title: argF_6 day starvation vs. day 0 replicate 1

city: bronx

first: Sangeeta

last: Tiwari

state: NY

address: 1300 Morris park ave

institute: Albert Einstein College of Medicine

description: Biological replicate 1 of 3

hyb_protocol: Differntially labelled Probes were suspended in standard gene expression hybridization solution and hybridized to microarray slides for 16 hours at 42 in water bath,  blocked in standard prehybridization solution. After hybridization, the slide was washed in stringent wash conditions (3 times 5 min 16xSSC 0.1% SDS, 3 times 5 min 0.16 xSSC 0.1% SDS, 3 times 5 min 0.16x SSC and a final wash in filtered MQ water).

scan_protocol: Arrays were scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: Spots were gridded and quantified with TIGR Spotfinder. The data was processed in TIGR MIDAS. Two color tiff images of the microarrays were visually inspected . pin-tip (block) intensity box plots were used to detect slides exhibiting spatial and/or pin biases before normalization ,post-normalization intensity box plots and MA plots were used to assess the effectiveness of normalization in correcting these biases. RI plots were also used to identify outlier slides and for assessing the effectiveness of the normalization process, and Z-score histograms were used to look for slides with abnormal intensity distributions. Slides that can not satisfy quality control  crireria were rejected. Post normalization (Total Intensity and LOWESS) the in-slide replicate spots were averaged before expression ratios were calculated. The results from 3 biological replicates were subjected to a t-test without false discovery correction in TIGR MeV software.

source_name: Mtb [delta]argF _0.1

label_protocol: The Institute of Genomic Research (TIGR)  protocol SOP# M007 was followed to perform labeling .

growth_protocol: Exponentially growing culture of Mycobacterium tuberculosis H37RvΔargB or  ΔargF in arginine supplemented (1mM)  media were harvested, washed and suspended in arginine deficient 7H9 OADC 0.2% glycerol 0.05% tyloxapol broth.

extract_protocol: Cells were harvested by centrifugation, suspended in 1mL Qiagen RNA protect and stored at 4°C. Later, cells were pelleted and resuspended in 1ml Trizol (Life Technologies, Fisher, Grand Island, NY) and transferred to a Fast-Prep lysing matrix Blue cap tube. Tubes are processed in Fast-Prep apparatus (MP Bio, Irvine, CA) for 2 X 45 seconds at 6.5 M per second then cooled on ice for 1 minute centrifuged to pellet debris. Following Direct-zol kit manufacturer instructions (Zymo Research Corporation, Irvine, CA),  RNA is isolated.

treatment_protocol: Samples  were incubated at 37°C shaker-incubator and harvested at indicated time points of arginine stravation day 0, 1, 3, 6.

value: Mtb [delta]argF

tag: condition

value: day 0 before arginine starvation

tag: replicate

source_name: Mtb [delta]argF _6.1

value: aginine starved for 6 days


title: D13-1

status: Public on Aug 31 2018

type: SRA

city: Boston

first: Alaattin

last: Kaya

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA

description:
Disomic yeast strain
D13.1

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Ensembl build R64-1-1 using Bowtie 2 v2.1.0 with default parameters
Read counts per gene were calculated using Feature Counts
To filter out genes with the low number of reads, only the genes with at least 1 count per million (cpm) in at least half of the strains were retained, resulting in an expression set of 6,059 genes across 32 evolved lines
Filtered data was then subjected to RLE normalization
Differential gene expression analysis was performed using the R package EdgeR, using a FDR of 10%.
Genome_build: Ensembl build R64-1-1
Supplementary_files_format_and_content: tab-delimited tsv file include normalized  count values per gene for each Sample ...

molecule: total RNA

organism: Saccharomyces cerevisiae W303

source_name: transcriptome  of chromosome XIII disomic yeast strain, evolved line 1

growth_protocol: 5 mL cells were grown at 30 oC to mid log phase and frozen immediately after centrifugation

extract_protocol:
We used epicentre masterpure yeast RNA purification kit for total RNA isolation
Cell-Seq method was used to generate transcriptome libraries; poly-A selection

tag: ploidy

value: Disomes

tag: background genetic strain


title: D15-1

description:
Disomic yeast strain
D15.1

source_name: transcriptome  of chromosome XV disomic yeast strain, evolved line 1


title: argF_3 day starvation vs. day 0 replicate 2

type: RNA

department: Microbiology and Immunology

description: Biological replicate 2 of 3

organism: Mycobacterium tuberculosis

source_name: Mtb [delta]argF _3.2

tag: genotype/variation

value: aginine starved for 3 days

source_name: Mtb [delta]argF _0.2


title: argF_6 day starvation vs. day 0 replicate2

description: Biological replicate 2 of 3

source_name: Mtb [delta]argF _6.2


title: ESC_DOX_Day6_1 (1)

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the mm10 genome using TopHat
Log2fold change of "noDox_day6" vs "Dox_Day6" or "NLS_Day6" or "E14_Day6"  was extracted by Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs and Log2fold change of RPKMs

organism: Mus musculus

growth_protocol: ESC were grown on 0.1% gelatin in DMEM supplemented with 15% heat-inactivated FBS, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1mM Sodium Pyruvate and no recombinant leukemia inhibitory factor.

extract_protocol:
RNA was extracted by lysing the whole cell in TRIzol
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

treatment_protocol: transgene expression was induced with 2.5 ug/ml doxycycline in ESC daily and LIF withdrawal for 6 days

tag: cells

value: ESC doxycycline-inducible expressing HA-Flag-AGO2

tag: passages

tag: genotype

value: ESC AGO1-4-/- expressing only AGO2 with doxycycline (called Dox)


title: argF_1 day starvation vs. day 0 replicate 3

description: Biological replicate 3 of 3

source_name: Mtb [delta]argF _1.3

value: aginine starved for 1 day

source_name: Mtb [delta]argF _0.3


title: argF_1 day starvation vs. day 0 replicate 2

description: Biological replicate 2 of 3

source_name: Mtb [delta]argF _1.2


title: ESC_E14_Day6_1 (1)

value: WT E14 ESC


title: argF_3 day starvation vs. day 0 replicate 1

description: Biological replicate 1 of 3

source_name: Mtb [delta]argF _3.1


title: D13

description:
Disomic yeast strain
D13.a

source_name: transcriptome  of chromosome XIII disomic yeast strain


title: argF_1 day starvation vs. day 0 replicate 1

description: Biological replicate 1 of 3

value: Mtb [delta]argB

source_name: Mtb [delta]argF _1.1

value: aginine starved for 1 days


title: D12-3

description:
Disomic yeast strain
D12.3

source_name: transcriptome  of chromosome XII disomic yeast strain, evolved line 3


title: D11-3

description:
Disomic yeast strain
D11.3

source_name: transcriptome  of chromosome XI disomic yeast strain, evolved line 3


title: D12-2

description:
Disomic yeast strain
D12.2

source_name: transcriptome  of chromosome XII disomic yeast strain, evolved line 2


title: D12-1

description:
Disomic yeast strain
D12.1

source_name: transcriptome  of chromosome XII disomic yeast strain, evolved line 1


title: D12

description:
Disomic yeast strain
D12.a

source_name: transcriptome  of chromosome XII disomic yeast strain


title: D11-2

description:
Disomic yeast strain
D11.2

source_name: transcriptome  of chromosome XI disomic yeast strain, evolved line 2


title: ESC_noDox_Day6_1 (1)

value: ESC AGO1-4-/- (called NoDOX)


title: argB_6 day starvation vs. day 0 replicate 3

description: Biological replicate 3 of 3

source_name: Mtb [delta]argB _6.3

source_name: Mtb [delta]argB _0.3


title: argB_6 day starvation vs. day 0 replicate 1

description: Biological replicate 1 of 3

source_name: Mtb [delta]argB _0.1

source_name: Mtb [delta]argB _6.1


title: USCF136

type: genomic

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

description: Miniature Schnauzer

hyb_protocol: Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).

data_processing:
Illumina Genome Studio (GSGT Version 1.9.4) was used to perform genotype calling to obtain the Final Report file.
Column headers for the  file "USCF_30JUN18_FinalReport.txt" are: SNP Name, Sample ID, Allele 1   Forward, Allele 2   Forward, Allele 1   Top, Allele 2   Top, Allele 1   AB, Allele2   AB, GC Score, X, Y.  This file contains the rawest form of the data available for this data set.
Processed data file includes: Genotype: AA,AB,BB,or NC (no call) and GC_score.

label: Cy3, Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Whole blood

extract_protocol: EDTA-stabilized whole blood or tissue was collected from the Australian Cattle Dogs and Miniature Schnauzers. Genomic DNA was extracted using the illustra Nucleon BACC 2 kit using the manufacturer's recommended protocols (GE Healthcare). This study was conducted with approval from the Animal Ethics Committee at the University of Sydney (approval number N00/9 2009/3/5109 and N00/10-2012/3/5837).

tag: tissue

value: Whole blood

tag: gender

value: female

tag: breed

value: Miniature Schnauzer


title: D11-1

description:
Disomic yeast strain
D11.1

source_name: transcriptome  of chromosome XI disomic yeast strain, evolved line 1


title: argB_3 day starvation vs. day 0 replicate 3

description: Biological replicate 3 of 3

source_name: Mtb [delta]argB _3.3


title: argB_6 day starvation vs. day 0 replicate 2

description: Biological replicate 2 of 3

source_name: Mtb [delta]argB _6.2

source_name: Mtb [delta]argB _0.2


title: D10-3

description:
Disomic yeast strain
D10.3

source_name: transcriptome  of chromosome X disomic yeast strain, evolved line 3


title: D11

description:
Disomic yeast strain
D11.a

source_name: transcriptome  of chromosome XI disomic yeast strain


title: USCF134

description: Miniature Schnauzer

scan_protocol: Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).

value: male


title: argB_1 day starvation vs. day 0 replicate 2

description: Biological replicate 2 of 3

source_name: Mtb [delta]argB _1.2


title: argB_3 day starvation vs. day 0 replicate 2

description: Biological replicate 2 of 3

source_name: Mtb [delta]argB _3.2


title: USCF301

description: Miniature Schnauzer

label_protocol: Samples were genotyped at 173,650 SNP loci on the CanineHD BeadChip array (Illumina) by GeneSeek (Lincoln, NE).


title: argB_1 day starvation vs. day 0 replicate 3

description: Biological replicate 3 of 3

source_name: Mtb [delta]argB _1.3


title: argB_3 day starvation vs. day 0 replicate 1

description: Biological replicate 1 of 3

source_name: Mtb [delta]argB _3.1


title: D10-2

description:
Disomic yeast strain
D10.2

source_name: transcriptome  of chromosome X disomic yeast strain, evolved line 2


title: argB_1 day starvation vs. day 0 replicate 1

description: Biological replicate 1 of 3

source_name: Mtb [delta]argB _1.1


title: USCF138

description: Miniature Schnauzer


title: Replicate 1: LIX50 versus LIX49

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.(Gene based analysis was performed).

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies). Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The recombinant H37Ra and H37Rv strains were cultivated in Middlebrook 7H9 medium supplemented with 0.05% Tween 80 and 10% ADS (0.5% albumin, 0.2% dextrose, 0.085% Saline) (7H9T medium) or on Middlebrook 7H10 agar plates at 37ºC to an OD600 ~0.2-0.3

extract_protocol: Total RNA was extracted using TRI reagent (Ambion) following the manufacturers instructions.

treatment_protocol: integrative plasmid pJFR19-devR (Hyg resistant) was electroporated in H37Ra and H37Rv to yield LIX48 and LIX50 strain respectively. Empty vector pJFR19 was electroporated into H37Ra and H37Rv to yield the respective control strains named here LIX47 and LIX49 respectively

tag: strain/genotype

value: empty vector control strain

value: H37Ra devR overexpressing strain


title: USCF1293

description: Australian Cattle Dog

value: Australian Cattle Dog


title: Replicate 2: LIX50 versus LIX49 (Dye Swap)

source_name: H37Rv19_ control_R3


title: Replicate 2: LIX48 versus LIX47 (Dye Swap)

source_name: H37Ra85_DevR _R3

source_name: H37Ra19 control_R3


title: H2-8Y_H2O2_30min_rep2

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

hyb_protocol: Microarray samples were hybridized and washed according to the manufacturer's instructions for two color eukaryotic microarrays.

scan_protocol: Slides were scanned with an GenePix 4100A GenePix reader and PMT was equal to 600 for both dye channels.

data_processing: Data were normalized using the LOWESS algorithm and analyzed for statistical significance using the MeV package.

organism: Nakaseomyces glabratus

source_name: H2-8Y, adaptive mutant with improved H2O2 tolerance, challenged with H2O2 for 30min

label_protocol: RNA was converted to amino-allyl cDNA using Superscript III RT, purified by ethanol precipitation, and resuspended in dye coupling buffer. Cy3 and Cy5 were utilized to label the experimental samples and reference as specified by GE Healthcare.

growth_protocol: Growth in YNB medium supplied with 2% (w/v) dextrose.

extract_protocol: After the challenge with H2O2, cultures were then harvested with rapid filtration and resuspended in RNALater to stop RNA degradation. The ZR Fungal/Bacterial RNA MiniPrep kit was used to extract pure RNA for subsequent analysis.

treatment_protocol: When OD600 reaches between 0.4 and 0.6, cells were subjected to 1 mM of H2O2 for 30 minutes at 30°C.

value: Adaptive mutant

tag: tag

value: YFP

tag: treatment

value: H2O2 for 30min

source_name: MHCg-Y, unevolved parent strain, challenged with H2O2 for 30min

value: Parental

tag: sample type

value: Reference


title: D10

description:
Disomic yeast strain
D10.a

source_name: transcriptome  of chromosome X disomic yeast strain

value: Disomes


title: H2-18Y_H2O2_30min_rep1

source_name: H2-18Y, adaptive mutant with improved H2O2 tolerance, challenged with H2O2 for 30min


title: H2-8Y_H2O2_30min_rep1


title: H2-22Y_H2O2_30min_rep2

source_name: H2-22Y, adaptive mutant with improved H2O2 tolerance, challenged with H2O2 for 30min


title: USCF1292

description: Australian Cattle Dog

source_name: Whole blood


title: D9-2

description:
Disomic yeast strain
D9.2

source_name: transcriptome  of chromosome IX disomic yeast strain, evolved line 2


title: D9

description:
Disomic yeast strain
D9.a

source_name: transcriptome  of chromosome IX disomic yeast strain


title: D9-1

description:
Disomic yeast strain
D9.1

source_name: transcriptome  of chromosome IX disomic yeast strain, evolved line 1


title: D8-3

description:
Disomic yeast strain
D8.3

source_name: transcriptome  of chromosome VIII disomic yeast strain, evolved line 3


title: H2-18Y_H2O2_30min_rep2


title: Input_RNC1-R1

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

country: France

institute: INRA/CNRS

description:
Input DNA
Input*R1 for all HxKx*R1 processed files

library_source: genomic

data_processing:
alignment using glint software with parameters glint map --best-score --mmis 3 --lrmin 80
Detection of H3K9Ac and  H3K9me2 narrow peaks was performed using MACS2 software (version :2.1.1.20160309, method : callpeak, custom parameters : --shift 100 --extsize 200) .
Identification of H3K27me3 broad domains was done with SICER software (version :1.1, parameters :redundancy threshold=1;window size=200;fragment size=150;effective genome fraction=0.860794380127;gap size=600;FDR=0.01 )
Supplementary_files_format_and_content: .narrowPeak.bed

organism: Medicago truncatula

growth_protocol: Aeroponic caisson

extract_protocol:
After plant material fixation in 1% (v/v) formaldehyde, tissues were homogenized, nuclei isolated and lysed. Cross-linked chromatin was sonicated using a Covaris S220 (PIP: 175W, DF: 20%, DPB: 200, time: 10min). Protein/DNA complexes were immunoprecipitated with antibodies, overnight at 4°C with gentle shaking, and incubated for 1h at 4°C with 50 µL of Dynabeads Protein A (Invitrogen, Ref. 100-02D). the beads were wash 2 x 5 min in ChIP Wash Buffer 1 (0.1% SDS, 1% Triton X-100, 20mMTris-HCl pH 8, 2 mM EDTA pH 8, 150 mMNaCl), 2 x 5 min in ChIP Wash Buffer 2 (0.1% SDS, 1% Triton X-100, 20 mMTris-HCl pH 8, 2 mM EDTA pH 8, 500 mMNaCl), 2 x 5 min in ChIP Wash Buffer 3 (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 10 mMTris-HCl pH 8,1 mM EDTA pH 8) and twice in TE (10 mMTris-HCl pH 8, 1 mM EDTA pH 8). ChIPed DNA was eluted by two 15-min incubations at 65°C with 250µL Elution Buffer (1% SDS, 0.1 M NaHCO3). Chromatin was reverse-crosslinked by adding 20µL of NaCl 5M and incubated over-night at 65°C. Reverse-cross-linked DNA was submitted to RNase and proteinase K digestion, and extracted with phenol-chloroform. DNA was ethanol precipitated in the presence of 20µg of glycogen and resuspended in 20µL of nuclease-free water (Ambion) in a DNA low-bind tube.
10 ng of IP or input DNA was used for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer recommendations. For all libraries, eleven cycles of PCR were used. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent), and the libraries were subjected to high-throughput sequencing by NextSeq 500 (Illumina).

treatment_protocol: non nitrogen-starved root systems, harvested after 14 days in caisson, frozen in liquid nitrogen and sent in dry ice from LIPM to IPS2

value: jemalong A17

tag: antibody


title: D8-2

description:
Disomic yeast strain
D8.2

source_name: transcriptome  of chromosome VIII disomic yeast strain, evolved line 2


title: Input_Nodules-R2

description:
Input DNA
Input*R2 for  HxKx*R2 processed files

treatment_protocol: nitrogen starvation after 7 days, 4 days of N starvation before S. meliloti 2011 inoculation, nodules harvested at 10 dpi, frozen in liquid nitrogen and sent in dry ice from LIPM to IPS2


title: D8-1

description:
Disomic yeast strain
D8.1

source_name: transcriptome  of chromosome VIII disomic yeast strain, evolved line 1


title: H2-22Y_H2O2_30min_rep1


title: Input_Nodules-R1


title: H2-11G_H2O2_30min_rep2

source_name: H2-11G, adaptive mutant with improved H2O2 tolerance, challenged with H2O2 for 30min

value: GFP

source_name: MHCg-G, unevolved parent strain, challenged with H2O2 for 30min


title: H2-11G_H2O2_30min_rep1


title: D10-1

description:
Disomic yeast strain
D10.1

source_name: transcriptome  of chromosome X disomic yeast strain, evolved line 1


title: H3K27me3_RNC1-R1_1

description:
ChIP assays were performed using anti-H3K27me3 (Millipore, ref. 07-449), using a procedure adapted from Veluchamy et al.
H3K27me3_RNC1-R1_W200-G600-FDR0.01-island.bed


title: USCF1294

description: Australian Cattle Dog

value: not determined


title: D8

description:
Disomic yeast strain
D8.a

source_name: transcriptome  of chromosome VIII disomic yeast strain


title: D9-3

description:
Disomic yeast strain
D9.3

source_name: transcriptome  of chromosome IX disomic yeast strain, evolved line 3


title: D5-2

description:
Disomic yeast strain
D5.2

source_name: transcriptome  of chromosome V disomic yeast strain, evolved line 2


title: D5-3

description:
Disomic yeast strain
D5.3

source_name: transcriptome  of chromosome V disomic yeast strain, evolved line 3


title: Replicate 1: LIX48 versus LIX47

source_name: H37Ra19 control_R2


title: Input_RNC1-R2


title: H3K27me3_Nodules-R2_1

description:
ChIP assays were performed using anti-H3K27me3 (Millipore, ref. 07-449), using a procedure adapted from Veluchamy et al.
H3K27me3_Nodules-R2_W200-G600-FDR0.01-island.bed


title: H3K27me3_Nodules-R1_1

description:
ChIP assays were performed using anti-H3K27me3 (Millipore, ref. 07-449), using a procedure adapted from Veluchamy et al.
H3K27me3_Nodules-R1_W200-G600-FDR0.01-island.bed


title: H3K9me2_RNC1-R1_2

description:
ChIP assays were performed using anti-H3K9me2 (Abcam, ref. ab1220), using a procedure adapted from Veluchamy et al.
H3K9me2_RNC1-R1_peaks.narrowPeak.bed


title: H3K9me2_RNC1-R1_1


title: D5

description:
Disomic yeast strain
D5.a

source_name: transcriptome  of chromosome V disomic yeast strain


title: D2-3

description:
Disomic yeast strain
D2.3

source_name: transcriptome  of chromosome II disomic yeast strain, evolved line 3


title: H3K9me2_Nodules-R1_1

description:
ChIP assays were performed using anti-H3K9me2 (Abcam, ref. ab1220), using a procedure adapted from Veluchamy et al.
H3K9me2_Nodules-R1_peaks.narrowPeak.bed


title: H3K9me2_Nodules-R1_2


title: H3K27me3_RNC1-R2_1

description:
ChIP assays were performed using anti-H3K27me3 (Millipore, ref. 07-449), using a procedure adapted from Veluchamy et al.
H3K27me3_RNC1-R2_W200-G600-FDR0.01-island.bed


title: RNA-seq 14 hpO Uninjected rep1

city: Beijing

first: Xiaotong

last: Wu

address: No. 1 Shuangqing Road, Haidian District

country: China

institute: Tsinghua University

data_processing:
RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads.
The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic.
RNA-seq signal were normalized using RPM (reads per million of mapped reads)
Genome_build: danRer7
Supplementary_files_format_and_content: Bigwig for RNA-seq tracks

molecule: polyA RNA

organism: Danio rerio

source_name: RNA-seq 14 hpO Uninjected

growth_protocol: The operated females were transferred into fish water containing 32 µg/ml tricaine (Sigma), 10 units/ml penicillin and 10 µg/ml streptomycin (HyClone, SV30010) after OMIS for 3 hours, and then transferred into fish water containing 16 µg/ml tricaine, 10 units/ml penicillin and 10 µg/ml streptomycin for another 11 hours. And at 14 hours post OMIS, in order to disconnect the surrounding somatic cells from oocytes, oocytes were isolated from ovary into special medium(90% Leibovitz's L-15 medium(Gibco),pH9.0,0.5mg/ml BSA(Amresco))for zebrafish oocytes maturation in vitro at room temperature.

extract_protocol:
Total RNA of oocytes were purified using RNeasy Mini kit (QIAGEN, 74104) as recommended protocols
First stand cDNA was synthesized using a commercial kit (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014), MgCl2, DTT, dNTP, dUTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2-hour incubation on thermomixer at 16°C. Synthesized cDNA was subjected to library preparation. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat. N808-0096) at 37°C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase (NEB, Cat. M0530L). The amplified DNA was size selected using AMPure Beads for 200-500bp DNA fragments.

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 12 uninjected oocytes were isolated at the same time points from the other ovary of the same female with OMIS samples at 14 hours post OMIS. The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.

tag: strain

value: India

tag: Stage

value: Stage III

value: gamete;  oocytes

tag: time point

value: 14 hours post-OMIS (hpO)


title: RNA-seq 14 hpO OMIS rep2

source_name: RNA-seq 14 hpO OMIS

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 11 microinjected oocytes (still arrested at prophase I) were isolated from the ovary at 14 hours post-OMIS (hpO). The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: RNA-seq 14 hpO Uninjected rep2

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 11 uninjected oocytes were isolated at the same time points from the other ovary of the same female with OMIS samples at 14 hours post OMIS. The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: RNA-seq 14 hpO OMIS rep1

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 12 microinjected oocytes (still arrested at prophase I) were isolated from the ovary at 14 hours post-OMIS (hpO). The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: H3K9ac_RNC1-R2_1

description:
ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352), using a procedure adapted from Veluchamy et al.
H3K9ac_RNC1-R2_peaks.narrowPeak.bed


title: RNA-seq 5 hpO Uninjected rep1

source_name: RNA-seq 5 hpO Uninjected

growth_protocol: The operated females were transferred into fish water containing 32 µg/ml tricaine (Sigma), 10 units/ml penicillin and 10 µg/ml streptomycin (HyClone, SV30010) after OMIS. And at 5 hours post OMIS, in order to dsiconnect the surrounding somatic cells from oocytes, oocytes were isolated from ovary into special medium(90% Leibovitz's L-15 medium(Gibco),pH9.0,0.5mg/ml BSA(Amresco))for zebrafish oocytes maturation in vitro at room temperature.

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 15 uninjected oocytes were isolated at the same time points from the other ovary of the same female with OMIS samples at 5 hours post OMIS. The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.

value: 5 hours post-OMIS (hpO)


title: D2

description:
Disomic yeast strain
D2.a

source_name: transcriptome  of chromosome II disomic yeast strain

tag: ploidy


title: D2-1

description:
Disomic yeast strain
D2.1

source_name: transcriptome  of chromosome II disomic yeast strain, evolved line 1

tag: background genetic strain


title: H3K9ac_RNC1-R1_2

description:
ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352), using a procedure adapted from Veluchamy et al.
H3K9ac_RNC1-R1_peaks.narrowPeak.bed


title: RNA-seq 5 hpO OMIS rep2

source_name: RNA-seq 5 hpO OMIS

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 11 microinjected oocytes (still arrested at prophase I) were isolated from the ovary at 5 hours post-OMIS (hpO). The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: H3K9ac_RNC1-R1_1


title: D1-3

description:
Disomic yeast strain
D1.3

source_name: transcriptome  of chromosome I disomic yeast strain, evolved line 3


title: RNA-seq 5 hpO OMIS rep1

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 15 microinjected oocytes (still arrested at prophase I) were isolated from the ovary at 5 hours post-OMIS (hpO). The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: RNA-seq 14 hpO OMIS rep3


title: H3K9ac_Nodules-R2_1

description:
ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352), using a procedure adapted from Veluchamy et al.
H3K9ac_Nodules-R2_peaks.narrowPeak.bed


title: D5-1

description:
Disomic yeast strain
D5.1

source_name: transcriptome  of chromosome V disomic yeast strain, evolved line 1


title: D1-2

description:
Disomic yeast strain
D1.2

source_name: transcriptome  of chromosome I disomic yeast strain, evolved line 2


title: H3K9ac_Nodules-R1_2

description:
ChIP assays were performed using anti-H3K9ac (Millipore, ref. 07-352), using a procedure adapted from Veluchamy et al.
H3K9ac_Nodules-R1_peaks.narrowPeak.bed


title: D1-1

description:
Disomic yeast strain
D1.1

source_name: transcriptome  of chromosome I disomic yeast strain, evolved line 1


title: H3K9ac_Nodules-R1_1


title: D1

description:
Disomic yeast strain
D1.a

source_name: transcriptome  of chromosome I disomic yeast strain


title: D2-2

description:
Disomic yeast strain
D2.2

source_name: transcriptome  of chromosome II disomic yeast strain, evolved line 2


title: RNA-seq 5 hpO Uninjected rep2

treatment_protocol: Following OMIS with rhodamine B in the afternoon, 11 uninjected oocytes were isolated at the same time points from the other ovary of the same female with OMIS samples at 5 hours post OMIS. The surrounding somatic cells of these oocytes were separated carefully by tweezers in a specific medium for culturing zebrafish oocytes.


title: H3K27me1_RNC1-R1_2

description:
ChIP assays were performed using anti-H3K27me1 (Millipore, ref. 07-448), using a procedure adapted from Veluchamy et al.
H3K27me1_RNC1-R1_peaks.narrowPeak.bed


title: H3K27me1_RNC1-R2_1

description:
ChIP assays were performed using anti-H3K27me1 (Millipore, ref. 07-448), using a procedure adapted from Veluchamy et al.
H3K27me1_RNC1-R2_peaks.narrowPeak.bed


title: H3K27me1_RNC1-R1_1


title: H3K27me1_Nodules-R2_1

description:
ChIP assays were performed using anti-H3K27me1 (Millipore, ref. 07-448), using a procedure adapted from Veluchamy et al.
H3K27me1_Nodules-R2_peaks.narrowPeak.bed


title: H3K27me1_Nodules-R1_2

description:
ChIP assays were performed using anti-H3K27me1 (Millipore, ref. 07-448), using a procedure adapted from Veluchamy et al.
H3K27me1_Nodules-R1_peaks.narrowPeak.bed


title: H3K27me1_Nodules-R1_1


title: PC3 SPINK3

status: Public on Aug 30 2018

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: sunyu_prostate_cellines_drugVswt.isoform.FPKM.txt

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: Prostate cancer cells

growth_protocol: Prostate cancer cells were routinely cultured and passaged (typically 0.5–1 × 106 cells in a T25 flask) in DMEM supplemented with 10% FBS.

extract_protocol:
At the end of cell coculture, media were removed, cells were lysed with Trizol reagent and total RNA was harvested. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101, RS-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Upon 80% confluency, cells were treated with conditioned media collected from control PSC27 cells or SPINK1-overexpressing PSC27 cells for consecutive 3 days.

tag: source

value: Derived from the metastatic site, bone of a prostate cancer patient

tag: type

value: Grade Iv, Adenocarcinoma

tag: culture

value: SPINK1+ stromal cell media


title: PC3 SPINK2


title: PC3 control 03

value: control media


title: PC3 control 01


title: PC3 SPINK1


title: PC3 control 02


title: DU145 SPINK2

value: Derived from the metastatic site, brain of a prostate cancer patient

value: Carcinoma


title: GROUP3 (SW480CSCs-NC)

city: Zunyi

first: Kunming

last: Wen

address: 149 DaLian Road, Zunyi, Guizhou 563000, People's Republic of China

institute: The Affiliated Hospital of Zunyi Medical University

hyb_protocol: 200 ng of purified total RNA was taken for the experiment. Using Agilent's miRNA Complete Labeling and Hyb Kit, the main steps include:1) Dephosphorylation, removal of the 5'-end phosphate group of RNA using the alkaline phosphatase CIP in the kit.2) Label the reaction, and connect Cyanine3-pCp to the 3' end of RNA using T4 RNA ligase in the kit. The reaction efficiency is >90%.3) The labeled reaction product is concentrated and drained.4) Hybrid overnight in an Agilent hybridization oven.

scan_protocol: After the hybridization, the solution was washed with 0.2% SDS, 2×SSC in the washing solution for 5 min at 42 °C, and then washed in 0.2×SSC lotion II for 5 min, and the slide was dried and used for scanning.The washed chip was scanned using an Agilent chip scanner (G2565CA) to obtain a hybrid image

data_processing: First, the hybrid image was analyzed and extracted using Agilent Feature Extraction (v10.7) software; then the data was normalized using Agilent GeneSpring software, and the difference analysis between groups was performed using GeneSpring software, such as T-test method. Two groups of differentially expressed genes were analyzed; ANOVA method was used to perform differential analysis of multiple groups of genes.

label_protocol: Total RNA was purified using the mirVanaTM miRNA Isolation Kit (AM1561). Re-quantify after purification.

growth_protocol: SW480 cell lines was grown in Leibovitz’ L-15 medium (M&C GENE TECH, China), supplemented with 10% fetal bovine serum (FBS) (Gibco, Australia) and maintained at 37°C in a humidified atmosphere; SW480CSCs were obtained by suspension culture of SW480 parental cells; SW480CSCs-NC group was transfected into NC-GFP-LV;SW480CSCs-OCT4B1-shR group was transfected into OCT4B1-shRNA-LV.

extract_protocol: 1. Total RNA from cell samples was extracted by Trizol method(Invitrogen p/n 15596-026), quantified by spectrophotometer, and the quality of total RNA detected by formaldehyde denaturing gel electrophoresis. 2. Purification of qualified total RNA3. Dephosphorylation and labeling of total RNA, 4. Chip cleaning and scanning 5. Data extraction and analysis

treatment_protocol: SW480CSCs-NC group was transfected into NC-GFP-LV; SW480CSCs-OCT4B1-shR group was transfected into OCT4B1-shRNA-LV.

tag: cell type

value: Human colorectal cells

tag: cell line

tag: transfection

value: NC-GFP-LV


title: GROUP1 (SW480 parental cell)

source_name: SW480 parental cells


title: DU145 control 02


title: BH13-rep2

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 5 ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. Subsequently, the samples were immediately hybridized onto  Agilent Yeast Oligo Microarray (V2) 8x15K G4813 in a rotating Agilent hybridization oven at 65 °C for 17 h.

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed using Feature Extraction Software 9.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Log-phase rep2

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

growth_protocol: Growth in Yeast Minimal Medium at 30 ºC and 150 rpm until log phase (OD600 ~1.0)

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturer’s instructions.  RNA quality based on Integrity Numbers (RIN) was checked with Agilent 2100 Bioanalyzer.  RNA samples with RIN values > 8 were used in the microarray analysis

treatment_protocol: No treatment

tag: genotype

value: mutant strain BH13


title: GROUP4 (SW480CSCs-OCT4B1-shR)


title: DU145 control 03


title: DU145 control 01


title: BH13-rep1

source_name: Log-phase rep1


title: BH13-rep3

source_name: Log-phase rep3


title: ML-1 without treatment,  biological rep2

city: Taipei

first: Ming-Hsun

last: Tsai

address: Rm513, No 1, Sec 1, Jen-Ai Rd

department: Graduate Institute of Immunology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from ML-1 cells

hyb_protocol: Samples were hybridized with GeneChip Mouse Clariom S Array  (Affymetrix) and scanned at the NHRI Microarray Core Facility.

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

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: biotin

source_name: ML-1 cell

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Wild-type/ PLS2KO ML-1 cells were cultured in DMEM containing 10% FBS and 50 μg/ml Gentamicin.

extract_protocol: RNA was extracted by TRIsure reagent according to manufacturer's instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with mouse IFN-α4 (1000U/ml) for 6h

value: Immortalized hepatocyte

value: Wild-type

tag: agent

value: control


title: PLS2KO ML-1 with IFN-α4 for 6h,  biological rep1

description: Gene expression data from IFN-α4 treated PLSCR2 knockout ML-1 cells

source_name: PLS2KO ML-1 cells

value: PLSCR2 knockout


title: PLS2KO ML-1 with IFN-α4 for 6h,  biological rep2


title: ML-1 with IFN-α4 for 6h,  biological rep1

description: Gene expression data from IFN-α4 treated ML-1 cells


title: ML-1 with IFN-α4 for 6h,  biological rep2


title: PLS2KO ML-1 without treatment,  biological rep2

description: Gene expression data from PLSCR2 knockout ML-1 cells


title: DU145 SPINK1


title: PLS2KO ML-1 without treatment,  biological rep1


title: GROUP2 (SW480CSCs)

source_name: SW480CSCs (SW480 in suspension)


title: DU145 SPINK3


title: peripheralblood-31b

first: Yuqing

last: Song

address: No.51 Huayuan Beilu, Haidian District

institute: Institute of  Mental Health, Peking University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: Total RNA was extracted from fresh peripheral blood using the Trizol reagent (Invitrogen) according to the manufacturer's instructions and quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies)..

tag: tissue

value: whole blood

tag: disease state

value: normal control

tag: gender

value: male

tag: age


title: peripheralblood-30b

value: female


title: peripheralblood-32b


title: peripheralblood-20b


title: peripheralblood-19b


title: peripheralblood-28b


title: peripheralblood-15b


title: peripheralblood-21b


title: peripheralblood-12b


title: peripheralblood-29b


title: peripheralblood-10b


title: peripheralblood-24b


title: peripheralblood-13b


title: peripheralblood-14b


title: peripheralblood-2b


title: ML-1 without treatment,  biological rep1

description: Gene expression data from ML-1 cells


title: peripheralblood-22b


title: peripheralblood-3b


title: peripheralblood-17b


title: peripheralblood-25b


title: peripheralblood-9b


title: peripheralblood-16b


title: peripheralblood-5b


title: peripheralblood-18b


title: peripheralblood-4b


title: peripheralblood-6b


title: peripheralblood-7b


title: peripheralblood-11b


title: peripheralblood-8b


title: peripheralblood-32a

value: Obsessive-Compulsive Disorder


title: peripheralblood-23b


title: peripheralblood-1b


title: peripheralblood-30a


title: peripheralblood-25a


title: peripheralblood-21a


title: peripheralblood-28a


title: peripheralblood-20a


title: peripheralblood-29a


title: peripheralblood-22a


title: peripheralblood-31a


title: peripheralblood-23a


title: peripheralblood-18a


title: peripheralblood-11a


title: peripheralblood-15a


title: peripheralblood-17a


title: 661W P27 serum starved

city: Southampton

first: Gabrielle

last: Wheway

address: Tremona Road

department: Faculty of Medicine

country: United Kingdom

institute: University of Southampton

description: P27 serum starved

data_processing:
Raw reads from 4 lanes per sample (4 FASTQ files) were aligned to the mouse (Mus musculus) full genome (GRCm38, UCSC mm10) using STAR with UCSC mm10.gtf gene model for splice junctions
Merge BAM files
Using UCSC mm10.gtf file, raw gene counts were estimated on merged BAM files using HTSeq, using the union method and –stranded=reverse options
Differential gene expression was analysed using DESeq2
data processing step
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of raw counts from HTseq. Excel file of differential expression between cells grown in serum/serum starved, from DESeq2.

source_name: cells of passage 27, serum starved

growth_protocol: Cells were cultured in DMEM high glucose + 10% FCS at 37°C, 5% CO2, and split at a ratio of 1:5 once per week.

extract_protocol:
Total RNA was extracted using TRI reagent,  samples treated with Dnase, and cleaned on an RNA clean and concentrate column
Libraries were prepared using Illumina TruSeq Stranded mRNA kit, using polyA selection, chemically fragmented to about 200 nt in size and cDNA synthesized using random hexamer primers. Each individual library received a unique Illumina barcode.

treatment_protocol: Cells were seeded at a density of 1 x 10e5 cells per mL in DMEM high glucose + 10% FCS and grown at 37°C, 5% CO2 for 48 hours. At this point, media was either replaced with fresh DMEM high glucose + 10% FCS or DMEM high glucose without FCS, and cells grown for a further 72 hours.

tag: growth condition

value: serum starvation

tag: passage


title: peripheralblood-12a


title: peripheralblood-13a


title: peripheralblood-9a


title: peripheralblood-10a


title: peripheralblood-19a


title: peripheralblood-6a


title: peripheralblood-3a


title: 661W P27

source_name: cells of passage 27, grown in complete media

value: complete media


title: peripheralblood-1a


title: peripheralblood-8a


title: 661W P26

source_name: cells of passage 26, grown in complete media


title: peripheralblood-7a


title: peripheralblood-4a


title: peripheralblood-5a


title: 661W P24 serum starved

description: P24 serum starved

source_name: cells of passage 24, serum starved


title: peripheralblood-14a


title: F8R6

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

country: Canada

institute: Center for Addiction and Mental Health

description: Pool of 125 cells captured using Laser Capture Microscopy

data_processing:
Sequence reads were aligned to Grcm38 reference genome using Hisat2 Aligner
The bam files generated used  generate counts data using the RNAseq work flow from bioconductor
Genome_build: Grcm38
Supplementary_files_format_and_content: tab-delimited text files include count values for each feature/gene across all samples

source_name: PYC Neurons

extract_protocol:
Fresh frozen tissue were section to 14um thickness and mounted on PEN membrane slite. After staning for PYC, PV, SST and VIP neuron (using Slc17a7, Pvalb,Sst and Vip markers respectively) 125 cells for each cell types were picked using laser capture microscopy and the total RNA was extracted using Picopure RNA isolation kit, Applied biosystem, KIT0204)
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq pico input kit (Clontech Laboratories, Cat.No.635007)

tag: strain

value: Brain Frontal Cortex

tag: age in months

value: Old 22 months


title: F8R9

source_name: SST Neurons

value: Young 2 months


title: F8R8

source_name: VIP Neurons


title: F8R7


title: 661W P26 serum starved

description: P26 serum starved

source_name: cells of passage 26, serum starved


title: 661W P24

source_name: cells of passage 24, grown in complete media


title: F8R5


title: F8R3


title: F8R4


title: peripheralblood-16a


title: F8R12

source_name: PV Neurons


title: F8R2


title: F8R11


title: F8R10


title: F8R1


title: F7R8


title: F7R9


title: F7R7


title: F7R2


title: F7R5


title: F7R4


title: F7R12


title: F6R9


title: F7R11


title: F7R10


title: F6R8


title: F6R7


title: F6R5


title: F7R1


title: F6R6


title: F6R11


title: F6R4


title: F6R2


title: F5R9


title: F6R1


title: F5R8


title: F6R10


title: F6R3


title: F5R7


title: F5R6


title: F7R6


title: F5R4


title: F5R5


title: F7R3


title: F5R3


title: F5R2


title: F6R12


title: F4R8


title: F5R12


title: F4R9


title: F4R5


title: F4R6


title: F4R2


title: F5R1


title: F4R12


title: F5R10


title: F4R10


title: F4R3


title: F4R4


title: F3R9


title: F3R8


title: F3R5


title: F3R6


title: F3R7


title: F3R4


title: F3R3


title: F3R2


title: F3R11


title: F3R12


title: F5R11


title: F4R7


title: F3R1


title: F3R10


title: F4R11


title: F2R8


title: F2R4


title: F2R7


title: F2R3


title: F4R1


title: F2R11


title: F2R10


title: F2R5


title: F2R1


title: F1R12


title: F2R2


title: Pons_3

city: New York

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

description: Standard sample

data_processing:
Adaptor sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed from reads using Trimmomatic 0.36
Trimmed reads were mapped using STAR 2.5.3a to the Ensembl mouse genome GRCm38.p5, release 90
Mapped reads were normalized to the total number of reads per sample (counts per million)
Genome_build: GRCm38.p5, release 90
Supplementary_files_format_and_content: STAR 2.5.3a quantification output, expressed as counts and normalized to counts per million

source_name: Labelled cells from ALM

growth_protocol: C57BL mice (~P56), with injections of rAAV2-retro in 4 targeted regions (Thalamus, IRN in medulla, superior colliculus, and pons)

extract_protocol:
For each sample, 50-120 labelled cells were isolated by manual cell sorting on a fluorescence dissecting scope, following micro-dissection, trituration and enzymatic digestion. Following pooling and lysis, total RNA was extracted by Picopure kit (KIT0204; Thermo-Fisher)
Amplified DNA was produced using Ovation RNA-seq System V2 kit (#7102; NuGEN), fragmented to ~200bp, ligated to Illumina sequencing adaptors with Encore Rapid kit (#0314; NuGEN), and sequenced on an Illumina HiSeq 2500 with 4-fold multiplexing (single end, 100bp read length)

tag: mouse strain

tag: virus

tag: fluorescent reporter

value: GFP

tag: injection site

value: Pons


title: Pons_2

description: Standard sample


title: Pons_1

description: Standard sample


title: Superior_Colliculus_3

description: Standard sample


title: Medulla_6

description: Standard sample

value: tdtomato

value: Medulla


title: Thalamus_6

description: Standard sample

value: Thalamus


title: Superior_Colliculus_1

description: Standard sample


title: Superior_Colliculus_2

description: Standard sample


title: Medulla_5

description: Standard sample


title: Thalamus_5

description: Standard sample


title: Medulla_4

description: Standard sample


title: F2R9


title: Thalamus_4

description: Standard sample


title: Thalamus_3

description: Standard sample


title: Thalamus_2

description: Standard sample


title: Medulla_3

description: Standard sample


title: Medulla_Outlier

description: Identified as outlier based on post-hoc Principal Component Analysis


title: Thalamus_1

description: Standard sample


title: Thalamus_Outlier


title: peripheralblood-2a


title: Medulla_1

description: Standard sample


title: Dppa2/4_OE_D11_GFPminus_Thy1minus_SSEA1minus

city: NEW HAVEN

first: Zheng

last: Wang

state: Connecticut

address: 10 amistad street, yale stem cell center, yale stem cell center

department: genetics

institute: YALE UNIVERSITY

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 11,GFPminus_Thy1minus_SSEA1minus

data_processing:
The reads were trimmed for quality and aligned to the mm10 genome using TopHat2.  The FPKM matrices were generated using cuffdiff and cummeRbund.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM Matrix

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Primary MEFs were isolated from 14-15dpc embryos. Prior to lentiviral transduction, cells were cultured in DMEM supplemented with L-glutamine, Na-pyruvate, β-Mercaptoethanol, Penicilin-Streptomycin and 10% FBS for one or two passages. Reprogramming was performed in DMEM supplemented with L-glutamine, Na-pyruvate, β-mercaptoethanol, penicilin-streptomycin, 15% ESC-grade FBS and 103units/ml of ESGRO (Millipore). Doxycyclin (Dox) was added at concentration 1μg/ml.

extract_protocol:
Total RNA was isolated using Trizol, treated with DNAse I (Ambion) to remove genomic DNA, extracted with phenol:chloroform (1:1), precipitated and diluted in water
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 ug/ml Doxycyclin were applicable.

value: Mouse Embryonic Fibroblasts

tag: media

tag: media supplement

value: 1μg/ml Doxycyclin

tag: treatment days


title: Dppa2/4_OE_D14_GFPminus_Thyminus_SSEA1plus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 14,GFPminus_Thyminus_SSEA1plus

tag: genotype

value: DMEM supplemented with L-glutamine, Na-pyruvate, β-mercaptoethanol, penicilin-streptomycin, 15% ESC-grade FBS and 103units/ml of ESGRO (Millipore)


title: Dppa2/4_OE_D8_GFPplus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 8,GFPplus


title: Dppa2/4_OE_D8_GFPminus_Thy1minus_SSEA1plus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 8,GFPminusThy1minusSSEA1plus


title: Dppa2/4_OE_D8_GFPminus_Thy1plus_SSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 8,GFPminus_Thy1plus_SSEA1minus


title: Dppa2/4_OE_D14_GFPminus_Thyplus_SSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 14,GFPminus_Thyplus_SSEA1minus


title: Dppa2/4_OE_D11_GFPminus_Thy1minus_SSEA1plus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 11,GFPminus_Thy1minus_SSEA1plus


title: Dppa2/4_OE_D11_GFPplus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 11,GFPplus


title: Dppa2/4_OE_D4_Thy1plusSSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 4,Thy1plusSSEA1minus


title: Dppa2/4_OE_D2_Thy1plusSSEA1plus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 2,Thy1plusSSEA1plus


title: Dppa2/4_OE_D4_Thy1plusSSEA1plus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 4,Thy1plusSSEA1plus


title: Dppa2/4_OE_D2_Thy1plusSSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 2,Thy1plusSSEA1minus


title: Dppa2/4_OE_D4_Thy1minusSSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 4,Thy1minusSSEA1minus


title: Dppa2/4_OE_D2_Thy1minusSSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 2,Thy1minusSSEA1minus


title: Medulla_2

description: Standard sample


title: Control_OE_D14_GFPplus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 14,GFPplus


title: Dppa2/4_OE_D2_rtTA-MEF

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 1

value: Rosa26-rtTA+/-; Oct4-GFP+/-


title: ES-WT

city: Suita

first: Ayumu

last: Asai

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

description: Sample 1

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned to GRCm.38 using CLC genomics workbench 9.0.
Data were quantified by TPM.
Genome_build: GRCm.38
Supplementary_files_format_and_content: csv file was listed quantified data of each sample.

source_name: v6.5 Mouse embryonic stem cells

extract_protocol:
Isogen (Nippon gene)
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero Kit (Illumina)

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: WT


title: ES-T29I

description: Sample 2


title: Dppa2/4_OE_D14_GFPplus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 14,GFPplus

tag: tissue


title: Dppa2/4_OE_D14_GFPminus_Thyminus_SSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 14,GFPminus_Thyminus_SSEA1minus


title: Control_OE_D14_GFPminus_Thy1plus_SSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 14,GFPminusThy1plusSSEA1minus


title: Control_OE_D14_GFPminus_Thy1minus_SSEA1plus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 14,GFPminusThy1minusSSEA1plus


title: Control_OE_D11_GFPplus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 11,GFPminusThy1minusSSEA1plus


title: Control_OE_D11_GFPminus_Thy1plus_SSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 11,GFPminusThy1plusSSEA1minus


title: Control_OE_D11_GFPminus_Thy1minus_SSEA1plus


title: Control_OE_D8_GFPminus_Thy1plus_SSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 8,GFPminusThy1plusSSEA1minus


title: Control_OE_D11_GFPminus_Thy1minus_SSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 11,GFPminusThy1minusSSEA1minus


title: Dppa2/4_OE_D8_GFPminus_Thy1minus_SSEA1minus

description: RNA-Seq from Dppa2/4 overexpression OSKM-rtTA MEF, day 8,GFPminusThy1minusSSEA1minus


title: Control_OE_D8_GFPminus_Thy1minus_SSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 8,GFPminusThy1minusSSEA1minus


title: Control_OE_D4_Thy1minusSSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 4,Thy1minusSSEA1minus


title: Control_OE_D8_GFPminus_Thy1minus_SSEA1plus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 8,GFPminusThy1minusSSEA1plus


title: Control_OE_D2_rtTA-MEF

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 1


title: Control_OE_D2_Thy1minusSSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 2,Thy1minusSSEA1minus


title: R_Dppa2-4_OE_InputS_ChIP

description: Input DNA from Dppa2/4 overexpression OSKM Reprogramming cells

data_processing:
Reads were mapped to the mm10 build of the mouse genome with Bowtie2 (version Bowtie2_2.2.9) with flag --local
Mapped reads were indexed and sorted with samtools 1.5
Peaks were called with MACS2 (version  2.1.1.20160309 ) with the options -g 1.87e9 -f BAMPE.
Intersection and merging between peaks were performed using BEDTools (version 2.27.1)
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak file generated by macs2

source_name: Mouse Reprogramming Embryonic Fibroblasts with Overexpression of OSKM

extract_protocol:
5-10x106 cells were cross-linked with 1% paraformaldehyde for 10 min and stopped by adding Glycine (to be 125 mM). The cross-linked material was washed with buffer 1 (0.25% Triton, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH7.5) and Buffer 2 (200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH7.5) supplemented with protease inhibitor cocktail (Roche). Cell pellet was lysed in SDS lysis buffer (50 mM Tris pH 8.0, 10mM EDTA, 1% SDS, 50 mM PMSF) and was sonicated to generate 200 to 600 bp fragments. Fragmented chromatin was immunoprecipitated with magnetic beads coupled with 5 μg of antibody. The beads were washed with low salt buffer (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), high salt buffer (50 mM Tris pH 8.0, 500 mM NaCl, 0.1% SDS, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), LiCl wash buffer (50 mM Tris pH 8.0, 250 mM LiCl, 0.5% Deoxycholate, 1% NP40, 1 mM EDTA), Morohashi RIPA buffer (50mM Tris pH7.5, 150mM NaCl, 5mM EDTA, 0.5% NP40, 0.1% SDS), DOC/Triton Buffer (25mM Tris pH7.5, 150mM NaCl, 5mM EDTA, 1% Triton-X-100, 0.5% DOC) and Tris-EDTA buffer (10 mM Tris pH 8.0, 1 mM EDTA) for 10 min at 4 °C. Complexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3) for 2 h at 65 °C and reverse cross-linked for 6 h at 65°C. Reverse cross-linked DNA was purified by QIAquick PCR purification kit
ChIP DNA samples for sequencing were prepared as described for ChIP above. PCR cleanup with MinElute PCR Purification kits (Qiagen) yielded 20 μl  ChIP DNA which was used immediately in a 23.3 μl combined end repair and A-tailing reaction using a KAPA Hyper Prep Kit (Kapa Biosciences) for 30 minutes at 20°C followed by 30 minutes at 65°C. 10 μl of ligase buffer, 3.7 μl of Y-Adapters diluted 1:50 (Illumina 5179206) and 3.3 μl ligase (KAPA Hyper Prep Kit) were added and incubated at 20°C for 4 hours. Double-stranded DNA fragments were purified from this reaction using KAPA Pure Beads (Kapa Biosciences) and eluted in 22 μl 10 mM Tris pH8.0. The amplification cycle number was determined empirically by using 1 μl  of the eluent in a 10 μl  test reaction containing a 1:10,000 dilution of SYBR Green I (Invitrogen), 2x KAPA HotStart ReadyMix (Kapa KM2618  and custom barcoding primers. An appropriate number of cycles was used in a subsequent 50 μl reaction with the remaining eluent in the absence of SYBR Green. Libraries were size-selected on a 2% E-Gel EX agarose gel (Invitrogen) and fragments between 150 and 350 bp were extracted using a QIAEX II Gel Extraction Kit (Qiagen) performed at room temperature. Libraries were quantitated with a high sensitivity Qubit dsDNA HS Assay Kit (Invitrogen Q32854) and pooled prior to submission quality control analyses and next-generation sequencing.

value: DMEM supplemented with L-glutamine, Na-pyruvate, β-mercaptoethanol, penicilin-streptomycin, 15%  FBS and 1,000 units/ml of ESGRO (Millipore)

tag: antibody

tag: fixation strategy

value: formaldehyde

tag: sonication strategy

value: Covaris S220


title: R_Control_OE_InputS_ChIP

description: Input DNA from Control overexpression OSKM Reprogramming cells

value: Mouse Reprogramming Embryonic Fibroblasts with Overexpression of OSKM


title: Control_OE_D4_Thy1plusSSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 4,Thy1plusSSEA1minus


title: Control_OE_D2_Thy1plusSSEA1minus

description: RNA-Seq from control overexpression OSKM-rtTA MEF, day 2,Thy1plusSSEA1minus


title: R_Dppa2-4_OE_InputP_ChIP

value: no fixative

value: Micrococcal nuclease treatment


title: R_Dppa2-4_OE_H3K9me3_ChIP

description: H3K9me3 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: Abcam ab8898


title: peripheralblood-24a

value: whole blood

tag: disease state

value: Obsessive-Compulsive Disorder

tag: gender

value: female

tag: age


title: R_Dppa2-4_OE_H3K4me3_ChIP

description: H3K4me3 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

tag: strain

value: Millipore 07-473


title: R_Dppa2-4_OE_H3K27Ac_ChIP

description: H3K27Ac ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: Active Motif AM39135


title: R_Dppa2-4_OE_H3K4me1_ChIP

description: H3K4me1 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: 1μg/ml Doxycyclin

value: Abcam ab8895


title: R_Control_OE_H3K4me3_ChIP

description: H3K4me3 ChIP from Control overexpression OSKM Reprogramming cells


title: R_Dppa2-4_OE_H3K27me3_ChIP

description: H3K27me3 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: Cell Signaling Technology 9733


title: R_Control_OE_InputP_ChIP


title: R_Dppa2-4_OE_Dppa4_ChIP

description: Dppa4 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: R&D Systems AF3730


title: R_Control_OE_H3K9me3_ChIP

description: H3K9me3 ChIP from Control overexpression OSKM Reprogramming cells


title: R_Dppa2-4_OE_Dppa2_ChIP

description: Dppa2 ChIP from Dppa2/4 overexpression OSKM Reprogramming cells

value: Millipore MAB4356


title: R_Control_OE_H3K4me1_ChIP

description: H3K4me1 ChIP from Control overexpression OSKM Reprogramming cells

value: DMEM supplemented with L-glutamine, Na-pyruvate, β-mercaptoethanol, penicilin-streptomycin, 15%  FBS and 1,000 units/ml of ESGRO (Millipore)


title: mES_H3K4me1_ChIP

description: H3K4me1 ChIP from WT mouse embryonic stem cells

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: Wild type

value: formaldehyde


title: mES_H3K4me3_ChIP

description: H3K4me3 ChIP from WT mouse embryonic stem cells

value: Covaris S220


title: R_Control_OE_H3K27me3_ChIP

description: H3K27me3 ChIP from Control overexpression OSKM Reprogramming cells

value: Mouse Reprogramming Embryonic Fibroblasts with Overexpression of OSKM


title: R_Control_OE_H3K27Ac_ChIP

description: H3K27Ac ChIP from Control overexpression OSKM Reprogramming cells


title: mES_H3K27Ac_ChIP

description: H3K27Ac ChIP from WT mouse embryonic stem cells


title: R_Control_OE_Dppa4_ChIP

description: Dppa4 ChIP from Control overexpression OSKM Reprogramming cells


title: R_Control_OE_Dppa2_ChIP

description: Dppa2 ChIP from Control overexpression OSKM Reprogramming cells


title: MEF_Input_ChIP

description: Input DNA from WT MEF cells

value: Mouse Embryonic Fibroblasts

value: DMEM supplemented with L-glutamine, Na-pyruvate, β-mercaptoethanol, penicilin-streptomycin, 10%  FBS


title: MEF_Dppa4_OE_Input_ChIP

description: Input DNA from Dppa4 overexpression MEF cells

value: Rosa26-rtTA+/+; Oct4-GFP+/+


title: MEF_H3K27Ac_ChIP

description: H3K27Ac ChIP from WT MEF cells


title: mES_Dppa2_ChIP

description: Dppa2 ChIP from WT mouse embryonic stem cells


title: mES_Dppa4_ChIP

description: Dppa4 ChIP from WT mouse embryonic stem cells


title: MEF_Dppa2-4_OE_Input_ChIP

description: Input DNA from Dppa2-4 overexpression MEF cells


title: MEF_Dppa4_OE_Dppa4_ChIP

description: Dppa4 ChIP from Dppa4 overexpression MEF cells


title: MEF_Dppa2-4_OE_Dppa4_ChIP

description: Dppa4 ChIP from Dppa2-4 overexpression MEF cells


title: MEF_Dppa2_OE_Input_ChIP

description: Input DNA from Dppa2 overexpression MEF cells


title: MEF_Dppa2-4_OE_Dppa2_ChIP

description: Dppa2 ChIP from Dppa2-4 overexpression MEF cells


title: MEF_Dppa2_OE_Dppa2_ChIP

description: Dppa2 ChIP from Dppa2 overexpression MEF cells


title: MEF_Control_OE_Input_ChIP

description: Input DNA from Control overexpression MEF cells


title: MEF_Control_OE_Dppa4_ChIP

description: Dppa4 ChIP from Control overexpression MEF cells


title: mES_Input_ChIP

description: Input DNA from WT mouse embryonic stem cells


title: MEF_Control_OE_Dppa2_ChIP

description: Dppa2 ChIP from Control overexpression MEF cells


title: MEF H3K4me1_ChIP

description: H3K4me1 ChIP from WT MEF cells


title: Total foam cells from ApoE -/- aorta (Single cell RNA-seq)

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: Foam cells from aortas of  ApoE -/- mouse fed with western diet

extract_protocol:
The whole aorta was carefully isolated, and the perivascular fat was removed. Then the aortic tissue was cut into 2–5 mm pieces and incubated at 37°C for 70 min with gentle shaking in enzyme mixture containing DNase I (90 U/ml), collagenase I (675 U/ml), collagenase XI (187.5 U/ml), hyaluronidase (90 U/ml). Live CD45+ cells or foam cells (PI-BODIPY493/503hiSSChi)  were sorted out using BD FACSAriaIII.
The cells are resuspended in final concentration of 1000cells/µL in 1X PBS containing 0.04% BSA to minimize cell loss and aggregation. ~17,400 cells are partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum recovery of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3’ Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell is tagged with a unique 16bp 10x barcode and 10bp Unique Molecular Identifier. Full length cDNA is then amplified to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size (~400bp) for library construction. The final library is sequence ready and contains four unique sample indexes. The concentration of the 10x single cell library will be accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 platform (Illumina). 26x98nt read lengths are generated targeting 50,000 reads per cell.

tag: mouse genotype

value: ApoE -/-

value: Foam cells


title: Total leukocytes from Ldlr -/- aorta (Single cell RNA-seq)

source_name: Leukocytes from aortas of  Ldlr -/- mouse fed with western diet

value: Ldlr -/-

value: Cd45+ cells


title: MEF H3K27me3_ChIP

description: H3K27me3 ChIP from WT MEF cells


title: mES H3K27me3_ChIP

description: H3K27me3 ChIP from WT mouse embryonic stem cells


title: Yaf2KO2 RNAseq

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

data_processing:
Mapping reads with the reference genome use TopHat 2.0.12
Assemble reads use Cufflinks 2.2.1
Gene expression level analysis HTSeq 0.6.0
Alternative splicing prediction use Cuffcompare 2.2.1
Differential expression gene analysis use DEGSeq 1.18.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: ES cells were cultured with mouse embryonic fibroblasts (MEFs) inactivated with mitomycin-C in DMEM supplemented with15% fetal calf serum , leukemia inhibitory factor , L-glutamine , non-essential amino acids , 0.1 mM betamercaptoethanol , and penicillin/streptomycin. All ES cell lines were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair、A-tailing and adapter added were implemented. The aimed products were retrieved by agarose gel electrophoresis and PCR was performed, then the library was completed.

treatment_protocol: Yaf2 KO ES cells were generated by Cas9 technology.


title: MEF H3K4me3_ChIP

description: H3K4me3 ChIP from WT MEF cells

value: Millipore 07-473


title: Yaf2KO3 RNAseq


title: wildtype2 RNAseq

value: wild type


title: HiC_0h

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: HiC experiment

data_processing:
TADbit’s fragment based mapping module (aligning with GEM) with the default parameters was used to align reads. TADbit’s filtering module was used to filter out non-informative contacts (self-circle, dangling ends, extra-dangling ends, errors, duplicated and random breaks). PUBMED: TADbit (28723903) and GEM (26094690)
Contact matrices were obtained and poor bins (containing low counts) were filtered out using TADbit’s routines. Raw counts at 100Kb resolution are stored as tab-separated files with bin in first column, second bin as second column, and number of contacts as third column.
Genome_build: mm9
Supplementary_files_format_and_content: Format:
Raw interaction matrices per chromosome are included in the abc format, which has commented lines (start with a “#” character) and the actual interaction counts (one per line) as three column with left-bin, rigth-bin and raw-counts.

source_name: mouse mammary epithelial cells

growth_protocol: NMuMG cells were maintained in Dubelcco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Invitrogen) supplemented with 10μg/ml of insulin (Sigma) at 37ºC in 5% CO2.

extract_protocol:
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014, PubmedID: 25497547).
Libraries were prepared according to Illumina instructions.

treatment_protocol: TGFβ was added at a final concentration of 1-5 ng/ml to induce EMT in NMuMG cells.

tag: cell line

value: NMuMG

tag: chip antibody


title: HiC_8h

description: HiC experiment


title: R_NORM_3

city: Gainesville

first: Hideko

last: Kasahara

state: Florida

address: 1345 Center Drive, Room M-557

department: Physiology and Functional Genomics

institute: University of Florida

description: Mutant normoxia

data_processing:
Quality of data was checked using FastQC, over-represented K-mers, GC content, and the presence of adaptors
The MM9 genome from Ensembl was indexed using Bowtie2, and the raw read were mapped to the MM9 genome using Tophat
A majority (75-85%; average 82%) of the reads were successfully mapped using Samstat
After mapping, the gene expression was quantified with Cufflinks software, which normalizes transcript length, number of reads, and sequencing biases
RT-PCR was performed using inventoried TaqMan gene expression assays: Nkx2-5 Mm00657783, Hey2 Mm00469280, Scn5a Mm00451971, KcneI Mm01215533, ANF Mm01255748, and hopx/HOD Mm00558629
Data were normalized to ß-actin expression (no. 4352933E) and duplicate experiments were averaged
Genome_build: MM9
Supplementary_files_format_and_content: The processed data consists of two excel files that list various data, including: gene ID, gene name, locus, sequencing value, log2(fold change), p value, and q value

source_name: heart

growth_protocol: Wild type female mice were separated and bred with either wild type males or mutant males, with plug checks the next day to determine possible pregnancies. On day 10 of gestation, pregnant mice were placed in the hypoxic chamber, which was lowered gradually to 14% oxygen, and left there (taken out daily for health checks and cleaning of the cages) until gestation day 18, or when the baby was birthed.

extract_protocol: All RNA samples had a RNA integrity number above 8, which was considered high quality. Poly-adenylated RNA via oligo dT purification was utilized for library preparation via standard TruSeq protocol. Reads were single-end and 40 bases pairs long each. The sequence depth was approximately 35 million reads per sample.

treatment_protocol: Hearts were dissected immediately, snap frozen, and stored at -80 degrees Celcius until RNA isolation

value: Nkx2-5 mutant

tag: treatment

value: normoxia

value: heart

tag: development stage

value: embryo


title: R_NORM_2

description: Mutant normoxia


title: saline male 5

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description:
S_276158_SALI_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx

data_processing:
alignment using STAR to mm10 (standard parameters, except with --outFilterMultimapNmax 1, clip3pAdapterSeq "TGGTATCAACGCAGAGTAC")
merging of bam files across lanes using samtools
cufflinks for expression level determination (including fragment bias, length and multi-read corrections)
cufflinks expression cut-off deemed mathematically and biologically appropriate: FPKM >= 1
featurecount (Liao et al. Bioinformatics 2014) was used to calculate raw read count and Deseq2 for differential expression level analysis (standard parameters)
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary Tables in .xls format: cufflinks derived FPKM values and DESeq2 output:
Supplementary Table 1 [alignment stats (flagstat outputs)]
Supplementary Table 2 [cufflinks FPKM values]
Supplementary Table 3 [DESeq2 output: male vs. female; CAIA vs. saline main effect]
Supplementary Table 4 [comparison to other historical data]
Supplementary Table 5 [power calculations]

source_name: lumbar dorsal horn microglia

growth_protocol: Adult male and female Balb/c AnNRJ (Janvier Labs)  mice were used and housed in groups (3-5 mice per cage) in a temperature and humidity controlled environment with a 12h light/dark cycle and access to food and water ad libitum.

extract_protocol:
Male and female Balb/c AnNRJ mice (naïve, saline injected or subjected to CAIA) were sacrificed by anesthetic overdose and transcardially perfused with ice-cold Hank’s Balanced Salt Solution (HBSS). Spinal cords were flushed out using a HBSS filled-syringe inserted in the tail end of the spinal column. Lumbar dorsal horns were dissected and dounce homogenized in FACS buffer (0.4% BSA; 15mM HEPES; 2mM EDTA in HBSS) into a cell suspension that was centrifuged (430 x g for 30 min at 17°C) over a 37%/70% Percoll gradient (Sigma). Microglial cells were isolated from the interface and the total cell number determined. For each experiment, the lumbar dorsal horns of two mice were pooled into one Percoll gradient, constituting one n per sample group (2 x saline/naïve and 2 x CAIA).
RNA was sent for batch-controlled library preparation (SMARTer Ultra Low Input HV kit, 634820, Clontech) and sequencing at the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics at Oxford University. After amplification, samples were multiplexed in replicate flow cells on an Illumina HiSeq4000 platform to yield 75 bp reads of at least 25 M read depth.

treatment_protocol: For induction of arthritis, mice were injected intravenously (1.25-1.5 mg) with an anti-collagen type-II cocktail containing 5 different monoclonal autoantibodies (Chondrex) at day 0 followed by an intraperitoneal injection of LPS (25 μg in 100 μl; serotype 0111:B4; Chondrex, or 35 μg in 100 μl; serotype 055:B5; Sigma) at day 5.

tag: background strain

value: Balb/c AnNRJ

value: lumbar dorsal horn microglia

tag: treatment condition

value: saline

tag: Sex

value: male


title: R_NORM_1

description: Mutant normoxia

tag: genotype/variation


title: saline male 4

description:
S_273194_SALI_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx

tag: tissue


title: WT_NORM_4

description: Wild type normoxia


title: saline male 3

description:
S_269147_SALI_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT_NORM_2

description: Wild type normoxia


title: WT_NORM_3

description: Wild type normoxia


title: WT_NORM_1

description: Wild type normoxia


title: saline female 8

description:
S_277146_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx

value: female


title: WT_HYPO_3

description: Wild type hypoxia

value: hypoxia


title: Yaf2KO1 RNAseq

tag: genotype


title: wildtype3 RNAseq


title: saline female 7

description:
S_275170_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: HiC_24h

description: HiC experiment


title: saline female 6

description:
S_274182_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: saline female 5

description:
S_271123_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: wildtype1 RNAseq


title: saline female 3

description:
S_263124_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: saline female 4

description:
S_266183_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT_HYPO_1

description: Wild type hypoxia


title: KI-2-2

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm9 whole genome using TopHat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks and raw counts were summarized by htseq-count for DESeq2 input
Gene differential expression was analyzed by DESeq2 according to its mannual
Genome_build: NCBI build37.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and tab-delimited text files include raw reads counts for each Sample

source_name: Lymph Node

growth_protocol: GFP-transduced wildtype or Pdcd1KI/KI OT-II T cells were transferred into B6 mice (5×105 sorted GFP+ cells per mouse) together with 5×105 dsRed-expressing MD4 B cells, and the recipients were subcutaneously immunized with HEL-OVA. CXCR5hi OT-II T cells were sorted from the two groups on day 5 and subjected to transcriptomic analysis by RNA-seq.

extract_protocol:
Cells were directly sorted into the lysis buffer and follow the modified the protocol initially developed for single-cell RNA-seq (Tang, 2011) to accommodate 100-200 sorted cells by doubling reaction volumes with extra buffers until the step for second strand DNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pdcd1KI/KICXCR5hiGFP+CD4+ OT-II T cells

value: HEL-OVA/LPS/Alum 5dpi


title: KI-2-3


title: saline male 2

description:
S_262136_SALI_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: saline male 1

description:
S_259172_SALI_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: KI-1-3


title: KI-1-2


title: KI-2-1


title: saline female 2

description:
S_260160_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA male 3

description:
S_278134_CAIA_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx

value: CAIA


title: KI-1-1


title: saline female 1

description:
S_258184_SALI_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA male 1

description:
S_257196_CAIA_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT-2-2

value: Pdcd1+/+CXCR5hiGFP+CD4+ OT-II T cells


title: CAIA female 7

description:
S_279122_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA female 6

description:
S_272111_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT-2-1


title: CAIA female 5

description:
S_270135_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT_HYPO_2

description: Wild type hypoxia


title: CAIA female 4

description:
S_268159_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT-1-3


title: WT-1-2


title: WT-1-1


title: CAIA female 3

description:
S_265195_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA female 2

description:
S_264112_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA female 1

description:
S_261148_CAIA_F
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: CAIA male 2

description:
S_267171_CAIA_M
processed data file:
Supplementary_Table_2.xlsx
Supplementary_Table_3.xlsx


title: WT-2-3


title: Boost-MA24h_rep1

city: Tehran

first: Mohammad Esmael

last: Akbari

address: Shahrdari

country: Iran

institute: Cancer Research Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapter sequences (standard TruSeq LT adapter sequence) were removed and short reads trimmed using eaUtils. Short read sequences were then aligned to the human genome (GRCh38 database; GRCh38.87) using the hierarchical indexing for spliced alignment of transcripts program, HISAT2
After spliced alignment, the set of expressed transcripts was identified using StringTie for transcriptome assembly on Binary Alignment/Map (BAM) files. All transcript assemblies were merged using cuffmerge.
Fragments per kilobase of transcript per million mapped reads (FPKM)-based, was used to identify the differentially expressed genes between the cases and controls.
The FPKM-based algorithm was implemented in the Cuffdiff package of Cufflinks2.2.1
Genome_build: GRCh38.87
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Breast

extract_protocol:
Margin of  tumor were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Patients were treated with irradiation following two separate strategies, including 12Gy and 21Gy treatment. The machine dose rate was adjusted to 1 cGy/MU during the irradiation. Approximately 100mg of samples retrieved from each patient for each types or treatment

value: Breast

tag: dose

value: Female


title: Boost-MAi_rep3


title: Radical-MA24h_rep1


title: Boost-MA24h_rep3


title: Boost-MA24h_rep2


title: Boost-MAi_rep1


title: Radical-MA24h_rep2


title: Radical-MAi_rep1


title: Radical-MB_rep2


title: Boost-MB_rep2


title: Boost-MB_rep3


title: Radical-MAi_rep2


title: Testis_N4_2_2

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

description:
polyA RNA
Testis_N4_2_2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the TPM values of RefSeq genes.  The file "sample_info.xls" contains the cell ID and cell barcode information and is available on the series record.

source_name: Human Testicular Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same adult sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

value: testis

tag: diagnosis

value: NOA

tag: ploidy

value: not available


title: Testis_N4_2_1

description:
polyA RNA
Testis_N4_2_1

tag: gender


title: Testis_N4_1_1

description:
polyA RNA
Testis_N4_1_1

tag: age


title: 4_GV_2N

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the TPM values of RefSeq genes. The file "sample_info.xls" contains the cell ID and cell barcode information and is available on the series record.

value: normal fertility or obstructive azoospermia (normal spermatogenesis)


title: 4_GV_2N_1

description: polyA RNA


title: 7_1N_2

description: polyA RNA


title: 4_GV_2N_2

description: polyA RNA


title: 7_4N

description: polyA RNA


title: 7_1N_1

description: polyA RNA


title: Boost-MAi_rep2


title: 6_1N

description: polyA RNA


title: Radical-MB_rep1


title: 6_4N

description: polyA RNA


title: Boost-MB_rep1


title: 2JY

description: polyA RNA


title: 1JJ

description: polyA RNA


title: 1JC

description: polyA RNA


title: 5_1N

description: polyA RNA


title: 1_SS

description: polyA RNA


title: 1_ST

description: polyA RNA


title: 1_SY

description: polyA RNA


title: 1_SJ

description: polyA RNA


title: 45_V_2N

description:
polyA RNA
This sample contains cells from two donors.


title: 2JJ

description: polyA RNA


title: V_2n_45


title: 1_SC

description: polyA RNA


title: 4N_7

description: polyA RNA


title: 4N_6

description: polyA RNA


title: 1N_6

description: polyA RNA


title: X10_4N_6_1

description: polyA RNA


title: Testis_N4_1_2

description:
polyA RNA
Testis_N4_1_2


title: X10_2N_5_1

description: polyA RNA


title: Gv_2n_4

description: polyA RNA


title: X10_2N_5_2

description: polyA RNA


title: X10_4N_6_2

description: polyA RNA


title: 1N_5

description: polyA RNA


title: X10_2N_4_2

description: polyA RNA


title: OE2-3

city: Hangzhou

first: Kang

last: Wei

address: Meiling South Road

institute: Tea Research Institute Chinese Academy of Agricult

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the Arabidopsis thaliana(TAIR10.13) genome assembly using hisat(0.1.6-beta)
Data were filtered using sickle(v1.33) with default parameters
The transcript abundances were measured as fragments per kilobase of exon per million fragments mapped (FPKM) follow trintiy script.EdgeR(Robinson et al. 2010) package(v3.1.2) was then used to determine significantly differential expression (FDR < 0.05)
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 9 d old seedlings

growth_protocol: seedlings were grown under 1/2 MS medium with 2% sucrose

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: overexpressing CsGSTF1


title: tt19-8-1

value: tt19 knock out


title: tt19-8-2


title: X10_2N_4_1

description: polyA RNA


title: tt19-8-3


title: X10_2N_2_1

description: polyA RNA


title: OE2-2


title: X10_2N_2_2

description: polyA RNA


title: OE1-2


title: OE1-3


title: X10_2N_1_2

description: polyA RNA


title: X10_1N_3_2

description: polyA RNA


title: X10_2N_1_1

description: polyA RNA


title: X10_1N_3_1

description: polyA RNA


title: OE1-1


title: 4_4N_2

description: polyA RNA


title: 5_4N_2

description: polyA RNA


title: 5_4N_1

description: polyA RNA


title: 4_4N_1

description: polyA RNA


title: LATS2 OE rep4

city: Münster

first: Jakob

last: Bonse

state: NRW

address: Albert-Schweitzer-Campus 1

department: Internal Medicine D

country: Germany

institute: Molecular Nephrology

data_processing:
Using a molecular barcode, the samples was demultiplexed (bcl2fastq2) to fastq data and quality controlled (FastQC)
Trimmomatic (Version 0.33) was used for adapter trimming and read filtering
reads were aligned to the human reference genome (HG19) using TopHat [Tarpnell et al.(2009)]
The aligned reads were assembled into transcripts in means of FPKM values (fragments per kilobase of exon per million fragments mapped) and differentially expressed genes and transcripts were reported using the Cufflinks package [Tarpnell et al.(2010)]
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text file containing FPKM means, log2(FC) and FDR values of all determined genes

growth_protocol: Immortalized human podocytes (AB8/13) were cultured on 10 cm plastic dish with 5 % CO2 and 33°C in RPMI1640 (with 10 % FCS, 0,8 % Supplements for cell culture and  1 % Penicillin/Streptomycin) up to 70 % confluence.

extract_protocol:
Media was removed and cells rinsed with PBS at 4°C. RNA was isolated using the GenEluteTM Mammalian total RNA Miniprep Kit according to the manufacturer’s instructions.
After determination of the concentration and RNA integrity number, the library was constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcode informatio:  Sample1,GTCCGC; Sample2,GTGAAA; Sample3,GTGGCC; Sample4,GTTTCG; Sample5,CGTACG; Sample6,GAGTGG; Sample7,ACTGAT; Sample8,ATTCCT

treatment_protocol: LATS2 overexpression was induced by doxycyclin treatment of 125 ng/mL for 8 h.

tag: cell type

value: Human immortalized podocytes

tag: protocol

value: 8 h doxycyclin induced


title: Untreated rep4

tag: cell line

value: untreated


title: LATS2 OE rep1


title: LATS2 OE rep3


title: 4_1N_2

description: polyA RNA

value: male


title: Untreated rep3


title: 4_1N_1

description: polyA RNA


title: N3_TESTIS_12

description: polyA RNA


title: Untreated rep2


title: N3_TESTIS_11

description: polyA RNA


title: N3_TESTIS_10

description: polyA RNA


title: Untreated rep1


title: OE2-1


title: N3_TESTIS_9

description: polyA RNA


title: N3_TESTIS_8

description: polyA RNA


title: N3_TESTIS_7

description: polyA RNA


title: N3_TESTIS_6

description: polyA RNA


title: N3_TESTIS_5

description: polyA RNA


title: N3_TESTIS_3

description: polyA RNA


title: N3_TESTIS_4

description: polyA RNA


title: N3_TESTIS_2

description: polyA RNA


title: N2_TESTIS_11

description: polyA RNA


title: LATS2 OE rep2


title: N3_TESTIS_1

description: polyA RNA


title: N2_TESTIS_12

description: polyA RNA


title: N2_TESTIS_8

description: polyA RNA


title: N2_TESTIS_9

description: polyA RNA


title: N2_TESTIS_6

description: polyA RNA


title: N2_TESTIS_10

description: polyA RNA


title: N2_TESTIS_4

description: polyA RNA


title: N2_TESTIS_3

description: polyA RNA


title: N2_TESTIS_5

description: polyA RNA


title: N2_TESTIS_1

description: polyA RNA


title: N2_TESTIS_7

description: polyA RNA


title: N2_TESTIS_2

description: polyA RNA