title: M2 BMDM of wild type mice_rep3

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from M2 mouse bone marrow derived macrophage of wild type mice, biological replicate 3

hyb_protocol: According to the Affymetrix expression protocol (HWS kit) including minor modifications according to the Nugen protocol

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G)

data_processing: Expression console (v.1.4.1.46, Affymetrix) was used for quality control and to obtain annotated normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation)

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (NuGEN Technologies, Inc, San Carlos, CA, USA)

growth_protocol: no

extract_protocol: Total RNA was isolated with peqGOLD total RNA kit (Peqlab) including digestion of remaining genomic DNA

treatment_protocol: As described in the paper. Briefly, bone marrow was flushed from femurs and tibias of C57BL/6N and Dner-/- mice with RPMI-1640 medium. Bone marrow cells were passed through 40µm filters (Miltenyi Biotec), counted and resuspended in 5% fetal bovine serum, 50μM β-mercaptoethanol and 100 U/ml penicillin and streptomycin RPMI-1640 medium. 2x10^6 cells/mL were plated in 24 well plates for RNA isolation. Medium was additionally supplemented with 20ng/mL of murine recombinant M-CSF to generate bone marrow derived macrophages (BMDM). Cells were maintained at 37°C, 5% CO2 for 7 days changing medium every 2-3 days and carefully discarding non-adherent cells. For BMDM, on day 7 fresh medium without M-CSF was added and left overnight. BMDM were stimulated with 1µg/mL LPS (from E.coli 0111:B4, Sigma-Aldrich) and 20ng/mL of recombinant murine IFNγ (M1 phenotype) or with 20ng/mL of recombinant murine IL-4 (M2 phenotype) for 24h.

tag: genotype

value: wild type


title: 3105-MS-66

status: Public on Mar 19 2019

type: SRA

city: Frederick

first: Kalyan

middle: C

last: Vinnakota

state: MD

address: 2405 Whittier Drive, Suite 200

country: USA

institute: Biotechnology HPC Software Applications Institute

library_source: transcriptomic

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
Software tool Kallisto was used to generate Rnor_6.0 transcriptome index from ENSEMBL genome assembly release 92
Software tool Kallisto was used to obtain transcript abundances (units of Transcripts Per Million) in each sample with the Rnor6 transcriptome index generated in the previous step
Software tool Sleuth was used to assess differential expression of genes from the transcript abundances obtained using Kallisto
Genome_build: Rnor_6.0 ENSEMBL genome assembly release 92
Supplementary_files_format_and_content: The output of Kallisto for each sample, provided here as a .tar.gz archive, consists of a folder with the following contents: abundance.tsv (a text file that contains a total summary of transcript abundances), 100 bs_abundance_<i>.tsv files (i ranges from 0 to 99, each file is one bootstrap of transcript abundances), and run_info.json (a text file that contains information on the Kallisto run)

molecule: total RNA

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was isolated from the liver, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA Mini Prep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche).

tag: fasting/treatment

tag: strain

value: Sprague-Dawley

tag: tissue

value: liver


title: Vehicle control_1

type: RNA

city: Pyeongchang

first: Joonghoon

last: Park

state: Kangwon

address: Pyeongchang daero 1447

department: International Agricultural Technology

country: South Korea

institute: Seoul National University

description: Gene expression data from mice after 6-week repeat oral administration

hyb_protocol: Approximately 5.5 μg of labeled cDNA was hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA) at 45°C for 16 h.

scan_protocol: The hybridized arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: All data analyses were performed with the GeneChip Command Console Software (Affymetrix). All data were normalized using the robust multi-array average (RMA).

label: biotin

organism: Mus musculus

source_name: STAM NASH-HCC mice

label_protocol: The cDNA was fragmented and biotin-labeled using GeneChip WT terminal labeling kit (Applied Biosystems).

growth_protocol: At 2 days after birth, the mice received a single subcutaneous injection of 200 μg streptozotocin (STZ; Sigma, St. Louis, MO, USA). Then, after 4 weeks of age, they received 60 kcal% fat HFD32 chow (CLEA Japan Inc., Tokyo, Japan) ad libitum and were assigned to receive either vehicle or telmisartan.

extract_protocol: Total RNA was extracted from the frozen liver tissues with a RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Telmisartan (Sigma) was dissolved in 0.5% (v/v) carboxymethyl cellulose (Sigma) and orally administered (5 mg/kg/day) to the mice from 6 to 12 weeks of age (n = 7 per group).

value: Liver

tag: agent

value: Vehicle


title: 3105-MS-67


title: SNAC1-D2-RNAseq

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

description: processed data file: All_gene_FPKM.txt

data_processing:
Sequencing reads were mapped to rice reference genome using Hisat2 (for RNA-seq) and Bowtie2 (for ChIP-seq).
RNA-seq transcripts were assembled and counted by StringTie and the differential expression was determined by DESeq2.
ChIP-seq peaks were called by MACS2 and peak annotation and differential binding identification were done by ChIPseeker and DiffBind, respectively.
Genome_build: Rice Genome Annotation Project (RGAP) Release 7
Supplementary_files_format_and_content: All_gene_FPKM.txt: Tab-delimited text file includes FPKM values for each RNA-seq sample.
Supplementary_files_format_and_content: Peaks_*.txt: Tab-delimited text files include normalized peak counts and fold changes for ChIP-seq samples.

organism: Oryza sativa Japonica Group

source_name: 4-leaf-stage seedling

growth_protocol: The transgenic and ZH11-WT seeds were sprouted on half-strength MS medium in the dark for 2-3 days at 28°C, and then 4-5 days in the greenhouse. The seedlings were then moved to pots with sand/paddy (1:3) soil under natural conditions at Wuhan, China.

extract_protocol:
The total RNAs were extracted from the leaves of SNAC1-OE lines and ZH11-WT plants using TRIzol reagent (InvitrogenTM) according to the manufacturer’s instructions. The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3g shoot tissues from 4-leaf-stage seedlings were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by custom-made anti-SNAC1 polyclonal antibody generated using full-length SNAC1 protein. The combined DNAs were eluted, purified, and dissolved in ddH2O.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After germination, the 1-week-old seedlings that were of uniform growth status were moved to pots filled with sandy soil. The transgenic and WT plants were grown in a half-and-half manner (10 plants each) in the pots. At the 4-leaf stage, the seedlings were subjected to drought stress treatment by stopping water for 10-15 days until the leaves were curled and turned yellow.

value: 4-leaf-stage seedling

tag: genotype/variation

tag: treatment

value: Drought

tag: sample type

value: RNA-seq


title: SNAC1-D1-RNAseq

description: processed data file: All_gene_FPKM.txt


title: Mpmycy_Wound_vs_Tak-1_Wound_repl2

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

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 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were  normalized by LOWESS algorithm followed by quantile normalization

organism: Marchantia polymorpha

label_protocol: 200 ng of total RNA were reverse transcribed used T7 primer and the cDNA converted to aRNA using T7 RNA polymerase, incorporating cyanine 3- or cyanine 5-labeled CTP, according to 'Two color Microarray-Based Gene Expression Analysis Protocol' (Agilent)

growth_protocol: Marchantia polymorpha accessions Takaragaike-1 (Tak-1; male) and Tak-2 (female) and mutants Mpmycy (male) and  Mpmycx (female) were used in this work. Plants were subcultivated on 0.5 Gamborg’s B5 medium containing 1% agar for 2 (OPDA) or 3 (wounding) weeks. Apical fragments of the plants, excluding gemma cups, were ground in liquid nitrogen prior RNA extraction. Every independent biological replicate contained 6-8 plants.

extract_protocol: Total RNA from Marchantia was extracted with either RNeasy Plant Mini Kit (Qiagen) and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.

treatment_protocol: 15-day-old Mpmycs and WT gemmalings treated with OPDA for 2 hours in liquid GB5 medium. 21-day-old gemmalings grown in GB5 1% agar were wounded with forceps and material collected after two hours

value: Mpmycy

value: Wounding


title: 3105-MS-30


title: M2 BMDM of wild type mice_rep2

country: Germany

description: Gene expression data from M2 mouse bone marrow derived macrophage of wild type mice, biological replicate 2


title: Mpmycy_Wound_vs_Tak-1_Wound_repl1


title: Vehicle control_2


title: Mpmycx_OPDA_vs_Tak-2_OPDA_repl3

value: Mpmycx

value: OPDA


title: Mpmycx_OPDA_vs_Tak-2_OPDA_repl1


title: M2 BMDM of wild type mice_rep1

description: Gene expression data from M2 mouse bone marrow derived macrophage of wild type mice, biological replicate 1


title: Marfan, Véh (did not pass QC 19)

city: Hamilton

first: Nadia

last: Milad

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing:
The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the SST-RMA procedure.  The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters. The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix.  affymetrix-algorithm-name = sst-rma-gene-full  affymetrix-algorithm-version = 1.0  affymetrix-array-type = Clariom_S_Mouse  program-name = Expression Console  program-version = 1.4.1.46
Samples 2, 3, 7 and 19 were removed due to poor cDNA quality, did not pass quality control criteria.

source_name: Lung

label_protocol: Microarray was performed at the GenomeQuebec in Montreal. RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 700 pg of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

growth_protocol: Sacrifice at 6 months of age

extract_protocol: QIAzol Rneasy

treatment_protocol: Treated with sildenafil in the drinking water from 6 weeks of age to 6 months

tag: age


title: Marfan, Sildenafil (did not pass QC 7)


title: 13h-vehicle (3438-MS-12)

value: 13h fasting


title: Mpmycy_OPDA_vs_Tak-1_OPDA_repl3


title: 3105-MS-24


title: 3105-MS-3


title: 3105-MS-5


title: Mpmycx_OPDA_vs_Tak-2_OPDA_repl2


title: 3105-MS-23


title: WT, Sildenafil (did not pass QC2 )


title: M1 BMDM of wild type mice_rep3

description: Gene expression data from M1 mouse bone marrow derived macrophage of wild type mice, biological replicate 3


title: M1 BMDM of wild type mice_rep2

description: Gene expression data from M1 mouse bone marrow derived macrophage of wild type mice, biological replicate 2


title: M1 BMDM of wild type mice_rep1

description: Gene expression data from M1 mouse bone marrow derived macrophage of wild type mice, biological replicate 1


title: M0 BMDM of wild type mice_rep3

description: Gene expression data from M0 mouse bone marrow derived macrophage of wild type mice, biological replicate 3


title: 3105-MS-4


title: Mpmycy_OPDA_vs_Tak-1_OPDA_repl2


title: M0 BMDM of wild type mice_rep2

description: Gene expression data from M0 mouse bone marrow derived macrophage of wild type mice, biological replicate 2


title: WT, Sildenafil (did not pass QC 3)


title: Mpmycy_OPDA_vs_Tak-1_OPDA_repl1


title: 3105-MS-21


title: M0 BMDM of wild type mice_rep1

description: Gene expression data from M0 mouse bone marrow derived macrophage of wild type mice, biological replicate 1


title: 3105-MS-2


title: 3105-MS-10


title: M2 BMDM of Dner-deficient mice_rep3

description: Gene expression data from M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 3

value: Dner deficient


title: 3105-MS-19


title: HS578T cells - pcDNA 3 with cloned EP300 cDNA - biological sample 2

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

country: United Kingdom

institute: Imperial College London

hyb_protocol: Following fragmentation and labeling, 3.5 µg of ss-cDNA were hybridized for 16 hr at 45°C on GeneChip® Cartridge Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite version 6.6  using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Homo sapiens

source_name: Total RNA isolated from cells in culture

label_protocol: Affymetrix GeneChipTM WT PLUS Reagent Kit

growth_protocol: Cells were grown in low-glucose DMEM containing 10% fetal calf serum, glutamine, insulin and G418

extract_protocol: Qiagen Rneasy total RNA extraction

tag: transfection

value: pcDNA 3 with cloned EP300 cDNA

tag: tumor

value: breast cancer

tag: cell line


title: HS578T cells - pcDNA 3 with cloned EP300 cDNA - biological sample 1


title: HS578T cells - pcDNA 3 with cloned EP300 cDNA - biological sample 3


title: 3105-MS-16


title: M2 BMDM of Dner-deficient mice_rep1

description: Gene expression data from M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 1


title: M2 BMDM of Dner-deficient mice_rep2

description: Gene expression data from M2 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 2


title: Marfan, Véh  23

description:
Marfan, Véh
23


title: 3105-MS-15


title: Marfan, Véh  24

description:
Marfan, Véh
24


title: 1370-RP-112-GAGATTCC-CAGGACGT_S148

source_name: Liver

tag: time point


title: 1370-RP-111-CGCTCATT-CAGGACGT_S147


title: HS578T cells - pcDNA 3 - biological sample 3

value: pcDNA 3


title: M1 BMDM of Dner-deficient mice_rep1

description: Gene expression data from M1 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 1


title: M1 BMDM of Dner-deficient mice_rep3

description: Gene expression data from M1 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 3


title: 1370-RP-62-GAGATTCC-CCTATCCT_S100


title: M1 BMDM of Dner-deficient mice_rep2

description: Gene expression data from M1 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 2


title: HS578T cells - pcDNA 3 - biological sample 2


title: Marfan, Véh  21

description:
Marfan, Véh
21


title: Marfan, Véh  22

description:
Marfan, Véh
22


title: 3105-MS-14


title: M0 BMDM of Dner-deficient mice_rep3

description: Gene expression data from M0 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 3


title: 1370-RP-110-TCCGGAGA-CAGGACGT_S146


title: Marfan, Véh  20

description:
Marfan, Véh
20


title: WT, Véh  18

description:
WT, Véh
18


title: 3105-MS-11


title: HS578T cells - pcDNA 3 - biological sample 1


title: 4dpi_Inhib_7_S12

city: Woods hole

first: Karen

last: Echeverri

state: MA

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

description:
4 days post injury miR-200 inhibitor
None

data_processing:
RNA-seq data were comprised of 2 ×126 bp paired-end reads. The RNA-seq reads from all samples were combined and then assembled by using Trinity (Grabherr et al., 2011) (v2.3.2) with default parameters. We used cd-hit-est (v4.6) (Fu et al., 2012) with parameter “-c 1” to remove shorter contigs with 100% identity with aligned longer contigs. These non-redundant contigs were mapped to Ensembl human proteins (v85) by BLASTX (v2.2.18). Contigs were assigned to human proteins by taking the best BLASTX hit with E-value < 10-5.    We used Bowtie (v0.12.1) (Langmead et al., 2009) to map the reads against all non-redundant contigs. Quantification of each contig was performed by RSEM v1.1.6 (Boido et al., 2011). RSEM employs an expectation maximization algorithm, so that for reads that match to multiple contigs, RSEM assigns a fraction of each read to each contig based on estimated abundances of contigs based on unique reads (Boido et al., 2011).  RNA-seq data were comprised of 2 ×126 bp paired-end reads. The RNA-seq reads from all samples were combined and then assembled by using Trinity (Grabherr et al., 2011) (v2.3.2) with default parameters. We used cd-hit-est (v4.6) (Fu et al., 2012) with parameter “-c 1” to remove shorter contigs with 100% identity with aligned longer contigs. These non-redundant contigs were mapped to Ensembl human proteins (v85) by BLASTX (v2.2.18). Contigs were assigned to human proteins by taking the best BLASTX hit with E-value < 10-5.    We used Bowtie (v0.12.1) (Langmead et al., 2009) to map the reads against all non-redundant contigs. Quantification of each contig was performed by RSEM v1.1.6 (Boido et al., 2011). RSEM employs an expectation maximization algorithm, so that for reads that match to multiple contigs, RSEM assigns a fraction of each read to each contig based on estimated abundances of contigs based on unique reads (Boido et al., 2011).
Relative abundances, in terms of transcripts per million (TPM), for genes were computed by first normalizing each gene’s fragment count by the sum of the “effective lengths” (weighted average of contigs’ length based on contigs’ abundance) of the contigs mapped to that gene and then scaling the resulting values such that they summed to one million over all genes. To identify differentially expressed genes the normalized counts from RSEM were imported into DESeq2 (version 1.16.1) (Love et al., 2014) as integers to determine moderated estimates of Log2 fold changes and Benjamini-Hochberg adjusted p-values between conditions.

organism: Ambystoma mexicanum

source_name: spinal cord

extract_protocol:
Trizol RNA extraction
Illumina

treatment_protocol: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota or at the MBL under the IACUC protocols #1710-35242A, #18-49. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: miR-200 inhibitor or control inhibitor  s pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. Four days post injury (4dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each RNA sample.

value: spinal cord

value: 4 days post injury miR-200 inhibitor


title: 1370-RP-108-AGCGATAG-TAATCTTA_S144

value: Sprague-Dawley

value: liver


title: 4dpi_Inhib_6_S11


title: WT, Véh  16

description:
WT, Véh
16


title: 1370-RP-107-TCTCGCGC-TAATCTTA_S143


title: 1370-RP-106-TCCGCGAA-TAATCTTA_S142


title: WT, Véh  15

description:
WT, Véh
15


title: 4dpi_Inhib_5_S10


title: 1370-RP-109-ATTACTCG-CAGGACGT_S145


title: WP group_Calf No. 25_Rumen epithelial RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description:
Gene expression in Rumen epithelium in the WP group Calf No. 25
Wood kraft pulp supplemented group

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Sure Scan) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Wood kraft pulp supplemented group_Calf No. 25_Rumen epithelium

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 500 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the rumen epithelium using Trizo (Invitrogen) according to the manufacturer's instructions.

value: Rumen epithelium

value: In vivo


title: Uninj_Inhib_7_S9

description:
uninjured mir-200 inhibor spinal cord
None

value: uninjured miR-200 inhibitor injected


title: Uninj_Inhib_6_S8


title: WT, Véh  17

description:
WT, Véh
17


title: 1370-RP-53-AGCGATAG-ATAGAGGC_S96


title: Uninj_Inhib_5_S7


title: 1370-RP-55-TCCGGAGA-CCTATCCT_S98


title: 1370-RP-52-TCTCGCGC-ATAGAGGC_S95


title: 4dpi_Cntl_6_S6

description:
4 day injured spinal cord
None

value: 4 days post injury spinal cord


title: WP group_Calf No. 24_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the WP group Calf No. 24
Wood kraft pulp supplemented group

source_name: Wood kraft pulp supplemented group_Calf No. 24_Rumen epithelium


title: M0 BMDM of Dner-deficient mice_rep2

description: Gene expression data from M0 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 2


title: 4dpi_Cntl_5_S5

description:
4 day injured spinal cord
None


title: Control group_Calf No. 21_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the Control group Calf No. 21
Control diet group

source_name: Control diet group_Calf No. 21_Rumen epithelium


title: M0 BMDM of Dner-deficient mice_rep1

description: Gene expression data from M0 mouse bone marrow derived macrophage of Dner-deficient mice, biological replicate 1


title: WT, Véh  13

description:
WT, Véh
13


title: Control group_Calf No. 23_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the Control group Calf No. 23
Control diet group

source_name: Control diet group_Calf No. 23_Rumen epithelium


title: 1370-RP-105-CGGCTATG-TAATCTTA_S141


title: WT, Véh  14

description:
WT, Véh
14


title: Control group_Calf No. 24_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the Control group Calf No. 24
Control diet group

source_name: Control diet group_Calf No. 24_Rumen epithelium


title: Marfan, Sildenafil  10

description:
Marfan, Sildenafil
10


title: Marfan, Sildenafil  11

description:
Marfan, Sildenafil
11


title: WP group_Calf No. 23_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the WP group Calf No. 23
Wood kraft pulp supplemented group

source_name: Wood kraft pulp supplemented group_Calf No. 23_Rumen epithelium


title: DEGRON_STH1_K501R biological replicate 2

first: Sofía

last: Muñoz

address: 1 Midland Rd

institute: The Francis Crick Institute

description: nucleosomal DNA

library_source: genomic

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”.
BWA (version 0.5.9-r16) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the yeast sacCer3 genome downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Genome-wide wig files were generated by treating each pair of reads as a single fragment, and normalising to 10 million reads.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in complete synthetic medium lacking methionine, arrested 1.5 hour with alpha-factor, and shifted to medium containing methionine and indole-3-acetic acid (IAA) for 2 hours before release from alpha-factor block into synchronous cell cycle progression until reaching a nocodazole-imposed mitotic arrest.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina HiSeq 2500 or 4000 platform. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehide. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (ThermoFisher) at 37°C for 20 minutes. The samples were then treated with Proteinase K and RNase A to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel.
Sequencing libraries were prepared using the Kapa Hyper Prep kit according to the manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2, STH1K501R-PK3::TRP1


title: 1370-RP-54-ATTACTCG-CCTATCCT_S97


title: Control group_Calf No. 25_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the Control group Calf No. 25
Control diet group

source_name: Control diet group_Calf No. 25_Rumen epithelium


title: DEGRON_STH1 biological replicate 2

description: nucleosomal DNA

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2, STH1-PK3::TRP1


title: 1370-RP-100-GAGATTCC-TAATCTTA_S136


title: 4dpi_Cntl_1_S4

description:
4 day injured spinal cord
None


title: 1370-RP-38-TCCGGAGA-ATAGAGGC_S86


title: Uninj_Cntl_5_S3

description:
spinal cord
None

value: uninjured spinal cord


title: Marfan, Sildenafil  12

description:
Marfan, Sildenafil
12


title: 1370-RP-98-TCCGGAGA-TAATCTTA_S134


title: Uninj_RNA_S2

description:
spinal cord
None


title: Cntl_Uninj_1_S1

description:
spinal cord
None


title: Marfan, Sildenafil  8

description:
Marfan, Sildenafil
8


title: WP group_Calf No. 21_Rumen epithelial RNA

description:
Gene expression in Rumen epithelium in the WP group Calf No. 21
Wood kraft pulp supplemented group

source_name: Wood kraft pulp supplemented group_Calf No. 21_Rumen epithelium


title: NSC4 [RNA-Seq]

status: Public on Mar 18 2019

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
The sequenced reads of RNA-seq experiments were aligned to human reference genome hg19/GRCh37 using STAR aligner (Dobin et al., 2013)
The expression of the genes was determined as FPKM by counting the number of uniquely mapping fragments and normalizing it by the length coding sequence and the library size.  Gene annotation was based on UCSC RefSeq. Genes expressed with > 1 FPKM in at least 50% of the samples of each group were considered to be expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file of raw fpkm expression values

source_name: neural stem cells

growth_protocol: Glioblastoma models were grown in Neurobasal medium supplemented with 2% B27, 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
Glioblastoma tissue was isolated from patients and flash frozen in liquid nitrogen followed by pulverization in a mortar and pestle. RNA was isolated using the Qiagen MiRNeasy kit according to manufacturers recommendations. Dnase treatment was performed on the samples.
Quality control and quantity of RNA was assessed on the Agilent Tape Station. RNA was prepared accoding to Illumina manufacturers conditions using a strand-specific RNA library preparation with ribosomal RNA depletion.
Total RNA was sequenced on a Illumina Hi-Seq in a 2x150bp configuration.

treatment_protocol: Cells were not treated in this manuscript for RNA-seq studies.

value: HFNSCFB

tag: cell type

value: neural stem cells


title: NSC2 [RNA-Seq]

value: ENSA


title: NSC6 [RNA-Seq]


title: NSC10 [RNA-Seq]


title: NSC7 [RNA-Seq]


title: Marfan, Sildenafil  9

description:
Marfan, Sildenafil
9


title: NSC5 [RNA-Seq]


title: WT, Sildenafil  5

description:
WT, Sildenafil
5


title: WT, Sildenafil  4

description:
WT, Sildenafil
4


title: NSC1 [RNA-Seq]


title: NSC9 [RNA-Seq]


title: WT biological replicate 2

description: nucleosomal DNA


title: NSC8 [RNA-Seq]


title: DEGRON biological replicate 2

description: nucleosomal DNA

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+, pADH1-OsTir1-Myc9::ADE2, URA3::pMET3::STH1-IAA17::KANMX6, SCC1-HA3::LEU2


title: WT, Sildenafil  6

description:
WT, Sildenafil
6


title: GSC7 [RNA-Seq]

source_name: glioblastoma stem cell

value: glioblastoma stem cell


title: GSC5 [RNA-Seq]


title: GSC6 [RNA-Seq]


title: GSC43 [RNA-Seq]


title: GSC9 [RNA-Seq]


title: GSC44 [RNA-Seq]


title: GSC42 [RNA-Seq]


title: GSC40 [RNA-Seq]


title: GSC41 [RNA-Seq]


title: GSC8 [RNA-Seq]


title: GSC4 [RNA-Seq]


title: GSC39 [RNA-Seq]


title: GSC37 [RNA-Seq]


title: WT, Sildenafil  1

description:
WT, Sildenafil
1


title: GSC36 [RNA-Seq]


title: GSC33 [RNA-Seq]


title: GSC34 [RNA-Seq]


title: GSC32 [RNA-Seq]


title: GSC3 [RNA-Seq]


title: GSC31 [RNA-Seq]


title: GSC29 [RNA-Seq]


title: GSC28 [RNA-Seq]


title: GSC24 [RNA-Seq]


title: GSC25 [RNA-Seq]


title: GSC27 [RNA-Seq]


title: GSC23 [RNA-Seq]


title: GSC21 [RNA-Seq]


title: GSC20 [RNA-Seq]


title: GSC2 [RNA-Seq]


title: GSC19 [RNA-Seq]


title: GSC22 [RNA-Seq]


title: GSC38 [RNA-Seq]


title: GSC17 [RNA-Seq]


title: GSC15 [RNA-Seq]


title: GSC18 [RNA-Seq]


title: GSC13 [RNA-Seq]


title: GSC12 [RNA-Seq]


title: GSC35 [RNA-Seq]


title: GSC11 [RNA-Seq]

value: RKI


title: GSC10 [RNA-Seq]


title: GSC1 [RNA-Seq]


title: GSC26 [RNA-Seq]


title: GBM81 [RNA-Seq]

source_name: glioblastoma multiforme

value: glioblastoma multiforme


title: GSC14 [RNA-Seq]


title: GBM80 [RNA-Seq]


title: GBM78 [RNA-Seq]


title: GBM79 [RNA-Seq]


title: GSC16 [RNA-Seq]


title: GBM76 [RNA-Seq]


title: GBM77 [RNA-Seq]


title: GBM84 [RNA-Seq]


title: GBM69 [RNA-Seq]


title: GBM70 [RNA-Seq]


title: GBM65 [RNA-Seq]


title: GBM71 [RNA-Seq]


title: GBM64 [RNA-Seq]


title: GBM72 [RNA-Seq]


title: GBM73 [RNA-Seq]


title: GBM74 [RNA-Seq]


title: GBM62 [RNA-Seq]


title: GBM63 [RNA-Seq]


title: GBM67 [RNA-Seq]


title: GBM59 [RNA-Seq]


title: GBM58 [RNA-Seq]


title: GBM82 [RNA-Seq]


title: GBM56 [RNA-Seq]


title: GBM57 [RNA-Seq]


title: GBM54 [RNA-Seq]


title: GBM55 [RNA-Seq]


title: GBM83 [RNA-Seq]


title: GBM53 [RNA-Seq]


title: GBM50 [RNA-Seq]


title: GBM51 [RNA-Seq]


title: GBM49 [RNA-Seq]


title: GBM5 [RNA-Seq]


title: GBM47 [RNA-Seq]


title: GBM46 [RNA-Seq]


title: GBM33 [RNA-Seq]


title: GBM32 [RNA-Seq]


title: NSC9_H3K27AC_INPUT

data_processing:
The H3K27ac ChIP-seq was processed following the guidelines of ENCODE (phase-3) using the AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline). This ChIP-seq processing pipeline, i) mapped the sequenced reads to the human reference genome hg19/GRCh37 using the Burrows-Wheeler Aligner (Li and Durbin, 2009), ii) filtered low-quality, duplicate, multimapping, unmapped reads along with reads mapping to the mitochondrial genome and iii) performed peak calling using MACS2 with P-value threshold of 1 × 10−5.
The H3K27a c ChIP-seq experiments with PBC1 > 0.8 with total mapped reads > 10M and MACS2 peaks (pvalue < 10^-05) > 5,000 were utilized for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in bedgraph format

extract_protocol:
5 million cells were crosslinked in 1% formaldehyde for 10 minutes, lysed, sonicated to ~500bp, and immunoprecipated using H3K27ac antibody (Active Motif 39133). In the case of tissue, 5-10mg of tissue was pulvarized in liquid nitrogen before cross-linking in the same manner as cell protocols (above) ChIP DNA was purified using the Qiagen PCR purification kit. Libraries were prepared according to manufacturers instructions using the Rubicon Thruplex DNA-seq kit
Libraries were constructed using the DNA-seq kit from Rubicon Genomics and quantified using Picogreen

treatment_protocol: Cells were not treated in this manuscript for ChIP-seq studies.

tag: input


title: GBM61 [RNA-Seq]


title: GBM4 [RNA-Seq]


title: GBM31 [RNA-Seq]


title: GBM30 [RNA-Seq]


title: GBM1 [RNA-Seq]


title: NSC9_H3K27AC

tag: antibody


title: GBM28 [RNA-Seq]


title: GBM21 [RNA-Seq]


title: GBM17 [RNA-Seq]


title: NSC8_H3K27AC_INPUT


title: NSC8_H3K27AC


title: NSC5_H3K27AC_INPUT


title: NSC6_H3K27AC_INPUT


title: NSC7_H3K27AC_INPUT


title: NSC5_H3K27AC


title: GBM48 [RNA-Seq]


title: NSC3_H3K27AC_INPUT

value: HFNSCHINDB


title: NSC4_H3K27AC_INPUT


title: GBM52 [RNA-Seq]


title: NSC6_H3K27AC


title: NSC7_H3K27AC


title: NSC3_H3K27AC


title: NSC4_H3K27AC


title: NSC2_H3K27AC


title: NSC1_H3K27AC_INPUT


title: NSC1_H3K27AC


title: GSC9_H3K27AC_INPUT

source_name: glioblastoma stem cells


title: NSC2_H3K27AC_INPUT


title: GSC8_H3K27AC


title: GSC44_H3K27AC_INPUT


title: GSC5_H3K27AC_INPUT


title: GSC6_H3K27AC_INPUT


title: GSC7_H3K27AC


title: GSC7_H3K27AC_INPUT


title: GSC6_H3K27AC


title: GSC44_H3K27AC


title: GSC8_H3K27AC_INPUT


title: GSC9_H3K27AC


title: GSC5_H3K27AC


title: GSC43_H3K27AC_INPUT


title: GSC30 [RNA-Seq]


title: GSC40_H3K27AC_INPUT


title: GSC41_H3K27AC


title: GSC4_H3K27AC_INPUT


title: GSC39_H3K27AC_INPUT


title: GSC4_H3K27AC


title: GSC38_H3K27AC_INPUT


title: GSC39_H3K27AC


title: GSC38_H3K27AC


title: GSC37_H3K27AC


title: GSC36_H3K27AC


title: GSC40_H3K27AC


title: GSC36_H3K27AC_INPUT


title: GSC34_H3K27AC_INPUT


title: GSC35_H3K27AC


title: GSC35_H3K27AC_INPUT


title: GSC34_H3K27AC


title: GSC33_H3K27AC_INPUT


title: GSC32_H3K27AC


title: GSC33_H3K27AC


title: GSC32_H3K27AC_INPUT


title: GSC31_H3K27AC_INPUT


title: GSC41_H3K27AC_INPUT


title: GSC30_H3K27AC_INPUT


title: GSC30_H3K27AC


title: GSC3_H3K27AC


title: GSC29_H3K27AC_INPUT


title: GSC29_H3K27AC


title: GSC27_H3K27AC


title: GSC27_H3K27AC_INPUT


title: GSC26_H3K27AC_INPUT


title: GSC28_H3K27AC_INPUT


title: GSC28_H3K27AC


title: GSC26_H3K27AC


title: GSC37_H3K27AC_INPUT


title: GSC25_H3K27AC_INPUT


title: GSC23_H3K27AC_INPUT


title: GSC25_H3K27AC


title: GSC24_H3K27AC


title: GSC31_H3K27AC


title: GSC3_H3K27AC_INPUT


title: GSC22_H3K27AC


title: GSC21_H3K27AC


title: GSC21_H3K27AC_INPUT


title: GSC20_H3K27AC


title: GSC2_H3K27AC_INPUT


title: GSC18_H3K27AC_INPUT


title: GSC18_H3K27AC


title: GSC19_H3K27AC


title: GSC17_H3K27AC_INPUT


title: GSC19_H3K27AC_INPUT


title: GSC17_H3K27AC


title: GSC16_H3K27AC


title: GSC14_H3K27AC_INPUT


title: GSC15_H3K27AC


title: GSC15_H3K27AC_INPUT


title: GSC16_H3K27AC_INPUT


title: GSC13_H3K27AC_INPUT


title: GSC14_H3K27AC


title: GSC13_H3K27AC


title: GSC24_H3K27AC_INPUT


title: GSC23_H3K27AC


title: GSC22_H3K27AC_INPUT


title: GSC11_H3K27AC_INPUT


title: GSC10_H3K27AC_INPUT


title: GSC12_H3K27AC


title: GSC10_H3K27AC


title: GSC2_H3K27AC


title: GSC11_H3K27AC


title: GSC12_H3K27AC_INPUT


title: GSC20_H3K27AC_INPUT


title: GSC1_H3K27AC


title: GBM84_H3K27AC


title: GBM84_H3K27AC_INPUT


title: GBM83_H3K27AC_INPUT


title: GBM82_H3K27AC


title: GBM82_H3K27AC_INPUT


title: GBM81_H3K27AC_INPUT


title: GBM81_H3K27AC


title: GBM83_H3K27AC


title: GBM78_H3K27AC


title: GBM80_H3K27AC_INPUT


title: GBM79_H3K27AC


title: GBM76_H3K27AC


title: GBM80_H3K27AC


title: GBM75_H3K27AC_INPUT


title: GBM79_H3K27AC_INPUT


title: GBM74_H3K27AC_INPUT


title: GSC1_H3K27AC_INPUT


title: GBM76_H3K27AC_INPUT


title: GBM74_H3K27AC


title: GBM73_H3K27AC_INPUT


title: GBM71_H3K27AC_INPUT


title: GBM71_H3K27AC


title: GBM73_H3K27AC


title: GBM75_H3K27AC


title: GBM70_H3K27AC_INPUT


title: GBM69_H3K27AC_INPUT


title: GBM69_H3K27AC


title: GBM68_H3K27AC_INPUT


title: GBM68_H3K27AC


title: GBM78_H3K27AC_INPUT


title: GBM66_H3K27AC


title: GBM64_H3K27AC


title: GBM64_H3K27AC_INPUT


title: GBM67_H3K27AC


title: GBM67_H3K27AC_INPUT


title: GBM63_H3K27AC


title: GBM66_H3K27AC_INPUT


title: GBM63_H3K27AC_INPUT


title: GSC43_H3K27AC


title: GBM62_H3K27AC_INPUT


title: GBM62_H3K27AC


title: GBM61_H3K27AC


title: GBM61_H3K27AC_INPUT


title: GBM59_H3K27AC_INPUT


title: GBM60_H3K27AC


title: GBM70_H3K27AC


title: GBM58_H3K27AC_INPUT


title: GBM59_H3K27AC


title: GBM58_H3K27AC


title: GBM54_H3K27AC_INPUT


title: GBM55_H3K27AC


title: GBM54_H3K27AC


title: GBM57_H3K27AC


title: GBM55_H3K27AC_INPUT


title: GBM53_H3K27AC_INPUT


title: GBM60_H3K27AC_INPUT


title: GBM52_H3K27AC


title: GBM51_H3K27AC_INPUT


title: GBM51_H3K27AC


title: GBM50_H3K27AC


title: GBM5_H3K27AC_INPUT


title: GBM49_H3K27AC_INPUT


title: GBM49_H3K27AC


title: GBM5_H3K27AC


title: GBM47_H3K27AC_INPUT


title: GBM48_H3K27AC_INPUT


title: GBM57_H3K27AC_INPUT


title: GBM48_H3K27AC


title: GBM47_H3K27AC


title: GBM45_H3K27AC_INPUT


title: GBM46_H3K27AC


title: GBM4_H3K27AC_INPUT


title: GBM45_H3K27AC


title: GBM53_H3K27AC


title: GBM4_H3K27AC


title: GBM33_H3K27AC_INPUT


title: GBM52_H3K27AC_INPUT


title: GBM33_H3K27AC


title: GBM32_H3K27AC_INPUT


title: GBM32_H3K27AC


title: GBM31_H3K27AC_INPUT


title: GBM30_H3K27AC


title: GBM31_H3K27AC


title: GBM28_H3K27AC_INPUT


title: GBM28_H3K27AC


title: GBM21_H3K27AC_INPUT


title: GBM17_H3K27AC


title: GBM21_H3K27AC


title: GBM1_H3K27AC_INPUT


title: GBM46_H3K27AC_INPUT


title: GBM1_H3K27AC


title: Brunello screen GFP+ (2)

city: NEW YORK

first: QINGL

last: LI

address: 1275 YORK AVE

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

description:
Amplicon Sequencing
sample 49 Brunello screen GFP+

data_processing:
Library strategy: Amplicon Sequencing
Raw FASTQ files demultiplexed by MSKCC IGO were further processed to contain only the unique gRNA sequences, and the processed reads were aligned to the designed gRNA sequences from the library using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The read counts were further normalized to total reads of that sample to offset differences in Hi-Seq depth.
genome build: GECKO v2 library B( Addgene, 1000000049)
Supplementary_files_format_and_content: Excel file (on series record)

source_name: HUES8 human embryonic stem cells (hESCs)

growth_protocol: Undifferentiated human ES and iPS cells were maintained in the chemically defined feeder-free E8 condition (Thermo Fisher Scientific, A1517001) at 37oC with 5% CO2, and routinely confirmed to be mycoplasma-free by the MSKCC Antibody and Bioresource Core Facility.

extract_protocol:
SOX17GFP+ and SOX17GFP- cells are sorted by fluorescence activated cell sorting. Genmoic DNA were extracted by using Qiagen Maxi Kit (Qiagen 13362)
A two-step PCR method was performed to amplify the gRNA sequence for Hi-Seq. For the first step, 380 _g of DNA per sample (6.6 _g of genomic DNA per 1 million cells) was used to perform PCR using Herculase II fusion DNA polymerase (Agilent, 600679) in order to achieve a 1,000-fold converge of the GECKO library containing 58,028 gRNAs. In total, we performed 38 separate 100 _l reaction with 10 _g genomic DNA per sample for 18 cycles and combined the resulting amplicons. For the second step, 5 _l of the product from the first PCR was used in a 100 _l PCR reaction for 24 cycles with primers to attach Illumina adaptors for barcoding. Gel purified amplicons from the second PCR were quantified, mixed and sequenced using a HiSeq 2500 (Illumina) at MKSCC Integrated Genomics Operation (IGO).

treatment_protocol: Human ES or iPS cells were cultured in E8 medium and routinely passaged by EDTA. When cells reached 80-90% confluence, cells were treated with TrypLE Select to dissociate them as single cells for passaging. Typically, 0.15 million human ES or iPS cells were plated in one well of the six-well plates with 10 μM ROCK inhibitor in 2 ml E8 media. 24 hours later, cells were washed with PBS once and culture medium was changed to Advanced RPMI (Thermo Fisher Scientific, 12633012) with penicillin/streptomycin (Thermo Fisher Scientific, 15070063), GlutaMAX (Thermo Fisher Scientific, 35050079), 0.003% BSA (Thermo Fisher Scientific, 15260037), 5 μM CHIR-99021 (Tocris, 4423) and 100 ng/ml Activin A (PeperoTech ,12014E). Over the next 2 days, culture medium was changed to Advanced RPMI with penicillin/streptomycin, GlutaMAX, 0.2% FBS and 100 ng/ml Activin A.

value: SOX17-GFP knockin

tag: parental cell line

tag: parental cell type

value: human embryonic stem cells (hESCs)

tag: differentiation status

value: ESC


title: Brunello screen GFP- (2)

description:
Amplicon Sequencing
sample 51 Brunello screen GFP-

tag: genotype


title: ESC-c ATAC

description:
ATAC-seq
Sup Data Set 4 (Motif analysis) .xlsx

data_processing:
Reads from ChIP-seq and ATAC-seq libraries were trimmed for quality and Illumina adapter sequences using trim_galore and aligned to human genome assembly hg19 with bowtie2 using the default parameters. Aligned reads with the same start site and orientation were removed using the Picard tool MarkDuplicates (http://broadinstitute.github.io/picard/). Density profiles were created by extending each read to the average library fragment size for ChIP and 0 bp for ATAC, then computing density using the BEDTools suite (http://bedtools.readthedocs.io). Enriched regions were discovered using MACS and scored against matched input libraries (fold change > 2 and p-value < 1e-5). Genomic    blacklisted    regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz) were filtered and peaks within 500 bp were merged. All genome browser tracks and read density tables were normalized to a sequencing depth of ten million mapped reads.
genome build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Nuclear Isolation: 50,000 cells were collected in an eppendorf tube, washed with 1mL of cold PBS and spun down at 1500rpm for 5 minutes at 4 oC. Cell were pelleted, and washed with 1mL of ice-cold ATAC Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2). Then cells were pelleted again and resuspended in 50μL of ATAC Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 or IGEPAL-Ca630) for 2 minutes on ice. 1 mL of cold ATAC Buffer was added to dilute out the lysis buffer. Cells were pelleted by centrifugation with 1500 RPM for 10 minutes at 4oC. Tagmentation: Supernatant was aspirated to leave behind ~22.5 μL sample liquid.  The resuspended pellet was transferred to a PCR tube containing 2.5 μL Tagmentation Enzyme (transposase) and 25 μL of Tagmentation Buffer (Illumina Nextera DNA Sample Preparation Kit). After incubating the reaction for 30 minutes at 37oC, 0.2% SDS was added to the reaction. After incubating the reaction for 5 minutes at room temperature, samples were purified with 2X Agencourt AMPure XP beads (Beckman Coulter A63881).
50μL of sample was mixed with 55 μL of NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB, catalogue M0543L) and 5 μL of primer mix. For the primer mix, we used the Nextera primers The universal primer Ad1 and the unique index primer 2.X  (ex. 2.1, 2.2, 2.3, etc.) were mixed so that each had a final concentration of 25 μM. The samples were amplified with the following PCR program: 65 ºC, 5 minutes; 98 ºC, 30 seconds; 98 ºC, 10 seconds, 65 ºC 30 seconds (12 times). The samples were purified with 1.5X AMPure XP beads and the concentration was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced PE50 on a HiSeq 2500.

treatment_protocol: DE cells were treated with JNKi or DMSO(control)


title: GBM30_H3K27AC_INPUT


title: DE Input Chip

description:
ChIP-seq
Sup Data Set 4 (Motif analysis) .xlsx

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Sigma, F1635) at 37°C for 15 min and quenched with 0.125 M glycine for 5 minutes at room temperature. Fixed cells were scraped off the plates in cold PBS buffer and washed twice in cold PBS buffer. Cell pellets were obtained by centrifugation at 3000 RPM for 5 minutes at 4 oC and frozen in liquid nitrogen immediately before transferring to the -80C freezer.  ~25 million cells were used for one ChIP reaction. Cell pellets were thawed on ice, resuspended in 1ml SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH8) containing proteinase and phosphatase inhibitor for one reaction in an eppendorf tube and incubated on ice for 10 minutes. Sonication was performed on a Branson Sonifier 250 with a 20% amplitude setting for 5.5 minutes (10 seconds on/off pulsing). Sonication products were spun down at 14000 RPM at 4oC for 10 minutes and 1ml supernatant containing chromatin and DNA were transferred to a falcon tube containing 9ml ChIP dilution buffer (0.01% SDS, 1.1% TritonX-100, 1.2mM EDTA, 16.7 mM Tris-HCl pH8, 167 mM NaCl) with proteinase and phosphatase inhibitor. 50 μl of dynabeads (Life Technologies 10009D) were added to samples and incubated at 4oC with rotation for 1 hour. After pre-clearing, dynabeads beads were removed and 200 μl of sample were collected as 2% input separately. 5 μg antibodies were added to the pre-cleared samples for overnight incubation at 4oC with rotation. 200 μl dynabeads were added into one ChIP reaction and incubated for 4-6 hours at 4 oC with rotation.  Dynabeads were collected by centrifugation with 3000 RPM at 4 oC for 5 minutes and washed in 1ml low salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) for 5 minutes at 4oC with rotations. Then beads were washed in 1ml high salt buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 500 mM NaCl) twice and TE buffer (10 mM Tris-HCl pH8, 1 mM EDTA) twice for 5 minutes at 4oC with rotation. After the last wash, beads were resuspended in 250 μl elution buffer (1% SDS, 0.1 M NaHCO3) and incubated in a thermomixer (850RPM) for 15 minutes at 60 oC. Supernatant were collected and added with 5 M NaCl for overnight decrosslinking at 65 oC. 10 μl 0.5 M EDTA, 20 μl 1 M Tris-HCl pH6.5 and 1 μl proteinase K (20 mg/ml) were added to decrosslinked product and incubated for 1 hour at 45 oC. DNA were isolated by using QIAquick PCR purification kit (Qiagen 28104).
Libraries were prepared using the NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina ® (NEB, E6240L) and quality controlled using Agilent Technologies 2200 TapeStation to determine fragment size and PicoGreen (Life Technologies/Invitrogen, P7589) to quantify the concentration. Samples were pooled and submitted to New York Genome Center for SE50 sequencing using a HiSeq 2500.

value: DE


title: DE GATA6 Chip (2)


title: ESC-a ATAC


title: ESC NANOG Chip (2)


title: ESC OCT4 Chip (2)


title: DE SMAD2/3 Chip (2)


title: ESC-b ATAC


title: ESC NANOG Chip


title: DE GATAT6 Chip


title: DE Input Chip (2)


title: DE SMAD2/3 Chip


title: ESC OCT4 Chip


title: GBM17_H3K27AC_INPUT


title: ESC Input (2)


title: ESC SMAD2/3 Chip (2)


title: JNKi DE Day 1 Input (2)


title: Brunello screen GFP- (1)

description:
Amplicon Sequencing
sample 50 Brunello screen GFP-


title: JNKi DE Day1 SMAD2/3 Chip (2)


title: JNKi DE Day1 GATA6 Chip (2)


title: Control DE Day1 Input (2)


title: Control DE Day1 GATA6 Chip (2)


title: Control DE Day1 JUN Chip (2)


title: Brunello screen GFP+ (1)

description:
Amplicon Sequencing
sample 48 Brunello screen GFP+


title: Control DE Day1 SMAD2/3 Chip  (2)


title: CF_TOFA-treated_2

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

institute: CWRU

data_processing:
Trimming and filtering of the reads to remove adaptor sequences and low-quality nucleotides were performed using Trimmomatic (v 0.36)
The filtered reads were aligned to the UCSC human genome hg19 as a reference using Bowtie2 (v 2.3.4.1) and Tophat (v 2.1.1). Assembly of transcriptomes and quantification of their expression was performed using Cufflinks (v 2.2.1).  Expression levels were expressed as fragments per kilobase of exon per million fragments mapped (FPKM).
Statistical significance in differential gene expression between groups was determined with Cuffdiff (v 2.2.1).  Both p and q values were determined and defined as uncorrected p-value of the test statistic and FDR-adjusted p-value of test-statistic, respectively.
Data were further analyzed and visualized using CummeRbund run under the R package (v 3.4.4)
Hierarchical clustering (heat map) of genes with differential expression was generated using Complete Linkage as the clustering method, Euclidian distance as the similarity measure, and Z-Score as normalization with TIBCO Spotfire Software (Palo Alto, CA). Pathway analysis was done using Gene Set Enrichment Analysis (GSEA) (Broad Institute, software.broadinstitute.org/gsea), a computational method that determines statistical significance of a priori defined set of genes between two groups. The Hallmark gene set from the Molecular Signature Database (MSigDB) collection was used to explore overrepresented pathways. It comprises of 50 hallmarks condensed from over 4,000 overlapping gene sets from v4.0 MSigDB collections C1 through C6.
Genome_build: hg19

source_name: Human nasal epithelial cultured cells

growth_protocol: Human nasal epithelial cells were obtained from the CWRU CF Center cell culture core facility. Briefly, nasal brushings were obtained from CF subjects (CF HNE) homozygous for F508del under UH IRB 10-04-14.  Samples were expanded by co-culture with irradiated 3T3 fibroblasts plus ROCK inhibitor (Y27632, 10 µM).  After expansion, CF HNE cells were seeded onto filter supports (Costar Snapwell #3801) and maintained in Airway 2 Media (DMEM/F12, pen/strep/gentamicin/Fungizone, Ultroser G).  After two days on filter inserts, apical media was removed and cells were cultured for 4-6 weeks as air/liquid interface cultures with media change on alternate days.

extract_protocol:
Total RNA was isolated with Qiazol Lysis Reagent (Qiagen Inc, Valencia, CA), cleaned-up using the RNeasy Mini Kit (Qiagen Inc), and eluted in 30 µl of RNase-free water (Qiagen Inc).
RNA-Seq libraries were generated using TruSeq stranded Total RNA Ribo-Zero human gold kit (Illumina, San Diego, CA) and the quality of resulting libraries was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Sequencing was carried out using an Illumina HiSeq 2500 Rapid Run flowcell – 2x100bp run.

treatment_protocol: CF F508del/F508del HNE cultured cells were mock treated or treated with TOFA (10 µg/mL) for 24 h (n=3: cells from separate patients for each replicate)

tag: diagnosis

value: cystic fibrosis

tag: tissue

value: Human nasal epithelial (HNE) cells

tag: Sex

value: Female


title: CF_TOFA-treated_3


title: CF_TOFA-treated_1


title: CF_Nontreated_3


title: ESC JUN Chip (2)


title: CF_Nontreated_1


title: X7b-3_shH3F3B_RNA-seq

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped to hg19 with internal pipeline StrongARM hat employs BWA and STAR
contaminant mouse reads were then removed from bam files with  internal pipeline XenoCP
reads were counted using htseq and converted to FPKM using hg19
Genome_build: hg19
Supplementary_files_format_and_content: matrix txt file with FPKM for each gene symbol  for each sample

source_name: SJ-DIPGx7 (PDX)

growth_protocol: human xenografts grown as implants in nude mouse brain

extract_protocol:
RNA extracted with Trizol following manufacturer's protocol
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit (Illumina.)

treatment_protocol: Xenografts dissected from mouse brain, cells dissociated and for each experiment, the same pool of cells was transduced with lentivirus expressing non-silencing control or specific shRNA, then cultured for 12 days under puro selection. Transduced cells were reimplanted into multiple mouse brains for each shRNA construct. The resulting tumors were dissected for ChIP-seq and RNAseq.

tag: cell source

value: in vivo xenograft dissected from mouse brain

tag: experiment id

tag: shRNA id

value: H3F3B shRNA

tag: shRNA backbone

value: miRE


title: XSUVI-6_shH3F3A_RNA-seq

source_name: SU-DIPGVI (established as neurospheres in vitro, implanted in brain for this experiment)

value: H3F3A shRNA #1


title: XSUVI-9_shH3F3A_RNA-seq

value: H3F3A shRNA #2


title: X7b-5_shH3F3A_RNA-seq


title: X7b-3_Ctl_RNA-seq

value: non silencing shRNA


title: X7b-2_shH3F3B_RNA-seq


title: X7b-4_shH3F3B_RNA-seq


title: XSUVI-10_shH3F3A_RNA-seq


title: CF_Nontreated_2

tag: age


title: X7b-2_shH3F3A_RNA-seq


title: X7b-3_shH3F3A_RNA-seq


title: X7b-2_Ctl_RNA-seq


title: X7b-1_shH3F3A_RNA-seq


title: X7a-9_shH3F3A_RNA-seq


title: X7b-4_shH3F3A_RNA-seq


title: X7b-1_shH3F3B_RNA-seq


title: X7b-1_Ctl_RNA-seq


title: X7a-3_Ctl_RNA-seq


title: X7a-7_shH3F3A_RNA-seq


title: X7a-4_Ctl_RNA-seq


title: X7a-6_shH3F3A_RNA-seq


title: X7a-5_Ctl_RNA-seq


title: X7a-2_Ctl_RNA-seq


title: X7a-19_Ctl_RNA-seq


title: X7a-20_Ctl_RNA-seq


title: X7a-18_Ctl_RNA-seq


title: X7a-16_shH3F3A_RNA-seq


title: X7a-14_shH3F3A_RNA-seq


title: X7a-15_shH3F3A_RNA-seq


title: X7a-12_Ctl_RNA-seq


title: X7a-10_Ctl_RNA-seq


title: X7a-11_Ctl_RNA-seq


title: X7a-17_Ctl_RNA-seq


title: X7a-8_shH3F3A_RNA-seq


title: X7a-1_Ctl_RNA-seq


title: X37-8_shH3F3A_RNA-seq

source_name: SJ-DIPGx37 (PDX)


title: XSUVI-8_shH3F3A_input_DNA

data_processing:
We used BWA (version 0.7.12, default parameter) to align the reads to the human hg19 + mouse mm9 + drosophila
marked duplicated reads with Picard with only nonduplicated reads kept by samtools
Only mapped human reads were extracted by samtools for quality contol and peak calling
To control the quality of the data and estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to draw cross-correlation with support of R (version 2.14.0)
peaks were called using MACS2 (for narrow peak histone marks) or Sicer V1.1 (for broad peak marks)
bam was converted to BigWig using bedtools (v2.25.0) and UCSC tools (20150811). Read coverage was scaled according to normalization factor using mouse contaminant reads as internal reference
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing locations of defined peaks
Supplementary_files_format_and_content: bigWig files containing normalized read coverage

extract_protocol:
ChIP and library construction for SJDIPGX7 xenografts using H3K27me3 (Millipore 07-449), H3K27ac (Active Motif 39133) and H3K4me3 (Active Motif 39159) was performed by Active Motif.  All other ChIP was performed at St. Jude using the following method.  Xenograft tumors were snap frozen and ground to a powder before fixation.  Single cell suspensions were generated from cultured cells then fixed. For histone ChIP, samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature.  For BMI1 and RNF2 ChIP, samples were fixed with 2mM disuccinimidyl glutarate in PBS for 45 minutes at room temperature followed by 1% paraformaldehyde in PBS for 15 minutes at room temperature following the method established in Gargiulo et al. (van Lohuizen lab, 2013 Cancer Cell 23:660-676). Bare nuclei were sheared on a Covaris M220.  For histone mark ChIPs, the reads arising from mouse cells entrapped within the xenograft to normalize the post ChIP samples to the human/mouse read ratio obtained for the pre-ChIP material (input library).  For some experiments, chromatin from drosophila S2 cells was also spiked-in and used to validate the use of mouse reads for normalization.  ChIP reactions were performed using a modified Upstate Biotechnology protocol. Antibodies used were (μl antibody per IP shown): H3K27me3 (Cell Signaling 9733, lot 8; 4 μl), H3K27ac (Cell Signaling 8173, lot 1; 4 μl), H3K4me3 (Cell Signaling 9751, lot 8; 5 μl), BMI1 (Bethyl A301-694A, lot 4; 5 μl) and RNF2 (Bethyl A302-869A, lot 1; 5 μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer).  Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

tag: chip antibody


title: X37-7_shH3F3A_RNA-seq


title: XSUVI-9_shH3F3A_H3K27me3_ChIP-seq

value: H3K27me3 (Cell Signaling, #9733, lot 8)


title: X7a-21_shH3F3A_RNA-seq


title: XSUVI-7_shH3F3A_H3K4me3_ChIP-seq

value: H3K4me3(Cell Signaling, #9751, lot 8)


title: XSUVI-9_shH3F3A_input_DNA


title: XSUVI-7_shH3F3A_input_DNA


title: XSUVI-8_shH3F3A_H3K27me3_ChIP-seq


title: XSUVI-8_shH3F3A_H3K4me3_ChIP-seq


title: XSUVI-7_shH3F3A_H3K27me3_ChIP-seq


title: XSUVI-6_shH3F3A_H3K4me3_ChIP-seq


title: XSUVI-5_Ctl_input_DNA


title: XSUVI-4_Ctl_input_DNA


title: XSUVI-2_Ctl_input_DNA


title: XSUVI-3_Ctl_input_DNA


title: XSUVI-6_shH3F3A_H3K27me3_ChIP-seq


title: X7a-13_Ctl_RNA-seq


title: XSUVI-1_Ctl_input_DNA


title: GBM50_H3K27AC_INPUT

tag: cell line


title: X7a-8_shH3F3A_H3K4me3_ChIP-seq

value: H3K4me3 (Active Motif, 39159)


title: X7a-7_shH3F3A_H3K27me3_ChIP-seq

value: H3K27me3 (Millipore, 07-449)


title: X7a-8_shH3F3A_H3K27me3_ChIP-seq


title: X7a-6_shH3F3A_H3K27me3_ChIP-seq


title: X7a-5_Ctl_H3K27me3_ChIP-seq


title: X7a-4_Ctl_H3K27me3_ChIP-seq


title: X7a-5_Ctl_H3K4me3_ChIP-seq


title: XSUVI-6_shH3F3A_input_DNA


title: prr7prr9_37C_ZT6_Rep2

city: Riverside

first: Dawn

last: Nagel

state: CA

address: 3401 Watkins Avenue (Batchelor Hall Rm 1123)

department: Botany and Plant Sciences

institute: University of Califonia, Riverside

description:
flowcell796_lane1_pair1_TTAGCCAG
processed data file:
prr7prr9Data.xlsm

data_processing:
Basic read processing
Filtering was performed with cutadapt with default settings
RNA-seqeuncing reads were aligned to the Araport11 gff file using TopHat2 (version 2.0.14) and Bowtie2 (version 2.2.5).
Relative gene expression was calculated using edgeR and limma
Genome_build: Araport 11 GFF (201606)
Supplementary_files_format_and_content: excel file with log2fold-change, false discovery rate, and counts per million by gene

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown for 12 days in diurnal conditions at 22°C

extract_protocol:
Qiagen RNeasy plant mini kit were used to extract total RNA
Libraries were constructed using protocol adapted from: A high-throughput method for Illumina RNA-Seq library preparation. See Temporal dynamics of temperature stress responses in Arabidopsis for details.

treatment_protocol: Plants were exposed to temperature stress for 1 hour at 0 or 5 hours after lights on

tag: ecotype background

tag: genotype/variation

tag: temperature

tag: time (hours)

value: 12-day-old whole seedling tissue

tag: replicate


title: X7a-20_Ctl_H3K27me3_ChIP-seq


title: X7a-3_Ctl_H3K27me3_ChIP-seq


title: X7a-21_shH3F3A_H3K27me3_ChIP-seq


title: prr7prr9_37C_ZT6_Rep1

description:
flowcell796_lane1_pair1_GTATCTCG
processed data file:
prr7prr9Data.xlsm


title: prr7prr9_22C_ZT6_Rep2

description:
flowcell796_lane1_pair1_TGCTCATG
processed data file:
prr7prr9Data.xlsm


title: Col-0_22C_ZT6_Rep2

description:
flowcell796_lane1_pair1_AATCACCT
processed data file:
prr7prr9Data.xlsm

value: wild type


title: X7a-2_Ctl_H3K27me3_ChIP-seq


title: X7a-18_Ctl_H3K27me3_ChIP-seq


title: prr7prr9_22C_ZT6_Rep1

description:
flowcell796_lane1_pair1_ATGTTGCG
processed data file:
prr7prr9Data.xlsm


title: X7a-16_shH3F3A_H3K4me3_ChIP-seq


title: prr7prr9_10C_ZT6_Rep2

description:
flowcell796_lane1_pair1_ATAGTATG
processed data file:
prr7prr9Data.xlsm


title: X7a-16_shH3F3A_H3K27me3_ChIP-seq


title: Col-0_22C_ZT6_Rep1

description:
flowcell796_lane1_pair1_TCGGTTGG
processed data file:
prr7prr9Data.xlsm


title: Col-0_10C_ZT6_Rep2

description:
flowcell796_lane1_pair1_AACGAGTC
processed data file:
prr7prr9Data.xlsm


title: X7a-19_Ctl_H3K27me3_ChIP-seq


title: X7a-15_shH3F3A_H3K27me3_ChIP-seq


title: X7a-14_shH3F3A_H3K4me3_ChIP-seq


title: Col-0_37C_ZT6_Rep2

description:
flowcell796_lane1_pair1_CGGCGATG
processed data file:
prr7prr9Data.xlsm


title: Col-0_10C_ZT6_Rep1

description:
flowcell796_lane1_pair1_CCTGGAAG
processed data file:
prr7prr9Data.xlsm


title: X7a-14_shH3F3A_H3K27me3_ChIP-seq


title: cca1lhy_37C_ZT1_Rep4

description:
flowcell664_lane1_pair1_CGATGCCA
processed data file:
cca1lhyData.xlsm


title: prr7prr9_10C_ZT6_Rep1

description:
flowcell796_lane1_pair1_TCGATATC
processed data file:
prr7prr9Data.xlsm


title: X7a-12_Ctl_H3K27me3_ChIP-seq


title: X7a-13_Ctl_H3K27me3_ChIP-seq


title: X7a-17_Ctl_H3K27me3_ChIP-seq


title: Col-0_37C_ZT6_Rep1

description:
flowcell796_lane1_pair1_CGTGTGTT
processed data file:
prr7prr9Data.xlsm


title: cca1lhy_37C_ZT1_Rep3

description:
flowcell664_lane1_pair1_TCATGCTG
processed data file:
cca1lhyData.xlsm


title: X7a-11_Ctl_H3K27me3_ChIP-seq


title: Col-0_37C_ZT1_Rep3

description:
flowcell664_lane1_pair1_CCTGGAAG
processed data file:
cca1lhyData.xlsm


title: X7a_shRNA_1_Pooled_Input_DNA


title: Col-0_37C_ZT1_Rep4

description:
flowcell664_lane1_pair1_CCATCAGG
processed data file:
cca1lhyData.xlsm


title: X7a-1_Ctl_H3K27me3_ChIP-seq


title: X7a-11_Ctl_H3K4me3_ChIP-seq


title: X7a-10_Ctl_H3K4me3_ChIP-seq


title: cca1lhy_37C_ZT1_Rep1

description:
flowcell664_lane1_pair1_CGGCAGAT
processed data file:
cca1lhyData.xlsm


title: cca1lhy_37C_ZT1_Rep2

description:
flowcell664_lane1_pair1_TCGATATC
processed data file:
cca1lhyData.xlsm


title: X7a_Ctrl_Pooled_Input_DNA


title: X7a-10_Ctl_H3K27me3_ChIP-seq


title: Col-0_37C_ZT1_Rep1

description:
flowcell664_lane1_pair1_TGCTCATG
processed data file:
cca1lhyData.xlsm


title: cca1lhy_22C_ZT1_Rep4

description:
flowcell664_lane1_pair1_GATGTGCC
processed data file:
cca1lhyData.xlsm


title: X37-9_shH3F3A_input_DNA


title: cca1lhy_22C_ZT1_Rep3

description:
flowcell664_lane1_pair1_CGGCGATG
processed data file:
cca1lhyData.xlsm


title: X37-8_shH3F3A_input_DNA


title: X37-8_shH3F3A_H3K4me3_ChIP-seq


title: cca1lhy_22C_ZT1_Rep1

description:
flowcell664_lane1_pair1_CTTGAACT
processed data file:
cca1lhyData.xlsm


title: X37-8_shH3F3A_H3K27me3_ChIP-seq


title: X37-7_shH3F3A_input_DNA


title: Col-0_22C_ZT1_Rep4

description:
flowcell664_lane1_pair1_GTATCTCG
processed data file:
cca1lhyData.xlsm


title: Col-0_22C_ZT1_Rep3

description:
flowcell664_lane1_pair1_CGTGTGTT
processed data file:
cca1lhyData.xlsm


title: Col-0_22C_ZT1_Rep2

description:
flowcell664_lane1_pair1_ATGTTGCG
processed data file:
cca1lhyData.xlsm


title: X37-7_shH3F3A_H3K27me3_ChIP-seq


title: X37-7_shH3F3A_H3K4me3_ChIP-seq


title: Col-0_22C_ZT1_Rep1

description:
flowcell664_lane1_pair1_TCGGTTGG
processed data file:
cca1lhyData.xlsm


title: X37-6_shH3F3A_input_DNA


title: X37-5_Ctl_input_DNA


title: cca1lhy_10C_ZT1_Rep4

description:
flowcell664_lane1_pair1_ATAGTATG
processed data file:
cca1lhyData.xlsm


title: cca1lhy_10C_ZT1_Rep1

description:
flowcell664_lane1_pair1_GTGCTACA
processed data file:
cca1lhyData.xlsm


title: cca1lhy_10C_ZT1_Rep2

description:
flowcell664_lane1_pair1_CGTGGTGC
processed data file:
cca1lhyData.xlsm


title: Col-0_10C_ZT1_Rep4

description:
flowcell664_lane1_pair1_AGCGTTAC
processed data file:
cca1lhyData.xlsm


title: Col-0_10C_ZT1_Rep3

description:
flowcell664_lane1_pair1_GCTATTCT
processed data file:
cca1lhyData.xlsm


title: X37-2_Ctl_input_DNA


title: X37-3_Ctl_input_DNA


title: X37-1_Ctl_input_DNA


title: Col-0_10C_ZT1_Rep2

description:
flowcell664_lane1_pair1_GACTGCCT
processed data file:
cca1lhyData.xlsm


title: ChIP-seq_ESC Input

description:
ChIP-seq
Sup Data Set 4 (Motif analysis) .xlsx

value: SOX17-GFP knockin

tag: parental cell line

tag: parental cell type

value: human embryonic stem cells (hESCs)

tag: differentiation status

value: ESC

tag: antibody

value: none (input)


title: X37-4_Ctl_input_DNA


title: cca1lhy_22C_ZT1_Rep2

description:
flowcell664_lane1_pair1_AATCACCT
processed data file:
cca1lhyData.xlsm

tag: tissue


title: ChIP-seq_ESC SMAD2_3

tag: genotype

value: SMAD2/3 (Cell Signaling Techology 8685)


title: ChIP-seq_ESC JUN

value: JUN (Cell Signaling Techology 9165S)


title: ChIP-seq_JNKi DE Day1-SMAD2_3

value: DE


title: ChIP-seq_JNKi DE Day1-GATA6

value: GATA6 (Cell Signaling Techology 5851)


title: Control DE Day1 Input


title: cca1lhy_10C_ZT1_Rep3

description:
flowcell664_lane1_pair1_AACGAGTC
processed data file:
cca1lhyData.xlsm


title: ChIP-seq_Control DE Day1-GATA6


title: ATAC-seq_JNKi DE Day1-c

description:
ATAC-seq
Sup Data Set 4 (Motif analysis) .xlsx


title: ChIP-seq_Control DE Day1-JUN


title: ChIP-seq_Control DE Day1-SMAD2_3


title: Advanced atherosclerotic plaque 3

city: Guangzhou

first: Jing-Jing

last: Zhao

state: Guangdong

address: No.1838, North of Guangzhou Avenue

institute: Laboratory Medicine Center, Nanfang Hospital, Southern Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: The arrays were scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: advanced atherosclerotic plaque

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method.

value: artery intima

tag: Sex

value: male

tag: lesion stage

value: V


title: ATAC_seq_JNKi DE Day1-b


title: Advanced atherosclerotic plaque 1

value: VI


title: ATAC-seq_Control DE Day1-b


title: ATAC-seq_JNKi DE Day1-a


title: ATAC-seq_Control DE Day1-c


title: JNKi DE Day1  Input


title: scRNA-Seq_Control DE_1

description:
scRNA-seq
This sample represents many single cells.
R1 contains cell bar code and R2 contains the biological  read

data_processing:
For scRNA-seq, the sequenced reads were processed and turned into a digital expression matrix using the Drop-Seq computational pipeline (v.1.2) of the McCarroll Lab (http://mccarrolllab.com/dropseq/). The reference genome was GRCh38, the gene annotation was from Ensembl release 76. The resulting count matrix was filtered to remove lowly covered cells and rarely captured transcripts, normalized for differences in sequencing depth, and de-noised using the MAGIC algorithm
genome build: GRCh38
Supplementary_files_format_and_content: count matrix

extract_protocol:
Definitive endoderm cells were washed with PBS once and treated with TrypLE for 5 minutes. E8 media was added to stop the digestion. Dissociated single cells were resuspended in PBS with 0.01% BSA, passed through a 40 micron filter and counted.  Cell concentration was adjusted to 100-120 cells/μl with >90% viability (in 1 ml volume).
Cell suspension were kept on and transferred to the Weill Cornell Genomics and Epigenomics Core Facility for drop-seq. Drop-seq experiment procedure follows the protocol published by the Steve McCarroll’s lab version 3.1 (12/18/15) http://mccarrolllab.com/download/905/.

treatment_protocol: DE cells were treated with JNKi or DMS(control)


title: Advanced atherosclerotic plaque 2


title: Normal arterial intima 2

source_name: normal arterial intima

value: normal


title: RNA-seq_MKK7 KO DE_2

description:
RNA-seq
Sup Data Set 3 (RNA-seq KO vs WT)
Sup Data Set 2 (RNA-seq DE vs ESC)

data_processing:
For RNA-seq, ESC and DE stage RNA-seq data from both WT and MKK7 KO cells were analyzed by Tophat, featureCounts and DESeq2. First, reads were mapped to the human genome (hg19) by Tophat (v.2.1.1) and read counts per gene were summarized by featureCounts from subread package. DESeq2 was used to analyze gene differential expression by comparing transcriptomes of WT and MKK7 KO cells from ESC and DE stages
genome build: hg19
Supplementary_files_format_and_content: Excel file (on series record)

source_name: H1 human embryonic stem cells (hESCs)

extract_protocol: Cell pellets were lysed in TRIzol (Thermo Fisher Scientific, 15596018). RNA was extracted from TRIzol lysate using the RNeasy Mini Kit (Qiagen, 74106). cDNA was produced using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814).

value: MKK7 KO


title: ATAC-seq_Control DE Day1-a


title: scRNA-seq_JNKi DE_2


title: RNA-seq_MKK7 KO DE_1


title: scRNA-seq_JNKi DE_1


title: scRNA-seq_Control DE_2


title: RNA-seq_WT DE_1

value: WT


title: RNA-seq_WT DE_2


title: RNA-seq_WT ESC_2


title: RNA-seq_MKK7 KO ESC_1


title: RNA-seq_WT ESC_1


title: RNA-seq_MKK7 KO ESC_2


title: Col-0_37C_ZT1_Rep2

description:
flowcell664_lane1_pair1_TTAGCCAG
processed data file:
cca1lhyData.xlsm

value: 12-day-old whole seedling tissue


title: Normal arterial intima 3


title: Amplicon-Seq_2_GFP-negative

description:
Amplicon Sequencing
Sup Data Set 1 (Screen Result)


title: Amplicon-Seq_1_GFP-negative


title: Amplicon-Seq_1_GFP-positive


title: Normal arterial intima 1


title: 9020331160_R05C01 genomic DNA from peripheral blood

type: genomic

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

description: peripheral blood sample

hyb_protocol: Bisulfite converted DNA was hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi (v1.16.0) for reading the data; MethylAid (v1.14.0) for quality control

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood was drawn and stored in EDTA to prevent coagulation. Erythrocytes were lysed before proteins were aggregated out of the sample. Genomic DNA was extracted through ethanol precipitation, after which the DNA was dissolved in tris-ethylenediaminetetraacetic buffer (Tris-EDTA) and stored at 4°C.

tag: gender

value: Male

tag: disease state

value: control

tag: growth

tag: facial

tag: cns


title: single sperm_4264

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

description: single sperm DNA sequence

data_processing:
Alignment with bwa-0.7.15
Use of platypus-0.5.2 to call variants de novo in bulk sperm samples, filtered as described in Hinch et al
Use of platypus-0.5.2 to call variants in each sperm at sites of de novo variants called in bulk sperm above
Calling crossover breakpoints using in-house algorithm (described in Hinch et al)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with column descriptions in commented header; each line corresponds to one crossover

source_name: single sperm

growth_protocol: Data were generated from sperm from a 10 week old male mouse - no culturing was performed.

extract_protocol:
Sperm samples were isolated mechanically and our novel single-cell DNA amplification protocol was performed on each sample followed by sequencing. Full experimental procedures are reported in accompanying manuscript (Hinch et al).
Libraries were prepared as per NEBNext library  preparation protocol with some modifications. Please see details in Hinch et al.

tag: strain

value: sperm

tag: prdm9 genotype

value: HUM/CAST


title: 9020331163_R04C01 genomic DNA from peripheral blood

description: peripheral blood sample

tag: age


title: single sperm_4263

description: single sperm DNA sequence


title: 9020331152_R06C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331152_R05C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4262

description: single sperm DNA sequence


title: 9020331163_R05C02 genomic DNA from peripheral blood

description: peripheral blood sample

value: Female


title: 9020331163_R01C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331108_R06C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331163_R01C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331124_R03C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331124_R02C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: Amplicon-Seq_2_GFP-positive

value: SOX17-GFP knockin

value: human embryonic stem cells (hESCs)

value: ESC


title: 9020331160_R01C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331082_R05C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4253

description: single sperm DNA sequence


title: single sperm_4250

description: single sperm DNA sequence


title: 9020331108_R02C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4258

description: single sperm DNA sequence


title: single sperm_4255

description: single sperm DNA sequence


title: single sperm_4257

description: single sperm DNA sequence


title: 9020331114_R05C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9003865063_R02C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331108_R05C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331077_R04C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4249

description: single sperm DNA sequence


title: single sperm_4243

description: single sperm DNA sequence


title: 9020331108_R04C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9003865063_R04C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9003865027_R06C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331082_R04C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331060_R01C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331077_R01C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331151_R01C02 genomic DNA from peripheral blood

description: peripheral blood sample

value: FASD


title: 9003865027_R06C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331124_R02C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9003865061_R03C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9003865027_R01C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9020331013_R03C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4239

description: single sperm DNA sequence


title: 9020331160_R06C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4234

description: single sperm DNA sequence


title: single sperm_4242

description: single sperm DNA sequence


title: single sperm_4241

description: single sperm DNA sequence


title: single sperm_4232

description: single sperm DNA sequence


title: single sperm_4246

description: single sperm DNA sequence


title: single sperm_4233

description: single sperm DNA sequence


title: single sperm_4230

description: single sperm DNA sequence


title: single sperm_4240

description: single sperm DNA sequence


title: 9020331175_R05C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4229

description: single sperm DNA sequence


title: 9020331060_R01C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4237

description: single sperm DNA sequence


title: 9985178087_R04C02 genomic DNA

description: peripheral blood sample


title: single sperm_4221

description: single sperm DNA sequence


title: single sperm_4245

description: single sperm DNA sequence


title: single sperm_4228

description: single sperm DNA sequence


title: single sperm_4225

description: single sperm DNA sequence


title: single sperm_4220

description: single sperm DNA sequence


title: 9985178082_R03C02 genomic DNA

description: peripheral blood sample


title: 9003865090_R04C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4214

description: single sperm DNA sequence


title: 9020331114_R04C02 genomic DNA from peripheral blood

description: peripheral blood sample


title: single sperm_4212

description: single sperm DNA sequence


title: 9986360122_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_4211

description: single sperm DNA sequence


title: 9985178087_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_4210

description: single sperm DNA sequence


title: 9020331060_R05C01 genomic DNA from peripheral blood

description: peripheral blood sample


title: 9986360121_R06C01 genomic DNA

description: peripheral blood sample


title: single sperm_4208

description: single sperm DNA sequence


title: single sperm_4236

description: single sperm DNA sequence


title: single sperm_4247

description: single sperm DNA sequence


title: 9985178130_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_4202

description: single sperm DNA sequence


title: single sperm_4206

description: single sperm DNA sequence


title: single sperm_3295

description: single sperm DNA sequence


title: single sperm_4201

description: single sperm DNA sequence


title: 9985178130_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_3294

description: single sperm DNA sequence


title: 9985178084_R01C01 genomic DNA

description: peripheral blood sample


title: 9979553088_R01C01 genomic DNA

description: peripheral blood sample


title: single sperm_3293

description: single sperm DNA sequence


title: 9985178082_R05C01 genomic DNA

description: peripheral blood sample


title: single sperm_3292

description: single sperm DNA sequence


title: 9986360121_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_4207

description: single sperm DNA sequence


title: single sperm_3291

description: single sperm DNA sequence


title: single sperm_3290

description: single sperm DNA sequence


title: 9979553082_R01C01 genomic DNA

description: peripheral blood sample


title: 9985178116_R04C01 genomic DNA

description: peripheral blood sample


title: 9986360121_R05C01 genomic DNA

description: peripheral blood sample


title: 9985178087_R03C02 genomic DNA

description: peripheral blood sample


title: single sperm_3287

description: single sperm DNA sequence


title: 9986360122_R01C02 genomic DNA

description: peripheral blood sample


title: single sperm_3288

description: single sperm DNA sequence


title: 9985178116_R02C02 genomic DNA

description: peripheral blood sample


title: single sperm_3289

description: single sperm DNA sequence


title: single sperm_3285

description: single sperm DNA sequence


title: single sperm_3281

description: single sperm DNA sequence


title: 9986360121_R02C02 genomic DNA

description: peripheral blood sample


title: 9986360122_R03C01 genomic DNA

description: peripheral blood sample


title: 9985178082_R02C02 genomic DNA

description: peripheral blood sample


title: 9986360122_R03C02 genomic DNA

description: peripheral blood sample


title: 9986360121_R03C02 genomic DNA

description: peripheral blood sample


title: 9985178084_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_3275

description: single sperm DNA sequence


title: 9985178087_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_3274

description: single sperm DNA sequence


title: single sperm_3268

description: single sperm DNA sequence


title: single sperm_3273

description: single sperm DNA sequence


title: 9985178087_R06C02 genomic DNA

description: peripheral blood sample


title: 9985178096_R03C02 genomic DNA

description: peripheral blood sample


title: single sperm_3278

description: single sperm DNA sequence


title: single sperm_3266

description: single sperm DNA sequence


title: 9979553088_R03C02 genomic DNA

description: peripheral blood sample


title: single sperm_3264

description: single sperm DNA sequence


title: single sperm_3261

description: single sperm DNA sequence


title: single sperm_3263

description: single sperm DNA sequence


title: 9986360109_R01C02 genomic DNA

description: peripheral blood sample


title: 9985178090_R04C02 genomic DNA

description: peripheral blood sample


title: 9986360109_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_3279

description: single sperm DNA sequence


title: 9979553088_R04C01 genomic DNA

description: peripheral blood sample


title: single sperm_3258

description: single sperm DNA sequence


title: 9985178096_R04C01 genomic DNA

description: peripheral blood sample


title: single sperm_3256

description: single sperm DNA sequence


title: 9985178082_R01C01 genomic DNA

description: peripheral blood sample


title: 9985178127_R04C02 genomic DNA

description: peripheral blood sample


title: 9986360122_R04C01 genomic DNA

description: peripheral blood sample


title: single sperm_3249

description: single sperm DNA sequence


title: single sperm_3248

description: single sperm DNA sequence


title: single sperm_3253

description: single sperm DNA sequence


title: single sperm_3252

description: single sperm DNA sequence


title: 9985178082_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_3246

description: single sperm DNA sequence


title: single sperm_3267

description: single sperm DNA sequence


title: 9985178084_R02C02 genomic DNA

description: peripheral blood sample


title: single sperm_3244

description: single sperm DNA sequence


title: 9985178084_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_3238

description: single sperm DNA sequence


title: 9985178096_R02C02 genomic DNA

description: peripheral blood sample


title: single sperm_3236

description: single sperm DNA sequence


title: single sperm_3235

description: single sperm DNA sequence


title: 9985178116_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_3255

description: single sperm DNA sequence


title: 9986360109_R01C01 genomic DNA

description: peripheral blood sample


title: 9985178090_R02C01 genomic DNA

description: peripheral blood sample


title: 9985178096_R06C02 genomic DNA

description: peripheral blood sample


title: 9986360121_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_3233

description: single sperm DNA sequence


title: single sperm_295

description: single sperm DNA sequence


title: single sperm_3234

description: single sperm DNA sequence


title: 9979553082_R02C01 genomic DNA

description: peripheral blood sample


title: 9985178127_R04C01 genomic DNA

description: peripheral blood sample


title: 9979553082_R06C01 genomic DNA

description: peripheral blood sample


title: 9979553082_R02C02 genomic DNA

description: peripheral blood sample


title: single sperm_294

description: single sperm DNA sequence


title: single sperm_293

description: single sperm DNA sequence


title: single sperm_292

description: single sperm DNA sequence


title: single sperm_291

description: single sperm DNA sequence


title: 9986360121_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_289

description: single sperm DNA sequence


title: 9985178127_R01C01 genomic DNA

description: peripheral blood sample


title: 9986360122_R01C01 genomic DNA

description: peripheral blood sample


title: single sperm_287

description: single sperm DNA sequence


title: 9985178090_R06C01 genomic DNA

description: peripheral blood sample


title: 9985178087_R01C02 genomic DNA

description: peripheral blood sample


title: 9979553082_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_284

description: single sperm DNA sequence


title: single sperm_285

description: single sperm DNA sequence


title: 9979553088_R04C02 genomic DNA

description: peripheral blood sample


title: single sperm_282

description: single sperm DNA sequence


title: 9985178127_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_281

description: single sperm DNA sequence


title: 9979553088_R02C02 genomic DNA

description: peripheral blood sample


title: 9979553088_R05C02 genomic DNA

description: peripheral blood sample


title: 9985178130_R05C01 genomic DNA

description: peripheral blood sample


title: single sperm_280

description: single sperm DNA sequence


title: single sperm_3242

description: single sperm DNA sequence


title: single sperm_277

description: single sperm DNA sequence


title: 9986360122_R02C01 genomic DNA

description: peripheral blood sample


title: 9985178084_R04C01 genomic DNA

description: peripheral blood sample


title: 9986360109_R06C01 genomic DNA

description: peripheral blood sample


title: single sperm_273

description: single sperm DNA sequence


title: single sperm_271

description: single sperm DNA sequence


title: single sperm_270

description: single sperm DNA sequence


title: single sperm_288

description: single sperm DNA sequence


title: single sperm_268

description: single sperm DNA sequence


title: 9986360122_R06C01 genomic DNA

description: peripheral blood sample


title: single sperm_276

description: single sperm DNA sequence


title: 9985178087_R02C02 genomic DNA

description: peripheral blood sample


title: 9985178090_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_265

description: single sperm DNA sequence


title: single sperm_262

description: single sperm DNA sequence


title: 9979553088_R05C01 genomic DNA

description: peripheral blood sample


title: single sperm_261

description: single sperm DNA sequence


title: 9985178130_R06C01 genomic DNA

description: peripheral blood sample


title: 9985178116_R06C01 genomic DNA

description: peripheral blood sample


title: single sperm_259

description: single sperm DNA sequence


title: 9985178096_R06C01 genomic DNA

description: peripheral blood sample


title: 9985178096_R05C02 genomic DNA

description: peripheral blood sample


title: single sperm_258

description: single sperm DNA sequence


title: single sperm_257

description: single sperm DNA sequence


title: 9979553082_R01C02 genomic DNA

description: peripheral blood sample


title: 9985178116_R04C02 genomic DNA

description: peripheral blood sample


title: 9985178116_R06C02 genomic DNA

description: peripheral blood sample


title: 9986360109_R04C02 genomic DNA

description: peripheral blood sample


title: single sperm_255

description: single sperm DNA sequence


title: 9985178127_R05C01 genomic DNA

description: peripheral blood sample


title: single sperm_256

description: single sperm DNA sequence


title: single sperm_252

description: single sperm DNA sequence


title: single sperm_254

description: single sperm DNA sequence


title: 9979553082_R06C02 genomic DNA

description: peripheral blood sample


title: 9985178096_R04C02 genomic DNA

description: peripheral blood sample


title: single sperm_248

description: single sperm DNA sequence


title: single sperm_250

description: single sperm DNA sequence


title: single sperm_246

description: single sperm DNA sequence


title: 9985178116_R01C01 genomic DNA

description: peripheral blood sample


title: 9985178084_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_247

description: single sperm DNA sequence


title: 9985178096_R02C01 genomic DNA

description: peripheral blood sample


title: single sperm_243

description: single sperm DNA sequence


title: single sperm_278

description: single sperm DNA sequence


title: single sperm_242

description: single sperm DNA sequence


title: single sperm_240

description: single sperm DNA sequence


title: 9985178082_R04C02 genomic DNA

description: peripheral blood sample


title: 9979553088_R02C01 genomic DNA

description: peripheral blood sample


title: 9985178084_R04C02 genomic DNA

description: peripheral blood sample


title: single sperm_236

description: single sperm DNA sequence


title: 9985178130_R04C02 genomic DNA

description: peripheral blood sample


title: 9985178127_R06C02 genomic DNA

description: peripheral blood sample


title: 9985178116_R01C02 genomic DNA

description: peripheral blood sample


title: Muscle__Cont__polyA.rep2

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Control), replicate 2

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d .
Genome_build: mm10
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script.  We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.

molecule: polyA RNA

source_name: control_P35 mouse  gastrocnemius skeletal muscle

extract_protocol:
Skeletal muscles were isolated and frozen in liquid nitrogen. Frozen muscle tissues were powdered in liquid nitrogen, lysed by Buffer RLT (QIAGEN), and digested by proteinase K. Total RNA was extracted using an RNeasy mini kit  (QIAGEN) according to the manufacturer’s instructions.
Ion Total RNA-Seq Kit (Life Technology)

value: gastrocnemius skeletal muscle

tag: genotype/variation


title: 9985178130_R01C02 genomic DNA

description: peripheral blood sample


title: single sperm_237

description: single sperm DNA sequence


title: single sperm_235

description: single sperm DNA sequence


title: 9985178090_R01C02 genomic DNA

description: peripheral blood sample


title: 9985178084_R01C02 genomic DNA

description: peripheral blood sample


title: single sperm_244

description: single sperm DNA sequence


title: 9985178090_R05C01 genomic DNA

description: peripheral blood sample


title: single sperm_234

description: single sperm DNA sequence


title: 9986360121_R06C02 genomic DNA

description: peripheral blood sample


title: 9985178130_R03C02 genomic DNA

description: peripheral blood sample


title: Muscle__Cont__polyA.rep3

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Control), replicate 3

value: male


title: 9986360121_R04C01 genomic DNA

description: peripheral blood sample


title: Muscle__SFPQ_KO__polyA.rep3

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Sfpq homo KO), replicate 3

source_name: SFPQ_KO_P35 mouse  gastrocnemius skeletal muscle


title: Muscle__SFPQ_KO__polyA.rep2

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Sfpq homo KO), replicate 2


title: single sperm_231

description: single sperm DNA sequence


title: Muscle__SFPQ_KO__polyA.rep1

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Sfpq homo KO), replicate 1


title: 9985178130_R03C01 genomic DNA

description: peripheral blood sample


title: single sperm_2296

description: single sperm DNA sequence


title: single sperm_2295

description: single sperm DNA sequence


title: Muscle__Cont__polyA.rep1

description: mRNA-seq (polyA+) data from gastrocnemius skeletal muscle of  P35 male mouse (Control), replicate 1


title: single sperm_245

description: single sperm DNA sequence


title: single sperm_2291

description: single sperm DNA sequence


title: single sperm_2290

description: single sperm DNA sequence


title: single sperm_2292

description: single sperm DNA sequence


title: Tln1 Pod-rtTA TetO with VPA 3

city: New Haven

first: Shuta

last: Ishibe

state: CT

address: 300 Cedar street

institute: Yale University

description: Gene expression data from Tln1 Pod-rtTA TetO-Cre mouse glomerulus with VPA treatment.

hyb_protocol: standard Affymetrix protocol

scan_protocol: The scanner is a 16-bit sophisticated opto-mechanical confocal scanner which measures fluorescence intensity emitted by the labeled cRNA/cDNA bound to the probe arrays. The scanner uses a high-quality, solid state 532nm Diode-Pumped, Frequency Doubled Nd:YAG (Neodymium-doped Yttrium Aluminum Garnet) Green Laser. The scanner optics are designed to condition the laser beam to deliver an excitation spot size of 3.5.

data_processing: Background correction was done individually for each data using RMA algorithm in limma package. Probes were mapped to gene symbols using the annotation file downloaded from Affymetrix website where probes with no annotation were discarded. The expression values with biological replicates were averaged. Z score for each gene was calculated following the method published by Cheadle et al. (2003). When comparing two samples, Z ratio of each gene was calculated.

source_name: kidney glomerulus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Doxycycline induction for 3 weeks in mice from 8 weeks old age

extract_protocol: RNA isolation of mouse glomerulus using Rneasy kit (Quiagen)

treatment_protocol: vehicle or valproic acid treatment for 2 weeks after completion of doxycyclin induction

value: 13 weeks old age

value: Tln1 Pod-rtTA TetO-Cre

tag: treatment

value: doxyclcline induction for 3 weeks + valproic acid


title: Tln1 Pod-rtTA TetO with VPA 2


title: 9985178127_R01C02 genomic DNA

description: peripheral blood sample


title: Tln1 Pod-rtTA TetO with VPA 1


title: 9985178116_R03C02 genomic DNA

description: peripheral blood sample


title: 9985178090_R01C01 genomic DNA

description: peripheral blood sample


title: 9985178090_R04C01 genomic DNA

description: peripheral blood sample


title: single sperm_2288

description: single sperm DNA sequence