kit (Qiagen) using a modification, where Trizol LS (Life Technologies) was used instead of the Qiazol reagent according to manufacturer's instructions. RNA consisted of total RNA, miRNA-enriched fraction was not purified separately. RNAs were eluted with 14 μl of RNAse-free water and stored in Low DNA binding Eppendorf tubes (Eppendorf) at −80 °C.
The integrity of total RNA in the samples was evaluated using Agilent Bioanalyzer RNA Nano/Pico chips (Agilent). Qubit fluorometer was used for the RNA quantitation, along with Qubit RNA-kit (Life Technologies). ScriptSeq Complete Gold System (Epicentre) was used to ripodeplete rRNA from the 1 μg of total RNA, and this ripodepleted RNA was then used for RNA-seq library preparation. The produced RNA-seq libraries were purified using SPRI beads (Agencourt AMPure XP, Beckman Coulter), and their quality control was evaluated on High Sensitivity chips using an Agilent Bioanalyzer (Agilent).

tag: age group

value: young control

value: plasma


title: Y4

value: female


title: Y7


title: LAB_LAB_6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD008

value: brain

value: SSp

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD007


title: Y3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD004


title: PV_LSPV_5


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD012


title: Y2


title: PV_LSPV_4


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD002


title: Y1


title: Y6


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B5_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD010


title: O7

value: nonagenarian


title: LAA_LAA_3

value: Male

value: Left Atrial Appendage


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD004


title: O6


title: LAA_LAA_2

value: White


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD007

value: SC


title: LAA_LAA_1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B4_AD006

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD002


title: O5


title: input_rep2

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Paired-end fastq files were aligned to the hg19 build of the human genome using Bowtie2 using the default settings. SAM files were converted to BAM and were sorted by chromosomal-coordinates using Picard SortSam. Duplicates were removed using Picard MarkDuplicates. BAM files were then used to call peaks using MACS2 using default settings with a q threshold of 0.05. To generate BigWig files, deepTools BamCoverage was used with default settings and a bin-size of 10 base pairs. Integrative Genome Viewer (IGV) was used to visualize BigWig files on the hg19 genome track. Homer was used to annotate ZNF416 binding sites to the nearest TSS as described above. Gene ontology of ZNF416 target genes was completed as described above.
Genome_build: hg19

source_name: lung

growth_protocol: IMR90's were grown in DMEM supplemented with 10% FBS and antibiotics. Lentiviral particles were used to generate stably expressing ZNF416-FLAG IMR90's. After transduction, IMR90s expressing ZNF416-FLAG were selected using puromycin. Surviving cells were then expanded for ChIPseq.

extract_protocol: ZNF416-FLAG expressing IMR90 cells were subjected to ChIP-seq for FLAG as previously described. Briefly, IMR90 cells (n=2 biological replicates) stably expressing ZNF416-FLAG were cross-linked with 1% formaldehyde (Sigma Aldrich, St. Louis, MO, USA) for 10 minutes, followed by quenching with 125 mM glycine (Sigma Aldrich, St. Louis, MO, USA) for 5 minutes at room temperature. Fixed cells were washed with 1X TBS (Thermo Fisher Scientific, Waltham, MA, USA). IMR90 cells were then resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 minutes. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) and incubated for 20 minutes at 37 °C in the presence of MNase. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysate was sonicated for 10 minutes (30 sec-on / 30 sec-off) in a Bioruptor instrument (Diagenode, Denville, NJ, USA) and then centrifuged at 15,000 rpm for 10 minutes. The cleared supernatant equivalent to about 15 million cells was incubated with 30 µl of prewashed anti-FLAG M2 magnetic beads (Sigma, Catalogue #: M8823) (Sigma Aldrich, St. Louis, MO, USA) on a rocker overnight. The beads were extensively washed with ChIP buffer, high salt buffer, LiCl2 buffer, and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65 °C overnight. DNA was treated with RNase A and Proteinase K (Qiagen, Valencia, CA, USA) and then purified using a Min-Elute PCR purification kit (Qiagen, Valencia, CA, USA). Sequencing libraries were prepared from 5 - 10 ng of ChIP and input DNA with the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) and were sequenced to 51 base pairs from both ends using an Illumina HiSeq 4000 instrument (Illumina, San Diego, CA, USA).

tag: cell line

value: IMR90 human lung fibroblasts

tag: antibody


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD012


title: input_rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD008


title: O3


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD010


title: O2


title: ZNF416_FLAG_rep2


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD002


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B3_AD006


title: O1


title: ZNF416_FLAG_rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD008


title: K9me3_Rep2_WT_(191204_DJ_MmEc_K9m3_W1_1031)

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: AUTOCUT&RUN for histone modification H3K9me3

data_processing:
Genome_build: UCSC mm10
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to mm10 of Mus musculus genomic sequence obtained from UCSC. 2. We extracted properly paired reads from the Mus musculus alignments to generate bed files <chr> <start> <stop> <length> (Supplementary file .bed.gz). 3. We made normalized count bedgraph files from the bed files (Supplementary file .bedgraph.gz). Normalized counts are the fraction of total counts at each base pair arbitrarily scaled by the size of mm10 so that if the counts were evenly distributed across the reference genome one count would be expected at each base pair.

source_name: CUT&RUN

value: Abcam, ab8898

tag: cell type

value: haploid spermatids WT


title: K9me3_Rep1_WT_(190603_DJ_MmEc_K9m3_W1_0521)


title: plastic - rep1

data_processing:
Paired-end reads were mapped to the mm10 genome using BWA. Sam files were converted to Bam files using picard SortSam (https://broadinstitute.github.io/picard/command-line-overview.html#SortSam) and sorted by chromosomal coordinates. PCR duplicates were removed using picard MarkDuplicates (https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). Pairs of reads with one or both reads uniquely mapped to chr1-22, chrX and chrY were retained. Processed bam files were used to call peaks using MACS2 with the following options “--keep-dup all -q 0.01 -no model”. To identify differentially accessible genomic loci, DiffBind was used with the processed bam files and peak files obtained from MACS2 using an FDR threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage files are provided as tdf files. Diffbind analyses are provided as .txt files.

growth_protocol: FACS purified primary mouse lung fibroblasts were seeded onto collagen I coated soft and stiff matrices. Fibroblasts were grown in DMEM supplemented with 10% FBS and antibiotics. 8 days after seeding, cells were subjected to ATACseq.

extract_protocol: FACS sorted mouse GFP+ lung fibroblasts were seeded (5,000 cells/cm2) onto 0.2 kPa PDMS, 32 kPa PDMS (Advanced Biomatrix, San Diego, CA, USA), or tissue-culture plastic. All culture plates were identically coated with collagen I (0.1 mg/mL diluted in PBS) (Advanced Biomatrix, San Diego, CA, USA) for one hour at room temperature. Cells were cultured for 8 days. Fibroblasts were then trypsinized and counted. 50,000 cells were subjected to Omni ATAC-seq following the published protocol22. The size of library DNA was determined from the amplified and purified library by a Fragment Analyzer (Advanced Analytical Technologies; AATI; Ankeny, IA), and the enrichment of accessible regions was determined by the fold difference between positive and negative genomic loci using real-time PCR. The following primer sequences were used: accessibility-positive control locus: AT-P7-F: 5’- GGCTTATCCGGAGCGGAAAT -3′, AT-P7-R: 5’-GGCTGGAACAGGTTGTGTTG -3′. Accessibility-negative control locus: AT-P13-F: 5’-TCCCCTTTACTGTTTTCCTCTAC-3′, AT-P13-R: 5’-GGATTGATGAGGAAACAGCCTC-3′. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument (Illumina, San Diego, CA, USA).

value: primary mouse lung fibroblasts

value: Col1a1-GFP transgenic mice

tag: culture

value: plastic


title: O4

value: plasma


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD007


title: 32 kPa - rep2

value: 32 kPa


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD004

value: brain


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD002

value: SSp


title: K9me3_Rep2_KO_(191204_DJ_MmEc_K9m3_N1_1031)

value: haploid spermatids H2A.B KO


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B2_AD006

value: male


title: 32 kPa - rep1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD001


title: K9me3_Rep1_KO_(190603_DJ_MmEc_K9m3_N1_0521)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD012

value: female


title: 0.2 kPa - rep2

value: 0.2 kPa


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD007


title: K4me3_Rep2_WT_(191204_DJ_MmEc_K4m3_W1_1031)

description: AUTOCUT&RUN for histone modification H3K4me3

value: Active Motif Cat#39159


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD008

value: SC


title: plastic - rep2


title: K4me3_Rep1_WT_(190603_DJ_MmEc_K4m3_W1_0521)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD004

value: MOp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B11_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B12_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B1_AD006


title: IgMnegB-1a (CKO#2)

first: Xiao

last: Li

state: OH

address: W123, Wood building

institute: CWRU

data_processing:
We aligned RNA-seq reads to the mouse reference genome (mm9) using TopHat (version 2.0.13). Both the mouse reference genome and transcript annotation were downloaded from illumina iGenomes.
We then assigned the mapped reads to gene using Python package HTseq (Python 2.7, HTseq version 0.6.0), with the default union-counting mode.
To perform differential gene expression analysis, we applied DESeq2 R package (R 3.3.1, DEseq 2 version 1.12.4), with an adjusted P-value of 0.05 as the cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements normalized by Deseq2

source_name: IgMneg B-1a cells in CKO mice

growth_protocol: Mice are breed and maintained  under the protocol approved by Stanford Veterinary Service Center (VSC)

extract_protocol:
RNA was isolated from 1-3x105 sorted cells using RNeasy plus Micro Kits (Qiagen), according to the manufacturer’s instructions. RNA concentration and integrity number were quantified by RNA quality control (QC) analysis conducted by Stanford Protein and Nucleic Acid (PAN) Facility. About 30ng of RNA per sample was used for preparing sequence library.
After the ribo-minus RNA was fragmented, cDNA was synthesized using superscript double strand cDNA synthesis kit (Invitrogen). The cDNA samples were then end repaired, ligated with illumine adaptor using NEB next ultra II end repair/dA-tailing and ligation module (New England Biolabs), and amplified with illumine sequencing primer.

treatment_protocol: special treatment has been applied to the mice

tag: strain background

value: Balb/c

tag: genotype/variation

value: CTLA-4 B cell conditional knockout (CKO)

value: spleen

value: B-1a cell


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B11_AD007


title: K4me3_Rep2_KO_(191204_DJ_MmEc_K4m3_N1_1031)


title: IgMnegB-1a (CKO#3)


title: K4me3_Rep1_KO_(190603_DJ_MmEc_K4m3_N1_0521)


title: IgMnegB-1a (CKO#1)


title: K27me3_Rep2_WT_(191204_DJ_MmEc_K27m_W1_1031)

description: AUTOCUT&RUN for histone modification H3K27me3

value: Cell Signaling Tech 9733S

value: haploid spermatids WT


title: IgMhiB-1a (CKO#2)

source_name: IgMhi B-1a cells in CKO mice


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B11_AD004


title: IgMhiB-1a (CKO#3)


title: K27me3_Rep1_WT_(190603_DJ_MmEc_K27m_W1_0521)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD006


title: 0.2 kPa - rep1

value: primary mouse lung fibroblasts

value: Col1a1-GFP transgenic mice


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD004

value: brain


title: K27me3_Rep2_KO_(191204_DJ_MmEc_K27m_N1_1031)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD001

value: SSp


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B10_AD012


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B11_AD001


title: K27me3_Rep1_KO_(190603_DJ_MmEc_K27m_N1_0521)

value: haploid spermatids H2A.B KO


title: IgMhiB-1a (control#2)

source_name: IgMhi B-1a cells in control mice

value: wild type


title: IgG_Rep2_WT_(191204_DJ_MmEc_IgG_W1_1031)

description: AUTOCUT&RUN for IgG

value: Abcam, ab46540


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD008

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD010

value: female


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD007

value: SC


title: IgMhiB-1a (control#1)


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD012


title: IgG_Rep1_WT_(190603_DJ_MmEc_IgG_W1_0521)

description: AUTOCUT&RUN for IgG


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD006

value: MOp


title: IgMhiB-1a (control#3)

value: Balb/c


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD004


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_B11_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD002


title: IgG_Rep2_KO_(191204_DJ_MmEc_IgG_N1_1031)

description: AUTOCUT&RUN for IgG


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A9_AD001


title: Pancreatic islets, ctrl3

city: Somerville

first: Daniel

last: Burkhardt

state: MA

address: 101 South Street, 6th Floor

institute: Cellarity

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the human transcriptome using 10X Cellranger v1.2
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_counts.csv.gz and metadata.csv; filtered_counts.h5ad is an AnnData object containing UMI counts for alpha, beta, and delta cells.

source_name: Donor islets cultured with CMRL media

growth_protocol: Islets were received on 3/21/18 and plated in 24 well tissue culture dishes in CMRL media (~200 islets per well, 4 wells for no treatment and 4 wells for IGNg treatment).  Cells were allowed to rest for 1 day and were not treated or treated with 25ng/ml IFNg on 3/22/18 for 24 hrs. The islets were harvested on 3/23/18 (the 4 untreated wells were pooled and the 4 treated wells were pooled), dissociated into single cells with 0.05% trypsin solution, stained with TMRE (for live cells) and Zinc stain (for beta cells) and live beta cells sorted and collected by flow cytometry.  Beta cells were spun down and immediately taken down for 10x genomics processing with target number 3,000 cells per sample.

extract_protocol:
10X Genomics 3' Single Cell RNA library preparation system
scRNA-seq libraries were prepared for sequencing with the 10X Genomics 3' Single Cell RNA v3 library preparation system per manufacturer's instructions.
RNA-seq (paired end reads with sample index)

value: Pancreatic islets

tag: treatment

value: Control


title: Pancreatic islets, ctrl2

treatment_protocol: Cells were allowed to rest for 1 day and were not treated or treated with 25ng/ml IFNg on 3/22/18 for 24 hrs.


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD012


title: Pancreatic islets, ctrl1


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD007


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD010


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD008


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD006


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD004


title: Pancreatic islets, ifng1

source_name: Donor islets cultured with CMRL media and IFNg

value: IFNg


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A8_AD001


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD012


title: PLX-27-707-R

city: ChengDu

first: Jinen

last: Song

address: Renmin road

country: China

institute: Sichuan university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using kallisto (Bray et al., 2016)
Transcripts Per Million (TPM) were calculated using sleuth (Pimentel et al., 2017)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: melanoma

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

value: melanoma

value: treated with PLX4032 for 27 days


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD010


title: PLX-27-706-R


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD008


title: PLX-27-706-L


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P3_180117_P4_A7_AD007


title: IgG_Rep1_KO_(190603_DJ_MmEc_IgG_N1_0521)

description: AUTOCUT&RUN for IgG


title: Pancreatic islets, ifng3


title: PLX-18-2

value: treated with PLX4032 for 18 days


title: Pancreatic islets, ifng2


title: Bolei_Xyl rep2

city: Ann Arbor

first: Gabriel

last: Vasconcelos Pereira

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

data_processing:
Standard Illumina 4000 protocol was used for base calling
Sequenced reads were trimmed for adaptor sequence, and trimmed based bellow quality score of 30 using Trimmomatic
Reads were aligned to the genome using BowTie2. Reads mapping to gene features were counted using htseq-count based on Anders, S. et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. 8, 1765-1786, (2013).
Differential expression analysis was performed using the edgeR package in R and the TMM method was used for library normalization
Genome_build: Bacteroides cellulosilyticus DSM 14838
Genome_build: Bacteroides intestinalis DSM 17393
Genome_build: Bacteroides oleiciplenusYIT 12058
Supplementary_files_format_and_content: tab-delimited table containing raw counts and edgeR tab-delimited table comparissons of each species in the two different growth carbon sources

organism: Bacteroides oleiciplenus

source_name: Bacterial cells

growth_protocol: The defined medium was composed of sodium chloride (15 mM), dipotassium hydrogen phosphate (5 mM), monopotassium hydrogen phosphate (5 mM), sodium bicarbonate (9.5 mM), cysteine hydrochloride (4 mM), magnesium (II) chloride heptahydrate (0.1 mM), calcium (II) chloride dihydrate (54 µM), iron (II) sulphate heptahydrate (1.4 µM), hemin chloride (1.9 µM), vitamin K3 (5.8 µM), vitamin B12 (7.3 nM), and appropriate carbon source (Xylose:Arabinose or Insoluble wheat arabinoxylan) (5 mg/mL).

extract_protocol:
The cells were rapidly mixed with RNAprotect bacterial reagent and collected by centrifugation, as described by the manufacturer and used for subsequent RNA extraction. RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Contaminating DNA was removed in-column using NEB DNase I (Ipswich, MA), and the quality of the RNA was assessed by using a Bioanalyzer 2100 with a RNA 6000 Nano Assay Reagent kit from Agilent (Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Different carbon sources

tag: carbon source


title: PLX-18-1


title: Bolei_Xyl rep1


title: heart_MI14days_rep_5

city: Hang Zhou

first: Feng

last: Zhang

state: Zhejiang

address: Kaixuan road number 258

institute: Zhejiang University

hyb_protocol: cDNA obtained were purified with RNeasy Minikit (Qiagen) and hybridized with Gene expression Hybridization kit (Agilent)

scan_protocol: Microarrays were scanned by Agilent G2505C scanner with the standard protocol of the manufacturer.

data_processing: Data pre-processing was performed using Limma (Smyth 2005) and vsn (Huber et al. 2002) packages rooted in the statistical computing environment R. The “bad spots”, i.e. signals were not well above the background, were removed. Normalization between arrays was performed with Agilent Spike-in probes.

source_name: Heart, myocardial infarction, 14 days, replicate5

label_protocol: 200 ng of total RNA of each sample was labeled and amplified with Low input Quick Amp labeling kit.

growth_protocol: Eight week-old male c57BL/6 mice

extract_protocol: Total RNA was isolated from fresh ventricular tissue using Trizol. mRNA was then purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: Myocardial infarction was performed on eight week-old male c57BL/6 mice by ligation of the left anterior descending coronary artery

value: Heart

value: 8 weeks

tag: sample type

value: myocardial infarction 14 days heart


title: PLX-6-712

tag: strain

value: treated with PLX4032 for 6 days


title: heart_MI14days_rep_4

source_name: Heart, myocardial infarction, 14 days, replicate4

tag: age


title: HS578T_HEYL_06h

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: Gene expression data from HS578T cells with inducible HEYL, induced for 6 hrs.

hyb_protocol: Standard Affymetrix protocol performed by core facility.

data_processing: The data were processed using the oligo package using RMA normalization.

label: biotin

growth_protocol: The cells containing both vectors were selected by treatment with 250 ug/ml hygromycin B, 200 ug/ml G418 and 20 ng/ml doxycyline. Individual clones were picked and cultured in 125 ug/ml hygromycin B, 100ug/ml G418 and 10ng/ml doxycycline for expansion

extract_protocol: RNeasy mini kit (Qiagen) was used to extract RNA after doxycycline withdrawal.

treatment_protocol: pcDNA3-hygro-HEYL, was transfected into breast cancer cell line HS578T with tTA-IRES-Neo vector to generate a HEYL inducible cell line. Cells were treated with doxycycline for 0, 6 or 24hrs.

value: breast

value: HEYL


title: heart_MI14days_rep_3

source_name: Heart, myocardial infarction, 14 days, replicate3

tag: tissue

value: male


title: heart_MI14days_rep_2

source_name: Heart, myocardial infarction, 14 days, replicate2


title: heart_MI14days_rep_1

source_name: Heart, myocardial infarction, 14 days, replicate1


title: PLX-6-711

value: female


title: heart_MI3days_rep_4

source_name: Heart, myocardial infarction, 3 days, replicate4

value: myocardial infarction 3 days heart


title: heart_MI3days_rep_5

source_name: Heart, myocardial infarction, 3 days, replicate5


title: HS578T_HEYL_00h

description: Gene expression data from HS578T cells with inducible HEYL, induced for 0 hrs.

scan_protocol: Standard Affymetrix protocol performed by core facility.


title: PLX-3-716

value: treated with PLX4032 for 3 days


title: Bolei_InWAX rep2

value: insoluble wheat arabinoxylan


title: PLX-27-707-L


title: Con-6-718

value: untreated


title: PLX-3-715


title: Bint_Xyl rep1

organism: Bacteroides intestinalis


title: Bint_Xyl rep2


title: Bcel_Xyl rep2

organism: Bacteroides cellulosilyticus


title: Bolei_InWAX rep1


title: Con-6-715


title: Bcel_Xyl rep1


title: Bint_InWAX rep2


title: Con-3-725


title: heart_MI3days_rep_2

source_name: Heart, myocardial infarction, 3 days, replicate2


title: HS578T_HEYL_24h

description: Gene expression data from HS578T cells with inducible HEYL, induced for 24 hrs.

label_protocol: Standard Affymetrix protocol performed by core facility.


title: Bcel_InWAX rep2


title: heart_MI3days_rep_1

source_name: Heart, myocardial infarction, 3 days, replicate1


title: heart_sham_rep_3

source_name: Heart, sham,replicate3

value: sham heart


title: heart_sham_rep_4

source_name: Heart, sham,replicate4


title: Bint_InWAX rep1


title: heart_MI3days_rep_3

source_name: Heart, myocardial infarction, 3 days, replicate3


title: Bcel_InWAX rep1


title: heart_sham_rep_2

source_name: Heart, sham,replicate2


title: DIV7A (BS-seq)

status: Public on Nov 13 2020

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

description:
Mixed Male and Female cells
geo_bs_lowcov2.tsv

data_processing:
Data were adapter-trimmed, mapped to mm9, then deduplicated and called for methylation using BS-seeker2. Methylation levels across regions was assessed using bedtools map -o sum, summing the number of reads mapping to Cs (supporting mC), and the amount of coverage in the region, then dividing those two numbers(Quinlan and Hall, 2010). Hydroxymethylation was calculated as the percent methylation found in the BS-seq minus the percent methylation found in the matching oxBS-seq. Due to count noise, this occasionally resulted in apparent negative hydroxymethylation. During bisulfite sequencing not all DNA can be efficiently bisulfite converted. Though our methods should maximize the amount of converted unmethylated C, there is still a small percentage of unmethylated cytosines that are called as methylated due to non-conversion (0.2-0.3%). Due to this non-conversion, very lowly methylated regions (e.g. mCA at CpG islands) may not show the same percent reduction in mCA as highly methylated regions. Data were visualized using the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Genome_build: mm9
Supplementary_files_format_and_content: mdt_table_GEO2.tsv: Tab-separated table (with header) of genes, and acetyl peaks, of mCA and mCG values of these regions in DNMT3A heterozygous KO and WT cortex.
geo_bs_lowcov2.tsv is a tab-separated table (with header) of the average genome-wide methylation values for each dinucleotide context (columns) for each sample (rows).

source_name: Cultured cortical neurons from E14.5

growth_protocol: For cortical cultures, samples were chosen for whole genome bisulfite sequencing if mutant and WT samples expressed equal amounts of Dnmt3a mRNA as measured by qRT-PCR. For tissue samples, tissue was taken from mice maintained under standard housing conditions.

extract_protocol:
For tissue samples, tissue was dissected from littermate mice in ice-cold PBS, flash-frozen in liquid nitrogen, and stored at -80°C. DNA was isolated from tissue and cultured cells using the DNEasy Kit.
DNA was bisulfite converted and prepared for sequencing using the Tecan Ovation Ultralow Methyl-Seq Kit and the Epitect Bisulfite Kit was used for bisulfite conversion. We used alternate bisulfite conversion cycling conditions ([95°C, 5 min; 60°C, 20 min] x 4 cycles, 20°C hold) to ensure lowest possible bisulfite non-conversion rate.
Libraries were either sequenced at a depth of 0.01-0.03x genomic coverage using an Illumina MiSeq 2x150 through the Spike-In Cooperative at Washington University in St. Louis, or sequenced at 6.4-7.8x coverage per biological rep with a Illumina HiSeq3000 at the Genome Technology Access Center at Washington University in St. Louis

value: wild type

tag: Sex

value: Pooled male and female

value: Cultured cortical neurons from E14.5

value: DIV 7


title: DIV4B (BS-seq)

value: DIV 4


title: DIV12_5A (BS-seq)

value: DIV 12


title: DIV7B (BS-seq)


title: heart_sham_rep_1

source_name: Heart, sham,replicate1

value: Heart

value: 8 weeks


title: DIV4A (BS-seq)


title: DIV12-5B (BS-seq)