title: B2_E1

source_name: P19_lymphatic endothelial cells

value: CD31+, LYVE1+, Podoplanin+


title: C_A4

status: Public on Feb 19 2020

type: SRA

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

library_source: transcriptomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: P21_lymphatic endothelial cells

extract_protocol:
Single lymphatic endothelial cells were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with 38/37 cycles paried-end high-output mode.

tag: strain

tag: age

tag: Sex

value: Male

tag: tissue

value: mouse back skin

tag: cell type

value: lymphatic endothelial cells

tag: sorting markers

value: CD31+, LYVE1-, Podoplanin+


title: C_A1


title: D_D6


title: B1_H9


title: C_B9


title: C_B5


title: C_B12


title: B1_F3


title: B1_H5


title: B1_E2


title: C_A6


title: B1_D3


title: B1_D11


title: B1_D1


title: B1_A11


title: B1_D5


title: B1_B3


title: B1_A12


title: B_C1


title: B_A1


title: B_B7


title: A_H3


title: A_G5


title: A1_A7


title: A_G8


title: A_E9


title: A_F5


title: A_G12


title: A_E1


title: A_D2


title: A_G1


title: A_D1


title: A_C8


title: A_B9


title: A_B10


title: A_B2


title: A_H5


title: Ana3_BulgeSC_Input

description: Input DNA

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10, build 38) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
tdf files were created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files; enrichment values in 25bp windows

molecule: genomic DNA

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were FACS-purified from CD1 WT mice at postnatal day 21.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to a ChIPmentation protocol (Schmidl et. al., Nature Methods, 2015 ). Briefly, immunoprecitiated nucleosomes on beads were tagmented by Tagmentation enzyme from the Nextera DNA Sample Prep Kit (Illumina). Follwoing tagmentation, the beads were washed and DNA elution, reerse cross-linking, DNA purification, and PCR amplification were performed. During PCR amplification, each sample were barcoded by different adaptor primers for illumina sequencing. Sequencing libraries were pooled and sequenced on the NextSeq 500 instrument with 37/38 cycles paried end high-output mode.

value: Female

tag: genotype

value: WT

value: bulge hair follicle stem cells

value: integrin α6, CD34, Sca-1

tag: chip antibody


title: A_H9


title: A_C1


title: 901b_H12

extract_protocol:
Single bulge hair follicle stem cells were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with 75 cycles paried-end high-output mode.

value: bulge hair follicle stem cell

value: GFP+, tdTomato+, integrin α6+, integrin b1+, CD34+


title: Ana3_BulgeSC_H3K4me1

description: Chromatin IP against H3K4me1


title: 901b_H10


title: 901b_H11


title: D_D12


title: 901b_E9


title: 901b_F12


title: 901b_F10


title: 901b_G3


title: 901b_G1


title: 901b_G4


title: 901b_F3


title: 901b_G2


title: 901b_G5


title: 901b_E8


title: 901b_E5


title: 901b_E7


title: Ana3_BulgeSC_H3K27ac

description: Chromatin IP against H3K27ac


title: 901b_H8


title: 901b_E3


title: 901b_E4


title: 901b_E10


title: 901b_E11


title: 901b_E2


title: 901b_H6


title: 901b_E12


title: 901b_D7


title: 901b_D5


title: 901b_D1


title: 901b_F6


title: 901b_D10


title: 901b_D6


title: 901b_D11


title: 901b_C7


title: 901b_C2


title: 901b_C3


title: 901b_C6


title: 901b_C5


title: 901b_B12


title: 901b_C1


title: 901b_B6


title: 901b_B4


title: 901b_B7


title: 901b_B2


title: 901b_B3


title: 901b_B5


title: 901b_B11


title: 901b_B10


title: 901b_A7


title: 901b_A5


title: 901b_A4


title: 901b_A3


title: 901b_A6


title: 901b_A9


title: 901b_A8


title: 901b_A2


title: 901b_A10


title: 901b_A12


title: 3-F12_HE_con_rep1

city: NEW YORK

first: Margot

last: Brandt

address: 101 AVENUE OF THE AMERICAS FL 4

institute: New York Genome Center

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to the GRCh37 whole genome using STAR 2-pass mapping.
Gene counts were calculated with FeatureCounts using Gencode v19 gene annotations.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited matrix showing read counts generated from featurecounts with genes as rows and samples as columns

organism: Homo sapiens

source_name: HEK293/hTLR4 cells

growth_protocol: HEK293/hTLR4A-MD2-CD14 (Invivogen)  were cultured in DMEM supplemented with 4.5 g/l glucose (Corning), 10% fetal bovine serum (Sigma-Aldrich), 1% penicillin/ streptomycin (Corning) and 1% L-glutaMAX (gibco). Cells were passaged using cell scraping to avoid damaging the cell surface receptors.

extract_protocol:
RNA was extracted using IBI Isolate (IBI Scientific), followed with the Direct-zol RNA MicroPrep kit (Zymo Research). RNA was then treated with DNAse I (Ambion) and enriched for mRNA using Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher).
cDNA was generated using a custom scaled-down modification of the SMART-seq protocol (Picelli et al., 2014). cDNA was synthesized from RNA input using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific). It was then amplified using Kapa HiFi 2X Ready Mix (Kapa Biosystems). cDNA was then cleaned using 0.9X Ampure beads. Finally, cleaned cDNA samples were tagmented and indexed using the Nextera XT DNA Library Prep Kit (Illumina)

treatment_protocol: 1 ug/mL of LPS was distributed to cells (for LPS 90m and LPS 12h samples) 24-hours after plating in 24 well plates with 180,000 cells per well.

tag: cell line

value: HE

tag: treatment

value: con

tag: clone

tag: replicate


title: 901b_B8


title: 3-F12_HE_12h_rep1


title: 3-E1_HE_90m_rep1


title: 3-E1_HE_12h_rep1


title: 3-E1_HE_con_rep1


title: 2-H1_HO_con_rep1

value: HO


title: 2-H1_HO_90m_rep1


title: 1-H1_WT_90m_rep1


title: 2-C10_HE_90m_rep1


title: 2-C10_HE_12h_rep1


title: 2-C10_HE_con_rep1


title: 2-H1_HO_12h_rep1


title: 1-G8_WT_12h_rep1


title: 1-H1_WT_12h_rep1


title: 1-G8_WT_90m_rep1


title: 1-H1_WT_con_rep1


title: 901b_A1


title: 1-G10_WT_con_rep1


title: 1-G10_WT_90m_rep1


title: 1-F9_WT_12h_rep1


title: 1-G10_WT_12h_rep1


title: 3-F12_HE_90m_rep1


title: 1-G8_WT_con_rep1


title: 1-F12_HO_90m_rep1


title: 1-F9_WT_con_rep1


title: 1-F12_HO_con_rep1


title: 1-F12_HO_12h_rep1


title: 1-F9_WT_90m_rep1


title: 1-C9_HO_90m_rep1


title: 1-C9_HO_con_rep1


title: 1-C9_HO_12h_rep1


title: 1-C8_HO_con_rep1


title: 1-C8_HO_12h_rep1


title: 1-C12_WT_90m_rep1


title: 1-C8_HO_90m_rep1


title: 1-C12_WT_con_rep1


title: 1-C12_WT_12h_rep1


title: 1-C1_HO_90m_rep1


title: 1-C1_HO_con_rep1


title: 3-F12_HE_90m_rep2


title: 3-E1_HE_90m_rep2


title: 3-E1_HE_con_rep2


title: 3-F12_HE_con_rep2


title: 3-F12_HE_12h_rep2


title: 2-H1_HO_12h_rep2


title: 3-E1_HE_12h_rep2


title: 1-C1_HO_12h_rep1


title: 2-H1_HO_con_rep2


title: 2-C10_HE_90m_rep2


title: 2-H1_HO_90m_rep2


title: 2-C10_HE_con_rep2


title: 2-C10_HE_12h_rep2


title: 1-H1_WT_con_rep2


title: 1-H1_WT_90m_rep2


title: 1-G8_WT_con_rep2


title: 1-G8_WT_90m_rep2


title: B_C11


title: 1-G8_WT_12h_rep2


title: 1-G10_WT_con_rep2


title: 1-G10_WT_90m_rep2


title: 1-G10_WT_12h_rep2


title: 1-F9_WT_90m_rep2


title: 1-F9_WT_con_rep2


title: 1-F12_HO_con_rep2


title: 1-F12_HO_12h_rep2


title: 1-C9_HO_90m_rep2


title: PVN, Control, rep2

city: SAO PAULO

first: André

middle: Souza

last: Mecawi

state: SÃO PAULO

address: Rua Botucatu, 862 - Vila Clementino,, Edifício de Ciências Biomédicas

department: Department of Biophysics

country: Brazil

institute: Federal University of Sao Paulo

data_processing:
Quality control (FastQC)
Adapter Trimming (BBDuk)
Alignment to reference genome (Rn6, Tophat)
Read counts (Ensembl Rn6, Htseq)
Differential Expression Analysis (EdgeR)
Genome_build: RN6
Supplementary_files_format_and_content: Raw counts as generated by HTSeq

organism: Rattus norvegicus

source_name: School of Dentistry-UNESP

extract_protocol:
QIAzol Lysis Reagent with RNeasy kit protocols (QIAgen, Crawley, UK)
Illumina TruSeq mRNA kit

value: Paraventricular Nucleus

value: Holtzman

value: control

tag: pooled

value: n=3 Pooled


title: PVN, Furosemide (10mg/kg), rep3

value: Furosemide

value: Male


title: PVN, Furosemide (10mg/kg), rep1


title: PVN, Control, rep1


title: Fluidigm C1 single cell RNA-Seq [Cell_276]

city: Bethesda

first: Michael

last: Hoa

state: MD

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using STAR pipeline using default settings.
Secondary analysis was performed using the Seurat2 package
Genome_build: mm10
Supplementary_files_format_and_content: Expression Matrix of Raw Counts; Cell-associated Metadata

molecule: polyA RNA

source_name: CD1_Lfng-EGFP_P120_Adult cochlear supporting cells

extract_protocol:
Cochleae from P60 and P120 LfngEGFP mice were used for FACS purification of GFP+ supporting cells (SCs) before single cell capture. Briefly, the inner ear was dissected from adult mice and the vestibular portions of the inner ear, including utricle, saccule and semicircular canal ampulla, were removed. Cochleae were then collected in a 1.5-ml tube (n = 4-5 cochleae per integrated fluidics chip (IFC) capture) and incubated in 0.05% crude trypsin (Worthington) in CMF-PBS (Life Technologies) at 37ºC for 8 min. Excess trypsin solution was removed and four volumes of 5% FBS (Thermo Fisher Scientific) in DMEM/F12 (Thermo Fisher Scientific) was added to stop the digestion. The tissue was then triturated for 2 min and passed through a 40-µm strainer (pluriSelect Life Science) to eliminate residual aggregates and bone fragments. The resulting single-cell suspension was then stained with propidium iodide (Life Technologies) to allow for exclusion of dead cells and debris from the samples during FACS-purification. Single cells were sorted on a FACSAria flow cytometer (BD Biosciences) with a compensated FITC setting and 488 nm excitation, using a 100-µm nozzle. In adult tissue, GFP+ SCs are the brightest population and typically comprised 2-7% of viable cells. The purpose of FACS purification was to enrich for a population of GFP+ SCs and gating was set based on wild type isotype controls to exclude the majority of GFP– cochlear cells. Scatter discrimination was used to eliminate doublets and samples were negatively selected with propidium iodide to remove dead cells. Cells were collected in 20% FBS in DMEM/F12 and stored on ice. After sorting, cells were spun at 200g for 10 min and then resuspended in 20% FBS
Library preparation was performed according to the manufacturer’s instructions for the Fluidigm C1 instrument (Fluidigm). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

tag: mouse model

value: Lfng-EGFP

tag: Stage

value: Adult cochlear supporting cells


title: PVN, Control, rep3


title: 1-C9_HO_con_rep2


title: 1-C9_HO_12h_rep2


title: 1-F12_HO_90m_rep2


title: 1-C8_HO_con_rep2


title: Fluidigm C1 single cell RNA-Seq [Cell_275]


title: Fluidigm C1 single cell RNA-Seq [Cell_273]


title: PVN, Furosemide (10mg/kg), rep2


title: Fluidigm C1 single cell RNA-Seq [Cell_274]


title: Fluidigm C1 single cell RNA-Seq [Cell_272]


title: 1-F9_WT_12h_rep2


title: 1-C8_HO_90m_rep2


title: 1-C8_HO_12h_rep2


title: ReN_OE_circARID1A_NC: negative control for overexpression of  circARID1A

type: RNA

city: Taipei

first: Trees-Juen

last: Chuang

address: 128, Academia Road, Sec. 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academic Sinica

description: Gene expreesion data from negative control for overexpression of circARID2A

hyb_protocol: Total RNA was hybridized to Affymetrix Human Genome Plus 2.0 Array (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanncer 3000 7G

data_processing: The microarray raw data was analyzed using Transcriptome Analysis Console (TAC 4.0) software (Affymetrix).

label: biotin

source_name: negative control for overexpression of circARID1A in ReNcell

label_protocol: Not provided

growth_protocol: ReNcell VM was commercially purchased from Sigma-Aldrich (SCC008). The cells were grown on 20μg/ml laminin (Merck) coated culture plates containing ReNCell NSC maintenance medium (Merck) supplemented with 20ng/ml of bFGF and EGF (Merck).

extract_protocol: Total RNA from cells were extracted using TRIzol reagent with PureLink RNA Mini Kit (Ambion) and PureLink DNase Set (Ambion).

treatment_protocol: Cells were transfected with siRNA (MDBio) or miRNA mimics (TOOLS) at final concentration of 10 nM using Lipofectamine RNAiMAX reagent (Invitrogen).

value: ReNcell


title: ReN_OE_circARID1A: overexpression of circARID1A

description: Gene expreesion data from overexpression of circARID1A

source_name: overexpression of circARID1A in ReNcell


title: Fluidigm C1 single cell RNA-Seq [Cell_271]


title: 1-C12_WT_con_rep2

value: WT


title: ReN_KB_circARID1A_NC: negative control for knockdown of circARID1A

description: Gene expreesion data from negative control for knockdown of circARID2A

source_name: negative control for knockdown of circARID1A in ReNcell


title: ReN_OE_miR-204-3p_NC: negative control for overexpression of  miR-204-3p

description: Gene expreesion data from negative control for overexpression of miR-204-3p


title: ReN_OE_miR-204-3p: overexpression of miR-204-3p

description: Gene expreesion data from overexpression of miR-204-3p

source_name: overexpression of miR-204-3p in ReNcell


title: ReN_KB_circARID1A: knockdown of circARID1A

description: Gene expreesion data from knockdown of circARID1A

source_name: knockdown of circARID1A in ReNcell


title: 1-C12_WT_90m_rep2


title: Fluidigm C1 single cell RNA-Seq [Cell_269]


title: Fluidigm C1 single cell RNA-Seq [Cell_270]


title: 1-C1_HO_con_rep2


title: 1-C1_HO_90m_rep2


title: 1-C12_WT_12h_rep2


title: 1-C1_HO_12h_rep2


title: promoter_3_90m

extract_protocol:
Cells were collected at their respective time point with TRIzol reagent (Thermo Fisher Scientific), followed with the Direct-zol RNA MicroPrep kit (Zymo Research). RNA was then treated with DNAse I (Ambion) and enriched for mRNA using Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher).
cDNA was generated using a custom scaled-down modification of the SMART-seq protocol (Picelli et al., 2014). cDNA was synthesized from RNA input using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific). It was then amplified using Kapa HiFi 2X Ready Mix (Kapa Biosystems). cDNA was then cleaned using 0.9X Ampure beads. Finally, cleaned cDNA samples were tagmented and indexed using the Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: HEK293-TLR4 cells were plated in three 24-well plates with 120,000 cells/well in 1 ml of DMEM. 24 hours later, the medium was replaced with 0.5 ml of OptiMem (Gibco) and cells were transfected with 1.5 ul of lipofectamine 3000 (Thermo Fisher Scientific), 200 ng of CRISPR-KRAB-MeCP2 vector (Addgene 110821) and 50 ng of gRNA gblock (IDT) (4 wells each received a gRNA targeting EGFP as a neutral control (‘GGTGGTGCAGATGAACTTCA’), 14 bp downstream of the IRF1 promoter (‘GTCTTGCCTCGACTAAGGAG’) or the enhancer (‘TTCTCTGTAGCCCTTGTATT’)). After 28 hours, 1 ug/mL of LPS (Invivogen) was added to the 90 m and 12 h samples and nothing to the control samples, with four biological replicates of each gRNA for each LPS treatment (36 total samples).

tag: grna

value: promoter

tag: lps treatment


title: Fluidigm C1 single cell RNA-Seq [Cell_263]

tag: strain


title: Fluidigm C1 single cell RNA-Seq [Cell_268]


title: Fluidigm C1 single cell RNA-Seq [Cell_266]


title: Fluidigm C1 single cell RNA-Seq [Cell_262]


title: promoter_2_0h


title: enhancer_3_0h

value: enhancer


title: Fluidigm C1 single cell RNA-Seq [Cell_261]


title: Fluidigm C1 single cell RNA-Seq [Cell_259]


title: Fluidigm C1 single cell RNA-Seq [Cell_260]


title: promoter_4_90m


title: control_4_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_265]


title: promoter_4_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_258]


title: Fluidigm C1 single cell RNA-Seq [Cell_256]


title: Fluidigm C1 single cell RNA-Seq [Cell_257]


title: Fluidigm C1 single cell RNA-Seq [Cell_255]


title: control_3_90m


title: promoter_2_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_267]


title: promoter_4_12h


title: enhancer_4_0h


title: enhancer_3_12h


title: Fluidigm C1 single cell RNA-Seq [Cell_252]


title: Fluidigm C1 single cell RNA-Seq [Cell_254]


title: enhancer_3_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_253]


title: Fluidigm C1 single cell RNA-Seq [Cell_251]


title: Fluidigm C1 single cell RNA-Seq [Cell_250]


title: enhancer_4_90m


title: enhancer_2_90m


title: control_2_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_248]


title: Fluidigm C1 single cell RNA-Seq [Cell_247]


title: Fluidigm C1 single cell RNA-Seq [Cell_249]


title: control_2_12h


title: control_1_12h


title: promoter_2_12h


title: Fluidigm C1 single cell RNA-Seq [Cell_246]


title: enhancer_2_12h


title: control_3_12h


title: Fluidigm C1 single cell RNA-Seq [Cell_245]


title: control_1_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_236]


title: Fluidigm C1 single cell RNA-Seq [Cell_237]


title: Fluidigm C1 single cell RNA-Seq [Cell_234]


title: Fluidigm C1 single cell RNA-Seq [Cell_233]


title: enhancer_1_12h


title: enhancer_1_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_231]


title: control_4_12h


title: enhancer_1_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_229]


title: promoter_3_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_230]


title: control_2_90m


title: control_4_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_228]


title: Fluidigm C1 single cell RNA-Seq [Cell_227]


title: control_3_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_224]


title: Fluidigm C1 single cell RNA-Seq [Cell_226]


title: Fluidigm C1 single cell RNA-Seq [Cell_223]


title: Fluidigm C1 single cell RNA-Seq [Cell_235]


title: enhancer_2_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_222]


title: promoter_1_12h


title: promoter_1_90m


title: Fluidigm C1 single cell RNA-Seq [Cell_220]


title: Fluidigm C1 single cell RNA-Seq [Cell_221]


title: Fluidigm C1 single cell RNA-Seq [Cell_218]


title: control_1_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_219]


title: s502

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing: counts

source_name: A375 cell line

extract_protocol: none provided by the submitter

tag: panobinostat treatment


title: promoter_1_0h


title: Fluidigm C1 single cell RNA-Seq [Cell_217]


title: s501


title: s03


title: Fluidigm C1 single cell RNA-Seq [Cell_215]


title: s02


title: s01


title: Fluidigm C1 single cell RNA-Seq [Cell_216]


title: promoter_3_12h


title: Fluidigm C1 single cell RNA-Seq [Cell_214]


title: Fluidigm C1 single cell RNA-Seq [Cell_212]


title: enhancer_4_12h


title: Fluidigm C1 single cell RNA-Seq [Cell_209]


title: s503


title: Fluidigm C1 single cell RNA-Seq [Cell_207]


title: Fluidigm C1 single cell RNA-Seq [Cell_206]


title: Fluidigm C1 single cell RNA-Seq [Cell_204]


title: Fluidigm C1 single cell RNA-Seq [Cell_205]


title: Fluidigm C1 single cell RNA-Seq [Cell_213]


title: Fluidigm C1 single cell RNA-Seq [Cell_201]


title: Fluidigm C1 single cell RNA-Seq [Cell_203]


title: Fluidigm C1 single cell RNA-Seq [Cell_199]


title: Fluidigm C1 single cell RNA-Seq [Cell_200]


title: Fluidigm C1 single cell RNA-Seq [Cell_210]


title: Fluidigm C1 single cell RNA-Seq [Cell_208]


title: Fluidigm C1 single cell RNA-Seq [Cell_198]


title: 1-H1_WT_12h_rep2


title: Testis sample with impaired spermatogenesis, Sample 13

city: Ljubljana

first: Alenka

last: Hodžić

address: Šlajmerjeva 3

department: Centre for Mendelian Genomics

country: Slovenia

institute: Clinical Institute of Medical Genetics University Medical Centre Ljubljana

description: Differential gene expression was measured in relation to the Agilent’s Universal Human Reference RNA and each experimental sample was hybridized against this common reference sample.

hyb_protocol: Hybridization was performed according to the manufacturer’s recommendations (Agilent Technologies).  Hybridization was performed for 17 h, rotating at a speed of 10 rpm at 65 °C in an  hybridization oven (Agilent technologies).

scan_protocol: Microarray slides were scanned using Agilent High Resolution  Microarray Scanner System, using the manufacturer's recommended scanning settings.

data_processing:
Microarray features were extracted using Agilent Feature Extraction  software v10.7.3.1. Background was substracted using Agilent's background detrend  algorithms, features with non uniform fluorescence profile were removed from further  analyses and linear lowess intra-array approach was used to account for and correct  possible dye bias. Consistency of log ratio values was inspected using manufacturers  provided spike-in probes and reproducibility was evaluated by investigating the extent of variance in the population of replicated probes.
Processed flouorescence values obtained in preceding steps  were read-in using slightly modified limma function. The complete dataset was then  inspected for NA values and other irregularities. Probe annotations were obtained from the Agilent's eArray service (earray.chem.agilent.com) and appended to initial datasets. Before  calculating log ratio values between flourescence signals originating from each color  channel, all the values were offset by 100 units, to prevent the undesirable increase in  variance in the population of features with low flouorescence values, ultimately causing  abnormalities in MA diagnostic plots. Statistical comparisons of expression values were  evaluated using moderated t-test approach implemented in limma. This test accounts for  the issue of small variance contributing to undesirably large t-test values occuring for some  genes, and uses Bayes inference to acknowledge similarities in gene expression profiles in  subsets of genes, thereby improving prioritization of genes with differences best related to  frank biological alterations. A linear model was set up, incorporating the effect of disease  status and gender, and expression values were fit to this model. Significance values and log  fold-change were calculated afterwards and p-values were controlled for the issue of  multiple testing by the method related to that described by Benjamini and Hochberg  (Benjamini et al., 1995) and implemented into the limma workflow

source_name: Testis tissue sample

label_protocol: For labeling reaction, 50 ng of RNA from  samples was used.  Sample labeling was performed according to the manufacturer’s recommendations (Agilent Technologies).

extract_protocol: Total RNA was isolated from frozen testis biopsy samples by using the TissueLyserLT  (Qiagen) apparatus and RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s  instructions. About 3.5-4.5 mg weight of tissue was disrupted and homogenized in 2 ml  centrifuge tubes containing 5-mm stainless steel beads and lysis buffer (Buffer RLT plus)  at a frequency of 50 Hz for 10 minutes in a TissueLyser device. Homogenate was  subsequently centrifuged for 3 minutes, collected and eluted in a gDNA eliminator spin  column. Ethanol was added to the flow-through to provide appropriate binding conditions  for RNA and samples were then applied to an RNeasy MinElute spin columns, where total  RNA was bound to the membrane and contaminants were efficiently whased away. RNA  was then eluted in 14µl of water. RNA concentrations were determined using NanoDrop  2000C Spectrophotometer (Thermo Scientific) and RNA quality was verified by Agilent  Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Testicular biopsy was performed under local anaesthesia. Following unilateral  hemiscrototomy, a small testicular incision was made and at least two samples of testicular  tissue were taken from each testis. The first sample was fixed in Bouin's solution, routinely  embedded in paraffin and cut at a section thickness of 5 μm. The sections were stained  with HE, PAS and van Gieson–Weigert.

tag: testis tissue

value: impaired spermatogensis

value: Experimental sample, impaired spermatogenesis

source_name: Agilent’s Universal Human Reference RNA

tag: sample type

value: Agilent’s Universal Human Reference RNA


title: Testis sample with normal spermatogenesis, Sample 14

value: normal spermatogenesis

value: Experimental sample, normal spermatogenesis


title: Fluidigm C1 single cell RNA-Seq [Cell_202]

tag: cell type


title: Fluidigm C1 single cell RNA-Seq [Cell_196]


title: Testis sample with impaired spermatogenesis, Sample 18


title: Testis sample with impaired spermatogenesis, Sample 20


title: Fluidigm C1 single cell RNA-Seq [Cell_191]

source_name: CD1_Lfng-EGFP_P60_Adult cochlear supporting cells


title: Testis sample with normal spermatogenesis, Sample 6


title: Testis sample with normal spermatogenesis, Sample 7


title: Testis sample with normal spermatogenesis, Sample 12


title: Testis sample with impaired spermatogenesis, Sample 9


title: Testis sample with impaired spermatogenesis, Sample 8


title: Testis sample with impaired spermatogenesis, Sample 17


title: Fluidigm C1 single cell RNA-Seq [Cell_192]


title: Testis sample with normal spermatogenesis, Sample 11


title: Testis sample with impaired spermatogenesis, Sample 5


title: Fluidigm C1 single cell RNA-Seq [Cell_185]


title: 293_smRNA_rep4

city: Chicago

first: Rui

last: Yi

state: Illinois

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

institute: Northwestern University

description:
Small RNA
smrna_293_counts.txt.gz

data_processing:
For the XPO5 HITS-CLIP, fastq files were trimmed using cutadapt (v1.8.3). For the miRNAseq, FASTQ files from XPO5cko experiments were trimmed to remove 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG), 5’ adapter (CTACAGTCCGACGATC) and randomized NN nucleotides introduced by the adapters from both the 5’ and 3’ end. FASTQ files from 293FT cells were trimmed to remove 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG), 5’ adapter (CTACAGTCCGACGATC) and randomized NN nucleotides introduced by the adapters from both the 5’ and 3’ end
For the XPO5 HITS-CLIP, reads were mapped to the human genome (hg19 build) using novoalign (v3.02.00). ). Reads greater than 25 nt after trimming were aligned with -l 25 -t 85 settings, whereas shorter reads were aligned with -l 20 -t 30 settings. PCR duplicates were removed using UMI-Tools (v. 0.5.3) with the "directional" option and alignments with MAPQ < 10 were discarded. For miRNAseq,  following trimming reads were then aligned with Bowtie2 (v.2.1.0) to the mouse genome (mm10) using local alignment.
For the XPO5 HITS-CLIP, peaks were called by merging all overlapping alignments using bedtools merge (v2.26.0). For the miRNAseq, a custom annotation file was built containing GENCODE annotations, v19 for human, M8 for mouse with Mt_rRNA, lincRNA, misc_RNA, rRNA, sRNA, sm_RNA, snRNA, snoRNA, vaultRNA, and tRNA biotypes, and miRBase microRNA annotations (release 19). Reads overlapping annotations were counted using Htseq-count (v.0.6.0), requiring a minimum MAPQ of 10.
For XPO5 HITS-CLIP, libraries were also independently mapped to a database of pre-microRNA sequences (mirBase release19) using blastn (v.2.2.28) to assess alignments with hairpin sequences.
Genome_build: hg19, Mm10
Supplementary_files_format_and_content: final_peaks_BC3_5reads.bed contains Xpo5 binding sites, read counts per hits-clip library, biological complexity and peak annotation information. Xpo5_normalized_counts.tsv contains normalized counts for small-RNA-Seq libraries from XPO5 cko and controls and log2 fold changes. smrna_293_counts.txt contains read counts for 293 small-RNA-Seq mapped via novoalign and counted via enumerating intersections with a pre-miRNA database from miRbase.

source_name: HEK293FT cells

growth_protocol: HEK293FT cells were cultured in DMEM (GIBCO) supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin (GIBCO) in the 5% CO2 incubator at 37 °C.

extract_protocol:
For the miRNA-seq, total RNA was extracted by Trizol reagent (Thermo Fisher Scientific) using HEK293Tcells and epidermis cells isolated from XPO5 het and KO animals .
For miRNA-seq, Total RNA samples from p2-p4 back skin epidermis and HEK293T cells were subject to high efficiency 3′ ligation. Products were resolved on 15% PAGE-urea gels and stained with SybrGold (Molecular Probes S-11494 Carlsbad, California, USA). The region corresponding to ligated miRNAs (46 nucleotides) was excised, gel slices were thoroughly minced, and eluted in HSCB (400 mM NaCl, 25 mM Tris-HCl pH 7.5, 0.1% SDS) overnight at 4°C. Nucleic acids were precipitated in the presence of glycogen carrier via 0.1 volumes sodium acetate and 2.5 volumes ethanol. Pellets were washed in 70% ethanol, and dissolved in the 5′ ligation mix without enzyme. Samples were briefly heated to 70°C, snap chilled on ice, and then enzyme was added. Following ligation reactions cDNA was prepared using Superscript III RT (Invitrogen) according to the manufacturer′s recommendation using 3′ linker-specific RT primer. cDNA libraries served as templates for PCR amplification; amplicons were resolved on 8% native acrylamide gels. Bands of the correct molecular weight were isolated and used for high-throughput sequencing on the Illumina HiSeq2000.


title: Fluidigm C1 single cell RNA-Seq [Cell_184]


title: Fluidigm C1 single cell RNA-Seq [Cell_183]


title: Testis sample with impaired spermatogenesis, Sample 4


title: Fluidigm C1 single cell RNA-Seq [Cell_181]


title: 293_smRNA_rep2

description:
Small RNA
smrna_293_counts.txt.gz


title: 293_smRNA_rep1

description:
Small RNA
smrna_293_counts.txt.gz


title: Fluidigm C1 single cell RNA-Seq [Cell_180]


title: Fluidigm C1 single cell RNA-Seq [Cell_186]


title: XPO5_HITS-CLIP_5

description:
final_peaks_BC3_5reads.bed.gz
processed data file sample name:
21_GTTTCG_L007_R1_001

extract_protocol:
HEK293T cells were UV-crosslinked, re-suspended in lysis buffer.RNA-XPO5 complexes were isolated with Anti-Exportin-5 antibody (Abcam).
For XPO5 HITS-CLIP, HEK293FT cell lysates were incubated with Anti-Exportin-5 antibody (Abcam) or control IgG for 1 hr on ice with or without RNase.  After incubation, dynabeads were added into the protein-RNA complexes solutions and incubate for 1h at 4°C, followed by labelling 3′ end of RNA with [γ- 32P] ATP using PNK. Then 5' Ligation Adapter-NN was linked to 5′ end of RNA using T4 RNA ligase 1 at room temperature for 2h. Protein-RNA complexes were incubated in 1x Nu-PAGE loading buffer (Invitrogen) at 70°C for 10 min, resolved on 8% Nu-PAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposed to a Fuji film. Bands corresponding to specific protein-RNA complexes were excised and then digested with proteinase K. RNAs were purified and adenylated linker was linked to 3’ end of purified RNAs. cDNAs were made using Superscript III(Invitrogen) with 3’ adenylated linker primers. cDNAs were separated on 15% denaturing urea polyacrylamide gel and one area around 100 bp were excised purified, followed by amplification by Phusion High Fidelity polymerase (NEB). PCR products were seperated by 6% denaturing urea polyacrylamide gel and three bands around 100-150 were purified. Obtained CLIP libraries were subjected to high throughput deep sequencing.

tag: antibody

value: Anti-Exportin-5 antibody (Abcam, Cat#ab131281)


title: XPO5_HITS-CLIP_3

description:
final_peaks_BC3_5reads.bed.gz
processed data file sample name:
19_GTGAAA_L007_R1_001


title: XPO5_HITS-CLIP_2

description:
final_peaks_BC3_5reads.bed.gz
processed data file sample name:
18_GTCCGC_L007_R1_001


title: XPO5_HITS-CLIP_1

description:
final_peaks_BC3_5reads.bed.gz
processed data file sample name:
17_GTAGAG_L007_R1_001


title: Fluidigm C1 single cell RNA-Seq [Cell_173]


title: Fluidigm C1 single cell RNA-Seq [Cell_174]


title: Fluidigm C1 single cell RNA-Seq [Cell_169]


title: WT-Neu-R848-6h2_S10

city: Tokyo

first: Hiroaki

last: Hatano

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Allergy and Rheumatology

country: Japan

institute: The University of Tokyo

data_processing:
Raw read quality was evaluated using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (v0.11.7).
After trimming off the adaptors using cutadapt (v1.16), reads containing many low quality bases (Phred quality score <20 in >20% of the bases) or very low quality bases (Phred quality score < 10) were removed using the FASTX toolkit. Mean of the total read count after QC was 1.02 × 10^6.
Filtered reads were mapped to the UCSC mm10 using STAR (v2.5.3a), and the read count was calculated using HTSeq (v0.6.1p1).
Genes expressed in less than two samples were omitted from further analysis. We compared changes in mRNA expression before and after R848 stimulation in WT and Padi4 KO neutrophils.
Genome_build: mm10
Supplementary_files_format_and_content: count table

extract_protocol:
RNA was harvested using TRIzol LS reagent (Life Technologies) and RNeasy micro kit (Qiagen). RNA sequencing libraries were prepared using a TrueSeq RNA sample preparation kit v2 (Illumina).
Paired-end sequencing was performed using a MiSeq Reagent V2 kit (Illumina) on the MiSeq system.RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Neutrophils at a concentration of 1 × 10^6/ml were incubated in 24-well plates and left unstimulated or stimulated with 1 µg/ml of R848 for 6 hours.

tag: strain background

tag: age

value: post natal week 8

tag: genotype

value: wild type

value: Neutrophil

value: 1 µg/ml of R848 for 6 h


title: KO-Neu-R848-6h1_S11

tag: treatment


title: WT-Neu-R848-6h1_S9


title: KO-Neu-Nostim-0h2_S4


title: Fluidigm C1 single cell RNA-Seq [Cell_168]


title: Testis sample with impaired spermatogenesis, Sample 19


title: KO-Neu-Nostim-0h1_S3


title: Testis sample with impaired spermatogenesis, Sample 16


title: Fluidigm C1 single cell RNA-Seq [Cell_164]


title: WT-Neu-Nostim-0h2_S2


title: Fluidigm C1 single cell RNA-Seq [Cell_161]


title: Fluidigm C1 single cell RNA-Seq [Cell_179]


title: Testis sample with normal spermatogenesis, Sample 1


title: 293_smRNA_rep3

description:
Small RNA
smrna_293_counts.txt.gz

tag: cell line


title: WT-Neu-Nostim-0h1_S1


title: Fluidigm C1 single cell RNA-Seq [Cell_175]


title: sgk1 inhibitor

city: Seoul

first: Oh-Chan

last: Kwon

address: 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea

department: Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse VM-derived glial cells

growth_protocol: Mixed glia were isolated from mouse or rat ventral midbrain(VM) on Postnatal day 1 (P1) ~P5, using the glial cell culture protocol . In brief, VMs were removed, triturated in DMEM (Thermo Scientific Inc., Waltham, MA) containing 10% FBS (HyClone, GE Healthcare Life Sciences, Pittsburgh, PA), and plated in 75-cm2 T-flasks. When cell confluence reached 80%–90%, cells were harvested with 0.125% trypsin and subcultured on a culture surface coated with poly-d-lysine (PDL) (Millipore Sigma, Louis, MO).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: For analyses, the cells were treated SGK1 inhibitors [GSK650394 (1-2μM) (Tocris Bioscience, Bristol, U.K.)] every-other-day with toxins.

value: ICR(CD-1) Outbred Mice

tag: tissue

value: brain

value: postnatal 5 day


title: Fluidigm C1 single cell RNA-Seq [Cell_160]

value: Lfng-EGFP

value: Adult cochlear supporting cells


title: Testis sample with normal spermatogenesis, Sample 2


title: Fluidigm C1 single cell RNA-Seq [Cell_159]


title: Cont


title: Fluidigm C1 single cell RNA-Seq [Cell_158]


title: Fluidigm C1 single cell RNA-Seq [Cell_166]


title: Sup RG33_S1

city: Linköping

first: Lech

middle: Tadeusz

last: Kaczmarczyk

address: Campus US

department: Cell Biology

country: Sweden

institute: Linköping University

description:
Sup
Input Supernatant

data_processing:
FastQC
BBduk alignment (bbmap.sh -Xmx30g in=xxx.fq out=xxx.bam qtrim=t usequality=t minaveragequality=0 local=f strictmaxindel=f xstag=us maxindel=100000 intronlen=10 ambig=toss threads=8)
Couting reads with SummarizeOverlaps()
DEseq2 robust RPKM calculation and quantification
Genome_build: GENCODE GRCm38
Supplementary_files_format_and_content: RPKM and sample table (csv files)

extract_protocol: none provided by the subimtter

tag: Sex

value: m


title: Fluidigm C1 single cell RNA-Seq [Cell_157]

tag: mouse model


title: Fluidigm C1 single cell RNA-Seq [Cell_154]

tag: Stage


title: Sup RG34_S1

description:
Sup
Input Supernatant

value: f


title: Fluidigm C1 single cell RNA-Seq [Cell_153]


title: Sup RG35_S1

description:
Sup
Input Supernatant


title: Sup RG36_S1

description:
Sup
Input Supernatant


title: Fluidigm C1 single cell RNA-Seq [Cell_151]


title: Sup RG16_S1

description:
Sup
Input Supernatant


title: Fluidigm C1 single cell RNA-Seq [Cell_182]


title: Testis sample with normal spermatogenesis, Sample 10


title: Sup RG17_S1

description:
Sup
Input Supernatant


title: Fluidigm C1 single cell RNA-Seq [Cell_148]


title: Sup RG19_S1

description:
Sup
Input Supernatant


title: IP RG34

description:
IP
RiboTag


title: Fluidigm C1 single cell RNA-Seq [Cell_147]


title: Fluidigm C1 single cell RNA-Seq [Cell_150]


title: Fluidigm C1 single cell RNA-Seq [Cell_146]


title: Fluidigm C1 single cell RNA-Seq [Cell_145]


title: Testis sample with normal spermatogenesis, Sample 3


title: IP RG36

description:
IP
RiboTag


title: IP RG27

description:
IP
RiboTag


title: Fluidigm C1 single cell RNA-Seq [Cell_144]


title: Fluidigm C1 single cell RNA-Seq [Cell_141]


title: Fluidigm C1 single cell RNA-Seq [Cell_152]


title: Fluidigm C1 single cell RNA-Seq [Cell_138]


title: Fluidigm C1 single cell RNA-Seq [Cell_134]


title: MEF16_WT

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Reads were mapped on mm10 mouse transcriptome with gencode M14 as gene annotation and quantified using RSEM v1.3.1
Read counts were normalized by calculating TPM (Transcripts Per Kilobase Million)
DESeq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads count, TPM and FPKM for each Sample

source_name: Wild Type MEFs (murine embryonic fibroblasts)

growth_protocol: MEFs cells were routinely grown on uncoated plastic in DMEM medium (Thermofisher) supplemented with Glutamine (Thermofisher).

extract_protocol:
MEFs were trypsinized, peletted, and RNA was harvested using Nucleospjin (Macherey). 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

value: mouse embryonic fibroblasts (MEFs)

tag: passage

tag: genotype/variation

value: Lztr1 +/+


title: MEF11_Het

source_name: Lztr1 +/- MEFs (murine embryonic fibroblasts)

value: Lztr1 +/-


title: Fluidigm C1 single cell RNA-Seq [Cell_137]

tag: strain


title: Fluidigm C1 single cell RNA-Seq [Cell_131]


title: IP RG35

description:
IP
RiboTag


title: SmoM2 rep 3

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan University

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using Hisat2（version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cortex from P0 WT mice, ShhN IUE mice and hGFAP-Cre,SmoM2f/+ mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

value: a mixed genetic background of C57BL/6J, 129S6 and CD1

value: Cortex

tag: developmental stage

value: Postnatal day 0

value: hGFAP-Cre, SmoM2f mice brain


title: SmoM2 rep 2


title: ShhN IUE rep 3

value: ShhN IUE brain


title: SmoM2 rep 1


title: Fluidigm C1 single cell RNA-Seq [Cell_126]


title: ShhN IUE rep 2


title: Fluidigm C1 single cell RNA-Seq [Cell_125]


title: ShhN IUE rep 1


title: Fluidigm C1 single cell RNA-Seq [Cell_139]


title: Fluidigm C1 single cell RNA-Seq [Cell_124]


title: IP RG29

description:
IP
RiboTag


title: Wild type rep 3

value: Wild type littermate


title: KO-Neu-R848-6h2_S12

value: post natal week 8

value: Neutrophil

value: 1 µg/ml of R848 for 6 h


title: Wild type rep 2


title: Fluidigm C1 single cell RNA-Seq [Cell_123]


title: XPO5_HITS-CLIP_4

description:
final_peaks_BC3_5reads.bed.gz
processed data file sample name:
20_GTGGCC_L007_R1_001

value: Anti-Exportin-5 antibody (Abcam, Cat#ab131281)


title: Wild type rep 1


title: Fluidigm C1 single cell RNA-Seq [Cell_165]

value: Lfng-EGFP


title: Fluidigm C1 single cell RNA-Seq [Cell_120]

value: Adult cochlear supporting cells


title: Reg_7d_Amp.26_R2.11182015.Left.P3

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
The gene expected read counts and TPMs were estimated by RSEM (v1.2.3)
TPMs were median-by-ratio normalized, and replicates were merged via calculating average normalized TPMs.
Genome_build: mm10
Supplementary_files_format_and_content: text and gene expression values

source_name: Amputated digit 3 (hindlimb distal phalanx (P3)

growth_protocol: A regenerating distal phalanx was generated by amputating ≤33% of the P3. Skin wounds were allowed to heal without suturing. Mice were subjected to micro-computed tomography (microCT) one day prior to surgery and immediately after amputation to confirm ≤ 33% removal of the P3. Any digit that did not fall within the   ≤ 33% amputation guideline was omitted from the study.

extract_protocol:
Total RNAs were isolated from tissues using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254).
One hundred nanograms of total RNA was used to prepare sequencing libraries using the LM-Seq (Ligation Mediated Sequencing) protocol (Hou, Z. et al. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Sci Rep 5, 9570 (2015).)
RNAs was selected using the NEB Next Poly A+ Isolation Kit (NEB #E7490S/L).  Poly A+ fractions were eluted, primed, and fragmented for 7 minutes at 85°C.  First stand cDNA synthesis was performed using SmartScribe Reverse Transcriptase (Takara Bio USA #639538) and RNA is then removed.  cDNA fragments were purified with AMpure XP beads (Beckman Coulter #A63881). The 5’ adapter was ligated and 18 cycles of amplification were performed.  These final indexed cDNA libraries were quantified, normalized, multiplexed, and run as single-end reads for 65bp on the HiSeq 2500 (Illumina, San Diego, CA).

treatment_protocol: P3 mice were collected at hours (0h, 3h, 6h ,12h, and 24h), and days (3d, 7d, 14d, and 21d). Each time point contained 3 mice, except day 7 (6 mice). At the time of P3 collection, samples were immediately immersed in RNAlater for 24h at 4C. The digits were then removed from RNAlater and stored at -80oC until performing RNA sequencing.

value: regenerative digits

tag: timepoint


title: Fluidigm C1 single cell RNA-Seq [Cell_177]


title: Reg_7d_Amp.24_M00.11182015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_130]


title: Fluidigm C1 single cell RNA-Seq [Cell_117]


title: Reg_7d_Amp.23_R1.11182015.Left.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_115]


title: Reg_7d_Amp.19_L1.11182015.Left.P3


title: Reg_7d_Amp.16_M00.07232015.Right.P3


title: Reg_6h_Amp.20_R1.07152015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_114]


title: Fluidigm C1 single cell RNA-Seq [Cell_111]


title: Fluidigm C1 single cell RNA-Seq [Cell_109]


title: Fluidigm C1 single cell RNA-Seq [Cell_110]


title: Reg_6h_Amp.20_M00.11192015.Right.P3


title: Reg_7d_Amp.16_L1.07232015.Right.P3


title: Reg_6h_Amp.10_M00.07152015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_108]


title: Fluidigm C1 single cell RNA-Seq [Cell_122]


title: Fluidigm C1 single cell RNA-Seq [Cell_129]


title: Fluidigm C1 single cell RNA-Seq [Cell_107]


title: Fluidigm C1 single cell RNA-Seq [Cell_106]


title: Reg_3h_Amp.19_R1.07142015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_105]


title: Reg_3h_Amp.17_M00.07142015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_103]


title: Fluidigm C1 single cell RNA-Seq [Cell_102]


title: Reg_3d_Amp.24_L1.07232015.Right.P3


title: Reg_3d_Amp.23_R1.07232015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_099]


title: Reg_3d_Amp.21_L1.11192015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_098]


title: Reg_24h_Amp.29_M00.12032015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_095]


title: Fluidigm C1 single cell RNA-Seq [Cell_094]


title: Reg_24h_Amp.21_R1.08132015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_171]


title: Reg_24h_Amp.16_L1.08132015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_093]


title: IP RG26

description:
IP
RiboTag

value: f


title: Fluidigm C1 single cell RNA-Seq [Cell_091]


title: Reg_21d_Amp.27_R1.12022015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_090]


title: Reg_3h_Amp.21_L1.07142015.Right.P3


title: Reg_21d_Amp.27_L1.01082016.Right.P3


title: Reg_21d_Amp.26_L2.01082016.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_086]


title: Reg_14d_Amp.42_L1.12012015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_085]


title: Fluidigm C1 single cell RNA-Seq [Cell_084]


title: Reg_14d_Amp.42_L2.12012015.Right.P3


title: Reg_12h_Amp.25_L1.07202015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_079]


title: Reg_12h_Amp.19_R1.07202015.Right.P3


title: Reg_14d_Amp.14_R1.07292015.Right.P3


title: Reg_12h_Amp.13_M00.07202015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_077]


title: Reg_0h_Amp.19_R1.07202015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_076]


title: Fluidigm C1 single cell RNA-Seq [Cell_074]


title: Reg_0h_Amp.13_L1.11302015.Right.P3


title: Reg_0h_Amp.11_R1.11302015.Right.P3


title: Fluidigm C1 single cell RNA-Seq [Cell_067]


title: H9 scramble p(A)+ RNA-seq replicate2

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

description: H9 scramble replicate2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq reads were first processed by using trimmomatic (version 0.35, parameters: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:80) to remove low quality bases and adaptor sequences, and then mapped by using HISAT2 (Kim et al., 2015) (version 2.0.5, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --dta -k 1 --max-seeds 20) to GRCh37/hg19 human reference genome with the GENCODE gene annotation (version 28lift27) or GRCm38/mm10 mouse reference genome with the GENCODE gene annotation (version M17). The HISAT2-mapped sam files were transferred to bam format by samtools (version 0.1.19).
Bam to Bedgraph using genomeCoverageBed  Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for H9 RNA-seq and mm10 for R1 RNA-seq
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: H9 cells

growth_protocol: H9 hESCs were maintained on irradiated-MEF feeder cells with daily changed hESC cultured medium and passaged weekly;  R1 cells were cultured in DMEM (Gibco, 12430) supplemented with 15% Fetal Bovine Serum (Gibco, 16000-044), 1mM Glutamin, 1% NEAA, 1% Nucleosides (Millipore) and 1% penicillin/streptomycin (Millipore), 0.1mM mercaptoethanol and 1 μM PD0325901, 3 μM CHIR99021 and 1000 units/ ml mouse LIF.

extract_protocol:
Total RNA from each cultured cell line or cultured cells with different treatments was extracted with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. Fractionation of the cytoplasmic and nuclear RNA in H9 and R1 cells was performed as following. 1 × 106 cells were rinsed twice with ice-cold PBS, and centrifuged at 1,000 rpm for 3 min. Cell pellet was suspended by gentle pipetting in 200 mL lysis buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1.5 mM MgCl2, 0.5% Igepal, 2 mM Ribonucleoside Vanadyl Complex), and incubated on ice for 5 min. During the incubation, one fifth of the lysate was added to 1 mL Trizol for total RNA extraction. The rest of the lysate was centrifuged at 1,000 g for 3 min at 4°C to pellet the nuclei and the supernatant was the cytoplasmic fraction. To obtain pure cytoplasmic RNA, the supernatant fraction was centrifuged at 14,000rpm for 10 min at 4°C and then collected the supernatant carefully to a new tube and extracted the RNA with Trizol. To obtain pure nuclear RNA, nuclear pellets underwent additional wash with 200 µL lysis buffer, one additional wash by adding 0.5% deoxycholic acid into the lysis buffer. Finally, the purified nuclei were resuspended in 200 µL lysis buffer followed by extraction with Trizol. Fractionated RNA from the same amount of cells was used for cDNA production, RT-PCR and RNA-seq analysis.
For RNA-seq samples from H9 and R1 cells, total/cytoplasmic/nuclear RNA was processed with the RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete ribosomal RNAs for sequencing (Ribo– RNA-seq). For hFAST KD total RNA-seq samples, polyadenylated (poly(A)+) RNA preparation was carried out as following. Briefly, total RNAs (8 μg) were incubated with oligo(dT) magnetic beads to isolate poly(A)+ RNAs, which were bound to beads, selection was performed three times to ensure the purity of poly(A)+ RNA populations. Ribo– and poly(A)+ RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Size-selected libraries were subjected to deep sequencing with Illumina HiSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China. Raw read qualities were evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

treatment_protocol: To knock down hFAST,  mPpie, DNA sequences for shRNAs were designed by the GPP Web Portal online tool (https://portals.broadinstitute.org/gpp/public/). DNA oligos of shRNA sequences for targeted RNAs or scramble shRNAs were individually cloned into pLKO.1-TRC vector.  To infect H9 cells with lentivirus, 2 × 105 cells were incubated MEF-CM containing 5 μL concentrated lentivirus, 5 μg/mL polybrene and 10 μM Y-27632 at 37°C for first day. To infect R1 cells with lentivirus, 2 × 105 cells were infected with 5 μL concentrated lentivirus, 5 μg/mL polybrene for first day. Cells were selected by 1mg/ml puromycine for two days, then harvest total RNA or cytoplasm RNA or nucleus RNA.

tag: type

value: cDNA

value: scramble


title: H9 scramble p(A)+ RNA-seq replicate1

description: H9 scramble replicate1


title: Fluidigm C1 single cell RNA-Seq [Cell_083]

tag: cell type


title: Fluidigm C1 single cell RNA-Seq [Cell_065]


title: Fluidigm C1 single cell RNA-Seq [Cell_066]


title: H9 FAST KD1 p(A)+ RNA-seq replicate1

description: H9 FAST KD1 replicate1

value: FAST shRNA KD


title: Fluidigm C1 single cell RNA-Seq [Cell_070]


title: H9 FAST KD1 p(A)+ RNA-seq replicate2

description: H9 FAST KD1 replicate2


title: H9 total cell ribo- RNA-seq replicate1

description: H9 total replicate1

data_processing:
Library strategy: Ribo-seq
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq reads were first processed by using trimmomatic (version 0.35, parameters: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:80) to remove low quality bases and adaptor sequences, and then mapped by using HISAT2 (Kim et al., 2015) (version 2.0.5, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --dta -k 1 --max-seeds 20) to GRCh37/hg19 human reference genome with the GENCODE gene annotation (version 28lift27) or GRCm38/mm10 mouse reference genome with the GENCODE gene annotation (version M17). The HISAT2-mapped sam files were transferred to bam format by samtools (version 0.1.19).
Bam to Bedgraph using genomeCoverageBed  Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for H9 RNA-seq and mm10 for R1 RNA-seq
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

value: untreated


title: Fluidigm C1 single cell RNA-Seq [Cell_063]


title: H9 total cell ribo- RNA-seq replicate2

description: H9 total replicate2


title: Fluidigm C1 single cell RNA-Seq [Cell_062]


title: H9 nucleus ribo- RNA-seq replicate1

description: H9 nucleus replicate1


title: H9 nucleus ribo- RNA-seq replicate2

description: H9 nucleus replicate2


title: Fluidigm C1 single cell RNA-Seq [Cell_061]


title: Fluidigm C1 single cell RNA-Seq [Cell_064]


title: Fluidigm C1 single cell RNA-Seq [Cell_058]


title: H9 cytoplasm ribo- RNA-seq replicate1

description: H9 cytoplasm replicate1


title: Fluidigm C1 single cell RNA-Seq [Cell_059]


title: H9 cytoplasm ribo- RNA-seq replicate2

description: H9 cytoplasm replicate2


title: Fluidigm C1 single cell RNA-Seq [Cell_071]


title: Fluidigm C1 single cell RNA-Seq [Cell_052]


title: G_6_3

city: Changsha

first: Touming

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
the raw reads for each sample were filtered, generating clean reads used in next analysis.
To estimate the expression level of garlic genes in various tissues and eight bulbs-developmental stages, the clean reads from transcriptome sequencing were aligned to garlic genome using the Bowtie2 software, and read number of each transcript was calculated using the RSEM software. The fragments per kilobase of transcript sequence, per millions base pairs sequenced (FPKM) were estimated to measure the expression of each transcript.
The DEGseq program based on the MA-plot algorithm was used to identify the differential expression genes during the bulbs growth.
Genome_build: The garlic genome has been submitted into the NCBI genome with the BioProject ID PRJNA606385. Gene annotation, CDS and protein sequences are also available at: https://doi.org/10.6084/m9.figshare.11860602.v1
The FASTA of CDS sequence is available on the series record.
Supplementary_files_format_and_content: the excel file contain the gene name, sample name, and FPKM value

organism: Allium sativum

source_name: the cultivar Ershuizao

growth_protocol: The garlic Ershuizao cultivated in the experimental farm of the Shandong Agricultural University, Taian, China, in Oct. 2018 was used for the transcriptome analysis. When the garlic buds, the shoots were collected. In May 6, 2019, the leaves, bulbs, pesudostems, garlic sprouts, roots and flowers were individually sampled. In addition, to characterize the expression of expanding bulbs dynamically, bulbs samples from eight stages of growth were collected, by sample each five day from April 11 to May 16 in 2019 when the bulbs have not start the expanding growth and have finished the expansion, respectively, and correspondingly, the sample names were designated orderly from S1 to S8. Three replicates were performed for each sample.

extract_protocol:
The samples were collected individually, immediately frozen in liquid nitrogen. Three replicates were sampled for exch tissues, respectively. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol.
Total RNAs for all 42 samples were separately extracted and used to construct the cDNA library with fragment lengths of ~250 bp.

value: roots

tag: cultivar

value: Ershuizao


title: QSLJ_1_2

value: flowers


title: Fluidigm C1 single cell RNA-Seq [Cell_055]


title: QSLJ_1_1


title: G_6_2


title: Fluidigm C1 single cell RNA-Seq [Cell_050]


title: Fluidigm C1 single cell RNA-Seq [Cell_049]


title: HJ_5_3

value: garlic sprouts


title: HJ_5_2


title: Fluidigm C1 single cell RNA-Seq [Cell_048]


title: G_6_1


title: Fluidigm C1 single cell RNA-Seq [Cell_047]


title: JJ_3_3

value: pesudostems


title: Fluidigm C1 single cell RNA-Seq [Cell_044]


title: HJ_5_1


title: JJ_3_2


title: Fluidigm C1 single cell RNA-Seq [Cell_045]


title: YP_2_3

value: leaves


title: JJ_3_1


title: QSLJ_1_3


title: Fluidigm C1 single cell RNA-Seq [Cell_046]


title: Fluidigm C1 single cell RNA-Seq [Cell_043]


title: YP_2_2


title: Fluidigm C1 single cell RNA-Seq [Cell_042]


title: Fluidigm C1 single cell RNA-Seq [Cell_041]


title: Fluidigm C1 single cell RNA-Seq [Cell_060]


title: Fluidigm C1 single cell RNA-Seq [Cell_051]


title: Fluidigm C1 single cell RNA-Seq [Cell_040]


title: Testis sample with normal spermatogenesis, Sample 15

tag: testis tissue

value: normal spermatogenesis

value: Experimental sample, normal spermatogenesis

tag: sample type

value: Agilent’s Universal Human Reference RNA


title: YP_2_1


title: Y_1_7

value: buds


title: Fluidigm C1 single cell RNA-Seq [Cell_038]

value: Lfng-EGFP

value: Adult cochlear supporting cells


title: Fluidigm C1 single cell RNA-Seq [Cell_082]


title: Y_1_1


title: Fluidigm C1 single cell RNA-Seq [Cell_039]


title: Fluidigm C1 single cell RNA-Seq [Cell_037]


title: Y_1_4


title: LJ_4_8_3

value: bulbs


title: Fluidigm C1 single cell RNA-Seq [Cell_035]


title: LJ_4_8_2


title: LJ_4_7_3


title: LJ_4_7_1


title: LJ_4_8_1


title: Fluidigm C1 single cell RNA-Seq [Cell_033]


title: LJ_4_7_2


title: LJ_4_6_3


title: LJ_4_6_2


title: Fluidigm C1 single cell RNA-Seq [Cell_029]


title: Fluidigm C1 single cell RNA-Seq [Cell_030]


title: Fluidigm C1 single cell RNA-Seq [Cell_032]


title: Fluidigm C1 single cell RNA-Seq [Cell_028]


title: Fluidigm C1 single cell RNA-Seq [Cell_027]


title: LJ_4_5_3


title: LJ_4_5_2


title: Fluidigm C1 single cell RNA-Seq [Cell_023]


title: Fluidigm C1 single cell RNA-Seq [Cell_036]


title: LJ_4_4_2


title: LJ_4_4_1


title: Fluidigm C1 single cell RNA-Seq [Cell_026]


title: Fluidigm C1 single cell RNA-Seq [Cell_024]


title: Fluidigm C1 single cell RNA-Seq [Cell_025]


title: LJ_4_3_2


title: Fluidigm C1 single cell RNA-Seq [Cell_021]


title: Fluidigm C1 single cell RNA-Seq [Cell_031]


title: LJ_4_3_1


title: Fluidigm C1 single cell RNA-Seq [Cell_019]


title: Fluidigm C1 single cell RNA-Seq [Cell_020]


title: LJ_4_2_2


title: Fluidigm C1 single cell RNA-Seq [Cell_018]


title: Fluidigm C1 single cell RNA-Seq [Cell_017]


title: LJ_4_6_1


title: LJ_4_1_3


title: Fluidigm C1 single cell RNA-Seq [Cell_015]


title: LJ_4_1_2


title: LJ_4_1_1


title: LJ_4_4_3


title: Fluidigm C1 single cell RNA-Seq [Cell_022]


title: LJ_4_3_3


title: Fluidigm C1 single cell RNA-Seq [Cell_012]


title: Surface Lab.1

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to Ensembl genome Astyanax mexicanus 2.0 with STAR aligner (version STAR_2.6.1c ), using Ensembl 96 gene models for annotations. Transcripts were quantified using RSEM  (version v1.3.0 ) to calculate the transcript abundance ‘TPM’ (Transcripts per Million).
Genome_build: Astyanax_mexicanus-2.0
Supplementary_files_format_and_content: TPM gene expression in csv file

organism: Astyanax mexicanus

source_name: Liver

growth_protocol: Animals were fasted for 12 hours before tissue dissection

extract_protocol: Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina). The resulting libraries were purified using Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and Qubit fluorometer (Life Technologies).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina NextSeq 500 instrument as High Output 75bp single read runs.

tag: group

value: Surface fish

tag: environment

value: lab

value: Adult


title: Surface Lab.3


title: Fluidigm C1 single cell RNA-Seq [Cell_013]


title: Fluidigm C1 single cell RNA-Seq [Cell_014]


title: Surface Lab.2


title: Fluidigm C1 single cell RNA-Seq [Cell_010]


title: Fluidigm C1 single cell RNA-Seq [Cell_011]


title: Surface Wild.2

value: wild-caught


title: LJ_4_2_3


title: Surface Wild.1


title: Fluidigm C1 single cell RNA-Seq [Cell_008]


title: Fluidigm C1 single cell RNA-Seq [Cell_006]


title: Pachón Lab.3

value: Cavefish


title: Pachón Lab.2


title: Fluidigm C1 single cell RNA-Seq [Cell_005]


title: Fluidigm C1 single cell RNA-Seq [Cell_016]


title: Pachón Lab.1


title: Fluidigm C1 single cell RNA-Seq [Cell_004]


title: Fluidigm C1 single cell RNA-Seq [Cell_003]


title: Pachón Wild.2


title: Pachón Wild.3


title: Surface Wild.3


title: Fluidigm C1 single cell RNA-Seq [Cell_001]


title: Pachón Wild.1


title: 201148310023_R11C01

type: genomic

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

institute: Langston University

description: Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping Beadchips (Illumina).

hyb_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.

data_processing:
Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping BeadChips (Illumina).
Image data was analyzed using Genome Studio and further analysis was conducted using PLINK, R, Qlik, and GoldenHelix SNP &Variation Suite

label: Cy3, Cy5

organism: Capra hircus

source_name: Milk Somatic Cells

extract_protocol: Norgen Biotek Corp. Milk DNA Preservation and Isolation Kit was used to extract genomic DNA from Bronopol preserved goat milk somatic cells.

treatment_protocol: Goat milk obtained from different sources and different locations throughout the United States were preserved by Bronopol tablet placement in the milk before shipment and downstream procedures.

value: Female

value: Milk Somatic Cells


title: 201148310023_R12C01

scan_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.


title: 201148310023_R11C02

label_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.


title: 201148310023_R08C02


title: 201148310023_R09C02


title: 201148310023_R09C01


title: 201148310023_R10C02


title: 201148310023_R10C01


title: 201148310023_R08C01


title: Fluidigm C1 single cell RNA-Seq [Cell_007]

extract_protocol:
Cochleae from P60 and P120 LfngEGFP mice were used for FACS purification of GFP+ supporting cells (SCs) before single cell capture. Briefly, the inner ear was dissected from adult mice and the vestibular portions of the inner ear, including utricle, saccule and semicircular canal ampulla, were removed. Cochleae were then collected in a 1.5-ml tube (n = 4-5 cochleae per integrated fluidics chip (IFC) capture) and incubated in 0.05% crude trypsin (Worthington) in CMF-PBS (Life Technologies) at 37ºC for 8 min. Excess trypsin solution was removed and four volumes of 5% FBS (Thermo Fisher Scientific) in DMEM/F12 (Thermo Fisher Scientific) was added to stop the digestion. The tissue was then triturated for 2 min and passed through a 40-µm strainer (pluriSelect Life Science) to eliminate residual aggregates and bone fragments. The resulting single-cell suspension was then stained with propidium iodide (Life Technologies) to allow for exclusion of dead cells and debris from the samples during FACS-purification. Single cells were sorted on a FACSAria flow cytometer (BD Biosciences) with a compensated FITC setting and 488 nm excitation, using a 100-µm nozzle. In adult tissue, GFP+ SCs are the brightest population and typically comprised 2-7% of viable cells. The purpose of FACS purification was to enrich for a population of GFP+ SCs and gating was set based on wild type isotype controls to exclude the majority of GFP– cochlear cells. Scatter discrimination was used to eliminate doublets and samples were negatively selected with propidium iodide to remove dead cells. Cells were collected in 20% FBS in DMEM/F12 and stored on ice. After sorting, cells were spun at 200g for 10 min and then resuspended in 20% FBS
Library preparation was performed according to the manufacturer’s instructions for the Fluidigm C1 instrument (Fluidigm). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).


title: 201148310023_R07C01


title: 201148310023_R06C02


title: Fluidigm C1 single cell RNA-Seq [Cell_034]


title: 201148310023_R05C01


title: 201148310023_R05C02


title: 201148310023_R04C02


title: Fluidigm C1 single cell RNA-Seq [Cell_002]


title: 201148310023_R04C01


title: 201148310023_R03C02


title: 201148310023_R03C01


title: 201148310023_R12C02


title: 201148310023_R02C02


title: 201148310023_R02C01


title: DLD-1 cells transfected miR-4711-5p

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: DLD-1 cells transfected miR-4711-5p

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: DLD-1 cells transfected miR-4711-5p

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: DLD-1 cells


title: LJ_4_5_1

value: Ershuizao


title: 201148310023_R07C02


title: DLD-1 cells transfected miR-negative control


title: 201148310023_R01C02


title: 201148310020_R11C01


title: 201148310020_R11C02


title: 201148310023_R01C01


title: 201148310020_R12C01


title: 201148310023_R06C01


title: H2170-MET-N375S

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
H2170 cell lines with MET N375S mutation.
processed data file: H2170_FPKM.xlsx

data_processing:
CASAVA v1.8 was used to convert bcl files into fastq files.
Alignment was made using TopHat2 v2.0.9 to hg19.
Quantification was performed using HTSeq v0.6.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: H2170_FPKM.xlsx: Excel file includes FPKM gene expression values.

source_name: lung carcinoma cultured cell line

growth_protocol: Cell lines were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 μg/mL streptomycin and 100 U/mL penicillin in a humidified 37°C incubator.

extract_protocol:
RNA was extracted with Qiagen RNeasy kit, RNA purity was determined with Nanodrop and Agilent 2100, and quantified by Qubit.
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Isogenic cell lines stably expressing pCMV6-AC-GFP vector, pCMV6-MET (wt) and pCMV6-MET (N375S) plasmids respectively, were generated by transfection and single-cell clonal selection.

tag: cell line

tag: expression


title: HCT116 cells transfected miR-4711-5p

description: HCT116 cells transfected miR-4711-5p

source_name: HCT116 cells transfected miR-4711-5p

value: HCT 116 cells


title: H2170-MET-WT

description:
H2170 cell lines with MET WT.
processed data file: H2170_FPKM.xlsx

value: MET-WT


title: HCT116 cells transfected miR-negative control


title: 201148310020_R10C02

tag: Sex

tag: tissue


title: 201148310020_R09C02


title: 201148310020_R09C01


title: 201148310020_R10C01


title: LJ_4_2_1


title: 201148310020_R08C02


title: 201148310020_R08C01


title: 201148310020_R12C02


title: 201148310020_R07C02


title: 201148310020_R07C01


title: 201148310020_R06C02


title: 201148310020_R05C02


title: 201148310020_R04C01


title: 201148310020_R06C01


title: Fluidigm C1 single cell RNA-Seq [Cell_009]

first: Michael

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using STAR pipeline using default settings.
Secondary analysis was performed using the Seurat2 package
Genome_build: mm10
Supplementary_files_format_and_content: Expression Matrix of Raw Counts; Cell-associated Metadata

tag: mouse model

tag: Stage


title: 201148310020_R05C01


title: 201148310020_R04C02


title: 201148310020_R03C02


title: 201148310020_R03C01


title: 201148310020_R02C02


title: UV-Treatment, 200 mg/L, Rep3

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: A custom microarray was developed featuring transcripts described in Villeneuve et al (2010) in addition to newly developed in-house sequence sets totaling ~50K unique P. promelas transcriptome sequences.  The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  The microarray experiment was executed as a completely randomized design with a 2 x 5 factorial treatment arrangement including either parent or UV-treated MeNQ with each including the dose series:  0 (control), 7, 22, 67, 200 mg/L (nominal concentrations).  All treatments included four exposure replicates where each replicate was hybridized to microarrays using a random number generator.

scan_protocol: An Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C) was used to scan microarray images at 2 μm resolution.  Data were extracted from microarray images using Agilent Feature Extraction software, version 10.7.3.1.

data_processing: Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.9 (Agilent Technologies). GeneSpring was also used to conduct statistical analyses to identify differentially expressed transcripts (DET) among treatments.  A two-way ANOVA (p = 0.05) with Benjamini-Hochberg multiple-test corrections was used to investigate the effects of MeNQ exposure, UV-treatment, and the interaction of these two independent variables on transcript expression.  Post-hoc tests were conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the 0 mg/L control and matching UV-exposure state.

organism: Pimephales promelas

source_name: whole animal

extract_protocol: All samples were flash frozen in liquid nitrogen to preserve RNA.  A total of 4 larval fish were sampled from each exposure replicate and 4 total exposure replicates were sampled for each treatment.  Samples were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals) before RNA isolation with RNeasy kits (Qiagen). Total RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer.  Criteria for acceptable RNA integrity included a RNA integrity number > 8.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0.

treatment_protocol: Preparation of exposure solutions:  Preparation of exposure solutions. A stock solution at 6140 mg/L (measured concentration) was created by dissolving MeNQ directly into dechlorinated tap water with no carrier solvent using magnetic stirring for 48 h.  The UV-treatment of MeNQ was performed by exposing that stock solution in a photo-reactor for 6 h, as previously described in Poda et al. (2013), and used as a standard UV-treatment for assessing the effects of UV-exposed IMs in Ceridaphnia dubia (Kennedy et al. 2017) and Danio rerio (Gust et al. 2017).  Briefly, a fan cooled Rayonet Reactor RPR-1000 (Southern New England Ultraviolet Company, CT, USA) equipped with a carousel and sixteen 14 W UV lamps (SNE Ultraviolet Company k = 300 ± 50 nm) with a flux of 2.50 ± 0.17 x 10-5 milli-Einsteins cm-2 s-1 measured by ferrioxalate actinometry using Ferrozine™ as the chelating reagent was used for all UV-treatment experiments (Goldstein and Rabani 2008; Rao et al. 2013).  These conditions were selected in accordance with EPA standard method 832.2210 (USEPA 1998) and represent the most active portion of light associated with photo-degradation (USEPA 1998).  Specific emission spectra are provided in (Kennedy et al. 2017).  UV-degradation was undertaken in two batches of ten 100 mL quartz beakers (3.2 cm ID, Technical Glass) where irradiation times were controlled by a timer controller (Control Company, Model # 5090). After photolysis, the first batch was refrigerated in an amber bottle to prevent further degradation. The batches were mixed immediately after photolysis of the second batch to find a final concentration of 5,940 mg/L of starting MeNQ remained. Upon combining the first and second batches, exposure solutions at the target concentrations 0 (control), 7, 22, 67, 200, and 600 mg/L were created by mixing the MeNQ stock (parent or UV-treated) and dechlorinated tap water.  Toxicity test:  Subchronic 7-d toxicity test using P. promelas was conducted in accordance with the USEPA (2002).  Larval P. promelas (2-d old within 24-h in age) from a single batch of offspring were acclimated to experimental conditions for 24 h. Each exposure concentration consisted of 5 replicates (250-mL glass beakers containing 10 fish and 200 mL test solution) and received a twice-daily feeding ration of Artemia nauplii to support growth. Fish were maintained at 25 °C and a 16:8 light:dark cycle.  Partial renewals (80% of the volume) of the test solutions were conducted daily.  Exposure water was collected from one tank per treatment at experiment initiation and before and after each exposure water renewal. Water quality (temperature, dissolved oxygen [DO], pH, and conductivity) was monitored using a 556 handheld multi-parameter field instrument (YSI Incorporated) daily in one replicate per treatment to minimize disturbance to test organisms. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  Survival, biomass, and growth (as dry biomass) were assessed after 7 d. At exposure termination, fish were killed with buffered Tricaine Methanesulfonate (MS-222; Western Chemical, Inc.), rinsed with deionized water, and placed by replicate on pre-weighed aluminum pans. Fish were dried for 24 h at 60°C and then weighed to the nearest 0.001mg.

value: larvae

tag: treatment

value: UV-Treatment, 200 mg/L


title: UV-Treatment, 200 mg/L, Rep2

label_protocol: The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.

growth_protocol: Larval P. promelas (2-d old within 24-h in age) from a single batch of offspring were acclimated to experimental conditions for 24 h. Each exposure concentration consisted of 5 replicates (250-mL glass beakers containing 10 fish and 200 mL test solution) and received a twice-daily feeding ration of Artemia nauplii to support growth. Fish were maintained at 25 °C and a 16:8 light:dark cycle.  Partial renewals (80% of the volume) of the test solutions were conducted daily.  Exposure water was collected from one tank per treatment at experiment initiation and before and after each exposure water renewal. Water quality (temperature, dissolved oxygen [DO], pH, and conductivity) was monitored using a 556 handheld multi-parameter field instrument (YSI Incorporated) daily in one replicate per treatment to minimize disturbance to test organisms.


title: 201148310020_R02C01


title: UV-Treatment, 22 mg/L, Rep4

value: UV-Treatment, 22 mg/L


title: UV-Treatment, 22 mg/L, Rep1


title: UV-Treatment, 22 mg/L, Rep2


title: UV-Treatment, 67 mg/L, Rep2

value: UV-Treatment, 67 mg/L


title: 201148310006_R11C02


title: 201148310006_R12C01


title: UV-Treatment, 7 mg/L, Rep2

value: UV-Treatment, 7 mg/L


title: UV-Treatment, 200 mg/L, Rep1


title: UV-Treatment, 67 mg/L, Rep3


title: 201148310020_R01C01


title: 201148310020_R01C02


title: UV-Treatment, 22 mg/L, Rep3


title: 201148310006_R10C02


title: UV-Treatment, 7 mg/L, Rep3


title: UV-Treatment, 200 mg/L, Rep4


title: UV-Treatment, 7 mg/L, Rep4


title: 201148310006_R10C01


title: 201148310006_R12C02


title: 201148310006_R09C02


title: UV-Treatment, 0 mg/L, Rep3

value: UV-Treatment, 0 mg/L


title: 201148310006_R08C02


title: 201148310006_R09C01


title: UV-Treatment, 67 mg/L, Rep1


title: 201148310006_R11C01


title: 201148310006_R08C01


title: UV-Treatment, 67 mg/L, Rep4


title: UV-Treatment, 0 mg/L, Rep1


title: UV-Treatment, 0 mg/L, Rep2


title: UV-Treatment, 7 mg/L, Rep1


title: No-UV treatment, 200 mg/L, Rep2

value: No-UV treatment, 200 mg/L


title: No-UV treatment, 200 mg/L, Rep4


title: No-UV treatment, 67 mg/L, Rep4

value: No-UV treatment, 67 mg/L


title: UV-Treatment, 0 mg/L, Rep4


title: No-UV treatment, 200 mg/L, Rep3


title: 201148310006_R07C01


title: No-UV treatment, 200 mg/L, Rep1


title: 201148310006_R06C02


title: 201148310006_R05C02


title: 201148310006_R06C01


title: 201148310006_R04C02


title: 201148310006_R05C01


title: 201148310006_R07C02


title: 201148310006_R04C01


title: 201148310006_R03C02


title: 201148310006_R03C01


title: 201148310006_R02C02


title: 201148310006_R02C01


title: 201148310006_R01C01


title: 201148310019_R12C02


title: No-UV treatment, 67 mg/L, Rep2


title: No-UV treatment, 67 mg/L, Rep3


title: No-UV treatment, 22 mg/L, Rep4

value: No-UV treatment, 22 mg/L


title: No-UV treatment, 22 mg/L, Rep3


title: No-UV treatment, 22 mg/L, Rep1


title: No-UV treatment, 22 mg/L, Rep2


title: 201148310019_R12C01


title: No-UV treatment, 7 mg/L, Rep2

value: No-UV treatment, 7 mg/L


title: No-UV treatment, 7 mg/L, Rep3


title: 201148310019_R11C02


title: 201148310019_R10C02


title: 201148310019_R11C01


title: 201148310006_R01C02


title: No-UV treatment, 7 mg/L, Rep4


title: AKO Chronic Cold iWAT, biological rep1

city: Ann Arbor

first: Siming

last: Li

state: MI

address: 210 Washtenaw Ave

department: CDB

institute: University of Michigan

description: Gene expression daftera from Baf60a AKO iWAT after after chronic cold

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 plate, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.1.1

source_name: inguinal white adipose tissue from AKO mice after Chronic cold

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Wild type and Baf60a knockout mice were maintained on standard rodent chow

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

treatment_protocol: Wild type and Baf60a knockout mice were either kept at ambient room temperature (22C) or subjected chronic 10oC expossure for 7 days following gradual cold temrature adaptation. Inguinal adipose tissue was harvested for total RNA isolation and microarray analysis.

value: inguinal adipose tissue

tag: genotype

value: Baf60a AKO

tag: age

value: 9 months

value: chronic cold


title: No-UV treatment, 67 mg/L, Rep1

tag: developmental stage


title: No-UV treatment, 7 mg/L, Rep1


title: No-UV treatment, 0 mg/L, Rep3

value: No-UV treatment, 0 mg/L


title: AKO Chronic Cold iWAT, biological rep3


title: AKO Room Temperature iWAT, biological rep2

description: Gene expression data from Baf60a AKO iWAT at RT

source_name: inguinal white adipose tissue from AKO mice at Room Temperature

value: RT


title: No-UV treatment, 0 mg/L, Rep1


title: flox Chronic Cold iWAT, biological rep3

description: Gene expression daftera from Baf60a flox iWAT after after chronic cold

source_name: inguinal white adipose tissue from flox mice after Chronic cold

value: Baf60a flox


title: No-UV treatment, 0 mg/L, Rep4

value: larvae


title: flox Chronic Cold iWAT, biological rep1


title: AKO Room Temperature iWAT, biological rep1


title: AKO Chronic Cold iWAT, biological rep2


title: flox Chronic Cold iWAT, biological rep2


title: No-UV treatment, 0 mg/L, Rep2


title: 201148310019_R08C02

value: Female

value: Milk Somatic Cells


title: AKO Room Temperature iWAT, biological rep3


title: 201148310019_R09C02


title: 201148310019_R08C01


title: 201148310019_R07C01


title: 201148310019_R07C02


title: 201148310019_R06C02


title: Rh41 SC B

first: Reshma

last: Taneja

state: Singapore

address: 2 Medical Drive, MD9, National University of Singapore

department: Department of Physiology

description: Patient derived

scan_protocol: Scanning was done using nCounter digital analyser

data_processing: The RCC files generated from nCounter were analysed using nSolver 3.0 software

source_name: RH41 ARMS cells

growth_protocol: Cells were culture in RPMI1640 (Gibco) supplemented with 10% FBS

extract_protocol: RNA was extracted uing Trizol and clean-up was performed using RNeasy MiniElute Clean up kit (Qiagen).  The hybridized RNA was scanned using nCounter digital analyser

treatment_protocol: Cells were transfected with 100nM of human G9a-specific siRNA (ON-TARGETplus EHMT2 siRNA SMARTpool, Dharmacon, Lafayette, CO, USA)  or 100nM scrambled siRNA (ON-TARGETplus, non-targeting pool, Dharmacon) using Lipofectamine RNAiMax

tag: transfection

value: scrambled siRNA

value: Human Alveolar Rhabdomyosarcoma


title: Rh41 SC A

description: Patient derived

tag: cell type


title: 201148310019_R10C01


title: 201148310019_R06C01


title: 201148310019_R09C01


title: Rh41 SiG9a B

description: Patient derived

value: G9a-specific siRNA


title: Combi_6h_3

city: Cologne

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

country: Germany

institute: University of Cologne, Medical Faculty and University Clinic Cologne

description:
Boedicker_Oncogene_RNA_seq_Rh30_6h_treatment
Time_6h_kombi_vs_Control.txt

data_processing:
Reads from fastq files were mapped against the human genome GRCh37/hg19 using STAR 2.5 with default parameters
Reads were count using summarizeOverlaps, mode="Union"
differential gene expression was calculated using DESeq2
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: excel file include read counts for each sample

source_name: Rh30 (RRID:CVCL_0041)

growth_protocol: Rh30 cells were maintained in RPMI 1640 or DMEM medium (Life Technologies, Eggenstein, Germany), supplemented with 10% fetal calf serum (FCS) (Biochrom, Berlin, Germany), 1 mM pyruvate and 1% penicillin/streptomycin (Invitrogen, Karlsruhe, Germany).

extract_protocol:
Total RNA was isolated by using the peqGOLD Total RNA kit (Peqlab, Erlangen, Germany) according to the manufacturer's instructions.
Library preparation was performed with the TrueSeq RNA Samples preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Rh30 cells were treated for 6h with either 1 µM JQ1 or 3 µM BYL719 or a combination of both: 1µM JQ1 and 3µM BYL719. Controls were treated with solvent alone. JQ1 was provided by Stefan Knapp (Darmstadt, Germany). BYL719 was purchased from Selleckchem (München, Germany).

value: alveolar Rhabdomyosarcoma cell line

value: 1µM JQ1 / 3µM BYL719


title: Byl_6h_3

description:
Boedicker_Oncogene_RNA_seq_Rh30_6h_treatment
Time_6h_BYL_vs_Control.txt

value: 3µM BYL719


title: JQ1_6h_3

description:
Boedicker_Oncogene_RNA_seq_Rh30_6h_treatment
Time_6h_JQ1_vs_Control.txt

value: 1µM JQ1


title: 201148310019_R05C01


title: Combi_6h_2


title: 201148310019_R04C02


title: flox Room Temperature iWAT, biological rep2

description: Gene expression data from Baf60a flox iWAT at RT

source_name: inguinal white adipose tissue from flox mice at Room Temperature

value: inguinal adipose tissue


title: flox Room Temperature iWAT, biological rep3


title: Rh41 SiG9a A

description: Patient derived


title: 201148310019_R04C01


title: 201148310019_R02C01


title: JQ1_6h_2


title: 201148310019_R03C01


title: Combi_6h_1


title: Byl_6h_2


title: control_6h_2

description: Boedicker_Oncogene_RNA_seq_Rh30_6h_treatment

value: Control (DMSO)


title: 201148310019_R02C02


title: flox Room Temperature iWAT, biological rep1

value: 9 months


title: Byl_6h_1


title: 201148310019_R03C02


title: 201148310019_R05C02


title: control_6h_1


title: 201148310018_R12C02


title: 201148310019_R01C01


title: JQ1_6h_1


title: Jurkat E6.1 cells, Stimulated + chemokine replicate 2

city: Oxford

first: Ling

last: Felce

state: Select State

address: Botnar Research Centre, Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were mapped and aligned to human GRCh37.EBVB95-8wt.ERCC reference genome using hisat.
Mapped reads converted to binary format and indexed using samtools.
featureCounts used to quantify binary indexed reads against annotated genome.
Example code: $featureCounts" "-T" "4" "-p" "-F" "GTF" "-a" "<annotation file>" "-o" "<output file>featureCount_Dup.txt" "<input file>.bam"
Genome_build: GRCh37.EBVB95-8wt.ERCC
Supplementary_files_format_and_content: text files include read counts for each sample

growth_protocol: Jurkat E6.1 cells were grown under standard tissue culture conditions, and two biological replicates were collected in separate experiments.

extract_protocol:
RNA was isolated from cells via TRIzol-chloroform extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either left unstimulated, or stimulated with anti-CD3, anti-CD28 beads for 2h in the presence or absence of CXCL12 and CCL19.

value: Jurkat E6.1 cells

value: CD4+ T cells

value: Stimulated + chemokine


title: 201148310019_R01C02


title: Jurkat E6.1 cells, Stimulated replicate 2

source_name: Jurkat E6.1 cells, Stimulated

value: Stimulated


title: Jurkat E6.1 cells, Stimulated + chemokine replicate 1


title: 201148310018_R11C02


title: 201148310018_R11C01


title: control_6h_3


title: 201148310018_R12C01


title: Jurkat E6.1 cells, Stimulated replicate 1


title: Jurkat E6.1 cells, Resting replicate 2

source_name: Jurkat E6.1 cells, Resting

value: Resting


title: Jurkat E6.1 cells, Resting replicate 1


title: 201148310018_R10C02

value: Female


title: 201148310018_R10C01

value: Milk Somatic Cells


title: P300-E24-5-IP-H3K27AC-10_SL024

city: New York

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-15
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain peak locations. Columns 1, 2, 3, and 4 contain the chromosome, start, end, and maximum height of the peak respectively.

source_name: SUDHL4 cell line, EP300 knock out

growth_protocol: Cells were grown in IMDM medium supplemented with 10% FBS and 1% Penicillin/Streptomicin at 37C and 5% CO2. Cells in log phase of growth were harversted and used for H3K27Ac ChIP-Seq experiments.

extract_protocol:
Purified cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 3ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 15nM, pooled and sequenced in an Illumina HiSeq 4000 instrument as paired-end 150 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Cells were engineered to disrupt the EP300 gene by using the CRISPR/Cas9 system and sgRNAs targeting the gene Exon 24 ; single clones were isolated by limiting dilution plating, verified for efficient deletion of the protein by sequencing analysis of the targeted region and western blot analysis, and kept as stable cell lines.

value: DLBCL cells

value: EP300 knock out

tag: antibody


title: 201148310018_R07C02


title: P300-E24-5-INPUT-10_SL022


title: 201148310018_R08C02


title: 201148310018_R08C01


title: 201148310018_R09C01


title: 201148310018_R09C02


title: 201148310018_R07C01


title: 201148310018_R06C02


title: N5-8-IP-H3K27AC-10_SL017

source_name: SUDHL4 cell line, CREBBP WT

treatment_protocol: Cells were engineered to edit a neutral region of the genome (in the PPP1R12C gene) by using the CRISPR/Cas9 system; single clones were isolated by limiting dilution plating, verified by sequencing analysis for editing of the targeted region and by western blot analysis for expression of CREBBP and EP300, and kept as stable cell lines.

value: CREBBP WT


title: P300-E17-17-IP-H3K27AC-10_SL021

treatment_protocol: Cells were engineered to disrupt the EP300 gene by using the CRISPR/Cas9 system and sgRNAs targeting the gene Exon 17 ; single clones were isolated by limiting dilution plating, verified for efficient deletion of the protein by sequencing analysis of the targeted region and western blot analysis, and kept as stable cell lines.


title: P300-E17-17-INPUT-10_SL019


title: 201148310018_R06C01


title: N5-8-INPUT-10_SL014


title: N4-8-IP-H3K27AC-10_SL012


title: 201148310018_R05C02


title: N4-8-INPUT-10_SL009


title: CBP-E20-9-IP-H3K27AC-10_SL006

source_name: SUDHL4 cell line, CREBBP knock-out

treatment_protocol: Cells were engineered to disrupt the CREBBP gene by using the CRISPR/Cas9 system and sgRNAs targeting the gene Exon 20 ; single clones were isolated by limiting dilution plating, verified for efficient deletion of the protein by sequencing analysis of the targeted region and western blot analysis, and kept as stable cell lines.

value: CREBBP knock-out


title: CBP-E20-9-INPUT-10_SL007


title: 201148310018_R04C02


title: 201148310018_R04C01


title: 201148310018_R03C02


title: CBP-E13-5-IP-H3K27AC-10_SL002

treatment_protocol: Cells were engineered to disrupt the CREBBP gene by using the CRISPR/Cas9 system and sgRNAs targeting the gene Exon 15 ; single clones were isolated by limiting dilution plating, verified for efficient deletion of the protein by sequencing analysis of the targeted region and western blot analysis, and kept as stable cell lines.


title: CBP-E13-5-INPUT-10_SL003


title: 201148310018_R02C02