title: KO #2-3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

description:
ZR-2-3_S6
ZR5_3

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat v2.0.22(Linux).
For FPKM, data processing and differential comparison were performed with cufflinks v2.1.1(Linux).
For TMM, gene counts were performed with featureCounts v1.4.6(Linux).
Differential comparison was performed with R program v3.4.2, package TCC v1.18.0 and package edgeR v3.20.1. tmm normalization was done by iDEGES/edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, counts

growth_protocol: Murine macrophage-like cells, RAW264 cells, were obtained from RIKEN cell bank. RAW264 cells were maintained in α-minimum Eagle's medium (Invitrogen) supplemented with 10% CELLect fetal bovine serum (MP Biomedicals), 1% antibiotic-antimycotic solution (Invitrogen), and 1% minimum Eagle's medium non-essential amino acids (Invitrogen).

extract_protocol:
Total RNA was extracted with ISOGEN (NIPPON GENE CO, JAPAN) and an RNeasy spin column kit (Qiagen, USA), followed by treatment with DNase I (Qiagen). RNA samples were confirmed RNA integrity number (RIN) greater than 8.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently library quality was checked using 2100 Bioanalyzer and Agilent DNA 1000 kit.

treatment_protocol: Guide-it-ZsGreen1 Vectors (Takara Bio Inc. Kusatsu, Japan) including Cas9 and gRNA sequence were transfected into RAW264 cells with electroporation using Neon® Transfection System (Life Technologies.) while single cell sorting with FACS-Aria (Becton, Dickinson and Company, Franklin Lakes, NJ).

value: macrophage-like cells

tag: mutation site

value: exon 5; Zscan10 KO

value: without RANKL treatment


title: DD KO timepoint6 rep1

status: Public on Mar 25 2019

type: SRA

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

country: Spain

institute: Institut for Research in Biomedicine (IRB-Barcelona)

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and quality correction with Trimmomatic
Then mapped to the mm10 reference genome with Tophat version 2.1.1 with parameters --no-novel-juncs --read-realign-edit-dist 0 -N 2 -p 4 -g 1 -r 200 --no-discordant --no-mixed –b2-sensitive
Read count over the Ensembl transcripts GRCm38.81 was performed with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of count data

molecule: total RNA

organism: Mus musculus

source_name: DD KO timepoint6_interfollicular epidermis

growth_protocol: For the transcriptomic studies of circadian oscillations 4 females (8 weeks old) were used per genotype at each of the six time points. Mice were maintained in a standard 12h light:12h darkness photoperiod at 22ºC degrees and had ad libitum access to standard chow diet. For the darkness experiment (DD) mice were transferred to 24h darkness per day at 7 weeks of age and kept in darkness in total for 156h to 176h.

extract_protocol:
Immediately after sacrifice 1cm2 backskin samples were collected for histology. Skin samples were scraped with a scalpel to remove the hypodermis and then floated on dispase 1mg/ml (Sigma-Aldrich) dissolved in PBS for approximately 40 min at 37ºC, allowing the interfollicular epidermis to be separated from the dermis. Dispase was inactivated with 15% chelated fetal bovine serum (GIBCO) diluted in EMEM medium without calcium (Lonza). The interfollicular epidermis was mechanically disaggregated and dissociated and sequentially filtered through a 100-mm and a 40-mm filter. Cells were counted and cell pellets of 1 million cells were frozen for later RNA extraction. RNA was extracted using TRIzol (Sigma-Aldrich).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 8 weeks

tag: genotype/variation

value: Bmal1-stopFL (KO)

tag: tissue

value: interfollicular epidermis


title: KO #2-2

country: Japan

description:
ZR-2-2_S5
ZR5_2

tag: cell line

tag: cell type

tag: treatment


title: Alcoholic_M_U_AA2181

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

country: USA

institute: Indiana University School of Medicine

description:
McClintick_LCL_data_2019.xlsx
21U

data_processing:
Sequencing reads (75 bases, single reads) were mapped to the human hg19 reference genome using an in-house mapping pipeline (Breese & Liu, 2013) that utilizes bfast-0.7.0a (Homer, Merriman, & Nelson, 2009)
reads were truncated where the average quality fell below 10 within a window size of 5, and then reads of <35 bases were discarded.
Reads mapped to rRNA/tRNAs were discarded. The remaining reads were mapped to reference genome hg19 and to a splice-junction library created in house. The genomic and splice-junction library maps were then merged. Reads mapped to multiple positions in the genome were excluded from further analysis.
The gene-based expression levels were calculated using bamutils from NGSUtils, based on the RefSeq gene annotation of hg19.
counts per million (CPM) from EdgeR
filter out low expressing genes, remove genes for which the cpm>=2 in fewer than 20 samples
Genome_build: hg19
Supplementary_files_format_and_content: CPM (count per million reads) for each gene

organism: Homo sapiens

source_name: Lymphoblastoid cell line

extract_protocol:
cells were harvested and lysed with buffer RLT plus, and RNA extractions were conducted using the QIAsymphony RNA extraction protocol
Samples were processed by polyA capture using Dynabeads mRNA DIRECT Micro Kit (Life Technologies, Carlsbad, CA) starting with 1.5 mg of total RNA. PolyA RNA was processed using Life Technologies SOLiDTM Total RNAseq kit (Life Technologies, Carlsbad, CA). Sequencing beads were produced separately for each batch using the SOLiDTM EZBeadTM System (Life Technologies, Carlsbad, CA). Each batch was sequenced separately on a SOLiD 5500xl DNA sequencer (ThermoFisher/ Life Technolgies, Carlsbad, CA).

treatment_protocol: For the RNA sequencing experiment, 2 x 106 LCLs from each of 21 AD and 21 control individuals were seeded in 10 ml of RPMI1640 medium supplemented with 15% FBS, 2 mM glutamine. Cells were cultured in the absence or presence of 75 mM ethanol for 48 h, at which time cells were harvested

tag: phenotype

value: Alcoholic

tag: gender

value: M

value: untreated

tag: library/sequencing batch

tag: ID


title: MDA_Lung_Rep2

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
MDA_Lung = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection, mouse lung was processed to get single cell suspension, and MDA231 cells were selected by culturing them in DMEM High glucose media with 10% Fetal Bovine Serum containing 200 ug/mL Hygromycin and 8 ug/mL Blasticidin, and RNA from the surviving cells were sequenced after 2 passages.
Counts_expressed_normalized_inVitro.csv

data_processing:
Samples were barcoded
run on a Hiseq 2000 platform in a 125bp/125bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 25 million paired reads were generated per sample.
The data were analyzed using the STAR-HTSeq-DESeq2 pipeline as previously described.
Flura-seq in vivo experiments were aligned to hybrid genome containing combined human and mouse genome. Mouse gene is indicated by "m" in front of the gene name whereas human gene is indicated by "h" in front of the gene name. For the other remaining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Two separate count files in csv format are provided for two different profiling methods (Counts_expressed_normalized_Fluraseq.csv, Counts_expressed_normalized_inVitro.csv)

source_name: MDA231 Lung Xenograft

growth_protocol: MDA231 cells  were cultured in DMEM with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 200 ug/mL Hygromycin and 8 ug/mL Blasticidin.

extract_protocol:
mRNAs were isolated by Oligo dT magnetic beads. Either the mRNAs were sequenced directly or immunoprecipitated with anti-BrdU antibody, and bound mRNAs were eluted using BrdU solution, and the eluted mRNAs were sequenced.
TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. For the immunopurified RNAs, the RNAs were amplified by SMARTer amplification and library was prepared by Nextera Kit followinf manufacturer's protocol.

tag: metastatic derivative

value: Lung

tag: reporter gene

value: Firefly Luciferase

tag: protocol

value: Isolated from Lung


title: MDA_Brain_Rep1

description:
MDA_Brain = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection, mouse brain was processed to get single cell suspension, and MDA231 cells were selected by culturing them in DMEM High glucose media with 10% Fetal Bovine Serum containing 200 ug/mL Hygromycin and 8 ug/mL Blasticidin, and RNA from the surviving cells were sequenced after 2 passages.
Counts_expressed_normalized_inVitro.csv

source_name: MDA231 Brain Xenograft

value: Brain

value: Isolated from brain


title: Alcoholic_M_T_AA2181

description:
McClintick_LCL_data_2019.xlsx
21T

value: ethanol 48h


title: Control_F_T_AA1927

description:
McClintick_LCL_data_2019.xlsx
19T

value: Control

value: F


title: Alcoholic_M_T_AA2314

description:
McClintick_LCL_data_2019.xlsx
22T


title: KO #2-1

description:
ZR-2-1_S4
ZR5_1

value: macrophage-like cells


title: 5WT3: LD WT timepoint5 rep3

description: LD WT timepoint5 rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence and quality correction with Trimmomatic
Then mapped to the mm10 reference genome with Tophat version 2.1.1 with parameters --no-novel-juncs --read-realign-edit-dist 0 -N 2 -p 4 -g 1 -r 200 --no-discordant --no-mixed –b2-sensitive
Read count over the Ensembl transcripts GRCm38.81 was performed with htseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of count data

source_name: interfollicular epidermis

growth_protocol: For the transcriptomic studies of circadian oscillations 4 females (8 weeks old) were used per genotype at each of the six time points. Mice were maintained in a standard 12h light:12h darkness photoperiod at 22ºC degrees and had ad libitum access to standard chow diet.

tag: genotype

value: K14-Cre (WT)


title: MDA_Lung_Rep1


title: KO #1-3

description:
ZR-5-3_S3
ZR2_3

value: exon 2; Zscan10 KO

value: without RANKL treatment


title: Control-3

description:
ZR-C-3_S9
ZR_C_3

value: none; control


title: Alcoholic_M_U_AA0342

description:
McClintick_LCL_data_2019.xlsx
25U


title: Control-2

description:
ZR-C-2_S8
ZR_C_2


title: Control_M_T_AA1888

description:
McClintick_LCL_data_2019.xlsx
18T


title: Control-1

description:
ZR-C-1_S7
ZR_C_1


title: DD KO timepoint5 rep3

source_name: DD KO timepoint5_interfollicular epidermis

value: 8 weeks

value: Bmal1-stopFL (KO)

value: interfollicular epidermis


title: PDD_P2_78

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

data_processing:
Illumina CASAVA v1.8.2  software used for basecalling and fastq file generation
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096)
Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample

organism: Escherichia coli BW25113

source_name: Trimethoprim

growth_protocol: bacteria were grown in iso-sensitest medium

extract_protocol:
after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer  (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification  using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies).
For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.

treatment_protocol: bacteria were treated with different antibiotics for ~ 25 min till  ~OD 0.2  in 2 ml tubes

tag: type

value: Gram-negative bacteria

tag: moa

value: Folic Acid synthesis inhibitor

value: EC90 of phenotype

tag: treatment time

value: ~ 25 min

tag: treatment concentration

value: 50 uM


title: Control_F_U_AA1927

description:
McClintick_LCL_data_2019.xlsx
19U

value: untreated


title: DD KO timepoint5 rep2

tag: strain

tag: age

tag: genotype/variation


title: KO #1-1

description:
ZR-5-1_S1
ZR2_1

tag: cell line

tag: cell type

tag: mutation site


title: PDD_P2_26

tag: phenotype


title: DD KO timepoint5 rep1

tag: tissue


title: PDD_P2_52


title: KO #1-2

description:
ZR-5-2_S2
ZR2_2

tag: treatment


title: PDD_P2_64

source_name: PolymyxineB

value: Membrane perturbation


title: Control_M_U_AA1567

description:
McClintick_LCL_data_2019.xlsx
17U

value: Control

tag: gender

value: M

tag: library/sequencing batch

tag: ID


title: PDD_P2_38


title: Control_M_U_AA1477

description:
McClintick_LCL_data_2019.xlsx
16U


title: DD KO timepoint5 rep4


title: DD KO timepoint4 rep4

source_name: DD KO timepoint4_interfollicular epidermis


title: MDA_MFP_IP_Rep3

description:
MDA_MFP_IP = MDA231 cells injected mammary fat pad in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later tumor in the mammary fat pad was harvested, homogenized, mRNAs were isolated, 5-FUtagged RNAs were immunopurified and sequenced.
Counts_expressed_normalized_Fluraseq.csv

data_processing:
Library strategy: Flura-seq
Samples were barcoded
run on a Hiseq 2000 platform in a 125bp/125bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 25 million paired reads were generated per sample.
The data were analyzed using the STAR-HTSeq-DESeq2 pipeline as previously described.
Flura-seq in vivo experiments were aligned to hybrid genome containing combined human and mouse genome. Mouse gene is indicated by "m" in front of the gene name whereas human gene is indicated by "h" in front of the gene name. For the other remaining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Two separate count files in csv format are provided for two different profiling methods (Counts_expressed_normalized_Fluraseq.csv, Counts_expressed_normalized_inVitro.csv)

organism:
Homo sapiens
Mus musculus

source_name: MDA231 MFP Xenograft

tag: metastatic derivative

value: Fat pad

tag: reporter gene

value: Firefly Luciferase

tag: protocol

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Fat pad, IP

tag: rip antibody

value: anti-BrdU (Abcam, catalog# ab6326, lot# GR254518-1)


title: Control_M_U_AA1888

description:
McClintick_LCL_data_2019.xlsx
18U


title: PDD_P2_76

source_name: Norfloxacin

tag: type

tag: moa

value: DNA replication inhibitor

tag: treatment time

tag: treatment concentration

value: 1 uM


title: PDD_P2_12

tag: strain


title: Control_M_T_AA1567

description:
McClintick_LCL_data_2019.xlsx
17T

value: ethanol 48h


title: MDA_MFP_IP_Rep2

tag: cell line


title: MDA_MFP_Input_Rep3

description:
MDA_MFP_Input = MDA231 cells injected in mammary fat pad in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later tumor from mammary fat pad was harvested, homogenized, mRNAs were isolated and sequenced.
Counts_expressed_normalized_Fluraseq.csv

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Fat pad, Input


title: Control_F_U_AA1264

description:
McClintick_LCL_data_2019.xlsx
15U

value: F


title: PDD_P2_50

value: Gram-negative bacteria


title: MDA_MFP_IP_Rep1


title: PDD_P2_24

value: EC90 of phenotype


title: DD KO timepoint4 rep2

tag: age

value: 8 weeks

tag: genotype/variation

value: Bmal1-stopFL (KO)

value: interfollicular epidermis


title: Control_F_T_AA1264

description:
McClintick_LCL_data_2019.xlsx
15T

tag: phenotype


title: PDD_P2_58

source_name: Nitroxolin

value: ~ 25 min


title: Control_F_U_AA2065

description:
McClintick_LCL_data_2019.xlsx
42U

value: Control

tag: treatment

value: untreated


title: DD KO timepoint3 rep3

source_name: DD KO timepoint3_interfollicular epidermis

tag: tissue


title: DD KO timepoint4 rep3


title: MDA_MFP_Input_Rep2

value: Fat pad


title: PDD_P2_32


title: MDA_Lung_IP_Rep3

description:
MDA_Lung_IP = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse lung was harvested, homogenized, mRNAs were isolated, 5-FUtagged RNAs were immunopurified and sequenced.
Counts_expressed_normalized_Fluraseq.csv

value: Lung

value: Firefly Luciferase

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Lung, IP


title: DD KO timepoint3 rep2


title: MDA_MFP_Input_Rep1


title: PDD_P2_06

value: DNA replication inhibitor


title: Control_F_T_AA2065

description:
McClintick_LCL_data_2019.xlsx
42T

tag: gender

tag: library/sequencing batch


title: DD KO timepoint3 rep1


title: PDD_P2_55

source_name: Nitrofurantoin

value: DNA damage

value: 50 uM


title: Control_M_U_AA4229

description:
McClintick_LCL_data_2019.xlsx
41U

value: M

tag: ID


title: Control_M_T_AA1477

description:
McClintick_LCL_data_2019.xlsx
16T

value: ethanol 48h


title: MDA_Lung_IP_Rep2

tag: metastatic derivative

tag: reporter gene

value: anti-BrdU (Abcam, catalog# ab6326, lot# GR254518-1)


title: Control_M_T_AA4229

description:
McClintick_LCL_data_2019.xlsx
41T


title: DD KO timepoint2 rep4

source_name: DD KO timepoint2_interfollicular epidermis


title: MDA_Lung_IP_Rep1

tag: protocol

tag: rip antibody


title: PDD_P2_29

tag: type

value: Gram-negative bacteria

tag: moa

value: EC90 of phenotype


title: DD KO timepoint2 rep3

value: 8 weeks

value: Bmal1-stopFL (KO)


title: MDA_Lung_Input_Rep3

description:
MDA_Lung_Input = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse lung was harvested, homogenized, mRNAs were isolated and sequenced.
Counts_expressed_normalized_Fluraseq.csv

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Lung, Input


title: DD KO timepoint4 rep1

value: interfollicular epidermis


title: MDA_Lung_Input_Rep2


title: PDD_P2_03

tag: treatment time

value: ~ 25 min

tag: treatment concentration


title: DD KO timepoint3 rep4

tag: strain


title: Alcoholic_F_U_AA4192

description:
McClintick_LCL_data_2019.xlsx
40U

value: Alcoholic

value: F

value: untreated


title: DD KO timepoint2 rep2

tag: age


title: Control_M_U_AA4445

description:
McClintick_LCL_data_2019.xlsx
39U

value: Control


title: DD KO timepoint2 rep1

tag: genotype/variation


title: Alcoholic_F_T_AA4192

description:
McClintick_LCL_data_2019.xlsx
40T

tag: phenotype


title: PDD_P2_56

source_name: Meropenem

value: cell wall synthesis inhibitor


title: DD KO timepoint1 rep4

source_name: DD KO timepoint1_interfollicular epidermis


title: PDD_P2_30


title: MDA_Brain_IP_Rep3

description:
MDA_Brain_IP = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse brain was harvested, homogenized, mRNAs were isolated, 5-FUtagged RNAs were immunopurified and sequenced.
Counts_expressed_normalized_Fluraseq.csv

tag: cell line

value: Brain

value: Firefly Luciferase

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Brain, IP


title: Control_M_T_AA4445

description:
McClintick_LCL_data_2019.xlsx
39T

value: M

tag: treatment

value: ethanol 48h


title: PDD_P2_04

value: Gram-negative bacteria


title: Alcoholic_M_U_AA0469

description:
McClintick_LCL_data_2019.xlsx
37U

tag: gender


title: MDA_Brain_IP_Rep2

value: anti-BrdU (Abcam, catalog# ab6326, lot# GR254518-1)


title: PDD_P2_66

source_name: Mecillinam

value: EC90 of phenotype

value: 5 uM


title: DD KO timepoint1 rep2

value: 8 weeks

value: Bmal1-stopFL (KO)

tag: tissue


title: Alcoholic_M_T_AA0469

description:
McClintick_LCL_data_2019.xlsx
37T

source_name: Lymphoblastoid cell line

tag: library/sequencing batch

tag: ID


title: PDD_P2_40

value: ~ 25 min


title: MDA_Brain_IP_Rep1

tag: metastatic derivative

tag: reporter gene


title: MDA_Brain_Input_Rep3

description:
MDA_Brain_Input = MDA231 cells injected intracardiacally in mouse, and 4 weeks after the injection CD/UPRT was induced by feeding Doxycycline diet for 2-3 days, and 250 mg/kg 5-fluorocytosine was injected intraperitoneally and 125 mg/kg thymine subcutaneously, and 12 hours later mouse brain was harvested, homogenized, mRNAs were isolated and sequenced.
Counts_expressed_normalized_Fluraseq.csv

tag: protocol

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Brain, Input


title: MDA_Brain_Input_Rep2


title: MDA_Lung_Input_Rep1

source_name: MDA231 Lung Xenograft

value: Lung

value: Dox 2d, 250 mg/Kg 5-FC, 12h, Lung, Input


title: PDD_P2_62

source_name: Levofloxacin

tag: type

value: DNA replication inhibitor


title: PDD_P2_14

tag: moa

value: cell wall synthesis inhibitor


title: Alcoholic_M_T_AA0466

description:
McClintick_LCL_data_2019.xlsx
36T

value: Alcoholic


title: PDD_P2_36

tag: treatment time


title: Alcoholic_M_U_AA0380

description:
McClintick_LCL_data_2019.xlsx
34U

value: untreated


title: MDA_Brain_Input_Rep1

source_name: MDA231 Brain Xenograft

value: Brain

value: Firefly Luciferase


title: DD KO timepoint1 rep3

value: interfollicular epidermis


title: DD KO timepoint1 rep1


title: PDD_P2_10

value: Gram-negative bacteria

tag: treatment concentration


title: Alcoholic_F_U_AA3969

description:
McClintick_LCL_data_2019.xlsx
38U

value: F


title: DD WT timepoint6 rep1

source_name: DD WT timepoint6_interfollicular epidermis

tag: strain

value: K14-Cre (WT)


title: DD WT timepoint5 rep4

source_name: DD WT timepoint5_interfollicular epidermis

tag: age


title: Alcoholic_F_T_AA3969

description:
McClintick_LCL_data_2019.xlsx
38T

value: ethanol 48h


title: DD WT timepoint6 rep2

value: 8 weeks

tag: genotype/variation


title: DD WT timepoint6 rep4


title: Alcoholic_M_T_AA0380

description:
McClintick_LCL_data_2019.xlsx
34T

tag: phenotype

value: M


title: PDD_P2_75

source_name: Globomycin

value: cell wall synthesis inhibitor / lipoprotein

value: EC90 of phenotype

value: ~ 25 min

value: 25 uM


title: DD WT timepoint6 rep3


title: DD WT timepoint5 rep2


title: PDD_P2_49


title: PDD_P2_61

source_name: Doxycycline

value: Protein synthesis


title: DD WT timepoint4 rep3

source_name: DD WT timepoint4_interfollicular epidermis


title: Control_M_U_AA3709

description:
McClintick_LCL_data_2019.xlsx
31U

value: Control


title: Alcoholic_M_U_AA0466

description:
McClintick_LCL_data_2019.xlsx
36U

value: Alcoholic


title: PDD_P2_23


title: Alcoholic_F_U_AA0460

description:
McClintick_LCL_data_2019.xlsx
35U

value: untreated


title: Alcoholic_F_T_AA0460

description:
McClintick_LCL_data_2019.xlsx
35T


title: Control_F_U_AA0614

description:
McClintick_LCL_data_2019.xlsx
33U


title: DD WT timepoint5 rep1


title: DD WT timepoint5 rep3


title: DD WT timepoint4 rep1


title: PDD_P2_53

source_name: DMSO

value: control


title: Alcoholic_M_U_AA3705

description:
McClintick_LCL_data_2019.xlsx
30U


title: PDD_P2_09


title: DD WT timepoint4 rep2


title: PDD_P2_35


title: Control_M_T_AA3709

description:
McClintick_LCL_data_2019.xlsx
31T


title: DD WT timepoint4 rep4


title: Control_F_T_AA0614

description:
McClintick_LCL_data_2019.xlsx
33T


title: HeLa EMT_2 m6A-IP

city: Guangzhou

first: Guoshi

last: Chai

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: SUN YAT-SEN UNIVERSITY

data_processing:
RNA-seq and m6A-seq reads were aligned to human genome hg19 by HISAT2 version 2.1.0
M6A enriched region were detected by MeTPeak software. RNA-Seq data(no IP, input RNA) in the same condition was used as input information
Genome_build: hg19
Supplementary_files_format_and_content: for  two duplicate m6A IP samples, bed files contain m6A enriched peaks. Format:chr chromStart chromEnd name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts

molecule: polyA RNA

source_name: HeLa cells

growth_protocol: Human cancer cells HeLa  were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in our lab with Dulbecco’s modified Eagle medium (DMEM, GIBCO, Carlsbad, CA, USA) with 10 % fetal bovine serum, and 1 % penicillin/streptomycin (Invitrogen).

extract_protocol:
Total polyadenylated RNA was isolated from HeLa cells treated with or without 10 ng/ml TGF-β for 3 days by use of TRIZOL reagent followed the using of FastTrack MAGMaxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed according to instructions of manufacture and the previously published protocol
Libraries were prepared according to Illumina's instructions accompanying the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA)

treatment_protocol: HeLa cells were treated with 10 ng/ml TGF-β treatment for 3 days  to induce EMT

tag: cell line

value: HeLa

tag: passages

tag: chip antibody

value: m6A Antibody (SYSY, Cat. No. 202 003)


title: PDD_P2_28

value: Gram-negative bacteria


title: DD WT timepoint3 rep4

source_name: DD WT timepoint3_interfollicular epidermis

tag: tissue

value: interfollicular epidermis


title: PDD_P2_27


title: Fasted_48 hrs RPF

city: Beijing

first: Shaonan

last: Liang

state: Beijing

address: Room D311, Medical Science Building, Tsinghua University

department: School of Medicine

institute: Institute for Immunology

data_processing:
library strategy: Ribosome profiling (Ribo-seq)
Cutadapt program was used to trim the 3’ adaptor in the raw reads from Ribo-seq
RPF reads with length between 25 and 35 nt were extracted
Low quality reads with Phred quality score >20 (>50% of bases) were removed using the FASTX-Toolkit
Sequencing reads originating from rRNAs were identified and discarded by aligning the reads to rRNA sequences of the particular species using Bowtie 1.1.2 with no mismatch allowed.
The remaining reads were mapped to the genome by STAR with end-to-end read alignment and maximum 1 mismatch was allowed.
Reads aligned to the first 15 and last 5 codons were excluded from the counting of RPF.
Only the reads uniquely mapped to the coding regions were counted for RPF using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: read counts of genes for each sample.

source_name: Ileum

extract_protocol:
Ileal tissues taken from fed and fasted mice were lysed with lysis buffer and treated with nuclease. Ribosome-protected fragments (RPF) were separated with a sucrose-cushion. Footprint fragments were purified and used to generate deep sequencing libraries.
After rRNA depletion DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~175 bp were band isolated from a polyacrylamide TBE-urea gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mice were fed or fasted for 48 hrs

value: wild type

value: post natal day 21

tag: treatment

value: fasted for 48hrs

value: Ileum

tag: molecule subtype

value: ribosome-protected mRNA


title: PDD_P2_01

value: EC90 of phenotype


title: Alcoholic_M_T_AA0376

description:
McClintick_LCL_data_2019.xlsx
28T

tag: gender

value: M

value: ethanol 48h

tag: library/sequencing batch

tag: ID


title: Fed RPF

value: fed


title: DD WT timepoint3 rep1

value: 8 weeks

value: K14-Cre (WT)


title: PDD_P2_02

tag: type

value: ~ 25 min


title: DD WT timepoint3 rep3


title: DD WT timepoint3 rep2


title: DD WT timepoint2 rep4

source_name: DD WT timepoint2_interfollicular epidermis


title: Alcoholic_M_T_AA3705

description:
McClintick_LCL_data_2019.xlsx
30T

value: Alcoholic


title: Alcoholic_M_U_AA0376

description:
McClintick_LCL_data_2019.xlsx
28U

value: untreated


title: PDD_P2_54

tag: moa

value: control


title: PDD_P2_41

source_name: Colistin

value: Gram-negative bacteria

value: Membrane perturbation

tag: treatment time


title: Control_M_T_AA2515

description:
McClintick_LCL_data_2019.xlsx
23T

value: Control


title: HeLa EMT_1 m6A-IP

value: HeLa

value: m6A Antibody (SYSY, Cat. No. 202 003)


title: PDD_P2_15

tag: treatment concentration


title: Control_F_U_AA0244

description:
McClintick_LCL_data_2019.xlsx
27U

value: F


title: PDD_P2_67

tag: strain


title: HeLa EMT_2 Input


title: Control_F_T_AA0244

description:
McClintick_LCL_data_2019.xlsx
27T


title: DD WT timepoint2 rep3

tag: age

value: interfollicular epidermis


title: HeLa EMT_1 input


title: HeLa Control_2 m6A-IP


title: PDD_P2_33

source_name: Clarithromycin

value: Protein synthesis

value: EC90 of phenotype

value: 50 uM


title: HeLa Control_2 Input


title: DD WT timepoint1 rep4

source_name: DD WT timepoint1_interfollicular epidermis

tag: genotype/variation


title: PDD_P2_07

tag: phenotype


title: Control_M_U_AA2515

description:
McClintick_LCL_data_2019.xlsx
23U

source_name: Lymphoblastoid cell line

value: M


title: DD WT timepoint2 rep2

value: 8 weeks


title: Alcoholic_M_U_AA1047

description:
McClintick_LCL_data_2019.xlsx
10U


title: DD WT timepoint1 rep2

value: K14-Cre (WT)


title: DD WT timepoint1 rep3


title: PDD_P2_59

value: ~ 25 min


title: PDD_P2_47

source_name: Ciprofloxacin

value: DNA replication inhibitor

value: 1 uM


title: DD WT timepoint1 rep1


title: DD WT timepoint2 rep1


title: Alcoholic_F_T_AA1803

description:
McClintick_LCL_data_2019.xlsx
11T

value: Alcoholic

value: ethanol 48h


title: PDD_P2_21

value: Gram-negative bacteria


title: PDD_P2_73


title: PDD_P2_57

source_name: Chloramphenicol

value: 25 uM


title: Alcoholic_F_U_AA1803

description:
McClintick_LCL_data_2019.xlsx
11U

value: untreated


title: Control_F_U_AA3238

description:
McClintick_LCL_data_2019.xlsx
5U

value: Control


title: Alcoholic_M_T_AA1047

description:
McClintick_LCL_data_2019.xlsx
10T


title: Control_F_U_AA2997

description:
McClintick_LCL_data_2019.xlsx
4U

value: F


title: Control_M_U_AA3405

description:
McClintick_LCL_data_2019.xlsx
6U


title: HeLa Control_1 m6A-IP

tag: cell line

value: HeLa

value: m6A Antibody (SYSY, Cat. No. 202 003)


title: PDD_P2_63

source_name: Ceftriaxone

value: cell wall synthesis inhibitor

value: EC90 of phenotype


title: PDD_P2_31

value: Protein synthesis


title: RNA-seq WT-6

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

country: United Kingdom

institute: University of Essex

description:
RNA-seq WT-6
Wiehle_et_al_2018_10.transcript_summary.tsv.gz
ctrl2

data_processing:
Paired-end MNase-ChIP-seq histone H3 reads were mapped to the mouse genome mm9 using Bowtie (Langmead et al. 2009) allowing up to two mismatches and only unique alignments. This resulted in 343 and 316 million mapped mono-nucleosome fragments correspondingly in WT and DKO cells. Single-end CTCF ChIP-seq produced 58 million mapped reads in WT (3 replicates) and 33 million mapped reads in DKO (2 replicates). Reads were then processed using the standard NucTools pipeline (Vainshtein et al. 2017) to calculate genome-wide occupancies and average aggregate profiles.
CTCF binding peaks were called with MACS (Zhang et al. 2008) using default parameters. Common sites were defined as peaks appearing in all replicates in both cell conditions. Lost sites were defined as appearing in all replicates in WT while not appearing in any of DKO replicates. Gained sites were defined as appearing in all replicates in DKO and not appearing in any of WT replicates. Precise positioning of CTCF binding sites within each category of CTCF peaks was done by scanning for the CTCF motif from JASPAR (Mathelier et al. 2016) using RSAT with default parameters (Castro-Mondragon et al. 2017).
RNA-seq was processed using Genomatix software
Genome_build: mm9
Supplementary_files_format_and_content: BED file format; MACS generated CTCF peaks in WT and DKO; NucTools generated positions of all mapped nucleosomal DNA fragments in WT and DKO
Abundance measurements and fold-change.

source_name: mouse embryonic stem cells

growth_protocol: Two WT and two Tet1/2-deficient (DKO) mouse ES cell lines were isolated from WT and Tet1/Tet2 double-mutant mice with a mixed 129 and C57BL/6 background as described (Dawlaty et al., 2013). ESCs were maintained in regular ESC medium (KnockOut DMEM supplemented with 15% fetal calf serum, 1x non-essential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin, 2 mM L-glutamine, 0.0008% β-mercaptoethanol and 1000 U/ml leukemia inhibiting factor) at 37 °C and 7% CO2 on inactivated MEF feeders seeded on gelatin (0.2%) coated dishes. For experiments cells were trypsinized and pre-plated on gelatin coated dishes three times to remove feeders.

extract_protocol:
Genomic DNA was isolated by lysing freshly prepared cell pellets in pre-lysis buffer (10 mM Tris-HCl (pH 8), 5 mM EDTA, 100 mM NaCl, 1.1% (v/v) SDS, 0.1 mg/ml Proteinase K and 0.04 mg/ml RNAse A) at 37°C overnight. The next day proteins were precipitated by addition of 5 M NaCl and the DNA was isolated by isopropanol precipitation. Total RNA was isolated from freshly harvested cells using TRIzol (Invitrogen).
Purified DNA was cloned into Illumina libraries with the NEBNext Ultra library preparation kit (NEB).
Illumina NEBNext Ultra

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: wild type


title: Control_M_T_AA3405

description:
McClintick_LCL_data_2019.xlsx
6T

value: M


title: Control_F_T_AA3238

description:
McClintick_LCL_data_2019.xlsx
5T


title: RNA-seq WT-4

description:
RNA-seq WT-4
Wiehle_et_al_2018_10.transcript_summary.tsv.gz
ctrl1


title: PDD_P2_05

value: ~ 25 min


title: Control_M_T_AA2985

description:
McClintick_LCL_data_2019.xlsx
3T


title: Input ChIP-seq WT-4

description: Input ChIP-seq

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: Alcoholic_M_U_AA2946

description:
McClintick_LCL_data_2019.xlsx
2U

tag: treatment


title: RNA-seq DKO-26

description:
RNA-seq DKO-26
Wiehle_et_al_2018_10.transcript_summary.tsv.gz
treat1

value: TET1/2 DKO


title: Control_M_U_AA2985

description:
McClintick_LCL_data_2019.xlsx
3U


title: PDD_P2_11


title: Input ChIP-seq DKO-51

description: Input ChIP-seq


title: PDD_P2_72

value: new hit

value: 50 uM


title: PDD_P2_37

value: Gram-negative bacteria


title: Input ChIP-seq WT-6

description: Input ChIP-seq


title: B.cereus_F837/76_Mucin2

city: Oberschleißheim

first: Nadja

last: Jessberger

address: Schönleutnerstr. 8

department: Department of Veterinary Sciences, Faculty of Veterinary Medicine

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
sample_1505_Mucin.genes.FPKM.table.tsv
sample_1505_MOD_vs_sample_1505_Mucin.SIGNIFICANT.gene_expression_table.tsv

data_processing:
Samples were sequenced via Illumina HiSeq 2500 Genome Sequencer with 50 bp paired-end mode.Sequence mode: HSHOv4 SR50. Data analysis included mapping of the samples against a reference genome (B. cereus F837/76; CP003187) and determination of gene expression.
The RNA-Seq reads are aligned to the reference genome or reference transcriptome using Bowtie generating genome / transcriptome alignments.
TopHat identies the potential exon-exon splice junctions of the initial alignment.
Then Cufflinks identifies and quantifies the transcripts from the preprocessed RNA-Seq alignment-assembly. After this, Cuffmerge merges the identi1ed transcript pieces to full length transcripts and annotates the transcripts based on the given annotations.
Finally, merged transcripts from two or more samples / conditions are compared using Cuffdiff to determine the differential expression levels at transcript and gene level including a measure of signigicance between samples / conditions.
Genome_build: CP003187.fasta
Supplementary_files_format_and_content: tsv format with FPKM

organism: Bacillus cereus

source_name: B.cereus_F837/76_mMOD minimal medium + 0.25 % PGM 2

growth_protocol: Reference strain F837/76 (=MIH 1505) was grown in triplicates in 50 ml mMOD minimal medium +/- 0.25 % PGM for three hours. Initial OD600 was 0.05.

extract_protocol:
Total RNA preparation and on-column DNase digestion were performed using RNeasy® Mini Kit (Qiagen) according to the instructions of the manufacturer. RNA quality was tested via spectrophotometer and agarose gel electrophoresis. RNA purity was confirmed via PCR for 16 S rRNA.
Random primed cDNA libraries were constructed according to the Illumina Genome Analyzer II protocol.

treatment_protocol: 10 ml samples were centrifuged for 10 min at 4,000 g and 4 °C. Cell pellets were stored at -80 °C.

tag: pgm


title: B.cereus_F837/76_Mucin3

source_name: B.cereus_F837/76_mMOD minimal medium + 0.25 % PGM 3


title: Input ChIP-seq DKO-26

description: Input ChIP-seq


title: PDD_P2_46


title: Control_F_T_AA2997

description:
McClintick_LCL_data_2019.xlsx
4T

tag: gender

value: ethanol 48h


title: B.cereus_F837/76_Mucin1

source_name: B.cereus_F837/76_mMOD minimal medium + 0.25 % PGM 1


title: CTCF ChIP-seq WT-6 rep2

description: CTCF ChIP-seq

value: CTCF antibody (Active Motif, catalog# 61311)


title: CTCF ChIP-seq WT-4

description: CTCF ChIP-seq


title: Alcoholic_M_T_AA2946

description:
McClintick_LCL_data_2019.xlsx
2T

value: Alcoholic

tag: library/sequencing batch


title: RNA-seq DKO-51

description:
RNA-seq DKO-51
Wiehle_et_al_2018_10.transcript_summary.tsv.gz
treat2


title: B.cereus_F837/76_mMOD2

description:
sample_1505_MOD.genes.FPKM.table.tsv
sample_1505_MOD_vs_sample_1505_Mucin.SIGNIFICANT.gene_expression_table.tsv

source_name: B.cereus_F837/76_mMOD minimal medium 2

value: no


title: B.cereus_F837/76_mMOD3

source_name: B.cereus_F837/76_mMOD minimal medium 3


title: PDD_P2_20


title: HeLa Control_1 input

source_name: HeLa cells

value: HeLa

tag: passages


title: I7it49_L1_383383

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

institute: Peking University

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

source_name: Bone marrow

growth_protocol: Immortalized bone marrow derived macrophages were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin on 10 cm dish for further experiments.

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by type II Toxoplasma gondii, ME49

value: ME49 infection


title: I3_L1_379379

value: Immortalized bone marrow derived macrophages

value: MOCK


title: CTCF ChIP-seq WT-6 rep1

description: CTCF ChIP-seq


title: H3 MNase-ChIP-seq DKO rep2

description: MNase-assisted H3 ChIP-seq

value: H3 antibody (Abcam, catalog# ab1791, lot# GR103864-1)


title: B.cereus_F837/76_mMOD1

source_name: B.cereus_F837/76_mMOD minimal medium 1


title: CTCF ChIP-seq DKO-51

description: CTCF ChIP-seq

value: mouse embryonic stem cells


title: PDD_P2_70

source_name: AZ-LolCDE

tag: type

value: cell wall synthesis inhibitor / lipoprotein

value: EC90 of phenotype


title: I7_L1_380380


title: PDD_P2_44

tag: moa

value: ~ 25 min


title: CTCF ChIP-seq DKO-26

description: CTCF ChIP-seq

value: TET1/2 DKO


title: PDD_P2_18

tag: treatment time


title: AKI_UPHD25_Rep3

city: Pittsburgh

first: Neil

middle: A

last: Hukriede

state: PA

address: 3501 Fifth Ave, 5061 BST3

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Reads were aligned using Hisat2 (v2.1.0) with the UCSC zebrafish genome version danRer11. Reads for multiple lanes of the same sample were pooled together.
Gene-level counts were calculated using featureCounts in the R package Rsubread (v1.24.2) with the Ensembl GTF file.
Genome_build: danRer11
Supplementary_files_format_and_content: Tab-delimited text file with gene-level counts for all samples.

organism: Danio rerio

source_name: zebrafish pronephros

growth_protocol: Larvae were incubated in E3 medium until treatment at 3dpf.

extract_protocol:
100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then, they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit (QIAGEN)
TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 rounds of PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay (Qubit) and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM, pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing, approximately 30-40 million reads per sample.

treatment_protocol: At 2dpi (5dpf), injured larvae were incubated with 1uM UPHD25 (1%DMSO) or control 1% DMSO for 24 hours at 28C

tag: genotype (transgenic line)

tag: tissue

value: pronephros

tag: microinjection

value: gentamicin

value: 1uM UPHD25


title: protoplasted rep1

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description:
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
RP1
processed data file: Root_bulk_tissue_datamatrix.txt

data_processing:
Cell Ranger 2.0.2 (10X Genomics) was used to process scRNA-seq data.
Bulk RNA Sequencing reads (pair-end, 75 bp) were trimmed using Trimmomatic (version 0.36), and aligned to the Arabidopsis TAIR10 reference genome with STAR. Gene expression values were calculated on uniquely mapped reads using HTSeq (version 0.7.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_datamatrix.csv: Comma-delimited text files include UMI counts values in each cell.
Supplementary_files_format_and_content: Root_bulk_tissue_datamatrix.txt: Tab-delimited text file includes read counts and RPM values for each Sample.

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown vertically on nylon mesh on ½ Murashige and Skoog 1% agar plates.

extract_protocol:
RNA extraction (for bulk RNA-seq samples) - either protoplasted (reduced to smallest possible volume) or unprotoplasted root tissue was flash-frozen in liquid nitrogen, ground to a powder and RNA extracted using the Spectrum Plant RNA Extraction Kit (Sigma). Quality and quantity were checked using Agilent Bioanalyzer chips and Nanodrop, respectively, prior to library construction.
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina. Single cell RNA-seq libraries were prepared from fresh protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. For each replicate, cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-‐ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.

treatment_protocol: For protoplasting: Roots of 6-day-old seedlings were cut approximately one centimetre from their tip, broadly diced with a scalpel blade, and treated with 7 ml protoplasting solution optimised for scRNA-seq from a protocol in Birnbaum et al., 2003. Immediately before use, 1.5% Cellulase R-10 and 0.1% Pectolyase (Duchefa Biochem.) were added to fresh protoplast buffer (0.1 M KCl, 0.02 M MgCl2, 0.02 M CaCl2, 0.1% BSA (Sigma Aldrich)), 0.08 M MES, and 0.6 M Mannitol adjusted to pH 5.5 with 0.1M Tris HCl) and mixed thoroughly. Root tissues were protoplasted for 2 hours at 20°C on an orbital shaker set at 200 evolutions/minute. The mixture was subsequently filtered through a 100 μm nylon filter and rinsed with 1-5 ml of root protoplast buffer. Protoplasts were then centrifuged for 10 minutes (500 g – 4°C), the supernatant gently removed, and the pellet resuspended in 10 ml root protoplast buffer containing 0.4 M Mannitol and no CaCl2. This wash procedure was repeated once more, the protoplasts centrifuged as before, and resuspended in ~500 μl or less protoplast buffer without CaCl2 and with 0.4 M Mannitol. Protoplasts were validated under a light microscope, and if necessary any excess debris or un-protoplasted tissues removed with an additional washing step. Cells were filtered through a 40 μm cell strainer (Flowmi Bel Art SP Scienceware), quantified using a haemocytometer, and adjusted to a density of approximately 800-‐900 cells per μl.

tag: strain/background

tag: genotype/variation

value: Wild type

value: Root

tag: age

value: 6-day-old seedlings

tag: condition

value: Protoplasted


title: vit49_L1_381381

tag: strain

tag: cell type

tag: genotype

value: wild type


title: protoplasted rep2

description:
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
RP2
processed data file: Root_bulk_tissue_datamatrix.txt


title: AKI_UPHD25_Rep1

tag: treatment


title: H3 MNase-ChIP-seq WT rep2

description: MNase-assisted H3 ChIP-seq

tag: chip antibody


title: Fasted_72 hrs

data_processing:
Datasets were excluded owing to low-quality reads.
Bowtie2 and HISAT were used to map clean reads to reference gene and genome respectively.
Gene expression level (FPKM) is quantified by RSEM
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values or read counts of genes for each Sample

source_name: Ileum

extract_protocol:
Ileum were removed, flash frozen in liquid nitrogen, and RNA was harvested using Total RNA Miniprep Purification Kit (GeneMarkbio,Cat# TR01).
cDNA was generated using random N6 primer followed by A-tailing. The adaptors were ligated to the A-tailed cDNA, then were amplified by PCR. The PCR products were heated to separate into single strand DNA which was cyclized with splint oligonucleotides to generate libraries.

treatment_protocol: Mice were fasted for 0 hr (also called fed), 48 hrs or 72 hrs.

value: post natal day 21

value: fasted for 72hrs

value: Ileum


title: AKI_UPHD25_Rep2


title: v_L1_378378

value: Immortalized bone marrow derived macrophages

value: MOCK


title: unprotoplasted rep2

description:
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
RU2
processed data file: Root_bulk_tissue_datamatrix.txt

value: Unprotoplasted


title: Fed

value: fed


title: H3 MNase-ChIP-seq WT rep1

description: MNase-assisted H3 ChIP-seq

value: mouse embryonic stem cells

value: H3 antibody (Abcam, catalog# ab1791, lot# GR103864-1)


title: Fasted_48 hrs RNA

value: fasted for 48hrs


title: unprotoplasted rep1

description:
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
RU1
processed data file: Root_bulk_tissue_datamatrix.txt


title: Fed RNA


title: Input MNase-ChIP-seq DKO rep1

description: Input MNase-ChIP-seq

value: TET1/2 DKO


title: AKI_DMSO_Rep2

value: pronephros

value: gentamicin

value: 1% DMSO


title: AKI_DMSO_Rep3


title: I3it49_L1_382382

value: ME49 infection


title: shr-3

description:
Single cell RNA-seq library was prepared from fresh shr-3 protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. Cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and the library were quantified using the NEBNext Library Quantification Kit for Illumina.
The R1 raw data files include the technical reads; the first 16 basepairs are barcode and the last 10 basepairs are UMI. The R2 raw data files include the biological reads.
processed data file: Root_single_cell_shr_datamatrix.csv

value: Col-0 and Ler backgrounds

value: shortroot-knockout mutant

value: Root

value: 6-day-old seedlings

value: Protoplasted


title: Ctrl_2nd

status: Public on Mar 24 2019

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
expressed_gene_reads.txt
expressed_gene_FPKM.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue < =0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene reads for each Sample
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

tag: clone

value: control plasmid

tag: cell line

value: HeLa


title: H3 MNase-ChIP-seq DKO rep1

description: MNase-assisted H3 ChIP-seq


title: Ctrl_1st


title: ZFP36_2nd

value: ZFP36 overexpression


title: AKI_DMSO_Rep1

extract_protocol:
100 larvae were pooled and treated with DTT and Collagenase I to disintegrate tissue. Then, they were titurated with p100 to reveal pronephros. GFP+pronephros were dissected and collected. Trizol based RNA isolation was used using RNAeasy Micro Kit (QIAGEN)
TruSeq Stranded mRNA kit was used according to the manufacturer's protocol. Fragmentation was performed for 8 minutes. 15 PCR amplification provided selective enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality assessment by fluorometric assay (Qubit) and Agilent DNA 1000 TapeStation assay respectively. Final libraries were normalized to 10 nM, pooled and diluted. Flowcells for the NextSeq 500 were seeded with 1.8 pM denatured library for automated cluster formation and 2 x 75 paired end sequencing, approximately 30-40 million reads per sample.


title: HomoC7_48hr_DMSO_rep2

type: RNA

first: Liang

middle: Jia

last: Zhang

address: 651 Dongfeng Road East, Yuexiu District,

institute: SYSUCC

description: miRNA expression treated with DMSO for 48h

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: HPDE6-C7, DMSO, 48h, replicate 2

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

growth_protocol: Incubate in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: Immortalized human pancreatic duct epithelial cells treated with 100ug/ml cigarette smoke condensate or DMSO diluted with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: immortalized human pancreatic duct epithelial cells


title: HomoC7_48hr_DMSO_rep3

source_name: HPDE6-C7, DMSO, 48h, replicate 3


title: HomoC7_48hr_CSC_rep2

description: miRNA expression treated with CSC for 48h

source_name: HPDE6-C7, CSC, 48h, replicate 2


title: HomoC7_48hr_CSC_rep3

source_name: HPDE6-C7, CSC, 48h, replicate 3


title: HomoC7_48hr_DMSO_rep1

source_name: HPDE6-C7, DMSO, 48h, replicate 1


title: HomoC7_48hr_CSC_rep1

source_name: HPDE6-C7, CSC, 48h, replicate 1


title: IMCbloodB16D111: B16 Day11 #1

city: Tel Aviv

first: Yoel

last: Bogoch

address: 6 Weizmann

country: Israel

institute: Sourasky Tel Aiv Meical Center

description: processed data file: IMC_3700_processed.xlsx

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 40).
Reads that had either a percentage of Adenine bases above 50% or a percentage of Thymine bases above 50% were discarded using a custom script.
TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10)
Counting reads on mm10 refseq genes was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: Peripheral blood

extract_protocol:
MDSCs were isolated from peripheral blood using MACS magnetic separation. RNA was extracted from the cells using qiagen mini prep kit
Inhouse poly A based RNA seq

value: MDSCs

value: Immature Myeloid Cells

value: Peripheral blood


title: PANC-1_NKAP-iCLIP

data_processing:
Reads were trimmed for adaptor sequence using cutadapt .
Paired-end fastq files were demultiplexed according to their experimental barcode using pyBarcodeFilter.py script of the pyCRAC suite
PCR-duplicates were removed based on their sequence with the pyFastqDuplicateRemover.py script of the pyCRAC suite.Headers compatible for subsequent analysis with the CIMS software were generated using in-house bash scripts.
For paired end data, reverse reads were reverse complemented and assigned with the reverse complement of the random barcode using in-house scripts and .Reads were aligned in single-end mode using bwa(bwa aln -n 0.06 -q 20)
For CIMS miCLIP ,The CIMS pipeline [Moore et al. 2014; PMID: 24407355] was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage (k) and the number of C-->T transitions (m) for each nucleotide. No FDR filter was applied. C-->T transition sites were filtered by the number transitions observed (m) and the ratio of transitions to unique tags covering that position (m/k)(50% >=m/k >= 1% ). For CITS miCLIP, reads were processed and mapped identically. The CITS pipeline [Weyn-Vanhentenryck et al. 2014; PMID: 24613350] was then used to determine sites with significant (p < 0.05) crosslinking-induced cDNA truncations.
Genome_build: GRCh38
Supplementary_files_format_and_content: wiggle files for miCLIP-seq tags and NKAP iCLIP-seq tags

molecule: nuclear RNA

source_name: pancreatic ductal adenocarcinoma cells

growth_protocol: Incubate in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Nuclear RNA from PANC-1 cells was isolated and fragmented. The ethanol precipitated RNA was diluted and incubated with anti-m6A. After cross-linking, the solution was incubated with Protein A/G beads (Millipore) overnight. Bead-bound antibody-RNA complexes were then recovered, multisteps washing,and 3′adaptor ligation with T4 RNA ligase (New England BioLabs) . The antibody-bound RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation.
Cells overexpressing FLAG-tagged NKAP were washed with ice-cold PBS and cross-linked and harvested on ice. Nuclear extraction was isolated and sonicated, followed by treating with DNase I and low dilution RNase A. Pre-washed Dynabeads protein A/G conjugated with anti-FLAG (F1804, Sigma) antibody were then incubated with the extraction. RNA were recovered by proteinase K treatment, followed by 3’ linker ligation, acidic phenol/chloroform extraction and ethanol precipitation.
The purified RNA was reverse transcribed with Superscript III reverse transcriptase (Life Technologies) according to the manufacturer’s protocol. First-strand cDNA was size-selected on an 8% TBE-Urea gel (Life Technologies), and regions corresponding to 100–180 nucleotides were used for further analysis. After circularization and re-linearization of cDNA, libraries were PCR amplified for 18–21 cycles and sequenced on an Illumina HiSeq X Ten.

treatment_protocol: For NKAP iCLIP, PANC-1 cells were transfected with FLAG-tag NKAP with lipofatamin2000. Nuclear fraction were isolated from cross-linked cells after transfacted for 48h.

value: NKAP-FLAG overexpression

tag: iclip antibody

value: anti-FLAG, Sigma, F1804


title: IMCbloodB16D8-1: B16 Day8 #1


title: IMCbloodB16D4-3: B16 Day4 #3


title: IMCbloodB16D4-1: B16 Day4 #1


title: IMCbloodB16D112: B16 Day11 #2


title: IMCbloodB16D0-2: B16 Day 0 #2


title: Input MNase-ChIP-seq WT rep1

description: Input MNase-ChIP-seq

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: wild type


title: IMCbloodB16D0-1: B16 Day 0 #1


title: IMCbloodB16D8-2: B16 Day8 #2


title: IMCbloodB16D8-3: B16 Day8 #3


title: PANC-1_miCLIP

value: Wild-type

value: anti-m6A, Synaptic Systems, 202003


title: ZFP36_1st


title: IMC_d11_2: CT26 Day11 #2

description: processed data file: IMC_1558_processed.xlsx

value: Balbc


title: IMCbloodB16D0-3: B16 Day 0 #3


title: mature DC day7

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

description:
mature DCs
This array contains ~19000 RefSeq coding genes and ~21001 long non-coding RNAs (lncRNA).

hyb_protocol: hybridization to the 12x135K LncRNA Expression Microarray (Arraystar, Rockville, USA)

scan_protocol: raw data were scanned and extracted using the Axon GenePix 4000B microarray scanner and the NimbleScan software (version 2.5).

data_processing: Implementation of RMA with NimbleScan software (v.2.5) offers quantile normalization and background correction. The sample data table contains values which are greater than or equal to Lower cut-off: 100.0, at least 3 out of 3 samples.

source_name: mature DC day7

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: Monocytes were purified from PBMCs using anti-CD14 microbeads (Miltenyi Biotech) and then cultured at 37°C in 24-well plates (5x10^5 cells per well) in 1 mL of RPMI-1640 Medium (PAA) with 10% (vol/vol) FCS (PAA) containing 100 ng/mL human GM-CSF and 20 ng/mL human IL-4 (R&D Systems, Minneapolis, MN). Half medium was replaced by fresh medium with GM-CSF and IL-4 at day 3 and day 5.

extract_protocol: Total RNA was isolated from purified monocytes, imDCs (day 5) and mature DCs (day 7) with Trizol and then subjected to double strand cDNA synthesis

treatment_protocol: DCs were matured by 300ng/ml LPS (0111:B4, Sigma) on day 5 and harvested on day 7 for mature DCs.

value: monocytes differentiated mature DCs

tag: harvested on

value: day 7


title: IMC_d11_3: CT26 Day11 #3


title: IMC_d4_1: CT26 Day4 #1


title: IMC_d8_2: CT26 Day8 #2


title: IMC_d8_3: CT26 Day8 #3


title: IMCbloodB16D113: B16 Day11 #3


title: IMC_d11_1: CT26 Day11 #1


title: IMC_d0_3: CT26 Day 0 #3


title: IMC_d8_1: CT26 Day8 #1


title: IMC_d4_3: CT26 Day4 #3


title: IMC_d0_2: CT26 Day 0 #2


title: Mouse OB 2016 10-cell random sample 23

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description:
Cspg4-CreER;Trp53F/F;Nf1F/F;Rosa26-LSL-tdT mice
janes2018_rsemcounts_mouse.csv

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to either the human (GRCh38.p12) or the mouse (GRCm38.p6) transcriptome using RSEM. If specified in character tag field, reference ERCC sequences were also provided for the alignment.
RSEM options  --bowtie2 --single-cell-prior (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Supplementary_files_format_and_content: Comma separated file includes read counts from RSEM

source_name: Brain olfactory bulb

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

value: Oligodendrocyte progenitor cells

tag: ercc spike ins

value: No spike ins

tag: days post-labeling


title: Mouse OB 2016 10-cell random sample 21


title: Mouse OB 2016 10-cell random sample 24


title: human monocytes

description:
monocytes
This array contains ~19000 RefSeq coding genes and ~21001 long non-coding RNAs (lncRNA).

source_name: human monocytes

value: peripheral blood monocytes

value: day 0


title: Mouse OB 2016 10-cell random sample 25


title: Mouse OB 2016 10-cell random sample 22


title: Mouse OB Tumor 2016 10-cell random sample 1

value: Glioma tumor cells


title: IMC_d0_1: CT26 Day 0 #1

value: MDSCs

tag: tissue


title: Mouse OB 2016 10-cell random sample 13


title: Mouse OB 2016 10-cell random sample 17


title: Mouse OB 2016 10-cell random sample 18


title: Mouse OB 2016 10-cell random sample 26


title: Mouse OB 2016 10-cell random sample 27


title: IMC_d4_2: CT26 Day4 #2

value: Immature Myeloid Cells


title: Mouse OB 2016 10-cell random sample 9


title: Mouse OB 2016 10-cell random sample 14


title: Mouse OB 2016 10-cell random sample 5


title: Mouse OB 2016 10-cell random sample 11


title: Mouse OB 2016 10-cell random sample 10


title: immature DC day5

description:
immature DCs
This array contains ~19000 RefSeq coding genes and ~21001 long non-coding RNAs (lncRNA).

source_name: immature DC day5

value: monocytes differentiated immature DCs

value: day 5


title: Mouse OB 2016 10-cell random sample 1


title: Mouse OB 2016 10-cell pool-and-split control replicate 20


title: Mouse OB 2016 10-cell random sample 12


title: Mouse OB 2016 10-cell random sample 3


title: Mouse OB 2016 10-cell random sample 2


title: Mouse OB 2016 10-cell random sample 7


title: Mouse OB 2016 10-cell random sample 16


title: Mouse OB 2016 10-cell random sample 6


title: Mouse OB 2016 10-cell pool-and-split control replicate 18


title: Mouse OB 2016 10-cell pool-and-split control replicate 13


title: Mouse OB 2016 10-cell pool-and-split control replicate 14


title: Mouse OB 2016 10-cell random sample 15


title: Mouse OB 2016 10-cell pool-and-split control replicate 17


title: Mouse OB 2016 10-cell random sample 8


title: Mouse OB 2016 10-cell pool-and-split control replicate 11


title: Mouse OB 2016 10-cell pool-and-split control replicate 15


title: Mouse OB 2016 10-cell pool-and-split control replicate 19


title: Mouse OB 2016 10-cell pool-and-split control replicate 16


title: Mouse OB 2016 10-cell random sample 4


title: Mouse OB 2016 10-cell pool-and-split control replicate 9


title: Mouse OB 2016 10-cell random sample 20


title: Mouse OB 2016 10-cell pool-and-split control replicate 7


title: Mouse OB 2016 10-cell pool-and-split control replicate 5


title: Mouse Cortex 2016 10-cell random sample 26

source_name: Brain cortex


title: Mouse Cortex 2016 10-cell random sample 27


title: Mouse Cortex 2016 10-cell random sample 18


title: Mouse OB 2016 10-cell pool-and-split control replicate 1


title: Mouse OB 2016 10-cell pool-and-split control replicate 8


title: Mouse OB 2016 10-cell pool-and-split control replicate 3


title: Mouse OB 2016 10-cell pool-and-split control replicate 12


title: Mouse OB 2016 10-cell pool-and-split control replicate 4


title: Mouse Cortex 2016 10-cell random sample 16


title: Mouse Cortex 2016 10-cell random sample 15


title: Mouse Cortex 2016 10-cell random sample 25


title: Mouse Cortex 2016 10-cell random sample 28


title: Mouse Cortex 2016 10-cell random sample 24


title: Mouse OB 2016 10-cell random sample 19


title: Mouse Cortex 2016 10-cell random sample 14


title: Mouse Cortex 2016 10-cell random sample 20


title: Mouse Cortex 2016 10-cell random sample 22


title: Mouse Cortex 2016 10-cell random sample 21


title: Mouse Cortex 2016 10-cell random sample 23


title: Mouse Cortex 2016 10-cell random sample 13


title: Mouse OB 2016 10-cell pool-and-split control replicate 2


title: Mouse Cortex 2016 10-cell random sample 17


title: Mouse OB Tumor 2016 10-cell random sample 2


title: Mouse OB 2016 10-cell pool-and-split control replicate 6


title: Mouse Cortex 2016 10-cell random sample 12


title: Mouse Cortex 2016 10-cell random sample 11


title: Mouse Cortex 2016 10-cell random sample 3


title: Mouse Cortex 2016 10-cell random sample 9


title: Mouse Cortex 2016 10-cell random sample 8


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 15


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 14


title: Mouse Cortex 2016 10-cell random sample 4


title: Mouse Cortex 2016 10-cell random sample 5


title: Mouse Cortex 2016 10-cell random sample 10


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 10


title: Mouse Cortex 2016 10-cell random sample 19


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 8


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 5


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 11


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 16


title: Mouse Cortex 2016 10-cell random sample 1


title: Mouse Cortex 2016 10-cell random sample 6


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 12


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 17


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 3


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 13


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 4


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 6


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 18


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 7


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 9


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 1


title: Mouse OB 2016 10-cell pool-and-split control replicate 10


title: Mouse OPC 2017 10-cell random sample 3

source_name: Brain


title: Mouse OPC 2017 10-cell random sample 2


title: Mouse OPC 2017 10-cell random sample 5


title: Mouse OPC 2017 10-cell pool-and-split control replicate 4


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 2


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 20


title: Mouse Cortex 2016 10-cell pool-and-split control replicate 19


title: Mouse OPC 2017 10-cell pool-and-split control replicate 3


title: Mouse OPC 2017 10-cell pool-and-split control replicate 2


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 5

description:
Trp53∆/∆Rb∆/∆ lung epithelium derive small cell lung cancer spheroids
janes2018_rsemcounts_mouse.csv

source_name: Small cell lung cancer spheroid

value: Explanted SCLC spheroid

value: ERCC spike ins


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 4


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 6


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 2


title: Mouse OPC 2017 10-cell random sample 4


title: Mouse OPC 2016 10-cell random sample 6 redo


title: Mouse OPC 2017 10-cell pool-and-split control replicate 5


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 3


title: Mouse OPC 2017 10-cell random sample 1


title: Mouse OPC 2017 10-cell pool-and-split control replicate 1


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 5


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 1


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 6


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 3


title: Mouse SCLC 2018 10-cell pool-and-split control cleanup replicate 1


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 2


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 4


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 1-3


title: Mouse SCLC 2018 10-cell pool-and-split control replicate 2


title: Mouse Cortex 2016 10-cell random sample 2


title: Mouse OPC 2018 10-cell pool-and-split control replicate 2


title: Mouse OPC 2018 10-cell pool-and-split control replicate 1-4


title: Mouse OPC 2018 10-cell pool-and-split control replicate 1-3


title: Mouse OPC 2018 10-cell pool-and-split control replicate 1-2


title: Mouse OPC 2018 10-cell pool-and-split control replicate 3


title: Mouse OPC 2017 10-cell pool-and-split control replicate 6


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 3


title: MCF10A 10-cell random sample 17

description:
Cells were grown as a matrigel overlay culture in DMEM/F12 containing 2% matrigel, 2% horse serum, 5 ng/ml EGF, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, 10 µg/ml insulin, and 1x penicillin-streptomycin for 10 days, with refeeding at days 4 and 8.
janes2018_rsemcounts_human.csv

source_name: ECM-attached MCF10A-5E cells grown in 3D culture for 10 days


title: MCF10A 10-cell random sample 18


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 1-2


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 1-1


title: Mouse OPC 2018 10-cell pool-and-split control replicate 1-1


title: Mouse OPC 2018 10-cell pool-and-split control cleanup replicate 1-4


title: MCF10A 10-cell random sample 13


title: MCF10A 10-cell random sample 6


title: MCF10A 10-cell random sample 7


title: MCF10A 10-cell random sample 16


title: MCF10A 10-cell random sample 4


title: MCF10A 10-cell random sample 2


title: MCF10A 10-cell random sample 9


title: MCF10A 10-cell random sample 12


title: MCF10A 10-cell random sample 14


title: MCF10A 10-cell random sample 10


title: MCF10A 10-cell random sample 11


title: MCF10A 10-cell random sample 8


title: Human breast 2017 10-cell random sample 6

description:
Breast cancer samples were collected as ultrasound-guided core needle biopsies during diagnostic visits in accordance with IRB Protocol #19272
janes2018_rsemcounts_human.csv

source_name: Breast

value: Human ER+ luminal breast cancer biopsy


title: MCF10A 10-cell random sample 15


title: MCF10A 10-cell random sample 3


title: MCF10A 10-cell pool-and-split control replicate 4


title: Human breast 2017 10-cell random sample 5


title: MCF10A 10-cell pool-and-split control replicate 3


title: MCF10A 10-cell pool-and-split control replicate 2


title: MCF10A 10-cell random sample 5


title: MCF10A 10-cell pool-and-split control replicate 1


title: MCF10A 10-cell pool-and-split control replicate 5


title: Human breast 2017 10-cell random sample 3


title: Human breast 2017 10-cell random sample 2


title: MCF10A 10-cell random sample 1


title: Human breast 2017 10-cell pool-and-split control replicate 6


title: MCF10A 10-cell no reverse transcription control


title: Human breast 2017 10-cell pool-and-split control replicate 4


title: Human breast 2017 10-cell random sample 4


title: Veh_5

city: San Diego

first: Wen

last: Luo

state: CA

address: 6331 Nancy Ridge Drive

institute: Denovo Biopharma

description: Gene expression data from CD34+ cells treated with Vehicle

hyb_protocol: The labeled target was subsequently hybridized to a human Affymetrix U133A microarray in an Affymetrix Hybridization Oven 640

scan_protocol: After washing and staining on Affymetrix Fluidics Station 450, the arrays were scanned with the Affymetrix GeneArray 2500 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

label: biotin

source_name: Human CD34+ bone marrow cells treated with vehicle control for 5 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: Human bone marrow hematopoietic CD34+ cells derived from five healthy donors were characterized for viability (90%-95% by Trypan blue dye exclusion) and CD34 expression (> 95% CD34+ by flow cytometry).

extract_protocol: Total RNA was isolated with RNA was isolated using RNeasy mini kit from Qiagen

treatment_protocol: Two million cells from each donor were subcultured at 500,000 cells per well of six-well culture dishes in IMDM with 20% FBS, rhSCF at 100 ng/mL, and either 100 ng/mL rhTPO, 1 µM LGD4665, or equivalent volume of vehicle and incubated at 37°C in 5% CO2 for five days.

tag: Human CD34+ bone marrow cells from donor 5


title: TPO_5

description: Gene expression data from CD34+ cells treated with TPO

source_name: Human CD34+ bone marrow cells treated with 100 ng/ml TPO for 5 days


title: LGD4665_5

description: Gene expression data from CD34+ cells treated with LGD-4665

source_name: Human CD34+ bone marrow cells treated with 1uM LGD-4665 for 5 days


title: TPO_3

description: Purified CD61+ cells derived from CD34+ cells treated with TPO

source_name: Purified CD61+ cells derived from CD34+ bone marrow cells treated with 100 ng/mL TPO for 10 days

growth_protocol: Human bone marrows from healthy donors were used to purifiy CD34+ cells, and cells were then cultured with rhSCF at 100 ng/mL, and either 100 ng/mL TPO, 3 µM eltrombopag, or 1 µM LGD-4665 for 10 days.

extract_protocol: Total RNA was isolated with Versagene RNA Cell Kit from Gentra Systems.

treatment_protocol: Purified human bone marrow CD34+ cells were cultured with rhSCF at 100 ng/mL, and either 100 ng/mL TPO, 3 µM eltrombopag, or 1 µM LGD-4665 for 10 days.  The mature megakaryocytes were enriched using anti-CD61 Miltenyi beads, and FACS analysis showed that more than 90% of the purified cells were CD61+ cells.

tag: Human CD34+ bone marrow cells from donor 3


title: Eltrom_5

description: Gene expression data from CD34+ cells treated with eltrombopag

source_name: Human CD34+ bone marrow cells treated with 1uM eltrombopag for 5 days


title: Eltrom_4

tag: Human CD34+ bone marrow cells from donor 4


title: Eltrom_3

description: Purified CD61+ cells derived from CD34+ cells treated with eltrombopag

source_name: Purified CD61+ cells derived from CD34+ bone marrow cells treated with 3 µM eltrombopag for 10 days


title: TPO_4


title: LGD4665_4


title: Eltrom_3


title: Eltrom_2

tag: Human CD34+ bone marrow cells from donor 2


title: TPO_4


title: Veh_4


title: Human breast 2017 10-cell random sample 1


title: Eltrom_2


title: Veh_3


title: LGD4665_4

description: Purified CD61+ cells derived from CD34+ cells treated with LGD-4665

source_name: Purified CD61+ cells derived from CD34+ bone marrow cells treated with 1 µM LGD-4665 for 10 days


title: TPO_3


title: LGD4665_3


title: Human breast 2017 10-cell pool-and-split control replicate 3


title: LGD4665_2


title: Human breast 2017 10-cell pool-and-split control replicate 5


title: Eltrom_1

tag: Human CD34+ bone marrow cells from donor 1


title: TPO_2


title: Human breast 2017 10-cell pool-and-split control replicate 2


title: LGD4665_2


title: TPO_2


title: LGD4665_1


title: LGD4665_1


title: TPO_1


title: Human breast 2017 10-cell pool-and-split control replicate 1


title: TPO_1


title: Veh_2


title: Eltrom_1


title: Veh_1


title: NK-HCC-1: NK cells from HCC patients, rep1

status: Public on Mar 23 2019

city: Parma

first: Alessandra

last: Zecca

state: Parma

address: via Gramsci 14

country: Italy

institute: Azienda Ospedaliero-Universitaria di Parma

hyb_protocol: RNA was hybridized to 60-mer oligonucleotide whole-human-genome microarrays (Human GE 8x60K v2 sureprint g3, Agilent Technologies), following the manufacturer's protocol.

scan_protocol: Microarray slides were scanned with an Agilent dual-laser DNA microarray scanner. The Agilent Feature Extraction software (user manual version 7.5) was used with default settings to obtain normalized expression values from the raw scans.

data_processing: The Agilent Feature Extraction software with default settings (user manual version 7.5) was used to obtain normalized expression values from the raw scans. The software package GeneSpring GX v13.1.1 (Agilent Technologies) was used for quality control checks, data normalization by the 75th percentile method.

source_name: peripheral blood NK cells from HCC patients 1

label_protocol: RNA was used to produce cRNA that was labeled with Cy3.

extract_protocol: RNA was purified from sorted NK cells  with the RNase-Free DNase I Kit (Norgen Biotek) according to the manufacturer's instructions. Total RNA concentration was determined with a Nanodrop spectrophotometer. RNA integrity was evaluated with a Bioanalyzer 2100 traces system (Agilent Technologies).

treatment_protocol: PBMCs were isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation and cryopreserved in liquid nitrogen until the day of analysis. After thawing of PBMCs, NK cells were isolated by cell sorting and labeled with 7-AAD, anti-CD3, anti-CD56, and anti-CD16. NK cells were sorted with a FACSAria III Cell Sorter (BD Biosciences).

tag: diagnosis

value: Hepatocellular Carcinoma (HCC) patient

value: Natural Killer (NK) cells


title: NK-HCC-6: NK cells from HCC patients, rep6

source_name: peripheral blood NK cells from HCC patients 6

tag: cell type


title: NK-HCC-7: NK cells from HCC patients, rep7

source_name: peripheral blood NK cells from HCC patients 7


title: NK-HCC-4: NK cells from HCC patients, rep4

source_name: peripheral blood NK cells from HCC patients 4


title: NK-HCC-8: NK cells from HCC patients, rep8

source_name: peripheral blood NK cells from HCC patients 8


title: NK-HCC-11: NK cells from HCC patients, rep11

source_name: peripheral blood NK cells from HCC patients 12


title: NK-LC-6: NK cells from cirrhotic patients, rep6

source_name: peripheral blood NK cells from cirrhosis patients 6

value: cirrhotic patient


title: NK-HCC-5: NK cells from HCC patients, rep5

source_name: peripheral blood NK cells from HCC patients 5


title: NK-LC-10: NK cells from cirrhotic patients, rep10

source_name: peripheral blood NK cells from cirrhosis patients 10


title: NK-HD-8: NK cells from healthy donor, rep6

source_name: peripheral blood NK cells from healthy donor 6

value: healthy donor


title: NK-HCC-2: NK cells from HCC patients, rep2

source_name: peripheral blood NK cells from HCC patients 2


title: NK-HD-9: NK cells from healthy donor, rep7

source_name: peripheral blood NK cells from healthy donor 7


title: NK-LC-7: NK cells from cirrhotic patients, rep7

source_name: peripheral blood NK cells from cirrhosis patients 7


title: NK-LC-5: NK cells from cirrhotic patients, rep5

source_name: peripheral blood NK cells from cirrhosis patients 5


title: NK-HCC-14: NK cells from HCC patients, rep14

source_name: peripheral blood NK cells from HCC patients 15


title: NK-HD-7: NK cells from healthy donor, rep5

source_name: peripheral blood NK cells from healthy donor 5


title: NK-HD-6: NK cells from healthy donor, rep4

source_name: peripheral blood NK cells from healthy donor 4


title: NK-LC-3: NK cells from cirrhotic patients, rep3

source_name: peripheral blood NK cells from cirrhosis patients 3


title: NK-LC-9: NK cells from cirrhotic patients, rep9

source_name: peripheral blood NK cells from cirrhosis patients 9


title: NK-HCC-9: NK cells from HCC patients, rep9

source_name: peripheral blood NK cells from HCC patients 10


title: NK-HCC-13: NK cells from HCC patients, rep13

source_name: peripheral blood NK cells from HCC patients 14


title: NK-HCC-3: NK cells from HCC patients, rep3

source_name: peripheral blood NK cells from HCC patients 3


title: NK-HCC-12: NK cells from HCC patients, rep12

source_name: peripheral blood NK cells from HCC patients 13


title: NK-LC-1: NK cells from cirrhotic patients, rep1

source_name: peripheral blood NK cells from cirrhosis patients 1


title: NK-HD-5: NK cells from healthy donor, technical rep2

source_name: peripheral blood NK cells from healthy donor 2


title: NK-LC-2: NK cells from cirrhotic patients, rep2

source_name: peripheral blood NK cells from cirrhosis patients 2


title: NK-HD-4: NK cells from healthy donor, technical rep1


title: NK-LC-4: NK cells from cirrhotic patients, rep4

source_name: peripheral blood NK cells from cirrhosis patients 4


title: NK-HCC-10: NK cells from HCC patients, rep10

source_name: peripheral blood NK cells from HCC patients 11


title: NK-HD-3: NK cells from healthy donor, rep3

source_name: peripheral blood NK cells from healthy donor 3


title: preoptic area neuron_H11

city: San Francisco

first: Lily

middle: Y

last: Jan

address: 1550 4th Street, Room RH-484A

department: Physiology

institute: UCSF

description:
raw_counts_for_stats.txt
normalized_counts.txt

data_processing:
quality control for sequencing was assessed using FastQC
raw reads were trimmed with R-package scythe for adapter contamination, and with sickle for low quality reads
reads were aligned to the mouse reference genome sequence mm10 with STAR, using UCSC annotation from iGenomes
raw read counts were generated by STAR; gene expression values were normalized based on library size as counts per million reads (CPM)
differential expression (DE) analysis was conducted using the Bioconductor package edgeR
principal component analysis (PCA) was conducted using a MATLAB toolbox SCell
Genome_build: mm10
Supplementary_files_format_and_content: text files of raw counts or CPM values for each sample

source_name: preoptic area neuron

extract_protocol:
glass pippette pick
Smart-seq2, Nextera XT

treatment_protocol: whole-cell patch-clamp recording prior to sample harvest

tag: strain

tag: age

value: 2-3 months

value: brain, hypothalamus

value: preoptic area neuron

tag: temperature sensitivity

value: unknown


title: preoptic area neuron_H7


title: control [Sample_95617]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: 2800 Plymouth Road

department: BRCF Bioinformatics Core

institute: University of Michigan

data_processing:
We downloaded the reads files from the Sequencing Core’s storage, and concatenated those into a single .fastq file for each sample.
We checked the quality of the raw reads data for each sample using FastQC (version 0.10.0) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).
We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads from the samples mm10 reference genome sequence using Tophat2 (version 2.0.13). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We used HTSeq (version 0.6.0) for expression quantitation, using respective reference genome sequence reference transcriptome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Pancreatic infiltrating myeloid cells

extract_protocol:
Cell lysates of FACS sorted cells were homogenized using QIAshredder, then total RNA samples were isolated using RNeasy Plus Micro Kit (Qiagen), including an on-column DNase treatment using RNase-Free DNase Set (Qiagen) according to manufacturer’s instruction.
RNA concentration and quality was determined and ribo depleted strand mRNA libraries were prepared by the University of Michigan Sequencing Core using SmartER-Pico kit. Libraries were multiplexed (7 per lane) and sequenced using paired end 50 cycle reads on a HiSeq 4000 (Illumina).

treatment_protocol: mice received DT for 3 weeks after 8 weeks’ recovery from 1- day caerulein treatment; pancreas tissues were harvested and digested for single cell suspension; pancreatic infiltrating myeloid cells were freshly sorted by FACS.

tag: group

value: control

tag: genotype/variation

value: KC


title: Treg depleted [Sample_95619]

value: Treg depleted


title: control [Sample_95616]


title: Treg depleted [Sample_95621]


title: preoptic area neuron_H10


title: preoptic area neuron_H4

value: warm-sensitive


title: preoptic area neuron_H9


title: preoptic area neuron_H6


title: preoptic area neuron_H8


title: preoptic area neuron_H3


title: control [Sample_95615]


title: Treg depleted [Sample_95622]


title: preoptic area neuron_H5


title: preoptic area neuron_G9

value: cold-sensitive


title: preoptic area neuron_G7

value: silent (temperature-insensitive)


title: preoptic area neuron_H2

value: temperature-insensitive


title: preoptic area neuron_H1


title: Treg depleted [Sample_95620]


title: preoptic area neuron_G11


title: preoptic area neuron_G8


title: preoptic area neuron_G10


title: preoptic area neuron_G6


title: preoptic area neuron_G12


title: NK-HD-1: NK cells from healthy donor, rep1

source_name: peripheral blood NK cells from healthy donor 1


title: NK-HD-2: NK cells from healthy donor, rep2


title: preoptic area neuron_G5


title: preoptic area neuron_F11


title: preoptic area neuron_F9


title: preoptic area neuron_F7


title: preoptic area neuron_F5


title: preoptic area neuron_F2


title: preoptic area neuron_H12


title: preoptic area neuron_E12


title: preoptic area neuron_F6


title: preoptic area neuron_G3


title: preoptic area neuron_G2


title: preoptic area neuron_G1

value: silent (temperature-sensitive)


title: preoptic area neuron_G4


title: preoptic area neuron_E10


title: preoptic area neuron_F3


title: preoptic area neuron_F8


title: preoptic area neuron_F12


title: preoptic area neuron_E9


title: preoptic area neuron_E8


title: preoptic area neuron_F1


title: preoptic area neuron_E5


title: preoptic area neuron_F4


title: preoptic area neuron_E4


title: preoptic area neuron_E7


title: preoptic area neuron_F10


title: preoptic area neuron_E2


title: preoptic area neuron_E11


title: preoptic area neuron_E3


title: preoptic area neuron_E6


title: preoptic area neuron_D9


title: preoptic area neuron_D12


title: preoptic area neuron_D10


title: preoptic area neuron_D8


title: preoptic area neuron_D11


title: preoptic area neuron_C11


title: preoptic area neuron_D2


title: preoptic area neuron_C9


title: preoptic area neuron_D4


title: preoptic area neuron_C10


title: preoptic area neuron_C4


title: preoptic area neuron_E1


title: preoptic area neuron_C6


title: preoptic area neuron_D7


title: preoptic area neuron_D3


title: preoptic area neuron_D5


title: preoptic area neuron_C12


title: preoptic area neuron_C1


title: preoptic area neuron_D1


title: preoptic area neuron_B10


title: preoptic area neuron_C2


title: preoptic area neuron_C8


title: preoptic area neuron_C7


title: preoptic area neuron_B12


title: preoptic area neuron_C5


title: preoptic area neuron_C3


title: preoptic area neuron_B9


title: preoptic area neuron_B11


title: preoptic area neuron_B7


title: preoptic area neuron_D6


title: preoptic area neuron_B5


title: preoptic area neuron_B4


title: preoptic area neuron_A11


title: preoptic area neuron_B8


title: preoptic area neuron_A9


title: NK-LC-8: NK cells from cirrhotic patients, rep8

source_name: peripheral blood NK cells from cirrhosis patients 8


title: preoptic area neuron_B1


title: preoptic area neuron_B6


title: preoptic area neuron_B3


title: preoptic area neuron_A4


title: preoptic area neuron_A2


title: preoptic area neuron_A12


title: preoptic area neuron_A8


title: preoptic area neuron_A7


title: preoptic area neuron_A3


title: L2V18DRBC15 invitro IL-33 stimulated ILC2s in absence of iBET151

city: Cambridge

first: Mayuri

last: Gogoi

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

institute: Laboratory of Molecular Biology

data_processing:
gene expression of iBET151 treated and untreated cells were compared
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: Blood

growth_protocol:
Purified human ILC2s were grown in media containing IL-2 and IL-7 (both at 10 ng/ml) with IL-33 (10 ng/ml) added to the cultures every alternate week.  ILC2s were then rested for 3 days in IL-2 and IL-7-containing media (no IL-33) before being divided and added to the following culture conditions: IL-2/IL-7, IL33 (all at 10 ng/ml) +/- iBET.
Lymphocytes were enriched from 150 ml human peripheral blood using lymphoprep (Axis-Shield) according to the manufacturer’s instructions. The collected PBMC fraction was washed with PBS/2% FCS followed by red blood cell lysis with ACK solution for 5 min at room temperature. To pre-enrich ILCs, cells were stained with biotinylated anti-CD3, CD14 and B220 in the presence of TruStain FcX (anti-CD16/CD32) followed by depletion with M280 streptavidin beads (Invitrogen). Subsequently, the enriched fraction was stained with CD45-AF488, CD127-PE-Cy7, CD117-PE, CRTH2-BV421, a lineage cocktail (APC-streptavidin, CD8a, CD11b, CD11c, FceRIa, CD123, CD20, CD56, CD71) and Draq7-viability dye, followed by sorting of ILCs as indicated on an Influx FACS. ILC2s designated as Draq7–(live cells)CD45+Lin–(streptavidin-APC, CD8a, CD11b, CD11c, FceRIa, CD123, CD20, CD56, CD71)CD127+CRTH2+ cells, were purified by flow cytometry from the peripheral blood of 3 individual donors and cultured separately s with IL-2, IL-7, and with  IL-33 (all at 10 ng/ml).

extract_protocol:
Cells from stimulation experiments were harvested by centrifugation, transferred to Trizol (Life Technologies) and stored at -80°C until further processing. RNA was extracted from the aqueous trizol/chloroform phase using the RNeasy Mini kit (Qiagen) followed by off-column DNA digestion using Turbo DNase (Ambion). DNA-free RNA was cleaned and concentrated using a RNeasy Micro Kit (Qiagen) and assessed using a Bioanalyser (Agilent). RNA was processed for RNA sequencing using Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220 and barcoded using Ovation Ultralow Library Systems (Nugen). Barcoded libraries were quantified using Qubit dsDNA BR assay (Invitrogen) and qPCR. Samples were sequenced using an Illumina Hiseq4000 (CRUK Cambridge Institute)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either treated with or without  250 nM iBET151

tag: culture conditions

value: In vitro


title: preoptic area neuron_A1


title: L2V18DRBC12 invitro IL-33 stimulated ILC2s in presence of iBET151

tag: ibet treatment

value: 125 nM iBET


title: L2V18DRBC16 invitro IL-33 stimulated ILC2s in presence of iBET151


title: L2V18DRBC06 invitro IL-33 stimulated ILC2s in presence of iBET151


title: L2V18DRBC10 invitro IL-33 stimulated ILC2s in absence of iBET151


title: L2V18DRBC04 invitro IL-33 stimulated ILC2s in absence of iBET151


title: preoptic area neuron_A6


title: preoptic area neuron_A5