title: H1944_A1186T_shNTC_R1 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: NT.T2_replicate 2

status: Public on Sep 10 2020

type: RNA

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

description: Corvina berries undergoing natural postharvest dehdration collected 33 days after harvest. It is the second of three biological replicates used in the study.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

molecule: total RNA

organism: Vitis vinifera

source_name: Corvina berries

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Grape bunches from Vitis vinifera L. cv. Corvina harvested during the 2011 vintage were grown in the Valpolicella region (Verona, north-east Italy) and collected at full commercial maturity. Approximately 200 kg of grape bunches were placed on wooden racks and stored for dehydration in Gargagnago di Sant’Ambrogio di Valpolicella, Italy (45◦31′20′′ N,10◦50′05′′ E). In the fruttaio, collected grapes were split into two dehydrating rooms where specific environmental conditions were set up to reproduce a natural (NT) and a forced (FR) dehydration process. Natural dehydration conditions were obtained as described in Zenoni et al. (2016). Forced dehydration conditions were obtained by using a fan close to the batch of grapes to promote a faster drying; in this way, FR grapes were exposed to an average airflow of about 1 m/s that in turn contributed to remove part of the humid air stacking around the clusters, almost without affecting temperature. Both drying processes were stopped when grapes reached ∼30% of the weight loss (i.e., after 120 and 65 days for NT and FR conditions, respectively).

extract_protocol: Total RNA extraction was performed from ~200 mg of berry tissue (pericarp without seeds) using the Spectrum Plant Total RNA kit (Sigma-Aldrich) as previously described (Fasoli et al., 2012).

tag: cultivar

value: Corvina

tag: year

tag: time point

value: 33 days after harvest

tag: treatment

value: natural postharvest dehdration


title: Day 6 Mature DC_Patient 12

city: Pittsburgh

first: Deena

middle: Marie

last: Maurer

address: 200 Lothrop Street

department: Immunology

country: USA

institute: University of Pittsburgh

description: Gene expression data from mDC, melanoma

hyb_protocol: the arrays were washed and stained on a GeneChip Fluidics Station 450

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control(all from Affymetrix, Santa Clara, CA).

data_processing: R/Bioconductor was used for the primary analysis. (Oligo & Limma Packages)

label: biotin

organism: Homo sapiens

source_name: Dendritic Cell, Melanoma

label_protocol: cDNAs were fragmented, biotinylated, and hybridized to the GeneChip Human Gene 2.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).

growth_protocol: Patient immature dendritic cells were generated from elutriated monocytes using GM-CSF and IL-4 for 5 days. On day 6, immature DC were matured using IFNG and LPS for 24hrs. 24hrs. Post-maturation, mDC were transduced with the adenovirus vaccine for 3hrs.

extract_protocol: Total RNA was extracted by using RNeasy kit (Qiagen, Germantown, , MD, USA). The RNA concentration was measured using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit).

treatment_protocol: Matured DC (mDC) were transduced with the recombinant Adenovirus vaccine (encoding three full length antigens: Tyrosinase, MART-1, MAGE-A6) for 3hrs at 37°C.

tag: subject id

value: Patient 12

tag: patient diagnosis

value: melanoma

tag: cell type

value: Dendritic Cell

tag: dc subtype

value: day 6 mDC

tag: clinical outcome

value: SD

tag: overall survival (months)


title: NT.T1_replicate 2

description: Corvina berries undergoing natural postharvest dehdration collected 22 days after harvest. It is the second of three biological replicates used in the study.

value: 22 days after harvest


title: Day 6 Mature DC_Patient 10

description: Gene expression data from monocyte-derived iDC, melanoma

value: Patient 10

value: day 5 iDC

value: PR


title: Day 5 Immature DC_Patient 9

value: Patient 9


title: NT.T2_replicate 3

description: Corvina berries undergoing natural postharvest dehdration collected 33 days after harvest. It is the third of three biological replicates used in the study.


title: H1944_G1162C_shSMARCA2_R1 (ATAC-seq)

type: SRA

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

library_source: genomic

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Genome_build: GRCh38
Supplementary_files_format_and_content: One bigWig file for each sample containing the normalized coverage in log counts per million

molecule: genomic DNA

source_name: NCI-H1944 cells

growth_protocol: RPMI 1640 supplemented with 10% FBS, 2 mM L-Glutamine and 100 U/mL penicillin-streptomycin

extract_protocol:
NCI-H1944 cells (100,000) transduced with LACZ, SMARCA4 WT or mutant were pelleted and resuspended in 50 mL cold ATAC-resuspension buffer (ATAC-RSB) (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% Igepal CA-630, 0.1% Tween-20 and 0.01% digitonin. Cells were incubated on ice for 3 min and lysis buffer was washed out using 1 mL cold ATAC-RSB containing 0.1% Tween-20. Cells were inverted several times and nuclei was pelleted at 500xg for 10 min at 4 °C. Supernatant was discarded and nuclei were resuspended in 50 μl transposition mixture (2.5 uL Tn5 transposase, 25uL 2x TD buffer, 16.5 uL PBS, 0.5 uL1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O). The transposase reaction was performed for 30 min at 37 °C in a thermomixer with 1000 rpm.
DNA was purified using the Qiagen MinElute purification kit. DNA libraries were PCR amplified using previously published protocols (PMID: 25559105; PMID: 28846090). The libraries were multiplexed and sequenced on Illumina HiSeq4000.

tag: cell line

value: lung cancer cell line NCI-H1944

tag: construct

value: Cells transduced with pLenti6.3-SMARCA4-G1162C, selected with 8ug/mL blasticidin for 5 days.

tag: hairpin

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

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

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: LSX

tag: Sex

value: male

tag: age

tag: strain


title: Day 6 Mature DC_Patient 11

description: Gene expression data from mDC, melanoma

value: Patient 11

value: PD


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad007


title: Day 5 Immature DC_Patient 8

value: Patient 8


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad006


title: H1944_G1162C_shNTC_R1 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: H1944_G1159V_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-G1159V, selected with 8ug/mL blasticidin for 5 days.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad010


title: T0_replicate 3

description: Corvina berries collected at harvest time. It is the third of three biological replicates used in the study.

tag: cultivar

value: Corvina


title: H1944_R1192C_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R1192C, selected with 8ug/mL blasticidin for 5 days.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad004


title: Day 5 Immature DC_Patient 7

value: Patient 7

value: melanoma

value: Dendritic Cell

value: SD


title: T0_replicate 2

description: Corvina berries collected at harvest time. It is the second of three biological replicates used in the study.

tag: year


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad002


title: NT.T1_replicate 1

description: Corvina berries undergoing natural postharvest dehdration collected 22 days after harvest. It is the first of three biological replicates used in the study.

tag: time point

value: 22 days after harvest

value: natural postharvest dehdration


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad012


title: Day 5 Immature DC_Patient 5

value: Patient 5

value: day 5 iDC


title: H1944_G1159V_shNTC_R1 (ATAC-seq)

value: lung cancer cell line NCI-H1944


title: Day 5 Immature DC_Patient 6

value: Patient 6


title: H1944_R1135W_shNTC_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R1135W, selected with 8ug/mL blasticidin for 5 days.


title: T0_replicate 1

description: Corvina berries collected at harvest time. It is the first of three biological replicates used in the study.


title: H1944_R1135W_shSMARCA2_R1 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: African Bush Elephant PBMC 14

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence with cuatadapt
STAR aligner
calculated expression counts with RSEM and FeatureCounts
Calculated differential expression with EdgeR
Genome_build: loxAfr3
Supplementary_files_format_and_content: BAM, RNA Expression Levels

organism: Loxodonta africana

source_name: Adult Female PBMC

extract_protocol:
Ficoll-Paque density gradient, 3 washes
Illumina TruSeq Stranded RNA kit with Ribo-Zero Gold

tag: tissue

value: PBMC

tag: gender

value: Female


title: 11_12_29_17_2L

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

data_processing: The alignment and quality control of RNA-Seq data followed the pipeline developed by The NCI's Genomic Data Commons(GDC,https://gdc.cancer.gov/). The quality assessment was performed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) on the pre-alignment and RNA-SeQC25 and Picard tools (http://broadinstitute.github.io/picard/) on the post-alignment. The sequence alignment was performed using a two-pass method using STAR226. Read Counts analysis were performed using SummarizedExperiment of DESeq227 and the count data normalized using BetweenLaneNormalization function of EDASeq28 using upper-quartile (UQ) normalization. The factors of unwanted variation were estimated using empirical control genes, e.g., least significantly differentially expressed (DE) genes based on a first-pass DE analysis performed prior to RUVg normalization29. Lastly, differential expression analysis was performed as implemented by DESeq2 by adding the factors of unwanted variation into design of DESeq2 in order to remove unwanted variation.

source_name: Brain Tumor

growth_protocol: Approximately 6x105 cells were implanted into the right frontal lobes of 6-8-week-old athymic Nu/Nu female mice obtained from Charles River Laboratories.  All applicable international, national, and or institutional guidelines for the care and use of animals were followed.  All procedures performed in studies involving animals were in accordance with the ethical standards of the institution at which the studies were conducted and approved by the Wake Forest Baptist Medical Center Institutional Animal Care and Use Committee (IACUC).  BTCOE 4795 was used as this cell line consistently formed tumors which on histology demonstrated necrosis and stained positive for HIF2aHIF2α. Mice were anesthetized with 0.1 mL/20g mouse weight IP ketamine/xylazine (87.5 mg/kg ketamine and 12.5 mg/kg xylazine) and placed on a small-animal head-holding frame.  A midline scalp incision exposed a burr-hole site 2-mm to the right and 1-mm anterior to lambda. A 27-gauge needle attached to a sterile Hamilton syringe (Hamilton, Reno, NV) was stereotactically inserted 3-mm below the cortical surface and cells were injected into the deep white matter in a volume of 7μL over 5 min.  The syringe was removed over an additional minute after completion of injection.  The scalp was closed with an interrupted 6-0 prolene suture. Mice recovered on a heating pad and returned to their cages after waking from anesthesia.  Treatments are detailed below. Brains of euthanized mice were collected and preserved in tissue-freezing medium (Triangle Biomedical Sciences, Durham, NC).

extract_protocol:
BTCOE 4795 tumor punches from extracted mouse brains (pathologist verified) were homogenized using the Bead Ruptor 24 (Omni International, Tulsa, OK).  Approximately 10 - 50 mg of tissue was placed into a 1.4 mm ceramic bead tube with 1 ml QIAzol lysis reagent. The tissue sample tube was processed on the Bead Ruptor for 1 cycle at a speed of 4.7 m/s for 20 sec. The homogenized lysates were extracted for total RNA using the RNeasy Microarray Tissue Mini kit (Qiagen, Venlo, Netherlands). Extracted RNA was DNase-treated and purified using the RNA Clean and Concentrator-5 kit (Zymo Research, Irvine, CA) and assessed for RNA quality using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).
Total RNA from 10 samples was used to prepare cDNA libraries using the Illumina® TruSeq Stranded Total RNA with Ribo-Zero Gold Preparation kit (Illumina Inc., San Diego, CA).  RIN values for the RNA samples ranged from 9.6 to 10. Briefly, 750 ng of total RNA was rRNA depleted followed by enzymatic fragmentation, reverse-transcription and double-stranded cDNA purification using AMPure XP magnetic beads. The cDNA was end repaired, 3′ adenylated, with Illumina sequencing adaptors ligated onto the fragment ends, and the stranded libraries were pre-amplified with PCR.  The library size distribution was validated, and quality inspected using a Fragment Analyzer (Advanced Analytical, Santa Clara, CA). The quantity of each cDNA library was measured using the Qubit 3.0 (Thermo Fisher, Waltham, MA). The libraries were pooled and sequenced to a target read depth of 40M reads per library using single-end (SE) 1X75bp sequencing on the Illumina NextSeq 500.

treatment_protocol: A stock solution of PT2385 was prepared in 30% PEG400, 10% ethanol, 0.5% tween80, and 0.5% methylcellulose.  PT2385 was administered 10 mg/kg PO BID in half the animals; the other half receiving vehicle treatment. As per company recommendations on dosing scheduled the drug was administered in 21 day on drug followed by 7 days off drug cycles repeated until endpoint met

tag: agent

value: Placebo

value: GBM Cells


title: H1944_R973L_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R973L, selected with 8ug/mL blasticidin for 5 days.


title: H1944_R973L_shNTC_R1 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: 10_12_29_17_2L

tag: cell type


title: African Bush Elephant PBMC 3


title: WT Colitis

city: Toyama

first: Shusaku

last: Hayashi

address: 2630 Sugitani

country: Japan

institute: University of Toyama

description: WT Colitis RNA sample was pooled from 3 mice with ear tag number 626, 647, & 641. Mice#626: body weight 78.0%; disease activity index 4; colon length 7.8 cm; mice#647: body weight 78.9%; disease activity index 3; colon length 8.2 cm; Mice #641: body weight 83.8%; disease activity index 4; colon length 8.0 cm.

hyb_protocol: A total of 0.6 ug of Cy3-labeled cRNA was fragmented at 60 ºC for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) at 65 ºC for 17 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature for 1 minute with GE Wash Buffer 1 (Agilent) and at 37 ºC for 1 minute with GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the GeneChip Scanner 3000 (Affymetrix)

data_processing: Gene expression was anlyzed using GeneChip Anlysis Suite Software (Affymetrix)

source_name: colon tissue

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1 ug total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent).

growth_protocol: WT and IL-4Ra-/- mice littermate were housed in the experimental animal facility at University of Toyama and were provided free access to food and water.

extract_protocol: Mice were sacrificed 7 days from the beginning of the DSS treatment, and distal colon tisues were collected. Total RNA was extracted using the RNeasy Total RNA Extraction kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Mice were treated with 3 % DSS in their drinking water for 7 days. Normal group received autoclave drinking water.

value: colon tissue

value: male

value: BALB/c

tag: day collected sample

value: day 7

tag: treatment

value: 3% DSS treated


title: WT Normal

description: WT Normal RNA sample was pooled from 4 mice with ear tag number 576, 580, 552, and 587. mice#576: Body weight 97.6%; disease activity index 0; colon length10.7cm ; mice#580: Body weight 103.5%; disease activity index 0; colon length 12.6cm; mice#552: body weight 101.9%; disease activity index 0; colon length 12.0 cm; mice#587: body weight 104.0%; disease activity index 0; colon length 10.5 cm.

value: water treated


title: African Bush Elephant PBMC 1


title: 9_12_29_17_2R


title: H1944_T910M_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-T910M, selected with 8ug/mL blasticidin for 5 days.


title: KO Colitis

description: KO Colitis RNA sample was pooled from 6 mice with ear tag number 634, 636, 637, 638, 639, and 643. Mice# 634: body weight 95.1%; disease activity index 1; colon length 10.0cm. Mice #636: body weight 95.3%; disease activity index 0; colon length 11.1cm. Mice #637: body weight 99.1%; disease activity index 0; colon length 10.4cm. Mice #638: body weight  97.3%; disease activity index 3; colon length 8.2cm. Mice #639: body weight 100.8% ; disease activity index 1; colon length 10.9cm. Mice #643: body weight  96.0%; disease activity index 1; colon length 11.3cm.


title: Day 5 Immature DC_Patient 33

tag: subject id

value: Patient 33

tag: patient diagnosis

value: melanoma

value: Dendritic Cell

tag: dc subtype

value: day 5 iDC

tag: clinical outcome

value: PD

tag: overall survival (months)


title: Day 5 Immature DC_Patient 4

value: Patient 4


title: Day 5 Immature DC_Patient 34

value: Patient 34

value: SD


title: Day 5 Immature DC_Patient 32

value: Patient 32


title: H1944_T910M_shNTC_R1 (ATAC-seq)

tag: cell line

value: lung cancer cell line NCI-H1944

tag: construct

tag: hairpin

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: 8_12_15_17_1R1L

value: Placebo

value: GBM Cells


title: African Bush Elephant PBMC 7

value: PBMC

value: Female


title: H1944_E882K_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-E882K, selected with 8ug/mL blasticidin for 5 days.

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: Day 5 Immature DC_Patient 31

value: Patient 31


title: VC48_2

city: Macau

first: wenwen

last: Zhang

address: University of Macau,  Avenida de Universidade, Taipa

country: Macau

institute: Zhang Wenwen

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  the V. parahaemolyticus RIMD2210633 genome  ( ASM19609v1) or C. elegans genome (WBcel235)using Tophat2 with the default parameterization, respectively
Reads aligned to annotated genes were quantified with the htseq-count program using gene annotations from Ensembl release 92
Determined uniquely mapped read counts were served as input to DESeq2 (version 1.14.1) for pairwise detection and quantification of differential gene expression with default parameterization (pmid 25516281)
Genome_build: V. parahaemolyticus RIMD2210633 genome  ( ASM19609v1) or C. elegans genome (WBcel235)
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample

organism:
Vibrio parahaemolyticus
Caenorhabditis elegans

source_name: Host and bacteria

extract_protocol:
Total RNA was then isolated from C. elegans containing bacteria using the mirVana kit (Ambion) following the user manual. The isolated total RNA was treated with DNase I (Fermentas) (0.25 U/1 μg of RNA) for 30 mins, followed by purification with ethanol. The Ribo-Zero Magnetic Gold Kit (Epidemiology) from Epicentre/Illumina was used to removed rRNA in the samples following the manufacturer’s instructions.
cDNA libraries for Illumina sequencing were constructed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) following the manufacture instruction. For organism dual RNA-Seq, ~ 100 ng rRNA-depleted RNA were used for cDNA library preparation

tag: strain

tag: genotype

value: WT

value: Whole organism


title: VC48_1


title: H1944_E882K_shNTC_R1 (ATAC-seq)


title: H1944_K785R_shSMARCA2_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-K785R, selected with 8ug/mL blasticidin for 5 days.


title: Day 5 Immature DC_Patient 30

value: Patient 30

value: melanoma

value: Dendritic Cell

value: day 5 iDC


title: 5_11_03_17_2L


title: VC36_3


title: H1944_T910M_shNTC_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-T910M, selected with 8ug/mL blasticidin for 5 days.


title: H1944_K785R_shNTC_R1 (ATAC-seq)

value: lung cancer cell line NCI-H1944


title: VC36_2


title: 7_10_19_17_1R1L


title: Day 5 Immature DC_Patient 35

value: Patient 35

value: SD


title: VC36_1


title: VC48_3


title: 2_10_19_17_2L

value: Placebo

value: GBM Cells


title: 3_10_06_17_2R


title: 6_10_29_17_1R1L


title: H1944_WT_shNTC_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-WT, selected with 8ug/mL blasticidin for 5 days.

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: VC24_3


title: VC24_2


title: Day 5 Immature DC_Patient 29

value: Patient 29


title: H1944_LACZ_shNTC_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-LACZ, selected with 8ug/mL blasticidin for 5 days.


title: VC24_1

value: WT


title: VC12_3

value: Whole organism


title: Day 5 Immature DC_Patient 27

value: Patient 27


title: Day 5 Immature DC_Patient 3

value: Patient 3

value: PD


title: Day 5 Immature DC_Patient 28

value: Patient 28

value: melanoma

value: Dendritic Cell


title: H1944_WT_shSMARCA2_R1 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: SAM24384965: Mlkl.C8.dko.dN4BP1.LPS.8h.BMDM

first: Rohit

last: Reja

institute: Genentech

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count and RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone Marrow

extract_protocol:
Bone marrow cells from femurs and tibia of wild-type C57BL/6N mice were cultured in Roswell Park Memorial Institute (RPMI) medium  supplemented with 10% heat-inactivated fetal bovine serum, 2 mM glutamine, 50 Î¼M 2-mercaptoethanol (Gibco), 100 U/ml penicillin, and 100 Î¼g/ml streptomycin (Gibco) and 50 ng/ml  of recombinant M-CSF (R&D Systems) on non-tissue culture treated 15 cm plates. On day 5 of culture, cells were harvested and 5 million cells were re-plated onto non-tissue culture  treated 10 cm plates in fresh media (same as that described above). After 2 additional days of culture, BMDMs from 3 individual mice (each corresponding to an independent biological replicate)  were harvested by scraping. Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol.  0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).  The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million  single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LPS treatment, 8hrs

value: Bone Marrow

value: MLKL -/- ,  Casp8 -/-  and N4bp1 -/-

value: Bone Marrow Derived Macrophages


title: 1_10_29_17_2R

value: GBM Cells


title: SAM24384962: Mlkl.C8.dko.ctrl.LPS.8h.BMDM

value: MLKL -/- and Casp8 -/-


title: Thymus of NP23-NHD13 double transgenic mouse M61-7589-NN

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description:
M61-7589-NN-Thy
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14.
Alignment performed using BWA v0.7.17.
Local realignment performed using GATK v3.8-1-0-gf15c1c3ef.
Somatic variant calling performed using MuTect2 v3.8-1-0-gf15c1c3ef.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv: Tab-separated text file includes somatic variant calling.

source_name: C57Bl6-NIH mouse

extract_protocol: Libraries were prepared according to the Nextera DNA Library Preparation protocol for the SureSelectXT Mouse All Exon Kit (Cat. No. 5190-4641, G7550C).

tag: strain/background

tag: genotype/variation

value: NP23-NHD13 double transgenic

tag: disease

value: Thymic AML

value: Thymus


title: VC12_1

value: WT

tag: tissue

value: Whole organism


title: VC12_2


title: P90 Spinal Cord GFP+ Oligodendrocytes 1

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description:
FACS sorted oligodendrocyte lineage cells based on reporter expression
IS
SeuratObjSpCrdGEO.Rdata

data_processing:
All individual samples were process with cellranger-2.1.1 with transcriptome reference refdata-cellranger-mm10-1.2.0
Raw files as aligned output bam files from Cellranger-2.1.1.  count output.
Genome_build: mm10
Supplementary_files_format_and_content: Expression and annotation matrix used in the study. Expression matrix of cells ( columns)  and genes ( rows) UMI counts. Annotation matrix of cells ( rows) and columns celltype clusters.

source_name: injury site (Spinal Cord) mouse

growth_protocol: Standard housing. 12h day/night cycle. Food and drinks at libitum

extract_protocol:
dissociation into single cells using the Miltenyi Biotec) accordingly to manufacture's instruction, excluding the red blood cells removal step.
cDNA libraries have been constructed with the kit from 10X Genomics Single Cell 3´v2 and were compatible with standars illumina sequencing

tag: health condition

value: Injured Spinal cord

value: spinal cord


title: P90 Spinal Cord GFP+ Oligodendrocytes 2

description:
FACS sorted oligodendrocyte lineage cells based on reporter expression
CTRL
SeuratObjSpCrdGEO.Rdata

source_name: Control (Spinal Cord) mouse

value: Healthy Spinal Cord


title: P90 Spinal Cord GFP+ Oligodendrocytes 3

description:
FACS sorted oligodendrocyte lineage cells based on reporter expression
WD
SeuratObjSpCrdGEO.Rdata

source_name: Wallerian degeneration (Spinal Cord) Mouse


title: Bone marrow of NP23-NHD13 double transgenic mouse M59-7489-NN

description:
M59-7489-NN-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: Bone marrow


title: SAM24384954: WT.control.untreated.BMDM

treatment_protocol: untreated

value: wild type

tag: cell type


title: SAM24384956: WT.control.LPS.8h.BMDM


title: H1944_LACZ_shSMARCA2_R1 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-LACZ, selected with 8ug/mL blasticidin for 5 days.


title: Bone marrow of NP23-NHD13 double transgenic mouse M58-7488-NN

description:
M58-7488-NN-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: B(HT-4)

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

country: China

institute: Newcore biotechnology

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina Novaseq 6000 sequencer. Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.2) software, high quality reads were generated. Then these high quality reads were aligned to reference genome (galGal6) using bowtie2 software (v2.2.4). Peak calling was performed with MACS software (v1.4.2).
Genome_build: galGal6
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: enriched peaks

organism: Gallus gallus

source_name: liver

extract_protocol:
cells were washed twice in Wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. 10 µL of concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at room temperature (RT) for 15 min. The bead-bound cells were resuspended in  Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2 mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform for 2 hours overnight at 4 °C. Then, the secondary antibody was diluted 1:50 in Dig-Wash buffer and cells were incubated at RT for 30 min. The pA-Tn5 adapter complex was added to the cells with gentle vortexing, and incubated at RT for 1 h. Next, cells were resuspended in Tagmentation buffer (10 mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. Then, DNA extraction was performed with proteinase K digestion and the following purification with Ampure XP beads (Beckman Counter). Cut&Tag libraries were amplified with NEBNext HiFi 2× PCR Master mix (New England Biolabs, Inc., USA). Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).
CUT&Tag

treatment_protocol: normal temperature and high temperature treatment

tag: treatment type

value: high temperature

value: liver


title: Day 5 Immature DC_Patient 24

tag: subject id

value: Patient 24

value: melanoma

value: Dendritic Cell

value: day 5 iDC

value: PD


title: SAM24384953: Mlkl.ko.dN4BP1.LPS.8h.BMDM

value: Bone Marrow

value: MLKL -/- and N4bp1 -/-

value: Bone Marrow Derived Macrophages


title: Day 5 Immature DC_Patient 25

value: Patient 25

tag: patient diagnosis


title: B(HT-3)


title: Day 5 Immature DC_Patient 22

value: Patient 22

tag: dc subtype


title: Day 5 Immature DC_Patient 26

value: Patient 26

tag: clinical outcome


title: SAM24384950: Mlkl.ko.dN4BP1.LPS.8h.BMDM


title: SAM24384947: Mlkl.ko.dN4BP1.LPS.8h.BMDM


title: B(HT-2)


title: B(HT-1)


title: Thymus of NP23-NHD13 double transgenic mouse M31-4399

description:
M31-4399-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: NP23-NHD13 double transgenic

value: Thymic AML

value: Thymus


title: Day 5 Immature DC_Patient 23

value: Patient 23

tag: overall survival (months)


title: Day 5 Immature DC_Patient 21

value: Patient 21


title: SAM24384944: Mlkl.ko.control.LPS.8h.BMDM

value: MLKL -/-


title: Day 5 Immature DC_Patient 2

value: Patient 2


title: Day 5 Immature DC_Patient 20

value: Patient 20

value: melanoma

value: PR


title: SAM24384941: Mlkl.ko.control.LPS.8h.BMDM


title: Bone marrow of NP23-NHD13 double transgenic mouse M60-7491-NN

description:
M60-7491-NN-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: Bone marrow


title: Day 5 Immature DC_Patient 19

description: Gene expression data from monocyte-derived iDC, melanoma

value: Patient 19

value: Dendritic Cell

value: day 5 iDC

value: SD


title: Day 5 Immature DC_Patient 18

value: Patient 18


title: A(NT-4)

value: normal temperature

value: liver


title: Bone marrow of NP23-NHD13 double transgenic mouse M23-4352

description:
M23-4352-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: NP23-NHD13 double transgenic

value: Thymic AML


title: A(NT-3)


title: Thymus of NP23-NHD13 double transgenic mouse M22-4324

description:
M22-4324-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: Thymus


title: A(NT-2)


title: Thymus of NP23-NHD13 double transgenic mouse M54-1286-NN

description:
M54-1286-NN-Thy
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: SAM24384938: Mlkl.ko.control.LPS.8h.BMDM

value: Bone Marrow

value: Bone Marrow Derived Macrophages


title: Thymus of NP23-NHD13 double transgenic mouse M53-1283-NN

description:
M53-1283-NN-Thy
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: SAM24384935: Mlkl.C8.dko.dN4BP1.LPS.8h.BMDM

value: MLKL -/- ,  Casp8 -/-  and N4bp1 -/-


title: SAM24384932: Mlkl.C8.dko.dN4BP1.LPS.8h.BMDM


title: Bone marrow of NP23-NHD13 double transgenic mouse M24-4360

description:
M24-4360-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: Thymus of NP23-NHD13 double transgenic mouse M21-4351

description:
M21-4351-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: A(NT-1)


title: Day 5 Immature DC_Patient 17

value: Patient 17

value: PD


title: Thymus of NP23-NHD13 double transgenic mouse M20-4361

description:
M20-4361-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: Day 5 Immature DC_Patient 13

value: Patient 13

value: melanoma


title: SAM24384926: Mlkl.C8.dko.ctrl.LPS.8h.BMDM

value: MLKL -/- and Casp8 -/-


title: SAM24384929: Mlkl.C8.dko.ctrl.LPS.8h.BMDM


title: Thymus of NP23-NHD13 double transgenic mouse M19-4318

description:
M19-4318-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: Day 5 Immature DC_Patient 14

value: Patient 14

value: Dendritic Cell


title: Day 5 Immature DC_Patient 16

value: Patient 16

value: day 5 iDC


title: Knockout 3

city: Boston

first: Yongjie

last: Yang

state: MA

address: 136 Harrison Ave

institute: Tufts University School of Medicine

description: Gene expression data from cultured astrocytes of a Fmr1+/- animal.

hyb_protocol: The labeled RNA was hybridized to the GeneChip miRNA version 4.0 Array for 18 hours in a GeneChip Hybridization oven 640 at 48oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw CEL files were normalized to produce expression values for all mouse and control probesets using Affymetrix Expression Console (version 1.4.1.46), using the Robust Multiarray Average (RMA) and Detection Above Background (DABG).

source_name: Cultured astrocytes

label_protocol: RNA was labeled with the FlashTag Biotin RNA Labeling Kit (Genisphere Inc., Hatfield, PA).

growth_protocol: Primary astrocyte cultures were obtained from P0-2 pups and maintained using standard astrocyte culture procedures.

extract_protocol: TRIzol reagent was added into culture wells after PBS wash to directly lyse cells and extract total RNA.

value: knockout


title: Thymus of NP23-NHD13 double transgenic mouse M18-4369

description:
M18-4369-Thymus
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: SAM24384917: WT.control.LPS.8h.BMDM

value: wild type


title: Day 5 Immature DC_Patient 15

value: Patient 15


title: C57Bl6-NIH WT mouse

description:
C57BL6-WT-Ref
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: WT

value: Tail


title: Knockout 1


title: Knockout 2


title: SAM24384915: WT.control.untreated.BMDM

value: Bone Marrow


title: P60 Corpus Callosum GFP+ Oligodendrocytes

description: FACS sorted oligodendrocyte lineage cells based on reperter expression

source_name: White matter (corpus callosum) mouse brain

extract_protocol:
Adult Brain Tissue dissociation into single cells using the Miltenyi Biotec) accordingly to manufacture's instruction, excluding the red blood cells removal step.
cDNA libraries have been constructed with the kit from 10X Genomics Single Cell 3´v2 and were compatible with standars illumina sequencing

value: Healthy adult brain

value: GFP+ Oligodendrocytes


title: Day 5 Immature DC_Patient 12

value: Patient 12

value: SD


title: SAM24384914: WT.control.LPS.8h.BMDM

value: Bone Marrow Derived Macrophages


title: P60 Corpus Callosum TdTom+ Oligodendrocytes

value: TdTom+ Oligodendrocytes


title: Day 5 Immature DC_Patient 11

value: Patient 11

value: melanoma

value: PD


title: SAM24384912: WT.control.untreated.BMDM

treatment_protocol: Untreated


title: Wild-type 2

description: Gene expression data from cultured astrocytes of a Fmr1+/y animal.

value: wild-type


title: Day 5 Immature DC_Patient 10

value: Patient 10

value: Dendritic Cell

value: day 5 iDC

value: PR


title: Wild-type 3


title: human spinal cord organoids - day 131

city: SEOUL

first: Ju-Hyun

last: Lee

address: 73 Inchon-ro

country: South Korea

institute: Korea University College of Medicine

description: Gene expression data from human spinal cord organoids

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16 h.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned with a GCS3000 Scanner (Affymetrix).

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Obtained raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).

source_name: hPSC

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: The Affymetrix Whole Transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) amplification kit as described by the manufacturer.

tag: developmental stage

value: On day 131 from hPSC


title: human spinal cord organoids - day 74

value: On day 74 from hPSC


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD006_indexed

status: Public on Sep 09 2020

tag: brain region

value: PAL

tag: Sex

value: male

tag: age


title: human spinal cord organoids - day 43

value: On day 43 from hPSC


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD004_indexed

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD007_indexed


title: human spinal cord organoids - day 15

value: On day 15 from hPSC


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD007_indexed


title: Wild-type 1

tag: genotype


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_C10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B6_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B6_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_B3_AD010_indexed


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title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD007_indexed


title: Total RNAseq wt 14mM CAF rep 2

city: Edinburgh

first: Sito

last: Torres-Garcia

address: 6.4 Michael Swann Building. Max Born Crescent

country: United Kingdom

institute: Wellcome Centre for Cell Biology. University of Edinburgh

description: Total RNA

data_processing:
RNA-Seq: Raw read were de-multiplexed. Adapter-trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using STAR (v2.2.1) and processed using Samtools (v1.3.1). Differential expression was analysed using the Bioconductor Rsamtools (v2.0.3), GenomicFeatures (v1.36.4) and DESeq2 (v.1.24) R libraries. Log2 fold changes were shrunk using the apeglm method58 and a MA-plot was generated using R. BigWig coverage files for forward and reverse strands were generated using BamCoverage (deepTools v2.0).
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: RNA-Seq: bigWig files of coverage for forward and reverse strands

organism: Schizosaccharomyces pombe

source_name: Total RNAseq wt 14mM CAF

growth_protocol: Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s instructions. Contaminating DNA was removed by treating with Turbo DNase (Invitrogen). rRNA was removed using the Ribo-Zero Gold rRNA removal kit (Yeast) (Illumina).
Libraries were prepared for Illumina sequencing with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced using NextSeq workflow.

value: h- ED972 wild-type (wt)

tag: phenotype

value: wild-type phenotype

tag: treatment

value: treated with 14 mM CAF for 18 hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD004_indexed


title: Total RNAseq wt 14mM CAF rep 1

description: Total RNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C2_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD012_indexed


title: liver D4-rep19

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

description:
test
M25J4

data_processing:
Results were analyzed using the Fluidigm real-time PCR analysis software v.4.1.3. The first part of the analysis is to clean up the data with the Fluidigm real-time PCR analysis software v.4.1.3.
Data were pre-processed for expression analysis as follows: the cycle threshold (Ct) values registered from amplifications that generated melting curves with aberrant Tm (melting temperature) or with products giving rise to a double peak in melting curves (corresponding to a mixture of expected and aberrant PCR products) were removed.
The selectHKgenes function with the Vandesompele method of the SLqPCR package was used with RStudio (Version 1.2.1335) to choose the five most stable housekeeping genes. The five housekeeping genes for the relative quantification of mRNA levels of target genes were SDHA, GLUT8, PDHA1, POL2 and Luciferase. In all cases, PCR efficiency values ranged between 1.90 and 2.
The analyses were done with RStudio with : Relative gene expression= (((E-target)^(ΔCt-target))/(geomean((E-ref)^(ΔCt-ref))). E = efficiency, Ct= threshold cycle, 〖ΔCt〗_target=〖Ct 〗_(control )-〖Ct 〗_sample, 〖ΔCt〗_ref=〖Ct 〗_(control )-〖Ct 〗_sample, 〖Ct 〗_(control ) = average Ct of all samples.
normalized expression = 2^-ΔCt, where ΔCt = Ct target- Ct HKG
fold change= relative expression = (((E-target)^(ΔCt-target))/(geomean((E-ref)^(ΔCt-ref))) with ΔCt_target (or ref)=〖Ct_control-Ct_sample and Ct_control = average Ct of all samples (for each gene)

label: EvaGreen

organism: Anas platyrhynchos x Cairina moschata

source_name: liver at post-hatching day 4

label_protocol: 6.5 ng of each cDNA were initially preamplified (10 min 95°C activation and 14 PCR cycles (15 sec 95°C and 4 min 60°C) with PreAmp Master Mix (100-5581, Fluidigm) and a pool containing all the primers targeting all the genes (200nM), excluding the 16S rRNA primer sets. Preamplified sample were diluted at 1/5 after an exonuclease treatment (M02935, NEB). In order to prepare samples for loading into the integrated fluidic circuits (IFC), a mix was prepared consisting of 440 μL 2X TaqMan Master Mix (Applied Biosystem, 4369016), 44 μL 20× DNA Binding Dye Sample Loading Reagent (100-7609, Fluidigm), 44µl 20X Evagreen (31000, Biotium) plus 132 μL TE, and 6 μL of this mix was dispensed to each well of a 96-well assay plate. 2µL of preamplified and diluted cDNA sample was added to each well and the plate was briefly vortexed and centrifuged. For the assays, 5 μL of each Assay (5 μM each primer in primer-mix (2X assay loading reagent (100-7611, Fluidigm) and Tris EDTA) were dispensed to each Detector Inlet of the 96.96 IFC. Following priming of the IFC in the IFC Controller HX, 5 μL of the cDNA sample + reagent mix and 5 µl of Assay were dispensed to each Sample Inlet of the 96.96 IFC. After loading the assays and samples into the IFC in the IFC Controller HX, the IFC was transferred to the BioMark and PCR was performed using the following thermal protocol : Thermal Mix of 50 °C, 2 min; 70 °C, 30min; 25°C, 10min, Hot Start at 50 °C, 2 min; 95°C, 10 min, PCR Cycle of 35 cycles of (95 °C, 15 s; 60 °C, 60 s), and Melting analysis (60°C, 30s; 95°C,1°C/3s)

extract_protocol: Samples were frozen in liquid nitrogen. Total RNA was isolated from frozen tissue according to the Ribozol method (VWR Life Science). Total RNA concentration was measured by spectrophotometry (optical density at 260 nm) using a Biotek EPOCH 2 microplate reader with Take3 Plate, and all the samples were normalized at 500 ng/ μl. The integrity of total RNA was analyzed by electrophoresis. An amount of 3µg RNA was reverse-transcribed to cDNA with Iscript Reverse Transcription Supermix for RTqPCR (Bio-Rad, USA) with duplicates of samples. DNA contamination was prevented by DNase treatment. Reverse transcription reaction was done in CFX384 (Bio-Rad, USA) according to this program: 25 °C/5 min, 46 °C/20 min, 95 °C/1 min.

tag: tissue

value: liver


title: liver D4-rep20

description:
test
M28J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD010_indexed


title: liver D4-rep18

description:
test
M24J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD008_indexed


title: liver D4-rep17

description:
test
M23J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD006_indexed


title: liver D4-rep14

description:
test
M20J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD008_indexed


title: liver D4-rep16

description:
test
M22J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C3_AD001_indexed


title: liver D4-rep15

description:
test
M21J4


title: liver D4-rep13

description:
test
M19J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C2_AD008_indexed


title: liver D4-rep12

description:
test
M16J4


title: liver D4-rep9

description:
test
M13J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD008_indexed


title: liver D4-rep10

description:
test
M14J4


title: liver D4-rep11

description:
test
M15J4


title: liver D4-rep7

description:
test
M11J4


title: liver D4-rep8

description:
test
M12J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C12_AD001_indexed


title: liver D4-rep3

description:
test
M4J4


title: liver D4-rep6

description:
test
M8J4


title: liver D4-rep4

description:
test
M5J4


title: liver D4-rep2

description:
test
M3J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD002_indexed


title: liver D4-rep1

description:
test
M2J4


title: liver D1-rep19

description:
test
M28J1

source_name: liver at post-hatching day 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C1_AD002_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD006_indexed


title: liver D1-rep18

description:
test
M25J1


title: liver D1-rep17

description:
test
M24J1


title: liver D1-rep16

description:
test
M23J1


title: liver D1-rep15

description:
test
M22J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD010_indexed


title: liver D1-rep14

description:
test
M21J1


title: liver D4-rep5

description:
test
M6J4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD008_indexed


title: liver D1-rep12

description:
test
M1J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD001_indexed


title: liver D1-rep13

description:
test
M20J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C10_AD004_indexed


title: liver D1-rep7

description:
test
M11J1


title: liver D1-rep9

description:
test
M14J1


title: liver D1-rep8

description:
test
M13J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_C11_AD004_indexed


title: liver D1-rep10

description:
test
M15J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD004_indexed


title: liver D1-rep5

description:
test
M6J1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B9_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD010_indexed


title: liver D1-rep2

description:
test
M3J1


title: liver D1-rep4

description:
test
M5J1


title: liver D1-rep3

description:
test
M4J1


title: liver D1-rep1

description:
test
M2J1


title: liver E28-rep20

description:
test
M24E28

source_name: liver at embryonic day 28


title: liver E28-rep17

description:
test
M20E28


title: liver D1-rep6

description:
test
M8J1


title: liver E28-rep18

description:
test
M21E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD004_indexed


title: liver E28-rep13

description:
test
M15E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD006_indexed


title: liver E28-rep10

description:
test
M12E28


title: liver E28-rep11

description:
test
M13E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD006_indexed


title: liver E28-rep12

description:
test
M14E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD012_indexed


title: liver D1-rep11

description:
test
M19J1


title: liver E28-rep9

description:
test
M11E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD010_indexed


title: liver E28-rep8

description:
test
M10E28