title: Flu02_050720_ROI_001_well_C02

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate


title: INFG_ID_103

status: Public on Aug 31 2022

type: RNA

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data were normalized using the R package ‘limma’ using the function backgroundCorrect with parameters: method=normexp, offset=50.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX).

treatment_protocol: A 2.5 ml peripheral blood sample (into PAXgene tubes) was obtained from each study participant. Routine investigations were performed, as determined by the admitting physician. Airway samples were tested for bacterial pathogens and common respiratory viruses.

tag: tissue

value: whole blood

tag: Sex

value: f

tag: age

tag: disease state


title: Covid17_050820_ROI_009_well_A10

type: SRA

city: Seattle

first: Tyler

last: Hether

state: WA

address: 530 Fairview Ave N

department: Translational Sciences

country: USA

institute: NanoString Technologies, Inc.

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

library_source: transcriptomic

data_processing:
library strategy: GeoMx Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx COVID19 Immune Response Atlas v1 Platform files (GeoMx_Hs_CTAv1.1.pkc and GeoMx_COVID19_v1.0.pkc)
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Values represented in the collapsed target counts tab (in GeoMx_processed_data.xlsx) are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: FFPE Rapid Autopsy Tissue

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

tag: virus

value: yes

tag: patient id

value: 1. Covid17

value: Geometric Segment

value: Alveolar

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes

value: Aveolar Zone with Type 2 Hyperplasia


title: INFG_ID_111

value: viral


title: INFG_ID_104

value: m


title: Covid02_050720_ROI_024_well_C01

tag: roi number

tag: segment type


title: Covid02_050720_ROI_023_well_B12

tag: condition

tag: roi x coordinate


title: Covid02_050720_ROI_022_well_B11

tag: tissue


title: Covid02_050720_ROI_021_well_B10


title: Flu02_050720_ROI_005_well_C06

value: Segment 1

value: Vascular

value: Flu


title: NAc, Caudate, and Putamen [1686P]

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment with HISAT2
Read counts using HTSeq
Assembly: Ensembl GRh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Putamen

extract_protocol:
Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepped for RNA-sequencing using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). 75bp paired-end dual-indexed sequencing was performed using the NextSeq 500 platform (Illumina, San Diego, CA).

tag: age

tag: gender

value: Male

value: Putamen

tag: race

value: Black

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [1605P]

value: Female

value: White

tag: disease state

value: match control


title: Covid02_050720_ROI_019_well_B08

tag: virus

value: yes

tag: patient id

tag: roi number

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: NAc, Caudate, and Putamen [1598P]

tag: age

tag: gender

tag: tissue

tag: race

tag: pmi

tag: sequence id

value: HFYYFBGXF

tag: library size

tag: rin


title: INFG_ID_102

value: whole blood

tag: Sex

value: f

tag: disease state


title: Flu02_050720_ROI_003_well_C04

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Large Airway

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: NAc, Caudate, and Putamen [1581P]

tag: age

tag: gender

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: NAc, Caudate, and Putamen [1543P]

tag: tissue

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin


title: Covid02_050720_ROI_017_well_B06

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Alveolar

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes

value: Aveolar Zone with Type 2 Hyperplasia


title: Covid02_050720_ROI_015_well_B04

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: Covid02_050720_ROI_016_well_B05

tag: tissue


title: Covid02_050720_ROI_014_well_B03


title: Covid02_050720_ROI_020_well_B09


title: Covid02_050720_ROI_013_well_B02


title: Covid02_050720_ROI_012_well_B01


title: NAc, Caudate, and Putamen [1455P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: Covid02_050720_ROI_008_well_A09

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: NAc, Caudate, and Putamen [1394P]

tag: age

tag: gender

tag: tissue

tag: race

tag: pmi

tag: disease state

tag: rin


title: NAc, Caudate, and Putamen [1420P]

tag: sequence id

tag: library size

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: INFG_ID_101

tag: Sex

value: viral


title: Covid02_050720_ROI_018_well_B07

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Covid02_050720_ROI_009_well_A10

tag: tissue

tag: sequencingsaturation

tag: notes


title: Covid02_050720_ROI_007_well_A08


title: INFG_ID_97

tag: age

tag: disease state


title: Covid02_050720_ROI_006_well_A07

tag: virus


title: NAc, Caudate, and Putamen [1518P]

tag: gender

value: Male

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: Covid02_050720_ROI_003_well_A04

tag: patient id

tag: roi number

tag: segment type

value: Vascular

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: Covid02_050720_ROI_005_well_A06

tag: virus

tag: tissue

tag: sequencingsaturation


title: Covid02_050720_ROI_002_well_A03


title: INFG_ID_94

tag: Sex

tag: age

tag: disease state


title: Covid02_050720_ROI_004_well_A05

tag: patient id


title: INFG_ID_99


title: INFG_ID_100

value: m


title: INFG_ID_98


title: NAc, Caudate, and Putamen [1391P]

tag: gender

value: Putamen

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: Covid02_050720_ROI_010_well_A11

tag: virus

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: notes


title: Covid02_050720_ROI_001_well_A02

tag: patient id

tag: tissue

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [1372P]

tag: age

tag: gender

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

value: Accidental


title: Normal04_050520_ROI_019_well_H12

tag: virus

value: no

value: 4. Normal04

tag: roi number

tag: segment type

tag: condition

value: Normal

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: NAc, Caudate, and Putamen [1371P]

tag: age

tag: gender

tag: tissue

tag: race

value: Black

tag: pmi

tag: disease state

value: match control

tag: manner of death


title: Normal04_050520_ROI_018_well_H11

tag: virus

tag: patient id

value: Geometric Segment

tag: deduplicatedreads

tag: sequencingsaturation


title: Normal04_050520_ROI_017_well_H10

tag: roi number

tag: segment type

value: Alveolar

tag: condition

tag: roi x coordinate


title: Normal04_050520_ROI_016_well_H09

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Normal04_050520_ROI_015_well_H08

tag: tissue

tag: alignedreads


title: Normal04_050520_ROI_014_well_H07


title: NAc, Caudate, and Putamen [1374P]

tag: age

tag: gender

tag: race

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: INFG_ID_61

value: whole blood

tag: Sex

value: f

tag: disease state


title: NAc, Caudate, and Putamen [1341P]

value: Female

tag: manner of death


title: INFG_ID_65


title: Normal04_050520_ROI_013_well_H06

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [1326P]

tag: age

tag: gender

value: Male

tag: tissue

tag: race

tag: pmi

tag: sequence id

value: HGCTCBGXF

tag: library size

tag: rin

tag: bmi


title: NAc, Caudate, and Putamen [1318P]

tag: disease state

value: HFYYFBGXF

tag: ph

tag: tissuestoragetime

tag: manner of death


title: INFG_ID_64

tag: Sex

value: m


title: INFG_ID_62


title: Normal04_050520_ROI_012_well_H05

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Normal04_050520_ROI_011_well_H04

value: Segment 2

tag: tissue

tag: deduplicatedreads

tag: sequencingsaturation


title: INFG_ID_63

tag: age

tag: disease state


title: Normal04_050520_ROI_010_well_H02


title: NAc, Caudate, and Putamen [13175P]

tag: gender

value: Putamen

tag: race

value: White

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: INFG_ID_59

tag: Sex


title: INFG_ID_60


title: Normal04_050520_ROI_010_well_H01

tag: virus

value: no

tag: patient id

value: 4. Normal04

tag: roi number

tag: segment type

value: Segment 1

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Normal04_050520_ROI_011_well_H03

tag: tissue

value: Normal

tag: deduplicatedreads

tag: sequencingsaturation


title: Normal04_050520_ROI_009_well_G12


title: NAc, Caudate, and Putamen [13149P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: INFG_ID_52

tag: Sex


title: INFG_ID_55


title: Normal04_050520_ROI_008_well_G10

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: Normal04_050520_ROI_008_well_G09

tag: tissue

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [13071P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: manner of death

value: Accidental


title: Normal04_050520_ROI_007_well_G08

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Vascular

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads


title: Normal04_050520_ROI_006_well_G07

tag: tissue

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: INFG_ID_58

value: whole blood

tag: Sex

tag: age

tag: disease state


title: Normal04_050520_ROI_005_well_G06

tag: virus


title: Sample_2-WT

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
The adaptor sequences were trimmed by the cutadapt (v1.4.2) and then aligned to the reference mouse genome (GRCm39) using the STAR aligner(ver 2.6.1).
The align data were quantified to the gene features (GRCm39.105.gtf) in gene count using HTSeq (ver 0.9.1). Gene count of each sample are attached (*.htseq.counts).
The gene count value of each sample were normalied with varience stabilizing transformation method (VST) using DESeq2.
Assembly: GRCm39
Supplementary files format and content: htseq.count.txt file

organism: Mus musculus

source_name: mouse muscle fibroadipogenic progenitor (FAP) cells, originated from wild-type mose

growth_protocol: Isolation of limb muscle mesenchymal fibroadipogenic progenitor cells (FAPs) was performed according to a previously reported protocol with minor modifications. Hindlimb and forelimb  muscles were dissected and mechanically dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; ThermoFisher Scientific, Waltham, MA, USA) at 37°C for 40 min. Digested suspensions were subsequently triturated by sterilized syringe with 20G1/2 needle (BD Biosciences, Franklin Lakes, NJ, USA), strained with 40μm cell strainer (SPL Lif eSciences, Pocheon, Korea) and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with corresponding antibodies. To exclude dead cells, 7-Aminoactinomycin D (Sigma-Aldrich; St. Louis, MO, USA) was used prior to FACS analysis. Stained cells were analyzed and 7AAD–Lin–Vcam–Sca1+ cells were isolated using a FACS Aria III cell sorter (BD Biosciences) with 4-way-purity precision. Isotype control density plots were used as a reference for positive gating.

extract_protocol:
total RNA was extracted from WT, ΔBap1, SMNWT-overexpressed ΔBap1, and SMNK186R-overexpressed ΔBap1 FAPs using TRIzol Reagent (Life Technologies, Carlsbad, CA, USA).
TruSeq technology was used to generate Illumina RNA-seq libraries, according to the manufacturer’s instructions.
RNA-seq libraries were sequenced as paired-ends on an Illumina Hi-Seq 4000 system.

treatment_protocol: Freshly isolated FAPs of indicated genotypes were cultured at 37 °C in alpha-MEM (Hyclone) supplemented with ZellShield (Minerva Biolabs; Skillman, NJ, USA) and 20% FBS (Hyclone). HEK293T cell line (ATCC, Manassas, VA) was grown at 37 °C in DMEM (Hyclone) supplemented with ZellShield and 10% FBS. The cell line was regularly tested for mycoplasma contamination. All transfections were performed using polyethyleneimine (PEI; Polysciences, Warrington, PA, USA). Full length and point-mutated constructs of human SMN were subcloned into the pcDNA4-HisMAX vector and pLVX vector. For Bap1 deletion under Rosa-CreER, FAPs were cultured with 1μM 4-Hydroxytamoxifen (4383 OHT). Equal concentration of ethanol was used as a control. Culture media was replaced by alpha-MEM supplemented with ZellShield and 20% FBS 24 hours after exposure to 4-OHT. Subsequent deletion of Bap1 gene was confirmed by qRT-PCR

value: limb muscle

tag: cell type

tag: treatment

value: EtOH

tag: genotype

value: WT

tag: culture media batch

value: B


title: Sample_1-WT

value: muscle fibroadipogenic progenitor (FAP) cells

value: A


title: NAc, Caudate, and Putamen [13068P]

tag: gender

value: Male

value: Putamen

tag: race

value: White

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: NAc, Caudate, and Putamen [13069P]

tag: age

tag: tissue

value: Natural


title: NAc, Caudate, and Putamen [13045P]

value: Female

tag: disease state

value: Undetermined


title: Normal04_050520_ROI_004_well_G05

tag: virus

value: no

tag: patient id

value: 4. Normal04

tag: roi number

tag: segment type

value: Segment 1

value: Large Airway

tag: condition

value: Normal

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Normal04_050520_ROI_003_well_G04


title: Normal04_050520_ROI_002_well_G03


title: Normal04_050520_ROI_009_well_G11

value: Alveolar


title: Sample_3-Smn1OE_K186R

source_name: mouse muscle fibroadipogenic progenitor (FAP) cells, originated from neuromuscular defects in SMNK186R-overexpressed Prrx1Cre;Bap1f/f (hereafter, cKO) mice

value: limb muscle

tag: cell type

tag: treatment

value: 4-OHT, SMNK186R overexpression vector transfected

tag: genotype

tag: culture media batch

value: F


title: Normal04_050520_ROI_001_well_G02

tag: virus

tag: tissue


title: INFG_ID_56

value: whole blood

tag: Sex

value: f

tag: age

tag: disease state


title: ARDS01_050520_ROI_024_well_G01

tag: patient id

value: 3. ARDS01

tag: roi number

tag: segment type

value: Geometric Segment

tag: condition

value: Non-viral

tag: roi x coordinate


title: ARDS01_050520_ROI_023_well_F12

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Sample_2-Smn1OE_K186R

tag: cell type

value: muscle fibroadipogenic progenitor (FAP) cells

tag: treatment

tag: genotype

value: E


title: ARDS01_050520_ROI_022_well_F11

tag: virus

tag: tissue

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [13032P]

tag: age

tag: gender

value: Male

value: Putamen

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [13112P]

value: Black


title: Sample_1-Smn1OE_K186R

tag: cell type

tag: treatment

tag: genotype

tag: culture media batch

value: D


title: NAc, Caudate, and Putamen [13017P]

tag: tissue


title: ARDS01_050520_ROI_021_well_F10

tag: virus

value: no

tag: patient id

tag: roi number

tag: segment type

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_3-WT

value: limb muscle

tag: cell type

tag: treatment

value: EtOH

value: WT

value: C


title: Sample_3-Smn1OE

source_name: mouse muscle fibroadipogenic progenitor (FAP) cells, originated from neuromuscular defects in SMN-overexpressed Prrx1Cre;Bap1f/f (hereafter, cKO) mice

value: 4-OHT, SMN overexpression vector transfected

tag: genotype

tag: culture media batch

value: F


title: ARDS01_050520_ROI_019_well_F08

tag: virus

value: 3. ARDS01

value: Geometric Segment

tag: tissue

value: Non-viral


title: INFG_ID_51

value: whole blood

tag: Sex

value: f

tag: age

tag: disease state


title: Sample_2-Smn1OE

value: muscle fibroadipogenic progenitor (FAP) cells

value: E


title: ARDS01_050520_ROI_018_well_F07

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate


title: NAc, Caudate, and Putamen [1298P]

tag: gender

value: Male

value: Putamen

tag: race

value: White

tag: pmi

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: ARDS01_050520_ROI_017_well_F06

tag: virus

value: no

tag: tissue

value: Alveolar

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Sample_1-Smn1OE

value: limb muscle

tag: cell type

tag: treatment

tag: genotype

tag: culture media batch

value: D


title: NAc, Caudate, and Putamen [1296P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi


title: ARDS01_050520_ROI_014_well_F03

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: ARDS01_050520_ROI_015_well_F04

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [1255P]

tag: age

tag: gender

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Accidental


title: ARDS01_050520_ROI_016_well_F05

tag: virus

tag: patient id

value: 3. ARDS01

tag: roi number

tag: segment type

value: Geometric Segment

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: NAc, Caudate, and Putamen [1268P]

tag: age

tag: gender

value: HFYYFBGXF

tag: rin

tag: bmi


title: ARDS01_050520_ROI_012_well_F01

value: Non-viral

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS01_050520_ROI_011_well_E12

tag: virus

tag: patient id


title: Sample_2-Bap1KO

source_name: mouse muscle fibroadipogenic progenitor (FAP) cells, originated from neuromuscular defects in Prrx1Cre;Bap1f/f (hereafter, cKO) mice

tag: cell type

tag: treatment

tag: genotype

tag: culture media batch

value: B


title: ARDS01_050520_ROI_020_well_F09

tag: roi number

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: NAc, Caudate, and Putamen [1247P]

tag: age

tag: gender

value: Female

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: ARDS01_050520_ROI_013_well_F02

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS01_050520_ROI_009_well_E10

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: ARDS01_050520_ROI_010_well_E11


title: Sample_1-Bap1KO

tag: cell type

value: muscle fibroadipogenic progenitor (FAP) cells

tag: treatment

tag: genotype

tag: culture media batch

value: A


title: Sample_3-Bap1KO

value: C


title: NAc, Caudate, and Putamen [1244P]

tag: age

tag: gender

value: Male

value: Putamen

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: ARDS01_050520_ROI_006_well_E07

tag: virus

value: no

tag: patient id

tag: roi number

tag: segment type

tag: tissue

value: Vascular

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: ARDS01_050520_ROI_008_well_E09

value: Alveolar


title: NAc, Caudate, and Putamen [1211P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

value: Natural


title: ARDS01_050520_ROI_007_well_E08

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate


title: C_9

data_processing:
Reads were quality checked with package FastQC, version 0.11.9, then trimmed using Trimgalore, version 0.6.7.
Trimmed reads were mapped to mouse genome annotation mm11 using STAR aligner, version 2.7.9a.
Mapped reads were feature counted (per gene) using RsubRead, version 2.8.1.
Raw counts were then normalized using DESeq2, version 1.26.0.
Genome_build: ENSMBL Mus_musculus.GRCm39, release 104
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: Lung

extract_protocol:
Mice were sacrificed, whole lungs prepared and immediately transferred to RNAlater solution (Qiagen). RNA was isolated using Qiagen Midi Kit according to the manufacturer's protocol.
Quality and integrity of total RNA was determined using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
A strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 60M reads per RNA sample.

treatment_protocol: Mice were intra-nasally infected with Infleunza A virus (IAV) and/or Streptococcus pneumoniae (S.p.) or PBS as control and lungs were collected for RNAseq analysis.

value: Lung

tag: treatment


title: C_7


title: NAc, Caudate, and Putamen [1207P]

tag: age

tag: gender

tag: race

tag: tissuestoragetime

tag: manner of death


title: ARDS01_050520_ROI_005_well_E06

value: 3. ARDS01

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: C_6


title: ARDS01_050520_ROI_004_well_E05

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Large Airway


title: ARDS01_050520_ROI_003_well_E04

tag: tissue

tag: condition

value: Non-viral

tag: roi x coordinate

tag: roi y coordinate


title: NAc, Caudate, and Putamen [1196P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

value: Accidental


title: C_4

tag: treatment


title: C_21


title: ARDS01_050520_ROI_001_well_E02

tag: virus

tag: patient id

tag: roi number

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_024_well_E01

value: yes

tag: segment type

tag: tissue

tag: roi x coordinate

tag: roi y coordinate


title: Flu01_050520_ROI_023_well_D12

tag: condition

value: Flu


title: Flu01_050520_ROI_021_well_D10


title: Flu01_050520_ROI_022_well_D11


title: NAc, Caudate, and Putamen [1188P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: tissuestoragetime

tag: manner of death


title: NAc, Caudate, and Putamen [1178P]

value: Female

value: Black

tag: ph


title: C_17

tag: treatment


title: NAc, Caudate, and Putamen [1159P]

value: Male

tag: tissue

value: Putamen


title: Flu01_050520_ROI_020_well_D09

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: roi x coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_019_well_D08

tag: condition

tag: roi y coordinate


title: NAc, Caudate, and Putamen [1171P]

tag: age

tag: gender

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: tissuestoragetime

tag: manner of death


title: Flu01_050520_ROI_016_well_D05

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

value: Vascular

tag: roi x coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: C_19

tag: treatment


title: C_16


title: C_20


title: Flu01_050520_ROI_017_well_D06

tag: condition

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_015_well_D04


title: NAc, Caudate, and Putamen [1121P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

value: HFYYFBGXF

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: ARDS01_050520_ROI_002_well_E03

tag: virus

value: no

tag: patient id

tag: roi number

tag: segment type

tag: tissue

tag: roi x coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: C_14

value: Lung

tag: treatment


title: Flu01_050520_ROI_014_well_D03

tag: condition

tag: roi y coordinate

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [1195P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [1105P]

tag: tissue

tag: tissuestoragetime


title: C_11

tag: treatment


title: Flu01_050520_ROI_013_well_D02

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: Flu01_050520_ROI_012_well_D01

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_011_well_C12


title: Flu01_050520_ROI_018_well_D07


title: NAc, Caudate, and Putamen [1099P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

value: HGCTCBGXF

tag: library size

tag: rin

tag: bmi

tag: ph

tag: manner of death


title: C_1

tag: tissue

tag: treatment


title: NAc, Caudate, and Putamen [1092P]

value: match control

tag: tissuestoragetime


title: Flu01_050520_ROI_009_well_C10

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads


title: C_46

extract_protocol:
Mice were scarified and heartblood was collected. 400 µl blood was transferred to RNAprotect Animal Blood Tube and RNA was isolated using RNeasy Protect Animal Blood Kit from Qiagen according to manufacturer instructions. Globin mRNA was depleted from total RNA using GLOBINclear kit by Thermofisher, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). PolyA+RNA were purified  from 1µg total RNA using Dynabeads mRNA DIRECT Micro Kit (ThermoFisher). The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (150 nucelotides, paired end) with an average of 60M reads per RNA sample.

treatment_protocol: mice were intra-nasally infected with Infleunza A virus (IAV) and/or Streptococcus pneumoniae (S.p.) or PBS as control and blood was collected for RNAseq analysis.

value: blood


title: Flu01_050520_ROI_008_well_C09

value: yes

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_010_well_C11

value: Flu


title: NAc, Caudate, and Putamen [1088P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: manner of death

value: Accidental


title: Flu01_050520_ROI_007_well_C08

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: C_45

tag: treatment


title: Flu01_050520_ROI_004_well_C05

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: Flu01_050520_ROI_006_well_C07


title: Flu01_050520_ROI_003_well_C04


title: C_43


title: Flu01_050520_ROI_005_well_C06


title: NAc, Caudate, and Putamen [1069P]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: NAc, Caudate, and Putamen [1067P]

tag: tissue

tag: manner of death


title: Flu01_050520_ROI_002_well_C03

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: C_40

tag: treatment


title: Flu01_050520_ROI_001_well_C02

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [1034P]

tag: age

tag: gender

value: Female

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: NAc, Caudate, and Putamen [1044P]

tag: tissue

tag: manner of death


title: C_39

tag: treatment


title: Covid01_050520_ROI_022_well_B11

tag: virus

tag: patient id

value: 1. Covid01

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: notes

value: Aveolar Zone/Endothelial cells


title: Covid01_050520_ROI_023_well_B12

tag: deduplicatedreads

tag: sequencingsaturation

value: Aveolar Zone with Type 2 Hyperplasia


title: Covid01_050520_ROI_024_well_C01

tag: tissue


title: C_37


title: NAc, Caudate, and Putamen [10025P]

tag: age

tag: gender

value: Male

value: Putamen

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: C_34

tag: treatment


title: Covid01_050520_ROI_021_well_B10

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: notes


title: EHT DMD 3

first: Christian

middle: J

last: Mandrycky

address: 850 Republican St

department: Bioengineering

institute: University of Washington

data_processing:
Base-calling and filtering was performed by BGI using SOAPnuke (DOI: 10.1093/gigascience/gix120) using the parameters  -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim
Reads were aligned to hg38 using subread and counts generated using featureCounts (both using Rsubread 2.8.1). Counts were generated at the meta-feature level. countChimericFragments, countMultiMappingReads, allowMultiOverlap were all set to FALSE. requireBothEndsMapped was set to TRUE.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Engineered heart tissue

growth_protocol: hiPSC-derived cardiomyocytes were differentiated as previously described (Lian, X., et al. 2012). After 25-27 days of differentiation, hiPSC-CMs were either cultured in 2D for another 3 weeks or cast into EHTs and cultured for three weeks as previously described (Leonard, A., et al. 2018).

extract_protocol:
Total RNA was isolated using Trizol and polyA enriched using oligo dT beads by BGI
Libraries were prepared by BGI using their standard DNA nanoball workflow, library type = DNBSEQ Eukaryotic mRNA library

treatment_protocol: hiPSC-CMs were harvested and stored in RNAlater at -80 ºC until they were sent for RNA extraction and sequencing. Engineered heart tissues were removed from posts and stored in RNAlater at -80 ºC until they were sent for RNA extraction and sequencing.

tag: cell type

value: hiPSC-derived cardiomyocytes and HS27a bone marrow stromal cells

tag: cell line

tag: genotype

value: DMD 263delG


title: NAc, Caudate, and Putamen [10023P]

tag: age

tag: gender

tag: tissue

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: NAc, Caudate, and Putamen [10003P]

value: White


title: C_32

tag: treatment


title: Covid01_050520_ROI_020_well_B09

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: EHT DMD 2

tag: cell type

tag: cell line

tag: genotype


title: Covid01_050520_ROI_019_well_B08

tag: virus

tag: tissue


title: EHT DMD 1


title: C_31

value: blood

tag: treatment


title: C_26


title: C_25


title: Covid01_050520_ROI_017_well_B06

value: yes

tag: patient id

tag: roi number

tag: segment type


title: NAc, Caudate, and Putamen [931C]

source_name: Caudate

tag: age

tag: gender

value: Caudate

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: EHT Control 1

tag: cell type

tag: cell line

tag: genotype

value: control


title: Covid01_050520_ROI_016_well_B05

tag: virus

tag: patient id

tag: roi number

tag: tissue

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: NAc, Caudate, and Putamen [933C]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

value: HWGYMBGXC

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: NAc, Caudate, and Putamen [878C]

tag: tissue

value: HWHWTBGXC


title: TMWT3

city: Hangzhou

first: Dan

last: Zhang

address: Yuhang Road 866

country: China

institute: Zhejiang University

data_processing:
The sequecnsing data was filtered with SOAPnuke(v1.5.2)
The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Bowtie2(v.2.2.5) was applied to align the clean reads to the gene set, a database built by BDI(Beijing Genomic Institute in ShenZhen)
Expression level of gene wad calculated by RSEM(v.1.2.12)
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: oocyte

extract_protocol:
TruePrep DNA Library Prep Kit V2 for Illumina （Vazyme #TD503）
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: C57BL/6 J

value: ovary

tag: cell type

value: oocyte

value: 12-weeks old

tag: genotype

value: wild type


title: C_24

tag: treatment


title: Covid01_050520_ROI_018_well_B07

tag: virus

tag: patient id

value: 1. Covid01

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes

value: Aveolar Zone with Type 2 Hyperplasia


title: TMWT2

tag: strain

tag: tissue

tag: cell type

tag: age


title: 2D DMD 3

source_name: hiPSC-CM

value: hiPSC-derived cardiomyocytes

tag: cell line

tag: genotype

value: DMD 263delG


title: NAc, Caudate, and Putamen [930C]

tag: gender

value: Male

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: EHT Control 2

value: hiPSC-derived cardiomyocytes and HS27a bone marrow stromal cells


title: NAc, Caudate, and Putamen [843C]

value: Female

value: Caudate

value: HWGNVBGXC

value: Suicide


title: Covid01_050520_ROI_014_well_B03

tag: virus

value: yes

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Alveolar

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: 2D DMD 2

tag: cell type

tag: cell line

tag: genotype


title: EHT Control 3

value: control


title: Covid01_050520_ROI_013_well_B02

tag: virus

tag: tissue

value: Aveolar Zone/Endothelial cells


title: Covid01_050520_ROI_015_well_B04

tag: patient id

tag: roi number


title: TMWT1

tag: strain

value: C57BL/6 J

value: ovary

value: oocyte

tag: age

value: 12-weeks old

value: wild type


title: NAc, Caudate, and Putamen [1180C]

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: 2D Control 3

tag: cell type

value: hiPSC-derived cardiomyocytes

tag: cell line

tag: genotype


title: NAc, Caudate, and Putamen [787C]

value: Male

tag: tissue

value: Black

value: HWFTVBGXC


title: 2D DMD 1

value: DMD 263delG


title: Covid01_050520_ROI_012_well_B01

tag: virus

tag: patient id

value: 1. Covid01

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes

value: Aveolar Zone with Type 2 Hyperplasia


title: TMHM3

tag: strain

tag: cell type

tag: age


title: TMHM2

tag: tissue

tag: genotype


title: Covid01_050520_ROI_011_well_A12

tag: virus

value: yes

tag: patient id

tag: roi number


title: Covid01_050520_ROI_010_well_A11

tag: segment type

value: Geometric Segment

tag: condition

tag: roi x coordinate


title: TMHM1


title: NAc, Caudate, and Putamen [722C]

tag: gender

value: Caudate

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: 2D Control 1

tag: cell type

tag: cell line

tag: genotype

value: control


title: Covid01_050520_ROI_009_well_A10

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

value: Alveolar

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation

tag: notes


title: NAc, Caudate, and Putamen [739C]

tag: age

tag: gender

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

value: HWHWTBGXC

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: Covid01_050520_ROI_008_well_A09

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: tissue

value: Vascular

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads


title: NAc, Caudate, and Putamen [694C]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size


title: Covid01_050520_ROI_007_well_A08

tag: virus

tag: patient id

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: meth3

city: Changsha

first: Yong

last: Wang

state: Hunan

address: No. 172 Tongzipo Road

institute: Central South University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: SH-SY5Y cells, methamphetamine treatment

growth_protocol: The cells were cultured in F12 medium (45%) and minimum essential medium (MEM, 45%) supplemented with 10% fetal bovine serum, 1% sodium pyruvate and 1% penicil lin/streptomycin. The incubator at the time of cell culture was set to 5% CO2 and 37°C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: METH group was treated with 2 mM methaphetamine for 24 hours while control group was treated with PBS.

tag: cell line

tag: cell type

value: neuroblastoma cells

tag: genotype

value: WT

tag: treatment

value: methamphetamine treatment

tag: time

value: Day 0


title: NAc, Caudate, and Putamen [697C]

tag: age

value: Male

tag: tissue

value: HWGNVBGXC

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: meth1


title: control3

source_name: SH-SY5Y cells, Control

value: PBS treatment


title: NAc, Caudate, and Putamen [822C]

tag: gender

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

value: HWFTVBGXC

tag: library size


title: meth2

tag: cell line

tag: cell type


title: Covid01_050520_ROI_006_well_A07

tag: virus

value: yes

tag: patient id

value: 1. Covid01

tag: roi number

tag: segment type

value: Geometric Segment

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: control2

tag: genotype

tag: treatment

tag: time


title: Covid01_050520_ROI_005_well_A06

tag: tissue

value: Large Airway


title: NAc, Caudate, and Putamen [656C]

tag: age

tag: gender

value: Female

value: Caudate

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: NAc, Caudate, and Putamen [625C]

value: HWHWTBGXC

value: Natural


title: control1

tag: cell line

tag: cell type

value: neuroblastoma cells

value: WT


title: 2D Control 2

value: hiPSC-derived cardiomyocytes

tag: genotype

value: control


title: Covid01_050520_ROI_004_well_A05

tag: virus

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads

tag: sequencingsaturation


title: siMESH1-03_2_HG-U133A+2

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Agilent 2100 Bioanalyzer G2939A

label: biotin

source_name: H1975 cells

label_protocol: Standard Affymetrix protocol

growth_protocol: All H1975 cells were cultured in the DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: H1975 cells were reverse transfected with the corresponding siRNA together with the Lipofectamine RNAiMAX reagent (ThermoFisher) and Opti-MEM according to the manufacture's instructions.

tag: transfection

value: TAZS89A and reverse transfeted with the siRNA targeting MESH1 CDS (siMESH1) for 72h


title: NAc, Caudate, and Putamen [700C]

tag: age

tag: gender

value: Male

tag: tissue

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

value: HWGNVBGXC

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: siMESH1-03_3_HG-U133A+2

tag: cell line


title: NAc, Caudate, and Putamen [604C]


title: Covid01_050520_ROI_003_well_A04

tag: virus

value: yes

tag: patient id

tag: roi number

tag: segment type

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: siMESH1-03_1_HG-U133A+2

tag: transfection


title: Covid01_050520_ROI_002_well_A03

value: 1. Covid01

tag: tissue

tag: sequencingsaturation


title: NAc, Caudate, and Putamen [587C]

tag: age

tag: gender

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: siMESH1-02_3_HG-U133A+2

tag: cell line

value: TAZS89A and reverse transfeted with the non-tagteing siRNA (siNT) for 72h


title: Covid01_050520_ROI_001_well_A02

tag: virus

tag: patient id

tag: roi number

tag: segment type

value: Geometric Segment

value: Large Airway

tag: condition

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: trimmedreads

tag: stitchedreads

tag: alignedreads

tag: deduplicatedreads


title: NAc, Caudate, and Putamen [1834C]

tag: age

tag: gender

value: Female

tag: tissue

value: Caudate

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

value: Undetermined


title: MM-5

city: Boston

first: Irene

last: Ghobrial

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: UMI count matrix and associated cell-level metadata

data_processing:
Generated libraries were combined according to Illumina specifications and paired-end sequenced on HiSeq 2500/4000 platforms with standard Illumina sequencing primers for both sequencing and index reads; 100 cycles were used to sequence Read1 and Read2.
Sample demultiplexing, barcode processing, alignment to the human genome (hg38) and single-cell 3’ gene counting was performed using the Cell Ranger Single-Cell Software Suite v.2.0.1.
Cells called by Cell Ranger were further filtered to those with <15% mitochondrial expression, >200 genes covered, <50,000 total unique molecular identifiers (UMIs), and <4,000 total genes detected.
Log-normalized expression values were calculated by dividing the UMIs in each cell by the total UMIs for that cell (excluding UMIs from genes that accounted for >20% of UMIs in any cell when calculating the total), multiplying by 10,000, adding one, and taking the natural log.
We removed cells incorrectly sorted during bead selection by Leiden clustering the data and using expression of known cell type markers to identify and remove clusters of cells containing non-CD138+ immune cells, red blood cells, and cells from the extracellular matrix.
Genome_build: hg38
Supplementary_files_format_and_content: umi-count-matrix.csv contains UMI counts from 10X Genomics for CD138+ plasma cells.

source_name: Bone marrow plasma cells

extract_protocol: Chromium Single Cell 3′ Library & Gel Bead Kit v3

treatment_protocol: CD138+ BM cell fractions were isolated using magnetic-activated cell sorting technology (Miltenyi Biotec). Selected cells were either viably cryopreserved in dimethylsulfoxide at a final concentration of 10% or used immediately for scRNA-seq. Before library prep, frozen BM cells were rapidly thawed, washed, counted and resuspended in PBS and 0.04% bovine serum albumin to a final concentration of 1,000 cells per µl.

tag: diagnosis

value: MM

tag: cell type

value: Bone marrow plasma cells


title: siMESH1-02_1_HG-U133A+2

tag: cell line

tag: transfection


title: MM-7


title: siMESH1-02_2_HG-U133A+2


title: MM-6


title: NAc, Caudate, and Putamen [1789C]

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: siMESH1-01_3_HG-U133A+2

value: plx304 vector and reverse transfeted with the siRNA targeting MESH1 CDS (siMESH1) for 72


title: NAc, Caudate, and Putamen [1807C]

tag: age

value: Male

value: Suicide


title: MM-4


title: MM-3


title: NAc, Caudate, and Putamen [1687C]

tag: gender

value: White

value: match control


title: NAc, Caudate, and Putamen [1686C]

tag: tissue


title: MM-8


title: NAc, Caudate, and Putamen [1605C]

tag: race


title: siMESH1-01_1_HG-U133A+2


title: NAc, Caudate, and Putamen [1598C]

tag: pmi

value: HWGYMBGXC


title: NAc, Caudate, and Putamen [1581C]

tag: disease state

value: HWHWTBGXC


title: SMM-12

value: SMM


title: SMM-11


title: siMESH1-01_2_HG-U133A+2


title: siNT-1_HG-U133A+2

value: plx304 vector and reverse transfeted with the non-tagteing siRNA (siNT) for 72h


title: Mutant_4_M

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Mutant for medial replicate 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for all 19 samples

source_name: mouse E14.5 embryonic cortex

extract_protocol:
Total RNA was extracted from dissected medial or lateral cortices of E14.5 embryonic brains by using the RNeasy Micro Kit (Qiagen)
A sequencing library was prepared using the TruSeq Stranded Total RNA Kit (Illumina).

value: medial cortex

tag: treatment

value: Mutant


title: Mutant_3_M

description: Mutant for medial replicate 3


title: NAc, Caudate, and Putamen [1518C]

tag: sequence id

tag: library size


title: NAc, Caudate, and Putamen [1543C]

value: Female

tag: rin

tag: bmi


title: Mutant_2_M

description: Mutant for medial replicate 2


title: Control_6_M

description: Control for medial replicate 5

value: Control


title: SMM-10

tag: diagnosis

tag: cell type


title: MM-2


title: SMM-9


title: siNT-3_HG-U133A+2

tag: cell line

tag: transfection


title: siNT-2_HG-U133A+2


title: Control_5_M

description: Control for medial replicate 4


title: NAc, Caudate, and Putamen [1455C]

value: Caudate

value: HWFTVBGXC

tag: ph

tag: tissuestoragetime


title: Mutant_1_M

description: Mutant for medial replicate 1


title: Control_4_M

description: Control for medial replicate 3


title: MM-1

value: MM

value: Bone marrow plasma cells


title: SMM-7


title: NAc, Caudate, and Putamen [1420C]

tag: age

tag: manner of death


title: NAc, Caudate, and Putamen [1394C]

tag: gender

tag: tissue

value: Natural


title: M10

city: Beijing

first: Mengling

address: No. 2 Yuanmingyuan West Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

data_processing:
Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
All identical sequences of sizes ranging from 18 to 32 nt were counted and eliminated from the initial data set. Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) was used to annotate the chromosomal location against the reference genome data.
Through a BLAST search of the miRbase, version 22.0 (http://www.mirbase.org/), the perfectly matched sequences were used to count and analyze the known miRNA expression profile. Then the assembled unique sequences were used for a BLAST search of the Rfam database, version 12.3 (http://rfam.sanger.ac.uk/), to remove non-miRNA sequences (rRNA, tRNA, snoRNA, etc.).
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miRDeep2 were integrated to predict novel miRNA. At the same time, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.
The expression level of each miRNA was calculated according to the transcripts per million reads (TPM) method. Significant differently expressed (DE) miRNAs were extracted with |log2FC| >1 and P adjust < 0.05 by edgeR.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Bos taurus

source_name: milk

extract_protocol:
Small RNA was extracted from milk EVs using the miRNeasy Mini kit (Qiagen)，3 ug of total RNA was used for the construction of sequencing libraries.
3μg of total RNA was ligated with sequencing adapters with TruseqTM Small RNA sample prep Kit (Illumina, San Diego, CA, USA).

value: milk

tag: group

value: clinical

value: extracellular vesicles


title: M9


title: Control_3_M

description: Control for medial replicate 2


title: M6


title: Control_2_M

description: Control for medial replicate 1


title: SMM-5


title: M5


title: SMM-8


title: SMM-4


title: Mutant_2_D

description: Mutant for dorsal replicate 2

value: dorsal cortex


title: NAc, Caudate, and Putamen [1374C]

value: Male

tag: race

value: White

tag: pmi

tag: disease state

value: match control


title: SMM-2

value: SMM


title: NAc, Caudate, and Putamen [1371C]

value: Black

tag: sequence id

tag: library size


title: NAc, Caudate, and Putamen [1372C]

tag: rin

tag: bmi

value: Accidental


title: Mutant_3_D

description: Mutant for dorsal replicate 3

tag: treatment

value: Mutant


title: M4

tag: cell type


title: SMM-3

tag: diagnosis


title: Mutant_4_D

description: Mutant for dorsal replicate 4


title: NAc, Caudate, and Putamen [1341C]

value: Female

tag: ph


title: SMM-6


title: Control_6_D

description: Control for dorsal replicate 6

value: Control


title: M3


title: M1


title: NAc, Caudate, and Putamen [1391C]

value: Caudate

tag: tissuestoragetime


title: NAc, Caudate, and Putamen [1326C]

tag: age


title: SM8

value: subclinical


title: Control_5_D

description: Control for dorsal replicate 5


title: NAc, Caudate, and Putamen [1318C]

value: HWHWTBGXC

tag: manner of death


title: SM6


title: SM5


title: Control_4_D

description: Control for dorsal replicate 4


title: MGUS-4

value: MGUS

value: Bone marrow plasma cells


title: NAc, Caudate, and Putamen [13175C]

tag: gender

value: Natural


title: MGUS-5


title: NAc, Caudate, and Putamen [13149C]

tag: tissue


title: SMM-1


title: Control_3_D

description: Control for dorsal replicate 3


title: SM4

value: milk

tag: group

value: extracellular vesicles


title: NAc, Caudate, and Putamen [13112C]

value: Male

tag: race


title: MGUS-3


title: Control_2_D

description: Control for dorsal replicate 2

value: dorsal cortex


title: MGUS-6


title: SM2


title: Mutant_1_D

description: Mutant for dorsal replicate 1


title: ovary tissue-BNC1-treated

library_source: genomic

data_processing:
Raw reads were first pre-processed by skewer(Version 0.2.2),  which filtered the low quality reads whose N content >=15% and mean quality score <=30. Meanwhile it removed the adapter at the 3’ end of read and filtered the reads whose length <50 after trimed.
Filtered reads were mapped to the genome by Bowtie2.
peaks were called using MACS(version 2.1.0).A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Overlap genes and annotatation genomic region of the peak. And then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected.Gene function and signaling pathway enrichment analysis using GO and KEGG database. The significantly enriched pathways were determined when P < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: ovary

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Preparation of the sequencing libraries of the DNA samples from IP and inputs was precisely followed the instructions of Illumina at Genergy Biotechnology Microarray Core Facility.   Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

tag: strain

value: C57BL/6 J

value: ovary

value: 8-weeks old

tag: genotype

value: wild type

tag: chip antibody


title: ovary tissue-input DNA


title: NAc, Caudate, and Putamen [13069C]

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

value: HWGNVBGXC

tag: library size


title: SM1

tag: cell type


title: NAc, Caudate, and Putamen [13045C]

value: Female

value: Caudate

tag: rin

tag: bmi

value: Undetermined


title: 4T1-GMP

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: experimental

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed with adaptor sequence using cutadapt v1.2.1  and mapped to mm10 reference with corresponding RefGene GTF annotation using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and RPKM estimation using edgeR_3.12.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with RPKM values of each sample

source_name: bone marrow

growth_protocol: cells purified by flow cytometry directly from bone marrow of the indicated groups

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 groups of mice:  1) non-tumor-bearing  (NTB) control; 2) mice orthotopically implanted with 4T1 mammary tumor cells (4T1-TB)

tag: mouse model

value: female 4T1 tumor-bearing mice

tag: mouse background

value: F1 semi-syngeneic (H-2b/d)


title: NAc, Caudate, and Putamen [13071C]

tag: age

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Accidental


title: MGUS-2

tag: diagnosis

value: MGUS

value: Bone marrow plasma cells


title: NBM-7

value: NBM (healthy control)


title: MGUS-1


title: NBM-8


title: H5

tag: tissue

value: milk

tag: group

value: healthy

value: extracellular vesicles


title: H9


title: NAc, Caudate, and Putamen [13068C]

tag: gender

value: Male

tag: race

value: Natural


title: NAc, Caudate, and Putamen [13017C]

value: White

tag: pmi

tag: disease state


title: NBM-11


title: NTB-GMP

description: control

value: female non-tumor-bearing mice


title: Fasted, neuronal, replicate 3

city: Cambridge

first: Ian

middle: Gordon

last: McLachlan

address: 77 Massachusetts Ave, 46-4243

department: Brain and Cognitive Sciences

institute: MIT

data_processing:
Reads pseudoaligned to genome and quantified for transcript abundance with kallisto.
Assembly: WBcel235
Supplementary files format and content: HDF5 binary files containing run info, abundance esimates, bootstrap estimates, and transcript length information.

organism: Caenorhabditis elegans

source_name: neuronal

growth_protocol: Animal growth on enriched peptone NGM plates

extract_protocol:
RNA collected via Agilent Absolutely RNA Nanoprep Kit and Clontech SMART-Seq v2 Low Input RNA kit
Illumina Nextera XT library preparation

treatment_protocol: Whole-animal samples directly lysed, neuronal ribotag samples were processed via HA-antibody ribotagging

value: neuronal

tag: treatment

value: fasted


title: NBM-10

tag: cell type


title: H4


title: NAc, Caudate, and Putamen [1298C]

value: Caudate

value: match control

tag: sequence id

tag: library size

tag: rin


title: H6


title: SM3

value: subclinical


title: ovary tissue-H3K4me3

tag: strain

value: C57BL/6 J

value: ovary

value: 8-weeks old

tag: genotype

value: wild type

tag: chip antibody

value: H3K4me3(Abcam, ab8580)


title: H3

value: milk


title: Control_1_D

description: Control for dorsal replicate 1

value: dorsal cortex

value: Control


title: NBM-3

value: NBM (healthy control)

value: Bone marrow plasma cells


title: H2

value: healthy

value: extracellular vesicles


title: Fed, neuronal, replicate 3

value: neuronal

value: fed


title: NAc, Caudate, and Putamen [1296C]

tag: age

value: Male

value: Caudate

value: White

tag: bmi

tag: ph

tag: tissuestoragetime

value: Natural


title: Fasted, whole-animal, replicate 3

source_name: whole-animal

tag: tissue

value: whole-animal

value: fasted


title: NAc, Caudate, and Putamen [13032C]

tag: gender

value: match control

tag: manner of death


title: H1

tag: group


title: NBM-6

tag: diagnosis


title: NAc, Caudate, and Putamen [1268C]

tag: race

value: Black

tag: pmi

tag: disease state

value: HWHWTBGXC


title: NBM-2

tag: cell type


title: U36: upstream24

city: Milwaukee

first: Rebecca

last: Klaper

state: WI

address: 600 E Greenfield Avenue

institute: University of Wisconsin - Milwaukee

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence data was quality-assessed using FastQC v0.11.5
Illumina TruSeq 3’-anchored primers were clipped using Cutadapt v1.18
Quality-controlled data was pseudoaligned and sample-quantified against the GCF_016745375.1 GenBank release of the fathead minnow reference genome using Kallisto v0.45.0
Genome_build: reference genome
Supplementary_files_format_and_content: estimated counts, tsv text

organism: Pimephales promelas

source_name: adult

growth_protocol: Fish were fed TetraMin Tropical Flakes twice a day and were maintained at a 16:8 h light:dark cycle. Tanks were kept at 19-23° C.

extract_protocol:
Brain tissues were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 96 h exposure 100 m upstream and 100 m downstream of effluent outfall

tag: Sex

value: male

value: WT

value: wild type

value: brain

tag: treatment

value: upstream exposure

value: adult

tag: exposure


title: Fed, whole-animal, replicate 3


title: NBM-4

value: NBM (healthy control)

value: Bone marrow plasma cells


title: NAc, Caudate, and Putamen [1247C]

value: Female

tag: sequence id

tag: library size

tag: rin


title: NAc, Caudate, and Putamen [1244C]

tag: age

value: Male

value: Caudate

value: HWGNVBGXC

tag: bmi

tag: ph

value: Accidental


title: NAc, Caudate, and Putamen [1211C]

tag: gender

tag: tissue

value: White

value: HWFTVBGXC

tag: tissuestoragetime

value: Natural


title: Fed, neuronal, replicate 2

value: neuronal

value: fed


title: U937_DAC+ATRA_3_ATAC

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

description: AML cell line U937 treated with DAC+ATRA for 72 h, replicate 3

data_processing:
read quality was checked with FastQC (≥95% >Q35)
alignment to the GRCh38/hg38 assembly was performed with Bowtie2
PCR duplicates were removed with MarkDuplicates
narrow peaks were called using MACS2 (FDR<0.05)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of called narrow peaks (in triplicates of each condition)

source_name: AML cell line

growth_protocol: Cell were cultured in RPMI supplemented with 20 % FCS and 1 % penicillin/streptomycin.

extract_protocol:
see below
For ATAC-sequencing (ATAC-seq), 50.000 fresh cells were processed in triplicates as described in the Omni-ATAC protocol by Corces et al. Size selection and purification was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA). Paired-end libraries were sequenced with 40 million read/sample.

treatment_protocol: Cells were either untreated or treated with 200 nM DAC ± 1 µM ATRA for 3 consecutive days, with daily medium changes and fresh administration of DAC.

value: AML cell line

tag: cell line

value: 200 nM decitabine + 1 uM ATRA


title: NBM-1

tag: diagnosis


title: U35: upstream23

value: female

tag: strain

value: WT

tag: genotype

value: wild type

value: brain


title: U937_DAC+ATRA_2_ATAC

description: AML cell line U937 treated with DAC+ATRA for 72 h, replicate 2


title: U937_DAC+ATRA_1_ATAC

description: AML cell line U937 treated with DAC+ATRA for 72 h, replicate 1


title: Fasted, whole-animal, replicate 2

value: whole-animal

value: fasted


title: U29: upstream20

value: male

value: upstream exposure

value: adult


title: Fed, whole-animal, replicate 2


title: NAc, Caudate, and Putamen [1207C]

value: Male

value: Caudate

tag: race

tag: pmi

tag: disease state

tag: manner of death


title: U27: upstream19

tag: Sex

tag: treatment

tag: exposure


title: Fed, neuronal, replicate 1


title: NAc, Caudate, and Putamen [1255C]

tag: age

value: Black

value: match control

tag: sequence id

tag: library size

tag: rin

value: Accidental


title: Fasted, neuronal, replicate 1

tag: tissue

value: neuronal


title: U26: upstream18


title: NAc, Caudate, and Putamen [1196C]

tag: gender

value: Female

value: White

tag: bmi

tag: ph

tag: tissuestoragetime


title: U34: upstream22

value: female

tag: strain

tag: genotype


title: NAc, Caudate, and Putamen [1188C]

tag: race

tag: pmi

value: HWGYMBGXC

value: Natural


title: U937_DAC_3_ATAC

description: AML cell line U937 treated with DAC for 72 h, replicate 3

value: AML cell line

tag: cell line

value: 200 nM decitabine


title: Fasted, whole-animal, replicate 1

value: whole-animal

value: fasted


title: U25: upstream17

tag: Sex

value: male

value: WT

value: wild type

value: brain

value: upstream exposure


title: U937_ATRA_1_ATAC

description: AML cell line U937 treated with ATRA for 72 h, replicate 1

tag: treatment

value: 1 uM ATRA


title: NAc, Caudate, and Putamen [1195C]

value: Male

value: Caudate

tag: disease state

tag: manner of death


title: U937_DAC_2_ATAC

description: AML cell line U937 treated with DAC for 72 h, replicate 2


title: U24: upstream16

tag: age

value: adult

tag: exposure


title: U31: upstream21


title: NAc, Caudate, and Putamen [1178C]

value: Female

value: Black

tag: sequence id

tag: library size

tag: rin


title: U937_ATRA_3_ATAC

description: AML cell line U937 treated with ATRA for 72 h, replicate 3

tag: tissue


title: Fed, whole-animal, replicate 1

value: fed


title: U937_DAC_1_ATAC

description: AML cell line U937 treated with DAC for 72 h, replicate 1


title: 6months_Control_rep4

city: Dunedin

first: Paulomi

middle: M

last: Mehta

state: Otago

address: 56 Hanover street

department: Department of Pathology

country: New Zealand

institute: University of Otago

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt (v 0.2.6) then mapped to Rnor6.0 whole genome using hisat2 v2.1.0 with parameters -p 4 -x
Aligned reads were counted by exon and summarized by gene using featureCounts (v2.0.0). The number of reads counts were normalised by the size of the library after variance stabilisation transformation (VST) and then differental gene analysis were perfromed between treatment groups for each time point individually using alpha of 0.5 and 'contrast' argument by Deseq2.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: raw counts matrix generated by featureCounts
Supplementary_files_format_and_content: DESeq2 derived abundance measurements for each comparison for all time points

organism: Rattus norvegicus

source_name: Kidney cortex

extract_protocol:
Kidney were removed, flash frozen with RNA later (cat#AM7021) and RNA was extracted using Trizol reagent and PureLink RNA mini kit (cat#12183018A) . Illumina TruSeq Stranded mRNA IDT for Illumina Unique Dual Indexing (cat#20020591) was used with 500ng/ul of total RNA for sequencing and Nanostring nCounter quantification ( only 6 months data).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats treated with lithium (60 mM Lithium carbonate in chow food), lithium+amiloirde (0.2 mM amiloirde in drinking water) or control (chow food) for 14 days, 28 days and 6 months.

value: Kidney cortex

value: wistar

value: Control

tag: length of treatment/study

value: 6 months


title: U22: upstream15


title: NAc, Caudate, and Putamen [1171C]

extract_protocol:
Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepped for RNA-sequencing using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). 75bp paired-end dual-indexed sequencing was performed using the NextSeq 500 platform (Illumina, San Diego, CA).

tag: gender

value: White

value: match control

value: HWFTVBGXC

tag: bmi

tag: ph

tag: tissuestoragetime

value: Natural


title: U937_ATRA_2_ATAC

description: AML cell line U937 treated with ATRA for 72 h, replicate 2

value: AML cell line


title: NAc, Caudate, and Putamen [1121C]

tag: race

tag: pmi


title: NAc, Caudate, and Putamen [1159C]

value: HWGYMBGXC


title: 6months_Control_rep3

tag: Sex

value: male

tag: strain


title: U17: upstream13

value: WT

tag: genotype

value: wild type

value: brain

tag: treatment

value: upstream exposure


title: U21: upstream14

value: female

tag: age

value: adult


title: NAc, Caudate, and Putamen [1105C]

value: Male

value: Caudate

tag: disease state

value: HWGNVBGXC

tag: manner of death


title: U937_untreated_2_ATAC

description: AML cell line U937 untreated 96 h, replicate 2

tag: cell line

value: untreated


title: U16: upstream12

tag: exposure


title: U15: upstream11

tag: tissue


title: 6months_Control_rep2

value: Kidney cortex

value: wistar

value: Control

tag: length of treatment/study

value: 6 months


title: NAc, Caudate, and Putamen [1099C]

tag: gender

value: Female

value: White

value: match control

tag: sequence id

tag: library size

tag: rin

value: Natural


title: 6months_Control_rep1

value: male


title: NAc, Caudate, and Putamen [1092C]

tag: race

value: Black

value: HWGYMBGXC

tag: bmi

tag: ph

tag: tissuestoragetime


title: U14: upstream10

tag: Sex

value: female

tag: strain

value: WT

tag: genotype

value: wild type

value: brain

value: upstream exposure


title: Fasted, neuronal, replicate 2

value: neuronal

tag: treatment

value: fasted


title: 6months_Lithium+Amiloride_rep4

value: Kidney cortex

value: wistar

value: Lithium+Amiloride


title: U937_DAC+ATRA_3

data_processing:
Read quality was determined by FastQC (all samples Q>32)
Alignment to reference genome (hg38) was performed with RNA STAR.
Counting of reads was performed with htseq-count (Mode: Intersection (nonempty), Stranded:reverse).
Differential expression analysis in each cell line was performed with DESeq2 (Factor levels: treatment versus ctrl, Type of fitting of dispersions to the mean intensity: parametric)
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix as tab-delimited .txt file, generated by DESeq2, with normalized read counts for every transcript in every samples.

growth_protocol: Cell were cultured in RPMI supplemented with 20 % FCS, 1 % penicillin/streptomycin and 5 ng/ml human GM-CSF.

extract_protocol:
Total RNA was extracted using the Macherey-Nagel NucleoSpin RNA Kit according to manufacturer's protocol. Concentration was measured with the Invitrogen Qubit Fluorometer and RNA integrity was determined using an Agilent TapeStation 2200 and the corresponding RNA Screen Tapes and reagents.
Total RNA was depleted for ribosomal RNA and paired-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit accoding to manufacturer's protocol.

tag: cell type

value: AML cell line

value: 200 nM decitabine + 1 microM ATRA


title: 6months_Lithium+Amiloride_rep3

value: 6 months


title: U937_ATRA_3

tag: cell line

value: 1 microM ATRA


title: U937_DAC+ATRA_2


title: U937_untreated_1_ATAC

description: AML cell line U937 untreated 96 h, replicate 1

value: untreated


title: U937_untreated_3_ATAC

description: AML cell line U937 untreated 96 h, replicate 3


title: 6months_Lithium+Amiloride_rep2

value: male


title: 6months_Lithium_rep3

value: Lithium


title: U13: upstream9

tag: age

value: adult

tag: exposure


title: U9: upstream6

value: female

value: WT

tag: tissue


title: NAc, Caudate, and Putamen [1044C]

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment with HISAT2
Read counts using HTSeq
Assembly: Ensembl GRh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

tag: gender

value: Female

value: Caudate

value: White

tag: pmi

tag: disease state

tag: manner of death

value: Natural


title: U937_DAC+ATRA_1


title: 6months_Lithium+Amiloride_rep1

value: Kidney cortex

tag: length of treatment/study


title: NAc, Caudate, and Putamen [1088C]

value: Male

tag: race

tag: sequence id

tag: library size

tag: rin

tag: bmi

value: Accidental


title: NAc, Caudate, and Putamen [1069C]

tag: ph

tag: tissuestoragetime


title: U10: upstream7

tag: Sex

tag: strain

tag: genotype

value: wild type

value: brain

tag: treatment

value: upstream exposure


title: U11: upstream8

tag: tissue

tag: age

tag: exposure


title: U937_ATRA_2

tag: cell type

value: AML cell line

tag: cell line

value: 1 microM ATRA


title: 6months_Lithium_rep4

value: male

value: wistar

tag: length of treatment/study

value: 6 months


title: U4: upstream4

value: female

value: adult


title: NAc, Caudate, and Putamen [1067C]

tag: gender

tag: race

tag: pmi

tag: disease state

value: match control

tag: manner of death


title: U937_DAC_2

value: 200 nM decitabine


title: NAc, Caudate, and Putamen [1034C]

value: Female

value: Caudate

value: White

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph


title: NAc, Caudate, and Putamen [10023C]

value: Black

tag: tissuestoragetime

value: Suicide


title: 6months_Lithium_rep2

tag: tissue

value: Kidney cortex

tag: Sex

tag: strain

tag: treatment

value: Lithium


title: U937_ATRA_1

tag: cell type

tag: cell line


title: U937_DAC_3


title: day28_Lithium+Amiloride_rep5

description: raw_counts_matrix_28 days.xlsx

value: Lithium+Amiloride

tag: length of treatment/study

value: 28 days


title: U2: upstream2

value: WT

tag: genotype

value: wild type

value: brain

value: upstream exposure

tag: age

tag: exposure


title: NAc, Caudate, and Putamen [10003C]

tag: gender

value: Male

tag: race

tag: pmi

tag: disease state

value: HFYWVBGXF

tag: manner of death

value: Accidental


title: U6: upstream5

value: male

value: adult


title: day28_Lithium+Amiloride_rep3

description: raw_counts_matrix_28 days.xlsx

value: wistar


title: day28_Lithium+Amiloride_rep2

description: raw_counts_matrix_28 days.xlsx


title: 6months_Lithium_rep1

value: 6 months


title: NAc, Caudate, and Putamen [933N]

source_name: Nac

value: Nac

value: White

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

value: Natural


title: U937_untreated_2

value: AML cell line

tag: treatment

value: untreated


title: U937_untreated_3

tag: cell type


title: U3: upstream3

tag: Sex

tag: strain

tag: tissue


title: D34: downstream24

value: female

tag: genotype

value: downstream exposure

tag: age


title: NAc, Caudate, and Putamen [931N]

tag: gender

value: Female

tag: tissuestoragetime


title: U937_untreated_1

tag: cell line


title: NAc, Caudate, and Putamen [10025C]

source_name: Caudate

value: Caudate

tag: race

value: Black

tag: pmi

tag: disease state


title: U1: upstream1

value: WT

value: wild type

value: brain

value: upstream exposure

tag: exposure


title: day28_Lithium_rep6

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex

value: male

value: Lithium

tag: length of treatment/study

value: 28 days


title: MOLM-13_DAC+ATRA_3

description: AML cell line MOLM-13 treated with DAC+ATRA for 72 h, replicate 3

treatment_protocol: Cells were either untreated or treated with 100 nM DAC ± 1 µM ATRA for 3 consecutive days, with daily medium changes and fresh administration of DAC.

value: 100 nM decitabine + 1 µM ATRA


title: U937_DAC_1

value: 200 nM decitabine


title: day28_Lithium+Amiloride_rep4

description: raw_counts_matrix_28 days.xlsx

value: wistar

value: Lithium+Amiloride


title: D32: downstream23

value: adult


title: day28_Lithium+Amiloride_rep1

description: raw_counts_matrix_28 days.xlsx


title: NAc, Caudate, and Putamen [878N]

value: Male

value: Nac

value: White

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: manner of death

value: Natural


title: MOLM-13_DAC+ATRA_2

description: AML cell line MOLM-13 treated with DAC+ATRA for 72 h, replicate 2

value: AML cell line

tag: treatment


title: D31: downstream22

tag: Sex

tag: strain

value: WT

value: wild type

tag: tissue

value: downstream exposure


title: NAc, Caudate, and Putamen [930N]

tag: age

tag: gender

tag: ph


title: day28_Lithium_rep5

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex


title: D30: downstream21

value: female

tag: genotype

value: brain


title: MOLM-13_DAC+ATRA_1

description: AML cell line MOLM-13 treated with DAC+ATRA for 72 h, replicate 1

tag: cell line


title: NAc, Caudate, and Putamen [843N]

value: Female

tag: race

tag: pmi

tag: disease state

tag: tissuestoragetime

value: Suicide


title: NAc, Caudate, and Putamen [822N]

value: Black

value: match control

tag: sequence id

tag: library size


title: D29: downstream20

tag: exposure


title: NAc, Caudate, and Putamen [787N]

tag: rin

tag: bmi

tag: manner of death


title: MOLM-13_ATRA_3

description: AML cell line MOLM-13 treated with ATRA for 72 h, replicate 3

tag: treatment

value: 1 µM ATRA


title: MOLM-13_ATRA_2

description: AML cell line MOLM-13 treated with ATRA for 72 h, replicate 2

tag: tissue


title: day28_Lithium_rep3

description: raw_counts_matrix_28 days.xlsx

tag: Sex

value: male

tag: strain

value: wistar

value: Lithium

tag: length of treatment/study

value: 28 days


title: D28: downstream19

tag: genotype

tag: age

value: adult


title: day28_Lithium_rep4

description: raw_counts_matrix_28 days.xlsx


title: D27: downstream18


title: day28_Lithium_rep2

description: raw_counts_matrix_28 days.xlsx


title: NAc, Caudate, and Putamen [739N]

tag: gender

value: Male

value: Nac

tag: race

value: White

tag: ph

value: Natural


title: MOLM-13_ATRA_1

description: AML cell line MOLM-13 treated with ATRA for 72 h, replicate 1

value: AML cell line

tag: cell line


title: MOLM-13_DAC_3

description: AML cell line MOLM-13 treated with DAC for 72 h, replicate 3

value: 100 nM decitabine


title: day28_Lithium_rep1

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex


title: D26: downstream17

value: female

value: WT

value: wild type

value: brain

value: downstream exposure


title: NAc, Caudate, and Putamen [722N]

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: tissuestoragetime


title: NAc, Caudate, and Putamen [700N]

value: match control

tag: library size

tag: rin

tag: bmi


title: day28_Control_rep6

description: raw_counts_matrix_28 days.xlsx

tag: tissue

value: male

value: wistar

tag: treatment

value: Control


title: D20: downstream16

tag: Sex

tag: strain

value: adult

tag: exposure


title: MOLM-13_DAC_2

description: AML cell line MOLM-13 treated with DAC for 72 h, replicate 2


title: NAc, Caudate, and Putamen [697N]

tag: age

value: Male

value: Nac

tag: manner of death

value: Suicide


title: D19: downstream15

tag: genotype


title: MOLM-13_DAC_1

description: AML cell line MOLM-13 treated with DAC for 72 h, replicate 1

value: AML cell line


title: NAc, Caudate, and Putamen [656N]

tag: gender

value: Female

tag: race

tag: ph


title: day28_Control_rep5

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex

tag: length of treatment/study

value: 28 days


title: D18: downstream14

value: female

value: WT


title: day28_Control_rep4

description: raw_counts_matrix_28 days.xlsx


title: MOLM-13_untreated_3

description: AML cell line MOLM-13 untreated 96 h, replicate 3

tag: cell line

value: untreated


title: D17: downstream13

description: D17: this sample had an insufficient number of reads to be included in the differential expression analysis and is therefore not present in any of the processed data files

value: wild type

value: brain

value: downstream exposure


title: NAc, Caudate, and Putamen [694N]

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: tissuestoragetime

value: Natural


title: day28_Control_rep3

description: raw_counts_matrix_28 days.xlsx

tag: tissue

value: male

value: wistar

value: Control


title: D16: downstream12

tag: treatment

value: adult


title: NAc, Caudate, and Putamen [604N]

value: Male

value: Nac

tag: library size

tag: rin

tag: bmi


title: NAc, Caudate, and Putamen [625N]

tag: age

value: Black


title: MOLM-13_untreated_1

description: AML cell line MOLM-13 untreated 96 h, replicate 1

value: AML cell line


title: D15: downstream11

tag: Sex

tag: strain

tag: exposure


title: MOLM-13_untreated_2

description: AML cell line MOLM-13 untreated 96 h, replicate 2


title: day28_Control_rep1

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex

value: 28 days


title: day14_Lithium+Amiloride_rep6

description: raw_counts_matrix_14 days.xlsx

value: Lithium+Amiloride

value: 14 days


title: NAc, Caudate, and Putamen [587N]

tag: gender

value: Female

tag: race

tag: manner of death


title: day14_Lithium+Amiloride_rep5

description: raw_counts_matrix_14 days.xlsx

tag: length of treatment/study


title: plko_S1

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: sample :RBMS1 knockdown

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: The gene expressiong matrix from RNA-seq

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in L15 medium containing 10% FBS and growed in the carbon dioxide free environment.

extract_protocol:
RNA samples were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We generated RBMS1 knockdown sample in MDA-MB-231 breast cancer cells

tag: cell type

value: human breast cancer cells

tag: cell line

tag: treated with

value: RBMS1 knocked down


title: D14: downstream10

value: female

value: WT

tag: genotype

value: wild type

value: brain

value: downstream exposure


title: plko_ctl

description: sample :RBMS1 knockdown ctrl

value: control


title: NAc, Caudate, and Putamen [1834N]

tag: tissue

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: ph

tag: tissuestoragetime

value: Undetermined


title: NAc, Caudate, and Putamen [1807N]

tag: age

value: Male

value: Nac

value: Black

tag: library size

tag: rin

tag: bmi

value: Suicide


title: D11: downstream8

tag: Sex

tag: strain

tag: treatment

value: adult

tag: exposure


title: D9: downstream7

value: male


title: day28_Control_rep2

description: raw_counts_matrix_28 days.xlsx

value: Kidney cortex

value: wistar

value: Control

tag: length of treatment/study

value: 28 days


title: NAc, Caudate, and Putamen [1687N]

tag: gender

tag: race

value: White

tag: manner of death

value: Natural


title: day14_Lithium+Amiloride_rep2

description: raw_counts_matrix_14 days.xlsx

tag: tissue

value: Lithium+Amiloride

value: 14 days


title: D8: downstream6

value: female

value: WT

tag: genotype

value: wild type

value: brain

value: downstream exposure


title: day14_Lithium+Amiloride_rep1

description: raw_counts_matrix_14 days.xlsx


title: day14_Lithium+Amiloride_rep4

description: raw_counts_matrix_14 days.xlsx


title: NAc, Caudate, and Putamen [1605N]

value: Female

value: Nac

tag: pmi

tag: disease state

value: match control

tag: sequence id


title: day14_Lithium_rep6

description: raw_counts_matrix_14 days.xlsx

value: male

value: Lithium


title: D7: downstream5

tag: age

value: adult


title: NAc, Caudate, and Putamen [1686N]

value: Male

value: Black

tag: library size

tag: ph

tag: tissuestoragetime


title: D5: downstream3

tag: Sex


title: NAc, Caudate, and Putamen [1789N]

value: White

tag: rin

tag: bmi


title: day14_Lithium_rep5

description: raw_counts_matrix_14 days.xlsx

value: Kidney cortex

tag: strain

value: wistar

tag: treatment


title: NAc, Caudate, and Putamen [1598N]

tag: gender

value: Natural


title: D6: downstream4

tag: exposure


title: D13: downstream9


title: D3: downstream2

value: female


title: day14_Lithium_rep3

description: raw_counts_matrix_14 days.xlsx

tag: length of treatment/study

value: 14 days


title: NAc, Caudate, and Putamen [1581N]

tag: tissue

tag: race

tag: manner of death


title: NAc, Caudate, and Putamen [1543N]

tag: pmi

tag: disease state


title: D2: downstream1

value: WT

tag: genotype

value: wild type

tag: age


title: C24: control16

value: brain

value: untreated


title: day14_Lithium_rep2

description: raw_counts_matrix_14 days.xlsx


title: NAc, Caudate, and Putamen [1518N]

value: Nac

tag: sequence id

tag: library size

tag: ph


title: day14_Lithium+Amiloride_rep3

description: raw_counts_matrix_14 days.xlsx

tag: Sex

value: Lithium+Amiloride


title: H375A SSU Processome rep_4 DMS

city: Jupiter

first: xin

last: liu

state: FL

address: 130 Scripps Way

institute: The Scripps Research

data_processing:
Library strategy: DMS-MaPseq
removing adaptors with skewer
trimming reads with seqtk
running shapemapper aligning to 35S rRNA
… S.c.35S_rRNA_profile.txt were extracted for further analysis.
Supplementary_files_format_and_content: Extract "Modified_effective_depth" and "modified_rate" of each nucleotide for further analysis.

organism: Saccharomyces cerevisiae

source_name: ribosome SSU Processome intermediate

growth_protocol: Cells were grown in YPD till mid-log phase before harvesting.

extract_protocol:
Phenol chloroform  precipitation
RNA-seq (DMS-MaPseq)

treatment_protocol: 1% DMS, 30°C, 5min

value: treated

tag: molecule subtype

value: ribosomal RNA


title: H375A SSU Processome rep_4 NC


title: NAc, Caudate, and Putamen [1455N]

tag: rin

tag: bmi

tag: tissuestoragetime


title: day14_Lithium_rep1

description: raw_counts_matrix_14 days.xlsx

value: male

tag: strain

tag: treatment

value: Lithium


title: C23: control15

tag: tissue

value: adult

tag: exposure


title: H375A SSU Processome rep_3 DMS


title: day14_Control_rep6

description: raw_counts_matrix_14 days.xlsx

value: Control

tag: length of treatment/study


title: day14_Lithium_rep4

description: raw_counts_matrix_14 days.xlsx

value: Kidney cortex


title: C22: control14


title: NAc, Caudate, and Putamen [1420N]

tag: gender

value: Male

tag: race

value: White

tag: pmi

tag: manner of death

value: Suicide


title: H375A SSU Processome rep_3 NC

tag: genotype


title: NAc, Caudate, and Putamen [1394N]

tag: age

tag: disease state

value: match control

tag: sequence id

tag: library size

value: Natural


title: H375A SSU Processome rep_2 DMS

tag: molecule subtype


title: day14_Control_rep4

description: raw_counts_matrix_14 days.xlsx

tag: Sex

value: wistar

value: 14 days


title: C18: control13

value: WT

value: wild type

value: brain

value: untreated


title: day14_Control_rep5

description: raw_counts_matrix_14 days.xlsx


title: NAc, Caudate, and Putamen [1374N]

value: Nac

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: day14_Control_rep3

description: raw_counts_matrix_14 days.xlsx

tag: tissue

value: male

tag: strain

tag: treatment


title: NAc, Caudate, and Putamen [1391N]

tag: gender

value: Female

tag: race


title: H375A SSU Processome rep_2 NC

value: ribosomal RNA


title: H375A SSU Processome rep_1 DMS

value: treated


title: C14: control11

value: adult

tag: exposure


title: C15: control12

value: female

tag: genotype


title: C13: control10

tag: age


title: day14_Control_rep2

description: raw_counts_matrix_14 days.xlsx

value: Kidney cortex

value: Control

tag: length of treatment/study


title: NAc, Caudate, and Putamen [1372N]

value: Male

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: manner of death

value: Accidental


title: day14_Control_rep1

description: raw_counts_matrix_14 days.xlsx

tag: Sex

value: wistar

value: 14 days


title: NAc, Caudate, and Putamen [1371N]

value: Black

tag: library size

tag: rin

tag: bmi

value: Natural


title: C12: control9

value: WT

value: wild type

tag: tissue

value: brain

value: untreated


title: H375A SSU Processome rep_1 NC

tag: molecule subtype

value: ribosomal RNA


title: NAc, Caudate, and Putamen [1341N]

value: Female

value: Nac

tag: ph

tag: tissuestoragetime


title: C10: control8

value: female

tag: strain

tag: treatment

value: adult


title: WT SSU Processome rep_4 NC

tag: genotype