title: LSCC_7 miRNA-Seq

description:
miRNA
C_7


title: LSCC_8 miRNA-Seq

status: Public on Jun 17 2020

type: SRA

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

description:
miRNA
C_8

library_source: transcriptomic

data_processing:
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads from the fq file were removed and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

molecule: total RNA

organism: Homo sapiens

source_name: Laryngeal squamous cell carcinoma tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumor and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US)  following the manufacturer’s instructions.

tag: tissue

tag: tumor stage

tag: tobacco smoking

value: Yes

tag: alcohol consumption

value: No


title: FC_pos_p1_N20_S59_mouse2

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 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: mm10
Supplementary_files_format_and_content: raw count tables

organism: Mus musculus

extract_protocol:
Brain tissues were dissociated with Worthington Papain Digestion Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
smart seq 2

tag: cell type

value: Primary brain cells  from muring mPFC


title: LSCC_6 miRNA-Seq

description:
miRNA
C_6

value: Laryngeal squamous cell carcinoma tissue


title: FC_neg_p3_A20_S196_mouse2


title: FC_pos_p1_M13_S29_mouse2


title: LSCC_5 miRNA-Seq

description:
miRNA
C_5


title: FC_pos_p1_K12_S282_mouse2


title: FC_pos_p1_M18_S34_mouse2


title: FC_pos_p1_O23_S85_mouse2


title: LSCC_4 miRNA-Seq

description:
miRNA
C_4


title: LSCC_2 miRNA-Seq

description:
miRNA
C_2


title: FC_pos_p1_G21_S199_mouse2


title: LSCC_3 miRNA-Seq

description:
miRNA
C_3


title: FC_pos_p10_H10_S143_mouse2


title: FC_pos_p1_F8_S163_mouse2


title: FC_pos_p1_H11_S212_mouse2


title: WGBS of hVSMCs [WGBS-VSMC_rep2]

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description:
WGBS of hVSMCs
WGBS-VSMC.bw

library_source: genomic

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2, histat2 or bsmap software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. Bigwig files of RPKM normalized read cout for each 10 bp bin size for ATAC-seq, ChIP-seq and ssDRIP-seq data. Bigwig files of CpG methylation for each site for WGBS data.

molecule: genomic DNA

source_name: Vascular smooth muscle cells

growth_protocol: The H9 hESC line (WA09, WiCell Research) and human induced pluripotent stem cells (hiPSCs) reprogrammed from hNSCs were cultured on Mitomycin C inactivated mouse embryonic fibroblast (MEF) feeders with cDF12 medium or Matrigel (BD)-coated plates with mTeSR1 medium, as previously described (Duan et al., 2015; Pan et al., 2016). hNSCs were cultured on Matrigel-coated plates with neural stem cell maintenance medium (NSMM) as previously described (Duan et al., 2015). hVECs were cultured on Collagen IV (Biocoat)-coated plates in EGM2 medium (Lonza) supplemented with 10 nM SB431542 (Selleck), 50 ng/ml VEGF (Stem Immune) and 20 ng/ml bFGF (Joint Protein Central). hVSMCs were cultured on Gelatin (Sigma Aldrich)-coated plates in VSMC medium with 10 ng/ml PDGF-AB (Pepro Tech) as previously described (Yan et al., 2019). hMSCs were cultured on Gelatin-coated plates in MEMalpha medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 1% non-essential amino acids (Gibco), 1% penicillin/streptomycin (Gibco), and 1 ng/ml bFGF (Joint Protein Central).

extract_protocol:
For ssDRIP-seq, 5 x 106 cells were harvested, lysed by SDS (final concentration: 0.5%) and treated with proteinase K (NEB, final concentration: 0.1 mg/ml) at 37 ºC overnight. Genomic DNA was extracted using the classic phenol-chloroform method. The genomic DNA was fragmented by endonucleases (Mse I, Dde I, Alu I and Mbo I; NEB) at 37 ºC overnight. Then, DRIP was performed as previously described (Xu et al., 2017).  For ChIP-seq, ChIP assay was performed as reported in previous studies with some minor modifications (Dahl and Collas, 2008). Briefly, 1 x 106 cells were harvested and crosslinked using 1% formaldehyde at room temperature for 6 min and then quenched with 2.5 mol/L glycine at room temperature for 5 min. The cells were then lysed in lysis buffer (1% SDS, 50 mM Tris-HCl, 10 mM EDTA) for 10 min and sonicated to 250-bp fragments using M220 Focused-ultrasonicator (Covaris, USA). The samples were incubated overnight with protein A beads (Thermo Fisher Scientific) linked with 2.4 µg antibody. After reverse-crosslinking and elution at 68 ºC, the IPed DNA was extracted by the aforementioned phenol-chloroform method.   For RNA-seq, total RNA was extracted using TRIzol (Thermo Fisher Scientific) from 1 x 106 cells per experimental replicate. For ATAC-seq, 3 x 104 cells were lysed in the lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.5% NP-40) for 10 min on ice. Then spun at 500 g for 5 min to remove the supernatant, followed by adding 50 μL transposition reaction mix from TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) at 37 ºC for 30 min.   For WGBS, genomic DNA was extracted using DNeasy Blood & Tissue Kits (Qiagen) according to the manufacturer’s instructions.
For ssDRIP-seq,  libraries were constructed using ACCEL-NGS 1S plus DNA Library Kit (Swift, USA) following manufacturer’s instructions. For ATAC-seq, library amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech).  For ChIP-seq, the enriched fragments were constructed into libraries without the incorporation of spike-in controls via KAPA Hyper Prep Kits with PCR Library Ampliﬁcation/Illumina series (KK8504) following the manufacturer’s instructions. For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For WGBS, genomic DNA were sonicated to 200 - 300 bp fragments followed by end repair and adenylation. Cytosine-methylated barcodes were added before bisulfite treatment. After the quantification of DNA concentration by Qubit® 2.0 FlurometerFluorometer (Life Technologies, CA, USA) and quantitative PCR, the libraries were sequenced on an Illumina Hiseq platform.

value: Vascular smooth muscle cells

tag: genotype

value: WT

tag: passage


title: FC_pos_p1_F19_S174_mouse2


title: FC_neg_p3_F22_S13_mouse2


title: WGBS of hNSCs [WGBS-NSC_rep2]

description:
WGBS of hNSCs
WGBS-NSC.bw

source_name: Neural stem cells

value: Neural stem cells


title: FC_pos_p1_F13_S168_mouse2


title: FC_pos_p1_L10_S3_mouse2


title: FC_neg_p2_F5_S228_mouse2


title: WGBS of hNSCs [WGBS-NSC_rep1]

description:
WGBS of hNSCs
WGBS-NSC.bw


title: FC_pos_p1_L17_S10_mouse2


title: FC_neg_p3_J22_S105_mouse2


title: LSCC_1 miRNA-Seq

description:
miRNA
C_1


title: FC_pos_p10_O1_S295_mouse2


title: WGBS of hiPSCs [WGBS-iPSC_rep2]

description:
WGBS of hiPSCs
WGBS-iPSC.bw

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: FC_neg_p2_N19_S126_mouse2


title: WGBS of hMSCs [WGBS-MSC_rep1]

description:
WGBS of hMSCs
WGBS-MSC.bw

source_name: Mesenchymal stem cell

value: Mesenchymal stem cell


title: WGBS of hESCs [WGBS-ESC_rep2]

description:
WGBS of hESCs
WGBS-ESC.bw

source_name: Embryonic stem cells

value: Embryonic stem cells


title: WGBS of hiPSCs [WGBS-iPSC_rep1]

description:
WGBS of hiPSCs
WGBS-iPSC.bw


title: WGBS of hESCs [WGBS-ESC_rep1]

description:
WGBS of hESCs
WGBS-ESC.bw


title: FC_pos_p1_N15_S54_mouse2


title: FC_pos_p1_E12_S144_mouse2


title: WGBS of hVECs [WGBS-EC_rep1]

description:
WGBS of hVECs
WGBS-EC.bw

source_name: Vascular endothelial cells

value: Vascular endothelial cells


title: WGBS of hVECs [WGBS-EC_rep2]

description:
WGBS of hVECs
WGBS-EC.bw


title: RNA sequencing of hVSMCs [RNA-VSMC_rep2]

description: RNA sequencing of hVSMCs


title: FC_pos_p10_F9_S96_mouse2


title: WGBS of hVSMCs [WGBS-VSMC_rep1]

description:
WGBS of hVSMCs
WGBS-VSMC.bw


title: RNA sequencing of hVSMCs [RNA-VSMC_rep1]

description: RNA sequencing of hVSMCs


title: FC_pos_p1_E13_S145_mouse2


title: FC_pos_p1_K23_S293_mouse2


title: WGBS of hMSCs [WGBS-MSC_rep2]

description:
WGBS of hMSCs
WGBS-MSC.bw


title: RNA sequencing of hNSCs [RNA-NSC_rep1]

description: RNA sequencing of hNSCs


title: RNA sequencing of hMSCs [RNA-MSC_rep2]

description: RNA sequencing of hMSCs


title: FC_pos_p1_N7_S46_mouse2


title: RNA sequencing of hiPSCs [RNA-iPSC_rep2]

description: RNA sequencing of hiPSCs


title: FC_pos_p1_K8_S278_mouse2


title: FC_pos_p1_O12_S74_mouse2


title: FC_pos_p10_M7_S255_mouse2


title: RNA sequencing of hiPSCs [RNA-iPSC_rep1]

description: RNA sequencing of hiPSCs


title: RNA sequencing of hESCs [RNA-ESC_rep1]

description: RNA sequencing of hESCs


title: FC_pos_p1_I9_S233_mouse2


title: FC_pos_p10_F10_S97_mouse2


title: RNA sequencing of hVECs [RNA-EC_rep2]

description: RNA sequencing of hVECs


title: RNA sequencing of hNSCs [RNA-NSC_rep2]

description: RNA sequencing of hNSCs


title: ssDRIP sequencing of hVSMCs [ssDRIP-VSMC_rep2]

description:
ssDRIP sequencing of hVSMCs
ssDRIP-VSMC.forward.bw  ssDRIP-VSMC.reverse.bw  ssDRIP-VSMC.unstrand.bw

data_processing:
Library strategy: ssDRIP-Seq
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2, histat2 or bsmap software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. Bigwig files of RPKM normalized read cout for each 10 bp bin size for ATAC-seq, ChIP-seq and ssDRIP-seq data. Bigwig files of CpG methylation for each site for WGBS data.


title: ssDRIP sequencing of hVSMCs [ssDRIP-VSMC_rep1]


title: RNA sequencing of hESCs [RNA-ESC_rep2]

description: RNA sequencing of hESCs


title: FC_pos_p1_I19_S243_mouse2


title: ssDRIP sequencing of hNSCs [ssDRIP-NSC_rep2]

description:
ssDRIP sequencing of hNSCs
ssDRIP-NSC.forward.bw  ssDRIP-NSC.reverse.bw  ssDRIP-NSC.unstrand.bw


title: FC_pos_p1_L16_S9_mouse2


title: RNA sequencing of hVECs [RNA-EC_rep1]

description: RNA sequencing of hVECs


title: FC_pos_p1_G9_S187_mouse2


title: FC_pos_p1_I22_S246_mouse2


title: ssDRIP sequencing of hNSCs [ssDRIP-NSC_rep1]


title: FC_pos_p10_L9_S234_mouse2


title: ssDRIP sequencing of hNSCs [ssDRIP-NSC_batch2_rep2]

description:
ssDRIP sequencing of hNSCs
ssDRIP-NSC.batch2.forward.bw  ssDRIP-NSC.batch2.reverse.bw  ssDRIP-NSC.batch2.unstrand.bw


title: RNA sequencing of hMSCs [RNA-MSC_rep1]

description: RNA sequencing of hMSCs


title: FC_pos_p1_P20_S105_mouse2


title: ssDRIP sequencing of hNSCs [ssDRIP-NSC_batch2_rep1]


title: FC_pos_p1_C15_S101_mouse2


title: FC_pos_p1_I23_S247_mouse2


title: ssDRIP sequencing of hMSCs [ssDRIP-MSC_rep2]

description:
ssDRIP sequencing of hMSCs
ssDRIP-MSC.forward.bw  ssDRIP-MSC.reverse.bw  ssDRIP-MSC.unstrand.bw


title: FC_pos_p1_H23_S224_mouse2


title: FC_pos_p10_C3_S21_mouse2


title: ssDRIP sequencing of hMSCs [ssDRIP-MSC_rep1]


title: FC_pos_p1_K6_S276_mouse2


title: ssDRIP sequencing of hiPSCs [ssDRIP-iPSC_rep2]

description:
ssDRIP sequencing of hiPSCs
ssDRIP-iPSC.forward.bw  ssDRIP-iPSC.reverse.bw  ssDRIP-iPSC.unstrand.bw


title: ssDRIP sequencing of hiPSCs [ssDRIP-iPSC_rep1]


title: FC_neg_p3_D20_S265_mouse2


title: FC_pos_p1_J15_S262_mouse2


title: FC_neg_p2_N15_S122_mouse2


title: ssDRIP sequencing of hiPSCs [ssDRIP-iPSC_batch2_rep1]

description:
ssDRIP sequencing of hiPSCs
ssDRIP-iPSC.batch2.forward.bw  ssDRIP-iPSC.batch2.reverse.bw  ssDRIP-iPSC.batch2.unstrand.bw


title: FC_pos_p10_M3_S251_mouse2


title: FC_pos_p1_A14_S54_mouse2


title: ssDRIP sequencing of hESCs [ssDRIP-ESC_rep2]

description:
ssDRIP sequencing of hESCs
ssDRIP-ESC.forward.bw  ssDRIP-ESC.reverse.bw  ssDRIP-ESC.unstrand.bw


title: FC_pos_p1_P14_S99_mouse2


title: ssDRIP sequencing of hESCs [ssDRIP-ESC_batch2_rep1]

description:
ssDRIP sequencing of hESCs
ssDRIP-ESC.batch2.forward.bw  ssDRIP-ESC.batch2.reverse.bw  ssDRIP-ESC.batch2.unstrand.bw


title: ssDRIP sequencing of hESCs [ssDRIP-ESC_batch2_rep2]


title: ssDRIP sequencing of hESCs [ssDRIP-ESC_rep1]


title: FC_neg_p3_K7_S113_mouse2


title: FC_pos_p1_K19_S289_mouse2


title: ssDRIP sequencing of hVECs [ssDRIP-EC_rep1]

description:
ssDRIP sequencing of hVECs
ssDRIP-EC.forward.bw  ssDRIP-EC.reverse.bw  ssDRIP-EC.unstrand.bw


title: ssDRIP sequencing of hVECs [ssDRIP-EC_rep2]


title: FC_neg_p3_H20_S57_mouse2


title: Input of hVSMCs [Input-VSMC_FKDL190741264-1a]

description: Input of hVSMCs


title: FC_pos_p1_D9_S118_mouse2


title: FC_pos_p1_P18_S103_mouse2


title: Input of hNSCs [Input-NSC_FKDL190741262-1a]

description: Input of hNSCs


title: FC_pos_p10_N4_S275_mouse2


title: Input of hMSCs [Input-MSC_FKDL190741265-1a]

description: Input of hMSCs


title: Input of hiPSCs [Input-iPSC_FKDL190741261-1a]

description: Input of hiPSCs


title: FC_pos_p1_L6_S299_mouse2


title: FC_neg_p3_C14_S236_mouse2


title: FC_pos_p1_B15_S78_mouse2


title: ssDRIP sequencing of hiPSCs [ssDRIP-iPSC_batch2_rep2]


title: Input of hESCs [Input-ESC_FKDL190741260-1a]

description: Input of hESCs


title: FC_pos_p1_D14_S123_mouse2


title: FC_pos_p1_N18_S57_mouse2


title: H3K4me3 ChIP sequencing of hVSMCs [H3K4me3-VSMC_rep3_FKDL190752811-1a]

description:
H3K4me3 ChIP sequencing of hVSMCs
H3K4me3-VSMC.bw

tag: antibody


title: H3K4me3 ChIP sequencing of hVSMCs [H3K4me3-VSMC_rep2_FKDL190752810-1a]


title: Input of hVECs [Input-EC_FKDL190741263-1a]

description: Input of hVECs


title: FC_pos_p1_E14_S146_mouse2


title: H3K4me3 ChIP sequencing of hVSMCs [H3K4me3-VSMC_rep1_FKDL190752809-1a]


title: FC_pos_p1_D19_S128_mouse2


title: H3K4me3 ChIP sequencing of hNSCs [H3K4me3-NSC_rep2_FKDL190752804-1a]

description:
H3K4me3 ChIP sequencing of hNSCs
H3K4me3-NSC.bw


title: H3K4me3 ChIP sequencing of hNSCs [H3K4me3-NSC_rep3_FKDL190752805-1a]


title: H3K4me3 ChIP sequencing of hNSCs [H3K4me3-NSC_rep1_FKDL190752803-1a]


title: FC_pos_p10_I7_S163_mouse2


title: FC_neg_p3_P15_S236_mouse2


title: FC_pos_p1_I12_S236_mouse2


title: H3K4me3 ChIP sequencing of hMSCs [H3K4me3-MSC_rep1_FKDL190752812-1a]

description:
H3K4me3 ChIP sequencing of hMSCs
H3K4me3-MSC.bw


title: FC_pos_p10_O2_S296_mouse2


title: FC_pos_p1_E22_S154_mouse2


title: FC_neg_p3_P19_S240_mouse2


title: H3K4me3 ChIP sequencing of hiPSCs [H3K4me3-iPSC_rep3_FKDL190752802-1a]

description:
H3K4me3 ChIP sequencing of hiPSCs
H3K4me3-iPSC.bw


title: H3K4me3 ChIP sequencing of hMSCs [H3K4me3-MSC_rep3_FKDL190752814-1a]


title: FC_pos_p1_H1_S202_mouse2


title: H3K4me3 ChIP sequencing of hiPSCs [H3K4me3-iPSC_rep1_FKDL190752800-1a]


title: FC_pos_p1_B4_S67_mouse2


title: FC_pos_p1_K9_S279_mouse2


title: H3K4me3 ChIP sequencing of hESCs [H3K4me3-ESC_rep3_FKDL190752799-1a]

description:
H3K4me3 ChIP sequencing of hESCs
H3K4me3-ESC.bw


title: FC_pos_p1_H17_S218_mouse2


title: FC_neg_p3_G22_S36_mouse2


title: FC_pos_p1_D12_S121_mouse2


title: H3K4me3 ChIP sequencing of hESCs [H3K4me3-ESC_rep1_FKDL190752797-1a]


title: FC_neg_p2_A23_S131_mouse2


title: FC_pos_p1_O15_S77_mouse2


title: H3K4me3 ChIP sequencing of hVECs [H3K4me3-EC_rep3_FKDL190752808-1a]

description:
H3K4me3 ChIP sequencing of hVECs
H3K4me3-EC.bw


title: H3K4me3 ChIP sequencing of hVECs [H3K4me3-EC_rep2_FKDL190752807-1a]


title: FC_pos_p1_I11_S235_mouse2


title: H3K4me3 ChIP sequencing of hVECs [H3K4me3-EC_rep1_FKDL190752806-1a]


title: H3K4me3 ChIP sequencing of hESCs [H3K4me3-ESC_rep2_FKDL190752798-1a]


title: FC_neg_p2_O17_S147_mouse2


title: H3K36me3 ChIP sequencing of hVSMCs [H3K36me3-VSMC_rep3_FKDL190743622-1a_H2VVCCCX2_L8]

description:
H3K36me3 ChIP sequencing of hVSMCs
H3K36me3-VSMC.bw


title: FC_pos_p1_F9_S164_mouse2


title: H3K36me3 ChIP sequencing of hVSMCs [H3K36me3-VSMC_rep2_FKDL190743621-1a_H2VVCCCX2_L5]


title: H3K4me3 ChIP sequencing of hMSCs [H3K4me3-MSC_rep2_FKDL190752813-1a]


title: FC_neg_p3_H21_S58_mouse2


title: FC_pos_p1_F20_S175_mouse2


title: FC_neg_p3_L18_S147_mouse2


title: FC_pos_p1_A19_S59_mouse2


title: H3K36me3 ChIP sequencing of hNSCs [H3K36me3-NSC_rep1_FKDL190743614-1a_H2VVCCCX2_L7]

description:
H3K36me3 ChIP sequencing of hNSCs
H3K36me3-NSC.bw


title: H3K36me3 ChIP sequencing of hNSCs [H3K36me3-NSC_rep2_FKDL190743615-1a_H2VVCCCX2_L5]


title: H3K4me3 ChIP sequencing of hiPSCs [H3K4me3-iPSC_rep2_FKDL190752801-1a]


title: H3K36me3 ChIP sequencing of hNSCs [H3K36me3-NSC_rep3_FKDL190743616-1a_H2VVCCCX2_L8]


title: H3K36me3 ChIP sequencing of hMSCs [H3K36me3-MSC_rep3_FKDL190743625-1a_H2VVCCCX2_L8]

description:
H3K36me3 ChIP sequencing of hMSCs
H3K36me3-MSC.bw


title: H3K36me3 ChIP sequencing of hVSMCs [H3K36me3-VSMC_rep1_FKDL190743620-1a_H2VVCCCX2_L7]


title: FC_pos_p1_M11_S27_mouse2


title: FC_pos_p1_P3_S88_mouse2


title: FC_pos_p10_B8_S3_mouse2


title: H3K36me3 ChIP sequencing of hMSCs [H3K36me3-MSC_rep2_FKDL190743624-1a_H2VVCCCX2_L5]


title: FC_pos_p1_G13_S191_mouse2


title: FC_neg_p2_A8_S116_mouse2


title: H3K36me3 ChIP sequencing of hiPSCs [H3K36me3-iPSC_rep2_FKDL190743612-1a_H2VVCCCX2_L5]

description:
H3K36me3 ChIP sequencing of hiPSCs
H3K36me3-iPSC.bw


title: FC_pos_p1_L23_S16_mouse2


title: FC_pos_p1_L20_S13_mouse2


title: FC_neg_p3_I13_S73_mouse2


title: H3K36me3 ChIP sequencing of hMSCs [H3K36me3-MSC_rep1_FKDL190743623-1a_H2VVCCCX2_L7]


title: FC_pos_p1_B14_S77_mouse2


title: FC_pos_p1_A18_S58_mouse2


title: FC_pos_p1_C20_S106_mouse2


title: H3K36me3 ChIP sequencing of hiPSCs [H3K36me3-iPSC_rep3_FKDL190743613-1a_H2VVCCCX2_L8]


title: FC_neg_p2_N5_S112_mouse2


title: H3K36me3 ChIP sequencing of hESCs [H3K36me3-ESC_rep3_FKDL190743610-1a_H2VVCCCX2_L8]

description:
H3K36me3 ChIP sequencing of hESCs
H3K36me3-ESC.bw


title: FC_pos_p1_N13_S52_mouse2


title: FC_pos_p1_F14_S169_mouse2


title: FC_neg_p2_M9_S93_mouse2


title: FC_neg_p3_P5_S226_mouse2


title: FC_pos_p1_E17_S149_mouse2


title: H3K36me3 ChIP sequencing of hESCs [H3K36me3-ESC_rep1_FKDL190743608-1a_H2VVCCCX2_L7]


title: H3K36me3 ChIP sequencing of hESCs [H3K36me3-ESC_rep2_FKDL190743609-1a_H2VVCCCX2_L5]


title: FC_neg_p2_J18_S33_mouse2


title: H3K36me3 ChIP sequencing of hiPSCs [H3K36me3-iPSC_rep1_FKDL190743611-1a_H2VVCCCX2_L7]


title: H3K36me3 ChIP sequencing of hVECs [H3K36me3-EC_rep3_FKDL190743619-1a_H2VVCCCX2_L8]

description:
H3K36me3 ChIP sequencing of hVECs
H3K36me3-EC.bw


title: FC_pos_p10_J9_S188_mouse2


title: H3K36me3 ChIP sequencing of hVECs [H3K36me3-EC_rep2_FKDL190743618-1a_H2VVCCCX2_L5]


title: FC_neg_p3_G2_S16_mouse2


title: FC_pos_p1_G22_S200_mouse2


title: 564016A09 - 21_Ct-1_2 vs 9_52CV_2

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis

hyb_protocol: 9_52CV_2 Cy5 / 21_Ct-1_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: rosette - Media: hydropony. Hygrometry: 100%. Shorts days, 21°C day, 17°C night.

treatment_protocol: Name:Nitrogen treatment 4mM - environmental treatment - nitrogen concentration,nitrogen:quantity 4mM time 7day .

tag: harvest date

value: leaf

tag: background ecotype

value: Columbia

tag: nuclear strain

tag: cytoplasm strain

value: Jea

tag: treatment


title: 564016A08 - 7_52CV_1 vs 19_Ct-1_1

hyb_protocol: 19_Ct-1_1 Cy5 / 7_52CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564016A05 - 11_52CV_3 vs 12_52CV-N_3

hyb_protocol: 12_52CV-N_3 Cy5 / 11_52CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

treatment_protocol: Name:Nitrogen treatment 0mM - environmental treatment - nitrogen concentration,nitrogen:quantity 0mM time 7day .


title: 564016A06 - 12_52CV-N_3 vs 11_52CV_3

hyb_protocol: 11_52CV_3 Cy5 / 12_52CV-N_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: D3_T7_C15_S199_mouse1


title: H5_T7_C18_S202_mouse1


title: B2_T8_G19_S299_mouse1


title: D3_T8_P20_S216_mouse1


title: 564016A10 - 9_52CV_2 vs 21_Ct-1_2

hyb_protocol: 21_Ct-1_2 Cy5 / 9_52CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H11_T2_N12_S232_mouse1


title: 564016A11 - 23_Ct-1_3 vs 11_52CV_3

hyb_protocol: 11_52CV_3 Cy5 / 23_Ct-1_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27me3 ChIP sequencing of hVSMCs [H3K27me3-VSMC_rep2_FKDL190763216-1a_H3YJJCCX2_L8]

description:
H3K27me3 ChIP sequencing of hVSMCs
H3K27me3-VSMC.bw


title: 564016A12 - 11_52CV_3 vs 23_Ct-1_3

hyb_protocol: 23_Ct-1_3 Cy5 / 11_52CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: B8_T8_M19_S143_mouse1


title: H3K27me3 ChIP sequencing of hVSMCs [H3K27me3-VSMC_rep1_FKDL190763215-1a_H3TMKCCX2_L3]


title: B8_T6_B8_S168_mouse1


title: 564016A07 - 19_Ct-1_1 vs 7_52CV_1

hyb_protocol: 7_52CV_1 Cy5 / 19_Ct-1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: A9_T8_B19_S179_mouse1


title: H3K27me3 ChIP sequencing of hVSMCs [H3K27me3-VSMC_rep3_FKDL190763217-1a_H3WLGCCX2_L4]


title: 564016A03 - 9_52CV_2 vs 10_52CV-N_2

hyb_protocol: 10_52CV-N_2 Cy5 / 9_52CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K36me3 ChIP sequencing of hVECs [H3K36me3-EC_rep1_FKDL190743617-1a_H2VVCCCX2_L7]


title: 564016A04 - 10_52CV-N_2 vs 9_52CV_2

hyb_protocol: 9_52CV_2 Cy5 / 10_52CV-N_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: A12_T1_L1_S173_mouse1


title: H3K27me3 ChIP sequencing of hNSCs [H3K27me3-NSC_rep3_FKDL190763211-1a_H3WLGCCX2_L4]

description:
H3K27me3 ChIP sequencing of hNSCs
H3K27me3-NSC.bw


title: A12_T8_E19_S251_mouse1


title: D8_T6_J9_S61_mouse1


title: 564016A01 - 7_52CV_1 vs 8_52CV-N_1

hyb_protocol: 8_52CV-N_1 Cy5 / 7_52CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27me3 ChIP sequencing of hNSCs [H3K27me3-NSC_rep2_FKDL190763210-1a_H3YJJCCX2_L8]


title: 564013A12 - 18_75CV-N_3 vs 17_75CV_3

hyb_protocol: 17_75CV_3 Cy5 / 18_75CV-N_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C11_T8_L20_S120_mouse1


title: 564016A02 - 8_52CV-N_1 vs 7_52CV_1

hyb_protocol: 7_52CV_1 Cy5 / 8_52CV-N_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C11_T2_B9_S241_mouse1


title: C10_T6_P8_S204_mouse1


title: H3K27me3 ChIP sequencing of hNSCs [H3K27me3-NSC_rep1_FKDL190763209-1a_H3TMKCCX2_L3]


title: D5_T7_E15_S247_mouse1


title: A3_T6_A7_S143_mouse1


title: D5_T6_G9_S289_mouse1


title: D5_T8_B21_S181_mouse1


title: H3K27me3 ChIP sequencing of hMSCs [H3K27me3-MSC_rep3_FKDL190763220-1a_H3WLGCCX2_L4]

description:
H3K27me3 ChIP sequencing of hMSCs
H3K27me3-MSC.bw


title: 564013A11 - 17_75CV_3 vs 18_75CV-N_3

hyb_protocol: 18_75CV-N_3 Cy5 / 17_75CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27me3 ChIP sequencing of hMSCs [H3K27me3-MSC_rep2_FKDL190763219-1a_H3YJJCCX2_L8]


title: H3K27me3 ChIP sequencing of hMSCs [H3K27me3-MSC_rep1_FKDL190763218-1a_H3TMKCCX2_L3]


title: C1_T9_C23_S207_mouse1


title: C9_T2_P8_S276_mouse1


title: H3K27me3 ChIP sequencing of hiPSCs [H3K27me3-iPSC_rep3_FKDL190763208-1a_H3WLGCCX2_L4]

description:
H3K27me3 ChIP sequencing of hiPSCs
H3K27me3-iPSC.bw


title: 564013A10 - 16_75CV-N_2 vs 15_75CV_2

hyb_protocol: 15_75CV_2 Cy5 / 16_75CV-N_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564013A09 - 15_75CV_2 vs 16_75CV-N_2

hyb_protocol: 16_75CV-N_2 Cy5 / 15_75CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E11_T6_I10_S38_mouse1


title: C1_T6_G8_S288_mouse1


title: C9_T1_A3_S211_mouse1


title: H3K27me3 ChIP sequencing of hiPSCs [H3K27me3-iPSC_rep2_FKDL190763207-1a_H3YJJCCX2_L8]


title: C9_T6_O8_S180_mouse1


title: H3K27me3 ChIP sequencing of hiPSCs [H3K27me3-iPSC_rep1_FKDL190763206-1a_H3TMKCCX2_L3]


title: C9_T8_J20_S72_mouse1


title: E11_T8_C22_S206_mouse1


title: H3K27me3 ChIP sequencing of hESCs [H3K27me3-ESC_rep3_FKDL190763205-1a_H3WLGCCX2_L4]

description:
H3K27me3 ChIP sequencing of hESCs
H3K27me3-ESC.bw


title: 564013A07 - 13_75CV_1 vs 14_75CV-N_1

hyb_protocol: 14_75CV-N_1 Cy5 / 13_75CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C2_T2_I8_S108_mouse1


title: 564013A06 - 6_Jea-N_3 vs 5_Jea_3

hyb_protocol: 5_Jea_3 Cy5 / 6_Jea-N_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564013A05 - 5_Jea_3 vs 6_Jea-N_3

hyb_protocol: 6_Jea-N_3 Cy5 / 5_Jea_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564013A08 - 14_75CV-N_1 vs 13_75CV_1

hyb_protocol: 13_75CV_1 Cy5 / 14_75CV-N_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 564013A04 - 4_Jea-N_2 vs 3_Jea_2

hyb_protocol: 3_Jea_2 Cy5 / 4_Jea-N_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: G5_T2_L11_S183_mouse1


title: H3K27me3 ChIP sequencing of hESCs [H3K27me3-ESC_rep2_FKDL190763204-1a_H3YJJCCX2_L8]


title: G5_T6_K11_S87_mouse1


title: 564013A03 - 3_Jea_2 vs 4_Jea-N_2

hyb_protocol: 4_Jea-N_2 Cy5 / 3_Jea_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27me3 ChIP sequencing of hESCs [H3K27me3-ESC_rep1_FKDL190763203-1a_H3TMKCCX2_L3]


title: G5_T7_H17_S21_mouse1


title: C2_T9_K23_S99_mouse1


title: H3K27me3 ChIP sequencing of hVECs [H3K27me3-EC_rep3_FKDL190763214-1a_H3WLGCCX2_L4]

description:
H3K27me3 ChIP sequencing of hVECs
H3K27me3-EC.bw


title: D10_T8_G21_S1_mouse1


title: D10_T3_L15_S187_mouse1


title: C6_T8_G20_S300_mouse1


title: G11_T3_A18_S226_mouse1


title: D10_T6_L9_S109_mouse1


title: H3K27me3 ChIP sequencing of hVECs [H3K27me3-EC_rep2_FKDL190763213-1a_H3YJJCCX2_L8]


title: C12_T8_M20_S144_mouse1


title: 564013A02 - 2_Jea-N_1 vs 1_Jea_1

hyb_protocol: 1_Jea_1 Cy5 / 2_Jea-N_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27me3 ChIP sequencing of hVECs [H3K27me3-EC_rep1_FKDL190763212-1a_H3TMKCCX2_L3]


title: C12_T2_C9_S265_mouse1


title: F8_T2_C11_S267_mouse1


title: H10_T7_H18_S22_mouse1


title: F5_T6_O10_S182_mouse1


title: C7_T8_H20_S24_mouse1


title: H3K27ac ChIP sequencing of hVSMCs [H3K27ac-VSMC_rep2_FKDL190741280-1a]

description:
H3K27ac ChIP sequencing of hVSMCs
H3K27ac-VSMC.bw


title: 564013A01 - 1_Jea_1 vs 2_Jea-N_1

hyb_protocol: 2_Jea-N_1 Cy5 / 1_Jea_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563965A12 - 24_Ct-1_N_3 vs 23_Ct-1_3

hyb_protocol: 23_Ct-1_3 Cy5 / 24_Ct-1_N_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C7_T6_M8_S132_mouse1


title: 563965A09 - 21_Ct-1_2 vs 22_Ct-1_N_2

hyb_protocol: 22_Ct-1_N_2 Cy5 / 21_Ct-1_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563965A10 - 22_Ct-1_N_2 vs 21_Ct-1_2

hyb_protocol: 21_Ct-1_2 Cy5 / 22_Ct-1_N_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: A11_T8_D19_S227_mouse1


title: C7_T3_M14_S210_mouse1


title: B9_T3_C14_S270_mouse1


title: B9_T7_A14_S150_mouse1


title: 563965A11 - 23_Ct-1_3 vs 24_Ct-1_N_3

hyb_protocol: 24_Ct-1_N_3 Cy5 / 23_Ct-1_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C5_T6_K8_S84_mouse1


title: C5_T2_L8_S180_mouse1


title: H3K27ac ChIP sequencing of hVSMCs [H3K27ac-VSMC_rep3_FKDL190741281-1a]


title: 563965A07 - 19_Ct-1_1 vs 20_Ct-1_N_1

hyb_protocol: 20_Ct-1_N_1 Cy5 / 19_Ct-1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27ac ChIP sequencing of hNSCs [H3K27ac-NSC_rep3_FKDL190741275-1a]

description:
H3K27ac ChIP sequencing of hNSCs
H3K27ac-NSC.bw


title: H3K27ac ChIP sequencing of hNSCs [H3K27ac-NSC_rep1_FKDL190741273-1a]


title: E5_T7_P15_S211_mouse1


title: H3K27ac ChIP sequencing of hNSCs [H3K27ac-NSC_rep2_FKDL190741274-1a]


title: H3K27ac ChIP sequencing of hVSMCs [H3K27ac-VSMC_rep1_FKDL190741279-1a]


title: H3K27ac ChIP sequencing of hMSCs [H3K27ac-MSC_rep3_FKDL190741284-1a]

description:
H3K27ac ChIP sequencing of hMSCs
H3K27ac-MSC.bw


title: E5_T1_E4_S8_mouse1


title: B9_T8_N19_S167_mouse1


title: B5_T1_A2_S210_mouse1


title: H3K27ac ChIP sequencing of hMSCs [H3K27ac-MSC_rep2_FKDL190741283-1a]


title: 563965A06 - 17_75CV_3 vs 23_Ct-1_3

hyb_protocol: 23_Ct-1_3 Cy5 / 17_75CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563965A08 - 20_Ct-1_N_1 vs 19_Ct-1_1

hyb_protocol: 19_Ct-1_1 Cy5 / 20_Ct-1_N_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27ac ChIP sequencing of hMSCs [H3K27ac-MSC_rep1_FKDL190741282-1a]


title: B3_T7_K13_S89_mouse1


title: G10_T3_P17_S285_mouse1


title: G10_T6_P11_S207_mouse1


title: 563965A02 - 13_75CV_1 vs 19_Ct-1_1

hyb_protocol: 19_Ct-1_1 Cy5 / 13_75CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27ac ChIP sequencing of hiPSCs [H3K27ac-iPSC_rep3_FKDL190741272-1a]

description:
H3K27ac ChIP sequencing of hiPSCs
H3K27ac-iPSC.bw


title: F4_T1_P4_S272_mouse1


title: 563965A05 - 23_Ct-1_3 vs 17_75CV_3

hyb_protocol: 17_75CV_3 Cy5 / 23_Ct-1_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563965A04 - 15_75CV_2 vs 21_Ct-1_2

hyb_protocol: 21_Ct-1_2 Cy5 / 15_75CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27ac ChIP sequencing of hiPSCs [H3K27ac-iPSC_rep2_FKDL190741271-1a]


title: F4_T6_N10_S158_mouse1


title: 563965A01 - 19_Ct-1_1 vs 13_75CV_1

hyb_protocol: 13_75CV_1 Cy5 / 19_Ct-1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: B12_T8_A20_S156_mouse1


title: B5_T6_O7_S179_mouse1


title: H3K27ac ChIP sequencing of hESCs [H3K27ac-ESC_rep3_FKDL190741269-1a]

description:
H3K27ac ChIP sequencing of hESCs
H3K27ac-ESC.bw


title: H8_T5_K6_S82_mouse1


title: A10_T8_C19_S203_mouse1


title: H3K27ac ChIP sequencing of hiPSCs [H3K27ac-iPSC_rep1_FKDL190741270-1a]


title: B12_T6_F8_S264_mouse1


title: B3_T9_B24_S184_mouse1


title: H8_T3_J18_S142_mouse1


title: H1_T9_H23_S27_mouse1


title: H3K27ac ChIP sequencing of hESCs [H3K27ac-ESC_rep2_FKDL190741268-1a]


title: H1_T6_C12_S196_mouse1


title: H1_T7_O17_S189_mouse1


title: F7_T1_C5_S261_mouse1


title: F6_T7_M16_S140_mouse1


title: 563907A11 - 5_Jea_3 vs 11_52CV_3

hyb_protocol: 11_52CV_3 Cy5 / 5_Jea_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563907A09 - 3_Jea_2 vs 9_52CV_2

hyb_protocol: 9_52CV_2 Cy5 / 3_Jea_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563907A12 - 11_52CV_3 vs 5_Jea_3

hyb_protocol: 5_Jea_3 Cy5 / 11_52CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563907A10 - 9_52CV_2 vs 3_Jea_2

hyb_protocol: 3_Jea_2 Cy5 / 9_52CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: F6_T3_P16_S284_mouse1


title: 563907A08 - 7_52CV_1 vs 1_Jea_1

hyb_protocol: 1_Jea_1 Cy5 / 7_52CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563907A06 - 17_75CV_3 vs 5_Jea_3

hyb_protocol: 5_Jea_3 Cy5 / 17_75CV_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H3K27ac ChIP sequencing of hVECs [H3K27ac-EC_rep3_FKDL190741278-1a]

description:
H3K27ac ChIP sequencing of hVECs
H3K27ac-EC.bw


title: 563907A07 - 1_Jea_1 vs 7_52CV_1

hyb_protocol: 7_52CV_1 Cy5 / 1_Jea_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: F6_T6_P10_S206_mouse1


title: G8_T6_N11_S159_mouse1


title: H3K27ac ChIP sequencing of hVECs [H3K27ac-EC_rep2_FKDL190741277-1a]


title: G8_T7_K17_S93_mouse1


title: H3K27ac ChIP sequencing of hVECs [H3K27ac-EC_rep1_FKDL190741276-1a]


title: ATAC sequencing of hVSMCs [ATAC-VSMC_rep2]

description:
ATAC sequencing of hVSMCs
ATAC-VSMC.bw


title: D11_T6_M9_S133_mouse1


title: ATAC sequencing of hVSMCs [ATAC-VSMC_rep1]

description:
ATAC sequencing of hVSMCs
ATAC-VSMC.bw


title: D11_T2_N9_S229_mouse1


title: D11_T1_O3_S247_mouse1


title: E6_T8_N21_S169_mouse1


title: H3K27ac ChIP sequencing of hESCs [H3K27ac-ESC_rep1_FKDL190741267-1a]


title: E6_T7_A16_S152_mouse1


title: F10_T7_A17_S153_mouse1


title: F12_T2_G11_S63_mouse1


title: ATAC sequencing of hNSCs [ATAC-NSC_rep2]

description:
ATAC sequencing of hNSCs
ATAC-NSC.bw


title: F10_T6_D11_S219_mouse1


title: F12_T3_F17_S45_mouse1


title: 563907A05 - 5_Jea_3 vs 17_75CV_3

hyb_protocol: 17_75CV_3 Cy5 / 5_Jea_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 563907A04 - 15_75CV_2 vs 3_Jea_2

hyb_protocol: 3_Jea_2 Cy5 / 15_75CV_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: G9_T3_O17_S261_mouse1


title: G9_T6_O11_S183_mouse1


title: ATAC sequencing of hMSCs [ATAC-MSC_rep1]

description:
ATAC sequencing of hMSCs
ATAC-MSC.bw


title: 563907A01 - 1_Jea_1 vs 13_75CV_1

hyb_protocol: 13_75CV_1 Cy5 / 1_Jea_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: ATAC sequencing of hiPSCs [ATAC-iPSC_rep2]

description:
ATAC sequencing of hiPSCs
ATAC-iPSC.bw


title: G9_T7_L17_S117_mouse1


title: G6_T2_M11_S207_mouse1


title: ATAC sequencing of hNSCs [ATAC-NSC_rep1]

description:
ATAC sequencing of hNSCs
ATAC-NSC.bw


title: ATAC sequencing of hiPSCs [ATAC-iPSC_rep1]

description:
ATAC sequencing of hiPSCs
ATAC-iPSC.bw


title: G1_T6_G11_S291_mouse1


title: Biofilm 2h 2 Co22

city: Hannover

first: Alexandra

last: Ingendoh-Tsakmakidis

address: Stadtfelddamm 34

department: Prosthetic Dentistry and Biomedical Materials Science

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 500ng of labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)     Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: Biofilm 2h 2 Co22

label_protocol: 70ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification), except that reaction volumes were halved. Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to each single sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies).

growth_protocol: HGF or HGEp were grown on titanium disks. For HGF, a density of 15,000 cells per mL per well in fully supplemented DMEM was used. For HGEp, a density of 45,000 cells per mL per well in CnT Prime medium was used. Incubation and culture was performed at 37 °C in a humidified atmosphere with 5 % CO2 for four days with a single medium replacement after two days. Fully supplemented DMEM --> 10 % FBS and 1 % v/v penicillin/streptomycin.

extract_protocol: The RNA from tissue cells was isolated using the RNeasy ® Mini Kit from QIAGEN (74104) according to the manufacturer’s instructions. The on-column DNAse I treatment was applied. The RLT buffer was supplemented with 1 % (v/v) β-mercaptoethanol and added to the tissue cells. A cell scraper was used to scratch the cells from the titanium disks.

treatment_protocol: HGF or HGEp grown on titanium disks were challenged with the S. oralis biofilm for 2 hours. The tissue cell culture media were used for the co-culture without addition of any antibiotic. The co-cultures were performed at 37 °C in a humidified atmosphere with 5 % CO2.

value: Primary human epithelila cells (HGEp)

tag: experimental run

tag: group

value: Biofilm


title: Control 2h 3 Co22

source_name: Control 2h 3 Co22

value: Control


title: G1_T3_G17_S69_mouse1


title: ATAC sequencing of hMSCs [ATAC-MSC_rep2]

description:
ATAC sequencing of hMSCs
ATAC-MSC.bw


title: Control 2h 1 Co22

source_name: Control 2h 1 Co22


title: Biofilm 2h 3 Co22

source_name: Biofilm 2h 3 Co22


title: ATAC sequencing of hESCs [ATAC-ESC_rep2]

description:
ATAC sequencing of hESCs
ATAC-ESC.bw


title: G1_T9_G23_S3_mouse1


title: G9_T2_P11_S279_mouse1


title: H6_T7_D18_S226_mouse1


title: Control 2h 2 Co21

source_name: Control 2h 2 Co21


title: 563907A03 - 3_Jea_2 vs 15_75CV_2

hyb_protocol: 15_75CV_2 Cy5 / 3_Jea_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: H6_T2_I12_S112_mouse1


title: H6_T6_H12_S16_mouse1


title: 563907A02 - 13_75CV_1 vs 1_Jea_1

hyb_protocol: 1_Jea_1 Cy5 / 13_75CV_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Control 2h 1 Co21

source_name: Control 2h 1 Co21


title: D7_T8_D21_S229_mouse1


title: Biofilm 2h 2 Co21

source_name: Biofilm 2h 2 Co21


title: F12_T1_H5_S81_mouse1


title: ATAC sequencing of hESCs [ATAC-ESC_rep1]

description:
ATAC sequencing of hESCs
ATAC-ESC.bw


title: ATAC sequencing of hVECs [ATAC-EC_rep2]

description:
ATAC sequencing of hVECs
ATAC-EC.bw


title: ATAC sequencing of hVECs [ATAC-EC_rep1]

description:
ATAC sequencing of hVECs
ATAC-EC.bw


title: D7_T3_I15_S115_mouse1


title: A1_T6_O6_S178_mouse1


title: A1_T2_P6_S274_mouse1


title: In Vitro Fertilized oocytes antisense 3 (IVF Anti3)

city: Yangling

first: Xiaoxu

address: Litai street

institute: Northwest A&F University

description:
total RNA
Embryo FPKM.txt

data_processing:
For small RNA analysis, we used a recently developed tool by Shi et.al published on Genomics, proteomics & bioinformatics    to analyze rRNA- and tRNA-derived small RNAs.
For single RNA sequencing, raw sequencing output was removed, clean data were mapped onto the reference genome (Sscrofa10.2.89) from Ensembl with TopHat v2.0.12. Total gene read counts were calculated as FPKM.
Genome_build: Sscrofa10.2.89

organism: Sus scrofa

source_name: 2-cell embryo

extract_protocol:
For small RNA sequencing, RNA was isolated by using Trizol (Takara) according to the manufacturer’s protocol. For single cell sequencing, every five 2-cell parthenogentically activated embryo or IVF embryo were pooled together. Embryos were lysed to release all RNAs and external RNA controls consortium (ERCC) was added into the released RNAs.
cDNA libraries of small RNAs were constructed using 10 ng of total RNA. After the adaptor ligation, first-strand cDNA synthesis and PCR amplification, the 130bp to 160bp DNA fragments corresponding to the small RNA fraction were acquired.For single cell sequencing, first strand cDNA was reverse transcribed into first cDNA strands by using the Smart-Seq2 method.

value: In Vitro Fertilized oocytes

tag: tag

value: tRNAGln-TTG antisense


title: A1_T3_O12_S256_mouse1

value: Primary brain cells  from muring mPFC


title: In Vitro Fertilized oocytes antisense 2 (IVF Anti2)

description:
total RNA
Embryo FPKM.txt


title: A1_T7_M12_S136_mouse1


title: In Vitro Fertilized oocytes antisense 1 (IVF Anti1)

description:
total RNA
Embryo FPKM.txt


title: D1_T2_D9_S289_mouse1


title: D7_T6_I9_S37_mouse1


title: Biofilm 2h 2 Co20

source_name: Biofilm 2h 2 Co20


title: In Vitro Fertilized oocytes control 3 (IVF NC3)

description:
total RNA
Embryo FPKM.txt

value: control


title: E10_T8_B22_S182_mouse1


title: E10_T3_H16_S92_mouse1


title: D1_T6_C9_S193_mouse1


title: E10_T2_I10_S110_mouse1


title: Biofilm 2h 1 Co20

source_name: Biofilm 2h 1 Co20


title: In Vitro Fertilized oocytes control 2 (IVF NC2)

description:
total RNA
Embryo FPKM.txt


title: E10_T6_H10_S14_mouse1


title: Biofilm 2h 3 Co18

source_name: Biofilm 2h 3 Co18

value: Primary human gingival fibroblasts (HGF)


title: A8_T7_D13_S221_mouse1


title: D1_T1_E3_S7_mouse1


title: Parthenogenetic-activated oocytes antisense 3 (PA Anti3)

description:
total RNA
Embryo FPKM.txt

value: Parthenogenetic-activated oocytes


title: A5_T8_N18_S166_mouse1


title: A5_T2_D7_S287_mouse1


title: Parthenogenetic-activated oocytes antisense 2 (PA Anti2)

description:
total RNA
Embryo FPKM.txt


title: Biofilm 2h 2 Co18

source_name: Biofilm 2h 2 Co18


title: Control 2h 1 Co20

source_name: Control 2h 1 Co20


title: C3_T1_K2_S150_mouse1


title: 563965A03 - 21_Ct-1_2 vs 15_75CV_2

hyb_protocol: 15_75CV_2 Cy5 / 21_Ct-1_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: C3_T7_G14_S294_mouse1


title: Control 2h 3 Co20

source_name: Control 2h 3 Co20


title: Control 2h 2 Co18

source_name: Control 2h 2 Co18


title: Control 2h 1 Co18

source_name: Control 2h 1 Co18


title: Biofilm 2h 2 Co15

source_name: Biofilm 2h 2 Co15


title: C3_T6_I8_S36_mouse1


title: Parthenogenetic-activated oocytes antisense 1 (PA Anti1)

description:
total RNA
Embryo FPKM.txt


title: In Vitro Fertilized oocytes control 1 (IVF NC1)

description:
total RNA
Embryo FPKM.txt


title: H9_T7_G18_S298_mouse1


title: H9_T3_K18_S166_mouse1


title: Parthenogenetic-activated oocytes control 3 (PA NC3)

description:
total RNA
Embryo FPKM.txt


title: H3_T9_H24_S28_mouse1


title: E1_T6_O9_S181_mouse1


title: H3_T7_A18_S154_mouse1


title: H3_T2_F12_S40_mouse1


title: Parthenogenetic-activated oocytes control 2 (PA NC2)

description:
total RNA
Embryo FPKM.txt


title: Biofilm 2h 1 Co18

source_name: Biofilm 2h 1 Co18


title: H3_T6_E12_S244_mouse1


title: E9_T6_G10_S290_mouse1


title: Parthenogenetic-activated oocytes control 1 (PA NC1)

description:
total RNA
Embryo FPKM.txt


title: Biofilm 2h 1 Co15

source_name: Biofilm 2h 1 Co15


title: E9_T8_A22_S158_mouse1


title: E9_T7_D16_S224_mouse1


title: Biofilm 2h 2 Co14

source_name: Biofilm 2h 2 Co14


title: E9_T1_I4_S104_mouse1


title: Control 2h 1 Co15

source_name: Control 2h 1 Co15

value: Cotrol


title: PANC-1_siMETTL3-14_rep3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

source_name: pancreas cancer derived cell line

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second stramd synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment. Completed libraries are sequenced on an Illumina HiSeq platform.

treatment_protocol: 96 hours upon transfection cells were harvested for RNA extraction.

tag: cell line

value: pancreas cancer derived cell line

tag: sirna

value: siRNA pool against METTL3 and METTL14

tag: collection time

value: harvested 96h upon transfection


title: C4_T1_L2_S174_mouse1


title: Control 2h 2 Co15

source_name: Control 2h 2 Co15


title: C4_T8_E20_S252_mouse1


title: Strain-4

city: Paris

first: Gwladys

last: Bertin

address: rue de l'observatoire

institute: Institut de Recherche pour le Développement

data_processing:
Genome index generation with STAR-2.7.1a(--sjdbOverhang 150 --genomeSAindexNbases 11-- sjdbGTFfile *gff file for each corresponding reference genome (from PlasmoDB)* --sjdbGTFtagExonParentTranscript Parent)
Mapping on reference genome with STAR-2.7.1a, default parameters
Sam to bam conversion and reads sort with Samtools-1.9
Absolute transcript abundance was evaluated by calculating Fragment Per Kilobase Million (FPKM) with Cufflinks-2.2.1
Genome_build: PlasmoDB release 43 - Pfalciparum3D7 for 3D7 strain samples - PfalciparumHB3 for HB3 strain samples - PfalciparumIT for ITG strain sample
Supplementary_files_format_and_content: Output files from cufflinks including FPKM values

organism: Plasmodium falciparum

source_name: Selected laboratory strain

growth_protocol: Parasites were cultivated in O+ red blood cells (EFS, Bichat Hospital, France) with RPMI1640 medium (Gibco) supplemented as described (Trager an Jensen, Science 1976). Parasites were cultivated at 37°C under 5% CO2, 20% O2, 75% N2. Parasitemia was monitored daily at ×100 immersion light microscopy using DiffQuick (RAL Diagnostics) reagent stained thin smear. Five independent samples were studied (S1-S5), corresponding to three parasites strains (ITG, Hb3, 3D7 respectively). ITG strain (S1) and 3D7 (S2) presented a background binding phenotype for human ICAM-1 receptor (obtained using binding to CHO-ICAM-1 transfected cells - ATCC® CRL-2093™ ), Hb3 (S4) and 3D7 (S3) for human brain endothelial cells (Hbec-5i ATCC® CRL-3245™ ) and Hb3 (S5) for CD36 human receptor (obtained with CHO-CD36 transfected cells - ATCC® CRL-2092™). Young trophozoites were preserved within an 18-24h time frame and development stage was assessed with Giemsa stain film microscopy assessment at ×100 oil immersion objective.

extract_protocol:
RNA was extracted as described in Ponts N et al 2012, then digested with DNAse I (Qiagen) and purified using RNEasy MinElute Cleanup kit column (Qiagen).. Absence of genomic DNA was assessed by the absence of amplification of p90 gene in qPCR from the direct use of the RNA extract, using Syber Green reagent (Life Technology) on Rotorgene 6000. RNA quality was assessed using Nanodrop (2000c) dosage and PicoChip Agilent 2100TM Bioanalyzeur profile (Agilent). Only RNA presenting a RNA Integrity Number (RIN) > 7 were retained for downstream analysis
RNA-seq libraries were performed by TruSeq Stranded mRNA protocol (Illumina®, California, U.S.A.)

tag: strain

tag: phenotype

value: Hbec-5i binding

tag: developmental stage

value: ring


title: Strain-5

value: CD36 binding


title: Control 2h 1 Co14

source_name: Control 2h 1 Co14

tag: cell type


title: Strain-3


title: PANC-1_siMETTL3-14_rep2


title: C4_T2_K8_S156_mouse1


title: C4_T9_K24_S100_mouse1


title: Strain-2

value: ICAM-1 binding


title: PANC-1_siMETTL3-14_rep1


title: C4_T3_J14_S138_mouse1


title: A4_T9_I24_S52_mouse1


title: PANC-1_siC_rep3_control_for_siMETTL

value: Control siRNA


title: A4_T1_D1_S281_mouse1


title: A4_T8_M18_S142_mouse1


title: PANC-1_siC_rep2_control_for_siMETTL


title: Strain-1

value: ITG


title: E8_T1_H4_S80_mouse1


title: A4_T6_B7_S167_mouse1


title: E8_T6_F10_S266_mouse1


title: E8_T8_P21_S217_mouse1


title: E8_T3_F16_S44_mouse1


title: G2_T3_H17_S93_mouse1


title: PANC-1_siE2F1-2-3_rep2

molecule: polyA RNA

value: siRNA pool against E2F1, E2F2 and E2F3


title: B11_T2_F8_S36_mouse1


title: SLR1431 50 ng/ml

city: Minneapolis

first: Frank

middle: Martin

last: Cichocki

state: Minnesota

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

description: FACS sorted

data_processing:
Quality of data in fastq files was assessed using FastQC
Reads were aligned using HISAT2 version 2.1.0
The Ensembl annotation release 87 was used.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw read counts were generated using featureCounts from the Subread R package version 1.6.2

source_name: Peripheral blood mononuclear cells

growth_protocol: FACS sorted human CD56bright NK cells were cultured in either DMSO or 25/50 ng/ml ascorbic acid.

extract_protocol:
RNA was extracted using the RNAeasy Kit from Qiagen.
RNA-seq libraries were generated using the TruSeq RNA Library Prep Kit v2. RNA was then multiplexed and sequenced on a NextSeq 550 Sequencing 150-paired end output.

treatment_protocol: Frozen PBMC aliqouts were thawed and rested overnight in RPMI media with 10% FBS prior to antibody staining and sorting the next day. No cytokines were added

value: CD56bright NK cells

tag: markers

value: 50 ng/ml ascorbic acid


title: SLR1425 25 ng/ml

description: FACS sorted

value: 25 ng/ml ascorbic acid


title: SLR1425 DMSO

description: FACS sorted

value: DMSO


title: SLR1431 DMSO

description: FACS sorted


title: Biofilm 2h 1 Co14

source_name: Biofilm 2h 1 Co14

value: Primary human gingival fibroblasts (HGF)

value: Biofilm


title: G2_T9_O23_S195_mouse1

value: Primary brain cells  from muring mPFC


title: E12_T8_D22_S230_mouse1


title: PANC-1_siE2F1-2-3_rep1

value: pancreas cancer derived cell line


title: B11_T8_P19_S215_mouse1


title: SLR1407 DMSO

description: FACS sorted


title: SLR1405 50 ng/ml

description: FACS sorted


title: E12_T3_J16_S140_mouse1


title: PANC-1_siC_rep2_control_for_siE2F


title: PANC-1_siC_rep3_control_for_siE2F


title: E12_T1_L4_S176_mouse1


title: B10_T6_D8_S216_mouse1


title: PANC-1_siC_rep1_control_for_siMETTL


title: SLR1405 DMSO

description: FACS sorted


title: F1_T1_M4_S200_mouse1


title: E12_T6_J10_S62_mouse1


title: PANC-1_siE2F1-2-3_rep3


title: SLR1407 50 ng/ml

description: FACS sorted


title: F1_T2_L10_S182_mouse1


title: F1_T7_H16_S20_mouse1


title: F1_T9_F23_S279_mouse1


title: F1_T6_K10_S86_mouse1


title: HepG2_siImp1_rep3

source_name: liver cancer derived cell line

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

value: liver cancer derived cell line

value: siRNA pool against IGF2BP1

value: harvested 72h upon transfection


title: E4_T9_M24_S148_mouse1


title: E4_T6_B10_S170_mouse1


title: G3_T9_G24_S4_mouse1


title: HepG2_siImp1_rep1


title: HepG2_siImp1_rep2


title: G4_T9_O24_S196_mouse1


title: G4_T6_J11_S63_mouse1


title: N1574_plus doxycycline 3

first: Christian

last: Bär

address: Carl-Neuberg-Str. 1

department: IMTTS

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422
nfcore/rnaseq (v1.3), pipeline: Nextflow (v18.10.1), FastQC (v0.11.8), TrimGalore (v0.5.0), STAR (vSTAR_2.6.1d), RSeQC (v3.0.0), dupRadar, Preseq (v2.0.3), featureCounts (v1.6.4), StringTie (v1.3.5), Sample_correlation, MultiQC (v1.7)
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: GRCh38; release 29
Supplementary_files_format_and_content: tab-delimited text files of raw read counts from each sample.

source_name: human iPSCs

extract_protocol:
iPSCs were harvested and RNA were isolated with miRNeasy mini kit (Qiagen). 500ng of total RNA was used for mRNA enrichment procedure with NEBNext PolyA mRNA magnetic Isolation Module.
Stranded cDNA library was generated using using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with an additional purification step using Agencourt® AMPure® XP Beads. cDNA libraries were barcoded by dual indexing approach with NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs.

value: iPSCs

value: treated with doxycycline

tag: genotype

value: knockdown of Cyrano


title: N1572_plus doxycycline 1


title: N1571_doxycycline control 3

value: control


title: HepG2_siC_rep2

value: Control siRNA


title: G4_T3_J17_S141_mouse1


title: N1569_doxycycline control 1


title: PANC-1_siC_rep1_control_for_siE2F

value: harvested 96h upon transfection


title: Imp1 KO_rep3

data_processing:
Sequenced reads were trimmed for adapter sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

source_name: lung cancer derived cell line

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second stramd synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment. Completed libraries are sequenced on an Illumina HiSeq platform.
poly-A RNA-Seq

treatment_protocol: 48 hours upon seeding cells were harvested for RNA extraction.

tag: genomic knockout

value: IGF2BP1 knockout

tag: passages

value: harvested 48h upon seeding


title: G4_T7_G17_S297_mouse1


title: HepG2_siC_rep1


title: D9_T1_M3_S199_mouse1


title: N1570_doxycycline control 2


title: E2_T9_M23_S147_mouse1


title: HepG2_siC_rep3


title: N1573_plus doxycycline 2


title: D9_T8_F21_S277_mouse1


title: D9_T3_K15_S163_mouse1


title: Imp1 KO_rep2


title: D9_T2_L9_S181_mouse1


title: D9_T6_K9_S85_mouse1


title: Imp1 KO_rep1


title: A7_T8_P18_S214_mouse1


title: A7_T6_E7_S239_mouse1


title: WT_rep3

value: Control


title: F3_T6_M10_S134_mouse1


title: WT_rep2


title: E7_T3_E16_S20_mouse1


title: WT_rep1


title: H2_T9_P23_S219_mouse1


title: A2_T6_P6_S202_mouse1


title: H7_T1_K6_S154_mouse1


title: H2_T6_D12_S220_mouse1


title: A6_T7_B13_S173_mouse1


title: GC1

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8. The _i.fastq.gz files contain sample barcodes, the _1.fastq.gz files contain feature barcodes and the _2.fastq.gz files contain reads. The data can be de-multiplexed using 10X Genomics CellRanger software.
RNA reads were mapped to the human genome (GRCh38) using 10x Genomics Cell Ranger v2.1
Antibody tags and cell barcodes were extracted using the feature barcoding function of 10x Genomics Cell Ranger v3.0. The feature references for mapping feature barcodes to antibody names are provided in the processed data files.
Genome_build: grch38
Supplementary_files_format_and_content: Tab delimited text files with cell barcodes, transcript counts and antibody tag counts. Antibody feature references are provided as CSV files for compatability with CellRanger.

source_name: Germinal Center B cells

growth_protocol: Surgically removed tonsil tissue was immediately processed to isolate mononuclear cells by Ficoll.

extract_protocol:
Single cells were captured and analyzed in the Chromium Controller using the Chromium Single Cell 3' kit v2 (10X Genomics) according to the manufacturer's instructions.
Libraries were prepared using the Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics).

treatment_protocol: Tonsillar dark zone (CD3-; IgD-; CD38+; CXCR4high; CD83low), light zone (CD3-; IgD-; CD38+; CXCR4low; CD83high) and total (CD3-; IgD-; CD38+) germinal center B cells were isolated by cytofluorimetric cell sorting.

tag: tissue

value: Tonsil


title: DZ1

source_name: Dark zone germinal center B cells


title: H7_T2_J12_S136_mouse1


title: H7_T3_I18_S118_mouse1


title: A6_T8_O18_S190_mouse1


title: A6_T2_E7_S11_mouse1


title: A6_T6_D7_S215_mouse1


title: Tonsil LZ_4

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (GRCh38) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -k 5. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v1.8 using the markdup option.
Reads were mapped to exons to produce count tables which were converted to transcript per million (TPM) values.
Genome_build: grch38
Supplementary_files_format_and_content: TPM tables containing the normalized transcripts per million mapped reads (TPM) counts for genes.

source_name: Light Zone Germinal Center B cells

extract_protocol:
Total RNA was isolated using the Trizol Reagent and cleaned up by  Qiagen RNAeasy kit, according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Tonsillar naïve, germinal center and memory B cells were isolated by magnetic cell separation, as described in Klein et al, Proc Natl Acad Sci U S A, 2003. Dark zone and light zone germinal center cells were isolated by magnetic cell separation, as described in Victora, Dominguez-Sola et al, Blood, 2012.

value: Light Zone Germinal Center B


title: A6_T3_D13_S293_mouse1


title: F3_T2_N10_S230_mouse1


title: F11_T1_G5_S57_mouse1


title: F11_T3_E17_S21_mouse1


title: F11_T6_E11_S243_mouse1


title: LZ1

source_name: Light zone germinal center B cells


title: C8_T8_I20_S48_mouse1


title: F11_T2_F11_S39_mouse1


title: C8_T6_N8_S156_mouse1


title: D2_T9_L23_S123_mouse1


title: D2_T2_E9_S13_mouse1


title: Tonsil DZ_3

source_name: Dark Zone Germinal Center B cells

value: Dark Zone Germinal Center B


title: Tonsil LZ_1


title: Biofilm 2h 1 Co21

source_name: Biofilm 2h 1 Co21

value: Primary human epithelila cells (HGEp)

value: Biofilm


title: D4_T9_L24_S124_mouse1

value: Primary brain cells  from muring mPFC


title: Tonsil DZ_2


title: D4_T8_A21_S157_mouse1


title: B4_T2_O7_S251_mouse1


title: B4_T9_J24_S76_mouse1


title: Tonsil DZ_1


title: B4_T8_I19_S47_mouse1


title: Tonsil LZ_3


title: Tonsil LZ_2


title: Tonsil M_3

source_name: Memory B cells

value: Memory B


title: D12_T1_P3_S271_mouse1


title: D12_T8_I21_S49_mouse1


title: Tonsil DZ_4


title: D12_T3_N15_S235_mouse1


title: Tonsil M_2


title: B7_T2_B8_S240_mouse1


title: Tonsil M_1


title: D4_T6_F9_S265_mouse1


title: B7_T1_C2_S258_mouse1


title: B7_T6_A8_S144_mouse1


title: H4_T2_G12_S64_mouse1


title: Tonsil CB_3

value: Germinal Center B


title: Tonsil CB_2


title: prostate_tissue-H-sf-replicate_RIB0034304

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate RP tissue specimen (prostate cancer)

hyb_protocol: We used 1.65 µg of labeled cRNA for hybridization with the custom microarray following manufacturer's instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) and following settings for scanning: Profile: AgilentG3_GX_1Color; Channels: Green; Scan Region: Agilent HD (61x 21,6 mm); Resolution: 3 µm double pass; Tiff: 20 bit; Green PMT Gain: 100 %. We extracted the result tables after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1).

data_processing: Three microarray were excluded from further processing due to scratches on array slides (data not included in GEO series). Quality control of remaining arrays (N=255) was performed by checking distribution of ``bright corner'', ``dark corner'' probes, and relative spike-in concentration versus normalized signal. Quality control confirmed high quality of the results and consequently all remaining microarray data were included in the downstream analysis. To retrieve a set of probes mapping to unique genomic positions in hg19 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites. All probes mapping to more than one distinct genomic region were discarded. Normalization between arrays was done by using quantile normalization. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least 20 arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model to detect expression variation between BPH and tumor specimens adjusted for array processing batches was fitted using limma v3.24.15 and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.

source_name: prostate

label_protocol: We prepared all samples assembled for expression analysis with the custom microarray using the Agilent Quick Amp Labeling Kit for single color following the manufacturer's instructions. Instead of the Oligo-dT/T7-primer delivered with the Quick Amp Labeling Kit, we used 120 pmol of a random N6/T7 primer synthesized by Metabion (Planegg, Germany) and used 200 ng RNA as input for the labeling procedure. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer's instructions.

extract_protocol: Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content (Supplementary Figure S1). Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.

tag: risk group

value: H-sf

value: prostate

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: prostate cancer


title: F2_T9_N23_S171_mouse1


title: prostate_tissue-C-replicate_RIB0034494

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: C

value: benign prostate hyperplasia


title: F2_T7_I16_S44_mouse1


title: Tonsil CB_1


title: F2_T1_N4_S224_mouse1


title: E3_T6_A10_S146_mouse1


title: Tonsil N_3

source_name: Naïve B cells

value: Naive B


title: prostate_tissue-C-replicate_RIB0034653


title: D6_T8_C21_S205_mouse1


title: Tonsil N_2


title: D6_T1_J3_S127_mouse1


title: prostate_tissue-C-replicate_RIB0034687


title: B7_T8_L19_S119_mouse1


title: prostate_tissue-H-sf-replicate_RIB0034829


title: B1_T6_K7_S83_mouse1


title: Tonsil N_1


title: prostate_tissue-C-replicate_RIB0034350


title: HUVEC.miRNA.oxPAPC_7h.rep1

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

data_processing:
For GRO-Seq and RNA-Seq, reads have been trimmed to remove 3' A-stretches from the library preparation and for all libraries the low quality reads were excluded (minimum 97% of bp over quality cutoff 10).
GRO-Seq reads have been aligned to hg19 with bowtie allowing up to two mismatches and only one alignment per read.
RNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for long RNA-seq pipeline.
microRNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for small RNA-seq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs and HAECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich); HASMC were cultrured in Medium 231 (Cascade Biologics®) supplemented with Smooth Muscle Growth Supplement (SMGS). CD14+/Macrophages were cultured in Medium RPMI 1640, supplemented with 10 % FBS, 100μg/ml streptomycin,100 U/ml penicillin, and 2 mM glutamine, 1 % Na-pyruvate, 1 % NEAA and supplemented with rHu M-CSF (50ng/ml; ThermoFisher Scientific).

extract_protocol:
Small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
The libraries were prepared at Finnish Microarray and Sequencing Centre (FMSC) Turku Centre for Biotechnology (Finland) using TruSeq small RNAseq protocol
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
RNA-seq, miRNA-seq: One hour after collection of GRO-Seq samples (reflecting the lag in nascent transcription and mature RNAs), cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confim the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. For RNA-Seq, larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). For miRNA-Seq, small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
GRO-seq, RNA-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). For GRO-Seq only immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. FOr both GRO-Seq and RNA-Seq libraries, the RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Hypoxia was achieved in Ruskinn Invivo2 400 hypoxia workstation (1% O2 and 5% CO2). OxPAPC has been generated from 1-palmitoyl-2-archidonoyl-sn-glycero-3-phophocholine [PAPC, 10 mg/ml (Avanti Polar Lipids, Inc)]. PAPC was exposed to air for 40h, then dissolved in chloroform and stored at -70 °C. At the start of the oxPAPC stimulation, chloroform was evaporated with nitrogen gas and lipids were re-suspended in growth medium to achieve a concentration of 30 μg/ml.

tag: timepoint

value: 7 hours

tag: stimulus

value: OxPAPC


title: D6_T3_H15_S91_mouse1


title: prostate_tissue-H+df-replicate_RIB0034344

value: H+df


title: HUVEC.miRNA.hypo+oxP_7h.rep1

value: Hypoxia+OxPAPC


title: HUVEC.miRNA.hypoxia_7h.rep1

value: Hypoxia


title: atrial.WT 2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Adapters were trimmed using Cutadapt (v2.3).
FastQC (v0.11.8) was used to ensure the quality of data
Reads were mapped to the reference genome using STAR (v2.7.3a)
count estimates were assigned to genes with RSEM  (v1.3.2)
Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw counts produced by RSEM in tab-delimited text format

source_name: heart atrium

extract_protocol:
Atrial tissue was removed, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy Plus kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: post-natal day 16

value: WT


title: atrial.WT 4


title: atrial.WT 1


title: HUVEC.miRNA.control.rep1

value: Control


title: atrial.KO 1

value: Scn1b  KO


title: atrial.KO 3


title: atrial.KO 2


title: Non-Irradiated Control_9 months [B18_S15]

city: Galveston

first: Anna

last: Nia

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

data_processing:
CLC Genomics Workbench v12.0.3 was used for bioinformatical analysis of the RNA-Seq data. Sequencing data was initially trimmed using the “Trim Reads” module. Reads containing nucleotides below the quality threshold of 0.05 (using the modified Richard Mott algorithm), those with two or more unknown nucleotides or sequencing adapters were trimmed out, 14 bases were trimmed from the 5’ of each read. Filtered sequencing reads were then processed using the “RNA-Seq Analysis” module. Reads were mapped using global alignment strategy against the mouse GRCm38 reference genome with 95% length fraction and similarity fraction scores with annotation version GRCm38.97.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: comma-seperated text file which includes RPKM (with corresponding ENSEMBL ID) for each sample

source_name: Non-Irradiated Control_9 months_Left liver lobes

extract_protocol:
Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA)
rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500.

tag: treatment type

value: Non-Irradiated Control

tag: time

value: 9 months

value: Left liver lobes

tag: replicate


title: atrial.KO 4


title: Non-Irradiated Control_9 months [B17_S47]

tag: strain


title: prostate_tissue-H+sf-replicate_RIB0034664

value: H+sf

value: prostate

value: male


title: prostate_tissue-C-replicate_RIB0034404

value: C

value: benign prostate hyperplasia


title: Non-Irradiated Control_9 months [B16_S31]


title: HAEC.miRNA.hypo+oxP_7h.rep1

source_name: primary human aortic endothelial cells

value: 7 hours


title: Non-Irradiated Control_4 months [B13_S45]

source_name: Non-Irradiated Control_4 months_Left liver lobes

value: 4 months


title: Non-Irradiated Control_4 months [B12_S29]


title: Non-Irradiated Control_4 months [B11_S12]


title: HAEC.miRNA.hypoxia_7h.rep1


title: prostate_tissue-C-replicate_RIB0034410


title: Non-Irradiated Control_2 months [B8_S43]

source_name: Non-Irradiated Control_2 months_Left liver lobes

value: 2 months


title: Non-Irradiated Control_2 months [B6_S21]


title: prostate_tissue-H+sf-replicate_RIB0034364

value: prostate cancer


title: prostate_tissue-C-replicate_RIB0034454


title: Non-Irradiated Control_12 months [B22_S16]

source_name: Non-Irradiated Control_12 months_Left liver lobes

value: 12 months


title: Non-Irradiated Control_12 months [B21_S33]


title: HAEC.miRNA.control.rep1


title: LN18-KPC1-2

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.
Fold change differences between samples were detected using the GFOLD version 1.1.4 algorithm.

source_name: Glioblastoma

extract_protocol:
Total RNA was extracted Direct-zol RNA MiniPrep kit (Zymo Research).
mRNA libraries were constructed using Illumina TruSeq RNA Sample Preparation kit v2.

value: Glioblastoma

tag: cell line

tag: passages after establishing stable clones

tag: genotype/variation


title: HAEC.miRNA.oxPAPC_7h.rep1

value: OxPAPC


title: Non-Irradiated Control_1 month [B3_S35]

source_name: Non-Irradiated Control_1 month_Left liver lobes

value: 1 month


title: Non-Irradiated Control_1 month [B1_S19]


title: LN18-KPC1-1


title: Non-Irradiated Control_2 months [B7_S27]


title: LN18-Ctrl-2

value: Control


title: Non-Irradiated Control_12 months [B25_S50]

value: Non-Irradiated Control


title: 56Fe Irradiated_9 months [E18_S7]

source_name: 56Fe Irradiated_9 months_Left liver lobes

value: 56Fe Irradiated

value: 9 months


title: LN18-Ctrl-1


title: 56Fe Irradiated_9 months [E17_S53]

value: Left liver lobes


title: 56Fe Irradiated_4 months [E13_S37]

source_name: 56Fe Irradiated_4 months_Left liver lobes


title: Non-Irradiated Control_1 month [B2_S4]


title: 56Fe Irradiated_9 months [E19_S9]


title: 56Fe Irradiated_4 months [E12_S21]


title: ANM_76

description:
whole transcriptome sequencing
P76

data_processing:
Basecalls performed using Perl package developed by Novogene.
Contaminant reads were filtered from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads.
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Then coding potential analysis was performed with CNCI, CPC, Pfam-sca, and phyloCSF, Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were candidate set of lncRNAs. Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cancer and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US) immediately following the manufacturer’s instructions.

tag: subject number

value: adjacent normal mucosa tissue

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption


title: 56Fe Irradiated_4 months [E11_S5]

tag: tissue


title: ANM_75

description:
whole transcriptome sequencing
P75


title: ANM_74

description:
whole transcriptome sequencing
P74


title: 56Fe Irradiated_12 months [E23_S27]

source_name: 56Fe Irradiated_12 months_Left liver lobes


title: 56Fe Irradiated_2 months [E8_S51]

source_name: 56Fe Irradiated_2 months_Left liver lobes


title: 56Fe Irradiated_12 months [E21_S57]


title: 56Fe Irradiated_12 months [E22_S41]


title: 56Fe Irradiated_2 months [E7_S35]


title: 56Fe Irradiated_1 month [E3_S3]

source_name: 56Fe Irradiated_1 month_Left liver lobes


title: ANM_65

description:
whole transcriptome sequencing
P65


title: 28Si Irradiated_9 months [A20_S25]

source_name: 28Si Irradiated_9 months_Left liver lobes

value: 28Si Irradiated


title: ANM_77

description:
whole transcriptome sequencing
P77


title: ANM_66

description:
whole transcriptome sequencing
P66


title: ANM_73

description:
whole transcriptome sequencing
P73


title: prostate_tissue-C-replicate_RIB0034760

source_name: prostate

tag: risk group

value: C

value: prostate

tag: gender

value: male

tag: gleason score

value: benign prostate hyperplasia


title: 28Si Irradiated_9 months [A17_S38]


title: 56Fe Irradiated_1 month [E2_S49]


title: 56Fe Irradiated_1 month [E1_S33]


title: ANM_64

description:
whole transcriptome sequencing
P64


title: prostate_tissue-H+sf-replicate_RIB0034883

value: H+sf

tag: diagnosis

value: prostate cancer


title: prostate_tissue-H+sf-replicate_RIB0034963


title: 28Si Irradiated_9 months [A16_S53]


title: 56Fe Irradiated_2 months [E6_S19]

value: 2 months


title: 28Si Irradiated_4 months [A13_S52]

source_name: 28Si Irradiated_4 months_Left liver lobes

value: 4 months


title: 28Si Irradiated_4 months [A12_S47]


title: 28Si Irradiated_4 months [A11_S46]


title: ANM_63

description:
whole transcriptome sequencing
P63


title: 28Si Irradiated_2 months [A7_S44]

source_name: 28Si Irradiated_2 months_Left liver lobes


title: 28Si Irradiated_12 months [A23_S33]

source_name: 28Si Irradiated_12 months_Left liver lobes

value: 12 months


title: 28Si Irradiated_2 months [A6_S43]


title: 28Si Irradiated_2 months [A8_S45]


title: ANM_61

description:
whole transcriptome sequencing
P61


title: ANM_62

description:
whole transcriptome sequencing
P62


title: 28Si Irradiated_12 months [A21_S1]


title: ANM_58

description:
whole transcriptome sequencing
P58


title: ANM_59

description:
whole transcriptome sequencing
P59


title: prostate_tissue-H-sf-replicate_RIB0034977

value: H-sf


title: ANM_60

description:
whole transcriptome sequencing
P60


title: 28Si Irradiated_1 month [A1_S40]

source_name: 28Si Irradiated_1 month_Left liver lobes

value: 1 month


title: prostate_tissue-H-sf-replicate_RIB0034815


title: ANM_57

description:
whole transcriptome sequencing
P57


title: 16O Irradiated_9 months [F19_S52]

source_name: 16O Irradiated_9 months_Left liver lobes

value: 16O Irradiated


title: 16O Irradiated_9 months [F18_S36]

value: 9 months


title: ANM_56

description:
whole transcriptome sequencing
P56


title: prostate_tissue-H+sf-replicate_RIB0034844


title: 16O Irradiated_4 months [F13_S20]

source_name: 16O Irradiated_4 months_Left liver lobes

value: Left liver lobes


title: 28Si Irradiated_1 month [A3_S42]


title: 28Si Irradiated_1 month [A2_S41]


title: 16O Irradiated_4 months [F12_S4]


title: 16O Irradiated_4 months [F11_S50]


title: ANM_54

description:
whole transcriptome sequencing
P54

value: adjacent normal mucosa tissue


title: ANM_53

description:
whole transcriptome sequencing
P53

value: Not Applicable


title: prostate_tissue-H-df-replicate_RIB0034228

value: H-df


title: prostate_tissue-C-replicate_RIB0034209

value: C


title: prostate_tissue-H+df-replicate_RIB0034220

value: H+df

value: prostate


title: ANM_55

description:
whole transcriptome sequencing
P55


title: 16O Irradiated_2 months [F7_S18]

source_name: 16O Irradiated_2 months_Left liver lobes


title: 16O Irradiated_12 months [F25_S44]

source_name: 16O Irradiated_12 months_Left liver lobes


title: 16O Irradiated_12 months [F24_S28]


title: 16O Irradiated_2 months [F6_S2]


title: prostate_tissue-H+sf-replicate_RIB0034217

value: male


title: 16O Irradiated_2 months [F8_S34]


title: 16O Irradiated_9 months [F20_S6]


title: 16O Irradiated_12 months [F23_S11]


title: ANM_52

description:
whole transcriptome sequencing
P52


title: 16O Irradiated_1 month [F5_S48]

source_name: 16O Irradiated_1 month_Left liver lobes


title: ANM_51

description:
whole transcriptome sequencing
P51


title: 16O Irradiated_1 month [F4_S32]


title: prostate_tissue-H+sf-replicate_RIB0034397

value: H+sf


title: 16O Irradiated_1 month [F3_S16]


title: ANM_50

description:
whole transcriptome sequencing
P50


title: d2_Control_3

first: Michel

address: 25 rue du Dr Roux

institute: Institut Pasteur

description:
rnaseq_apcnle_deseqnorm_counts.tsv.gz
rnaseq_apcnle_est_counts.tsv.gz
rnaseq_apcnle_tpm.tsv.gz

data_processing:
Paired end RNA-seq reads were quantified against the mm9 transcriptome using Kallisto 0.43 with default options. Rounded estimated counts were normalised by DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with estimated counts, deseq normalised counts and TPM for each sample

extract_protocol:
Total RNA was extracted according to the Trizol-chloroform extraction protocol provided by Invitrogen. RNAseq was performed on these extracted RNA.
RNA-seq libraries were prepared and sequenced by Novogene Co Ltd.

treatment_protocol: Mice at 5 to 10 weeks of age were injected intraperitoneally with 56mg/kg tamoxifen for three consecutive days. For crypts isolation, 5–10 cm of jejunum were collected, opened longitudinally and processed as described in Guo et al. J. Biol. Chem. 2009

value: Intestinal crypt

value: Control

tag: time point


title: d2_NlecKO_3

value: NlecKO


title: ANM_46

first: Yongyan

description:
whole transcriptome sequencing
P46


title: d2_Control_2


title: d2_NlecKO_2


title: d2_NlecKO_1


title: d2_Control_1


title: ANM_37

description:
whole transcriptome sequencing
P37


title: ANM_36

description:
whole transcriptome sequencing
P36


title: d2_ApccKO_3

value: ApccKO


title: ANM_35

description:
whole transcriptome sequencing
P35


title: d2_ApccKO_1


title: ANM_34

description:
whole transcriptome sequencing
P34


title: d2_ApccKO_2


title: atrial.WT 3

source_name: heart atrium

tag: age

value: post-natal day 16

tag: genotype

value: WT


title: d2_ApccKO;NlecKO_1

value: ApccKO;NlecKO


title: d2_ApccKO;NlecKO_3


title: ANM_31

description:
whole transcriptome sequencing
P31


title: d1_ApccKO;NlecKO_3


title: prostate_tissue-C-replicate_RIB0034917

value: benign prostate hyperplasia


title: d2_ApccKO;NlecKO_2


title: d1_ApccKO;NlecKO_2


title: ANM_30

description:
whole transcriptome sequencing
P30


title: d1_ApccKO_3


title: d1_ApccKO_2


title: ANM_28

description:
whole transcriptome sequencing
P28


title: ANM_29

description:
whole transcriptome sequencing
P29


title: d1_ApccKO_1


title: prostate_tissue-H-sf-replicate_RIB0034347

value: H-sf

value: prostate cancer


title: d1_ApccKO;NlecKO_1


title: d1_NlecKO_3


title: ANM_26

description:
whole transcriptome sequencing
P26

value: adjacent normal mucosa tissue

value: Not Applicable


title: ANM_27

description:
whole transcriptome sequencing
P27


title: d1_Control_2


title: d1_NlecKO_1


title: d1_Control_3


title: ANM_23

description:
whole transcriptome sequencing
P23


title: ANM_24

description:
whole transcriptome sequencing
P24


title: ANM_22

description:
whole transcriptome sequencing
P22


title: prostate_tissue-C-replicate_RIB0034993

value: C


title: d1_Control_1


title: d1_NlecKO_2


title: PDGF 24

city: Moscow

first: Mikhail

last: Arbatsky

address: Lomonosovskiy 27 bld 10

country: Russia

institute: MSU IRM

hyb_protocol: Whole-genome gene expression was assessed using a direct hybridization approach. To amplify starting material, a single-round IVT amplification was carried out using the Illumina RNA Amplification Kit, manufactured by Ambion®, Inc.

scan_protocol: Illumina protocol

data_processing:
Lumi package is a very convenient tool for Illumina data preprocessing
The processing included following steps: Quality control of raw data; Background subtraction; Variance stabilization using algorithm VST, developed for Illumina data. Values after this processing step should be treated as log-transformed. Quantile normalization.
Enrichment Fold (1.3, 2)

label: biotin

source_name: Mesenchymal stem cells

label_protocol: Illumina protocol

growth_protocol: Cells were cultured in AdvanceSTEM™ Mesenchymal Stem Cell Media containing 10 % AdvanceSTEM™ Supplement (HyClone, USA), 1 % antibiotic–antimycotic solution (HyClone) at 37 °C in 5 % CO2 incubator.

extract_protocol: Total cellular RNA was isolated from cultured ADSCs using RNeasy Kit (Qiagen, cat # 74104) according to manufacturer instructions.

treatment_protocol: For assessment of transcriptome content ADSCs were cultured under standard conditions (5 % CO2 and 21 % O2) at 37 °C for 12 or 24 h with or without PDGF-BB.

tag: cell type

value: Human adipose-derived mesenchymal stem/stromal cells (ADSCs

tag: treatment

value: (5 % CO2 and 21 % O2) at 37 °C for 24 h with  PDGF-BB


title: ANM_20

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

institute: Shanxi Medical University

description:
whole transcriptome sequencing
P20

source_name: adjacent normal mucosa tissue


title: ANM_25

description:
whole transcriptome sequencing
P25


title: ANM_19

description:
whole transcriptome sequencing
P19


title: Control sample

value: untreated


title: prostate_tissue-C-replicate_RIB0034472

value: prostate

value: male


title: prostate_tissue-H-df-replicate_RIB0034995

value: H-df


title: ANM_18

description:
whole transcriptome sequencing
P18


title: RNAseq_Syn_WH7803_LL_UV_T6_E1

city: Roscoff

first: Laurence

last: Garczarek

address: Place Georges Teissier

department: UMR7144-Adaptation and Diversity in Marine Ecosystems

institute: Station Biologique (Sorbonne University and CNRS)

data_processing:
Reads quality checks were performed with the FastQC tool.
Illumina adapters, found in 23.5 +/- 4.5 % of all reads, were removed using Cutadapt v1.8.3.
rRNA, constituting 5.0 +/- 5.9 % of all reads, were removed with Sortmerna v2.1.
Reads under 50 bp size and with a mean quality score lower than 25 were filtered out using Prinseq v0.20.4.
Remaining reads were then aligned on the reference genome of Synechococcus sp. WH7803 using Bowtie2 v2.2.9 software with ‘--non-deterministic --end-to-end –sensitive’ parameters and by selecting only the properly paired reads (i.e. SAM flagged as 99, 147, 163 or 83)
Read counts table were obtained using HTSeq Count v0.6.0 with following parameters: ‘--stranded=reverse -a 10 -m intersection-nonempty’.
Genes expression level between stress and control conditions as well as adjusted p-value based on the Benjamini-Hochberg procedure were determined using SARTools v1.4.0 with embedded DESeq2 v1.14.1.
Genome_build: NC_009481.1
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each sample, log2FC and  their associated pvalues and adjusted pvalues

organism: Synechococcus sp. WH 7803

source_name: culture of Synechococcus sp. WH7803 cells

growth_protocol: Synechococcus sp. WH7803, an axenic strain retrieved from the Roscoff culture collection (RCC752; http://roscoff-culture-collection.org/), was grown in modified PCR-S11 culture medium with 1 mM sodium nitrate and 1 μg/L vitamin B12. Cultures were acclimated for at least two weeks at 22°C (hereafter medium temperature: MT) and 20 μmol photon.m-2.s-1 (LL and μE.m-2.s-1) or 250 μE.m-2.s-1 (HL) provided by multicolor (cool white: 6500K, blue: 470 nm, green: 530 nm) LED systems (Alpheus, France). For each growth irradiance, 9 L of exponentially growing culture were split in 500 mL aliquots in 1 L flasks (Nalgene, St. Louis, MO, USA) and left under their initial growth irradiance overnight before being submitted to light, UV or temperature stress conditions and sampled at different times for various parameters.

extract_protocol:
RNA extractions were performed from 150 mL of culture harvested by centrifugation for 7 min at 10,414 × g and 4°C in an Eppendorf 5804R, followed by 2 min centrifugation at 20,817 × g in Eppendorf tubes and 4°C in an Eppendorff 5417R centrifuge. Cell pellet was then resuspended in 1 mL Qiazol (Qiagen, Valencia, CA, USA) and quickly frozen in liquid nitrogen. After thawing the tubes at 65 °C, followed by and additional incubation of 5 min at this temperature, RNA was extracted using the Direct-Zol kit (Zymo Research Corp, Proteigene) as recommended by the manufacturer. Three successive DNase treatments were performed on the Zymo-Spin™-IIC Column using the Qiagen RNase-free DNase Set (Qiagen), followed by elution from the column in 30 L DEPC-treated water. RNA quantification and quality check were performed using a Qubit (Invitrogen) and a BioAnalyzer 2100 with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA), respectively. RNA samples were then frozen in liquid nitrogen and stored at -80°C.
Ribodepletion was performed at the Genotoul platform (Toulouse, France) from 5 µg of RNA using the Ribo-Zero Bacteria Magnetic Kits (Illumina) in presence of RiboGuard RNase Inhibitor (Epicentre) and treated RNA samples were purified and concentrated using RNA Clean & Concentrator™-5 columns (Zymo research). 0.5 µL of ribo-depleted RNA was then used for quantification (Qubit RNA HS Assay Kit) and quality check (Bioanalyzer RNA Pico kit or Labchip GX). Libraries were then prepared using 100 to 400 ng of RNA with the Illumina TruSeq Stranded mRNA kit and sequenced as 150 bp paired-end reads on Illumina HiSeq 3000 System (Illumina, San Diego, CA, USA) at Genotoul (Toulouse, France). 18.5 +/- 4.7·10^6 paired-end reads were generated per sample.

treatment_protocol: For shift experiments, High light (HL) stress was induced by a shift from LL acclimated conditions (LL, 20 μE m-2 s-1) to HL ((250 μE m-2 s-1). Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). UV stress was induced by a shift from LL-acclimated conditions or HL-acclimated conditions to 3 W.m −2  of UV-A and 0.3 W.m −2  of UV-B. Cultures were then sampled after 20 min (T0.3), 1h (T1), 3h (T3) and 6h (T6). Low temperature (LT) stress was performed on LL- or HL-acclimated culture by shifting them from 22 °C to 13 °C. Cultures were then sampled after 12h (J0-5), 24h (J1), 48h (J2), 72h (J3) or after 4h (J0-17), 8h (J0-33), 16h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. High temperature (HT) stress was performed on LL- or HL-acclimated culture by shifting them from 22°C to 30 °C. Cultures were then sampled after 12h (J0-5), 1 day (J1), 2 days (J2), 3 days (J3) and after 4h (J0-17), 8h (J0-33), 14.5h (J0-67), 24h (J1), for LL and HL-acclimated cultures, respectively. UVA and UVB radiations, generated from UVA-351 and UVB-313 fluorescent bulbs (Q-Panel Lab products, Cleveland, OH, USA), were measured between 280–320 and 320–400 nm, respectively using a USB2000 spectroradiometer (Ocean Optics, Ew Duiven, The Netherlands). Temperature stress were performed in temperature-controlled chambers (Liebherr-Hausgeräte, Lienz, Austria).  For diel cycle experiments, run at two temperatures (21 and 27°C), a bell-shaped 12/12 h L/D cycle, triggering a good synchronization of cell division, was generated using the multicolor LED systems and the Ether software (Alpheus, France). The maximal irradiance (at virtual noon) was set at 669 μE.m-2.s-1. Two replicate cultures per temperature were acclimated to L/D cycles for at least 2 weeks prior to start monitoring the different parameters. During the experiment, two replicate cultures were grown with a continuous input of fresh medium, in order to maintain cells in exponential growth throughout the whole sampling period. To study the kinetics of the response of cells to light fluctuations, cultures were sampled at 6:00, 9:00, 12:00, 15:00, 18:00, 20:00, 22:00, and 2:00 over 3 days.

tag: strain

tag: acclimation condition

value: Low Light

tag: stress condition

value: UV exposition

tag: timepoint

value: 6 hours

tag: replicate


title: ANM_16

city: Taiyuan

last: Wu

description:
whole transcriptome sequencing
P16

tag: subject number

tag: tumor stage

tag: tobacco smoking


title: ANM_17

description:
whole transcriptome sequencing
P17

tag: tissue

tag: alcohol consumption


title: ANM_15

description:
whole transcriptome sequencing
P15


title: RNAseq_Syn_WH7803_LL_UV_T6_C1


title: RNAseq_Syn_WH7803_LL_UV_T6_D1


title: ANM_14

description:
whole transcriptome sequencing
P14


title: ANM_13

description:
whole transcriptome sequencing
P13


title: RNAseq_Syn_WH7803_LL_UV_T3_E1

value: 3 hours


title: ANM_12

description:
whole transcriptome sequencing
P12


title: RNAseq_Syn_WH7803_LL_UV_T3_D1


title: ANM_11

description:
whole transcriptome sequencing
P11


title: prostate_tissue-C-replicate_RIB0034871

tag: risk group

tag: gender

tag: gleason score


title: RNAseq_Syn_WH7803_LL_UV_T3_C1


title: prostate_tissue-H+sf-replicate_RIB0034958

value: H+sf

tag: diagnosis


title: RNAseq_Syn_WH7803_LL_UV_T1_E1

value: 1 hour


title: prostate_tissue-H-sf-replicate_RIB0034498

value: H-sf


title: 28Si Irradiated_12 months [A25_S3]

tag: treatment type

value: 28Si Irradiated

tag: time

value: 12 months

value: Left liver lobes


title: prostate_tissue-H-sf-replicate_RIB0034843

value: prostate cancer