title: Phase I melanoma ROI13 rep2.2 [NS4-B-13-2]

tag: patient

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % tme


title: Phase I melanoma ROI14 rep2.1 [NS4-B-14-1]

status: Public on Mar 03 2021

type: SRA

city: Seattle

first: Michelle

last: Kriner

state: WA

address: 500 Fairview Ave North

country: USA

institute: NanoString Technologies

library_source: transcriptomic

data_processing:
Library strategy: GeoMX-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
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 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: Summarized count files generated by parsing DCC files and merging with sample annotations. Count values are the geometric mean of the probes for a given target, after removing any probes flagged as outliers.
Supplementary_files_format_and_content: For Phase II (MK008), genes not detected in any AOIs were removed from the dataset, and the counts for each AOI were normalized to the upper quartile, yielding finalData file

molecule: total RNA

organism: Homo sapiens

source_name: FFPE skin biopsy

extract_protocol:
Following standard ISH protocols, samples were incubated with 1) DNA oligo-barcoded ISH probes containing a UV-photocleavable linker and 2) flourescently labeled antibodies for visualization of morphological structures. Areas of interest (AOI) 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. Concentration and purity of the resulting libraries was measured using a Bioanalyzer high-sensitivity DNA assay and Qubit high-sensitivity dsDNA kit.

tag: case class

value: melanoma

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: immune

value: ND

tag: % other

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI2 rep2.1 [NS4-B-2-1]

tag: patient

tag: dsp replicate


title: Phase I melanoma ROI13 rep2.1 [NS4-B-13-1]

tag: roi type

value: melanocyte

tag: % keratinocyte


title: Phase II melanoma in situ NS11 ROI3 [NS11-03]

value: melanoma in situ

value: Mixed

tag: % melanocyte

tag: % immune cells


title: Phase I melanoma ROI12 rep2.2 [NS4-B-12-2]

tag: case class

value: keratinocyte/melanocyte

tag: % tme


title: Phase I melanoma ROI12 rep2.1 [NS4-B-12-1]

tag: roi number

tag: sequencing replicate


title: 32_ZIKV

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: isolation_time is the time from death to cell isolation.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome with hisat v2.1.0 with default parameters.
Alignments to genes were counted with FeatureCounts and Ensembl 93 annotation.
Differential expression analysis and normalization were conducted with EdgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.featureCounts.txt: Tab-delimited text files include raw read counts from FeatureCounts.

source_name: Human iris pigment epithelial cell

growth_protocol: Iris pigment epithelial cells were isolated from human cadaveric donor eyes using enzymatic digestion of tissue, followed by culture in Epithelial Cell Medium (ScienCell Research Laboratories) supplemented with 2% FBS and 100 U/ml penicillin-100 μg/ml streptomycin.

extract_protocol:
Total RNA was extracted using Thermo Fisher Scientific TRIzol Reagent, following the manufacturer’s instructions.
The library was constructed using the Illumina TruSeq Stranded Total RNA Sample Preparation kit, following the manufacturer’s instructions.

treatment_protocol: Cells were infected with Zika virus (PRVABC59 strain, MOI 5) or mock-infected for 90 minutes and held for a total of 24 hours before RNA extraction.

tag: age

value: 68 yr

tag: cell type

value: Iris pigment epithelial cell

tag: treatment

value: Zika virus infection

tag: donor

tag: batch


title: 31_UI

value: Mock infection


title: Phase II melanoma in situ NS11 ROI1 [NS11-01]

tag: roi diameter (um)

value: Keratinocyte

tag: % other

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Phase II melanoma in situ NS11 ROI2 [NS11-02]

tag: patient

tag: dsp replicate

tag: roi type

value: Keratinocyte/melanocyte

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: sequencingsaturation


title: Phase I melanoma ROI2 rep2.2 [NS4-B-11-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % tme


title: 35_UI

tag: age

value: 61 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase II melanoma in situ NS11 ROI5 [NS11-05]

tag: roi diameter (um)

tag: % other

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: 30_ZIKV

value: 62 yr


title: Phase I melanoma ROI1 rep2.1 [NS4-B-11-1]

tag: patient

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: sequencingsaturation


title: Phase I melanoma ROI10 rep2.2 [NS4-B-10-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % tme


title: Phase II dysplastic nevus NS10 ROI15 [NS10-15]

value: dysplastic nevus

tag: roi diameter (um)

tag: % other


title: Phase I melanoma ROI1 rep2.1 [NS4-B-1-1]

tag: rawreads

tag: trimmedreads


title: Phase I melanoma ROI10 rep2.1 [NS4-B-10-1]

tag: stitchedreads

tag: alignedreads


title: Phase II dysplastic nevus NS10 ROI16 [NS10-16]

tag: patient

value: Immune

tag: deduplicatedreads


title: Phase I melanoma ROI9 rep1.2 [NS4-A-9-2]

value: melanoma

tag: dsp replicate

tag: roi type


title: 28_ZIKV

tag: age

value: 44 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: 27_UI


title: 29_UI


title: Phase II dysplastic nevus NS10 ROI13 [NS10-13]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: sequencingsaturation


title: Phase II dysplastic nevus NS10 ROI14 [NS10-14]

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: 26_ZIKV

tag: age

value: 60 yr

tag: cell type

tag: treatment


title: Phase I melanoma ROI8 rep1.1 [NS4-A-8-1]

tag: patient

tag: case class

tag: dsp replicate

tag: roi type

value: ND

tag: deduplicatedreads


title: Phase I melanoma ROI7 rep1.2 [NS4-A-7-2]

tag: roi number

tag: sequencing replicate

value: immune

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: Phase I melanoma ROI9 rep1.1 [NS4-A-9-1]

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: Phase II dysplastic nevus NS10 ROI12 [NS10-12]

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: 25_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: 24_ZIKV


title: Phase I melanoma ROI6 rep1.2 [NS4-A-6-2]

tag: patient

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi type

tag: deduplicatedreads


title: Phase I melanoma ROI5 rep1.2 [NS4-A-5-2]

tag: roi diameter (um)

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: Phase I melanoma ROI6 rep1.1 [NS4-A-6-1]

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase I melanoma ROI7 rep1.1 [NS4-A-7-1]

tag: patient

tag: case class


title: Phase II dysplastic nevus NS10 ROI10 [NS10-10]

tag: dsp replicate

tag: roi number


title: Phase I melanoma ROI1 rep2.2 [NS4-B-1-2]

tag: sequencing replicate

tag: roi type


title: Phase I melanoma ROI5 rep1.1 [NS4-A-5-1]

tag: roi diameter (um)

tag: deduplicatedreads


title: Phase II dysplastic nevus NS10 ROI9 [NS10-09]

tag: % keratinocyte

tag: % melanocyte


title: Phase II dysplastic nevus NS10 ROI11 [NS10-11]

tag: % immune cells

tag: % other


title: Phase I melanoma ROI8 rep1.2 [NS4-A-8-2]

tag: % tme

tag: rawreads


title: 22_ZIKV

tag: age

value: 66 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: 23_UI


title: Phase II dysplastic nevus NS10 ROI8 [NS10-08]

tag: patient

tag: case class

tag: dsp replicate

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase I melanoma ROI4 rep1.1 [NS4-A-4-1]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: control (keratinocyte)

tag: % keratinocyte

tag: % melanocyte

tag: deduplicatedreads


title: Phase I melanoma ROI3 rep1.2 [NS4-A-3-2]

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: Phase I melanoma ROI3 rep1.1 [NS4-A-3-1]

tag: patient

tag: case class


title: 21_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI2 rep1.2 [NS4-A-2-2]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase I melanoma ROI4 rep1.2 [NS4-A-4-2]

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: Phase I melanoma ROI2 rep1.1 [NS4-A-2-1]

tag: patient

tag: case class

tag: % tme

tag: rawreads


title: Phase II dysplastic nevus NS10 ROI7 [NS10-07]

tag: dsp replicate

tag: roi number


title: 20_ZIKV

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI17 rep1.2 [NS4-A-17-2]

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase II dysplastic nevus NS10 ROI6 [NS10-06]

tag: patient

tag: case class

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: Phase I melanoma ROI17 rep1.1 [NS4-A-17-1]

tag: dsp replicate

tag: roi number

tag: % tme

tag: rawreads


title: 19_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI16 rep1.2 [NS4-A-16-2]

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: melanocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase II dysplastic nevus NS10 ROI5 [NS10-05]

tag: patient

tag: case class

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: Phase I melanoma ROI16 rep1.1 [NS4-A-16-1]

tag: dsp replicate

tag: roi number

tag: % tme

tag: rawreads


title: 18_ZIKV

tag: age

value: 71 yr

tag: cell type

value: Iris pigment epithelial cell

tag: treatment

tag: donor

tag: batch


title: Phase II dysplastic nevus NS10 ROI4 [NS10-04]

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: Phase I melanoma ROI15 rep1.1 [NS4-A-15-1]

tag: patient

tag: case class

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: Phase I melanoma ROI15 rep1.2 [NS4-A-15-2]

tag: dsp replicate

tag: roi number

tag: % tme

tag: rawreads


title: Phase I melanoma ROI14 rep1.2 [NS4-A-14-2]

tag: sequencing replicate

tag: roi diameter (um)


title: 17_UI

tag: age

tag: cell type

tag: treatment

value: Mock infection

tag: donor

tag: batch


title: Phase I melanoma ROI14 rep1.1 [NS4-A-14-1]

tag: patient

tag: case class

tag: roi type

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: sequencingsaturation


title: 16_ZIKV

value: 52 yr

value: Zika virus infection


title: Phase I melanoma ROI13 rep1.1 [NS4-A-13-1]

tag: dsp replicate

tag: roi number

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: 15_UI

tag: age

tag: cell type

tag: treatment


title: Phase II dysplastic nevus NS10 ROI2 [NS10-02]

tag: patient

tag: sequencing replicate

tag: roi diameter (um)

value: Keratinocyte/melanocyte

tag: % tme

tag: rawreads


title: Phase II dysplastic nevus NS10 ROI3 [NS10-03]

tag: case class

tag: roi type

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase I melanoma ROI1 rep1.2 [NS4-A-1-2]

tag: dsp replicate

tag: roi number

value: keratinocyte/melanocyte

tag: % keratinocyte

tag: % melanocyte

tag: sequencingsaturation


title: Phase I melanoma ROI12 rep1.1 [NS4-A-12-1]

tag: % immune cells

tag: % other

tag: deduplicatedreads


title: Phase II dysplastic nevus NS10 ROI1 [NS10-01]

tag: patient

value: dysplastic nevus

tag: sequencing replicate

value: Keratinocyte


title: 14_ZIKV

tag: age

value: 77 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase II dysplastic nevus NS9 ROI9 [NS09-09]

tag: case class

tag: roi diameter (um)

tag: roi type

value: Mixed

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Phase I melanoma ROI12 rep1.2 [NS4-A-12-2]

value: melanoma

tag: dsp replicate

tag: roi number

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: alignedreads

tag: sequencingsaturation


title: Phase I melanoma ROI11 rep1.2 [NS4-A-11-2]

tag: patient

tag: sequencing replicate

value: ND

tag: % other

tag: deduplicatedreads


title: Phase I melanoma ROI11 rep1.1 [NS4-A-11-1]

tag: case class

tag: roi diameter (um)


title: Phase II dysplastic nevus NS9 ROI8 [NS09-08]

tag: roi type

value: Immune

tag: % tme


title: Phase I melanoma ROI1 rep1.1 [NS4-A-1-1]

tag: rawreads

tag: trimmedreads


title: 12_ZIKV

tag: age

value: 61 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma ROI10 rep1.2 [NS4-A-10-2]

tag: dsp replicate

tag: roi number

value: immune

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: stitchedreads

tag: alignedreads


title: Phase II dysplastic nevus NS9 ROI7 [NS09-07]

tag: patient

tag: case class

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma in situ ROI9 rep2.2 [NS3-B-9-2]

value: melanoma in situ

tag: roi type

tag: % tme

tag: rawreads

tag: trimmedreads


title: Phase I melanoma in situ ROI9 rep2.1 [NS3-B-9-1]

tag: dsp replicate

tag: roi number


title: Phase II dysplastic nevus NS9 ROI5 [NS09-05]

tag: % keratinocyte

tag: % melanocyte


title: 10_ZIKV

tag: age

value: 47 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma in situ ROI8 rep2.2 [NS3-B-8-2]

tag: patient

tag: case class

tag: sequencing replicate

tag: roi diameter (um)

tag: % immune cells

tag: stitchedreads

tag: alignedreads


title: Phase II dysplastic nevus NS9 ROI6 [NS09-06]

tag: roi type

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma ROI13 rep1.2 [NS4-A-13-2]

tag: dsp replicate

tag: roi number

value: melanocyte

tag: % keratinocyte

tag: % melanocyte


title: Phase I melanoma in situ ROI7 rep2.2 [NS3-B-7-2]

tag: patient

tag: case class

value: mixed


title: 9_UI

tag: age

tag: cell type

value: Iris pigment epithelial cell

tag: treatment

value: Mock infection

tag: donor

tag: batch


title: Phase I melanoma in situ ROI7 rep2.1 [NS3-B-7-1]

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % immune cells

tag: % other

tag: stitchedreads

tag: alignedreads


title: Phase II dysplastic nevus NS9 ROI4 [NS09-04]

tag: dsp replicate

tag: roi number

value: Keratinocyte/melanocyte

tag: % tme

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: 8_ZIKV

tag: age

value: 71 yr

tag: cell type

tag: treatment

value: Zika virus infection


title: Phase I melanoma in situ ROI6 rep2.2 [NS3-B-6-2]

tag: patient

tag: case class

tag: sequencing replicate

tag: % keratinocyte

tag: % melanocyte


title: 13_UI

tag: donor

tag: batch


title: Phase I melanoma in situ ROI6 rep2.1 [NS3-B-6-1]

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % immune cells

tag: % other

tag: stitchedreads

tag: alignedreads


title: Phase II dysplastic nevus NS9 ROI3 [NS09-03]

value: dysplastic nevus

tag: roi number

tag: % tme

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma in situ ROI5 rep2.2 [NS3-B-5-2]

tag: patient

tag: case class

tag: sequencing replicate

tag: % keratinocyte


title: 6_ZIKV

tag: age

value: 78 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase I melanoma in situ ROI5 rep2.1 [NS3-B-5-1]

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % melanocyte

tag: % immune cells

tag: % other

tag: stitchedreads


title: Phase I melanoma in situ ROI4 rep2.2 [NS3-B-4-2]

tag: roi number

tag: % tme

tag: rawreads

tag: trimmedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: 7_UI

tag: age

tag: cell type

tag: treatment


title: Phase II dysplastic nevus NS9 ROI2 [NS09-02]

tag: patient

tag: case class

tag: dsp replicate

tag: sequencing replicate

tag: % keratinocyte


title: 5_UI

tag: donor

tag: batch


title: Phase II dysplastic nevus NS9 ROI1 [NS09-01]

tag: roi number

tag: roi diameter (um)

tag: roi type

value: Keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: stitchedreads


title: Phase I melanoma ROI10 rep1.1 [NS4-A-10-1]

value: melanoma

tag: % tme

tag: rawreads

tag: trimmedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma in situ ROI3 rep2.2 [NS3-B-3-2]

tag: patient

tag: case class

tag: dsp replicate

tag: sequencing replicate

value: ND


title: 11_UI

tag: age

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase II dysplastic nevus NS8 ROI12 [NS08-12]

tag: roi number

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other


title: Phase I melanoma in situ ROI4 rep2.1 [NS3-B-4-1]

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I melanoma in situ ROI3 rep2.1 [NS3-B-3-1]

tag: patient

tag: case class

tag: dsp replicate

tag: sequencing replicate


title: Phase I melanoma in situ ROI8 rep2.1 [NS3-B-8-1]

tag: roi number

tag: roi diameter (um)


title: 4_ZIKV

tag: age

value: 45 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase II dysplastic nevus NS8 ROI11 [NS08-11]

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: 3_UI


title: Phase I melanoma in situ ROI2 rep2.2 [NS3-B-2-2]

tag: patient

tag: case class

value: keratinocyte/melanocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: S6: Heart, DAC

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

country: China

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Original data were filtered to remove reads with joints, indeterminate base information and low quality, followed by sequencing error rate check and GC content distribution check to obtain clean reads used in subsequent analysis.
Clean  reads were than mapped to susScr11 genome with HISAT2 compares software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids.
Genome_build: susScr11
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Sus scrofa

source_name: Heart

extract_protocol:
Total RNAs from the ventricular tissues of Sham (n=3) and DAC (n=3) minipigs were isolated using TRIzol® Reagent(Thermo Fisher Scientific, USA). Each group contains three independent samples. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Tibetan minipig

tag: tissue

value: heart

tag: group

value: descending aortic constriction (DAC)


title: 2_ZIKV

tag: age

value: 63 yr

tag: cell type

tag: treatment

tag: donor

tag: batch


title: Phase II dysplastic nevus NS8 ROI10 [NS08-10]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: Immune

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme


title: S5: Heart, DAC

tag: breed

tag: tissue


title: Phase I melanoma in situ ROI2 rep2.1 [NS3-B-2-1]

tag: patient

tag: case class

value: melanoma in situ

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: S3: Heart, Sham

tag: group

value: Sham


title: S4: Heart, DAC


title: Phase II dysplastic nevus NS8 ROI9 [NS08-09]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: Keratinocyte/melanocyte


title: Phase II dysplastic nevus NS8 ROI8 [NS08-08]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme


title: 1_UI

tag: age

tag: cell type

value: Iris pigment epithelial cell

tag: treatment

value: Mock infection

tag: donor

tag: batch


title: S2: Heart, Sham

tag: breed

tag: tissue


title: Phase I melanoma in situ ROI1 rep2.1 [NS3-B-1-1]

tag: patient

tag: case class

tag: dsp replicate

value: mixed

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase II dysplastic nevus NS8 ROI7 [NS08-07]

value: dysplastic nevus

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme


title: Phase I melanoma in situ ROI1 rep2.2 [NS3-B-1-2]

tag: patient

tag: case class


title: Phase I melanoma in situ ROI10 rep2.1 [NS3-B-10-1]

tag: dsp replicate

tag: rawreads


title: Phase I melanoma in situ ROI10 rep2.2 [NS3-B-10-2]

tag: trimmedreads

tag: stitchedreads


title: Phase II dysplastic nevus NS8 ROI6 [NS08-06]

value: Mixed

tag: alignedreads

tag: deduplicatedreads


title: MHCIIΔCcl19_1

city: Würzburg

first: Haroon

last: Shaikh

state: Bayern

address: Zinklesweg 10

department: Department of Internal Medicine II

country: Germany

institute: University Hospital Würzburg

data_processing:
Read quality of sequenced libraries was evaluated with FastQC.
Sequencing reads were aligned to the reference mouse genome assembly GRCm38 using STAR (version 2.40e) (Dobin et al. Bioinformatics 2013).
Reads aligned to annonated genes were quantified with htseq-count (Anders S et al. Bioinformatics 2015).
Protein-coding genes with at least five reads in at leasrt two replicates were included in the analysis. The calculated read counts were further processed with DESeq2 (version 1.26.0) for quantification of differentially gene expression (Love MI et al. Genome Biol. 2014).
Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values. Genes were considered as differentially expressed at log2(fold change) >0.75 and adjusted p-value of <0.05.
Genome_build: mm9
Supplementary_files_format_and_content: count matrix for T cells as a tab-delimited txt file but FPKM is not included in the txt file

organism: Mus musculus

source_name: Spleen

extract_protocol:
Spleens were removed, processed and enriched for CD4+ T cells using Dynabeads™ Untouched™ Mouse CD4 Cells Kit and stained with anti-CD4, anti-CD90.1 and LIVE/DEAD™ Fixable Violet Dead Cell Stain Kit and 12000 cells sorted on FACS Aria III equipment into extraction buffer of Arcturus PicoPure RNA isolation kit and flash frozen on dry ice, and RNA was harvested usingArcturus PicoPure RNA isolation kit with 750 pg of total RNA , for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module

treatment_protocol: Conditional knockout of MHC class II on Ccl19 expressing fibroblastic reticular cells versus Cre negative controls.

tag: strain

value: FVB/N

tag: cell type

value: CD4+ CD90.1+ T cells

tag: treatment

value: allo-HCT into MHCIIΔCcl19 mice

tag: time-point

value: day +30 after allo-HCT


title: MHCIIΔCcl19_2


title: S1: Heart, Sham

tag: breed

value: Tibetan minipig

tag: tissue

tag: group


title: H2-Ab1fl_3

value: allo-HCT into B6.H2-Ab1fl mice


title: Phase II dysplastic nevus NS8 ROI5 [NS08-05]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: sequencingsaturation


title: H2-Ab1fl_2


title: CSF1_1

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

data_processing:
Low-quality reads were removed using Trimmomatic v0.36
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
Bigwig files were generated with custom bash scripts and BEDtools
RNA-seq differential expression analysis was performed using DESeq2
Genome_build: RNA-seq reads were aligned to sequences of the whole genome shotgun sequencing project of strain Acinetobacter baumannii A118F (DDBJ/ENA/GenBank accession VCCO01000000)
Supplementary_files_format_and_content: tsv file generated by DESeq2 provides gene ID, base mean reads, log2 fold-change, log2 fold-change standard error, Wald statistic, Wald test p-value, and Bonferroni Hochberg corrected p-value for the expression of each gene.

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii A118

growth_protocol: Bacteria were grown in a rotary shaker with agitation at 37oC.

extract_protocol:
Total RNA was extracted using the TRI REAGENT® Kit
Illumina RNA-seq

treatment_protocol: Bacteria were cultured in Luria-Bertani broth (LB) with or without CSF for 18 h. Overnight cultures were then diluted 1:10 in fresh LB broth and incubated for additional 7 h.

tag: condition

value: LB + 4% CSF

tag: biological replicate

tag: experiment

value: RNA-seq 150PE


title: LB2_1 (CSF control)

value: LB


title: Phase II dysplastic nevus NS8 ROI4 [NS08-04]

tag: patient

tag: case class

tag: dsp replicate

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: CSF2_1


title: Phase I melanoma in situ ROI9 rep1.1 [NS3-A-9-1]

value: melanoma in situ

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: immune

tag: % keratinocyte

value: ND


title: H2-Ab1fl_1

tag: strain

tag: cell type

tag: treatment

tag: time-point


title: LB1_1 (CSF control)

tag: condition

tag: biological replicate

tag: experiment


title: Phase I melanoma in situ ROI8 rep1.2 [NS3-A-8-2]

tag: patient

tag: case class

tag: dsp replicate

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: Phase II dysplastic nevus NS8 ROI2 [NS08-02]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Phase I melanoma in situ ROI8 rep1.1 [NS3-A-8-1]

tag: patient

tag: case class


title: Phase II dysplastic nevus NS8 ROI3 [NS08-03]

tag: dsp replicate

tag: % melanocyte


title: Sample_SS4_young_97

city: Los Angeles

first: Albina

state: California

address: 1425 San Pablo Street

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

data_processing:
STAR,2.7,default parameters for PE reads
RSEM,1.3,default parameters
Genome_build: mm10
Supplementary_files_format_and_content: csv file with RSEM count estimates for each sample
Supplementary_files_format_and_content: csv file with RSEM TPM normalized estimates for each sample
Supplementary_files_format_and_content: csv file with cell subtype groupings identified by k-means clustering

source_name: Dentate Gyrus

extract_protocol:
Homozygous Nestin:CFPnuc mice (Encinas et al., 2006) (Strain: B6.Cg-Tg(Nes-CFP)1Enik/J) were used for all single-cell RNA-seq experiments (Shin et al., 2015). Mice were euthanized by cervical dislocation, and brains were immediately immersed into cold Hibernate A solution (BrainBits). Dentate gyri were dissected under a stereomicroscope as previously described (Hagihara et al., 2009). All procedures were performed with approved protocols in accordance with institutional animal guidelines. The single cell suspension was prepared by using Neural Tissue Dissociation Kit (P), with the addition of one cleaning step with Percoll (1:10 dilution) to remove myelin layer and cellular debris. Propidium Iodide was added to determine cell viability and cells were sorted on a BD FACs Aria II with a 70μm nozzle at 13 psi (Figure S3). Single cells were collected onto the ice-cold 8-sample parafilm-covered glass slides with 1.25uL of 1X lysis mixture (Clontech Laboratories SMART-Seq v4 Ultra Low Input RNA Kit for sequencing) and immediately transferred in individual 0.2-ml RNase-free 8-well strip (Figure S3).  To avoid any effects due to the FACs sorting protocol, cells were kept on ice the entire procedure, and the actual collection was performed at 4°C.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories) for sequencing with modifications to bring down the cost. Briefly, all reagents from the kit (for Reverse transcription and cDNA amplification) were miniaturized 10-fold by utilizing FACs collection in a very low volume of the lysis buffer. The same quality of cDNA was achieved as for the original kit. The amplification product was purified using Ampure XP beads according to the manufacturer’s protocol. Quality control and validation were performed by using qPCR for Actin expression and Agilent TapeStation 4200 (Agilent Technologies). The amplification product was sheared using library preparation Nextera XT Kit (Illumina Inc.) following the manufacturer’s protocol. In brief, the purified cDNA was tagmented and fragmented using a miniaturized protocol. cDNA fragments were barcoded using i5 and i7 indices (Illumina Inc.) and the product was purified using Ampure RNA clean beads. The purified ligation product underwent 13 cycles of PCR. A Mantis Liquid Handler (Formulatrix, Inc.) was used to handle low volume pipetting. The libraries were multiplexed and sequenced using Illumina NextSeq 550 (Illumina Inc.) 75 paired end run. To minimize the batch effect on the sequencing all cells were loaded into one chip.

tag: strain

tag: tissue

value: Dentate Gyrus

tag: age

value: 2 months old


title: Sample_SS4_young_94


title: Phase I melanoma in situ ROI7 rep1.2 [NS3-A-7-2]

value: mixed

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: Phase II benign nevus NS7 ROI10 [NS07-10]

value: benign nevus

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

value: Immune/melanocyte

tag: % keratinocyte


title: Phase I melanoma in situ ROI7 rep1.1 [NS3-A-7-1]

tag: patient

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Sample_SS4_young_92

tag: strain

tag: tissue


title: Phase I melanoma in situ ROI9 rep1.2 [NS3-A-9-2]

tag: case class

tag: dsp replicate

tag: % melanocyte

tag: % immune cells


title: Phase II dysplastic nevus NS8 ROI1 [NS08-01]

value: dysplastic nevus

value: Keratinocyte

tag: % other

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: Sample_SS4_young_91

tag: age


title: Phase I melanoma in situ ROI6 rep1.2 [NS3-A-6-2]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte


title: Phase II benign nevus NS7 ROI9 [NS07-09]

tag: patient

value: Melanocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Phase I melanoma in situ ROI6 rep1.1 [NS3-A-6-1]

tag: case class

tag: dsp replicate

tag: % melanocyte


title: Phase II benign nevus NS7 ROI8 [NS07-08]

value: Keratinocyte/melanocyte

tag: % immune cells

tag: % other

tag: % tme


title: Phase II benign nevus NS7 ROI7 [NS07-07]

tag: rawreads

tag: sequencingsaturation


title: Phase I melanoma in situ ROI5 rep1.2 [NS3-A-5-2]

tag: roi number

tag: sequencing replicate


title: Sample_SS4_young_89

tag: strain

tag: tissue

tag: age


title: Sample_SS4_young_9


title: Phase II benign nevus NS7 ROI6 [NS07-06]

tag: patient

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: trimmedreads


title: Phase I melanoma in situ ROI5 rep1.1 [NS3-A-5-1]

tag: case class

tag: dsp replicate

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Sample_SS4_young_85


title: Phase I melanoma in situ ROI4 rep1.2 [NS3-A-4-2]

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads


title: Sample_SS4_young_84

tag: strain

tag: tissue


title: Sample_SS4_young_81

tag: age


title: Sample_SS4_young_90


title: Phase I melanoma in situ ROI4 rep1.1 [NS3-A-4-1]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: sequencingsaturation


title: Phase II benign nevus NS7 ROI4 [NS07-04]

tag: case class

tag: dsp replicate

tag: roi type

value: Mixed

tag: % keratinocyte

tag: trimmedreads


title: Phase II benign nevus NS7 ROI3 [NS07-03]

tag: % melanocyte

tag: % immune cells

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Phase II benign nevus NS7 ROI2 [NS07-02]

tag: % other

tag: % tme

tag: rawreads


title: Sample_SS4_young_80

tag: strain

tag: tissue

tag: age


title: Phase I melanoma in situ ROI3 rep1.1 [NS3-A-3-1]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: sequencingsaturation


title: Sample_SS4_young_78


title: Phase I melanoma in situ ROI3 rep1.2 [NS3-A-3-2]

tag: case class

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: trimmedreads


title: Phase I melanoma in situ ROI2 rep1.2 [NS3-A-2-2]

value: keratinocyte/melanocyte

tag: % melanocyte

tag: % immune cells

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Sample_SS4_young_74

tag: strain

tag: tissue


title: Phase II benign nevus NS6 ROI6 [NS06-06]

tag: patient

tag: % other

tag: % tme

tag: rawreads


title: Phase II benign nevus NS7 ROI5 [NS07-05]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: Immune

tag: sequencingsaturation


title: hiPSC_rep4

type: RNA

city: Singapore

first: Alison

middle: P

last: Lee

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Raw data from CEL files was RMA-normalized and summarized to transcript clusters using R ‘oligo’ package.

label: biotin

source_name: Human iPSC differentiated erythroid cells

label_protocol: Labelled single-stranded cDNA targets were prepared from 250 ng total RNA using the GeneChip WT PLUS Reagent Kit (Life Technologies, Carlsbad, CA) and assayed on the Human Clariom D Array according to manufacturer’s protocol.

extract_protocol: RNA was extracted from 1 to 2e6 cells per sample using Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA).

tag: cell type


title: hiPSC_rep7

value: Human iPSC differentiated erythroid cells


title: adult_RBC_rep4

source_name: Adult peripheral blood differentiated erythroid cells


title: hiPSC_rep6


title: adult_RBC_rep1

value: Adult peripheral blood differentiated erythroid cells


title: Phase I melanoma in situ ROI2 rep1.1 [NS3-A-2-1]

tag: case class

value: melanoma in situ

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: trimmedreads


title: hiPSC_rep1


title: adult_RBC_rep6


title: Phase I melanoma in situ ROI1 rep1.1 [NS3-A-1-1]

tag: % melanocyte

tag: % immune cells

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Phase I melanoma in situ ROI10 rep1.2 [NS3-A-10-2]

tag: patient

tag: % other

tag: % tme


title: Phase II benign nevus NS6 ROI4 [NS06-04]

tag: roi number

tag: sequencing replicate

tag: rawreads


title: Phase II benign nevus NS7 ROI1 [NS07-01]

tag: roi diameter (um)

tag: sequencingsaturation


title: cord_blood_rep3

source_name: Cord blood differentiated erythroid cells

tag: cell type


title: hiPSC_rep5


title: Phase II benign nevus NS6 ROI3 [NS06-03]

tag: case class

tag: dsp replicate

tag: roi type


title: Sample_SS4_young_73

tag: strain

tag: tissue

tag: age


title: cord_blood_rep2

value: Cord blood differentiated erythroid cells


title: Sample_SS4_young_70


title: Sample_SS4_young_72


title: mock-treated group

city: Wuhan

first: Bo

last: Wang

address: No.215 Zhongshan Avenue, Wuhan City, Hubei Province

institute: Wuhan no1 hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Next, Genespring software (version 14.8; Agilent Technologies) was employed  to finish the basic analysis with the raw data.  The raw data was normalized with the RMA algorithm.

source_name: human mesenchymal stem cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: These cells were cultured in complete culture medium of low glucose Dulbecco’s modifed Eagle’s medium (L-DMEM) (HyClone, USA), 10% fetal bovine serum (FBS) (Gibco, USA), 100 IU/ml penicillin/streptomycin and incubated at 37 °C with 5% carbon dioxide and 95% humidity.

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

treatment_protocol: Lentiviral knockdown HDAC9 (lenti-HDAC9) particles and lentiviral GFP particles, used as the control group (lenti-control), were prepared by Western Biomedical technology. For infections, 70% confluent hBMSCs were incubated with lentiviral particles and 5.0 μg/ml polybrene in growth medium at a multiplicity of infection of 40. After 24 h, 95% of the cells were still viable, and the culture medium was then changed. Three days later, all transfected cells were passaged for use in subsequent experiments.

value: human mesenchymal stem cell

tag: treartment

value: mock-treated


title: control group

value: control


title: Phase II benign nevus NS6 ROI2 [NS06-02]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Sample_SS4_young_64

value: Dentate Gyrus

value: 2 months old


title: Phase II benign nevus NS6 ROI1 [NS06-01]

tag: patient

value: benign nevus

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads


title: Sample_SS4_young_63

tag: strain

tag: tissue


title: Phase I dysplastic nevus ROI9 rep2.2 [NS2-B-9-2]

tag: case class

value: dysplastic nevus

tag: dsp replicate

tag: roi type

value: mixed

value: ND

tag: sequencingsaturation


title: lenti-HDAC9 group

tag: cell type

tag: treartment


title: Phase I dysplastic nevus ROI9 rep2.1 [NS2-B-9-1]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase I melanoma in situ ROI10 rep1.1 [NS3-A-10-1]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: deduplicatedreads


title: Sample_SS4_young_57

tag: strain

tag: tissue

tag: age


title: Phase II benign nevus NS5 ROI6 [NS05-06]

tag: case class

tag: dsp replicate

tag: roi type

value: Immune/melanocyte

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: cord_blood_rep1

tag: cell type


title: Sample_SS4_young_55


title: Sample_SS4_young_53


title: Phase I dysplastic nevus ROI8 rep2.2 [NS2-B-8-2]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase II benign nevus NS5 ROI5 [NS05-05]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: deduplicatedreads


title: Phase II benign nevus NS5 ROI4 [NS05-04]

tag: case class

tag: dsp replicate

tag: roi type

value: Melanocyte


title: Phase I dysplastic nevus ROI8 rep2.1 [NS2-B-8-1]

value: keratinocyte/melanocyte

tag: % tme

tag: rawreads

tag: sequencingsaturation


title: Phase II benign nevus NS5 ROI3 [NS05-03]

value: Keratinocyte/melanocyte

tag: % keratinocyte

tag: % melanocyte


title: Phase I dysplastic nevus ROI7 rep2.1 [NS2-B-7-1]

value: melanocyte/immune

tag: % immune cells

tag: trimmedreads


title: Phase II benign nevus NS5 ROI2 [NS05-02]

value: Immune

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_young_52

tag: strain

tag: tissue

tag: age


title: Sample_SS4_young_47


title: Sample_SS4_young_51


title: Phase II benign nevus NS5 ROI1 [NS05-01]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: Keratinocyte

tag: % other


title: Phase I dysplastic nevus ROI6 rep2.2 [NS2-B-6-2]

tag: case class

tag: dsp replicate

tag: roi type

value: immune

tag: % tme

tag: deduplicatedreads


title: Phase I dysplastic nevus ROI5 rep2.2 [NS2-B-5-2]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: Sample_SS4_young_46

tag: strain

tag: tissue


title: Sample_SS4_young_44

tag: age


title: RNA-Seq 1592

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
1592
FACS purified myeloma cells

data_processing:
RNA-seq FASTQ sequencing files were quality and adapter trimmed using Trim Galore! (v0.6.4; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and CutAdapt (v2.5; https://github.com/marcelm/cutadapt/) prior to mapping the GRCh37 genome accounting for the Ensembl GRCh37.74 transcription database using the STAR aligner (v2.5.3a).
Putative PCR duplicate reads were marked in BAM files using Samtools (v1.7).
Gene read counts were calculated in R (v3.6.2) by reading in BAM files using the function readGAlignmentPairs and counting the number of reads that overlap any exonic region of an Ensemble (v74) gene using the function summarizeOverlaps of the GenomicAlignments package (v1.2).
Gene expression data was normalized for sequencing depth using reads per million (RPM) or fragments per kilobase per million reads (FPKM) where read depth was the total number of reads on autosomal chromosomes only
Genome_build: GRCh37
Supplementary_files_format_and_content: geneCts.exon.csv - Comma delimited file of gene level raw sequencing counts calculated based on exonic reads.
Supplementary_files_format_and_content: geneFpkm.exon.csv - Comma delimited file of gene level FPKM normalized reads calculated based on exonic reads

molecule: polyA RNA

source_name: multiple myeloma patient bone marrow aspirates

extract_protocol:
50,000 CD138+CD38+PI- cells were FACS isolated directly into 600 uL of RLT lysis buffer with 1% B-ME (Sigma-Aldrich M6250) prior to vortexing 1 min at max speed and freezing in a dry ice ethanol mixture. RNA was isolated (Qiagen RNeasy Mini 74104) and quality assessed using an Agilent BioAnalyzer.
Stranded mRNA-seq libraries were made using the mRNA HyperPrep kit (Kapa 08098115702) following the manufacturer’s protocol and using custom short TruSeq compatible sequencing adapters (IDT) (see Supplementary Table 1 from Barwick et al. Clinical Cancer Research 2021).  Barcodes were added to each library using long PCR primers (see Supplementary Table 1 from Barwick et al. Clinical Cancer Research) during 8 cycles of PCR amplification.

tag: markers

tag: cryopreserved

value: TRUE


title: RNA-Seq 1591

description:
1591
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI6 rep2.1 [NS2-B-6-1]

tag: patient

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: RNA-Seq 1588

description:
1588
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI5 rep2.1 [NS2-B-5-1]

tag: case class

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: Sample_SS4_young_38

tag: strain

tag: tissue

tag: age


title: Phase II benign nevus NS6 ROI5 [NS06-05]

tag: patient

tag: % melanocyte

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: RNA-Seq 1586

description:
1586
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI4 rep2.1 [NS2-B-4-1]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_young_37

tag: strain


title: Sample_SS4_young_36

tag: tissue


title: Phase I dysplastic nevus ROI7 rep2.2 [NS2-B-7-2]

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: Phase I dysplastic nevus ROI4 rep2.2 [NS2-B-4-2]

tag: patient

tag: % melanocyte

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: Phase I dysplastic nevus ROI3 rep2.2 [NS2-B-3-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)


title: RNA-Seq 1581

description:
1581
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI3 rep2.1 [NS2-B-3-1]

tag: dsp replicate

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_young_35

tag: strain

tag: tissue

tag: age


title: RNA-Seq 1575

description:
1575
FACS purified myeloma cells


title: Sample_SS4_young_33


title: Sample_SS4_young_32


title: RNA-Seq 1563

description:
1563
FACS purified myeloma cells


title: Sample_SS4_young_41


title: Phase I dysplastic nevus ROI2 rep2.1 [NS2-B-2-1]

tag: patient

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: Phase I dysplastic nevus ROI12 rep2.2 [NS2-B-12-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: RNA-Seq 1573

description:
1573
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Sample_SS4_young_3

tag: strain

tag: tissue

tag: age


title: Sample_SS4_young_28


title: RNA-Seq 1562

description:
1562
FACS purified myeloma cells


title: RNA-Seq 1562-fresh

description:
1562-fresh
FACS purified myeloma cells

value: FALSE


title: Phase I dysplastic nevus ROI1 rep2.2 [NS2-B-1-2]

tag: patient

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: RNA-Seq 1585

description:
1585
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI11 rep2.2 [NS2-B-11-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % melanocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: Sample_SS4_young_27

tag: strain


title: Sample_SS4_young_19

tag: tissue


title: Sample_SS4_young_20

tag: age


title: RNA-Seq 1561

description:
1561
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI11 rep2.1 [NS2-B-11-1]

tag: patient

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: Phase I dysplastic nevus ROI10 rep2.2 [NS2-B-10-2]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % keratinocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase I dysplastic nevus ROI2 rep2.2 [NS2-B-2-2]

tag: % melanocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: Sample_SS4_young_175

tag: strain

tag: tissue

tag: age


title: RNA-Seq 1555-fresh

description:
1555-fresh
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI10 rep2.1 [NS2-B-10-1]

tag: patient

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: Phase I dysplastic nevus ROI1 rep2.1 [NS2-B-1-1]

tag: case class

tag: roi number

tag: sequencing replicate

tag: % keratinocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_young_173

tag: strain

tag: tissue

tag: age


title: RNA-Seq 1539

description:
1539
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI12 rep2.1 [NS2-B-12-1]

tag: patient

tag: dsp replicate

tag: roi diameter (um)

tag: % melanocyte

tag: % other

tag: % tme

tag: deduplicatedreads


title: RNA-Seq 1541

description:
1541
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI9 rep1.1 [NS2-A-9-1]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi type

tag: % immune cells

tag: rawreads

tag: sequencingsaturation


title: RNA-Seq 1563-fresh

description:
1563-fresh
FACS purified myeloma cells


title: Sample_SS4_young_145

tag: strain

tag: tissue

tag: age


title: Sample_SS4_young_161


title: Phase I dysplastic nevus ROI8 rep1.2 [NS2-A-8-2]

tag: patient

tag: % keratinocyte

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase I dysplastic nevus ROI9 rep1.2 [NS2-A-9-2]

tag: dsp replicate

tag: roi diameter (um)

tag: % melanocyte

tag: % other

tag: % tme


title: RNA-Seq 1511-3

description:
1511-3
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Sample_SS4_young_113


title: Sample_SS4_young_112


title: RNA-Seq 1525

description:
1525
FACS purified myeloma cells


title: RNA-Seq 1557-fresh

description:
1557-fresh
FACS purified myeloma cells


title: RNA-Seq 1511-2

description:
1511-2
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI7 rep1.1 [NS2-A-7-1]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi type

tag: % immune cells

tag: rawreads

tag: deduplicatedreads


title: RNA-Seq 1517

description:
1517
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI7 rep1.2 [NS2-A-7-2]

tag: patient

tag: % keratinocyte

tag: trimmedreads

tag: sequencingsaturation


title: RNA-Seq 1557

description:
1557
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI8 rep1.1 [NS2-A-8-1]

tag: dsp replicate

tag: roi diameter (um)

tag: stitchedreads

tag: alignedreads


title: Phase I dysplastic nevus ROI6 rep1.2 [NS2-A-6-2]

tag: % melanocyte

tag: % other

tag: % tme


title: RNA-Seq 1426

description:
1426
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI6 rep1.1 [NS2-A-6-1]

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi type


title: Sample_SS4_young_108

tag: strain

tag: tissue

tag: age


title: RNA-Seq 1379

description:
1379
FACS purified myeloma cells


title: Sample_SS4_young_172


title: Sample_SS4_old_99

value: 4.5 months old


title: Sample_SS4_old_96

value: Dentate Gyrus


title: RNA-Seq 1225-2

description:
1225-2
FACS purified myeloma cells


title: Sample_SS4_old_95


title: Phase I dysplastic nevus ROI4 rep1.2 [NS2-A-4-2]

tag: patient

tag: % keratinocyte

tag: % immune cells

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_SS4_old_87


title: Phase I dysplastic nevus ROI4 rep1.1 [NS2-A-4-1]

tag: dsp replicate

tag: roi diameter (um)

tag: % melanocyte

tag: % other

tag: % tme

tag: stitchedreads

tag: alignedreads


title: RNA-Seq 1318

description:
1318
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: RNA-Seq 1223

description:
1223
FACS purified myeloma cells


title: Sample_SS4_young_110

tag: strain

tag: tissue

tag: age

value: 2 months old


title: Phase I dysplastic nevus ROI5 rep1.1 [NS2-A-5-1]

tag: patient

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi type

tag: % keratinocyte

tag: % immune cells


title: RNA-Seq 1238_PB

description:
1238_PB
FACS purified myeloma cells

source_name: multiple myeloma patient peripheral blood


title: Sample_SS4_old_84


title: Phase I dysplastic nevus ROI3 rep1.2 [NS2-A-3-2]

tag: dsp replicate

tag: roi diameter (um)

tag: % melanocyte

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_SS4_old_83

tag: strain


title: Phase I dysplastic nevus ROI3 rep1.1 [NS2-A-3-1]

tag: % other

tag: % tme

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_old_80

tag: tissue

tag: age


title: RNA-Seq 1201-2

description:
1201-2
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: RNA-Seq 1232_PB

description:
1232_PB
FACS purified myeloma cells


title: Sample_SS4_young_1


title: RNA-Seq 1461

description:
1461
FACS purified myeloma cells


title: RNA-Seq 1255

description:
1255
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI2 rep1.2 [NS2-A-2-2]

tag: patient

tag: case class

tag: roi number

tag: sequencing replicate

tag: roi type

tag: % keratinocyte

tag: % immune cells


title: Phase I dysplastic nevus ROI2 rep1.1 [NS2-A-2-1]

tag: dsp replicate

tag: roi diameter (um)

tag: % melanocyte

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I dysplastic nevus ROI5 rep1.2 [NS2-A-5-2]

tag: % other

tag: % tme

tag: stitchedreads

tag: alignedreads


title: ATAC-Seq 1575

description:
1575
FACS purified myeloma cells

library_source: genomic

data_processing:
ATAC-seq FASTQ files were quality and adapter trimmed using Trim Galore! (v0.6.4; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and CutAdapt (v2.5; https://github.com/marcelm/cutadapt/) prior to mapping the GRCh37 genome using bowtie2 (v2.2.6) for alignment
Aligned SAM files were converted to BAM files and putative PCR duplicates were marked with Samtools (v1.7)
Regions of chromatin accessibility were identified in each sample using MACS2 (v2.1.0.20151222)
The union of all accessible regions was determined and reads mapping into these regions were determined for each sample using the summarizeOverlaps of the GenomicAlignments package (v1.2) in R (v3.6.2)
Regions that overlapped ENCODE blacklisted regions were removed
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS2_q_0.01.union.annot.clean.cts - Tab delimited file of chromatin accessible regions (w/ annotation) and raw sequencing counts
Supplementary_files_format_and_content: MACS2_q_0.01.union.annot.clean.rppm.cov - Tab delimited file of chromatin accessible regions (w/ annotation) and reads per peak million (rppm) normalized ATAC-seq signal. See Barwick et al Clinical Cancer Research 2021 for RPPM normalization details.

molecule: genomic DNA

extract_protocol:
20,000 CD138+CD38+PI- viable myeloma cells were sorted into PBS and kept on ice. Cells were isolated by centrifugation at 500 g for 10 minutes at 4°C and the supernatant was carefully removed by pipet.   Cells were resuspended in 50 uL of nuclei-lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL) prior to centrifugation at 500 g for 30 minutes at 4°C and careful removal of nuclei-lysis buffer by pipet.
Nuclei were resuspended in 25 uL of tagmentation mix consisting of 10.5 uL H2O, 12.5 uL TD Buffer (Illumina) and 2 uL Tn5 transposase (Illumina) and incubated at 37 °C for 1 hour. After tagmentation, DNA was isolated by digesting with 20 mg Proteinase K for 1 hour in 25 uL of tagmentation clean-up buffer (326 mM NaCl, 109 mM EDTA, 0.63% SDS). High molecular weight DNA was excluded by 0.6 x volume negative selection with SPRI beads (Kapa Biosystems) followed by a 1.2 x SPRI bead positive selection, which was repeated twice. ATAC libraries were amplified for 12 PCR cycles using Nextera adapters (Illumina) prior to sequencing on an Illumina HiSeq 4000.

tag: markers

tag: cryopreserved


title: Phase I dysplastic nevus ROI12 rep1.2 [NS2-A-12-2]

tag: patient

tag: case class

tag: roi number

tag: sequencing replicate


title: Sample_SS4_old_67

tag: strain

tag: tissue

tag: age


title: Sample_SS4_old_73


title: Sample_SS4_old_69


title: Phase I dysplastic nevus ROI12 rep1.1 [NS2-A-12-1]

tag: dsp replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: rawreads


title: Sample_SS4_old_62


title: ATAC-Seq 1573

description:
1573
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI1 rep1.2 [NS2-A-1-2]

tag: % other

tag: % tme

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_SS4_old_60

tag: strain


title: ATAC-Seq 1563

description:
1563
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: ATAC-Seq 1563-fresh

description:
1563-fresh
FACS purified myeloma cells


title: Sample_SS4_old_53

tag: tissue

tag: age


title: Phase I dysplastic nevus ROI11 rep1.2 [NS2-A-11-2]

tag: patient

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type


title: Sample_SS4_old_52


title: Phase I dysplastic nevus ROI11 rep1.1 [NS2-A-11-1]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: ATAC-Seq 1562

description:
1562
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: ATAC-Seq 1562-fresh

description:
1562-fresh
FACS purified myeloma cells


title: ATAC-Seq 1561

description:
1561
FACS purified myeloma cells


title: Sample_SS4_old_38

tag: strain

tag: tissue

tag: age


title: Sample_SS4_old_46


title: Sample_SS4_old_5


title: Phase I dysplastic nevus ROI10 rep1.1 [NS2-A-10-1]

tag: patient

tag: case class

tag: dsp replicate

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: RNA-Seq 1183

description:
1183
FACS purified myeloma cells


title: Phase I dysplastic nevus ROI1 rep1.1 [NS2-A-1-1]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: ATAC-Seq 1560-fresh

description:
1560-fresh
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: ATAC-Seq 1557

description:
1557
FACS purified myeloma cells


title: Sample_SS4_old_32

tag: strain

tag: tissue

tag: age


title: Phase I benign nevus ROI9 rep2.2 [NS1-B-9-2]

tag: patient

tag: case class

value: benign nevus

tag: dsp replicate

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: Sample_SS4_old_34


title: Phase I benign nevus ROI9 rep2.1 [NS1-B-9-1]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I benign nevus ROI8 rep2.2 [NS1-B-8-2]

tag: roi type

value: melanocyte

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: ATAC-Seq 1557-fresh

description:
1557-fresh
FACS purified myeloma cells

tag: markers

tag: cryopreserved


title: Sample_SS4_old_31

tag: strain

tag: tissue

tag: age


title: ATAC-Seq 1555

description:
1555
FACS purified myeloma cells


title: Phase I benign nevus ROI8 rep2.1 [NS1-B-8-1]

tag: patient

tag: case class

tag: dsp replicate

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: Sample_SS4_old_3


title: ATAC-Seq 1555-fresh

description:
1555-fresh
FACS purified myeloma cells


title: ATAC-Seq 1539

description:
1539
FACS purified myeloma cells


title: Phase I benign nevus ROI7 rep2.2 [NS1-B-7-2]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I benign nevus ROI7 rep2.1 [NS1-B-7-1]

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells


title: Phase I benign nevus ROI6 rep2.2 [NS1-B-6-2]

tag: patient

tag: case class

value: negative (empty)


title: Sample_SS4_old_22

tag: strain

tag: tissue

tag: age


title: input DNA PBS_Repl2

city: Stanford

first: Jan

middle: K

last: Hennigs

address: 269 Campus Dr

department: Wall Center for Pulmonary Vascular Diseases, Cardiovascular Institute and Pediatrics - Cardiology

institute: Stanford University

data_processing:
Raw reads trimmed using FASTQ groomer.
Aligned to the human genome using BWA-aln
Peaks were called using MACS2.
MACS2 narrowPeak files from two biological replicates were submitted into Irreproducible Discovery Rate (IDR) pipeline.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt files were generated using IDR pipeline.

source_name: input DNA

growth_protocol: 293T were cultured in supplemented DMEM media (DMEM, 1x Penicilln/Streptomycin and 10% FBS, ScienCell, Carlsbad, CA).

extract_protocol:
Cells were treated with hypotonic buffer for 10 min on ice and then were homogenized using a glass homogenizer.  Nuclear pellets were re-suspended in RIPA buffer (Millipore) and incubated for 30 min on ice. Chromatin was sheared with SFX250 Sonifier (Branson, Dunbury, CT).
The ChIP-DNA samples were end-repaired and A-tailed.  Illumina TruSeq adapters (Illumina, San Diego, CA) were ligated and size-selected from the gel before performing PCR amplification.

treatment_protocol: 293T were kept in complete DMEM media and treated  for 24 h with Doxorubicin (0.5 µg/ml) or PBS vehicle control before performing p53 ChIP. Cells were then trypsinized and cross-linked with 1% formaldehyde (EMD Millipore), for 10 min at room temperature on a stirrer.  To neutralize formaldehyde, 2M glycine (ThermoFisher Scientific) were added and incubated for five minutes at room temperature while stirring.  The cells were washed with ice cold PBS twice, snap-frozen and stored at -80°C.

tag: cell line

tag: passages

tag: agent

value: PBS (20 microL)

tag: time point

tag: chip antibody


title: Phase I dysplastic nevus ROI10 rep1.2 [NS2-A-10-2]

value: dysplastic nevus

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: mixed

value: ND

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_old_28

tag: strain

tag: tissue


title: Sample_SS4_old_21

tag: age


title: Sample_SS4_old_2


title: Phase I benign nevus ROI5 rep2.2 [NS1-B-5-2]

tag: patient

tag: case class

tag: roi type

value: control (keratinocyte)

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: input DNA Dox_Repl2

tag: cell line

tag: passages

tag: agent

value: Doxorubicin (0.5 microg/ml)

tag: time point

tag: chip antibody


title: input DNA Dox_Repl1


title: Phase I benign nevus ROI5 rep2.1 [NS1-B-5-1]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_old_190

tag: strain

tag: tissue

tag: age


title: Sample_SS4_old_188


title: Sample_SS4_old_187


title: Phase I benign nevus ROI4 rep2.2 [NS1-B-4-2]

tag: patient

tag: case class

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: p53_ChIP_Seq_PBS_Repl1

tag: cell line

tag: passages

tag: agent

tag: time point

tag: chip antibody

value: p53 (Cell Signaling Technology, #2425, clone 1C12, lot #10)


title: Phase I benign nevus ROI4 rep2.1 [NS1-B-4-1]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: p53_ChIP_Seq_Dox_Repl2


title: Sample_SS4_old_176

tag: strain

tag: tissue

tag: age


title: p53_ChIP_Seq_PBS_Repl2

tag: cell line

tag: passages


title: Sample_SS4_old_173


title: p53_ChIP_Seq_Dox_Repl1

tag: agent

tag: time point


title: Phase I benign nevus ROI3 rep2.2 [NS1-B-3-2]

tag: patient

tag: case class

tag: dsp replicate

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I benign nevus ROI3 rep2.1 [NS1-B-3-1]

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_old_166

tag: strain

tag: tissue

tag: age


title: input DNA PBS_Repl1

tag: cell line

tag: passages

tag: agent

tag: time point

tag: chip antibody


title: GW26E1_smRNA_Day0_4

city: Beijing

first: Yuanyuan

last: Fu

address: 5 Yiheyuan Road

institute: BIOPIC, Peking University

description: Sample 40

data_processing:
For data from Illumina, Illumina CASAVA (Version 1.8) was used to the basecalling
The ‘trimfq’ function within ‘seqtk’ software was applied to obtain clean reads.
Clean data were mapped to hg38 genome by ‘STAR’ software
Python package ‘umi_tools’ was used to extract barcodes and UMIs, and then gene tags were added by ‘featureCounts’ to enable ‘umi_tools’ to recognize and then quantify the number of UMIs of each gene within each cell.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg38
Supplementary_files_format_and_content: tab-delimited text file includes UMI values for each Cell

source_name: embryonic brain, single cell

extract_protocol:
The dissected tissue was digested with 2 mg ml-1 collagenase IV (Gibco, 17104-019), 10 U μl -1 DNase I (NEB, M0303L), after pipetting up and down with 1 ml pipette for a while, and next with 1 mg ml-1 papain (Sigma, P4762) at 37℃ for about 30 min to fully digest. After removing undigested clumps with a 40 μm strainer (BD, 352340), cells were centrifuged at 300 g for 5min at 4℃, and the supernatant was removed, cells were resuspended with 200 μl Hibernate E medium, and then incubated with 2μl EGFR antibody (1:100, Abcam, ab231) for 30 min at 4℃. After incubation, the cell suspension was centrifuged at 600 g for 5 min and resuspended again.
After sorting, every EGFR-positive single cell was picked into the lysis buffer by mouth pipette for scRNA-seq library preparation with the previous protocol (Li et al., 2017). Briefly, oligo (dT) primers, which anchored with cell barcodes and unique molecular identifiers (UMIs), were used to perform reverse transcription reaction, and then 4 (98°C 20 s, 65°C for 30 s, 72°C for 5 min) and 16 (98°C 20 s, 67°C 15 s, 72°C for 5 min) cycles of PCR were done for pre-amplification. After pooling cells with different barcodes together and purification their cDNAs, PCR reaction was performed with biotinylated primers, which ligated with P7 index. Then followed by DNA fragment and biotin enrichment, KAPA Hyper Prep Kit (Kapa Biosystems, kk8504) was used to construct libraries and then sequenced on Illumina Hiseq 4000 platform.

treatment_protocol: The aborted fetuses were immediately dissected for the frontal lobe of brains.

tag: developmental stage

value: embryonic stage GW26

value: frontal lobe of brain

tag: cell type

value: EGFR+ cells


title: GW26E1_smRNA_Day0_3

description: Sample 39


title: GW26E1_smRNA_Day0_5

description: Sample 41


title: Phase I benign nevus ROI6 rep2.1 [NS1-B-6-1]

tag: patient

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_SS4_old_15

tag: strain

tag: tissue

tag: age


title: Sample_SS4_old_164


title: Sample_SS4_old_155


title: GW26E1_smRNA_Day0_1

description: Sample 38

tag: developmental stage


title: Sample_SS4_old_146


title: Phase I benign nevus ROI1 rep2.1 [NS1-B-1-1]

value: immune

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_SS4_old_145

value: 4.5 months old


title: Phase I benign nevus ROI9 rep1.2 [NS1-A-9-2]

tag: patient

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

value: melanocyte/immune


title: GW25E3_smRNA_Day0_8

description: Sample 36

value: embryonic stage GW25

tag: cell type


title: Phase I benign nevus ROI9 rep1.1 [NS1-A-9-1]

value: benign nevus

tag: roi type

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: GW25E3_smRNA_Day0_9

description: Sample 37

tag: developmental stage

tag: tissue


title: Sample_SS4_old_143

tag: strain

value: Dentate Gyrus

tag: age


title: GW25E3_smRNA_Day0_7

description: Sample 35


title: Sample_SS4_old_122


title: GW25E3_smRNA_Day0_6

description: Sample 34


title: Sample_SS4_old_118


title: Phase I benign nevus ROI8 rep1.1 [NS1-A-8-1]

tag: patient

value: melanocyte

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: GW25E3_smRNA_Day0_5

description: Sample 33

tag: cell type


title: Phase I benign nevus ROI8 rep1.2 [NS1-A-8-2]

tag: case class

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte


title: Phase I benign nevus ROI7 rep1.2 [NS1-A-7-2]

value: keratinocyte/melanocyte

tag: % melanocyte

tag: % immune cells

tag: deduplicatedreads

tag: sequencingsaturation


title: Phase I benign nevus ROI2 rep2.2 [NS1-B-2-2]

tag: patient

tag: % other

tag: % tme


title: Sample_SS4_old_108

tag: strain

tag: tissue

tag: age


title: Phase I benign nevus ROI2 rep2.1 [NS1-B-2-1]

tag: case class

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Phase I benign nevus ROI1 rep2.2 [NS1-B-1-2]

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type


title: GW25E3_smRNA_Day0_4

description: Sample 32

tag: developmental stage

tag: cell type


title: Phase I benign nevus ROI7 rep1.1 [NS1-A-7-1]

tag: patient

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: deduplicatedreads

tag: sequencingsaturation


title: GW25E3_smRNA_Day0_3

description: Sample 31

tag: tissue


title: Phase I benign nevus ROI6 rep1.2 [NS1-A-6-2]

tag: case class

value: negative (empty)

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: neural progenitor cells_NIM-rep2

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

institute: University of Sydney

data_processing:
RNA-seq reads were aligned to Ensembl GRCm38 M. musculus reference transcriptome using Hisat2
. StringTie was utilized to assemble and quantify expressed transcripts.
The transcript abundance and differential expression tables were generated using Ballgown.
The statistical analysis of between-group differences was performed using EdgeR package
Gene ontology (GO) enrichment analysis was done using the NetworkAnalyst platform and the Reactome database as reference for transcripts with p<0.001
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited csv files generated using EdgeR: scores represent log2fold change and FDR

source_name: Mouse neural progenitor cells

growth_protocol: The established mouse multipotent neural stem cells (C17.2) were purchased from CellBank Australia (Children’s Medical Research Institute, Australia). Growth medium for NSCs consisted of DMEM/F12 supplemented with 10% fetal Bovine serum and Antibiotic-Antimycotic (100X, Life Technologies).

extract_protocol:
RNA was harvested using Bioline RNA isolation kit. 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

treatment_protocol: To induce neural differentiation, NSCs were cultured in Knockout™ DMEM (Gibco), GlutaMAX™ supplement, N2 supplement (Gibco), and brain-derived neurotrophic factor (BDNF, 10 ng/ml, Sigma).

tag: cell line

tag: strain

value: CD1 x C57BL/6

tag: treatment

value: Neural induction


title: GW25E3_smRNA_Day0_2

description: Sample 30

tag: developmental stage

tag: cell type


title: Sample_SS4_old_106

tag: age


title: neural progenitor cells_NIM-rep1

value: mouse multipotent neural stem cells (C17.2)


title: Phase I benign nevus ROI6 rep1.1 [NS1-A-6-1]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

value: ND

tag: % melanocyte

tag: alignedreads


title: GW25E2_smRNA_Day0_4

description: Sample 29

tag: tissue


title: neural progenitor cells_heme-rep2

value: Heme-treated


title: Phase I benign nevus ROI5 rep1.2 [NS1-A-5-2]

tag: case class

value: control (keratinocyte)

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: GW25E2_smRNA_Day0_3

description: Sample 28

tag: developmental stage

value: frontal lobe of brain

tag: cell type


title: neural progenitor cells_Ct-rep2

tag: cell line

tag: strain

tag: treatment

value: Growth medium


title: Phase I benign nevus ROI4 rep1.2 [NS1-A-4-2]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: roi type

tag: % keratinocyte

tag: % melanocyte


title: Phase I benign nevus ROI5 rep1.1 [NS1-A-5-1]

tag: case class

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads

tag: alignedreads


title: GW25E2_smRNA_Day0_2

description: Sample 27

tag: developmental stage

tag: tissue

tag: cell type

value: EGFR+ cells


title: neural progenitor cells_heme-rep1

tag: cell line

tag: strain

tag: treatment


title: neural progenitor cells_Ct-rep1


title: Phase I benign nevus ROI4 rep1.1 [NS1-A-4-1]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: stitchedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: GW25E1_smRNA_Day0_3

description: Sample 25


title: Prdm16_mutant_FB_ATAC-seq_Rep3

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
ATAC-Seq: The replicated Prdm16 KO (x3) and control (x3) ATAC-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the UCSC Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The high quality and uniquely mapped reads (with mapping quality >= 20) were used for further analysis. ATAC-seq differential expression analysis between Prdm16 mutants and wild types on the Prdm16 bound ChIP-seq peaks were performed by Limma R package. The ATAC-seq peak calling was performed by HOMER using the “broad peak” option with parameters “-region -size 1000 -minDist 2500”, separately for the mutant and wild type. To compare active enhancers between E13.5 and E15.5, we further re-analyzed the publicly available histone mark H3K27ac and PRDM16 ChIP-seq data at E15.5. We called the peaks against Input using “narrow peak” option by HOMER with the default parameters.
RNA-Seq: After trimming the adaptor sequences using Trimmomatic, we mapped RNA-seq reads from the replicated Prdm16 wild type (x3) and mutant samples (x3) to the UCSC Mus musculus (mm10) genome assembly using HISAT2. We normalized RNA-seq by the “Relative Log Expression” method implemented in the DESeq2 Bioconductor library (Love et al., 2014). Gene annotation was obtained from the iGenomes UCSC Mus musculus gene annotation. Differentially expressed mRNAs between Prdm16 mutants versus wild type were identified, and FDR (Benjamini-Hochberg) was estimated, using DESeq2.
ChIP-Seq: The replicated Prdm16 KO (x3) and control (x3) ChIP-seq samples, after the adaptor trimming by Trimmomatic, were mapped to the UCSC Mus musculus (mm10) genome assembly using Bowtie2 with the default parameters. The uniquely mapped reads (with mapping quality >= 20) were used for further analysis. The PRDM16 peaks were called by HOMER (v4.10) (Heinz et al., 2010). The peak replicate reproducibility was estimated by Irreproducibility Discovery Rate (IDR), using the HOMER IDR pipeline (https://github.com/karmel/homer-idr). As suggested by the Encode IDR guideline that IDR requires to initially call peaks permissively for the replicates, we used a relatively relaxed parameter “-F 2 -fdr 0.3 -P .1 -L 3 -LP .1” for the true/pseudo/pooled replicates by the HOMER peak calling. The final confident peaks were determined by an IDR < 5%. The peaks that were overlapped with mm10 blacklist were also removed.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage; xlsx file for RNA-seq count table

source_name: forebrain

extract_protocol:
Forebrain from E13.5 wt and mut embryos were collected, nuclei were extracted according to published protocol (Buenrostro et al. 2013).
The ATAC-seq libraries were made according to the published method (Buenrostro et al. 2013) and using the Illumina Nextera DNA library kit. In brief, cortices were dissected from 3 control and 3 Prdm16 KO E13.5 brains. Tn5 enzyme reaction was performed at 37 degrees for 30mins, followed by DNA purification. 11 cycles of PCR amplification was performed using barcoded adaptors and primers on purified DNA template. Libraries were purified and pooled before sequencing with illumina Next-seq platform.

value: forebrain

tag: genotype

value: homozygous mutant


title: Phase I benign nevus ROI3 rep1.2 [NS1-A-3-2]

tag: case class

tag: roi type

value: mixed

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme

tag: rawreads

tag: trimmedreads


title: GW25E1_smRNA_Day0_2

description: Sample 24

tag: developmental stage

value: embryonic stage GW25

tag: tissue

tag: cell type


title: GW25E1_smRNA_Day0_1

description: Sample 23


title: Prdm16_mutant_FB_ATAC-seq_Rep2


title: Phase I benign nevus ROI3 rep1.1 [NS1-A-3-1]

tag: patient

value: benign nevus

tag: dsp replicate

tag: roi number

tag: sequencing replicate

tag: roi diameter (um)

tag: alignedreads


title: Phase I benign nevus ROI2 rep1.2 [NS1-A-2-2]

tag: case class

tag: roi type

value: melanocyte

tag: stitchedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: GW24E3_smRNA_Day0_2

description: Sample 22

value: embryonic stage GW24


title: Phase I benign nevus ROI2 rep1.1 [NS1-A-2-1]

tag: % keratinocyte

tag: % melanocyte

tag: % immune cells

tag: % other

tag: % tme


title: Prdm16_mutant_FB_ATAC-seq_Rep1

tag: tissue

tag: genotype

tag: developmental stage


title: Prdm16_control_FB_ATAC-seq_Rep3

value: heterozygous or willd-type control little


title: GW24E3_smRNA_Day0_1

description: Sample 21

tag: cell type


title: Phase I benign nevus ROI1 rep1.2 [NS1-A-1-2]

tag: patient

tag: dsp replicate

tag: roi number

tag: sequencing replicate

value: immune

tag: rawreads

tag: trimmedreads


title: Prdm16_control_FB_ATAC-seq_Rep2


title: Phase I benign nevus ROI1 rep1.1 [NS1-A-1-1]

tag: case class

tag: roi diameter (um)

tag: roi type

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: GW24E2_smRNA_Day0_5

description: Sample 19


title: GW24E2_smRNA_Day0_7

description: Sample 20


title: WT_small RNA

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description:
small RNA
Single-end small RNA-Seq libraries constructed using standard Illumina protocols (Illumina)

data_processing:
Bowtie v1.1.2 was used to map sRNA-Seq reads; Tophat was used to map RNA-seq reads
Sequence reads were trimmed using Cutadapt version 1.13 (Martin, 2011) and trimmed reads, 18-26 nucleotides in length, aligned to the maize B73 RefGen_v3 genome (release 5a.57) using Bowtie version 1.1.2 (Langmead et al., 2009), allowing no mismatches and a maximum of 20 alignments per read; For RNA-seq, reads were trimmed using trimmomatic verstion 0.36. Trimmed RNA-Seq reads were aligned to the B73 RefGen_V3 using tophat, and uniquely mapped reads were used for subsequent analyses
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: SAM_datamatrix.txt.gz includes bulk RNA-seq tab-delimited text file includes RPM values for each Sample
Supplementary_files_format_and_content: miRNA_info.txt includes name, sequence, raw reads count and normalized data (reads per million)

organism: Zea mays

growth_protocol: maize B73 seedlings were grown in growth-chambers at 16 hour 25 oC/light and 8 hour 21 oC/dark cycles

extract_protocol:
For small RNA-seq, total RNA was extracted using TRIzol reagent (Invitrogen) followed by treatment with DNase I (Promega). For bulk RNA-seq, RNA was extracted with the PicoPure RNA isolation kit (Arcturus), treated with DNaseI (Qiagen) and linearly amplified with the TargetAmp 2-Round aRNA Amplification kit 2.0 (Epicentre Biotechnologies).
sRNA-Seq libries were prepared from 1.2 𝝁g total RNA using TruSeq small RNA sample preparation kit (Illumina). Libraries were quantified with the KAPA Illumina library Quantification Kit (KAPABIOSYSTEMS) and sequenced on the Illumina HiSeq2000 platform; RNA-Seq Libraries were constructed from linearly amplified RNA using the TruSeq RNA Library Kit from Illumina following the recommended protocols.

treatment_protocol: Cells of interest were captured by LCM from 2-week-old B73 apices as described (Knauer et al., 2019).

tag: strain

value: whole shoot apex

tag: age

value: 14-day-old seedlings

value: wild type


title: GW24E2_smRNA_Day0_4

description: Sample 18

tag: tissue


title: GW24E2_smRNA_Day0_3

description: Sample 17

tag: developmental stage


title: GW25E2_smRNA_Day0_1

description: Sample 26

tag: cell type


title: GW24E2_smRNA_Day0_2

description: Sample 16


title: FMA2 22.2: NRG1 mutant (fwd)

city: Monterrey

first: Jose

middle: Alejandro

last: Sánchez-Arreguin

state: Nuevo León

address: Pedro de Alba S/N

department: Facultad de ciencias Biológicas

country: Mexico

institute: Universidad Autónoma de Nuevo León

data_processing:
Quality-control checkpoints (Bioconductor QuasR v1.09.0 utility "preprocessReads"): Raw reads were processed by fitering Quality <Q20, minimum lengths of 130nt (after adapter removal), trimmed read lengths of 130nt (to remove low quality sequences). Other parameters that were taken in consideration for filtration were GC content, overrepresented k-mers and duplicated reads.
Read alignment (Bioconductor QuasR v1.09.0 utility "qAlign"): The reads were mapped to the reference genome of Ustilago maydis 521, GenBank assembly accession: GCA_000328475.2
Differential gene expression (DEG) (Blas2GO v 5.0): BAM files were employed to generate the count tables, All differentially expressed genes were classified into the categories of molecular function, cellular component, and biological process in the Gene Ontology (GO) database (http://www.geneontology.org/). FB2 samples were consider to be basal and FMA luminal
GSEA analysis (Blas2GO v 5.0): Default BLAST2GO parameters were used and only GO terms with P<0.005 were included in the present study. GSEA Enrichment analysis was used to find enriched GO terms, p-value P<0.005.
The read files are paired end but the mapping was made like single end, and in the differential expression analysis the samples were concatenated.

organism: Mycosarcoma maydis

source_name: Yeast cells from Basidiomycota

growth_protocol: Cells cultures were grown on minimum media at pH 4, and recovered after 14 h of growth.

extract_protocol:
RNA was extracted from frozen and ground fungal tissue using the PureLink RNA Mini Kit (Invitrogen)
1 µg of total RNA was subjeted to library synthesis using the TruSeq RNA sample prep LT

treatment_protocol: The pH was modified to acidic conditions

value: genetic background a2b2 Dnrg1

tag: genotype/variation

value: NRG1 mutant

value: Yeast cells from Basidiomycota


title: FMA2 11.1: NRG1 mutant (fwd)


title: muscle of well endurance trained aged subject #4

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

country: Italy

institute: University of Bologna

description: 80X2 paired-end sequence reads

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for sequance adapters and low-quality tails, then mapped to hg19 reference using tophat (2.0.9)
Raw count  were computed using the Python package HTSeq-count (0.6.1p1) adopting the gene annotations Ensembl GRCh37.72. Data were normalized as count per million adopting the the R-bioconductor package edgrR (3.8.6)
Genome_build: hg19
Supplementary_files_format_and_content: text file include count per million (cpm) for every gene

source_name: muscle  vastus lateralis

extract_protocol:
TRIZOL® (Invitrogen SRL, Milan, Italy)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: age (years)

tag: % of resistance training

tag: % of endurance training

tag: average weekly hours of training


title: FB2 22.1: Wild type (rev)

value: genetic background a2b2


title: FMA2 11.1: NRG1 mutant (rev)


title: muscle of well endurance trained aged subject #5

description: 80X2 paired-end sequence reads


title: muscle of well endurance trained aged subject #3

description: 80X2 paired-end sequence reads


title: GW24E1_smRNA_Day0_5

description: Sample 15

value: frontal lobe of brain

value: EGFR+ cells


title: GW24E1_smRNA_Day0_4

description: Sample 14


title: GW24E1_smRNA_Day0_3

description: Sample 13


title: FB2 22.1: Wild type (fwd)


title: WT-LT-HSC

city: Tokyo

first: Noriko

last: Sorimachi

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biophysics and Biochemistry

country: Japan

institute: Graduate School of Science, The University of Tokyo

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used according to the manufacturer's instruction

scan_protocol: DNA Microarray Scanner (Agilent SureScan G4900DA) was used according to the manufacturer's instruction

data_processing: The scanned images were analyzed with Feature Extraction Ver.11.5.1.1 (Agilent). Normalization method was 75 percentile shift for each sample.

source_name: HSC

label_protocol: Gene Expression Hybridization Kit (5188-5242 : Agilent) was used according to the manufacturer's instruction

extract_protocol: Fresh WT or p38KO HSCs were sorted into SF-O3 medium and then centrifuged at 340 x g for 5 minutes at 4℃. Cell pellets were lysed in 75uL of RLT buffer plus 1% 2-ME, followed by RNA extraction using Qiagen RNeasy micro kit (74004 : Qiagen) according to the manufacturer's instruction.

value: 2 years old

value: Bone marrow

value: CD150+CD48-Flt3-CD34- LSK

value: wild-type


title: muscle of well endurance trained aged subject #2

description: 80X2 paired-end sequence reads


title: muscle of well endurance trained aged subject #1

description: 80X2 paired-end sequence reads


title: Prdm16_control_FB_ATAC-seq_Rep1

value: forebrain

tag: genotype


title: muscle of well resistance trained aged subject #4

description: 80X2 paired-end sequence reads


title: GW24E1_smRNA_Day0_2

description: Sample 12

value: embryonic stage GW24


title: Mtb_colony_morphotype

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: comparision of RNA from 50 pooled spreading and 150 pooled raised colonies

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: Mtb spread colonies

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Proper dilutions of single cell preparation from a liquid culture of mc27000 (Mtb delta RD1 delta panCD) were spread on 7H10 OADC agar plates supplemented with D-pantothenic acid at 2ug/ml, and incubated at 37C for 4 weeks.

extract_protocol: Colonies were suspended in 1mL buffer RLT from a Qiagen RNeasy kit. The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus. After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube. 525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications. At this point the RNA is purified as recommended by the Qiagen protocol.

treatment_protocol: 50 spread and 150 raised were identified and picked into separate tubes.

source_name: Mtb raised colonies


title: FB2 11.1: Wild type (rev)


title: GW23E1_smRNA_Day0_1

description: Sample 10

value: embryonic stage GW23


title: mRNA_Th17-23_KO_rpt3_OS1457

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
BCL conversion and demultiplexing (Casava 1.8.2 for ChIP, miRNA and mRNA)( Bcl2fastq and CellRanger for scRNA).  scRNA-seq raw files: read1_26/i7index_8/read2_98.
Mapping (Tophat 2.0.8 and Bowtie 2-2.1.0  for mRNA) (Bowtie v0.12.8 for ChIP and miRNA) (CellRanger for scRNA)
peak calling (MACS v1.4.2: default p-value threshold of 1E-5 for ChIP-seq)
BigWig tracks (BEDTOOLS v2.24, UCSC tool bedGraphToBigWig)
Genome_build: mm9 (ChIP, miRNA, mRNA); mm10 (scRNA)
Supplementary_files_format_and_content: BigWig files (ChIP, miRNA, mRNA); Robj, CellRanger output files (scRNA)

source_name: in vitro cultured CD4+ T cells

growth_protocol: CD4+ T cells were enriched by negative selection (Miltenyi), then purified to naïve population by sorting (CD4+CD62L+CD44-CD25-), then cultured with plate-bound anti-CD3 and anti-CD28 for 3 days with cytokines/antibodies indicated in treatment section.

extract_protocol:
Total RNA was isolated using TRIzol or mirVana miRNA Isolation kit (Thermo Fisher Scientific)
TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) using 200 ng of total RNA

value: spleen and lymph node

tag: growth condition

value: 3 day in vitro culture

tag: treatment

value: IL-6, IL-23, anti-IFNg, anti-IL4


title: GW24E1_smRNA_Day0_1

description: Sample 11


title: cKO-LT-HSC


title: FMA2 22.2: NRG1 mutant (rev)

value: genetic background a2b2 Dnrg1


title: muscle of well resistance trained aged subject #3

description: 80X2 paired-end sequence reads


title: GW21E4_smRNA_Day0_4

description: Sample 9

value: embryonic stage GW21


title: GW21E4_smRNA_Day0_3

description: Sample 8


title: muscle of well resistance trained aged subject #2

description: 80X2 paired-end sequence reads


title: mRNA_Th17-23_KO_rpt2_OS1456


title: GW21E4_smRNA_Day0_2

description: Sample 7


title: muscle of well resistance trained aged subject #1

description: 80X2 paired-end sequence reads


title: GW21E3_smRNA_Day0_5

description: Sample 6


title: mRNA_Th17-23_KO_rpt1_OS1455


title: muscle of sedentary aged subject # 5

description: 80X2 paired-end sequence reads


title: mRNA_Th17-23_WT_rpt3_OS1441

value: Wild type


title: FB2 11.1: Wild type (fwd)

value: wild type

value: Yeast cells from Basidiomycota


title: GW21E3_smRNA_Day0_4

description: Sample 5

value: frontal lobe of brain


title: muscle of sedentary aged subject # 3

description: 80X2 paired-end sequence reads

value: male


title: GW21E3_smRNA_Day0_3

description: Sample 4

value: EGFR+ cells


title: mRNA_Th17-23_WT_rpt1_OS1416


title: muscle of sedentary aged subject # 2

description: 80X2 paired-end sequence reads


title: muscle of sedentary aged subject # 1

description: 80X2 paired-end sequence reads

source_name: muscle vastus lateralis


title: GW21E3_smRNA_Day0_2

description: Sample 3


title: mRNA_Th1_KO_rpt2_OS1450

value: IL-12, anti-IL4


title: mRNA_Th1_KO_rpt3_OS1451


title: Immunocastrated pigs (pooled RNA)_adipose 2

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

data_processing:
Raw reads were filtered by (1) discarding the reads with adaptor contamination, (2) removing the reads with more than 10% of uncertain nucleotides, (3) discarding reads with low-quality nucleotides (base quality less than 20) constituting more than 50% of the read.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12 (default parameters allowing up to 2 bases mismatches).
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor.
Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P-values were adjusted using the Benjamini & Hochberg method.
Genome_build: Sus scrofa 11.1 (Gene bank assembly GCA_000003025.6)
Supplementary_files_format_and_content: tab-delimited csv file with FPKM values or read counts

source_name: subcutaneous adipose tissue (at withers)

extract_protocol:
The inner layer of subcutaneous adipose tissue at withers (i.e., between first thoracal and last cervical vertebra) was sampled, immediately frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted using RNeasy plus Universal Mini Extraction Kit. Extracted RNA samples were pooled in equal quantities for each group.
cDNA sequencing libraries were generated using NEBNext Ultra RNA Library preparation Kit for Illumina.

treatment_protocol: Immunocastrated pigs were vaccinated at the age of 12 and 21 weeks with a vaccine against GnRH (Improvac® vaccine, Zoetis) and surgically castrated pigs were castrated within the first week of life.

tag: breed

value: Landrace x Pietrain crosses

value: immunocastration

value: subcutaneous adipose tissue


title: Entire male pigs (pooled RNA)_adipose 1

value: no treatment


title: Surgically castrated pigs (pooled RNA)_adipose 3

value: surgical castration


title: GW21E2_smRNA_Day0_1

description: Sample 2


title: mRNA_Th1_WT_rpt3_OS1412

value: spleen and lymph node


title: Recovered_rep3

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Read counts of each gene was counted by featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: Line 3 recovered hiPSC-CM

extract_protocol: hiPSC-CMs RNA was harvested using Trizol reagent

value: hiPSC-CMs

tag: differentiation day

value: Recovered


title: Recovered_rep2

source_name: Line 2 recovered hiPSC-CM


title: GW21E1_smRNA_Day0_1

description: Sample 1