title: GFP

city: SEOUL

first: JUNG

middle: HOON

last: KIM

state: MAPOGU

address: SOGANG R 1206

department: LIF SCIENCE

institute: SOGANG UNIV

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the Affymetrix GeneChip® Mouse Gene 2.0 ST Array for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained using SAPE (Streptavidin Phycoerythrin) and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix). the image data was extracted through Affymetrix Commnad Console software1.1.

data_processing: The raw .cel file generated through above procedure meant expression intensity data and was used for the next step.  Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: NIWA ESC

label_protocol: Per RNA sample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: GFP and EWS OCT4A-GFP Niwa stable cell lines, both were cultured in ESC media with LIF.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, USA), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: We treated 1ug/ml Doxycycline to down-regulate endogenous OCT-4 respectively in stable cell lines.

value: Niwa-GFP stable cell line


title: adult human lung stromal cells from distal portion enriched in alveoli

status: Public on Aug 08 2018

type: SRA

city: San Francisco

first: Peng

last: Tien

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

country: USA

institute: University of California San Francisco

description: single cell RNA sequencing of adult human distal alveolar lung (EPCAM-/CD45-/CD11b-/CD31-) stromal cells

library_source: transcriptomic

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 using default parameteres.
Genome_build: hg19
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

molecule: total RNA

organism: Homo sapiens

source_name: adult human lung distal alveolar stromal cells

extract_protocol:
The human lung tissue (~10 cm3) was dissected from the whole lung and washed with HBSS X 4 times in 15 min. The piece of lung was further diced with razor blades and was added into the digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (100 U/ml, Sigma). The mixture was incubated for 2 h at 37 ºC and vortexed intermittently. The mixture was then liquefied with a blender and passed through 4X4 gauze, a 100 µm and a 70 µm cell strainer. The mixture was resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 ºC and washed with FACS buffer. The following antibodies were used at 1:200 for staining: anti-CD45-APC-Cy7 (BioLegend), anti-CD31-APC-Cy7 (BioLegend), anti-CD11b-APC-Cy7 (BD Biosciences) and anti- EPCAM-APC-Cy7 (BioLegend). DRAQ7 (CST, 1:1000) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DRAQ7 fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.
droplet-based single cell RNA-Seq

tag: tissue

value: lung

tag: developmental stage

value: adult

tag: cell type

value: lung distal alveolar stromal cells


title: 28_HM_1_FC2

city: Chicago

first: Bryan

middle: J

last: Pavlovic

state: IL

department: Human Genetics

institute: University of Chicago

data_processing:
100 bp single-end RNA-seq reads from each species were mapped to the appropriate genome (hg38 or panTro5) using Hisat2 (version 2.0.4) (Kim et al. 2015). Only reads that mapped uniquely were used.
The number of reads falling into orthologous meta-exons across 44,125  Ensembl genes from hg38, panTro5 was determined using featureCounts within SubRead (version 1.5.1) (Liao et al. 2014).
Genome_build: hg38 & panTro5
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

source_name: induced pluripotent stem cells

growth_protocol: Feeder free iPSC cultures were initially maintained on Growth Factor Reduced Matrigel using Essential 8 Medium (E8) as previously described. After 10 passages in E8, all cell lines were transitioned to a 50/50% ratio of iDEAL/E8 feeder free medium that was prepared in house as specified previously (Marinho et al. 2015). Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

extract_protocol:
RNA was extracted using the ZR-Duet DNA/RNA MiniPrep kit (Zymo) with the addition of an on column DNAse I treatment step prior to RNA elution.
Samples were pooled together in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.Samples were pooled  in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

treatment_protocol: Cardiomyocytes were generated following a recently protocol ((Rana et al. 2012; Burridge et al. 2014; Burridge et al. 2015)) with minimal modification. At 12 hours prior to initiating differentiation, iPSC lines at 70-90% confluence were seeded to achieve a starting density of 150,000-250,000 cells/cm2. Differentiations were initiated by removing stem cell maintenance media and adding RPMI base media (with HEPES LifeTechnologies# 22400105) supplemented with 6 μM CHIR9902 (LClabs# C-6556), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390), 0.3 μg/mL sodium selenite (Sigma-Aldrich# S5261), 5 μg/mL Holo-transferrin (Sigma-Aldrich# T3705), 1 μg/mL Linolenic acid (Sigma-Aldrich# L2376), 1 μg/mL Linoleic acid (Sigma-Aldrich# 1012) and 1x Pen/Strep (Days 0-1 media). After 48 hours the media was changed to RPMI base media (with HEPES LifeTechnologies# 22400105) supplemented with 2 μM Wnt-c59 (Tocris# 5148), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390 and 1x Pen/Strep (Days 2-3 media).  After another 48 hours, the media was changed to RPMI base (with HEPES LifeTechnologies# 22400105) supplemented 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep. Media was changed every 48 hours until day 10 (total of 2 additional media changes). At day 10 the media was switched to RPMI media (no glucose, Cellgro#10-043-CV) supplemented with 5 mM Sodium D/L Lactate (Sigma-Aldrich# L4263), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep, media was changed every 48 hours (total of 2 additional media changes). At day 15, cells were dissociated using TrypLE and split to a density of 0.4 x 106 cells/cm2 onto Matrigel coated dishes. Cells were replated in RPMI media (no glucose, Cellgro#10-043-CV) supplemented with 5% FBS, 10 mM D-galactose (Sigma-Aldrich# G5388), 1 mM Sodium Pyruvate (LifeTechnologies# 11360070), 1X NEAA (LifeTechnologies# 11140076), 5 mM HEPES (LifeTechnologies# 15630080), mM Sodium D/L Lactate (Sigma-Aldrich# L4263), 0.5 mg/mL BSA (Sigma-Aldrich# A2153), 0.213 mg/mL ascorbic acid (Santa Cruz Bio# sc-228390) and 1x Pen/Strep (Galactose media). After 24 hours, the media was changed to Galactose media without FBS. Media was changed every 48 hours (total of 1 additional media change). At day 20 media was changed to Galactose media supplemented with 3 ng/mL Triiodothyronine (T3, Sigma-Aldrich# T6397). Media was changed every 48 hours until cells were harvested at day 27 (total of 3 additional media changes). For the first two media changes (Days 0 and 2) cultures were supplies with an excess of media (0.499 mL/cm2), all other days media was added at (0.2495 mL/cm2).

tag: cell line

tag: Sex

value: Male

tag: population

value: Caucasian

value: induced pluripotent stem cells


title: EWS-OCT4A-GFP

type: RNA

country: South Korea

label: biotin

organism: Mus musculus

value: Niwa EWS-OCT4A-GFP stable cell line


title: ALCL02

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

description: Gene expression data from human anaplastic large cell lymphoma biopsies

hyb_protocol: Following fragmentation, cRNA were hybridized to a HG-133_Plus_2 gene chip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: CEL files were processed to extract perfect match probes (PMPs) and raw intensities were normalized using robust multi-array average (RMA) with background correction. Normalized intensities were log2-transformed prior to further analysis

source_name: Lymphnode biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Total RNA was extracted from frozen tumor tissue using PerfectPure (5 PR IME, Gaithersburg, MD). RNA quality was confirmed on an Agilent Bioanalyzer (Agilent Technologies,Santa Clara, CA).

treatment_protocol: Tissue biopsies were fixed in OCT and frozen.

tag: age/gender

tag: who diagnosis

value: ALCL, ALK negative

tag: genetic subtype

value: Other


title: FVB heart replicate 1

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9/rn5 using bowtie2
For 3'READs data, reads with a mapping quality score (MAPQ) ?10 were kept for further analysis. Reads with ?2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: mm9 for mouse, rn5 for rat
Supplementary_files_format_and_content: tab-delimited text files include reads count for each PAS position

source_name: heart

extract_protocol:
TRIzol
See the "extraction protocol" column in the SAMPLES section.
3'READS: The 3’READS procedure has been described in (Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina NextSeq 500 (1x75 bases).

value: heart

tag: protocol

tag: purpose

value: Analysis of APA in heart, testis and heart between mouse and rat

tag: strain

value: FVB/NJ


title: 7452 Epididymis, Cre-

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description: Gene expression data from the epididymis of Cre- TGFbR2fl/fl males

hyb_protocol: According to manufacturer's (Affymetrix) protocol

data_processing: The data were analyzed with GeneSpring 14.9, using  ExonRMA16 summarization algorithm; quantile sample normalization with baseline transformation to median of all samples

source_name: mouse epididymis

growth_protocol: 8-10 week old mice housed in  a barrier animal facility monitored and free of common murine pathogens (MHV, MPV, MVM, TMEV, Mycoplasma pulmonis, Sendai, EDIM, MNV, and eco- and endoparasites)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by column purification (Qiagen Mini RNA kit)

treatment_protocol: Anaysis was performed at baseline, with no treatment

value: epididymis

tag: genotype

value: Cre-

tag: treatment

value: untreated


title: 146_HM_1_FC2


title: C57 heart replicate 2


title: 60_HM_1_FC1


title: C57 heart replicate 1


title: 28_HM_1_FC1


title: 146_HM_1_FC1


title: FVB brain replicate 1

source_name: brain

value: brain


title: C57 brain replicate 3


title: 90_HF_1_FC2

value: Female


title: C57 brain replicate 2


title: FVB brain replicate 2


title: 75_HF_1_FC2


title: 48_HF_1_FC2


title: 13_HF_1_FC2


title: C57 heart replicate 3


title: FVB testis replicate 2

source_name: testis

value: testis


title: 124_HF_1_FC2


title: FVB heart replicate 2


title: adult mourin lung stromal cells from proximal portion enriched in airways

description: single cell RNA sequencing of adult human proximal airway lung (EPCAM-/CD45-/CD11b-/CD31-) stromal cells

source_name: adult human lung proximal airway stromal cells

value: lung

value: adult


title: C57 brain replicate 1


title: 90_HF_1_FC1


title: 75_HF_1_FC1


title: 110_HF_1_FC2


title: 48_HF_1_FC1


title: 13_HF_1_FC1


title: SAM24345996 vismo 6d

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

library_source: genomic

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Genome_build: GRCm38
Supplementary_files_format_and_content: One bigWig file for each sample containing the normalized coverage in log counts per million

molecule: genomic DNA

source_name: Skin

extract_protocol:
Tumour cells were collected in FACS buffer, centrifuged for 8 minutes at 500g, and 100,000 cells were resuspended in 100 μL of lysis buffer (Tris HCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0,1%) and centrifuged (500 g) for 25 min at 4°C. Supernatant was discarded and nuclei were resuspended in 50 μL of reaction buffer (Tn5 transposase 2,5 μL, TD buffer 22,5 μL and 25 μL H2O - Nextera DNA sample preparation kit, Illumina). The transposase reaction was performed for 30 min at 37°C and then blocked by addition of 5μL of clean up buffer (NaCl 900mM, EDTA 300mM). .
DNA was purified using the MinElute purification kit (QIAGEN). DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected for 200 to 800 bp (BluePippin, Sage Sciences) following manufacturers' protocols

value: Skin

tag: tissue diagnosis

value: Carcinoma Basal Cell

tag: strain/genotype

value: K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP

value: vismodegib - 6 days


title: SAM24350077 vismo 14d

value: vismodegib - 14 days


title: SAM24350080 vismo 14d


title: SAM24350076 vismo 14d


title: SAM24345995 MCT

value: control


title: SAM24345999 vismo 6d


title: SAM24345994 MCT


title: SAM24345403 vismo 6d


title: SAM24345402 MCT


title: 124_HF_1_FC1

value: Caucasian

value: induced pluripotent stem cells


title: 57_HM_3_FC2

source_name: Primary Heart Tissue

value: Male

value: Primary Heart Tissue


title: 71_HM_3_FC2


title: 110_HF_1_FC1


title: 160_HM_3_FC2


title: 158_HM_3_FC2


title: 25_HM_3_FC2


title: 143_HM_3_FC2


title: 57_HM_3_FC1


title: 71_HM_3_FC1


title: 25_HM_3_FC1


title: 160_HM_3_FC1


title: 143_HM_3_FC1


title: 165_HF_3_FC2


title: 163_HF_3_FC1


title: 69_HF_3_FC1


title: 140_HF_3_FC2


title: 36_HM_2C_FC1

source_name: iPSC-derived cardiomyocytes day 27 Not T3 treated

value: iPSC-derived cardiomyocytes

value: Not T3 treated


title: 45_HM_3_FC2


title: 126_HF_2C_FC2


title: 99_HF_2C_FC1


title: 126_HF_2C_FC1


title: 134_HF_2C_FC1


title: 158_HM_3_FC1


title: 7_HM_2A_FC2

source_name: iPSC-derived cardiomyocytes day 27 T3 treated

value: T3 treated


title: 103_HM_2B_FC2


title: 96_HM_2A_FC2


title: 121_HM_2A_FC2


title: 45_HM_3_FC1


title: 36_HM_2C_FC2


title: 121_HM_2A_FC1


title: 95_HF_2A_FC2

value: Female


title: 103_HM_2B_FC1


title: 65_HF_2A_FC2


title: 53_HF_2A_FC2


title: 52_HF_2B_FC2


title: 39_HF_2A_FC2


title: 37_HF_2B_FC2


title: 23_HF_2A_FC2


title: 96_HM_2A_FC1


title: 65_HF_2A_FC1


title: 85_HF_2B_FC1


title: 95_HF_2A_FC1


title: 120_HF_2B_FC2


title: 53_HF_2A_FC1


title: 39_HF_2A_FC1


title: 52_HF_2B_FC1


title: 37_HF_2B_FC1


title: 23_HF_2A_FC1


title: 120_HF_2B_FC1


title: 85_HF_2B_FC2


title: 34_HM_2_FC2

source_name: iPSC-derived cardiomyocytes day 15

tag: time

value: day 15


title: 98_HM_2_FC2


title: 118_HM_2_FC2


title: 98_HM_2_FC1


title: 118_HM_2_FC1


title: 34_HM_2_FC1


title: 49_HF_2_FC2


title: 17_HF_2_FC2


title: 132_HF_2_FC2


title: 117_HF_2_FC2


title: 49_HF_2_FC1


title: 2_HF_2_FC1


title: 117_HF_2_FC1


title: 17_HF_2_FC1


title: 132_HF_2_FC1


title: 82_HF_2_FC1


title: S2_L002: ET2DA rep2

first: Seok Hoon

last: Hong

address: 10 West 33rd Street, Perlstein Hall 127

department: Chemical and Biological Engineering

institute: Illinois Institute of Technology

description: gene expression during persister cell formation

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to E.Coli MG1655 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: E. coli MG1655
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Overnight culture of E. coli BW25113 was diluted 100 times with LB medium and incubated at 37°C with shaking (220 rpm) until OD = 0.5. Cells were washed twice using 0.85% NaCl and resuspended with fresh LB to adjust the OD = 1.0.

extract_protocol:
Total RNA was isolated using Zymo RNA isolation kit (Zymo Research, Irvine, CA) by following the manufacturer’s suggested protocol. Total RNA was quantified by Qubit and the RNA integrity (RIN) was assessed by Agilent 2200 TapeStation.  Ribo-Zero rRNA removal Kit (Illumina, San Diego, CA) was used to remove ribosomal RNA from 1 µg of total RNA sample by following the protocol supplied in the kit.
cDNA was synthesized by reverse transcription and amplified to generate library using ScriptSeq Complete Kit (Epicenter, Madison, WI) and thermal cycler by following the library preparation protocol provided by the manufacturer. Libraries were sequenced on an Illumina NextSeq500 with 2x75bp reads on a Mid Output Sequencing Flow Cell.

treatment_protocol: Cells were divided to two cultures with 25 mL each. The one culture was treated with 1 µg/ml of ciprofloxacin as a control, and the other culture was treated with both 1 µg/ml of ciprofloxacin and 500 µM of ET2DA. After one-hour incubation, cells were pelleted by centrifuging at 12,000 ´g for 5 min and washed twice with 25 mL of cold 0.85% NaCl. The cell pellet was resuspended in 2 mL of RNAlater (Invitrogen, Carlsbad, CA) and incubated for one hour at 4°C. Then, RNAlater was removed by centrifugation, and the cell pellet obtained was stored in -80°C until use.

tag: antibioic treatment

value: 1 ug/mL of ciprofloxacin

tag: fatty acid treatment

value: 500 µM of ET2DA

tag: treatment time

value: 1 hour


title: S2_L003: ET2DA rep3


title: S1_L004: Control rep4

source_name: Control


title: S2_L001: ET2DA rep1


title: S1_L002: Control rep2


title: S1_L003: Control rep3


title: H3: Heat

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the Arabidopsis thaliana genome database downloaded from TAIR10 using TopHat2 software with default parameters.
The read counts for each gene was calculated by HTSeq v0.6.1.
Genome_build: TAIR 10
Supplementary_files_format_and_content: The tab-delimited text files files include genes read count for each sample (.txt)

organism: Arabidopsis thaliana

source_name: Heat

growth_protocol: 23°C/18°C (day/night); photoperiod: 16h/8h (day/night) with photosynthetically active radiation (PAR) in the day photoperiod at about 350 μmol m-2 s-1 provided by fluorescent tubes (Philips Electronics Trading & Services Co Ltd, Shanghai, China)

extract_protocol:
The leaves of control, warming and heat treatments were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Control:The day/night temperatures were set at 23/18°C as the “control temperature (CK)” based on published studies using the Col-0 ecotype; Warming:set the “warming temperature” at 5°C above CK, and plants were subjected to 28/23°C (day/night) at 23 days after sowing for 7 days; Heat: plants at 30 days after sowing to 38°C for 6 hours

tag: tissue

value: leaves

value: 38°C for 6 hours


title: H2: Heat


title: W3: Warming

source_name: Warming

value: 28/23°C (day/night) at 23 days after sowing for 7 days


title: W2: Warming


title: S2_L004: ET2DA rep4


title: W1: Warming


title: CK3: Control

value: 23°C/18°C (day/night) for 30 days


title: 99_HF_2C_FC2

tag: cell line

tag: Sex

tag: cell type


title: 91_CM_1_FC2

organism: Pan troglodytes

tag: population

value: Chimpanzee


title: 14_CM_1_FC2


title: 145_CM_1_FC2


title: Library sequencing in 16 expression bins

city: Cambridge

first: Shira

last: Weingarten-Gabbay

state: MA

address: 75 Ames St

institute: The Broad Institute

data_processing:
Single-end  reads in the length of 75 to 45nt containing the unique 11nt barcode
Trimmed reads were mapped to the synthetic library sequences using Novoalign aligner
The number of reads for each designed oligo was counted in each expression bin
Expression scores were computed according to the distrubution of reads across expression bins (see methods in the paper)
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: Tab delimited file that holds the synthetic oligo id number, sequence, cap-independnet translation activity, promoter activitiy and cDNA/gDNA ratio

organism: synthetic construct

source_name: Designed oligonucleotides

extract_protocol:
Genomic DNA (gDNA) was purified from K562 cells using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer protocol. Library oligos were amplified from gDNA using two-step nested PCR reaction and PCR product was extracted from gel. Finally, Illumina adaptors were ligated to the purified PCR product
Illumina adaptors ligation

tag: functional assay

value: promoter activity measurements

tag: master plasmid

value: pZDonor with mCherry and eGFP


title: CK1: Control


title: CK2: Control


title: 111_CM_1_FC2

value: Male

value: induced pluripotent stem cells


title: 91_CM_1_FC1


title: 14_CM_1_FC1


title: 145_CM_1_FC1


title: S1_L001: Control rep1


title: 111_CM_1_FC1


title: 72_CF_1_FC2


title: H1: Heat


title: 7_HM_2A_FC1

value: Caucasian

value: iPSC-derived cardiomyocytes


title: 59_CF_1_FC2


title: 140_HF_3_FC1

value: Primary Heart Tissue


title: 27_CF_1_FC2

value: Female


title: 47_CF_1_FC2


title: 163_HF_3_FC2


title: 72_CF_1_FC1


title: C57 testis replicate 3

value: testis

tag: protocol

tag: purpose

value: Analysis of APA in heart, testis and heart between mouse and rat


title: Quizalofop-p-ethyl_0.1uM (RM-Sample-90)

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

data_processing:
The RNA-seq data analysis was performed using the new version of the Tuxedo protocol with HISAT, StringTie and Ballgown
Sequences were then aligned to the human genome (prebuilt indexes H. sapiens, GRCh38 downloaded from HISAT2 website) using the hierarchical indexing for spliced alignment of transcripts program HISAT2
StringTie was used to assemble and quantify the transcripts in each sample using the Homo_sapiens.GRCh38.89 database
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with Ballgown following the protocol described in the Tuxedo protocol publication (Nat Protoc. 2016 Sep; 11(9): 1650–1667.)
Genome_build: Homo_sapiens.GRCh38.89 database
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HepaRG

growth_protocol: Differentiated HepaRG cells (HPR 116) were purchased from Biopredic International (Rennes, France). Cells were thawed, suspended and plated in the general purpose medium (Williams’E medium + GlutaMAXTM) containing with ADD670 supplement. A total of 72,000 and 2,000,000 cells were plated in collagen-coated 96 well-plates (Greiner Bio-One, Germany), and 6 well-plates (Biopredic), respectively. All cells were grown at 37°C (5% CO2). The medium was refreshed at day 3, 5 and 7. The cells were kept in the general purpose medium until day 8, when the culture becomes well organized and includes well-delineated trabeculae and many canaliculi-like structures. At this time, the culture is composed of primitive biliary epithelial cells and mature hepatocytes with basal metabolic activities similar to fresh cells.

extract_protocol:
RNA extraction was performed using the Qiagen’s RNeasy kit according to the manufacturer's instructions.
A 100ng aliquot of total RNA from each sample was used to prepare total RNA libraries using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Massachusetts, USA), and samples were randomised before preparation. Fragmentation prior to first strand cDNA synthesis was carried out using incubation conditions recommended by the manufacturer for intact RNA samples (94°C for 6 minutes). Polymerase chain reaction (PCR) was performed for 14 cycles for final library amplification. Resulting libraries were quantified using the Qubit 2.0 spectrophotometer (Life Technologies, California, USA) and average fragment size assessed using the Agilent 2200 Tapestation (Agilent Technologies UK Limited). The transcriptome of HepaRG cells exposed to glyphosate was sequenced employing the same strategy, except that the libraries were prepared as previously described (Mesnage et al., 2018). A total of three separate sequencing pools were created using equimolar quantities of each sample with compatible indexes; two with 17 samples each, and one with 16 samples. Paired-end reads of 75bp were generated for each library using the Illumina NextSeq®500 in conjunction with the NextSeq®500 v2 High-output 150-cycle kit (Illumina Inc., Cambridge, UK).

treatment_protocol: From day 8 to day 14, cells were switched to the test medium composed of Williams’E medium + GlutaMAXTM supplemented with 2% Fetal Bovine Serum (FBS; GE Healthcare Life Sciences, Buckinghamshire, UK) and 1% DMSO, as well as different concentrations of the different pesticide active ingredients

value: HepaRG

value: terminally differentiated hepatic cells

tag: agent

value: Quizalofop-p-ethyl

tag: concentration


title: Control (RM-Sample-9)

value: Control


title: Quizalofop-p-ethyl_10uM (RM-Sample-89)


title: Quizalofop-p-ethyl_1mM (RM-Sample-88)


title: 123_CF_1_FC2

source_name: induced pluripotent stem cells


title: 88_CM_3_FC2


title: Isoxaflutole_1mM (RM-Sample-85)

value: Isoxaflutole


title: 58_CF_1_FC1


title: Isoxaflutole_10uM (RM-Sample-86)


title: Isoxaflutole_0.1uM (RM-Sample-87)


title: 47_CF_1_FC1


title: 70_CM_3_FC2


title: 69_HF_3_FC2


title: 44_CM_3_FC2


title: 58_CF_1_FC2


title: 150_CM_3_FC2


title: 151_CM_3_FC2


title: Mesotrione_1mM (RM-Sample-82)

value: Mesotrione


title: Mesotrione_10uM (RM-Sample-83)


title: Quizalofop-p-ethyl_0.1uM (RM-Sample-72)


title: Control (RM-Sample-81)


title: 27_CF_1_FC1

value: Chimpanzee


title: Quizalofop-p-ethyl_10uM (RM-Sample-71)


title: Quizalofop-p-ethyl_1mM (RM-Sample-70)


title: 123_CF_1_FC1


title: 11_CM_3_FC2


title: Mesotrione_0.1uM (RM-Sample-84)


title: Isoxaflutole_0.1uM (RM-Sample-69)


title: 70_CM_3_FC1


title: Isoxaflutole_10uM (RM-Sample-68)


title: 44_CM_3_FC1


title: 88_CM_3_FC1


title: Mesotrione_0.1uM (RM-Sample-66)


title: Mesotrione_10uM (RM-Sample-65)


title: Isoxaflutole_1mM (RM-Sample-67)


title: 151_CM_3_FC1


title: 24_CM_3_FC2


title: Mesotrione_1mM (RM-Sample-64)


title: 150_CM_3_FC1


title: 147_CM_3_FC2


title: Quizalofop-p-ethyl_10uM (RM-Sample-53)


title: 11_CM_3_FC1


title: 107_CM_3_FC2


title: 107_CM_3_FC1


title: 8_CF_3_FC2


title: Quizalofop-p-ethyl_1mM (RM-Sample-52)


title: 55_CF_3_FC2


title: Isoxaflutole_0.1uM (RM-Sample-51)


title: 6_HM_2B_FC1

tag: treatment

value: T3 treated


title: 157_CF_3_FC2


title: Isoxaflutole_1mM (RM-Sample-49)


title: 24_CM_3_FC1


title: 155_CF_3_FC2


title: Mesotrione_0.1uM (RM-Sample-48)


title: Mesotrione_1mM (RM-Sample-46)


title: 154_CF_3_FC2


title: 153_CF_3_FC2


title: Control (RM-Sample-45)


title: Control (RM-Sample-63)


title: 147_CM_3_FC1


title: Quizalofop-p-ethyl_0.1uM (RM-Sample-54)


title: 152_CF_3_FC2


title: Quizalofop-p-ethyl_0.1uM (RM-Sample-36)


title: 149_CF_3_FC2


title: Mesotrione_10uM (RM-Sample-47)


title: 139_CF_3_FC2


title: Quizalofop-p-ethyl_10uM (RM-Sample-35)


title: Quizalofop-p-ethyl_1mM (RM-Sample-34)


title: 104_CF_3_FC2


title: 55_CF_3_FC1


title: Isoxaflutole_1mM (RM-Sample-31)


title: 156_CF_3_FC1


title: Mesotrione_0.1uM (RM-Sample-30)


title: 155_CF_3_FC1


title: Mesotrione_10uM (RM-Sample-29)


title: 154_CF_3_FC1


title: 153_CF_3_FC1


title: Mesotrione_1mM (RM-Sample-28)


title: 4_HM_2C_FC1

value: Not T3 treated


title: 152_CF_3_FC1


title: Quizalofop-p-ethyl_0.1uM (RM-Sample-18)


title: 149_CF_3_FC1


title: Quizalofop-p-ethyl_10uM (RM-Sample-17)


title: Control (RM-Sample-27)


title: 139_CF_3_FC1


title: 104_CF_3_FC1


title: Isoxaflutole_10uM (RM-Sample-14)


title: 119_CM_2C_FC2

value: Male


title: 83_CM_2C_FC2


title: Isoxaflutole_10uM (RM-Sample-32)


title: 8_CF_3_FC1


title: Isoxaflutole_1mM (RM-Sample-13)


title: Isoxaflutole_0.1uM (RM-Sample-33)


title: 100_CM_2C_FC2


title: Mesotrione_0.1uM (RM-Sample-12)


title: 83_CM_2C_FC1


title: 119_CM_2C_FC1


title: 100_CM_2C_FC1


title: Mesotrione_1mM (RM-Sample-10)


title: yheO-KO rep2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_000913.2) using bowtie with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM).
Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: reference genome (NC_000913.2)
Supplementary_files_format_and_content: tab-delimited text files containing FPKM values for each sample

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with the glucose M9 minimal medium for each TF candidate. The concentration of carbon sources was 0.2% (w/v). M9 minimal media was also supplemented with 1 ml trace element solution (100X). The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5)

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

tag: genotype

value: yheO deletion


title: 3_CF_2C_FC2

value: iPSC-derived cardiomyocytes


title: yddM-KO rep2

value: yddM deletion


title: 35_CF_2C_FC2

value: Female


title: yheO-KO rep1


title: 133_CF_2C_FC2


title: Isoxaflutole_0.1uM (RM-Sample-15)


title: yddM-KO rep1


title: 3_CF_2C_FC1


title: 35_CF_2C_FC1


title: ydcI-KO-high-ph rep2

value: glucose M9 minimal pH8.5

value: ydcI deletion


title: ydcI-KO-high-ph rep1


title: 133_CF_2C_FC1


title: ydcI-KO-low-ph rep2

value: glucose M9 minimal pH5.5


title: 165_HF_3_FC1

value: Caucasian

value: Primary Heart Tissue


title: ydcI-KO-low-ph rep1


title: 67_CM_2A_FC2


title: 5_CM_2B_FC2


title: Mesotrione_10uM (RM-Sample-11)

value: HepaRG

value: terminally differentiated hepatic cells


title: ybiH-KO rep2

value: ybiH deletion


title: 54_CM_2A_FC2

value: Chimpanzee

value: T3 treated


title: 40_CM_2A_FC2

value: Male


title: ybiH-KO rep1

value: glucose M9 minimal


title: 38_CM_2B_FC2


title: ybaQ-KO rep2

value: mid-log phase

value: ybaQ deletion


title: ybaQ-KO rep1


title: ybaO-KO rep2

value: ybaO deletion


title: 5_CM_2B_FC1

value: iPSC-derived cardiomyocytes


title: 67_CM_2A_FC1


title: ybaO-KO rep1

value: ybaOdeletion


title: 136_CM_2B_FC2


title: WT-high-ph rep2

value: glucose M9 minimal pH8.5

value: wild type


title: WT-high-ph rep1


title: 54_CM_2A_FC1


title: WT-low-ph rep1

value: glucose M9 minimal pH5.5


title: 38_CM_2B_FC1


title: YdcI_ph8_2_ChIPexo

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
MACE program  was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, peaks with signal-to-noise (S/N) ratio less than 1.5 were removed
The noise level was set to the top 5% of signals at genomic positions because top 5% makes a background level in plateau and top 5% intensities from each ChIP-exo replicates across conditions correlate well with the total number of reads.The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: E.coli genome(NC_000913.2)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

tag: myc-tagging

value: ydcI myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: WT-low-ph rep2


title: 40_CM_2A_FC1


title: 86_CF_2A_FC2

value: Female


title: YdcI_ph8_1_ChIPexo


title: 84_CF_2B_FC2


title: YdcI_ph5_1_ChIPexo


title: YdcI_ace2_ChIPexo


title: YdcI_ph5_2_ChIPexo


title: 80_CF_2B_FC2


title: 51_CF_2B_FC2


title: 32_CF_2A_FC2


title: 66_CM_2A_FC1


title: yieP-KO rep2

tag: strain

value: yieP deletion


title: YdcI_ace1_ChIPexp


title: 138_CF_2A_FC2

tag: cell line


title: 135_CF_2B_FC2

tag: Sex


title: 86_CF_2A_FC1

tag: cell type


title: yiaJ-KO rep1

value: yiaJ deletion


title: yieP-KO rep1


title: yiaJ-KO rep2


title: yeiE-KO rep2

value: yeiE deletion


title: 102_CF_2B_FC2

tag: population

value: Chimpanzee

value: T3 treated


title: 136_CM_2B_FC1

value: Male


title: yeiE-KO rep1

value: glucose M9 minimal

value: mid-log phase


title: yafC-KO rep2

value: yafC deletion


title: yafC-KO rep1


title: 32_CF_2A_FC1

value: iPSC-derived cardiomyocytes


title: 80_CF_2B_FC1


title: rat heart replicate 2

organism: Rattus norvegicus

source_name: heart

tag: tissue

value: heart

value: Analysis of APA in heart, testis and heart between mouse and rat


title: rat heart replicate 1


title: 138_CF_2A_FC1


title: WT rep2

value: wild type


title: rat testis replicate 1

value: testis


title: rat testis replicate 2


title: 51_CF_2B_FC1


title: WT rep1


title: rat brain replicate 2

value: brain


title: 102_CF_2B_FC1


title: RpoB_glc2_ChIPexo

value: wild type cells

value: purified anti E.coli RNA polymerase β, clone NT63, catalog 663006,BioLegend


title: RpoB_glc1_ChIPexo


title: 84_CF_2B_FC1

value: Female


title: YieP_glc2_ChIPexo

value: yieP myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: 63_CM_2_FC2

value: Chimpanzee

tag: time

value: day 15


title: 50_CM_2_FC2

value: Male


title: YieP_glc1_ChIPexo


title: YiaJ_glc2_ChIPexo

value: yiaJ myc-tagging cells


title: YiaJ_glc1_ChIPexo


title: OsCPK21RNAi-stage12

city: Beijing

first: Shenghua

last: Jia

address: No. 19, XinJieKouWai St., HaiDian District

institute: Beijing Normal University

description: Gene expression in OsCPK21-RNAi spikelets at stage 12 of anther development

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Oryza sativa

source_name: spikelets, OsCPK21-RNAi, anther development stage 12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA

growth_protocol: ZH11 and OsCPK21-RNAi (3 lines) plants were grown under natural conditions in a field of Beijing Normal University (Beijing, China).

extract_protocol: Total RNAs were extracted from rice spikelets using the TRIzol reagent (Invitrogen) and purified with the PureLink RNA Mini kit (Invitrogen) combined with the PureLink DNase kit (Invitrogen) according to the manufacturer’s protocols.

treatment_protocol: ZH11 and OsCPK21-RNAi (3 lines) plants were grown under natural conditions. No treatment.

tag: genetic background

tag: source tissue

value: spikelet

tag: age

value: anther development stage 12


title: ZH11-stage12

description: Gene expression in ZH11 spikelets at stage 12 of anther development

source_name: spikelets, ZH11, anther development stage 12


title: rat brain replicate 1

source_name: brain

tag: protocol

tag: purpose


title: 33_CM_2_FC2

value: iPSC-derived cardiomyocytes


title: 63_CM_2_FC1


title: YheO_glc1_ChIPexo

value: yheO myc-tagging cells


title: 18_CM_2_FC2


title: 33_CM_2_FC1


title: ZH11-stage9

description: Gene expression in ZH11 spikelets at stage 9 of anther development

source_name: spikelets, ZH11, anther development stage 9

value: anther development stage 9


title: 135_CF_2B_FC1

tag: treatment

value: T3 treated


title: 18_CM_2_FC1


title: YeiE_glc2_ChIPexo

value: yeiE myc-tagging cells


title: YeiE_glc1_ChIPexo


title: YheO_glc2_ChIPexo


title: PV of control brain [68_CPV]

city: Barcelona

first: Anna

last: PLANAS

state: - If in U.S, Select a State -

address: Rossello 161 planta 6

country: Spain

institute: Spanish Research Council (CSIC)

description: Gene expression data from  perivascular and meningeal macrophages sorted from the control rat brain

hyb_protocol: The ds-cDNA is fragmented and labeled and hybridized onto the  Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneCHip Scanner 3000 System.Data was analyzed with Expression Console Software using RMA analysis.

data_processing: Data were processed using the limma (v3.18) package in the R (v3.3.1) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Non-specific filtering of 50% less intense and variable data was applied before testing.

source_name: PV of control brain

label_protocol: FFPE samples were processed using the Affymetrix 3' IVT Pico reagent Kit. Starting from 500pg-50ng of purified total RNA from FFPE tissues, a reverse transcription reaction is initiated at the Poly-A tail as well as throughout the entire length of RNA to capture both coding and multiple forms of non-coding RNA. Complementary RNA (cRNA) amplification is achieved using low-cycle PCR followed by linear amplification using T7 in vitro transcription (IVT) technology. The cRNA is then converted to biotinylated double-stranded cDNA (ds-cDNA) hybridization targets for unbiased coverage of the transcriptome.

growth_protocol: Rats were kept under standardized conditions. Animal work was conducted with approval of the Ethical Committee of the University of Barcelona (CEEA) (ref. 716/15)

extract_protocol: RNA was extracted from sorted cells with PureLink RNA Micro Kit (Invitrogen) following the manufacturer instructions. On-column DNAse step was performed to avoid genomic DNA contamination. RNA purity was assessed by RNA PicoChip BioAnalyzer2100. All RIN values were >9.2

treatment_protocol: The right brain hemisphere was processed with the Neural Dissociation kit (Miltenyi Biotec) we used a 30%-0% percoll gradient to obtain a single-cell suspension of living cells that were immunostained for CD11b and CD163. CD163+ PV were sorted by FACS (Aria II cell sorter, BD Biosciences) and collected in RNAse-free PBS. Each sample corresponds to a different rat.

value: Sprague-Dawley

value: male

value: adult

tag: condition

value: Control

value: CD163+ perivascular and meningeal macrophages (PV)


title: PV of ischemic brain [66_IPV]

description: Gene expression data from  perivascular and meningeal macrophages sorted from the ischemic rat brain

source_name: PV of ischemic brain

value: Ischemia


title: PV of ischemic brain [64_IPV]


title: OsCPK21RNAi-stage9

description: Gene expression in OsCPK21-RNAi spikelets at stage 9 of anther development

source_name: spikelets, OsCPK21-RNAi, anther development stage 9

tag: genotype

value: wild type


title: PV of control brain [69_CPV]


title: PV of ischemic brain [65_IPV]


title: 97_CF_2_FC2

value: Female

value: Chimpanzee

value: day 15


title: YddM_glc2_ChIPexo

tag: myc-tagging

value: yddM myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: ECFCs_CTR_2

city: Rozzano

first: Domenico

last: Mavilio

address: Via Manzoni 113

department: Dept of Medical Biotechnologies and Translational Medicine

country: Italy

institute: University of Milan - Humanitas Clinical and Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The Matrix normalized includes quantile normalized signal count data and  detection p-value

label: Biotin

source_name: ECFCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Rneasy micro kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: Healthy control


title: 2-B6-TGFbeta

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek

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

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: genotype/variation

value: B6-TGFß (WT)

tag: disease state

value: induced renal fibrosis


title: ECFCs_CTR_5


title: 81_CF_2_FC2

source_name: iPSC-derived cardiomyocytes day 15

tag: cell line

tag: Sex

value: iPSC-derived cardiomyocytes


title: 4-CBAxB6-TGFbeta

value: CBAxB6-TGFß (KO)


title: ECFCs_CTR_3


title: YddM_glc1_ChIPexo

tag: strain

tag: chip-exo antibody


title: ECFCs_CTR_4


title: 5-CBAxB6-TGFbeta


title: YdcI_glc2_ChIPexo

value: ydcI myc-tagging cells


title: 1_CF_2_FC2

tag: population

tag: cell type

tag: time


title: 131_CF_2_FC2


title: YdcI_glc1_ChIPexo


title: 1-B6-TGFbeta


title: 6-CBAxB6-TGFbeta


title: 116_CF_2_FC2


title: ECFCs_CTR_1


title: ECFCs_uVTE_7

value: uVTE


title: ECFCs_uVTE_5


title: ECFCs_uVTE_8


title: ECFCs_uVTE_6


title: 115_CF_2_FC2


title: Ybih_glc2_ChIPexo

value: ybiH myc-tagging cells


title: Quizalofop-p-ethyl_1mM (RM-Sample-16)

value: HepaRG

value: terminally differentiated hepatic cells

tag: agent

value: Quizalofop-p-ethyl

tag: concentration


title: YbiH_glc1_ChIPexo


title: YbaQ_glc2_ChIPexo

value: ybaQ myc-tagging cells


title: YbaQ_glc1_ChIPexo


title: 81_CF_2_FC1

value: Female


title: 97_CF_2_FC1

value: Chimpanzee


title: 1_CF_2_FC1

value: day 15


title: 131_CF_2_FC1


title: ECFCs_uVTE_2


title: ECFCs_uVTE_3


title: YbaO_glc1_ChIPexo

value: ybaO myc-tagging cells


title: YafC_glc2_ChIPexo

value: yafC myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: 115_CF_2_FC1


title: 116_CF_2_FC1


title: YbaO_glc2_ChIPexo


title: YafC_glc1_ChIPexo


title: 59_CF_1_FC1

value: induced pluripotent stem cells


title: control, biological rep3

city: Nanjing

first: Zhikui

last: Gao

address: 87# Dingjiaqiao Road

institute: Southeast University

description: Gene expression data of the control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

growth_protocol: Cells were grown in RPMI-1640 containing 10% fetal bovine serum (Gibico), 100U/mL Penicillin-Streptomycin Solution(Gibico) at 37℃ in incubator containing 5% CO2 humidified atmosphere.

treatment_protocol: To obtain pri-miR-144/451 cluster plasmid, a synthetic sequence within the range of upstream 200bp to downstream 200bp of pri-miR-144/451 was cloned into the PCDH-CMV-MCS-EF1-Puro lentivirus plasmid. Plasmids of pMDLg/Prre, pRSV-Rev, pMD2G and PCDH-CMV-MCS-EF1-Puro were transfected into HEK-293T for packaging lentivirus.


title: ECFCs_uVTE_1


title: control, biological rep2

description: Gene expression data of the control

value: control


title: control, biological rep1

description: Gene expression data of the control


title: cells overexpressing miR-144/451,  biological rep2

description: Gene expression data of ECa9706 overexpressing miR-144/451 cluster

value: overexpressing miR-144/451


title: Wildtype Uterus

status: Public on Aug 07 2018

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
read1 = barcode, read2 = biological
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene counts per cell

source_name: Uterus

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

tag: age

value: Wildtype


title: A910D91011 Uterus

value: Hox mutant


title: A91011D91011 Uterus


title: 469 2nd generationp53 Mut MSC TL (3)

city: Rehovot

first: Dan

last: Ben-Avraham

address: Herzl 234

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

description: 2nd generationp53 Mut MSC TLs are derived from tumors generated from the injection of 1st generationp53 Mut MSC TL

data_processing:
Adapter trimming - cutadapt tool with -m 40 (Martin, 2011)
Alignement to mm10 mouse geno,e using TopHat v2.0.10
Counting reads on exons based on the refseq annotation (downloaded from igenomes) using HTSeq-count (version 0.6.1p1) (Anders, Pyl, & Huber, 2014).
Differential expression analysis was performed using DESeq2 (1.6.3) (Anders et al., 2013; Love, Huber, & Anders, 2014)
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated text file with counts for each gene and sample

source_name: Mesenchymal stem cell derived tumor line

growth_protocol: BM nucleated cells were obtained from femurs and tibias of R172H knock-in C57BL/6 mice. The bone was flushed with PBS containing 2% fetal cow serum. The cells were dissociated to single-cell suspension and were centrifuged at 300 g for 5 min at room temperature. Red blood cells (RBCs) were removed by RBC lysis buffer. the pellet BM cells were re-suspended to single-cell suspension and seeded in six-well plates containing MSC medium. Tumor derived cells were culture on agar coated plates in DMEM medium supplemented with 15% (vol/vol) FCS, 1 mM sodium pyruvate, 2 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, 1,000 units/mL leukemia inhibitory factor (ESG1107; [BD] at a ratio of 1:1). Cells were incubated at 37˚ in a humidified atmosphere of 5% CO2. All cells were checked for mycoplasma contamination and in all the analyses, we verify that the cells did not exceeded 20 in-vitro passages.

extract_protocol:
RNA extraction by The Direct-zol™ RNA Kit from ZYMO
Total RNA was fragmented followed by reverse transcription and second strand cDNA synthesis. The double strand cDNA was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 22 samples on a 2 lane of Illumina HiSeq 2500 V4 instrument, resulting in ~18 million single-end 60-bp reads per sample.

treatment_protocol: No treatment

value: Tumor line derived from MSC tumors

tag: passage

value: R172H knock-in C57BL/6 mice


title: 458 1st generation p53 Mut MSC TL  clone


title: 467 2nd generationp53 Mut MSC TL (2)


title: 460 1st generation p53 Mut MSC TL  clone


title: 468 1st generation p53 Mut MSC TL  (3)


title: 457 1st generation p53  KO MSC TL  clone


title: 459 1st generation p53  KO MSC TL  clone


title: cells overexpressing miR-144/451,  biological rep3


title: Isoxaflutole_10uM (RM-Sample-50)

value: HepaRG

value: Isoxaflutole


title: shControl 1_Rep_1

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: Gene expression data upon H157 cells after sheGFP treatment

hyb_protocol: The standard protocol of 900720-  GeneChip® kit  was followed for hybridization, wash, and, staining.

scan_protocol: GeneChip Command Software (AGCC4.3.3) was used for imaging and acquisition.

data_processing: The data was processed with Transcriptome Analysis Console (TAC) version 4.0 and .CHP files were generated with sst-rma-combined dabg normalization.

source_name: HNC cells H157

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250 ng of total RNA.

growth_protocol: H157 cells were cultured in media recommended by Public Helath England guideline in a humidified chamber at 37  degree Centigrade with 5% CO2

treatment_protocol: H157 cells were infected with shControl and shPAK2 lentivirus and cells were selected for three days with 1 ug /ml puromycin containing cell culture media. Post selection, cells were harvested and total RNA was isolated.

value: PAK2 Control


title: shPAK2 2_Rep_2

description: Gene expression data upon H157 cells after shPAK2 treatment

value: PAK2 knockdown


title: shPAK2 1_Rep_1


title: cells overexpressing miR-144/451,  biological rep1


title: 464 1st generationp53 Mut MSC TL (2)


title: 471 1st generationp53 Mut MSC TL (3)


title: shControl 2_Rep_2


title: 476 1st generation p53 Mut MSC TL  (2)


title: 483 1st generationp53 Mut MSC TL (1)


title: 482 1st generation p53 Mut MSC TL  (1)


title: 466 2nd generationp53 Mut MSC TL (1)


title: 477 2nd generationp53 Mut MSC TL (2)


title: 463 p53 Mut MSCs (3)

source_name: Mesenchymal stem cells

value: Bone marrow mesenchymal stem cells


title: 461 p53 Mut MSCs (1)


title: Adult12wk Mammary 10X

city: LA JOLLA

first: Rajshekhar

last: Giraddi

state: California

address: 10010 north torrey pines road, Wahl Lab Salk Institute

department: Gene Expression Laboratory

institute: Salk Institute of Biological Sciences

description: AdultEpithelial

data_processing:
Sequencing reads were quality checked by FastQC and NGS-QC generator
Sequence reads aligned to custom mouse transcriptome compatible with RSEM and comprised of gene models from MM10 sequences and sequences for the ERCC RNA spike-in set.  Transcript counts were enumerated using RSEM
A Single Cell 3’ Library comprises standard Illumina® paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ v2 16 bp 10x™ Barcodes are encoded at the start of Read 1, while sample index sequences are incorporated as the i7 index read. Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. Read 1 is used to sequence the 16 bp 10x Barcode and 10 bp UMI, while Read 2 is used to sequence the cDNA fragment. Each sample index provided in the Chromium™ i7 Sample Index Kit combines 4 different sequences in order to balance across all 4 nucleotides.
Relationships between samples, cell stages and clusters were visualized using t-SNE and diffusion coordinates as implemented in the tsne and Destiny packages for R, respectively
Genome_build: Custom mouse transcriptome of gene models from MM10 sequences
Supplementary_files_format_and_content: tSNE, diffusion component and negative matrix factorization

source_name: Mouse mammary gland

extract_protocol: 10X Chromium V2

value: wild type

tag: developemental stage

value: Adult Virgin

tag: tissue

value: mouse mammary gland


title: E18 Mammary 10X

value: Embryonic


title: P4 Mammary 10X

value: Postnal


title: E16 Mammary 10X


title: 50_CM_2_FC1

city: Chicago

first: Bryan

last: Pavlovic

institute: University of Chicago

data_processing:
100 bp single-end RNA-seq reads from each species were mapped to the appropriate genome (hg38 or panTro5) using Hisat2 (version 2.0.4) (Kim et al. 2015). Only reads that mapped uniquely were used.
The number of reads falling into orthologous meta-exons across 44,125  Ensembl genes from hg38, panTro5 was determined using featureCounts within SubRead (version 1.5.1) (Liao et al. 2014).
Genome_build: hg38 & panTro5
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

extract_protocol:
RNA was extracted using the ZR-Duet DNA/RNA MiniPrep kit (Zymo) with the addition of an on column DNAse I treatment step prior to RNA elution.
Samples were pooled together in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.Samples were pooled  in 8 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  100 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

value: Male

value: Chimpanzee

value: iPSC-derived cardiomyocytes

value: day 15


title: 462 p53 Mut MSCs (2)


title: 41_CF_3_FC2

source_name: Primary Heart Tissue

value: Female

value: Primary Heart Tissue


title: Py8119T1 biological rep1

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

description: Gene expression data form Py8119  tumor in mouse

hyb_protocol: Following fragmentation, 2.3 ug of ss-DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridization and wash GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: The array data was analyzed using R\Bioconductor package (oligo and limma), RMA method for normalization.

source_name: Py8119 cells formed Tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA (GeneChipTM WT PLUS assay manual, 2017, Thermo Fisher)

growth_protocol: Py8119 and Py117 Hams F12K media, 5% FBS, Orthotopic implantation of 1x10^6 PyMT cells in the mammary fat pad #4 in 50% PBS and 50% matrigel without phenol red and low growth factor clones from transgenic MMTV-PyMT mice

extract_protocol: Tumors were harvested from mice on the day RT would typically occur for the Py117, Py8119, and the Py5050 mix tumors then tissue was homogenized 100 mg per 500 µL centrifuged and RNA was extracted from the supernatants

treatment_protocol: Untreated cells and tumor

value: Py8119 cells formed Tumor


title: Py8119T4 biological rep4


title: Py5050T4 mixed Tumor biological rep4

description: Gene expression data form mixed tumor Py5050 tumor in mouse

source_name: Py117-Py8119 Mixed cells formed Tumor with 1:1 ratio


title: Py117T1 biological rep1

description: Gene expression data form Py117 tumor in mouse

source_name: Py117 cells formed Tumor

value: Py117 cells formed Tumor


title: Py117T4 biological rep4


title: Py8119C2 biological rep2

description: Gene expression data form Py8119 cell line in culture

source_name: Py8119 at cell cultured condition


title: Py5050T5 Mixed Tumor biological rep5

value: Py117-Py8119 Mixed cells formed Tumor with 1:1 ratio


title: Py8119T2 biological rep2


title: PV of control brain [63_CPV]

value: Sprague-Dawley

value: male

value: adult

tag: condition

value: Control

value: CD163+ perivascular and meningeal macrophages (PV)


title: Py8119C1 biological rep1


title: Py117T3 biological rep3


title: Py117T2 biological rep2


title: Py5050T2 Mixed tumor biological rep2


title: Py8119T3 biological rep3


title: Py5050T1 Mixed tumor biological rep1


title: Py117T5 biological rep5


title: Py8119C3 biological rep3


title: 3W_Sm_10: 10th  fraction of S series slicing

city: Wako-shi

first: Yuko

last: Okamura-Oho

state: Saitama

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: sample for Transcriptome Tomography

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 GE 028005 Microarrays 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the one color scan setting for 8x60k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (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. Data were normalized using per chip: normalize to 75th percentile.

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf10

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

growth_protocol: Mice were grown in pathogen-free conditions.

extract_protocol: RNA was prepared using the Mag-max-96 for Microarrays Total RNA Isolation Kit (Ambion) following the manufacturer's recommendations of the spin column protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: brain

tag: gender

value: 3 weeks post-natal age

tag: section type

value: sagittal plane

tag: mouse id


title: Py117C1 biological rep1

description: Gene expression data form Py117 cell line in culture

source_name: Py117 at cell cultured condition

tag: cell line


title: 3W_Sm_09: 9th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf09


title: Py8119T5 biological rep5


title: 3W_Sm_08: 8th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf08


title: 3W_Sm_07: 7th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf07


title: 3W_Sm_06: 6th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf06


title: Py117C2 biological rep2


title: Py5050T3 Mixed tumor biological rep3


title: 3W_Sm_05: 5th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf05


title: 3W_Sm_04: 4th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf04


title: R59C46

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: Fast-neutron mutant/ wild-type parent comparison

hyb_protocol: Arrays are hybridized at 67C for approximately 72 hours at a rotation speed of 20rpm. Arrays are washed in Wash Buffer 1 for 5 minutes at room temperature, Wash Buffer 2 for 1.5 minutes at 37C, followed by a 1minute wash in room temperature Acetonitrile. All other processing follow Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

scan_protocol: Arrays are immediately and individually scanned using Roche NimbleGen MS200 array scanner using NimbleGen MS200 v1.2 acquisition software. The array is inserted “active side up” with a Scan Resolution of 2micons, Gain at 100% for both channels, Laser Intensity at 100% for both channels, Autogain is deselected and a Multi Tiff File Setting.

data_processing: Image extraction and grid alignment is done using Agilent Feature Extraction (FE) 12.0.0.7.  The CGH module portion of Agilent Genomic Workbench (AWB) 7.0.4.0 software is used to generate data.  Analysis settings include: Aberration Algorithm is ADM-2, Threshold is 6.0, Fuzzy Zero is selected, GC correction is selected with a window size of 2 Kb, Legacy is selected with a bin size of 10, Diploid Peak is deselected, Manually Reassign Peaks is deselected and Combine Intra-Array Replicates is selected. The Aberration Filter is set to call amplification or deletion as having 2 consecutive probes with an absolute log ratio greater or equal to +/- 1.

organism: Glycine max

source_name: Fast neutron mutant individual R59C46CSCW08YB#1ar176aMN15

label_protocol: Individual reactions with 500ng of Soybean DNA are labeled with Cy3 and Cy5 following Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

extract_protocol: Soybean DNA is extracted from approximately 90 mg of fresh, young tissue disrupted with mortar and pestle and liquid nitrogen. The tissue is processed using Qiagen DNeasy Plant Mini Kit catalog number 69106. The Qiagen protocol is followed with 2 elution’s of DNA from the column using 60uL – 50% AE / 50% Water.

value: Leaf

tag: genotype

value: Fast-neutron mutant

value: wild type parent (M92-220-Long)


title: 3W_Sm_03: 3rd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf03

tag: strain


title: 3W_Hm_05: 5th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf05

value: horizontal plane


title: 3W_Sm_02: 2nd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf02


title: 3W_Hm_06: 6th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf06


title: 3W_Hm_04: 4th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf04


title: 3W_Hm_02: 2nd  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf02


title: 3W_Sm_01: 1st  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf01


title: 3W_Cm_08: 8th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf08

value: coronal plane


title: 3W_Cm_10: 10th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf10


title: 3W_Hm_03: 3rd  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf03


title: 3W_Cm_09: 9th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf09


title: 3W_Cm_07: 7th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf07


title: 3W_Cm_11: 11th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf11


title: 3W_Cm_06: 6th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf06


title: 3W_Cm_12: 12th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf12 plus Cf13


title: 3W_Hm_01: 1st  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf01


title: Py117C3 biological rep3

source_name: Py117 at cell cultured condition


title: 3-B6-TGFbeta

tag: genotype/variation

value: B6-TGFß (WT)

tag: disease state

value: induced renal fibrosis


title: 3W_Cm_03: 3rd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf03


title: 3W_Cm_05: 5th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf05


title: P7_Sm_02: 2nd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf03

value: 3 days, post-natal stage


title: P7_Sm_06: 6th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf07, Sf08 plus Sf09


title: P7_Sm_05: 5th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf06


title: P7_Hm_03: 3rd  fraction of H series slicing

description: sample for Transcriptome Tomography


title: P7_Hm_04: 4th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf04


title: P7_Sm_04: 4th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf05


title: P7_Cm_08: 8th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf08


title: 3W_Cm_02: 2nd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf02


title: 3W_Cm_04: 4th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf04


title: P7_Hm_06: 6th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf06


title: P7_Sm_01: 1st  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf01 plus Sf02


title: P7_Hm_05: 5th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf05


title: P7_Cm_10: 10th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf10 plus Cf11


title: P7_Cm_07: 7th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf07


title: P7_Hm_02: 2nd  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf02


title: P7_Hm_01: 1st  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf01


title: P7_Cm_04: 4th  fraction of C series slicing

description: sample for Transcriptome Tomography


title: P7_Sm_03: 3rd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf04


title: 3W_Cm_01: 1st  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf01


title: P7_Cm_05: 5th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf05


title: P7_Cm_09: 9th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf09


title: P7_Cm_06: 6th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf06


title: P3_Sm_10: 10th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf11

value: 3 days post-natal age


title: P3_Sm_09: 9th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf10


title: P3_Sm_11: 11th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf12 plus Sf13


title: P7_Cm_01: 1st  fraction of C series slicing

description: sample for Transcriptome Tomography


title: P3_Sm_04: 4th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf05


title: P7_Cm_02: 2nd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf02


title: P3_Sm_02: 2nd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf03


title: P3_Hm_07: 7th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf07


title: P7_Cm_03: 3rd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf03


title: P3_Sm_07: 7th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf08


title: ECFCs_uVTE_4

source_name: ECFCs

tag: disease

value: uVTE


title: P3_Sm_01: 1st  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf01 plus Sf02

value: male


title: P3_Sm_08: 8th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf09


title: P3_Sm_05: 5th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf06


title: P3_Hm_04: 4th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf04


title: P3_Hm_06: 6th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf06


title: P3_Sm_06: 6th  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf07


title: P3_Hm_08: 8th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf08


title: P3_Hm_03: 3rd  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf03


title: P3_Cm_15: 15th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf15


title: P3_Hm_01: 1st  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf01


title: P3_Hm_02: 2nd  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf02


title: P3_Hm_05: 5th  fraction of H series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 holizontal slices (500 micron width) of the brain, Hf05


title: P3_Cm_13: 13th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf13


title: iNPC_FMR1KO_experiment2

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

institute: ASUBIO PHARMA CO., LTD.

description: Gene expression of iNPC_FMR1KO, experiment2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v3 8x60K Microarray (G4851C) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: iNPC, FMR1KO, experiment2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. Purified RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: iPSCs-derived NPCs


title: iNPC_WT_experiment2

description: Gene expression of iNPC_WT, experiment2

source_name: iNPC, WT, experiment2

value: WT


title: P3_Cm_12: 12th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf12


title: P3_Cm_14: 14th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf14


title: P3_Cm_10: 10th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf10


title: iNPC_WT_experiment1

description: Gene expression of iNPC_WT, experiment1

source_name: iNPC, WT, experiment1


title: 3_729_Hippocampus

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Illumina base-calling
Adapters trimmed from reads using CutAdapt with Trim Galore wrapper script
Reads aligned to hg38 (plus ERCC sequences and in silico chromosome) using STAR v2.5.3a
Alignments assembled intro transcript models using Stringtie v1.3.3
Individual sample transcriptomes merged into consensus using Stringtie --merge
Genome_build: hg38
Supplementary_files_format_and_content: .gtf files provide assembled transcript coordinates and expression values (FPKM) for each sample

source_name: Brain tissue

extract_protocol:
RNA was extracted using the QIAGEN miRNeasy kit.
RNA CaptureSeq was performed as per the protocol from Mercer, T.R. et al Nature Protocols 9, 989-1009 (2014), using the KAPA Stranded RNA-seq library prep kit.

tag: donor id

value: C

tag: brain region

value: Hippocampus


title: 4_729_SupCol

tag: age

value: Superior colliculus


title: 4_729_ACCx

value: Anterior cingulate cortex


title: 3_692_Thalamus

value: B

value: Thalamus


title: 4_683_ACCx

value: A


title: 4_683_SupCol


title: 3_683_Thalamus


title: 2_729_PFC

value: Prefrontal cortex


title: P3_Cm_11: 11th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf11

value: brain

value: coronal plane


title: P3_Cm_08: 8th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf08


title: 2_729_Cerebellum

value: Cerebellum


title: 2_692_Hippocampus


title: 2_692_Cerebellum


title: P3_Cm_05: 5th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf05


title: P3_Cm_04: 4th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf04


title: 2_692_Caudate

value: Caudate


title: P3_Sm_03: 3rd  fraction of S series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 sagittal slices (500 micron width) of the brain, Sf04

value: 3 days post-natal age

value: sagittal plane


title: P3_Cm_02: 2nd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf02

value: male


title: P3_Cm_03: 3rd  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf03


title: P3_Cm_07: 7th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf07


title: iNPC_FMR1KO_experiment1

description: Gene expression of iNPC_FMR1KO, experiment1

source_name: iNPC, FMR1KO, experiment1

value: iPSCs-derived NPCs


title: P3_Cm_06: 6th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf06


title: 1_729_VCx

value: Visual cortex


title: P3_Cm_01: 1st  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf01


title: 1_692_VCx


title: 1_729_Caudate

value: C


title: 3_692_PFC


title: P3_Cm_09: 9th  fraction of C series slicing

description: sample for Transcriptome Tomography

source_name: 5 micron x 100 coronal slices (500 micron width) of the brain, Cf09


title: DP cells donor 2

city: Incheon

first: Nahyun

last: Choi

state: Incheon

address: gwahackro 85

department: college of pharmacology

institute: Yonsei University

description:
human-DP-donor2_1
GeneExpression.txt
DESeq8_DP_ASL.txt

data_processing:
Trimmed low base quality
Mapping with UCSC hg19 reference using Hisat2
FPKM(Fragment per Kilobase of transcript per Million mapped reads) were calculated using StringTie
DEG analysis(Differentially Expressed Gene)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: xlsx file include FPKM values for each Sample, xlsx file include DEG result

source_name: Dermal papilla of hair

growth_protocol: ASCs were cultured in alpha-MEM medium (Hyclone, Logan, UT) with 10% fetal bovine serum (Gibco, CA, USA) and 1% penicillin/streptomycin (Gibco). We purchased human DP cells from PromoCell (#C-12071). Human DP cells were cultured in follicle DP cell medium with supplementMix (PromoCell, Heidelberg, Germany) and 0.1% anti-antibiotics (Gibco). DP cells for all experiment were used at passages 2~3, but used at passages 5~6 for analysis of alkaline phosphatase activity. ASCs and tfASCs were used at passages 5~8 and 7~10, respectively. For tfASCs were cultured in the partial DP culture medium (alpha-MEM; follicle DP cell medium = 1;1). ASCs, DP cells and tfASCs were maintained at 37 °C in a humidiﬁed 5% CO2 incubator.

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the Stranded mRNA LT Sample Prep Kit.
TruSeq

treatment_protocol: Total RNA of ASC, tfASC and DP cells was extracted using total RNA purification mini kit (FAVORGEN, Ping-Tung, Taiwan), and then sent to Macrogen (Seoul, South Korea) for library construction and sequencing.

value: dermal papilla


title: ASCs donor 3

description:
ASL-donor3_1
GeneExpression.txt
DESeq4_DP_ASL.txt
DESeq4_DPlike_ASL.txt

source_name: Fat

value: adipose-derived stem cells


title: tfASCs rep1

description:
DP-like-1-P3_1
GeneExpression.txt
DESeq5_DPlike_ASL.txt

value: three trichogenic factors platelet-derived growth factor-A, SOX2, and beta-catenin to ASCs


title: 13C-Casp11-neg-neg-LPS

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the mouse (GRCm38.p3) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCm38.p3 from ENCODE (GRCm38.p3.genome.fa, gencode.vM3.annotation.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Ileum

extract_protocol:
For transcriptome (RNASeq/RefSeq) analysis , ileum from each WT, Casp8–/–Ripk3–/– and Casp11-negative mouse (5 male mice per group) harvested at 1.5 hpc was placed in RNAlater (Thermo-Fisher) at 4C. 24 h post-harvest, intestines were cleaned with cold RNAlater and mucus was scraped, homogenized and pelleted as described for immunoblot analysis. RNA isolation and further steps for transcriptome analysis were carried out as described (Sandler et al., 2014) in the NHP Genomics Core, Yerkes National Primate Research Center. Briefly, total RNA was isolated from mucus pellet for each sample using RNeasy Micro and RNA integrity was tested using Agilent Bioanalyzer capillary electrophoresis.
cDNA libraries were prepared using Illumina Stranded RNATruSeq kits and barcoded as well as sequenced on an Illumina HiSeq 3000. Five million 150-base pair mapping reads were obtained per sample, with >90% reads having Q-Scores of >30 (>99.9% estimated accuracy for 150 base reads).

value: C57BL/6 backcrossed

value: Ileum

tag: stress

value: LPS-challenge


title: ASCs donor 2

description:
ASL-donor2_1
GeneExpression.txt
DESeq3_DP_ASL.txt
DESeq3_DPlike_ASL.txt


title: ASCs donor 1

description:
ASL-donor1_1
GeneExpression.txt
DESeq2_DP_ASL.txt
DESeq2_DPlike_ASL.txt


title: 12C-Casp11-neg-neg-LPS


title: tfASCs rep2

description:
DP-like-2-P2_1
GeneExpression.txt
DESeq6_DPlike_ASL.txt


title: 10C-Casp8-Rip3-LPS


title: DP cells donor 3

description:
human-DP-donor3_1
GeneExpression.txt
DESeq9_DP_ASL.txt


title: kda3: MOCS2 RNAi knockdown replicate 3

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Raw reads were demultiplexed into fastq format allowing up to one mismatch in the barcode using illumina bcl2fastq version 2.18.
Reads were aligned to UCSC genome hg38 with Tophat 2.0.13 with "--library-type fr-firststrand" using Ensembl 87 gene models.
Read counts were generated using HTSeq-count with "-m intersection-nonempty"
Genome_build: hg38
Supplementary_files_format_and_content: comma seperated values of htseq-count generated counts of reads on Ens 87 gene models.

source_name: HEK293 cells

growth_protocol: Control or MOCS2 knockdown HEK293 cells were cultured in DMEM-High Glucose (4500 mg/L) (D6429, SigmaAldrich, Missouri, USA) with 10% fetal bovine serum with 500 mg/ml Geneticin (Life Technologies)

extract_protocol:
Total RNA from control or MOCS2 knockdown HEK293 CELLS were extracted by TRIZol (Life technology) and were then purified by Direct-zol RNA Miniprep Plus (Zymo Research).
TruSeq stranded Total RNA Kit with Ribo-Zero Gold was used for library construction.

value: MOCS2 knockdown


title: DP cells donor 1

description:
human-DP-donor1_1
GeneExpression.txt
DESeq7_DP_ASL.txt


title: 11C-Casp11-neg-neg-LPS


title: 14C-Casp11-neg-neg-LPS


title: 15C-Casp11-neg-neg-LPS


title: kda2: MOCS2 RNAi knockdown replicate 2


title: 8C-Casp8-Rip3-LPS


title: kda1: MOCS2 RNAi knockdown replicate 1


title: 9C-Casp8-Rip3-LPS


title: 7C-Casp8-Rip3-LPS


title: cont3: Control replicate 3

value: wild type


title: 3C-WT-3-LPS

value: WT


title: 6C-Casp8-Rip3-LPS


title: 4C-WT-4-LPS


title: cont1: Control replicate 1


title: cont2: Control replicate 2


title: 2C-WT-2-LPS


title: 1C-WT-1-LPS


title: 5C-WT-5-LPS