title: ATAC_S2_gst_RNAi_1


title: MDS BM sample 21

status: Public on Dec 05 2018

type: RNA

city: Tapei

first: Yi

middle: Tsung

last: Yang

address: No.7, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist., Taipei City 10002, Taiwan (R.O.C.)

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Samples were hybridized with Affymetrix Human Transcriptome 2.0 Array and scanned at the Microarray Core Lab of the National Health Research Institutes according to Affymetrix protocols.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The data was analyzed with Affymetrix AGCC software, Affymetrix Expression Console software and Transcriptome Analysis Console (TAC) version 3.0 software with Affymetrix default settings.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDS patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA then labeled with biotin according to the standard Affymatrix protocols

growth_protocol: Whole bone marrow mononuclear cells were collected and then stored at liquid nitrogen temperature at once with ptotected by RNase inhibitor

extract_protocol: RNA was isolated from bone marrow mononuclear cells according to the manufacturer’s instructions.

tag: subject status

value: myelodysplastic syndrome (MDS) patient

tag: subject id

tag: gender

value: male

tag: tissue

value: bone marrow


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_37

type: SRA

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description:
Sm22-Cre;tdTomato
Plikus_C1_PWD12_v1_Mv13_Matrix.txt

library_source: transcriptomic

data_processing:
RSEM was used for alignment, mapping and quantification of single cell transcripts.
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/gencode.Mv13) using Bowtie (version 1.0.0) with the following standard parameters: rsem-prepare-reference --bowtie --gtf and quantified using the RNA-seq by Expectation-Maximization algorithm (RSEM) (version 1.2.31) with the following standard parameters: rsem-calculate-expression -p $CORES --paired-end. (B. Li, C. N. Dewey. BMC bioinformatics 12, 323 (2011).
FPKM values were used. FPKM values were added pseudo-count of 1. Gene expression values for each cell were scaled by the total number of transcripts and multiplied by 10,000. This scaled expression data were then natural-log transformed before further downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (txt) text files include unprocessed FPKM values.

organism: Mus musculus

source_name: Skin wound cells

extract_protocol:
Skin wound tissues were harvested and dissegragated into single cell suspensions with collagenase. Cells were FACS sorted as viable tdTomatoHi. Pre-sorted, viable tdTomatohi single cells were re-suspended at appropriate concentrations in DMEM supplemented with 10% FBS, antibiotics and antifungals, diluted with suspension reagent for attribution of optimal buoyancy, and loaded onto a large 17-25μm 96-well microfluidic IFC (Fluidigm) for single cell capture in the automated C1 system for single-cell genomics (Fluidigm). Lysis, RT and cDNA pre-amplification were performed in loco (protocol 1.773x) with ultra-low input RNA reagents as suggested per manufacturer (Clonetech). RNA spike-in controls were omitted.
cDNA concentrations were estimated using Qubit 2.0 (Thermo) and cDNAs with concentration ≥ 1.0 ng/μl were used for downstream library preparation. Libraries were amplified using the Nextera XT v2 Index Kit (Illumina). Quality control on multiplexed libraries was performed using the Agilent Bioanalyzer and quantification was performed using KAPA for Illumina Sequencing Platforms (Illumina). Multiplexed libraries were sequenced as paired-end on an Illumina Next-Seq500 platform (Illumina).
SMART-seq2 - Fluidigm.

treatment_protocol: 3-8 week old mice were wounded as previously described. Briefly, 1.5 x 1.5 cm squared excisional wounds were inflicted on the dorsum of adult mice. Skin wound tissues (n=2-3/time point) were collected from Sm22-Cre;tdTomato mice on PWD 12, 15 and 21.

tag: strain

value: Mixed background

tag: cell type

value: Skin wound cells

tag: treatment

value: Post wounding day 12


title: MDS BM sample 20


title: ATAC_S2_clamp_RNAi_3

city: Planegg-Martinsried

first: Christian

last: Albig

address: Großhaderner Strasse 9

department: Biomedical Center

country: Germany

institute: Ludwig-Maximilians-University Munich

library_source: genomic

data_processing:
For ChIP‑seq and DIP‑seq samples, sequence reads were aligned to the D. melanogaster release 6 reference genome using Bowtie (Langmead et al., 2009) version 1.1.2 (parameter –m 1). Aligned reads were extended to 200 bp fragments.
For ATAC-seq samples, sequence reads were aligned to the D. melanogaster release 6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) version 2.2.9 (parameters --very-sensitive, --no-discordant, --no-mixed, -X 100) considering read‑pairs as non‑nucleosome if less than 100 bp according to (Buenrostro et al., 2013).
bigWig files were generated by counting overlapping fragments at each genomic position.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files with coverage

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1 mg/mL streptomycin (Sigma‑Aldrich).

extract_protocol:
ATAC‑seq was performed as described earlier (Buenrostro et al., 2013; Buenrostro et al., 2015) with some modification for Drosophila cells. In brief, 50,000 S2 or Kc cells, also with prior RNAi, were used per reaction. Cells were washed in 100 µL PBS, resuspended in 100 µL Lysis Buffer (10 mM Tris/HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA‑630) with cOmplete, EDTA‑free Protease Inhibitor Cocktail (Sigma‑Aldrich) and incubated for 3 min on ice. Nuclei were spun down at 4°C for 10 min at 600 g, resuspended in 50 µL 1x TD buffer with 2.5 µL TD Enzyme (Illumina) and incubated with slight agitation for 30 min at 37°C. Tagmented DNA was purified with MinElute kit (QIAGEN). Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).
Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).

treatment_protocol: RNAi against target genes in S2 and Kc cells was performed as previously described (Villa et al., 2016). In brief, double-stranded RNA fragments (dsRNA) were generated with MEGAscript kit (Thermo Fisher) from PCR products. Cells were incubated with 10 µg dsRNA per 1x10e6 cells at a concentration of 10 µg/mL in serum‑free medium (1x10e6 cells in 6‑well plate for ATAC‑seq) or 4.2 µg dsRNA at 6.3 µg/mL serum free medium per 1x10e6 cells (12x10e6 cells in 75 cm^2 flask for ChIP‑seq) for 1 hour. Two volumes of growth medium were added and cells were incubated for 5 days at 26°C. Then, 1x of initial volume (6‑well plate) or 0.75x of initial volume (75 cm2 flask) of growth medium was added and cells were incubated for further 2 days at 26°C.

tag: cell line

value: clamp RNAi


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_35


title: Mix-end_vs_Mix-core5

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replicate 5 of 5,  Mix-end_vs_Mix-core

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Raw Agilent data files were transferred to limma for further processing and final statistical analysis. Pre-processing: background correction (normexp), followed by within- (global loess) and between-array (Aquantile) normalization. Linear modelling was performed both with and without incorporation of intraspot-correlations.

organism: Tetranychus urticae

source_name: Mix-end

label_protocol: 100 ng of total RNA (+ RNA-Spike-In control) was used to generate Cy3- or Cy5-labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Spider mites were reared on bean (Phaseolus vulgaris cv Prelude) under controlled laboratory conditions (23°C, 16:8 LD photoperiod)

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion).

treatment_protocol: Briefly, the experimental range consisted of a linear system of populations: bean leaf squares, connected by parafilm bridges. The metapopulations were founded by ten mated one-day-old females on the core patch. Bean leaves were weekly refreshed to ensure the mites had an unlimited food supply.

tag: age

value: adult

value: female

source_name: Mix-core


title: Mix-end_vs_Mix-core4

description: Replicate 4 of 5,  Mix-end_vs_Mix-core


title: ATAC_S2_clamp_RNAi_2

extract_protocol:
ATAC‑seq was performed as described earlier (Buenrostro et al., 2013; Buenrostro et al., 2015) with some modification for Drosophila cells. In brief, 50,000 S2 or Kc cells, also with prior RNAi, were used per reaction. Cells were washed in 100 µL PBS, resuspended in 100 µL Lysis Buffer (10 mM Tris/HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA‑630) with cOmplete, EDTA‑free Protease Inhibitor Cocktail (Sigma‑Aldrich) and incubated for 3 min on ice. Nuclei were spun down at 4°C for 10 min at 600 g, resuspended in 50 µL 1x TD buffer with 2.5 µL TD Enzyme (Illumina) and incubated with slight agitation for 30 min at 37°C. Tagmented DNA was purified with MinElute kit (QIAGEN).
Cycle number for library amplification was determined by qPCR. Cycle number at quarter maximal intensity was used for library amplification (typically 11‑13 cycles). ATAC libraries were purified with MinElute kit (QIAGEN).


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_33


title: ATAC_S2_clamp_RNAi_1


title: Mix-end_vs_Mix-core3

description: Replicate 3 of 5,  Mix-end_vs_Mix-core


title: MDS BM sample 19


title: MDS BM sample 25


title: ATAC_Kc_untreated_4

source_name: Kc cells

value: Kc

value: untreated


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_34


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_31


title: ATAC_Kc_untreated_3


title: MDS BM sample 16


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_32


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_30


title: ATAC_Kc_untreated_2


title: Mix-end_vs_Mix-core1

description: Replicate 1 of 5,  Mix-end_vs_Mix-core


title: Control-end _vs_Control-core6

description: Replicate 6 of 6, Control-end _vs_Control-core

source_name: Control-end

source_name: Control-core


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_29


title: ATAC_Kc_untreated_1


title: MDS BM sample 13


title: ATAC_S2_gst_RNAi_2

value: gst RNAi


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_28


title: ATAC_Kc_gst_RNAi_3


title: MDS BM sample 15


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_27


title: MDS BM sample 10


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_26


title: MDS BM sample 17


title: ATAC_Kc_gst_RNAi_1


title: MDS BM sample 14


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_25


title: Control-end _vs_Control-core3

description: Replicate 3 of 6, Control-end _vs_Control-core


title: ATAC_Kc_gst_RNAi_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_24


title: Mix-end_vs_Mix-core2

description: Replicate 2 of 5,  Mix-end_vs_Mix-core


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_22


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_21


title: ATAC_Kc_clamp_RNAi_1


title: Control-end _vs_Control-core4

description: Replicate 4 of 6, Control-end _vs_Control-core


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_23


title: Control-end _vs_Control-core1

description: Replicate 1 of 6, Control-end _vs_Control-core


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_20


title: MDS BM sample 18


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_19


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_16


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_18


title: Control-end _vs_Control-core5

description: Replicate 5 of 6, Control-end _vs_Control-core


title: MDS BM sample 7


title: Control-end _vs_Control-core2

description: Replicate 2 of 6, Control-end _vs_Control-core


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_15


title: MDS BM sample 9


title: ATAC_Kc_clamp_RNAi_2


title: MDS BM sample 11


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_13


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_14


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_11


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_10


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_8


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_9


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_7


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_5


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_3


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_2


title: MDS BM sample 4


title: ATAC_Kc_clamp_RNAi_3


title: Control-34

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Reads from each RNA-Seq sample were aligned to the hg38 genome using STAR.
Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes and other analyses in the study. Statistical tests in this study were performed using custom Python scripts.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files include a expression text file that contains expression values for each sample (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to hg38 human assembly.

molecule: polyA RNA

source_name: Monocyte cells

extract_protocol:
Isolation of untouched monocytes from PBMCs by using the Pan Monocyte Isolation Kit (Order No. 130-096-537)
According to Gosselin et al., Cell, 2014

tag: group

value: Control

tag: age [y]

tag: Sex


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_4


title: sihnRNPL/siUPF1_2

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

data_processing:
Sequencing reads in FASTQ format were aligned to the reference genome hg19 using the Tophat2 aligner.
Differential gene expression analysis was performed using the DEseq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM and fold expression change values

source_name: HEK-293TO cells

growth_protocol: HEK-293TO cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml of penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml of L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Transient depletion for 72 hours by reverse transfection.

tag: sirna

value: treated with hnRNP L and UPF1 siRNAs


title: sihnRNPL/siUPF1_3


title: PD-07

value: Parkinson's disease


title: MDS BM sample 12


title: MDS BM sample 3


title: sihnRNPL/siUPF1_1


title: siUPF1_3

value: treated with UPF1 siRNA


title: MDS BM sample 2


title: MDS BM sample 8


title: Control-32


title: MDS BM sample 5


title: MDS BM sample 6


title: sihnRNPL_3

value: treated with hnRNP L siRNA


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_12


title: MDS BM sample 1

value: myelodysplastic syndrome (MDS) patient


title: sihnRNPL_1


title: sihnRNPL_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_6


title: MR_I_D_R3

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

description: mRNA

data_processing:
The quality of the fastq files was evaluated with the fastQC program.
The reads obtained were pseudomapped to the T. atroviride V2 transcriptome using kallisto to quantify transcript abundance.
For the differential expression analysis only those genes that had at least three reads per million in at least ten libraries were considered as transcribed. All analyses were carried out using the edgeR package.
For determining differential expression between the comparisons, we used the generalized linear model (GLM) likelihood ratio test. False discovery rates (FDR) were calculated and genes with an FDR < 0.05 were considered differentially expressed.
In the case of small RNAs, with the help of Minion and Reaper, which are part of the Kraken tool (Davis et al., 2013), adapters were detected and removed.
Using the ShortStack tool (Johnson et al., 2016), and the BAM files from mapping all the libraries to the T. atroviride genome, 11718 clusters that produce Dicer dependent sRNAs were detected (Dicer call). All mapping was performed with Bowtie1 (Angmead et al., 2009).

organism: Trichoderma atroviride

source_name: mycelium

growth_protocol: growth in PDA at 28 degrees celsius.

extract_protocol:
Trizol
TruSeq RNA and TruSeq Small RNA

treatment_protocol: Mycelial plugs of the different T. atroviride strains were inoculated in PDA plates and allowed to grow for 36 hours in the dark at 28 °C, mycelia were then cut using a scalpel or a cookie mold under a red safety light (Hernández-Oñate et al., 2012)

tag: genotype/variation

value: knockout milRNA2

tag: experiment

value: Injury


title: MR_I_D_R2

description: mRNA


title: MR_I_D_R1

description: mRNA


title: WT_I_D_R3

description: mRNA

value: Wild-type


title: siNS_3

value: treated with non-specific (NS) siRNA


title: WT_I_D_R2

description: mRNA


title: siNS_2


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_17

value: Mixed background

value: Skin wound cells

value: Post wounding day 12


title: siUPF1_1


title: siUPF1_2


title: siNS_1


title: TX,CD25+

city: Tokushima

first: Naozumi

last: Ishimaru

address: Kuramoto

department: Oral Molecular Pathology

country: Japan

institute: Tokushima University Graduate School

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: thymectomy, CD25+

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling 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: Total RNA was extracted from mouse ear and purified using the RNeasy Mini Kit (Qiagen). Samples are pooled from 4 mice for each treatment. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

value: spleen

value: T cells

tag: cell markers

value: thymectomy


title: RD_I_B_R3

description: mRNA

value: knockout rdr3


title: nonTX,CD25-

source_name: no thymectomy, CD25-

value: no thymectomy


title: Sample 1_PWD12_WoundDermis_SingleCells_Fluidigm_Cell_1


title: sRNA_DC_I_R3

description: small RNA

value: knockout dcr2


title: sRNA_DC_I_R2

description: small RNA


title: TX,CD25-

source_name: thymectomy, CD25-


title: RD_I_B_R1

description: mRNA


title: sRNA_DC_I_R1

description: small RNA


title: RD_C_B_R3

description: mRNA

value: vegetative growth (control)


title: sRNA_DC_C_R3

description: small RNA


title: RD_C_B_R2

description: mRNA


title: RD_I_B_R2

description: mRNA


title: WT_I_D_R1

description: mRNA


title: sRNA_DC_C_R2

description: small RNA


title: RD_C_B_R1

description: mRNA


title: nonTX,CD25+

source_name: no thymectomy, CD25+


title: BeS sample 7 [cbdmeth]

type: genomic

city: Aurora

first: Ivana

state: CO

institute: University of Colorado - Anschutz Medical Campus

description: Bisulfite-converted DNA from primary patient cells

hyb_protocol: Illumina standard protocol

scan_protocol: iScan

data_processing: SWAN normalization and logit transformation for methylation arrays

label: Cy3, Cy5

source_name: BALF

label_protocol: Illumina standard protocol

extract_protocol: DNA and RNA extracted using the AllPrep kit from Qiagen from freshly collected cells

tag: dx

value: BeS

value: Male

tag: race

value: W

tag: ethnicity

value: non-hispanic

tag: smoking status

value: Former

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Untreated


title: sRNA_DC_C_R1

description: small RNA

tag: treatment


title: WT_I_B_R2

description: mRNA

value: Wild-type

value: Injury


title: sRNA_WT_I_R3

description: small RNA


title: sRNA_WT_I_R1

description: small RNA


title: sRNA_WT_I_R2

description: small RNA


title: WT_I_B_R1

description: mRNA


title: WT_C_B_R3

description: mRNA


title: Sarcoidosis sample 5 [cbdmeth]

value: Sarcoidosis

value: female

tag: age


title: BeS sample 6 [cbdmeth]

value: Never


title: CBD sample 8 [cbdmeth]

value: CBD

value: Treated

value: Steroids


title: BeS sample 8 [cbdmeth]


title: CBD sample 7 [cbdmeth]


title: Sarcoidosis sample 7 [cbdmeth]


title: Sarcoidosis sample 6 [cbdmeth]


title: sRNA_WT_C_R3

description: small RNA


title: Sarcoidosis sample 8 [cbdmeth]


title: WT_I_B_R3

description: mRNA


title: WT_C_B_R2

description: mRNA


title: WT_C_B_R1

description: mRNA


title: sRNA_WT_C_R1

description: small RNA


title: 2L12.2

city: Córdoba

first: Muñoz Marin

last: Maria del Carmen

state: Córdoba

address: Campus Rabanales

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

description: Gene expression after 12hr from sunrise (actual sunset)

hyb_protocol: The hybridization of cDNA samples (1.0 mg of ds-cDNA) to the microarray was done with Gene Expression Hybriditation kit (Cat#5188-5242) at Roy J. Carver Center for Genomics (CCG) Facility (University of Iowa, Iowa city, Iowa, USA) according to the protocol in Agilent Technology for arrays

scan_protocol: Slides were scanned immediately after washing (Gene Expression wash buffer Cat#5188-5377) on the Agilent DNA Microarray Scanner using one color scan setting for two 8x60k array slides and one color scan setting for 4x180k array slide. It was done at Roy J. Carver Center for Genomics (CCG) Facility (University of Iowa, Iowa city, Iowa, USA).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 060208_G2_D_F_20130916) to obtain background subtracted and spatially detrended Processed Signal intensities. It was done at Roy J. Carver Center for Genomics (CCG) Facility (University of Iowa, Iowa city, Iowa, USA).
Transcription values for each gene were obtained using median polish summarization and values were normalized using quantile normalization. The transcription values of L6, L9, D3 and 2L12 are the median transcription of two different replicates (L6.1, L6.2, L9.1, L9.2, D3.1, D3.2, 2L12.1 and 2L12.2).

source_name: seawater, 6 pm, replicate 2

label_protocol: The labeling of cDNA samples (1.0 mg of ds-cDNA) to the microarray was done with SureTag DNA labeling kit (Cat#5190-3400) at Roy J. Carver Center for Genomics (CCG) Facility (University of Iowa, Iowa city, Iowa, USA) according to the protocol in Agilent Technology for arrays

extract_protocol: RNA for UCYN-A was extracted using the Ambion RiboPure kit (Life Technologies, Grand Island, NY, USA) with modifications that included mechanical lysis using glass beads as described in Shilova et al. (2014). Extracted RNA was cleaned and concentrated with Zymo Research RNA Clean & Concentrator TM-5 (Irvine, CA, USA) and treated with DNase (Ambion Turbo-DNA-freeTM Kit, (Life Technologies, Grand Island, NY, USA) to remove genomic DNA. cDNA was synthesized from 400 ng RNA from each sample, which was then amplified using the TransPlex Whole Transcriptome Amplification kit (WTA-2, Sigma-Aldrich, St Louis, MO, USA) and antibody-inactivated hot-start Taq DNA Polymerase (Sigma-Aldrich). The amplified cDNA was purified with the GenElute PCR cleanup kit (Sigma-Aldrich).

tag: kind of sample

value: Environmental samples

tag: synonym

value: UCYN-A


title: Sarcoidosis sample 3 [cbdmeth]

tag: Sex

value: Current

value: MTX


title: DC_I_A_R3

description: mRNA

value: knockout dcr2


title: 2L12.1

source_name: seawater, 6 pm, replicate 1


title: D6

description: Gene expression after 6hr from sunset

source_name: seawater, 12 am


title: DC_I_A_R2

description: mRNA


title: 2L9

description: Gene expression after 9hr from sunrise

source_name: seawater, 3 pm


title: D3.2

description: Gene expression after 3hr from sunset

source_name: seawater, 9 pm, replicate 2


title: DC_I_A_R1

description: mRNA


title: 2L3

description: Gene expression after 3hr from sunrise

source_name: seawater, 9 am


title: 2D12

description: Gene expression after 12hr from sunset (actual sunrise)

source_name: seawater, 6 am


title: BeS sample 5 [cbdmeth]

value: BeS

value: Male

value: W

value: hispanic


title: D3.1

description: Gene expression after 3hr from sunset

source_name: seawater, 9 pm, replicate 1


title: BeS sample 4 [cbdmeth]

value: Former

value: Untreated


title: L9.2

description: Gene expression after 9hr from sunrise

source_name: seawater, 3 pm, replicate 2


title: Sarcoidosis sample 4 [cbdmeth]

value: Sarcoidosis

value: non-hispanic


title: sRNA_WT_C_R2

description: small RNA

value: Wild-type

value: vegetative growth (control)


title: L9.1

description: Gene expression after 9hr from sunrise

source_name: seawater, 3 pm, replicate 1


title: Sarcoidosis sample 2 [cbdmeth]

value: Never


title: BeS sample 2 [cbdmeth]


title: CBD sample 6 [cbdmeth]

value: CBD

value: Treated

value: Steroids


title: BeS sample 3 [cbdmeth]

value: Current


title: L6.2

description: Gene expression after 6hr from sunrise

source_name: seawater, 12 pm, replicate 2

value: Environmental samples

value: UCYN-A


title: DC_C_A_R2

description: mRNA

source_name: mycelium

value: knockout dcr2


title: WT_I_A_R2

description: mRNA

value: Injury


title: DC_C_A_R3

description: mRNA


title: WT_I_A_R3

description: mRNA


title: DC_C_A_R1

description: mRNA


title: WT_I_A_R1

description: mRNA


title: L6.1

description: Gene expression after 6hr from sunrise

source_name: seawater, 12 pm, replicate 1


title: CBD sample 5 [cbdmeth]

value: female

value: W


title: WT_C_A_R3

description: mRNA


title: CBD sample 4 [cbdmeth]

value: Male


title: individual 2 of crossbred Duroc x (Landrace x Yorkshire)

city: ChengDu

first: Yu

last: Lin

state: SiChuan

address: GongPing

country: China

institute: Sichuan Agricultural University

description:
SAMPLE 6
DLY-2

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland)

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on iScan (Illumina Inc.)(Illumina).

data_processing: Genomic DNA extracted from ear and liver was genotyped using porcine 60K BeadChip genotyping array (Illumina)

organism: Sus scrofa

source_name: liver

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1)

extract_protocol: Genomic DNA for each individual was extracted from the ear and liver tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany)

tag: breed

tag: gender

value: male

tag: tissue

value: liver


title: individual 6 of crossbred Duroc x (Landrace x Yorkshire)

description:
SAMPLE 10
DLY-6


title: individual 5 of crossbred Duroc x (Landrace x Yorkshire)

description:
SAMPLE 9
DLY-5


title: individual 4 of crossbred Duroc x (Landrace x Yorkshire)

description:
SAMPLE 8
DLY-4


title: individual 1 of crossbred Duroc x (Landrace x Yorkshire)

description:
SAMPLE 5
DLY-1


title: individual 3 of crossbred Duroc x (Landrace x Yorkshire)

description:
SAMPLE 7
DLY-3


title: WT_C_A_R1

description: mRNA

tag: genotype/variation

tag: experiment


title: WT_C_A_R2

description: mRNA


title: individual of crossbred Landrace x Yorkshire

description:
SAMPLE 4
LY

source_name: ear

value: crossbred Landrace x Yorkshire

value: ear


title: HepG2_5-AZA_day12

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description:
Gene expression after 12 days of treatment
7-D12

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The raw data were processed using Agilent’s Feature Extraction Software version 10.7.3.1 to analyze the array and calculate the intensities of the measured spots.

source_name: HepG2, 5-AZA (2.5µM), 12 days

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol. Cyanine-3 (Cy3)

growth_protocol: Human HepG2 cells were purchased from the American Type Culture Collection and maintained in DMEM (Gibco) supplemented with penicillin (50 IU/mL; Gibco), streptomycin (50 µg/mL; Gibco), and 10 % fetal bovine serum (FBS; Thermo Scientific).

extract_protocol: mRNA and miRNA were purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Total RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and the integrity of the RNA was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For assessment of epigenetically silenced miRNAs, total RNA samples were collected from HepG2 cells every 48 hours from the beginning of treatment until day 12. The demethylating agent 5-azacytidine (5-AZA; PubChem CID: 9444) was from Sigma (#A2385). The compound was dissolved in phosphate-buffered saline as a 10 mM stock, filtered (0.22 µM), and stored at -20°C. The cells were treated with 5-AZA at a concentration of 2.5 µM. The drug and medium were replaced daily.

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: time


title: HepG2_5-AZA_day10

description:
Gene expression after 10 days of treatment
6-D10

source_name: HepG2, 5-AZA (2.5µM), 10 days


title: HepG2_5-AZA_day8

description:
Gene expression after 8 days of treatment
5-D8

source_name: HepG2, 5-AZA (2.5µM), 8 days


title: 2: rfpC_FRL

city: University Park

first: Donald

middle: Ashley

last: Bryant

state: PA

address: Althouse

department: Biochemistry and Molecular Biology

institute: The Pennsylvania State University

data_processing:
Mapping against the Chlorogloeopsis fritschii PCC 9212 genome was performed using the BWA software package using modified scripts to accommodate the Illumina sequences as shown in Li and Durbin (2009). Bioinformatics 25, 1754-1760.
The resulting alignment files were further analyzed with self-developed scripts modified from Ludwig and Bryant (2011). Frontiers in Microbiology 2, 41. to extract expression levels for each gene.
Supplementary_files_format_and_content: Tab-delimited text files including reads of each gene in each sample. Locust tags are searchable on the JGI/IMG website.

organism: Chlorogloeopsis fritschii PCC 9212

source_name: whole cells

extract_protocol:
Cells were harvested, immediately frozen in liquid nitrogen, and stored at -80 oC. Total RNA was extracted with phenol and further purified with High Pure RNA Isolation Kit (Roche, Indianapolis,IN). Ribosomal RNA  was removed using Ribo-Zero rRNA Removal Kit  (Bacteria) (Illumina, Inc.)
Library was generated by using the TruSeq Stranded mRNA Kit with skipping of poy(A) selection (Illumina, Inc.)

tag: genotype

value: rfpC knockout mutant

tag: antibiotic


title: 2: rfpB_FRL

value: rfpB knockout mutant


title: Progressive sarcoidosis sample 9 [sarcmeth]

data_processing: SWAN normalization and logit transformation using Partek Genomics Suite

source_name: BALF

tag: group

value: Prog Sarc

tag: race

tag: ethnicity

value: hispanic

tag: smoking status

value: Former

tag: scadding

tag: total lung capacity, percent predicted

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

value: Treated

value: Steroid

value: MTX


title: 2: WT_FRL + Em

value: wild type

value: erythromycin


title: Sarcoidosis sample 1 [cbdmeth]

tag: dx

value: Sarcoidosis

tag: Sex

value: AA

value: non-hispanic

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

tag: treatment

value: Untreated


title: Duroc breed

description:
SAMPLE 1
D

tag: breed

value: Duroc breed

tag: gender

value: male

tag: tissue


title: BeS sample 1 [cbdmeth]

value: BeS

value: Male

value: W

value: Never


title: Landrace breed

description:
SAMPLE 2
L

value: Landrace breed

value: ear


title: HepG2_5-AZA_day4

description:
Gene expression after 4 days of treatment
3-D4

source_name: HepG2, 5-AZA (2.5µM), 4 days

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: time


title: Progressive sarcoidosis sample 6 [sarcmeth]

tag: group

value: Prog Sarc

value: female

tag: race

tag: ethnicity

value: Former

value: Treated

value: Steroid


title: HepG2_5-AZA_day2

description:
Gene expression after 2 days of treatment
2-D2

source_name: HepG2, 5-AZA (2.5µM), 2 days


title: CBD sample 2 [cbdmeth]

value: CBD

tag: smoking status

tag: total lung capacity, percent predicted


title: Progressive sarcoidosis sample 7 [sarcmeth]

value: non-hispanic

tag: scadding

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

value: untreated

value: MTX


title: Yorkshire breed

description:
SAMPLE 3
Y

value: Yorkshire breed


title: Progressive sarcoidosis sample 5 [sarcmeth]

tag: Sex

tag: diffusing capacity of the lung for carbon monoxide, percent predicted


title: Progressive sarcoidosis sample 8 [sarcmeth]

tag: age

tag: treatment


title: CBD sample 1 [cbdmeth]

tag: dx

value: Untreated


title: PBMC-Induced Microglia #3

city: Boston

first: Roy

middle: H.

last: Perlis

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: Gene Expression (Clarion_S_Human Array) PBMC-Induced Microglia #3

hyb_protocol: Whole-genome gene expression profiling was performed using the ClariomTM S Pico human gene expression array. GeneChipTM Fluidics Station 450 performed all liquid handling steps

scan_protocol: Chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: Quality control (QC) was performed using the manufacturer’s software Transcriptome Analysis Console (TAC) v4.0 (Affymetrix Inc.), as per manufacturer's instructions (PCA, labeling controls, hybridization controls, Pos vs. Neg AUC, and Signal Box Plot) with no indication of outliers. Normalization was performed according to a Robust Multi-chip Analysis (RMA) approach.

source_name: PBMC-Induced Microglia #3

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (QIAGEN, Hilden, Germany) as per manufacturer's instructions

tag: subject #


title: Remitting sarcoidosis sample 15 [sarcmeth]

value: Remit Sarc

value: Male


title: 2: rfpC_WL

tag: genotype

value: rfpC knockout mutant

tag: antibiotic


title: PBMC-Induced Microglia #5

description: Gene Expression (Clarion_S_Human Array) PBMC-Induced Microglia #5

source_name: PBMC-Induced Microglia #5


title: Remitting sarcoidosis sample 14 [sarcmeth]

value: W


title: 2: rfpB_WL

value: rfpB knockout mutant


title: HepG2_No-5-AZA

description:
Gene expression in control HepG2 cells
1-D0

source_name: HepG2, no 5-AZA treatment

tag: cell line

tag: cell type

value: hepatocellular carcinoma

value: control

tag: time


title: 2: WT_WL + Em

value: wild type

value: erythromycin


title: HepG2_5-AZA_day6

description:
Gene expression after 6 days of treatment
4-D6

source_name: HepG2, 5-AZA (2.5µM), 6 days


title: CBD sample 3 [cbdmeth]

tag: race

tag: ethnicity

value: Former


title: PBMC-Induced Microglia #2

description: Gene Expression (Clarion_S_Human Array) PBMC-Induced Microglia #2

source_name: PBMC-Induced Microglia #2


title: sog1_bleomycin_rep2

city: Ikoma

first: Naoki

last: Takahashi

state: Nara

address: Takayama 8916-5

institute: Nara Institute of Science and Technology

description:
Gene expression after bleomycin treatment
US45103077_253459210074_S01_GE1_107_Sep09_2_4

hyb_protocol: 600 ng of cRNAs were hybridized to an Arabidopsis Agilent custom microarrays at 65 ˚C. for 17 h, using Gene Expression Hybridization kit. After hybridization, the microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned by Agilent DNA Microarray Scanner (G2539A ver.C).

data_processing: When Agilent feature extraction software outputted raw data, the software omitted rows associated with spots where DNA proves were not spotted.

organism: Arabidopsis thaliana

label_protocol: 200 ng of total RNA was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Arabidopsis plants were grown in Murashige and Skoog (MS) medium under continuous light at 23 ˚C.

extract_protocol: Total RNA was extracted from two biological replicates with Plant Total RNA Mini Kit (FAVORGEN) according to the manufacturer’s instructions.

treatment_protocol: Five-day-old WT, anac044-1 anac085-1, and sog1-101 plants were transferred to MS medium with or without 0.6 µg/ml bleomycin for 10 h.

tag: ecotype background

tag: genotype/variation

value: Five-day-old plant

value: 0.6 µg/ml bleomycin for 10 h

tag: tissue

value: roots


title: PBMC-Induced Microglia #1

description: Gene Expression (Clarion_S_Human Array) PBMC-Induced Microglia #1

source_name: PBMC-Induced Microglia #1


title: PBMC-Macrophage #3

description: Gene Expression (Clarion_S_Human Array) PBMC-Macrophage #3

source_name: PBMC-Macrophage #3


title: Remitting sarcoidosis sample 13 [sarcmeth]

tag: group

value: AA

value: non-hispanic

tag: smoking status

tag: scadding

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted

value: untreated


title: 2: WT_WL


title: Remitting sarcoidosis sample 11 [sarcmeth]

tag: Sex

value: Never

tag: total lung capacity, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

tag: age

tag: treatment

value: Untreated


title: 2: WT_FRL

tag: genotype

tag: antibiotic


title: Progressive sarcoidosis sample 4 [sarcmeth]

value: Prog Sarc

value: Male

tag: race

value: Current


title: Remitting sarcoidosis sample 12 [sarcmeth]

value: Remit Sarc

value: female

tag: ethnicity


title: Remitting sarcoidosis sample 10 [sarcmeth]

value: W


title: Progressive sarcoidosis sample 3 [sarcmeth]

value: Treated

value: Steroid


title: sog1_bleomycin_rep1

description:
Gene expression after bleomycin treatment
US45103077_253459210074_S01_GE1_107_Sep09_2_3

tag: ecotype background


title: 1: rfpC_FRL + Em

value: rfpC knockout mutant

value: erythromycin


title: PBMC-Induced Microglia #4

description: Gene Expression (Clarion_S_Human Array) PBMC-Induced Microglia #4

source_name: PBMC-Induced Microglia #4

tag: subject #


title: sog1_mock_rep2

description:
Gene expression under control condition
US45103077_253459210074_S01_GE1_107_Sep09_2_2

tag: genotype/variation

value: Five-day-old plant

value: mock

tag: tissue


title: 1: rfpB_FRL + Em

value: rfpB knockout mutant


title: Remitting sarcoidosis sample 9 [sarcmeth]

description: Bisulfite-converted DNA from primary patient cells

tag: group

value: non-hispanic

tag: smoking status

value: MTX


title: sog1_mock_rep1

description:
Gene expression under control condition
US45103077_253459210074_S01_GE1_107_Sep09_2_1

value: roots


title: 1: rfpA_FRL + Em

value: rfpA knockout mutant


title: anac044anac085_bleomycin_rep2

description:
Gene expression after bleomycin treatment
US45103077_253459210075_S01_GE1_107_Sep09_1_4

value: 0.6 µg/ml bleomycin for 10 h


title: 1: rfpC_WL + Em


title: Remitting sarcoidosis sample 8 [sarcmeth]

value: Former

tag: scadding

tag: forced vital capacity, percent predicted

value: untreated


title: PBMC-Monocyte #1

description: Gene Expression (Clarion_S_Human Array) PBMC-Monocyte #1

source_name: PBMC-Monocyte #1


title: Remitting sarcoidosis sample 7 [sarcmeth]

value: Remit Sarc

tag: Sex

value: Male

value: Never

tag: forced expiratory volume in one second, percent predicted


title: PBMC-Macrophage #1

description: Gene Expression (Clarion_S_Human Array) PBMC-Macrophage #1

source_name: PBMC-Macrophage #1


title: 1: rfpB_WL + Em


title: 1: WT_FRL

value: wild type


title: PBMC-Macrophage #2

description: Gene Expression (Clarion_S_Human Array) PBMC-Macrophage #2

source_name: PBMC-Macrophage #2


title: 1: rfpA_WL + Em


title: anac044anac085_bleomycin_rep1

description:
Gene expression after bleomycin treatment
US45103077_253459210075_S01_GE1_107_Sep09_1_3


title: Progressive sarcoidosis sample 2 [sarcmeth]

value: Prog Sarc

value: female

value: W

tag: total lung capacity, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted

value: Untreated


title: Stat6_ISC

city: Beijing

first: Pingping

last: Zhu

state: Beijing

address: Datun Road 15#

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
RNA-seq was performed using a BGISEQ-500 platform and the raw reads were filtered for adaptor sequence, masked for low-complexity or low-quality sequence. Clean reads were mapped to mm9 using HISAT/Bowtie2 tool. Gene expression level was quantified by RSEM and FPKM was calculated. RNA-seq analysis was completed by BGI company (Shenzhen,China).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_ISC expression.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Stat6 ISC

growth_protocol: ISC cells were cultured in Dulbecco’s modified Eagle’s medium/F12 medium (Invitrogen) was supplemented with N2 (Invitrogen), B27 (Invitrogen), 50 ng/ml EGF (Rockland), 1.25 mM N-acetylcysteine (Sigma-Aldrich), 1 mg/ml Rspo1 (peprotech), 20 ng/ml EGF (Peprotech), 20 mM Y27632 (Sigma-Aldrich).

extract_protocol:
Total RNA isolated using Trizol reagent (Ambion).
Construction of RNA-seq library was completed by BGI company (Shenzhen, China).
Single-ended 50 bp reads (59 million per sample on average) were generated using a BGISEQ-500 platform (BGI America Co., Cambridge, MA).

treatment_protocol: ISC cells were infected with CRISPR/Cas Lentivirus containing Stat6-sgRNAs. Stat6-deficient ISC cells were screened out.

value: Lgr5GFP-CreERT2 Stat6 KO

tag: cell type

value: intestinal stem cells

tag: age

value: 2 months


title: iPSC-derived Neuron #4

description: Gene Expression (Clarion_S_Human Array) iPSC-Derived Neuron #4

source_name: iPSC-derived Neuron #4


title: PBMC-Monocyte #2

description: Gene Expression (Clarion_S_Human Array) PBMC-Monocyte #2

source_name: PBMC-Monocyte #2


title: anac044anac085_mock_rep2

description:
Gene expression under control condition
US45103077_253459210075_S01_GE1_107_Sep09_1_2

value: Five-day-old plant

tag: treatment

value: mock


title: Remitting sarcoidosis sample 6 [sarcmeth]

source_name: BALF

tag: race

value: non-hispanic


title: iPSC-derived Neuron #2

description: Gene Expression (Clarion_S_Human Array) iPSC-Derived Neuron #2

source_name: iPSC-derived Neuron #2


title: iPSC-derived Neuron #3

description: Gene Expression (Clarion_S_Human Array) iPSC-Derived Neuron #3

source_name: iPSC-derived Neuron #3


title: WT_bleomycin_rep2

description:
Gene expression after bleomycin treatment
US45103077_253459210074_S01_GE1_107_Sep09_1_4

value: WT

value: 0.6 µg/ml bleomycin for 10 h

value: roots


title: iPSC-derived Neuron #1

description: Gene Expression (Clarion_S_Human Array) iPSC-Derived Neuron #1

source_name: iPSC-derived Neuron #1


title: anac044anac085_mock_rep1

description:
Gene expression under control condition
US45103077_253459210075_S01_GE1_107_Sep09_1_1


title: 1: WT_WL

source_name: whole cells

tag: genotype

tag: antibiotic


title: WT_ISC

source_name: WT ISC

value: Lgr5GFP-CreERT2 WT


title: Progressive sarcoidosis sample 1 [sarcmeth]

value: Male

value: AA

tag: ethnicity

value: Former

value: Treated

value: Steroid


title: SKMNC_DMSO_6hr

status: Public on Dec 04 2018

city: Guangzhou

first: Lehang

address: 107, West Yanjiang Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
STAR aligner with ensemble gtf (v75) was used to align 100 bp paired-end sequencing reads to human reference genome (build GRCh37/hg19)
Cufflinks were used to measure the expression in terms of FPKM (Fragments Per  Kilobase of transcript per Million mapped reads) against Ensemble transcripts (v75)
Genome_build: GRCh37/hg19

source_name: Ewing sarcoma cells

growth_protocol: A673 and SKNMC Ewing sarcoma cells were both grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and kept at 37℃ with 5% CO2.

extract_protocol: QIAGEN RNA extract kit

treatment_protocol: Ewing sarcoma cell lines(A673 and SKNMC) were both treated with DMSO, 50 nM THZ1 or 200 nM THZ1 for 6 hours

tag: cell line

value: SKNMC

value: Ewing sarcoma cells

tag: cell number


title: A673_50nM_6hr

tag: tissue


title: A673_DMSO_6hr


title: SKMNC_200nM_6hr


title: Remitting sarcoidosis sample 5 [sarcmeth]

tag: group

value: Remit Sarc

value: W

tag: smoking status

value: Never

value: untreated

value: MTX


title: iPSC #2

description: Gene Expression (Clarion_S_Human Array) iPSC#2

source_name: iPSC #2

tag: subject #


title: NLRP2_over_rep1

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Reads quality was evaluated using FastQC (version 0.11.2, Babraham Institute Cambridge, UK) tool.
Reads were mapped to the human Ensembl GRCh38 build reference genome using STAR version 2.5.0a.The Ensembl annotation release 91 was used to build a transcriptome index that was then provided to STAR during the alignment.
The same gene annotations were used to quantify the gene-level read counts using HTSeq-count version 0.8.0 script.
The differential analysis for gene expression was performed using Bioconductor R version 3.4.4 package DESeq2 version 1.18.1.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes sample raw counts of the gene-level reads

source_name: conditionally immortalized PTEC (ciPTEC)

extract_protocol:
Total RNA was extracted using Trizol Reagent (Ambion)
Libraries were prepared for sequencing according to Lexogen's instructions accompanying the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.

tag: vector transfected

value: pEZ-M68 containing full length NLRP2


title: NLRP2_over_rep2


title: CTRL_rep1

value: empty pEZ-M68


title: CTRL_rep2


title: Remitting sarcoidosis sample 4 [sarcmeth]

tag: Sex

value: non-hispanic

tag: scadding

tag: forced vital capacity, percent predicted

tag: forced expiratory volume in one second, percent predicted


title: SKMNC_50nM_6hr


title: WT_mock_rep1

description:
Gene expression under control condition
US45103077_253459210074_S01_GE1_107_Sep09_1_1

tag: ecotype background

tag: genotype/variation

value: WT

tag: age

value: Five-day-old plant

value: mock

value: roots


title: WT_mock_rep2

description:
Gene expression under control condition
US45103077_253459210074_S01_GE1_107_Sep09_1_2

tag: treatment


title: A673_200nM_6hr


title: Remitting sarcoidosis sample 2 [sarcmeth]

description: Bisulfite-converted DNA from primary patient cells

value: female

tag: race

tag: total lung capacity, percent predicted

tag: diffusing capacity of the lung for carbon monoxide, percent predicted


title: iPSC #1

description: Gene Expression (Clarion_S_Human Array) iPSC#1

source_name: iPSC #1


title: Remitting sarcoidosis sample 1 [sarcmeth]

value: Male

tag: ethnicity

value: Untreated


title: Remitting sarcoidosis sample 3 [sarcmeth]


title: KO_young_bleo2

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

institute: INER

description: Gene expression data from young Zmpste24-/-

hyb_protocol: After fragmentation,cRNA were hybridized  with rotation at 60 rpm for 16 hr at 45°C  on Mouse Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChipTM Scanner 3000 7G Thermo Fisher P/N 00-0212 (North America) P/N 00-0213 (International)

data_processing: The results were analyzed by R software (http://www.r-project.org/) and Bioconductor (http://www.bioconductor.org/). To identify significant differences between gene expression in each condition, all data were analyzed by Limma linear model based on Bayes empirical method. Representative data were considered significantly with higher p-values (adjusted p-value < 0.05).

source_name: Lung tissue from bleomycin injured mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA (GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Array ).

growth_protocol: Mice were bred under specific pathogen-free conditions.

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

treatment_protocol: Lung injury was induced by oropharyngel administration of bleomycin  at a single dose of 1U/g of mice in 50 μl of vehicle. Control groups received the same volume of vehicle. Mice were sacrificed at  21 days after  treatment. Microarray experiments were performed in two different moments described here as set1, and set2.

tag: set

tag: strain

tag: tissue

value: Lung

value: 7 weeks

tag: genotype

value: Zmpste24 -/-


title: KO_young_v2_sal1

source_name: Lung tissue from saline treated mice


title: WT_old_bleo3

description: Gene expression data from old Zmpste24+/+

value: 82 weeks

value: zmpste24 +/+


title: KO_young_v2_sal2


title: WT_old_bleo2


title: KO_young_v2_sal3


title: KO_young_bleo1


title: WT_old_bleo1


title: WT_young_v2_sal2

description: Gene expression data from young Zmpste24 +/+


title: WT_young_bleo3

value: 16 weeks


title: WT_young_v1_sal1


title: WT_young_v2_sal1


title: WT_old_sal1


title: WT_old_sal3


title: KO_young_v1_sal1


title: WT_old_sal2


title: WT_young_bleo1


title: KO_young_v1_sal3


title: WT_young_v1_sal3


title: WT_young_v1_sal2


title: KO_old_bleo3

description: Gene expression data from old Zmpste24-/-


title: WT_young_v2_sal3


title: KO_old_bleo1


title: KO_old_sal3


title: WT_young_bleo2


title: KO_old_bleo2


title: BPVinf3

city: São Cristóvão

first: Marcus

last: Batista

state: Sergipe

address: Av Marechal Rondon, s/n

department: Department of Biology

country: Brazil

institute: Federal University of Sergipe

data_processing:
HiSeq 2500 Version 4 (Illumina Inc.), running HCS software v2.2.6
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD3.1 Bos taurus 8 whole genome using Tophat v2.0.11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using using Cufflinks v2.2.1. Identification of the differentially expressed genes was performed using Cuffdiff v 2.2.1 software and visualization was generated by CummeRbund
Genome_build: UMD3.1 Bos taurus 8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Bos taurus

source_name: BPV infected_Epithelial tissue

extract_protocol:
Total RNA were purified using RealipredTM RNA Tissue Miniprep System Kit (Promega), according to manufacturer’s instructions
Libraries were generated from 1000 ng of total RNA using the TruSeq stranded mRNA Sample Preparation LS Protocol Kit (Illumina Inc. San Diego, CA, USA), as per the manufacturer’s recommendations

value: 2 years old

value: BPV infected

value: Skin; Epithelial tissue


title: BPVnon1

source_name: BPV non-infected_Epithelial tissue

value: BPV non-infected


title: KO_old_sal2


title: BPVnon4


title: BPVinf2


title: BPVinf1


title: KO_young_bleo3


title: KO_old_sal1


title: BPVnon2


title: D. ananassae_stage5_replicate3

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dana-all-chromosome-r1.3.fasta
annotation file used: dana-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila ananassae

source_name: single embryo

growth_protocol: All species were maintained on molasses food in uncrowded conditions

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Libraries were constructed using Illumina Tru-Seq kits and indices

treatment_protocol: Eggs were collected from vials, and imaged to determine stage

tag: embryonic stage

value: stage 5

tag: replicate number

value: replicate 3

tag: raw data mixed with d. melanogaster?

value: no


title: D. ananassae_stage5_replicate1

value: replicate 1


title: D. ananassae_stage5_replicate2

value: replicate 2


title: D. ananassae_stage2_replicate3

value: stage 2


title: D. ananassae_stage2_replicate2


title: D. ananassae_stage2_replicate1


title: pse_latest5_M_1 [reanalyzed]

data_processing:
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Genome_build: See sample for information
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila pseudoobscura

source_name: embryo

value: embryo

tag: maternal genotype

value: Flagstaff 14

tag: paternal genotype

tag: Sex

value: M

tag: illumina index


title: pse_latest5_F_3 [reanalyzed]

value: F


title: pse_latest5_M_3 [reanalyzed]


title: pse_latest5_M_2 [reanalyzed]


title: pse_latest5_F_1 [reanalyzed]


title: pse_latest5_F_2 [reanalyzed]


title: WT_bleomycin_rep1

description:
Gene expression after bleomycin treatment
US45103077_253459210074_S01_GE1_107_Sep09_1_3

tag: ecotype background

tag: genotype/variation

value: WT

tag: age

value: Five-day-old plant

value: 0.6 µg/ml bleomycin for 10 h

value: roots


title: KO_young_v1_sal2

value: Lung

value: 7 weeks

value: Zmpste24 -/-


title: pse_st2_5 [reanalyzed]

tag: notes

value: possibly unfertilized


title: pse_st2_4 [reanalyzed]


title: pse_st2_3 [reanalyzed]


title: pse_st2_6 [reanalyzed]


title: D. mojavensis_stage5_replicate4

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dmoj-all-chromosome-r1.3.fa
annotation file used: dmoj-all-r1.3.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila mojavensis

value: stage 5

value: replicate 4

value: yes


title: D. mojavensis_stage5_replicate2

value: replicate 2


title: pse_st2_1 [reanalyzed]


title: pse_st2_2 [reanalyzed]


title: D. mojavensis_stage5_replicate1

value: replicate 1


title: D. mojavensis_stage5_replicate3

value: replicate 3


title: D. mojavensis_stage2_replicate5

value: stage 2

value: replicate 5


title: D. mojavensis_stage2_replicate3


title: D. mojavensis_stage2_replicate6

value: replicate 6


title: D. mojavensis_stage2_replicate1


title: D. mojavensis_stage2_replicate2


title: D. mojavensis_stage5_replicate5


title: Murine_Hep_Orgs_sc

city: Utrecht

first: Huili

last: Hu

address: Upsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: single cell sequencing from murine hepatocyte organoids

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4or 8 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: normalised abundance counts

source_name: Liver organoids

growth_protocol: Isolated hepatocytes were filtered by 70m filter, washed twice with cold AdDMEM/F12, counted and mixed with MatrigelR in suspension plates (Greiner). 20,000-50,000 cells were used per well of a 24 well plate. After MatrigelR was solidified, Hep-Medium was added. Hep-Medium consists of AdDMEM/F12 (Thermo Scientific, with Hepes, GlutaMax and Penicillin-Streptomycin ) plus 15% RSPO1 conditioned medium (home-made), B27 (minus vitamin A), 50ng/ml EGF (Peprotech), 1.25mM N-acetylcysteine (Sigma), 10 nM gastrin (Sigma), 3m CHIR99021 (Sigma), 25ng/ml HGF (Peprotech), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Peprotech), 1M A83-01 (Tocris), 10 mM Nicotinamide (Sigma), and 10M Rho Inhibitor -27632 (Calbiochem). 14 days after seeding, organoids were mechanically fragmented and re-seeded into new MatrigelR. During culturing, medium was refreshed at most every three days. Organoids are usually passaged with a split ratio of 1:3 every 7-10 days.

extract_protocol:
Hepatocytes were isolated by two steps of collagenase perfusion. Organoids were withdrawn from Matrigel. For bulk sequencing, mRNA were isolated by trizol method according to manufacter's protocol. RNA-sequencing libraries were prepared based on the DESeq2 method (Hashimshony et al., 2016; Love et al., 2014). For single cell sequencing, Organoids were digested by triple into single cells. Live positive single cells were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 8bp random molecular barcode (UMI), a cell-specific barcode, the 5'Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain background

value: C57/BL6 mice Hep-Orgs

tag: tissue/cell type

value: hepatocyte organoids (Hep-Orgs)


title: Sox2_M_PFA_1

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
ChIP-seq: Reads aligned with Bowtie2 with options “-k 10”. Reads were filtered for mapping quality 255 and edit distance <= 4. Reads with identical barcode, alignment position & strand  were treated as PCR-duplicates and collapsed. Peaks called with MACS2 with options “callpeak -q 0.2 -g mm”. BigWig files were generated by extending reads to mean fragment length.
Mnase-seq & ATAC-seq:  Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4.
RNA-seq: Stranded Reads pairs were aligned to the mm9 genome using RSEM-STAR pipeline with options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 –paired-end”.
MNase/ATAC-seq Meta Plot Library: Mid-points of MNase-fragments (140-200 bp), cut sites of ATAC-seq fragments (0-100 bp), counted at base pair resolution and normalised per million reads, in +/- 1000bp of TSS, EP300 summits, Esrrb Bookmarked Sites, Esrrb Lost Sites and Oct4/Sox2 sites. Mid-point/cutsite data smoothed by sparse Gaussian process regression using Gpy.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BigWig files, MNase-seq/ATAC-seq: Library of meta-plots in tab-separated format; RNA-seq: Raw and normalised read-counts tab-separated format.

growth_protocol: ES cells were cultured on 0.1% gelatine in DMEM + GlutaMax-I (Gibco, Cat# 31966-021) 10% FCS, 100 μM 2-mercaptoethanol, 1× MEM non-essential amino acids, and 10 ng×ml−1 recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895). When required medium was supplemented with 1 µM PD0325901 and 3 µM CHIR99021 (Axon Medchem Bv).

extract_protocol:
ATAC-Seq: 5x104 cells pellets were resuspended in 25 µl TD buffer (Nextera kit; Illumina, Cat# FC-121-1030). After the addition of 2.5 µl of transposase TDE1 and 22.5 µl nuclease free water, reactions were mixed and incubated for 30min at 37oC. Reactions were stopped by adding the appropriate volume of Binding Buffer and the DNA was purified using the Qiagen MinElute PCR Kit according to manufacturer’s protocol. The purified DNA was either stored at -20oC or used directly for library preparation.
ATAC-seq: Reactions were prepared mixing 10 µl transposed DNA, 2.5 µl 25 µM primer Ad1.noMX, 2.5 µl 25 µM primer Ad2 from (Buenrostro et al. 2013), 9 µl Nuclease Free Water, 1 µl of a 1:8 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496) and 25µl of KAPA HiFi HotStart 2× Master Mix (Kapa Bioscience Cat# KK2502). Amplification was carried out under the following conditions: Pre-amplification: 1 cycle: 5’ at 72°C; 30” at 98°C; 5 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C; Amplification: 1 cycle: 30” at 98°C; 11/12 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C. After amplification libraries were purified with SPRI beads, using a sample to bead ratio of 1: 1.4.
Cell-cycle RNA-seq: ES cells were sorted on the basis of Hoechst and GFP levels in three populations (early G1, late G1 and G2) as previously described (Festuccia et al. 2016). RNA was extracted with TRIzol (ThermoFisher, Cat# 15596026). Samples were DNAse I treated (Qiagen, Cat# 79254), phenol/chloroform extracted and ethanol precipitated.
ChIP-seq and MNase-seq: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC. DNA was purified with 90µl of SPRI beads and 50µl isopropanol and eluted in 21µl of water. DNA was mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water and mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters (See below), and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 Illumina primers. The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with SPRI beads using 70µl beads, no isopropanol, and eluting in water. Barcoded adaptor: 5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-IIIIII-NNNNNNNN-ATCTCGTATGCCGTCTTCTGCTTG. 5’P indicates the presence of a 5’phosphate group. IIIIII represent the six base index nucleotides, and NNNNNNNN a stretch of 8 random nucleotides used for single molecule barcoding. Universal adapter: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T. * indicates the presence of a phosphorothioate bond between the last C and T.
ChIP-seq/Mnase-seq Chromatin preparation: Interphase cells were resuspended in 2 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) and 0.5% IGEPAL. After 30 min on ice, the suspension was passed 40 times in a dounce homogenizer. Both mitotic and interphase cells were resuspended in 300 μl of TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1× PIC. Samples were sonicated in 1.5 ml tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power. After centrifugation (30 min, full speed, 4 °C), the supernatant was either used immediately for immunoprecipitation or stored at −80 °C until use.
ChIP-seq: Chromatin was pre-cleared for 3 hours rotating on-wheel at 4 °C in 300 μl of TSE150 containing 50 μl of protein G Sepharose beads 50% slurry, previously blocked with BSA and yeast tRNA. Immunoprecipitations with anti-ESRRB mouse monoclonal (1µg per 2x106cells, 5 μg per 107 cells; Perseus Proteomics, Cat# H6-705-00), anti-NANOG rabbit polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Cosmobio, Cat#  REC-RCAB001P); anti-POU5F1 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc-5279); anti-SOX2 goat polyclonal (0.6 μg per 2x106cells, 3 μg per 107 cells; Santa Cruz Biotechnology, Cat # sc- 17320), were performed overnight rotating on-wheel at 4 °C in 500 μl of TSE150. Twenty-five microliters of blocked protein G beads 50% slurry was added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 5 min rotating on-wheel at room temperature with 1 ml of buffer in the following order: 3 × TSE150, 1 × TSE500 (as TSE150 but 500 mM NaCl), 1× washing buffer (10 mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and 2 × TE (10 mM Tris-HCl pH8, 1 mM EDTA). Elution was performed in 100 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) for 15 min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150 μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
Chip-seq: Fixation DSG+FA.  ES cells were crosslinked in PBS-DSG 2 mM at pH 7.0 (Sigma, Cat# 80424-5 mg) for 50 min at room temperature with occasional shaking and incubated for 10 min in 2 ml PBS 1% formaldehyde after washing in PBS. Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. Fixation FA: ES cells crosslinked in 3 ml of pre-warmed DMEM/FCS/LIF for 10 min at room temperature adding 1% formaldehyde (Thermo, Cat# 28908). Crosslinking was stopped with 0.125 M glycine for 5 min at room temperature.
H3 ChIP-seq:  ChIP was performed as described using 5 µg of anti-Histone H3 rabbit polyclonal (Abcam, Cat# ab1791).
MNase-seq: Cells fixed in formaldehyde as for ChIP were pre-incubated for 10 min at 37°C and ½ U, 16 U or 128 U of MNase (Expressed in KUntiz, 1 Kunitz is equivalent to 10 gel units, NEB Cat# M0247S) added to the reaction. Cells were incubated for further 10 min at 37°C, inverting the tubes occasionally. The reaction was stopped on ice by adding 500ul of 2 × STOP buffer (2% Triton X-100, 0.2% SDS, 300mM NaCl, 10mM EDTA). Tubes were left rotating overnight on a wheel to allow diffusion of the digested fragments. The cell suspension was spun down and the supernatant stored at -80°C. Samples were then incubated over night at 65°C in TE 1% SDS to revert the crosslinking, and treated with Proteinase K. DNA was phenol/chloroform extracted, ethanol precipitated, and RNase treated. 50 µl of DNA was purified with 90µl of SPRI beads and 50 µl isopropanol.
RNA-seq:Ribo-depleted, stranded and paired-end RNA-seq libraries were prepared and sequenced by Novogene Co Ltd.

treatment_protocol:
ChIP-seq and MNase-seq: E14tg2a cells grown in T150 flasks were treated for 4-5 h with 50 ng×ml−1 nocodazole. Shake-off was performed and the cell suspension was filtered through a 10µm filter (pluriSelect, Cat# 43-50010-03). For interphase samples, untreated cells were trypsinised and collected in parallel.
Cell-cycle RNA-seq: GFP Sox2-AID ES cells were cultured in the presence of 0.5mM of auxin (Sigma, Cat# I5148) for 3 hours. During the last 20 minutes 20μM Hoechst-33342 was added.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: fixative

value: FA

tag: cellcycle

value: M

tag: chip antibody

value: Sox2 (Santa Cruz Biotechnology, sc-17320, K0813)

tag: barcode


title: Sox2_M_DSGPFA_1

value: DSGFA


title: Sox2_A_PFA_1

value: I


title: Oct4_A_PFA_1

value: Oct4 (Santa Cruz Biotechnology, sc-5279, F1016)


title: Oct4_A_DSGPFA_1


title: Nanog_M_PFA_1


title: D. mojavensis_stage2_replicate4

tag: embryonic stage

tag: replicate number

value: replicate 4

tag: raw data mixed with d. melanogaster?


title: Nanog_M_DSGPFA_1


title: Input_A_PFA_1

value: none (Input)


title: Input_M_DSGPFA_1


title: Input_M_PFA_1


title: Input_A_DSGPFA_1


title: Nanog_A_DSGPFA_1


title: Nanog_A_PFA_1


title: Esrrb_M_PFA_2

value: Esrrb (Perseus Proteomics, PP-H6705-00, A-2)


title: Esrrb_M_PFA_1


title: WT2: Contol

city: Cambridge

first: Matthew

middle: C

last: Hill

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description: We performed scRNA-seq on dissociated olfactory bulbs from control animals.

data_processing:
Sequencing data was handled using the 10X Genomics Cell Ranger software  (version 2.0.0). Subsequently, expression matrices from each experiment were merged and imported into Seurat (version 2.2.1)(Butler et al. 2018), where Log normalization and scaling was performed (Thulasi Raman et al. 2016). The minimum gene per cell threshold was set to 200 for inclusion into the final digital expression matrix. Batch effects were corrected for by regressing out the number of molecules per cell, mitochondrial genes, and the batch identity with the RegressOut function (Seurat package). Next, principle components analysis (PCA) was performed and significant PCs were used as input for graph-based clustering. 2-dimensional visualization of the multi-dimensional data set was done with t-SNE. Differential expression of the individual clusters was performed using the likelihood-ratio test for single cell gene expression (Seurat FindMarkers function, default parameters). To account for over-clustering, clusters that were not transcriptionally distinct were merged together into a single cluster. Clusters composed of doublets (2 different cell types within single droplet) were removed from the data set.
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression (dge) files for the raw merged data, and processed and scaled data were exported directly from Seurat as csv files.

source_name: Olfactory bulb

extract_protocol:
Animals were deeply anesthetized using isoflurane, and perfused intracardially with phosphate-buffered saline (PBS). Brains were dissected, and OBs were removed from the rest of the brain. To ensure inclusion of the most anterior parts of the OB, brains were dissected out with the tissues surrounding them. Since olfactory epithelium is juxtaposed to the OB at the most anterior part of the brain, our data include some olfactory epithelium cells.  OB tissue was dissociated according to the 10X Genomics Chromium sample preparation protocol. Briefly, the tissue was cut into 1 mm3 pieces and placed in 2 mL papain solution (Worthington, PAPL) prepared according to manufacturer’s protocol in Hibernate E-Calcium (BrainBits, HECA100). Tissue was incubated in papain solution at 37oC for 20 min. Papain solution was removed and discarded by leaving the tissue at the bottom of the tube. 2 mL of HEB medium (BrainBits, HEB100) was added to the samples and triturated with a fire polished Pasteur pipette, passing the tissue through the pipette 10 – 15 times. Un-dissociated tissue was allowed to settle to the bottom of the tube for 1 minute. The supernatant containing the dissociated cells was moved to a different tube after passing through 70 µm mesh three times. Samples were centrifuged for 2 minutes at 200 rcf and the supernatant was discarded. Cells were resuspended in NbActiv1 (BrainBits, NbActiv1 100) solution and placed on ice until the single cell RNA-seq experiment. Cells were counted and diluted in 1X PBS with 0.04% Bovine Serum Albumin (BSA) prior to loading onto the 10X Genomics Chromium instrument.
The scRNA-seq libraries were generated using the 10X Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions and were sequenced on an Illumina Nextseq500.

tag: mouse strain

tag: tissue

value: Olfactory bulb

tag: manipulation


title: Esrrb_M_DSGPFA_2


title: Esrrb_A_PFA_1


title: WT1: Contol


title: Esrrb_M_DSGPFA_1


title: Sox2_A_DSGPFA_1


title: Esrrb_A_DSGPFA_1


title: Oct4_M_PFA_1


title: TR2: Trained

description: We performed scRNA-seq on dissociated olfactory bulbs from animals which were olfactory enriched through training on an olfactory discrimination learning paradigm

value: Olfactory training


title: Oct4_M_DSGPFA_1


title: OC1: Naris occlusion

description: We performed scRNA-seq on dissociated olfactory bulbs from olfactory deprived animals.

value: olfactory deprivation, naris occlusion


title: OC2: Naris occlusion


title: 8 wk after TAM 3

city: Shinjuku-ku

first: Yusuke

last: Mizuno

state: Tokyo

address: Shinanomachi 35

department: Pediatrics

institute: Keio University

data_processing:
bcl2fastq2 v2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using TopHat 2.0.14.
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using Genedata Profiler Genome software 10.1.15a.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt

source_name: adrenal gland

extract_protocol: RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit and standard Illumina protocols

tag: strain

value: adrenal gland

tag: duration after star ko

value: 8 wks


title: 8 wk after TAM 4


title: 8 wk after TAM 2


title: 24h after TAM 4


title: 8 wk after TAM 1


title: Esrrb_A_PFA_2


title: Esrrb_A_DSGPFA_2


title: 24h after TAM 3


title: 24h after TAM 1


title: Before TAM 5

value: before


title: Before TAM 4


title: 24h after TAM 2


title: Before TAM 3


title: Before TAM 2


title: Before TAM 1


title: Sox2_A_DSGPFA_4


title: Sox2_A_DSGPFA_5


title: TR1: Trained


title: Sox2_M_DSGPFA_5


title: Oct4_M_DSGPFA_3


title: Sox2_M_DSGPFA_4


title: Oct4_M_DSGPFA_4


title: Sox2_M_DSGPFA_2


title: Sox2_A_DSGPFA_3


title: Sox2_A_DSGPFA_2


title: Oct4_A_DSGPFA_4


title: Nanog_M_DSGPFA_2


title: Oct4_A_DSGPFA_2


title: Oct4_A_DSGPFA_3


title: Input_M_DSGPFA_3


title: Nanog_A_DSGPFA_2


title: Input_M_DSGPFA_2


title: Input_A_DSGPFA_4


title: Input_A_DSGPFA_3


title: Input_A_DSGPFA_2


title: Oct4_M_DSGPFA_2


title: Sox2_M_DSGPFA_3


title: Atxn1-154Q/2Q KI Replicate 1 Inferior Olive 12 Weeks Old

city: New Haven

first: Janghoo

last: Lim

state: CT

address: 295 Congress Ave, BCMM

institute: Yale University

data_processing:
TopHat2 v2.1.0 was utilized to align reads to the mouse reference genome (mm10).
The iGenomes mm10 gtf file was used for annotation.
Cuffquant from Cufflinks v2.2.1 was used for gene expression quantification.
Differential expression analyis was carried out using Cuffdiff from Cufflinks v2.2.1.
Cuffnorm was utilized for generating normalized expression values.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain normalized FPKMs for each biological sample, as well as Cuffdiff output for each comparison.
Supplementary_files_format_and_content: ATXN1_82Q_Tg_Cerebellum_5weeks.txt: Normalized FPKM for WT and ATXN1-82Q Tg 5 week cerebellum, and Cuffdiff comparison
Supplementary_files_format_and_content: ATXN1_82Q_Tg_Cerebellum_12weeks.txt: Normalized FPKM for WT and ATXN1-82Q Tg 12 week cerebellum, and Cuffdiff comparison
Supplementary_files_format_and_content: ATXN1_82Q_Tg_Inferior_Olive_5weeks.txt: Normalized FPKM for WT and ATXN1-82Q Tg 5 week inferior olive, and Cuffdiff comparison
Supplementary_files_format_and_content: ATXN1_82Q_Tg_Inferior_Olive_12weeks.txt: Normalized FPKM for WT and ATXN1-82Q Tg 12 week inferior olive, and Cuffdiff comparison
Supplementary_files_format_and_content: Atxn1_154Q_KI_Cerebellum_5weeks.txt: Normalized FPKM for WT and Atxn1 154Q/2Q KI 5 week cerebellum, and Cuffdiff comparison
Supplementary_files_format_and_content: Atxn1_154Q_KI_Cerebellum_12weeks.txt: Normalized FPKM for WT and Atxn1 154Q/2Q KI 12 week cerebellum, and Cuffdiff comparison
Supplementary_files_format_and_content: Atxn1_154Q_KI_Inferior_Olive_5weeks.txt: Normalized FPKM for WT and Atxn1 154Q/2Q KI 5 week inferior olive, and Cuffdiff comparison
Supplementary_files_format_and_content: Atxn1_154Q_KI_Inferior_Olive_12weeks.txt: Normalized FPKM for WT and Atxn1 154Q/2Q KI 12 week inferior olive, and Cuffdiff comparison

source_name: inferior olive

growth_protocol: Not applicable

extract_protocol:
Cerebella and inferior olive were dissected out, flash frozen, and kept at -80°C until further processing. For inferior olive, the brainstem was removed and the inferior olive dissected using the decussation of the pyramid and pons as a reference. Anatomical location was verified under a dissection microscope. The same individual conducted all tissue extractions to eliminate variability in sample collection. RNA was extracted using a Qiagen RNeasy Mini Kit, following the manufacturer's protocol. RNA was sent to the Yale Center for Genome Analysis for library prepration and sequencing.
The RNA libraries for all experiments were conducted using standard Illumina protocols.

treatment_protocol: Mice were maintained on a 12 hour light/dark cycle with standard chow and ad libitum access to water. ATXN1-82Q Tg mice were maintained on a FVB/NJ background, and Atxn1 154Q/2Q KI mice on a pure C57BL/6J background (Burright et al., 1995; Watase et al., 2002). All procedures were approved by the Yale University Institutional Animal Care and Use Committee. For RNA-sequencing, male mice were used.

value: inferior olive

tag: age

value: 12 weeks old

tag: genotype

value: Atxn1-154Q/2Q KI


title: Atxn1-154Q/2Q KI Replicate 2 Inferior Olive 12 Weeks Old

description: Atxn1_154Q_KI_Inferior_Olive_12weeks.txt


title: Atxn1-154Q/2Q KI Replicate 3 Inferior Olive 12 Weeks Old


title: WT/C57 Replicate 3 Inferior Olive 12 Weeks Old

value: wild-type


title: WT/C57 Replicate 2 Inferior Olive 12 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 3 Inferior Olive 5 Weeks Old

value: 5 weeks old


title: WT/C57 Replicate 1 Inferior Olive 12 Weeks Old


title: WT/C57 Replicate 1 Inferior Olive 5 Weeks Old


title: WT/C57 Replicate 2 Inferior Olive 5 Weeks Old


title: WT/C57 Replicate 3 Inferior Olive 5 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 3 Cerebellum 12 Weeks Old

source_name: cerebellum

value: cerebellum


title: Atxn1-154Q/2Q KI Replicate 2 Cerebellum 12 Weeks Old


title: WT/C57 Replicate 3 Cerebellum 12 Weeks Old


title: WT/C57 Replicate 1 Cerebellum 12 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 1 Cerebellum 12 Weeks Old


title: WT/C57 Replicate 2 Cerebellum 12 Weeks Old


title: WT/C57 Replicate 3 Cerebellum 5 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 2 Cerebellum 5 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 1 Cerebellum 5 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 3 Cerebellum 5 Weeks Old


title: WT/C57 Replicate 1 Cerebellum 5 Weeks Old


title: WT/C57 Replicate 2 Cerebellum 5 Weeks Old


title: ATXN1-82Q Tg Replicate 2 Inferior Olive 12 Weeks Old

value: FVB/NJ

value: ATXN1-82Q Tg


title: ATXN1-82Q Tg Replicate 3 Inferior Olive 12 Weeks Old


title: ATXN1-82Q Tg Replicate 1 Inferior Olive 12 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 1 Inferior Olive 5 Weeks Old


title: Atxn1-154Q/2Q KI Replicate 2 Inferior Olive 5 Weeks Old


title: WT/FVB Replicate 3 Inferior Olive 12 Weeks Old


title: WT/FVB Replicate 2 Inferior Olive 12 Weeks Old


title: WT/FVB Replicate 1 Inferior Olive 12 Weeks Old


title: ATXN1-82Q Tg Replicate 3 Inferior Olive 5 Weeks Old


title: WT/FVB Replicate 2 Inferior Olive 5 Weeks Old


title: ATXN1-82Q Tg Replicate 1 Inferior Olive 5 Weeks Old


title: ATXN1-82Q Tg Replicate 3 Cerebellum 12 Weeks Old


title: ATXN1-82Q Tg Replicate 2 Inferior Olive 5 Weeks Old


title: WT/FVB Replicate 1 Inferior Olive 5 Weeks Old


title: WT/FVB Replicate 3 Inferior Olive 5 Weeks Old


title: ATXN1-82Q Tg Replicate 3 Cerebellum 5 Weeks Old


title: ATXN1-82Q Tg Replicate 2 Cerebellum 12 Weeks Old


title: WT/FVB Replicate 2 Cerebellum 12 Weeks Old


title: WT/FVB Replicate 1 Cerebellum 12 Weeks Old


title: WT/FVB Replicate 3 Cerebellum 12 Weeks Old


title: WT/FVB Replicate 2 Cerebellum 5 Weeks Old


title: ATXN1-82Q Tg Replicate 2 Cerebellum 5 Weeks Old


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_8_B

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Standard Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 using tophat
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, normalization, and differential expression analysis were calculated using Cufflinks and cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements

source_name: WNT5A treated LT-HSC sorted from young mouse (daughter cell)

growth_protocol: Cells were cultured in IMDM + 10% FBS + Cytokines mSCF,GCSF, and mTPO 50ng/ml at 37°C (5% CO2, 3% O2). Mother cells were collected 16hrs after culture. Daughter cells were cultured for 40 to 44 hrs, for first cell division.

extract_protocol:
For single cell transcriptome profiling, SMART-Seq v4 Ultra Low Input RNA kit from Clontech (Catalog # 634892) was used. The cDNA synthesis and amplification were performed as recommended by Clontech. The kit generates Illumina compatible cDNA library.
The amplified cDNA generated from single cells were used to make libraries using Illumina’s Nextera XT DNA Library Preparation kit (Catalog # FC-131-1096) as per Illumina’s instructions.

treatment_protocol: 5µM CASIN (CASIN treatment); 100 ng/ml Wnt5a directly added to the medium at the beginning of culture.

tag: treatment

value: B6.SJL mice

value: Long-term Hematopoietic stem cells (LT-HSC)


title: WT/FVB Replicate 1 Cerebellum 5 Weeks Old


title: WT/FVB Replicate 3 Cerebellum 5 Weeks Old


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_8_A


title: ATXN1-82Q Tg Replicate 1 Cerebellum 12 Weeks Old


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_5_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_6_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_7_A


title: ATXN1-82Q Tg Replicate 1 Cerebellum 5 Weeks Old


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_5_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_4_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_4_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_7_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_3_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_3_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_13_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_13_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_2_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_2_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_11_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_12_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_12_A


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_11_A


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_8_M

source_name: Untreated (Control) LT-HSC sorted from young mouse (mother cell)

value: CONTROL


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_3_M


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_10_M


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_5_M


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_9_M


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_1_M


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_6_M


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_9_A

source_name: Untreated (Control) LT-HSC sorted from young mouse (daughter cell)


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_5_B


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_5_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_6_B


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_4_B


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_6_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_3_B


title: WNT5A_Young_Daughter TY3_WNT5A_D_Y_1_Y6_6_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_4_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_2_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_2_B


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_3_A


title: CONTROL_Young_Daughter TY3_CONTROL_D_Y_1_Y6_9_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_6_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_6_A


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_5_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_4_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_4_A


title: CONTROL_Young_Mother TY3_CONTROL_M_Y_1_Y6_4_M


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_3_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_3_A


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_2_A


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_2_B


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_1_A


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_1_B


title: CONTROL_Young_Daughter TY2O3P2_CONTROL_D_Y_1_Y5_4_B


title: CONTROL_Aged_Mother TY2O3P2_CONTROL_M_O_1_O5_1_M

source_name: Untreated (Control) LT-HSC sorted from aged mouse (mother cell)


title: CONTROL_Aged_Mother TY2O3P2_CONTROL_M_O_1_O5_3_M


title: CONTROL_Young_Daughter TY2O3P2_CONTROL_D_Y_1_Y5_4_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_8_B

source_name: CASIN treated LT-HSC sorted from aged mouse (daughter cell)


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_8_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_7_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_5_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_7_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_4_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_5_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_6_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_6_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_3_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_4_A


title: WNT5A_Young_Daughter TY2O3P2_WNT5A_D_Y_1_Y5_5_A


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_2_B


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_2_A


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_7_M


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_8_M


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_6_M


title: CONTROL_Aged_Daughter TY2O3P2_CONTROL_D_O_1_O5_3_A


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_5_M


title: CONTROL_Aged_Mother TY2O3P2_CONTROL_M_O_1_O5_7_M


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_4_M


title: CONTROL_Aged_Mother TY2O3P2_CONTROL_M_O_1_O5_5_M


title: CONTROL_Aged_Mother TY2O3P2_CONTROL_M_O_1_O5_6_M


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_1_M


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_3_A


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_2_B


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_3_B


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_1_A


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_1_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_7_A

value: CASIN


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_8_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_8_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_6_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_4_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_5_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_7_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_5_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_4_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_3_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_2_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_2_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_3_A


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_1_B


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_2_M


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_3_B


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_2_B


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_3_A


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_1_B


title: CONTROL_Young_Daughter TY2O3P1_CONTROL_D_Y_1_Y5_2_A


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_1_A


title: CONTROL_Young_Mother TY2O3P1_CONTROL_M_Y_1_Y5_3_M


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_6_B


title: CONTROL_Young_Mother TY1_CONTROL_M_Y_1_Y4_4_M


title: WNT5A_Young_Daughter TY1_WNT5A_D_Y_1_Y4_2_A


title: CONTROL_Young_Mother TY1_CONTROL_M_Y_1_Y4_1_M


title: CONTROL_Young_Mother TY1_CONTROL_M_Y_1_Y4_3_M


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_5_B


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_5_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_4_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_4_B


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_3_B


title: CASIN_Aged_Daughter TY2O3P1_CASIN_D_O_1_O5_1_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_2_B


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_2_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_1_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_1_B


title: CONTROL_Aged_Mother TO4_CONTROL_M_O_1_O6_3_M


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_7_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_5_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_4_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_5_A


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_6_A


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_3_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_2_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_4_A


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_3_A


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_1_B


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_2_A


title: CONTROL_Young_Mother TY1_CONTROL_M_Y_1_Y4_2_M


title: CONTROL_Aged_Daughter TO4_CONTROL_D_O_1_O6_1_A


title: CONTROL_Young_Daughter TY1_CONTROL_D_Y_1_Y4_3_A


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_7_A


title: CASIN_Aged_Daughter TO4_CASIN_D_O_1_O6_6_B


title: D. virilis_stage5_replicate11

data_processing:
Genome_build:flybase genome used for alignment/processing: dana-all-chromosome-r1.3.fasta dvir-all-chromosome-r1.2.fa
annotation file used: dvir-all-r1.2.gff
a preprocessing step using cutadapt removed adapters, barcodes and low quality regions of reads
reads were aligned using Tophat2
transcriptome assembly was carried out using cufflinks
the assemblies were merged using cuffmerge
abundance estimates were calculated with cuffquant (using the merged assemblies) followed by cuffnorm
differential expression was determined using cuffdiff
Supplementary_files_format_and_content: Mean FPKM values for each species at each stage. One file (gene_exp_orthologs_any) provides FPKM values for all genes with any orthology in any species, the other (gene_exp_orthologs_all_14_species_present) provides FPKM values for all genes with one-to-one orthologs in all 14 species. The FPKM value for each gene is the sum of the FPKM values for all isoforms of that gene.

organism: Drosophila virilis

value: stage 5

value: replicate 11

value: no


title: D. virilis_stage5_replicate10

value: replicate 10