title: Sleep deprived subject 6166 blood collection 03 [D6]

description:
SD_6166_t03
Sample SD_6166_t03 in GSE98564


title: 68: 1X choline female rep 1 (mRNA)

status: Public on Apr 10 2018

type: SRA

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

country: USA

institute: Cornell University

description:
allSamples_gene_exp.diff: N_0
allSamples_genes.read_group_tracking: N_0
female_gene_exp.diff: NF_0
female_genes.read_group_tracking: NF_0

library_source: transcriptomic

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited cuffdiff2 output text files including individual sample results (raw counts, FPKM values in read_groups_tracking files) and differential gene expression results (log2FC, p-values, and q-values [corrected for multiple hypothesis testing] in gene_exp.diff files)

molecule: total RNA

organism: Mus musculus

source_name: Mouse placenta

growth_protocol: Prior to euthanization and tissue harvesting, the mice in this study had ad libitum access to the diet and water, and were housed in microisolator cages in an environmentally-controlled room (22-25°C, 70% humidity) with a 12-hour light-dark cycle.

extract_protocol:
Placenta tissues were removed from the mice after they were sacrificed at gestational day 15.5 and were immediately flash frozen in liquid nitrogen. RNA were extracted from the tissues using Trizol following the manufacturer's protocol.
RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Directional Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Prior to euthanization and tissue harvesting, the mice in this study were fed the AIN-93G diet, with either 1X choline concentration (1.4g choline chloride/kg diet; Dyets Cat #103345) or 4X choline concentration (5.6g choline chloride/kg diet; Dyets Cat #103347).

tag: strain

value: non-Swiss Albino (NSA)

tag: tissue

value: Placenta

tag: developmental stage

value: Gestational day 15.5

tag: fetal sex

value: Female

tag: diet treatment

value: 1X choline


title: 269: 4X choline male rep 3 (mRNA)

description:
allSamples_gene_exp.diff: CH_4
allSamples_genes.read_group_tracking: CH_4
male_gene_exp.diff: CHM_2
male_genes.read_group_tracking: CHM_2

value: Male

value: 4X choline


title: Sleep deprived subject 6166 blood collection 01 [D6]

type: RNA

city: Oklahoma City

first: Hilary

middle: A

last: Uyhelji

state: OK

address: 6500 S. MacArthur Blvd.

department: Civil Aerospace Medical Institute

institute: Federal Aviation Administration

description:
SD_6166_t01
Sample SD_6166_t01 in GSE98564

hyb_protocol: Hybridization cocktail was prepared according to the NuGEN Encore® Biotin module manual. Affymetrix GeneChip Human Gene 1.0 ST arrays were prewet with hybridization solution, and then incubated with hybridization cocktail.

scan_protocol: Affymetrix Wash and Stain kit reagents and fluidics protocol were used with the GeneChip Fluidics Station 450 for post-hybridization chip processing. Scanning was done on an Affymetrix Scanner with G7 upgrade.

data_processing: Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6.

label: biotin

organism: Homo sapiens

source_name: blood

label_protocol: Reverse transcription was performed with Ovation Pico WTA System V2 kit (NuGEN), and fragmentation and biotin labeling was performed using the Encore® Biotin module (NuGEN).

growth_protocol: Blood was collected in PAXgene tubes from healthy adult human volunteers.

extract_protocol: RNA was extracted from blood collected in PAXgene™ tubes using a QIAcube robotic workstation (Qiagen).

treatment_protocol: Blood was drawn every 4 hours during time awake on day 2 (Baseline), day 4 (Experimental), and day 6 (Recovery) of the 7 days in the sleep lab, amounting to 4 draws per day for 12 total timepoints per subject. On all 7 days, Control (C) subjects had 10 h TIB. The Sleep Deprived (SD) subjects experienced 10 h TIB during Baseline and Recovery days, but underwent 62 h continued wakefulness in the Experimental phase. Blood draws on day 4 (Experimental) for the Sleep Deprived subjects correspond to hours 24-36 of continued wakefulness.

tag: subject id

value: susceptible

tag: subject group

value: Sleep Deprived

tag: study phase

value: baseline

tag: timepoint


title: Sleep deprived subject 6125 blood collection 15 [D6]

description:
SD_6125_t15
Sample SD_6125_t15 in GSE98564

value: resistant

value: recovery


title: Sleep deprived subject 6125 blood collection 13 [D6]

description:
SD_6125_t13
Sample SD_6125_t13 in GSE98564


title: Sleep deprived subject 6125 blood collection 14 [D6]

description:
SD_6125_t14
Sample SD_6125_t14 in GSE98564


title: 241: 4X choline male rep 2 (mRNA)

description:
allSamples_gene_exp.diff: CH_3
allSamples_genes.read_group_tracking: CH_3
male_gene_exp.diff: CHM_1
male_genes.read_group_tracking: CHM_1


title: Sleep deprived subject 6125 blood collection 11 [D6]

description:
SD_6125_t11
Sample SD_6125_t11 in GSE98564

value: experimental


title: Sleep deprived subject 6125 blood collection 12 [D6]

description:
SD_6125_t12
Sample SD_6125_t12 in GSE98564


title: 71: 1X choline female rep 2 (mRNA)

description:
allSamples_gene_exp.diff: N_1
allSamples_genes.read_group_tracking: N_1
female_gene_exp.diff: NF_1
female_genes.read_group_tracking: NF_1


title: 223: 4X choline male rep 1 (mRNA)

description:
allSamples_gene_exp.diff: CH_1
allSamples_genes.read_group_tracking: CH_1
male_gene_exp.diff: CHM_0
male_genes.read_group_tracking: CHM_0


title: 273: 1X choline male rep 3 (mRNA)

description:
allSamples_gene_exp.diff: N_5
allSamples_genes.read_group_tracking: N_5
male_gene_exp.diff: NM_2
male_genes.read_group_tracking: NM_2


title: Sleep deprived subject 6125 blood collection 04 [D6]

description:
SD_6125_t04
Sample SD_6125_t04 in GSE98564


title: 222: 1X choline male rep 1 (mRNA)

description:
allSamples_gene_exp.diff: N_2
allSamples_genes.read_group_tracking: N_2
male_gene_exp.diff: NM_0
male_genes.read_group_tracking: NM_0


title: Sleep deprived subject 6125 blood collection 09 [D6]

description:
SD_6125_t09
Sample SD_6125_t09 in GSE98564


title: 234: 1X choline male rep 2 (mRNA)

description:
allSamples_gene_exp.diff: N_3
allSamples_genes.read_group_tracking: N_3
male_gene_exp.diff: NM_1
male_genes.read_group_tracking: NM_1


title: Sleep deprived subject 6125 blood collection 08 [D6]

description:
SD_6125_t08
Sample SD_6125_t08 in GSE98564


title: Murine myeloid precursors treated with CSF-1and RANKL for 3 days 2

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: Gene expression levels were estimated from Expression console software from affymetrix (RMA-Gene-Core)

label: Biotin

source_name: Murine myeloid precursors_CSF-1and RANKL for 3 days

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: Murine bone marrow cells were flushed, grown on plastic plates with 100 ng/ml CSF-1 in DMEM supplemented with 10% FBS, L glutamine and 1X Pen-Strep for 3 days at 5% CO2 water jacketed incubator at 37 degree C.

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

treatment_protocol: Enriched myeloid precursors from mouse as well as Lonza Poietics human osteoclast precurosrs were seeded at 100,000 cells/ml in OCP-BlueKit (PT-8001, Lonza) according to manufacturer's protocol for indicated time.

tag: cell type

value: Murine enriched myeloid precurosrs

tag: treated with

value: CSF-1and RANKL for 3


title: Sleep deprived subject 6125 blood collection 01 [D6]

description:
SD_6125_t01
Sample SD_6125_t01 in GSE98564


title: Murine myeloid precursors treated with CSF-1and RANKL for 3 days 3


title: Sleep deprived subject 6093 blood collection 15 [D6]

description:
SD_6093_t15
Sample SD_6093_t15 in GSE98564


title: Sleep deprived subject 6125 blood collection 10 [D6]

description:
SD_6125_t10
Sample SD_6125_t10 in GSE98564


title: Cip_93_ALL_D6_S38

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: genes_cpm_filter_expression_nonmerged.tsv

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: reprogramming cells

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: reprogramming cells

tag: treatment

value: all chemical

tag: day of reprogramming


title: Murine myeloid precursors treated with CSF-1and RANKL for 3 days 1


title: Cip_93_MEF_D0_S37

source_name: mouse embryonic fibroblast

value: MEF cells


title: Sleep deprived subject 6093 blood collection 13 [D6]

description:
SD_6093_t13
Sample SD_6093_t13 in GSE98564


title: Cip_93_ALL_D40_S44


title: Sleep deprived subject 6093 blood collection 14 [D6]

description:
SD_6093_t14
Sample SD_6093_t14 in GSE98564


title: Cip_93_ALL_D30_S42


title: Cip_93_ALL_D36_S43


title: Murine myeloid precursors treated with CSF-1and RANKL for 1.5 days 3

source_name: Murine myeloid precursors_CSF-1and RANKL for 1.5 days

value: CSF-1and RANKL for 1.5 days


title: Murine myeloid precursors treated with CSF-1and RANKL for 1.5 days 2


title: Murine myeloid precursors treated with CSF-1and RANKL for 1.5 days 1


title: Sleep deprived subject 6311 blood collection 10 [D6]

description:
SD_6311_t10
Sample SD_6311_t10 in GSE98564


title: Sleep deprived subject 6125 blood collection 02 [D6]

description:
SD_6125_t02
Sample SD_6125_t02 in GSE98564


title: Sleep deprived subject 6093 blood collection 12 [D6]

description:
SD_6093_t12
Sample SD_6093_t12 in GSE98564


title: Cip_93_ALL_D22_S41


title: Sleep deprived subject 6125 blood collection 03 [D6]

description:
SD_6125_t03
Sample SD_6125_t03 in GSE98564


title: Cip_93_ALL_D18_S40


title: Sleep deprived subject 6093 blood collection 09 [D6]

description:
SD_6093_t09
Sample SD_6093_t09 in GSE98564


title: Sleep deprived subject 6093 blood collection 10 [D6]

description:
SD_6093_t10
Sample SD_6093_t10 in GSE98564


title: Murine myeloid precursors treated with CSF-1 alone 1

source_name: Murine myeloid precursors_CSF-1 alone

value: CSF-1 alone


title: Sleep deprived subject 6093 blood collection 11 [D6]

description:
SD_6093_t11
Sample SD_6093_t11 in GSE98564


title: Sleep deprived subject 6093 blood collection 03 [D6]

description:
SD_6093_t03
Sample SD_6093_t03 in GSE98564


title: Sleep deprived subject 6093 blood collection 08 [D6]

description:
SD_6093_t08
Sample SD_6093_t08 in GSE98564


title: Sleep deprived subject 6093 blood collection 04 [D6]

description:
SD_6093_t04
Sample SD_6093_t04 in GSE98564


title: Cip_93_ALL_Chir_D6_S52

value: minus Chir


title: Cip_93_ALL_Chir_D30_S56


title: Murine myeloid precursors treated with CSF-1 alone 3


title: Cip_93_ALL_Chir_D22_S55


title: Cip_93_ALL_Chir_D18_S54


title: Cip_93_ALL_Chir_D12_S53


title: Cip_93_ALL_D12_S39


title: Cip_93_ALL_Brdu_D6_S45

value: minus Brdu


title: Control subject 6297 blood collection 15 [D6]

description:
C_6297_t15
Sample C_6297_t15 in GSE98564

value: unknown

value: Control


title: fetal fibroblasts_control clone_2-C121

type: genomic

city: Würzburg

first: Anna

last: Maierhofer

address: Biozentrum, Am Hubland

department: Institute of Human Genetics

country: Germany

institute: University of Würzburg

description:
control clone
SAMPLE 48

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings

data_processing:
Chip Analysis Methylation Pipeline (ChAMP) (Morris et al., 2014)
supplementary files contain normalized (BMIQ normalization method) average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: fetal fibroblast strain 2

label_protocol: Standard Illumina Protocol

growth_protocol: cells were cultured in T25 flasks in Chang Medium with L-glutamine (Irvine Scientific) at 37°C in an incubator with 5% CO2 atmosphere

extract_protocol: genomic DNA was extracted from fetal fibrobalsts using Quick-gDNA MiniPrep Kit (Zymo Research) according to standard instructions

treatment_protocol: cultures were exposed at room temperature to a single X-ray dose of 2 Gray (8 Gy/min) using a Siemens Primus L linear accelerator

value: fetal fibroblast

tag: group

value: non-irradiated

tag: stability


title: Cip_93_ALL_Brdu_D40_S51


title: Sleep deprived subject 6093 blood collection 02 [D6]

description:
SD_6093_t02
Sample SD_6093_t02 in GSE98564

value: Sleep Deprived

value: baseline


title: fetal fibroblasts_irradiated clone_2-217

description:
irradiated clone
SAMPLE 47

value: irradiated

value: stable


title: Sleep deprived subject 6093 blood collection 01 [D6]

description:
SD_6093_t01
Sample SD_6093_t01 in GSE98564

value: resistant


title: fetal fibroblasts_irradiated clone_2-2B

description:
irradiated clone
SAMPLE 46


title: Cip_93_ALL_Brdu_D36_S50


title: fetal fibroblasts_control clone_2-C13

description:
control clone
SAMPLE 45


title: APNL

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

country: South Korea

institute: Dongguk Uvi.

description: SAMPLE 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: APNL

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: Total RNA was extracted from the cells using the Trizol reagent (Invitrogen, Carlsbad, CA, USA).

value: APNL


title: Cip_93_ALL_Brdu_D30_S49

value: reprogramming cells


title: Murine myeloid precursors treated with CSF-1 alone 2

value: Murine enriched myeloid precurosrs


title: Control subject 6297 blood collection 13 [D6]

description:
C_6297_t13
Sample C_6297_t13 in GSE98564

value: recovery


title: Control subject 6297 blood collection 14 [D6]

description:
C_6297_t14
Sample C_6297_t14 in GSE98564


title: Control subject 6297 blood collection 12 [D6]

description:
C_6297_t12
Sample C_6297_t12 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2308

description:
irradiated clone
SAMPLE 44

value: unstable


title: APNL+AuEMF

description: SAMPLE 3

source_name: APNL+AuEMF

value: APNL+AuEMF


title: Control

description: SAMPLE 1

source_name: fibroblast

value: fibroblast


title: Control subject 6297 blood collection 11 [D6]

description:
C_6297_t11
Sample C_6297_t11 in GSE98564

value: experimental


title: Fibroblast

description: SAMPLE 1

source_name: Fibroblast

value: Fibroblast


title: Cip_93_ALL_Brdu_D22_S48

description: genes_cpm_filter_expression_nonmerged.tsv

value: minus Brdu


title: Primary neuron

description: SAMPLE 4

source_name: Primary neuron

value: Primary neuron


title: Control subject 6297 blood collection 09 [D6]

description:
C_6297_t09
Sample C_6297_t09 in GSE98564

value: unknown

value: Control


title: Control subject 6297 blood collection 10 [D6]

description:
C_6297_t10
Sample C_6297_t10 in GSE98564


title: EMF+AuNPs

description: SAMPLE 2


title: Cip_93_ALL_Brdu_D18_S47


title: Control subject 6297 blood collection 08 [D6]

description:
C_6297_t08
Sample C_6297_t08 in GSE98564


title: Cip_93_ALL_Brdu_D12_S46


title: fetal fibroblasts_control clone_2-C101

description:
control clone
SAMPLE 40

value: fetal fibroblast

value: non-irradiated


title: fetal fibroblasts_irradiated clone_2-2114

description:
irradiated clone
SAMPLE 42

value: irradiated

value: stable


title: fetal fibroblasts_irradiated clone_2-2103a

description:
irradiated clone
SAMPLE 41


title: Control subject 6297 blood collection 04 [D6]

description:
C_6297_t04
Sample C_6297_t04 in GSE98564

value: baseline


title: cips192d6-plus-input_S9

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ChIIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using MACS14, using input as control
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

extract_protocol:
ChIP was performed as described previously(Liu et al., 2015), Briefly, cells were fixed in 18 ml DMEM (Hyclone) containing 1% formaldehyde for 15 min at room temperature with rotation, the reaction was quenched by the addition of 2 ml of 0.125 M glycine. And then the cells were washed with PBS 3 times. Cells were lysed in ChIP buffer A (50mM HEPES-KOH, 140 mM NaCl, 1mM EDTA (pH 8.0), 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 50 mM Tris-HCl (pH 8.0), and protease inhibitor cocktail) for 10 min at 4°C. Pellets were lysed in ChIP buffer B (1% SDS, 50 nM Tris-HCl (pH 8.0), 10mM EDTA and protease inhibitor cocktail) for 5 min at 4°C. The DNA was fragmented to 100-500 bp by sonication, and then centrifuged at 12,000g for 2 min. The supernatant was diluted with ChIP IP buffer (0.01% SDS, 1% Triton X-100, 2mM EDTA, 50mM Tris-HCl (pH 8.0), 150 mM NaCl and protease inhibitor cocktail). Immunoprecipitation was performed using 2μg of H3K27ac antibody added to protein A/G Dynabeads, and incubated overnight at 4°C. Beads were washed, eluted and reverse crosslinked. DNA was purified by using the MinElute Reaction Clean up Kit (QIAGEN).
The ChIP DNA library for NextSeq 500 sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to manufacturer’s instructions. AMPure XP beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech). Libraries were sequenced on an Illumina NextSeq 500 v2 using 50bp paired-end reads.

value: reprogramming cells

value: all chemical

tag: chip antibody

value: input


title: cips192d6-plus-H3K27ac-rp1_S4


title: cips192d6-minus-input_S1


title: fetal fibroblasts_irradiated clone_2-2103n

description:
irradiated clone
SAMPLE 39

value: unstable


title: Control subject 6297 blood collection 02 [D6]

description:
C_6297_t02
Sample C_6297_t02 in GSE98564


title: fetal fibroblasts_control clone_2-C42

description:
control clone
SAMPLE 38


title: Control subject 6297 blood collection 03 [D6]

description:
C_6297_t03
Sample C_6297_t03 in GSE98564


title: fetal fibroblasts_irradiated clone_2-244

description:
irradiated clone
SAMPLE 37


title: fetal fibroblasts_control clone_2-C100

description:
control clone
SAMPLE 43


title: cips192d6-minus-H3K27ac-rp1_S1


title: cips192d40-plus-input_S21


title: fetal fibroblasts_control clone_2-C6

description:
control clone
SAMPLE 36


title: cips192d40-plus-H3K27ac_S23


title: fetal fibroblasts_irradiated clone_2-2M

description:
irradiated clone
SAMPLE 35


title: cips192d22-plus-input_S13


title: Control subject 6296 blood collection 15 [D6]

description:
C_6296_t15
Sample C_6296_t15 in GSE98564

value: recovery


title: Control subject 6296 blood collection 13 [D6]

description:
C_6296_t13
Sample C_6296_t13 in GSE98564


title: Control subject 6296 blood collection 14 [D6]

description:
C_6296_t14
Sample C_6296_t14 in GSE98564


title: Control subject 6297 blood collection 01 [D6]

description:
C_6297_t01
Sample C_6297_t01 in GSE98564


title: fetal fibroblasts_control clone_2-C52

description:
control clone
SAMPLE 34


title: Control subject 6296 blood collection 12 [D6]

description:
C_6296_t12
Sample C_6296_t12 in GSE98564


title: cips192d22-minus-input_S5


title: fetal fibroblasts_control clone_2-C20

description:
control clone
SAMPLE 32


title: cips192d22-minus-H3K27ac-rp1_S2


title: cips192d22-plus-H3K27ac-rp1_S6


title: Control subject 6296 blood collection 11 [D6]

description:
C_6296_t11
Sample C_6296_t11 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2301

description:
irradiated clone
SAMPLE 31


title: fetal fibroblasts_irradiated clone_2-2200

description:
irradiated clone
SAMPLE 30


title: Control subject 6296 blood collection 09 [D6]

description:
C_6296_t09
Sample C_6296_t09 in GSE98564


title: Control subject 6296 blood collection 04 [D6]

description:
C_6296_t04
Sample C_6296_t04 in GSE98564


title: CiPS-B-D40_S3

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: wig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

extract_protocol:
A total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

value: day 40


title: CiPS-B-D36_S2

value: day 36


title: Control subject 6296 blood collection 10 [D6]

description:
C_6296_t10
Sample C_6296_t10 in GSE98564

value: experimental


title: Control subject 6296 blood collection 08 [D6]

description:
C_6296_t08
Sample C_6296_t08 in GSE98564


title: fetal fibroblasts_irradiated clone_2-210

description:
irradiated clone
SAMPLE 28


title: CiPS-B-D30_S1

value: day 30

value: minus Brdu


title: fetal fibroblasts_starting culture_2-rep2

description:
mass culture
SAMPLE 27

value: starting culture


title: CiPS-B-D22_S12

value: day 22


title: fetal fibroblasts_irradiated clone_2-2A

description:
irradiated clone
SAMPLE 33

value: fetal fibroblast


title: Control subject 6296 blood collection 03 [D6]

description:
C_6296_t03
Sample C_6296_t03 in GSE98564

value: unknown

value: Control


title: Control subject 6296 blood collection 02 [D6]

description:
C_6296_t02
Sample C_6296_t02 in GSE98564


title: fetal fibroblasts_control clone_2-C26

description:
control clone
SAMPLE 25

value: non-irradiated


title: CiPS-A-D6_S1

value: day 6


title: Control subject 6231 blood collection 14 [D6]

description:
C_6231_t14
Sample C_6231_t14 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2205

description:
irradiated clone
SAMPLE 26

value: irradiated

value: stable


title: CiPS-B-D18_S11

value: reprogramming cells

value: day 18


title: CiPS-B-D12_S5

value: day 12


title: Control subject 6231 blood collection 15 [D6]

description:
C_6231_t15
Sample C_6231_t15 in GSE98564

value: recovery


title: Control subject 6296 blood collection 01 [D6]

description:
C_6296_t01
Sample C_6296_t01 in GSE98564

value: baseline


title: Control subject 6231 blood collection 12 [D6]

description:
C_6231_t12
Sample C_6231_t12 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2L

description:
irradiated clone
SAMPLE 24

value: unstable


title: CiPS-B-D6_S4


title: fetal fibroblasts_control clone_2-C4

description:
control clone
SAMPLE 23


title: Control subject 6231 blood collection 13 [D6]

description:
C_6231_t13
Sample C_6231_t13 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2W

description:
irradiated clone
SAMPLE 22


title: CiPS-A-D36_S6

value: day 36

value: all chemical


title: Control subject 6231 blood collection 11 [D6]

description:
C_6231_t11
Sample C_6231_t11 in GSE98564

value: experimental


title: fetal fibroblasts_irradiated clone_2-29

description:
irradiated clone
SAMPLE 20


title: fetal fibroblasts_control clone_2-C14

description:
control clone
SAMPLE 29


title: CiPS-A-D40_S7

value: day 40


title: fetal fibroblasts_control clone_2-C2

description:
control clone
SAMPLE 21

value: fetal fibroblast


title: fetal fibroblasts_irradiated clone_2-2337

description:
irradiated clone
SAMPLE 19


title: CiPS-A-D30_S5

value: day 30


title: CiPS-A-D22_S4

value: day 22


title: CiPS-A-D12_S2


title: fetal fibroblasts_control clone_2-C103

description:
control clone
SAMPLE 18

value: non-irradiated


title: fetal fibroblasts_irradiated clone_2-2106

description:
irradiated clone
SAMPLE 17


title: CiPS-A-D18_S3


title: fetal fibroblasts_irradiated clone_2-2302

description:
irradiated clone
SAMPLE 13


title: fetal fibroblasts_control clone_2-C104

description:
control clone
SAMPLE 11


title: Control subject 6231 blood collection 10 [D6]

description:
C_6231_t10
Sample C_6231_t10 in GSE98564

value: unknown

value: Control


title: fetal fibroblasts_control clone_2-C9

description:
control clone
SAMPLE 14


title: fetal fibroblasts_control clone_2-C102

description:
control clone
SAMPLE 16


title: Control subject 6231 blood collection 09 [D6]

description:
C_6231_t09
Sample C_6231_t09 in GSE98564


title: Control subject 6231 blood collection 04 [D6]

description:
C_6231_t04
Sample C_6231_t04 in GSE98564


title: Control subject 6231 blood collection 08 [D6]

description:
C_6231_t08
Sample C_6231_t08 in GSE98564


title: Control subject 6231 blood collection 02 [D6]

description:
C_6231_t02
Sample C_6231_t02 in GSE98564


title: Control subject 6231 blood collection 03 [D6]

description:
C_6231_t03
Sample C_6231_t03 in GSE98564


title: Control subject 6089 blood collection 13 [D6]

description:
C_6089_t13
Sample C_6089_t13 in GSE98564


title: Control subject 6089 blood collection 12 [D6]

description:
C_6089_t12
Sample C_6089_t12 in GSE98564


title: fetal fibroblasts_control clone_2-C1

description:
control clone
SAMPLE 7


title: Control subject 6089 blood collection 15 [D6]

description:
C_6089_t15
Sample C_6089_t15 in GSE98564


title: Control subject 6089 blood collection 14 [D6]

description:
C_6089_t14
Sample C_6089_t14 in GSE98564


title: Control subject 6089 blood collection 09 [D6]

description:
C_6089_t09
Sample C_6089_t09 in GSE98564


title: fetal fibroblasts_control clone_2-C48

description:
control clone
SAMPLE 9


title: fetal fibroblasts_irradiated clone_2-2300

description:
irradiated clone
SAMPLE 15

value: irradiated


title: fetal fibroblasts_irradiated clone_2-2309

description:
irradiated clone
SAMPLE 12


title: Control subject 6231 blood collection 01 [D6]

description:
C_6231_t01
Sample C_6231_t01 in GSE98564


title: Control subject 6089 blood collection 10 [D6]

description:
C_6089_t10
Sample C_6089_t10 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2237

description:
irradiated clone
SAMPLE 10


title: fetal fibroblasts_irradiated clone_2-2113

description:
irradiated clone
SAMPLE 6


title: fetal fibroblasts_control clone_2-C3

description:
control clone
SAMPLE 2


title: fetal fibroblasts_starting culture_2-rep1

description:
mass culture
SAMPLE 8

value: starting culture


title: Control subject 6089 blood collection 11 [D6]

description:
C_6089_t11
Sample C_6089_t11 in GSE98564


title: fetal fibroblasts_irradiated clone_2-2203

description:
irradiated clone
SAMPLE 1


title: Control subject 6089 blood collection 02 [D6]

description:
C_6089_t02
Sample C_6089_t02 in GSE98564


title: Control subject 6089 blood collection 04 [D6]

description:
C_6089_t04
Sample C_6089_t04 in GSE98564


title: Control subject 6089 blood collection 01 [D6]

description:
C_6089_t01
Sample C_6089_t01 in GSE98564


title: fetal fibroblasts_control clone_2-C25

description:
control clone
SAMPLE 4


title: Control subject 6089 blood collection 08 [D6]

description:
C_6089_t08
Sample C_6089_t08 in GSE98564


title: Control subject 6089 blood collection 03 [D6]

description:
C_6089_t03
Sample C_6089_t03 in GSE98564


title: fetal fibroblasts_irradiated clone_2-21

description:
irradiated clone
SAMPLE 3

value: stable


title: fetal fibroblasts_irradiated clone_2-2310

description:
irradiated clone
SAMPLE 5


title: Control subject 6068 blood collection 10 [D6]

description:
C_6068_t10
Sample C_6068_t10 in GSE98564


title: Control subject 6068 blood collection 13 [D6]

description:
C_6068_t13
Sample C_6068_t13 in GSE98564


title: Control subject 6068 blood collection 15 [D6]

description:
C_6068_t15
Sample C_6068_t15 in GSE98564


title: Control subject 6068 blood collection 09 [D6]

description:
C_6068_t09
Sample C_6068_t09 in GSE98564


title: Control subject 6068 blood collection 14 [D6]

description:
C_6068_t14
Sample C_6068_t14 in GSE98564


title: Control subject 6068 blood collection 12 [D6]

description:
C_6068_t12
Sample C_6068_t12 in GSE98564


title: Control subject 6068 blood collection 03 [D6]

description:
C_6068_t03
Sample C_6068_t03 in GSE98564


title: Control subject 6068 blood collection 08 [D6]

description:
C_6068_t08
Sample C_6068_t08 in GSE98564


title: Control subject 6068 blood collection 04 [D6]

description:
C_6068_t04
Sample C_6068_t04 in GSE98564


title: Control subject 6068 blood collection 02 [D6]

description:
C_6068_t02
Sample C_6068_t02 in GSE98564


title: Control subject 6068 blood collection 01 [D6]

description:
C_6068_t01
Sample C_6068_t01 in GSE98564


title: Control subject 6068 blood collection 11 [D6]

description:
C_6068_t11
Sample C_6068_t11 in GSE98564


title: Control subject 6045 blood collection 14 [D6]

description:
C_6045_t14
Sample C_6045_t14 in GSE98564


title: Control subject 6045 blood collection 13 [D6]

description:
C_6045_t13
Sample C_6045_t13 in GSE98564


title: Control subject 6045 blood collection 12 [D6]

description:
C_6045_t12
Sample C_6045_t12 in GSE98564


title: Control subject 6045 blood collection 11 [D6]

description:
C_6045_t11
Sample C_6045_t11 in GSE98564


title: Control subject 6045 blood collection 09 [D6]

description:
C_6045_t09
Sample C_6045_t09 in GSE98564


title: MRC5_si-Dicer1_rep2

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

description: microRNA expression data from MRC5-CAFs transfected with si-Dicer1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: PICR scanner 3000

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

value: CAFs


title: MRC5_si-Dicer1_rep3

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 3


title: MRC5_si-Dicer1_rep1

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 1


title: Control subject 6045 blood collection 08 [D6]

description:
C_6045_t08
Sample C_6045_t08 in GSE98564


title: Control subject 6045 blood collection 15 [D6]

description:
C_6045_t15
Sample C_6045_t15 in GSE98564

value: recovery


title: Control subject 6045 blood collection 04 [D6]

description:
C_6045_t04
Sample C_6045_t04 in GSE98564

value: baseline


title: AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock_Rep3

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

description: Biological replicate 3 of 3. AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation.

scan_protocol: Images were scanned at 2mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and they were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

organism: Marchantia polymorpha

label_protocol: 200 ng of total RNA was reverse transcribed used T7 promotor  primer and the cDNA was converted to aRNA using T7 RNA polimerase, wich simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two color Microarray-Based GeneExpression Analysis Protocol )

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male) and Takaragaike-2 (Tak-2; female) were used as wild-type. Mutants Mpcoi1-1 (female) and Mpcoi1-2 (male) and complemented line proMpEF:AtCOI1/Mpcoi1-1 (female) were also analysed. Gemmae were grown for 13 days on 0.5 Gamborg’s B5 medium containing 0.5% agar.

extract_protocol: Every independent biological replicate contained 6-8 plants. Total RNA from Marchantia was extracted with Trizol (Invitrogen) and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.

treatment_protocol: Plants were transferred to 0.5 Gamborg’s B5 liquid medium for 2 hours for hormone treatments (OPDA 25 µM, coronatine 0.5 µM or the equivalent amount of ethanol as mock). Mechanical wounding was performed with tweezers all over the 21-day-old thalli of Tak-1 grown on 0.5 Gamborg’s B5 0.5% agar. Plants were then ground in liquid nitrogen prior RNA extraction.

tag: genotype/variation

value: COR

value: Mock


title: MRC5_si-Ctrl_rep3

description: microRNA expression data from MRC5-CAFs transfected with si-Ctrl .

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 3


title: Control subject 6045 blood collection 02 [D6]

description:
C_6045_t02
Sample C_6045_t02 in GSE98564


title: MRC5_si-Ctrl_rep1

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 1


title: Control subject 6045 blood collection 01 [D6]

description:
C_6045_t01
Sample C_6045_t01 in GSE98564

source_name: blood


title: Lichtheimia_H2_controlnacl

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description: CTRL for NaCl replicate 2

data_processing:
Base calling and adapter clipping performed by the Ion Proton System
Quality trimming by Qtrim v1.1 parameterized by sliding window of length 10, mean phred score 20 and minimum read length 20
Segemehl v0.2 was used for mapping with enabled split option
Unique mapped reads were extracted using the Bio::ViennaNGS Perl modules script bam_uniq.pl
Per gene read counts were inferred in-house by split aware usage of Bio::DB::SAM Perl modules applied on reference annotations
Genome_build: Lichtheimia corymbifera JMRC:FSU:09682 (NCBI WGS accession CBTN000000000), Lichtheimia hyalospora JMRC:FSU:10163 (v1.0 JGI Project ID 1015499 ), Lichtheimia ramosa JMRC:FSU:06197 (ENA Study PRJEB6289)
Supplementary_files_format_and_content: Tab separated text file containing gene ids in column 1 an raw read counts in column 2

organism: Lichtheimia hyalospora

source_name: mRNA extracted from mycelia

growth_protocol: Spores incubated in SUP medium for 22h (CTRL) or 16h (HEAT, NaCl) or 20h (GDA, DTT)

extract_protocol:
Total RNA extracted using RNAeasy Plant kit (Quiagen), Poly-A purified using Dynabeads mRNA DIRECT Micro Purification Kit (Ambion)
Ion Total RNA-Seq Kit v2.0 (Life Technologies), SuperScript III Enzyme Mix (Life Technologies) for reverse transcription and amplified using Platinum PCR High Fidelity polymerase (Life Technologies) for sequencing on an on an Ion Proton Sequencer (Life Technologies)

treatment_protocol: Spores in SUP medium incubated for additional 6h (HEAT, NaCl) or 2h (GDA, DTT)

tag: strain

tag: incubation


title: Lichtheimia_H1_controlnacl

description: CTRL for NaCl replicate 1


title: AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock_Rep1

description: Biological replicate 1 of 3. AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock


title: Lichtheimia_H2_heatnacl

description: NaCl replicate 2

value: NaCl (final concentration:0.5 M)

value: 16h pre-grown + 6h HEAT,NaCl


title: Floral nectary secretory replicate 2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Normalized contig counts mapped to Glycine max and Arabidopsis thaliana
Glycine max mapped counts tested for differential expression using DESeq
Genome_build: NCBI RefSeq mRNA used for Glycine max, Araport 11 build 201606 used for Arabidopsis thaliana
Supplementary_files_format_and_content: bean_to_Gmax.xls: The UQN (upper quartile normalized) count data is normalized on the contig count level (reads mapped to assembled contigs), to get consistent upper-quartile counts across all of the samples.  No further normalization was performed after mapping those counts to the Glycine max sequences.

organism: Phaseolus vulgaris

source_name: Floral nectary tissue

growth_protocol: Phaseolus vulgaris cv. Blue Lake 274 was grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle, photosynthetic photon flux of 250 μmol m-2 s-1 at leaf level, and a temperature of 23°C.

extract_protocol:
Triplicate RNA samples were isolated from seven tissues: (1) leaf, (2) extrafloral nectaries at the base of terminal trifoliate leaves (EFN_leaf), (3) extrafloral nectaries located on stems at the base of lateral trifoliate leaves (EFN_stem), (4) ‘pre-secretory #1’ floral nectaries (‘pre1’, 24 hours prior to anthesis/nectar secretion), (5) ‘pre-secretory #2’ floral nectaries (‘pre2’, 12 hours prior to anthesis/nectar secretion), (6) ‘secretory’ floral nectaries (‘sec’, full anthesis, 3 hours after dawn), and (7) ‘post-secretory’ floral nectaries (‘post’, 12 hours after the ‘secretory’ stage). All nectary tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-one TruSeq RNA v2 libraries were created (7 tissues in triplicate) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two full lanes. This generated 150 M reads for each lane and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: cultivar

value: Blue Lake 274

tag: tissue

value: Floral nectary

tag: nectary stage

value: secretory


title: Floral nectary pre-secretory stage 2 replicate 2

value: pre-secretory


title: Lichtheimia_H2_heat

description: HEAT replicate 2

value: Heat (42°C)

value: 16h pre-grown + 6h HEAT


title: AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock_Rep2

description: Biological replicate 2 of 3. AtCoi1/Mpcoi1-1 treated with COR vs Mpcoi1-1 Mock


title: HDF1429_3

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Human dermal fibroblasts, replicate 3

hyb_protocol: Manufature's protocol

scan_protocol: Fluorescent signals were read on an Illumina BeadStation GX scanner.

data_processing: Normalization and calculation of beta-values, the ratio of methylated to unmethylated cytosine, was performed using GenomeStudio (Illumina).

source_name: Human dermal fibroblasts, replicate 3

label_protocol: Manufature's protocol

growth_protocol: HDFs were maintained in Dulbecco’s modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies) and 0.5% Penicillin/Streptomycin (Pen/Strep, Life Technologies).

extract_protocol: Cells were lysed with Cell lysis solution (QIAGEN), and genomic DNA was purified using a DNeasy blood and tissue kit (QIAGEN) according to manufacturer’s protocol.

value: Human dermal fibroblasts


title: HDF1429_2

description: Human dermal fibroblasts, replicate 2

source_name: Human dermal fibroblasts, replicate 2


title: Floral nectary secretory replicate 1


title: WTC11_2_teratoma_fibroblasts_2

description: Teratoma, replicate 2

source_name: Teratoma, replicate 2

value: Teratoma


title: WTC11_2_teratoma_fibroblasts_3

description: Teratoma, replicate 3

source_name: Teratoma, replicate 3


title: Floral nectary pre-secretory stage 2 replicate 3


title: Tak-1 mechanical wounded vs Tak-1 Mock_Rep3

description: Biological replicate 3 of 3. Tak-1 wound vs Tak-1 Mock

value: wound


title: WTC11_2_teratoma_fibroblasts_1

description: Teratoma, replicate 1

source_name: Teratoma, replicate 1


title: Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA_Rep3

description: Biological replicate 3 of 3. Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA

value: 25 uMOPDA


title: Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA_Rep2

description: Biological replicate 2 of 3. Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA


title: MRC5_si-Ctrl_rep2

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 2

value: CAFs


title: Lichtheimia_H1_heatnacl

description: NaCl replicate 1


title: Tak-1 mechanical wounded  vs Tak-1 Mock_Rep2

description: Biological replicate 2 of 3. Tak-1 wound vs Tak-1 Mock


title: HDF1429_1

description: Human dermal fibroblasts, replicate 1

source_name: Human dermal fibroblasts, replicate 1


title: Floral nectary pre-secretory stage 1 replicate 3


title: Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA_Rep1

description: Biological replicate 1 of 3. Mpcoi1-2 treated with OPDA vs Tak-1 treated with OPDA


title: Floral nectary pre-secretory stage 2 replicate 1


title: Lichtheimia_H1_heat

description: HEAT replicate 1


title: Lichtheimia_H2_dtt

description: DTT replicate 2

value: Dithiothreitol (DTT)

value: 20h pre-grown + 2h DTT


title: Tak-1 mechanical wounded vs Tak-1 Mock_Rep1

description: Biological replicate 1 of 3. Tak-1 wound vs Tak-1 Mock


title: Lichtheimia_H1_dtt

description: DTT replicate 1


title: Lichtheimia_H2_gda

description: GDA replicate 2

value: Geldanamycin (GDA)

value: 20h pre-grown + 2h GDA


title: Floral nectary pre-secretory stage 1 replicate 1


title: Lichtheimia_H1_gda

description: GDA replicate 1


title: Floral nectary post-secretory replicate 1

value: post-secretory


title: Leaf replicate 3

source_name: Leaf tissue

value: Leaf


title: Floral nectary post-secretory replicate 3

value: Blue Lake 274


title: Floral nectary pre-secretory stage 1 replicate 2

value: Floral nectary


title: Floral nectary post-secretory replicate 2


title: Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA_Rep2

description: Biological replicate 2 of 3. Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA


title: Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA_Rep1

description: Biological replicate 1 of 3. Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA


title: Lichtheimia_H1_control

description: CTRL replicate 1


title: Leaf replicate 1


title: Mpcoi1-2 treated with OPDA vs Mpcoi1-2 Mock_Rep2

description: Biological replicate 2 of 2. Mpcoi1-2 treated with OPDA vs Mpcoi1-2 Mock

value: Mock


title: Lichtheimia_C2_dtt

description: DTT replicate 2

organism: Lichtheimia corymbifera


title: Tak-2 treated with OPDA vs Tak-2 Mock_Rep2

description: Biological replicate 2 of 3. Tak-2 treated with OPDA vs Tak-2 Mock


title: Mpcoi1-2 treated with OPDA vs Mpcoi1-2 Mock_Rep1

description: Biological replicate 1 of 2. Mpcoi1-2 treated with OPDA vs Mpcoi1-2 Mock


title: Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA_Rep3

description: Biological replicate 3 of 3. Mpcoi1-1 treated with OPDA vs Tak-2 treated with OPDA


title: Tak-2 treated with OPDA vs Tak-2 Mock_Rep3

description: Biological replicate 3 of 3. Tak-2 treated with OPDA vs Tak-2 Mock


title: Lichtheimia_R2_heat

description: HEAT replicate 2

organism: Lichtheimia ramosa


title: Leaf replicate 2


title: Lichtheimia_C2_heat

description: HEAT replicate 2


title: Lichtheimia_H2_control

description: CTRL replicate 2


title: Lichtheimia_R2_dtt

description: DTT replicate 2


title: Lichtheimia_R1_heat

description: HEAT replicate 1


title: Control subject 6045 blood collection 03 [D6]

description:
C_6045_t03
Sample C_6045_t03 in GSE98564

tag: subject id

value: unknown

value: Control

value: baseline


title: Stem extrafloral nectary replicate 3

source_name: Extrafloral nectary tissue

value: Stem Extrafloral nectary


title: Lichtheimia_C1_dtt

description: DTT replicate 1


title: Tak-2 treated with OPDA vs Tak-2 Mock_Rep1

description: Biological replicate 1 of 3. Tak-2 treated with OPDA vs Tak-2 Mock


title: Stem extrafloral nectary replicate 1


title: Lichtheimia_C1_heat

description: HEAT replicate 1

value: Heat (42°C)

value: 16h pre-grown + 6h HEAT


title: Lichtheimia_R1_dtt

description: DTT replicate 1


title: Lichtheimia_C2_control

description: CTRL replicate 2


title: Lichtheimia_R2_control

description: CTRL replicate 2


title: Stem extrafloral nectary replicate 2


title: Lichtheimia_C2_gda

description: GDA replicate 2


title: Leaf extrafloral nectary replicate 2

value: leaf Extrafloral nectary


title: Lichtheimia_C1_control

description: CTRL replicate 1


title: Lichtheimia_R1_control

description: CTRL replicate 1


title: Leaf extrafloral nectary replicate 1


title: Lichtheimia_R2_gda

description: GDA replicate 2


title: Lichtheimia_C1_gda

description: GDA replicate 1


title: 2D_mouseastrocytes(ma)_rep2

status: Public on Apr 09 2018

city: Cambridge

first: Halil

last: Tekin

state: MA

address: 75 Ames St.

institute: Broad Institute of MIT and Harvard

description:
mouse astrocytes cultured on 2D
count_matrix.txt
16B-070517_S47

data_processing:
RSEM v1.3 was run on fastq files using a joint human (hg19 annotation from UCSC) and mouse (mm10 annotation from UCSC) transcriptome and STAR v2.5.2, with the options --star --star-gzipped-read-file --paired-end. The STAR bams output by RSEM were used to filter the original fastq files with seqtk. In particular, all reads that mapped to the mouse transcriptome were removed, as were all unmapped reads. These filtered fastq files were run through RSEM with default parameters using human hg19 UCSC genome to estimate gene expression values, which were then used to create an un-normalized count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: "count_matrix.txt", tab-delimited un-normalized count matrix, contains count reads per gene for each Sample.
Supplementary_files_format_and_content: "singleCell_count1.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.
Supplementary_files_format_and_content: "singleCell_count2.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.

source_name: cortex

growth_protocol: desribed in H. Tekin et al., Nat Biomed Eng, 2018

extract_protocol:
RNA lysis buffer was used to lyse cells. Each lysate was then transferred to a 1.5 ml centrifuge tube, which was then placed on dry ice for rapid freezing and then stored at -80 °C. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.

tag: strain/cell type

tag: culture condition

tag: age

value: newborn

tag: genotype

value: wild type


title: JRGC_KO_5

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Single-end RNAseq.

data_processing:
Reads with poor quality were trimmed with Trimmomatic v0.32.
Trimmed reads were aligned to mm10 using tophat v2.0.10.
Aligned reads were counted using Htseq v0.6.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files, one per sample, include raw counts of sequencing reads.

source_name: Postnatal day 4-5 retina

extract_protocol:
J-RGCs were purified by flow cytometry and collected in pools of 100 cells per 100ul cell lysis buffer (2% beta-mercaptoethanol in TCL buffer, Qiagen) for RNA extraction and purification.
cDNA libraries were prepared from the RNA using Smartseq2 and Nextera XT DNA library preparation kit (FC-131-1024).

tag: strain/background

value: Mixed (C57BL/6 and CD1)

value: Tbr1 KO

value: Postnatal day 4-5

tag: cell type

value: J-RGC retinal ganglion cells


title: JRGC_KO_3

description: Single-end RNAseq.


title: JRGC_KO_6

description: Single-end RNAseq.


title: Leaf extrafloral nectary replicate 3


title: Lichtheimia_R1_gda

description: GDA replicate 1

tag: treatment

value: Geldanamycin (GDA)

value: 20h pre-grown + 2h GDA


title: JRGC_WT_4

description: Single-end RNAseq.

value: WT


title: 2D_mouseastrocytes(ma)_rep3

description:
mouse astrocytes cultured on 2D
count_matrix.txt
16C-070517_S48


title: Non-targeted differentiating GFP-D

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: GFP-D

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: mm9
Supplementary_files_format_and_content: File lists gene name, RefSeq id, locus, RPKM value of each gene in each sample

source_name: brain

growth_protocol: NPCs were grown in N2 media with 20 ng/ml of EGF and bFGF. For differentiation cells were kept in neurobasal media with 1X B27 supplement for 5 days.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For knockdown of FUBP1 cells were infected with lentivirus for FUBP1 hairpins and selected by puromycin treatment for 3 days.

value: brain neural progenitors

value: brain

value: Non-targeted differentiating


title: Non-targeted differentiating 7


title: JRGC_KO_2

description: Single-end RNAseq.


title: JRGC_KO_4

description: Single-end RNAseq.


title: 2D_mouseastrocytes(ma)_rep1

description:
mouse astrocytes cultured on 2D
count_matrix.txt
16A-070517_S46


title: FUBP1-targeted differentiating

value: FUBP1-targeted differentiating


title: JRGC_KO_1

description: Single-end RNAseq.


title: Non-targeted proliferating TRC

description: TRC

value: Non-targeted proliferating


title: JRGC_WT_5

description: Single-end RNAseq.


title: JRGC_WT_1

description: Single-end RNAseq.


title: JRGC_WT_3

description: Single-end RNAseq.


title: JRGC_WT_2

description: Single-end RNAseq.


title: CIC-targeted proliferating

description: CIC

value: CIC-targeted proliferating


title: Floral nectary secretory replicate 3

value: Blue Lake 274

value: Floral nectary

value: secretory


title: FUBP1-targeted proliferating

value: FUBP1-targeted proliferating


title: Non-targeted proliferating GFP

description: GFP


title: MDS98_Normal_RNA-seq

city: Stanford

first: Varsha

last: Rao

state: California

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description:
MDS_65
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR or TopHat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C et al. Read Counts (cpm) were generated using EdgeR package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MDS_isoform_fpkm.txt: Combined matrix of normalized abundance measurement - isoform expression (fpkm) using CuffDiff2.
Supplementary_files_format_and_content: MDS_genes_edgeR.txt: Combined matrix of normalized abundance measurement - gene expression (counts) using EdgeR.

source_name: Hematopoietic stem cells

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA) from magnetic bead affinity-enriched CD34+ cells (>90%) obtained from marrow aspirates (Miltenyi Biotec, Auburn, CA). The samples were snap frozen in liquid nitrogen and stored at -80oC on the day of collection. Quality check was performed by Bioanalyzer2100 (Agilent Technologies, Palo Alto, CA) using High Sensitivity RNA Chips.
5-10ng of total RNA (RIN>7) was amplified by using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech Laboratories, Inc., Mountain View, CA) after testing for the fidelity of the protocol on HeLa cell derived RNA (Supplementary Methods, Suppl Figure 1 of publication). cDNA library synthesis and sequencing were performed as previously described (See Supplementary Methods of publication). The libraries were sequenced on the Illumina HiSeq 2000 platform at the Stanford Sequencing Center.

value: CD34+ hematopoietic stem cells

tag: disease status

value: Healthy


title: MDS97_Normal_RNA-seq

description:
MDS_63
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS107_Normal_RNA-seq

description:
MDS_62
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS94_Normal_RNA-seq

description:
MDS_66
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS99_Normal_RNA-seq

description:
MDS_67
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDSBM791_Normal_RNA-seq

description:
MDS_57
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: CIC-targeted differentiating

description: CIC-D

value: CIC-targeted differentiating


title: MDS96_Normal_RNA-seq

description:
MDS_64
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1280_Normal_RNA-seq

description:
MDS_55
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1278_Normal_RNA-seq

description:
MDS_56
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1274_Normal_RNA-seq

description:
MDS_51
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS121_Normal_RNA-seq

description:
MDS_59
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS78_Normal_RNA-seq

description:
MDS_60
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS92_Normal_RNA-seq

description:
MDS_61
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS125_Normal_RNA-seq

description:
MDS_58
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDSBM800_Normal_RNA-seq

description:
MDS_53
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDSBM862_Normal_RNA-seq

description:
MDS_54
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1277_Normal_RNA-seq

description:
MDS_50
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1271_sMDS_RNA-seq

description:
MDS_43
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt

value: Myelodysplastic syndrome

tag: myelodysplastic syndrome stage

value: sMDS


title: MDS1245_sMDS_RNA-seq

description:
MDS_44
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1226_Normal_RNA-seq

description:
MDS_45
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDSBM802_Normal_RNA-seq

description:
MDS_52
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1243_sMDS_RNA-seq

description:
MDS_39
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1126_sMDS_RNA-seq

description:
MDS_34
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1265_sMDS_RNA-seq

description:
MDS_41
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1045_sMDS_RNA-seq

description:
MDS_38
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1208_sMDS_RNA-seq

description:
MDS_42
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: single_cell_3D_iN_ma

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 30 million cells per ml.
singleCell_count1.txt
SingleCell1

data_processing:
CellRanger count function was run on fastq files with the option --force-cells=10,000. The count data was extracted from the Cellranger output. We removed all cells expressing less than 1000 human genes or more than 300 mouse genes, and retained the count data from all human genes.
Genome_build: hg19
Supplementary_files_format_and_content: "count_matrix.txt", tab-delimited un-normalized count matrix, contains count reads per gene for each Sample.
Supplementary_files_format_and_content: "singleCell_count1.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.
Supplementary_files_format_and_content: "singleCell_count2.txt, tab-delimited un-normalized count matrix, with one column for each cell and one row for each gene.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: HUES66 and mouse cortex

extract_protocol:
3D culture hydrogel was dissociated. Cell suspension of human neuronal cells and mouse astrocytes was loaded onto the 10x Chromium Instrument to generate single-cell gel bead in emulsions.
Single-cell RNA-Seq libraries were constructed using 10x Chromium 3' Solution following the manufacturer’s protocol.

value: wild type


title: MDS1209_Normal_RNA-seq

description:
MDS_48
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1204_sMDS_RNA-seq

description:
MDS_37
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1239_Normal_RNA-seq

description:
MDS_46
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_50ul_CH_2X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
16B060216_S47

extract_protocol:
3D culture hydrogel was transferred to a 1.5 ml centrifuge tube and immersed in RNA lysis buffer, which was placed on dry ice for rapid freezing and then stored at -80 °C. 3D culture hydrogel was homogenized in lysis buffer. Total RNA isolation was performed using a kit following the manufacturer’s protocol. Further purification step was performed on the eluted RNA samples.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.


title: MDS1203_Normal_RNA-seq

description:
MDS_49
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1064_sMDS_RNA-seq

description:
MDS_32
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1195_tMDS_RNA-seq

description:
MDS_40
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt

value: tMDS


title: 3D_50ul_CH_2X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
16A060216_S46


title: MDS1098_tMDS_RNA-seq

description:
MDS_33
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1100_sMDS_RNA-seq

description:
MDS_36
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_50ul_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
6C060216_S18


title: MDS1249_sMDS_RNA-seq

description:
MDS_29
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_50ul_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
6B060216_S17


title: MDS1065_sMDS_RNA-seq

description:
MDS_35
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_50ul_CH_2X_CRS_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS at 30 million cells per ml.
count_matrix.txt
7B060216_S20


title: 3D_50ul_CH_2X_CRS_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS at 30 million cells per ml.
count_matrix.txt
7A060216_S19


title: MDS1240_Normal_RNA-seq

description:
MDS_47
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_50ul_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
6A060216_S16


title: 3D_CH_8X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
9B060216_S26


title: 3D_CH_4X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
15B060216_S44


title: MDS1224_sMDS_RNA-seq

description:
MDS_28
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1200_tMDS_RNA-seq

description:
MDS_22
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_8X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
9C060216_S27


title: MDS1216_sMDS_RNA-seq

description:
MDS_24
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS199_sMDS_RNA-seq

description:
MDS_25
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_8X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
9A060216_S25


title: MDS1141_tMDS_RNA-seq

description:
MDS_26
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1044_sMDS_RNA-seq

description:
MDS_23
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
15C060216_S45


title: MDS1131_tMDS_RNA-seq

description:
MDS_27
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
15A060216_S43


title: 3D_CH_1X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
13C060216_S39


title: 3D_CH_1X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
13B060216_S38


title: MDS1039_sMDS_RNA-seq

description:
MDS_30
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_2X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
11C060216_S33


title: 3D_50ul_CH_2X_CRS_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 50 microliter CH 2X CRS at 30 million cells per ml.
count_matrix.txt
7C060216_S21


title: MDS123_tMDS_RNA-seq

description:
MDS_21
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1199_tMDS_RNA-seq

description:
MDS_20
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1134_tMDS_RNA-seq

description:
MDS_15
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1028_tMDS_RNA-seq

description:
MDS_17
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_2X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
11A060216_S31


title: MDS1217_tMDS_RNA-seq

description:
MDS_18
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1232_tMDS_RNA-seq

description:
MDS_31
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_1X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
13A060216_S37


title: MDS1212_sMDS_RNA-seq

description:
MDS_16
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_8X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
8A060216_S22


title: 3D_CH_8X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
8C060216_S24


title: MDS1142_sMDS_RNA-seq

description:
MDS_11
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1083_tMDS_RNA-seq

description:
MDS_10
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1114_sMDS_RNA-seq

description:
MDS_14
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1242_tMDS_RNA-seq

description:
MDS_9
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
5C060216_S15


title: 3D_CH_8X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
8B060216_S23


title: MDS1234_tMDS_RNA-seq

description:
MDS_7
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1283_tMDS_RNA-seq

description:
MDS_13
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_2X_CRS_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
11B060216_S32


title: MDS1116_tMDS_RNA-seq

description:
MDS_19
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1058_sMDS_RNA-seq

description:
MDS_8
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
5A060216_S13


title: MDS1075_tMDS_RNA-seq

description:
MDS_12
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1112_sMDS_RNA-seq

description:
MDS_3
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: MDS1259_sMDS_RNA-seq

description:
MDS_5
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
5B060216_S14


title: 3D_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
10C060216_S30


title: 3D_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
10B060216_S29


title: MDS1197_tMDS_RNA-seq

description:
MDS_6
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_2X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
10A060216_S28


title: 3D_CH_1X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
12C060216_S36


title: MDS1251_tMDS_RNA-seq

description:
MDS_2
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_8X_CRS_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 30 million cells per ml.
count_matrix.txt
16A_S46


title: MDS1258_sMDS_RNA-seq

description:
MDS_4
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_4X_CRS_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 30 million cells per ml.
count_matrix.txt
2C060116_S6


title: 3D_CH_1X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
12A060216_S34


title: 3D_CH_8X_CRS_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 30 million cells per ml.
count_matrix.txt
16C_S48


title: 3D_CH_1X_CRS_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
12B060216_S35


title: 3D_CH_4X_CRS_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 30 million cells per ml.
count_matrix.txt
2B060116_S5


title: MDS1281_tMDS_RNA-seq

description:
MDS_1
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt


title: 3D_CH_8X_CRS_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 30 million cells per ml.
count_matrix.txt
16B_S47


title: 3D_CH_2X_CRS_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 30 million cells per ml.
count_matrix.txt
3C060116_S9


title: 3D_CH_2X_CRS_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 30 million cells per ml.
count_matrix.txt
3B060116_S8


title: P13-NS-1-RNASeq

city: Oklahama city

first: David

last: Jones

address: 825 NE 13th st

department: Functional and chemical genomics

institute: Oklahama medical research foundation

description:
9807X2
rRNA-depleted total RNA

data_processing:
Reads were aligned to the genome with Novalign (v2.08.01) using default settings
USeq (8.4.6) SamTranscriptomeParser was used to convert spliced alignments to genomic coordinates
Useq (8.4.6) DefinedRegionDifferentialSeq was used to generate read counts for each gene
EdgeR (3.2.4) was used to determine differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing raw counts per gene
Supplementary_files_format_and_content: Excel file (S2.xlsx) reporting genes with expression changes in SSP compared to NA (fold change >2, FDR 0.01)

source_name: colon

extract_protocol:
RNA was extracted from O.C.T embeded frozen colon biopsies (P1-SSP-3, P2-SSP-4, P5-SSP-7, P6-SSP-8, P8-TSA-2, P9-FAP-2, P10-FAP-3, P11-Ca-1, P12-Ca-2, P1-GU-1, P13-NA-1, P13-NS-1, P14-NS-2, P15-NA-3) as explained above. Total RNA was DNase treated using TURBO DNA-free Kit (Ambion), and its quality was assessed on Bioanalyzer RNA 6000 Nano Chip. For ribosomal RNA depletion, the total RNA was treated with RiboMinus kit (Life Technologies).
Directional RNAseq library was performed according to Illumina’s protocol. Libraries were sequenced using 50bp single-end format on Illumina HiSeq 2000.

value: colon

value: Normal sigmoid


title: P14-NS-2-RNASeq

description:
10132X4
rRNA-depleted total RNA


title: P15-NA-3-RNASeq

description:
10132X1
rRNA-depleted total RNA

value: Normal ascending


title: Blood-WGBS

description: Bisulfite treated genomic DNA

data_processing:
Reads were aligned to the human genome using Novoalign (v2.08.01)
USeq NovoalignBisulfiteParser was used to parse Novoalign output into point data for each cytosine in the genome
The point data was parsed into CpG context using USeq ParsePointDataContexts
USeq BisStat was used to calculate fraction methylation
USeq FilterPointData was used to filter the point data for the regions of interest
USeq BisSeq was used to find differentially methylated regions
Genome_build: hg19
Supplementary_files_format_and_content: Excel file (S1.xlsx) listing the enhanced methylated regions (EMRs) with more than 10 fold gain of methylation in SSP compared to GU (p-value <0.001).

source_name: Blood

extract_protocol:
Three micrograms of genomic DNA (extracted from P1-SSP-3, P1-GU-1 and P1-blood) were sheared using Covaris S2 Focused-ultrasonicator, in a 130 µl volume, with 5.0 intensity, 10% duty cycle, 200 cycles per burst, and 6:00 minutes treatment time. Sheared DNA was purified using QIAquick PCR purification kit. Unmethylated DNA of lambda phage was added at 1% concentration to each sample as an internal control of monitoring the conversion efficiency.
Libraries were made according to the Illumina library preparation protocol using the methylated adaptors. The libraries were purified using QIAquick PCR purification kit and bisulfite converted using EpiTect bisulfite kit (Qiagen). To increase the conversion efficiency we performed the denaturation steps at 98°C for 10 minutes, and the samples were incubated for another 120 minutes at 60°C at the end of thermocycling reaction. The bisulfite converted libraries were amplified using PfuTurbo HotStart DNA Polymerase (Agilent) for 16 cycles. The libraries were then size selected (200-300bp) and gel purified. The quality of libraries were checked using DNA 1000 Bioanalyzer chip. Libraries were then quantitated by qPCR using KapaBiosystems Kapa Library Quant kit and were run through 101 paired-end Illumina HiSeq 2000.

value: Blood sample from patient #1 (P1)

value: Blood


title: GU-WGBS

description: Bisulfite treated genomic DNA

value: Grossly uninvolved biopsy from patient #1 (P1)


title: 3D_CH_1X_CRS_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 30 million cells per ml.
count_matrix.txt
17B060216_S49


title: 3D_CH_1X_CRS_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 30 million cells per ml.
count_matrix.txt
17C060216_S50


title: P10-FAP-3-RNASeq

description:
9179X5
rRNA-depleted total RNA

value: Familial adenomatous polyp


title: 3D_CH_1X_CRS_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 30 million cells per ml.
count_matrix.txt
17A060216_S48


title: SSP-WGBS

description: Bisulfite treated genomic DNA

value: sessile serrated polyp biopsy (BRAF-V600E) from patient #1 (P1) [P1-SSP-3]


title: P11-Ca-1-RNASeq

description:
9673X9
rRNA-depleted total RNA

value: Carcinoma


title: 3D_CH_2X_CRS_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 30 million cells per ml.
count_matrix.txt
3A060116_S7


title: 3D_CH_8X_CRS_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 20 million cells per ml.
count_matrix.txt
19A_S55


title: P6-SSP-8-RNASeq

description:
9673X18
rRNA-depleted total RNA

value: Sessile serrated polyp


title: P9-FAP-2-RNASeq

description:
9179X3
rRNA-depleted total RNA


title: P8-TSA-2-RNASeq

description:
9179X1
rRNA-depleted total RNA

value: Traditional serrated adenoma


title: P13-NA-1-RNASeq

description:
9807X1
rRNA-depleted total RNA


title: P12-Ca-2-RNASeq

description:
9673X11
rRNA-depleted total RNA


title: P5-SSP-7-RNASeq

description:
9673X17
rRNA-depleted total RNA


title: 3D_CH_8X_CRS_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 20 million cells per ml.
count_matrix.txt
19C_S57


title: 3D_CH_8X_CRS_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 8X CRS at 20 million cells per ml.
count_matrix.txt
19B_S56


title: P1-SSP-3-RNASeq

description:
9673X15
rRNA-depleted total RNA


title: 3D_CH_2X_CRS_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 20 million cells per ml.
count_matrix.txt
4B060216_S11


title: P2-SSP-4-RNASeq

description:
9503X1
rRNA-depleted total RNA


title: 3D_CH_4X_CRS_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 20 million cells per ml.
count_matrix.txt
1B060116_S2


title: 3D_CH_4X_CRS_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 20 million cells per ml.
count_matrix.txt
1C060116_S3


title: P5-SSP-7

description:
whole exome-DNA
9563x3

data_processing:
Library strategy: Exome-seq
Reads were aligned to the genome with Novalign (v2.08.01) using default settings
SAMtools (v0.1.18) was used to create mpileup files from the alignments
VaScan (v2.3.5) was used to identify mutations.
Genome_build: hg19
Supplementary_files_format_and_content: VCF files

extract_protocol:
The characterized biopsies were subjected to sample isolation from the affected areas of the blocks using 1mm diameter disposable biopsy punches (Miltex). The QIAamp DNA FFPE Tissue kit (Qiagen) was used to extract DNA from FFPE tissues. The Qiagen AllPrep kit was used to extract both DNA and RNA from frozen O.C.T. embedded tissues. DNeasy Blood & Tissue kit (Qiagen) was used to extract DNA from blood samples. Library construction for exome sequencing was performed using Agilent Technologies SureSelect XT Reagent Kit, HSQ as described below. Briefly, 1-3 µg genomic DNA was sheared using Covaris S2 Focused-ultrasonicator, in a 130 µl volume, with 5.0 intensity, 10% duty cycle, 200 cycles per burst, and 6:00 minutes treatment time. Sheared DNA was purified using QIAquick PCR Purification kit (Qiagen).
Using a combination of enzymes with filling and exonuclease activity, the DNA fragments became blunt ended. To prepare the fragments for accepting adaptors and to block concatamerization, an A overhang was added to the 3’ end of the fragments, followed by ligation to adaptors with T overhangs. Adaptor-ligated fragments were amplified using 6 cycle PCR and followed by PCR product purification using Agencourt AMPure XP beads. Concentrations and fragment size ranges of the libraries were measured using NanoDrop spectrophotometer and D1K ScreenTape assay in the Agilent 2200 TapeStation system. Exome capture was performed on about 750 ng of the amplified libraries via biotinylated RNA bait molecules of SureSelect Human All Exon 50Mb (Agilent). The captured molecules were purified using Dynabeads MyOne Streptavidin T1, and index tagged in 10 PCR cycles. The amplified exome-enriched fragments were purified on Agencourt AMPure XP beads. Concentration and size measurements were done using Invitrogen Qubit dsDNA HS Assay and High Sensitivity D1K assay. The KapaBiosystems Kapa Library Quant kit was used to quantitate the concentration of adaptor ligated libraries. The captured libraries were sequenced using HiSeq 2000 101 cycle paired-end sequencing.

value: Sessile serrated polyp biopsy from patient #5


title: 3D_CH_2X_CRS_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 20 million cells per ml.
count_matrix.txt
4A060216_S10


title: P3-blood

description:
whole exome-DNA
9482x4

source_name: blood

value: blood

value: blood from patient #3


title: P4-SSP-6

description:
whole exome-DNA
9563x1

value: Sessile serrated polyp biopsy from patient #4


title: 3D_CH_4X_CRS_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 20 million cells per ml.
count_matrix.txt
1A060116_S1

value: wild type


title: 3D_CH_2X_CRS_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 2X CRS at 20 million cells per ml.
count_matrix.txt
4C060216_S12


title: 3D_7.36mg/ml_Mtrgl_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
19B060216_S55

extract_protocol:
3D culture hydrogel was transferred to a 1.5 ml centrifuge tube and immersed in RNA lysis buffer, which was placed on dry ice for rapid freezing and then stored at -80 °C. 3D culture hydrogel was homogenized in lysis buffer. Total RNA isolation was performed using a kit following the manufacturer’s protocol.
RNA-Seq libraries were prepared following the Smart-seq2 protocol. 1 ng of total RNA was used. cDNA was synthesized and then used in each NexteraXT (Illumina) reaction.


title: P2-SSP-4

description:
whole exome-DNA
9482x1

value: Sessile serrated polyp biopsy from patient #2


title: P6-SSP-8

description:
whole exome-DNA
9563x4

value: colon

value: Sessile serrated polyp biopsy from patient #6


title: 3D_CH_4X_CRS_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 4X CRS at 30 million cells per ml.
count_matrix.txt
2A060116_S4


title: 3D_7.36mg/ml_Mtrgl_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
19C060216_S56


title: 3D_CH_1X_CRS_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 20 million cells per ml.
count_matrix.txt
14A060216_S40


title: P4-blood

description:
whole exome-DNA
9563x2

value: blood from patient #4


title: 3D_CH_1X_CRS_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 20 million cells per ml.
count_matrix.txt
14B060216_S41


title: P1-SSP-3

description:
whole exome-DNA
8122x3

value: Sessile serrated polyp biopsy from patient #1


title: P3-SSP-5

description:
whole exome-DNA
9482x3

value: Sessile serrated polyp biopsy from patient #3


title: P1-SSP-1

description:
whole exome-DNA
8122x1


title: 3D_7.36mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
15B_S44


title: 3D_7.36mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
15C_S45


title: P1-blood

description:
whole exome-DNA
8122x4

value: blood from patient #1


title: 3D_7.36mg/ml_Mtrgl_1.5mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1.5 mg/ml HA at 30 million cells per ml.
count_matrix.txt
19A060216_S54


title: 3D_7.36mg/ml_Mtrgl_1mg/ml_HA_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
18B060216_S52


title: 3D_7.36mg/ml_Mtrgl_1mg/ml_HA_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
18A060216_S51


title: 3D_7.36mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
8C_S24


title: P1-SSP-2

description:
whole exome-DNA
8122x2


title: 3D_4.6mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
11C_S33


title: 3D_7.36mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
15A_S43


title: P2-blood

description:
whole exome-DNA
9482x2

value: blood from patient #2


title: 3D_4.6mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
11A_S31


title: 3D_7.36mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
6C_S18


title: 3D_7.36mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
8B_S23


title: 3D_CH_1X_CRS_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D CH 1X CRS at 20 million cells per ml.
count_matrix.txt
14C060216_S42


title: 3D_7.36mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
6B_S17


title: 3D_7.36mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
6A_S16


title: 3D_7.36mg/ml_Mtrgl_1mg/ml_HA_30mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel with 1 mg/ml HA at 30 million cells per ml.
count_matrix.txt
18C060216_S53


title: 3D_4.6mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
4A_S10


title: 2D_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
18C-070517_S54


title: C3-2

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

description:
processed data file:
Neuron_rawCounts.txt
DESeq_Neuron_results.txt

data_processing:
The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina.
Analysis of library complexity and per-base sequence quality (i.e. q > 30) was assessed using FastQC (v0.11.2) software. Low quality bases (q < 10) were trimmed from the 3’ end of reads. Adaptor sequences and reads shorter than 40 nucleotides were removed using Trimmomatic.
Reads were aligned to GRCh37/hg19 using TopHat2 (v2.0.14, --b2-very-sensitive --keep- --nocoverage-search --library-type fr-firststrand). High quality mapped reads (MAPQ > 10) were filtered with SAMtools (v0.1.19).
Gene level counts were obtained using the GRCh37 Ensembl annotation with Rsubread (v 1.18.0, strandSpecific = 2, GTF.featureType = "exon", countMultiMappingReads = FALSE).
Differential expression of genes was determined using DESeq (v1.24.0) software with the options “per-condition”, “maximum”, and “local” for dispersion calculations. Significance was assigned to genes with an FDR less than 10%.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts as well as DESeq results.

source_name: disomic_IPSC Derived Neurons

growth_protocol: iPSCs were dissociated with Accutase, and plated on Geltrex-coated dishes at 10-20 x 103 cells/cm2 in mTeSR1 medium + 10 uM Y27632 ROCK inhibitor (Tocris). After 2-4 days, the cells formed a meshwork of dense ridges with mostly open spaces in between. The differentiation process was begun (day 0) by feeding the cells every other day for 12 days with NIM neural induction medium (Stem Cell Technologies), followed by DDM medium supplemented with 2% B27 [13] every other day for 12 days. On day 24, the dense ridges or islands containing neural progenitors were manually dissociated, resuspended in DDM + 2% B27 + 10 uM Y27632, and plated on dishes and chamber slides coated with poly-ornithine and laminin [14]. Every 4-5 days, half the medium was changed to fresh Neurobasal + 2% B27 + 2mM GlutaMax (Invitrogen). Colonies that were clearly nonneuronal were removed by scraping, rinsing and refeeding the cultures. After 40 days of differentiation, the cells were rinsed with PBS and harvested 140 with ice-cold Trizol or fixed with 4% para-formaldehyde + 4% sucrose in PBS. Successful differentiation of iPSCs into cortical neuronal cultures was confirmed by immunofluorescence staining for markers of cortical layers V (transcription factor Ctip2, encoded by BCL11B) and VI (transcription factor TBR1), as well as for glutamatergic markers vGLUT1 (encoded by SLC17A7) and GRIK2.

extract_protocol:
RNA for poly(A) RNA sequencing libraries was extracted from IPSC and neuronal cultures via TRIzol extraction. Genomic DNA was removed using TURBO DNase (Invitrogen).
Single-end sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Targeted removal of CHR 21 in IPSC using TKNEO transgene. Li et al., Trisomy correction in Down syndrome induced pluripotent stem cells. Cell Stem Cell 11, 615-619 (2012).

value: IPSC-derived Neurons

tag: ploidy

value: disomic

tag: differentiation length

value: 40 days


title: C2-2

source_name: trisomic_IPSC Derived Neurons

value: trisomic


title: C244-B

description:
processed data file:
IPSC_rawCounts.txt
DESeq_IPSC_result.txt

growth_protocol: IPSC lines were grown on Geltrex (Life Technologies) under feeder-free conditions in mTeSR1 medium according to the protocol of Stem Cell Technologies. iPSC colonies were passaged with dispase, and differentiating colonies were removed manually by scraping. Periodically, live iPSC colonies were stained with anti-Tra-1- 60 or Tra-1-81 conjugated to Dylight fluor 488 to confirm the stem cell character of the colonies. Likewise, fixed cells were shown 117 to express Oct4 by immunostaining. We used ABI/Thermo Fisher TaqMan Copy Number Assays (Hs01180853_cn; Hs02928366_cn; Hs01533676 corresponding to APP, DYRK1A and RCAN1 respectively) to evaluate the number of copies of Chr. 21 in the iPSC lines.

value: human induced pluripotent stem cells (iPSCs)

tag: passages


title: C2-1


title: 3D_4.6mg/ml_Mtrgl_20mpml_1wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
4C_S12


title: C3-1


title: 3D_4.6mg/ml_Mtrgl_30mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 30 million cells per ml.
count_matrix.txt
11B_S32


title: C244-A


title: C243


title: 3D_7.36mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 7.36 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
8A_S22


title: 3D_4.6mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
10C_S30


title: 2D_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
18A-070517_S52


title: 3D_4.6mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
10B_S29


title: C3-4


title: C2A


title: 2D_1wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
17B-070517_S50


title: C2-3


title: 3D_4.6mg/ml_Mtrgl_20mpml_5wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured in 3D 4.6 mg/ml Matrigel at 20 million cells per ml.
count_matrix.txt
10A_S28


title: 2D_1wk_iN_ma_rep1

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
17A-070517_S49


title: 2D_1wk_iN_ma_rep3

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
17C-070517_S51


title: C2B


title: 2D_5wk_iN_ma_rep2

description:
human neuronal cells and mouse astrocytes co-cultured on 2D
count_matrix.txt
18B-070517_S53


title: single_cell_3D_iN_astrocytic-cell

description:
human neuronal cells and differentiated human astrocytic cells co-cultured in 3D CH 4X CRS at 30 million cells per ml.
singleCell_count2.txt
SingleCell2

extract_protocol:
3D culture hydrogel was dissociated. Cell suspension of human neuronal cells and differentiated human astrocytic cells was loaded onto the 10x Chromium Instrument to generate single-cell gel bead in emulsions.
Single-cell RNA-Seq libraries were constructed using 10x Chromium 3' Solution following the manufacturer’s protocol.