title: 15_6


title: 15_58

status: Public on Feb 08 2019

type: SRA

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
All reads were aligned to the mouse (mm10) genome plus EGFP sequence using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl  (May 2014) and ERCC-spike in annotations.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

molecule: polyA RNA

organism: Mus musculus

source_name: single cell

extract_protocol:
Single cells have been extracted from tissue using Neuronal Tissue Dissociation Kit (Miltenyi Biotec) for embryonic and early postnatal stages. Papain Dissociation System (Worthington) was used for the adult mice. cDNA was generated from FACS sorted single cells using Smart-seq2 protocol (Picelli et al. Nature Methods 2013). For some of the samples, ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

tag: cell type

value: neuron

tag: genotype

value: Pitx3tm1Mli heterozygote

tag: age

value: embryonic day 15.5

tag: spike-in

value: no


title: 15_70


title: 15_54


title: Aug29_Cell_77

city: Cincinnati

first: Yael

last: Haberman

state: OH

address: 3333 Burnet Ave

department: Gastroenterology

country: USA

institute: Cincinnati Children's Hospital

data_processing:
Basecalling was performed with Illumina's bcl2fastq v2.15.0
Identifying information was removed from the fastqs with desnp v1.0 (manuscript in preparation)
kallisto v0.42.5 was used to quantify transcripts from two different models: Gencode v26 and the UCSC knownGenes table (Dec 2014).  Parameters: --bias
Genome_build: GRCh38
Supplementary_files_format_and_content: Abundance.tsv files from kallisto: tab-separated, containing abundance estimates in TPM

molecule: total RNA

organism: Homo sapiens

source_name: esophagus

extract_protocol:
Single cells were isolated on the Fluidigm C1 system using the 7-10 uM capture chip and manually examined to remove empty chambers and chambers with multiple cells
Libraries were constructed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 system (CloneTech)

tag: disease

value: Remission

tag: cell isolation batch

tag: cluster


title: Aug29_Cell_84


title: Aug29_Cell_73


title: Aug29_Cell_71


title: Aug29_Cell_74


title: 15_53


title: Aug29_Cell_72


title: 15_51


title: 15_5


title: Aug29_Cell_69


title: 15_45


title: 15_52


title: 15_42


title: 15_55


title: Aug29_Cell_64


title: 15_46


title: Aug29_Cell_66


title: 15_36


title: 15_43


title: 15_41


title: Aug29_Cell_67


title: Aug29_Cell_70


title: 15_33


title: Aug29_Cell_61


title: 15_59


title: Aug29_Cell_60


title: 15_27


title: Aug29_Cell_63


title: Aug29_Cell_59


title: Aug29_Cell_57


title: 15_35


title: 15_26


title: Aug29_Cell_65


title: Aug29_Cell_58


title: 15_25


title: Aug29_Cell_54


title: 15_29


title: Aug29_Cell_55


title: Aug29_Cell_56


title: 15_203


title: 15_22


title: 15_207


title: 15_208


title: 15_201


title: 15_202


title: Aug29_Cell_53


title: Aug29_Cell_52


title: 15_21


title: Aug29_Cell_68


title: Aug29_Cell_51


title: Apr4_Cell_53


title: Apr4_Cell_47


title: Apr4_Cell_52


title: 15_20


title: Apr4_Cell_51


title: Aug29_Cell_62


title: 15_198


title: 15_2


title: Apr11_Cell_95

value: ActiveEOE


title: Apr4_Cell_49


title: 15_199


title: Apr4_Cell_48


title: 15_190


title: Apr4_Cell_50


title: 15_189


title: 15_193


title: Apr11_Cell_94


title: Apr11_Cell_96


title: 15_206


title: Apr11_Cell_92


title: 15_197


title: 15_195


title: 15_187


title: 15_188


title: Apr11_Cell_91


title: Apr11_Cell_89


title: Apr11_Cell_9


title: Apr11_Cell_87


title: 15_183


title: Apr11_Cell_90


title: 15_182


title: 15_186


title: 15_185


title: 15_194


title: 15_184


title: 15_18


title: Apr11_Cell_84


title: Apr11_Cell_88


title: Apr11_Cell_93


title: Apr11_Cell_86


title: Apr11_Cell_85


title: 15_180


title: Apr11_Cell_82


title: Apr11_Cell_83


title: Apr11_Cell_81


title: 15_175


title: 15_181


title: 15_204


title: 15_174


title: 15_171


title: 15_168


title: Apr11_Cell_79


title: Apr11_Cell_80


title: 15_172


title: Apr11_Cell_8


title: Apr11_Cell_76


title: Apr11_Cell_78


title: Apr11_Cell_77


title: 15_167


title: 15_166


title: Apr11_Cell_74


title: 15_160


title: 15_164


title: 15_173


title: Apr11_Cell_73


title: 15_163


title: 15_165


title: Apr11_Cell_70


title: Apr11_Cell_7


title: 15_17


title: 15_158


title: 15_16


title: Apr11_Cell_68


title: 15_159


title: 15_157


title: Apr11_Cell_67


title: Apr11_Cell_75


title: 15_151


title: 15_156


title: 15_152


title: 15_150


title: Apr11_Cell_65


title: Apr11_Cell_66


title: Apr11_Cell_64


title: Apr11_Cell_72


title: 15_15


title: 15_149


title: Apr11_Cell_62


title: Apr11_Cell_63


title: Apr11_Cell_69


title: Apr11_Cell_61


title: 15_143


title: Apr11_Cell_60


title: 15_142


title: Apr11_Cell_6


title: Apr11_Cell_59


title: 15_147


title: 15_140


title: Apr11_Cell_57


title: 15_141


title: Apr11_Cell_56


title: 15_14


title: 15_139


title: 15_138


title: Apr11_Cell_58


title: Apr11_Cell_54


title: Apr11_Cell_55


title: 15_137


title: Apr11_Cell_5


title: 15_133


title: Apr11_Cell_34


title: Apr11_Cell_4


title: Apr11_Cell_71


title: 15_132


title: Apr11_Cell_32


title: 15_130


title: 15_131


title: 15_129


title: 15_125


title: Apr11_Cell_31


title: Apr11_Cell_29


title: 15_126


title: 15_123


title: Apr11_Cell_27


title: 15_124


title: Apr11_Cell_33


title: 15_134


title: 15_120


title: 15_122


title: Apr11_Cell_26


title: Apr11_Cell_24


title: Apr11_Cell_25


title: Apr11_Cell_30


title: 15_13


title: Apr11_Cell_22


title: Apr11_Cell_23


title: 15_118


title: Apr11_Cell_20


title: Apr11_Cell_21


title: Apr11_Cell_2


title: 15_115


title: 15_116


title: Apr11_Cell_3


title: Apr11_Cell_19


title: Apr11_Cell_28


title: 15_114


title: 15_112


title: Apr11_Cell_17


title: Apr11_Cell_18


title: Apr11_Cell_15


title: Apr11_Cell_14


title: 15_109


title: Apr11_Cell_16


title: 15_107


title: 15_119


title: 15_117


title: Apr11_Cell_12


title: 15_108


title: 13_99

value: embryonic day 13.5


title: 13_96


title: Apr11_Cell_10


title: Apr11_Cell_1


title: 13_97


title: 24_D7_inf_RMD

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
CASAVA
Sequenced reads were trimmed for adaptor sequence and filtered for low quality sequences, then mapped to hg38 whole genome using TopHat v2.0.13 with parameters --bowtie1 --transcriptome-index --no-coverage-search --library-type fr-firststrand
Read counts were calculated with HTSeq (htseq-count) using the following parameters:  --stranded=reverse.  Mapped files were counted against the Gencode v21 database with all level 3 annotations removed.
Data filtering was performed for both genes and ERCC spikes before differential expression analysis with EdgeR. Any gene which did not achieve 1 count per million in at least 4 samples or any ERCC that did not achieve at least 5 total reads in at least 4 samples was removed from further analysis. Data was upper quartile normalized and ERCC spikes were used in conjunction with the program RUVSeq to create a variable to remove unwanted technical variation. That variable was then used as a blocking factor in general linear modeling tests within EdgeR. Significance was determined at an FDR corrected p-value < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Comma separated files with all rows for host genes, ERCC spikes or HIV designation and columns for sample label.

source_name: CD4+ T-cell RNA extract

extract_protocol:
Total RNA was extracted from cell samples using the RNeasy Mini Kit (QIAGEN, Cat. No. 74104) with the addition of an on-column DNase treatment (RNase-free DNase Set, QIAGEN, Cat. No. 79254).
Paired end RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were plated at 500,000 cells per well in 200 ul of RPMI-1640 media containing 5% human serum on a 96-well tissue culture plate and either treated with SAHA (1uM), RMD (15 nM), or DMSO for a period of 24 hours.

tag: individual

value: donor 7

value: CD4+ T cell

tag: infection status

value: Model of HIV latency

tag: treatment

value: RMD


title: 13_95


title: 13_93


title: 15_110


title: 22_D7_inf_DMSO

value: DMSO


title: 13_92


title: 21_D7_uninf_RMD

value: Mock-infected


title: 23_D7_inf_SAHA

value: SAHA


title: 20_D7_uninf_SAHA


title: 13_91


title: 18_D4_inf_RMD

value: donor 4


title: 13_85


title: 17_D4_inf_SAHA


title: 13_84


title: 15_111


title: 15_1


title: 16_D4_inf_DMSO


title: 13_83


title: 13_81


title: 14_D4_uninf_SAHA


title: 13_D4_uninf_DMSO


title: 13_8


title: 13_94


title: 13_86


title: 15_D4_uninf_RMD


title: 13_77


title: 12_D2_inf_RMD

value: donor 2


title: 13_76


title: 19_D7_uninf_DMSO


title: 13_74


title: 10_D2_inf_DMSO


title: 8_D2_uninf_SAHA


title: 9_D2_uninf_RMD


title: 6_D1_inf_RMD

value: donor 1


title: 13_70

value: neuron


title: 13_73

value: Pitx3tm1Mli heterozygote


title: 5_D1_inf_SAHA


title: Apr11_Cell_13


title: 13_82


title: 13_68


title: 13_7


title: 13_69


title: 7_D2_uninf_DMSO


title: 3_D1_uninf_RMD


title: 2_D1_uninf_SAHA


title: 13_67


title: 4_D1_inf_DMSO


title: 13_66


title: 13_65


title: 1_D1_uninf_DMSO


title: 13_75


title: 13_62


title: 13_61


title: 19_9_11_p60_GiWi_d30_Lac

city: Madison

first: Timothy

last: Kamp

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

description: hPSC-derived cardiomyocytes

data_processing:
FASTQ ﬁles were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome (RefGene v1.2.3) using Bowtie (v0.12.8) (Langmead et al., 2009) allowing 2-mismatches and a maximum of 20 multiple hits. The gene expression values TPMs (Transcript per Million Reads) were calculated by RSEM (v1.2.3) (Li and Dewey, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: genes.tpm.tab (tab-delimited RSEM-generated Transcripts Per Million expression estimates)

source_name: iPS DF19-9-11T.H derived cardiomyocytes

growth_protocol: Human iPSC line DF19-9-11T, human primary adult ventricular cardiac fibroblasts (Lonza, NHCF-V) and primary dermal fibroblasts (hDFs) were used in the RNA-seq expermentation. hPSCs were cultured on Matrigel (GFR, BD Biosciences) coated 6-well plates in mTeSR1 medium (Stem Cell Technologies). hPSC-CMs were diferentiated using the GiWi protocol (Lian X. et al., Nat. Protoc 2013) and were purified in the lactate medium of RPMI without glucose plus B27 supplement (Gibco) and 5 mM Sodium DL-lactate (Sigma-Aldrich) for 10 days. hPSC-CFs at 20 days of differentiation were dissociated with 0.05% Trypsin-EDTA (Gibco) and plated in 6-well non-coding plastic plates at the density of 300,000 cells/well in 2ml of FibroGRO medium (Millipore EMD, SCMF001) plus 2% FBS (Gibco). The hPSC-CFs were fed every other day with FibroGRO+2% FBS medium and passaged every 4-6 days using 0.05% Trypsin-EDTA. The plating density for passaging hPSC-CFs was 5,800 cells/cm2 and the hPSC-CFs at passage 3-4 were used for RNA-seq. The human primary adult CFs (Lonza, NHCF-V) were thawed at passage 2 in FGM-3 medium (Lonza, CC-4526) in non-coding plastic T75 flasks at the plating density of 3,500 cells/cm2, and were passaged every 4-8 days using 0.05% Trypsin-EDTA, and the cells at passage 3-4 were used in RNA-seq. The primary hDFs (020a) were thawed at passage 5 in DMEM high glucose with GlutaMAX supplement (Gibco 10566-016) plus 10% FBS (Gibco 10437) in non-coding plastic T75 flasks at the plating density of 1,900 cells/cm2 and were passaged every 6-8 days using 0.05% Trypsin-EDTA, and the passage 8 cells were used in RNA-seq.

extract_protocol:
Cell samples were collected using 0.25% trypsin-EDTA (Invitrogen) to remove the cells from cell culture plates. Total RNA was purified using QIAGEN RNeasy® Mini kit. Possible genomic DNA contamination was removed by RNase-Free DNase Set (QIAGEN) with the RNeasy columns. Total RNA was qualified with the Life Technologies Qubit fluourometer (Q32857) and Agilent Bioanalyzer (G2940CA).
To prepare cDNA, the Ligation Mediated RNA sequencing library protocol was performed (Hou Z. et. al. Sci Rep 2015).  Briefly, mRNA was isolated from purified 100 ng total RNA using oligo-dT beads (NEB). Isolated mRNA was fragmented in reverse transcription buffer and reverse transcribed with SmartScribe reverse transcriptase (Clontech).   RNase A and RNase H treatments were then performed to remove RNA. The 5’ adapter was ligated to the cDNA using RNA ligase 1 (NEB) and purified using Ampure XP Beads (Beckman).  The cDNA was then amplified with 18 cycles of PCR.  The indexed cDNA libraries were normalized and pooled at thirty samples per lane and sequenced on an Illumina HiSeq 2500 with a single 51bp read and a 10bp index read.

tag: source, catalog, lot

value: iPS DF19-9-11T.H derived cardiomyocytes

value: hPSC-derived cardiomyocyte

tag: passages


title: 19_9_11_p46_cFib_p3___sample_3

description: hiPSC-derived cardaic fibroblasts

source_name: iPS DF19-9-11T.H derived cardaic fibroblasts

value: hPSC-derived cardaic fibroblast


title: 19_9_11_p70_GiWi_d30_Lac

description: hPSC-derived cardiomyocytes


title: 13_59

value: no


title: 19_9_11_p46_cFib_p3___sample_1

description: hiPSC-derived cardaic fibroblasts

value: iPS DF19-9-11T.H derived cardaic fibroblasts


title: 13_58

value: embryonic day 13.5


title: 13_57


title: 19_9_11_p52_stem_cell___sample_3

description: Human induced pluripotent stem cells (hiPSCs)

value: WiCell, iPS DF19-9-11T.H

value: Human pluripotent stem cell (hPSC)


title: 13_55


title: 13_53


title: 13_54


title: NHCF_V_27277_p4_sample_2

description: Human primary adult ventricular cardiac fibroblasts

source_name: Normal Human Ventricular Cardiac Fibroblasts, NHCF-V

value: Human primary cardiac fibroblst


title: 13_52


title: 13_56


title: 11_D2_inf_SAHA

value: CD4+ T cell

value: Model of HIV latency


title: 19_9_11_p52_stem_cell___sample_2


title: 13_5


title: 13_6


title: 13_51


title: Oct24_Cell_64

value: normal


title: Oct24_Cell_8


title: 13_48


title: Oct24_Cell_63


title: Oct24_Cell_62


title: NHCF_V_27277_p4_sample_3


title: 13_46


title: Oct24_Cell_61


title: 13_47


title: Oct24_Cell_7


title: 13_45


title: Oct24_Cell_60


title: 020a_p8_with_DMEM___sample_2

description: Human primary adult dermal fibroblasts

source_name: Human dermal fibroblasts

value: Healthy donor, 020a

value: Human primary dermal fibroblst


title: 13_43


title: Oct24_Cell_6


title: 020a_p8_with_DMEM___sample_1

description: Human primary adult dermal fibroblasts


title: 13_4


title: Oct24_Cell_58


title: 13_36


title: 13_37


title: Oct24_Cell_56


title: Oct24_Cell_57


title: 13_35


title: Oct24_Cell_55


title: Oct24_Cell_54


title: Oct24_Cell_53


title: 13_34


title: 13_33


title: 13_30


title: 13_28


title: Oct24_Cell_51


title: 13_3


title: Oct24_Cell_5


title: Oct24_Cell_50


title: Oct24_Cell_52


title: 13_29


title: Oct24_Cell_59


title: 13_26


title: Oct24_Cell_49


title: 13_38


title: 13_25


title: 13_23


title: Oct24_Cell_46


title: Oct24_Cell_44


title: Oct24_Cell_45


title: 13_202


title: 13_201


title: Oct24_Cell_9


title: Oct24_Cell_43


title: 13_198


title: 15_12

value: embryonic day 15.5


title: 13_27

value: neuron


title: 13_197

value: Pitx3tm1Mli heterozygote


title: 13_196


title: Oct24_Cell_39


title: Oct24_Cell_41


title: Oct24_Cell_4


title: 13_194


title: Oct24_Cell_40


title: Oct24_Cell_47


title: 13_20


title: 13_193


title: Oct24_Cell_37


title: Oct24_Cell_48


title: 13_22


title: Oct24_Cell_36


title: 13_19


title: Oct24_Cell_35


title: 13_190


title: Oct24_Cell_42


title: 13_186


title: Oct24_Cell_38


title: Oct24_Cell_34


title: Oct24_Cell_33


title: 13_188


title: 13_185


title: 13_195


title: Oct24_Cell_31


title: Oct24_Cell_32


title: 13_183


title: 13_182


title: 13_184


title: Oct24_Cell_3


title: Oct24_Cell_30


title: 13_181


title: Oct24_Cell_29


title: 13_173


title: Oct24_Cell_26


title: 13_172


title: 13_18


title: Oct24_Cell_24


title: Oct24_Cell_25


title: 13_170


title: Oct24_Cell_23


title: 13_169


title: 13_165


title: 13_166


title: Oct24_Cell_20


title: Oct24_Cell_21


title: Oct24_Cell_18


title: Oct24_Cell_19


title: 13_162


title: Oct24_Cell_2


title: Oct24_Cell_16


title: 13_164


title: 13_168


title: 13_161


title: 13_163


title: Oct24_Cell_27


title: Oct24_Cell_28


title: 13_180


title: 13_158


title: 13_171


title: Oct24_Cell_17


title: Oct24_Cell_13


title: Oct24_Cell_15


title: Oct24_Cell_12


title: 13_157


title: Oct24_Cell_22


title: Apr11_Cell_11

value: ActiveEOE


title: 13_156


title: 13_154


title: Oct24_Cell_10


title: Oct24_Cell_11


title: 13_155


title: 13_153


title: Oct24_Cell_14


title: Nov28_Cell_96


title: Nov28_Cell_95


title: 13_151


title: 13_15


title: 13_150


title: Oct24_Cell_1


title: Nov28_Cell_91


title: 13_147


title: 13_144


title: Nov28_Cell_9


title: 13_149


title: 13_148


title: 13_142


title: Nov28_Cell_88


title: Nov28_Cell_90


title: 13_16


title: 13_152


title: Nov28_Cell_92


title: Nov28_Cell_89


title: Nov28_Cell_87


title: 13_140


title: Nov28_Cell_94


title: Nov28_Cell_86


title: 13_141


title: 13_134


title: Nov28_Cell_84


title: Nov28_Cell_82


title: Nov28_Cell_93


title: 13_132


title: 13_137


title: Nov28_Cell_81


title: Nov28_Cell_85


title: 13_133


title: 13_131


title: Nov28_Cell_83


title: 13_130


title: Nov28_Cell_80


title: 13_143


title: 13_13


title: Nov28_Cell_79


title: 13_129


title: 13_120


title: Nov28_Cell_78


title: 13_127


title: Nov28_Cell_77


title: Nov28_Cell_75


title: Nov28_Cell_74


title: Nov28_Cell_76


title: 13_12


title: 13_117


title: 13_119


title: 13_116


title: Nov28_Cell_73


title: 13_115


title: 13_113


title: Nov28_Cell_70


title: Nov28_Cell_7


title: 13_111


title: Nov28_Cell_71


title: Nov28_Cell_68


title: 13_114


title: 13_110


title: Nov28_Cell_67


title: 13_112


title: Nov28_Cell_8


title: Nov28_Cell_69


title: Nov28_Cell_66


title: 13_109


title: 13_118


title: 13_108


title: Nov28_Cell_65


title: 13_11


title: 13_107


title: Nov28_Cell_64


title: 13_104


title: 13_103


title: 13_102


title: Nov28_Cell_62


title: Nov28_Cell_61


title: Nov28_Cell_6


title: Nov28_Cell_63


title: 13_100


title: Nov28_Cell_72


title: 13H_6_H9

value: Pitx3tm1Mli homozygote

value: ERCC


title: Nov28_Cell_59


title: 13H_6_H8


title: 13H_6_H7


title: Nov28_Cell_42


title: Nov28_Cell_40


title: Nov28_Cell_41


title: Nov28_Cell_5


title: 13H_6_H12


title: 13H_6_H11


title: 13H_6_H10


title: Nov28_Cell_39


title: Nov28_Cell_38


title: 13H_6_H2


title: Nov28_Cell_37


title: 13H_6_G8


title: 13H_6_G9


title: Nov28_Cell_60


title: 13H_6_H1


title: 13H_6_G3


title: 13H_6_G2


title: 13H_6_G12


title: Nov28_Cell_36


title: Nov28_Cell_33


title: 13H_6_G11


title: Nov28_Cell_30


title: Nov28_Cell_34


title: 13H_6_H3


title: Nov28_Cell_32


title: Nov28_Cell_3


title: Nov28_Cell_4


title: Nov28_Cell_31


title: 13H_6_G10


title: 13H_6_G1


title: Nov28_Cell_28


title: 13H_6_F8


title: 13H_6_F7


title: Nov28_Cell_29


title: Nov28_Cell_27


title: 13H_6_F3


title: Nov28_Cell_26


title: 13H_6_F9


title: 13H_6_F2


title: 13H_6_G7


title: 13H_6_F12


title: Nov28_Cell_23


title: Nov28_Cell_35


title: 13H_6_F1


title: 13H_6_F11


title: Nov28_Cell_24


title: Nov28_Cell_22


title: 13H_6_E9


title: Nov28_Cell_21


title: Nov28_Cell_2


title: Nov28_Cell_20


title: 13H_6_E7


title: 13H_6_F10


title: Nov28_Cell_18


title: Nov28_Cell_19


title: 13H_6_E8


title: Nov28_Cell_17


title: Nov28_Cell_25


title: 13H_6_E12


title: Nov28_Cell_16


title: Nov28_Cell_14


title: Nov28_Cell_12


title: Nov28_Cell_15


title: Nov28_Cell_13


title: 13H_6_D9


title: 13H_6_E10


title: 13H_6_D8


title: 13H_6_E11


title: 13H_6_E1


title: Nov28_Cell_10


title: 13H_6_D7


title: Nov28_Cell_11


title: 13H_6_D2


title: 13H_6_E2


title: 13H_6_D12


title: 13H_6_E3


title: 13H_6_D3


title: Nov14_Cell_57


title: 13H_6_D10


title: Nov14_Cell_54


title: Nov14_Cell_58


title: 13H_6_D11


title: 13H_6_D1


title: Nov14_Cell_56


title: Nov14_Cell_55


title: 13H_6_C9


title: Nov14_Cell_53


title: Nov14_Cell_52


title: 13H_6_C8


title: Nov14_Cell_51


title: 13H_6_C3


title: 13H_6_C7


title: 13H_6_C2


title: Nov14_Cell_49


title: Nov14_Cell_50


title: Nov28_Cell_1


title: Nov14_Cell_47


title: 13H_6_C11


title: Nov14_Cell_48


title: 13H_6_C10


title: Nov14_Cell_45


title: 13H_6_C1


title: 13H_6_B9


title: Nov14_Cell_43


title: Nov14_Cell_46


title: 13H_6_B8


title: Nov14_Cell_44


title: 13H_6_B7


title: 13H_6_B2


title: Nov14_Cell_40


title: Nov14_Cell_39


title: 13H_6_B3


title: Nov14_Cell_37


title: Nov14_Cell_41


title: 13H_6_B12


title: Nov14_Cell_36


title: 13H_6_B1


title: 13H_6_B11


title: 13H_6_A8


title: 13H_6_B10


title: Nov10_Cell_94


title: Nov10_Cell_95


title: 13H_6_A7


title: 13H_6_A3


title: Nov10_Cell_93


title: Nov10_Cell_96


title: Nov14_Cell_42


title: 13H_6_C12


title: 13H_6_A9


title: 13H_6_A11


title: 13H_6_A12


title: Nov10_Cell_91


title: 13H_6_A2


title: 13H_6_A10


title: Nov10_Cell_89


title: Nov10_Cell_9


title: Nov10_Cell_88


title: 13H_6_A1


title: Nov10_Cell_86


title: 13H_5_H6


title: 13H_5_H4


title: 13H_5_H5


title: Nov10_Cell_87


title: Nov10_Cell_85


title: 13H_5_G6


title: 13H_5_G5


title: Nov14_Cell_38


title: Nov10_Cell_84


title: Nov10_Cell_83


title: Nov10_Cell_82


title: 13H_5_F6


title: 13H_5_F4


title: Nov10_Cell_92


title: Nov10_Cell_80


title: 13H_5_F5


title: Nov10_Cell_81


title: Nov10_Cell_8


title: 13H_5_E5


title: Nov10_Cell_78


title: 13H_5_E4


title: Nov10_Cell_90


title: 13H_5_D6


title: Nov10_Cell_79


title: Nov10_Cell_76


title: 13H_5_D4


title: 13H_5_D5


title: 13H_5_C5


title: Nov10_Cell_75


title: 13H_5_G4


title: Nov10_Cell_74


title: Nov10_Cell_73


title: 13H_5_C4


title: Nov10_Cell_72


title: 13H_5_B6


title: Nov10_Cell_71


title: Nov10_Cell_7


title: 13H_5_B5


title: Nov10_Cell_69


title: 13H_5_E6


title: Nov10_Cell_77


title: 13H_5_B4


title: Nov10_Cell_65


title: Nov10_Cell_66


title: 13H_4_H9


title: 13H_5_A6


title: Nov10_Cell_6


title: Nov10_Cell_68


title: 13H_5_A5


title: 13H_5_C6


title: 13H_5_A4


title: 13H_4_H6


title: Nov10_Cell_67


title: 13H_4_H8


title: Nov10_Cell_70


title: Nov10_Cell_4


title: 13H_4_H3


title: 13H_4_H12


title: 13H_4_H2


title: Nov10_Cell_35


title: 13H_4_H5


title: 13H_4_H11


title: Nov10_Cell_32


title: Nov10_Cell_31


title: 13H_4_H10


title: Nov10_Cell_30


title: 13H_4_H7


title: Nov10_Cell_3


title: 13H_4_H1


title: Nov10_Cell_5


title: Nov10_Cell_34


title: 13H_4_G8


title: Nov10_Cell_27


title: Nov10_Cell_28


title: Nov10_Cell_29


title: 13H_4_H4


title: Nov10_Cell_33


title: Nov10_Cell_26


title: 13H_4_G5


title: Nov10_Cell_25


title: 13H_4_G4


title: 13H_4_G3


title: 13H_4_G6


title: Nov10_Cell_21


title: Nov10_Cell_22


title: 13H_4_G12


title: 13H_4_G2


title: Nov10_Cell_2


title: 13H_4_G9


title: Nov10_Cell_20


title: Nov10_Cell_19


title: 13H_4_G1


title: 13H_4_G11


title: Nov10_Cell_17


title: 13H_4_G7


title: Nov10_Cell_18


title: 13H_4_G10


title: 13H_4_F9


title: Nov10_Cell_24


title: 13H_4_F8


title: 13H_4_F6


title: Nov10_Cell_23


title: Nov10_Cell_15


title: Nov10_Cell_13


title: Nov10_Cell_14


title: Nov10_Cell_12


title: Nov10_Cell_11


title: 13H_4_F7


title: Nov10_Cell_10


title: Nov10_Cell_1


title: May2_Cell_94


title: 13H_4_F11


title: May2_Cell_92


title: 13H_4_F12


title: May2_Cell_93


title: 13H_4_F2


title: 13H_4_F1


title: 13H_4_F5


title: 13H_4_F4


title: 13H_4_F3


title: Nov10_Cell_16


title: May2_Cell_91


title: 13H_4_E8


title: 13H_4_F10


title: 13H_4_E9


title: May2_Cell_90


title: 13H_4_E7


title: May2_Cell_89


title: 13H_4_E6


title: May2_Cell_88


title: May2_Cell_86


title: 13H_4_E5


title: May2_Cell_87

value: Low Del


title: 13H_4_E3


title: 13H_4_E4


title: May2_Cell_85


title: 13H_4_E12


title: May2_Cell_83


title: 13H_4_E11


title: May2_Cell_81


title: 13H_4_D9


title: May2_Cell_82


title: May2_Cell_78


title: 13H_4_E10


title: May2_Cell_77


title: 13H_4_D7


title: 13H_4_E1


title: May2_Cell_79


title: May2_Cell_76


title: 13H_4_D6


title: May2_Cell_80


title: 13H_4_D8


title: May2_Cell_75


title: 13H_4_D4


title: May2_Cell_74


title: 13H_4_E2


title: May2_Cell_72


title: May2_Cell_84


title: 13H_4_D3


title: May2_Cell_71


title: May2_Cell_70


title: 13H_4_D12


title: 13H_4_D2


title: 13H_4_D11


title: May2_Cell_69


title: 13H_4_D10


title: 13H_4_D5


title: 13H_4_D1


title: 13H_4_C9


title: May2_Cell_67


title: 13H_4_C6


title: 13H_4_C8


title: 13H_4_C5


title: 13H_4_C7


title: May2_Cell_66


title: 13H_4_C3


title: May2_Cell_63


title: May2_Cell_65


title: May2_Cell_64


title: May2_Cell_62


title: 13H_4_C4


title: May2_Cell_61


title: May2_Cell_73


title: 13H_4_C12


title: May2_Cell_60


title: 13H_4_C2


title: May2_Cell_59


title: May2_Cell_58


title: 13H_4_C1


title: May2_Cell_57


title: May2_Cell_56


title: 13H_4_C11


title: 13H_4_B9


title: May2_Cell_55


title: May2_Cell_68


title: 13H_4_B8


title: 13H_4_B7


title: 13H_4_B6


title: May2_Cell_53


title: 13H_4_B5


title: 13H_4_B2


title: May2_Cell_49


title: 13H_4_B4


title: 13H_4_B3


title: May2_Cell_52


title: May2_Cell_50


title: 13H_4_B12


title: 13H_4_B11


title: May2_Cell_47


title: May2_Cell_48


title: May2_Cell_51


title: May2_Cell_46


title: May2_Cell_45


title: 13H_4_A9


title: 13H_4_C10


title: May2_Cell_44


title: May2_Cell_54


title: May2_Cell_42


title: 13H_4_B10


title: 13H_4_A8


title: May2_Cell_43


title: 13H_4_A4


title: 13H_4_A3


title: May2_Cell_38


title: May2_Cell_40


title: May2_Cell_37


title: May2_Cell_41


title: May2_Cell_39


title: May2_Cell_36


title: 13H_4_A11


title: 13H_4_A2


title: 13H_4_A10


title: 13H_4_A12


title: May2_Cell_35


title: May16_Cell_96


title: 13H_4_A7


title: May16_Cell_8


title: 32s:Salt:YPK3:YPD:Cocktail

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

data_processing:
bases called by Illumina software
aligned to sacCer3 from UCSC using STAR
reads normalized using DESeq2::vst in R
Genome_build: sacCer3
Supplementary_files_format_and_content: .tab files with counts per gene

organism: Saccharomyces cerevisiae

source_name: Bulk population

growth_protocol: From saturation dilution into exponential growth for 20 hours in 2ml deep well plates

extract_protocol: Illumina tru-seq

treatment_protocol: 1. add kinase inhibitor 2. wait 5 min 3. add stress perturbation 4. wait 20 min. 5. freeze in liquid nitrogen and extract mRNA

tag: strain background

tag: media

value: YPD

tag: stress

value: Salt

tag: perturbation

tag: kinase inhibitor

value: Cocktail


title: 32t:Tunicamycin:YPK3:YPD:Cocktail

value: Tunicamycin

value: 5 ug/ml


title: 32c:SDC:YPK3:SDC:None

value: SDC


title: 13H_4_A6

tag: cell type

value: embryonic day 13.5


title: May16_Cell_7


title: 32d:SDC:YPK3:SDC:Cocktail

tag: genotype


title: 32r:Rapamycin:YPK3:YPD:Cocktail

value: Rapamycin

value: 1 ug/ml


title: May16_Cell_6


title: 32yd:YPD:YPK3:YPD:Cocktail


title: May16_Cell_5


title: 32yc:YPD:YPK3:YPD:None


title: May16_Cell_44


title: 32h:Heatshock:YPK3:YPD:Cocktail

value: Heatshock

value: 39 Degrees


title: May16_Cell_43


title: 32g:Glucose_Dropout:YPK3:YPD:Cocktail

value: YPsorbitol (2.02%)


title: May16_Cell_95


title: May16_Cell_42


title: 32a:Azetidine:YPK3:YPD:Cocktail

value: Azetidine


title: May16_Cell_40

value: ActiveEOE


title: 31c:SDC:YPK1:SDC:None


title: 32f:Fluconazole:YPK3:YPD:Cocktail

value: Fluconazole

value: 250 ug/ml


title: May16_Cell_41


title: May16_Cell_39


title: 31t:Tunicamycin:YPK1:YPD:Cocktail


title: 13H_4_A5

value: neuron

value: Pitx3tm1Mli homozygote

tag: age

value: ERCC


title: May16_Cell_9


title: 31r:Rapamycin:YPK1:YPD:Cocktail

value: YPD

value: Cocktail


title: May16_Cell_38


title: 31m:Menadione:YPK1:YPD:Cocktail

value: Menadione


title: May16_Cell_35


title: May16_Cell_36


title: May16_Cell_37


title: 31yc:YPD:YPK1:YPD:None


title: 31yd:YPD:YPK1:YPD:Cocktail


title: May16_Cell_34


title: 31g:Glucose_Dropout:YPK1:YPD:Cocktail


title: May16_Cell_32


title: 31h:Heatshock:YPK1:YPD:Cocktail


title: May16_Cell_33


title: 31f:Fluconazole:YPK1:YPD:Cocktail


title: 31a:Azetidine:YPK1:YPD:Cocktail


title: 32m:Menadione:YPK3:YPD:Cocktail


title: May16_Cell_4


title: May16_Cell_30


title: 30d:SDC:YGK3:SDC:Cocktail

value: SDC


title: May16_Cell_31


title: 30t:Tunicamycin:YGK3:YPD:Cocktail

value: Tunicamycin

value: 5 ug/ml


title: 30c:SDC:YGK3:SDC:None


title: May16_Cell_28


title: May16_Cell_29


title: May16_Cell_3


title: 30yd:YPD:YGK3:YPD:Cocktail


title: 30r:Rapamycin:YGK3:YPD:Cocktail

value: Rapamycin

value: 1 ug/ml


title: 30s:Salt:YGK3:YPD:Cocktail

value: Salt


title: May16_Cell_26


title: May16_Cell_22


title: 30yc:YPD:YGK3:YPD:None


title: 30g:Glucose_Dropout:YGK3:YPD:Cocktail

value: YPsorbitol (2.02%)


title: May16_Cell_24


title: May16_Cell_25


title: 30h:Heatshock:YGK3:YPD:Cocktail

value: Heatshock

value: 39 Degrees


title: May16_Cell_23

value: ActiveEOE


title: 30m:Menadione:YGK3:YPD:Cocktail


title: May16_Cell_21


title: 30a:Azetidine:YGK3:YPD:Cocktail

value: Azetidine


title: May16_Cell_2


title: 30f:Fluconazole:YGK3:YPD:Cocktail

value: Fluconazole

value: 250 ug/ml


title: May16_Cell_20


title: May16_Cell_19


title: 29t:Tunicamycin:YAK1:YPD:Cocktail


title: May16_Cell_18


title: 29c:SDC:YAK1:SDC:None


title: 29s:Salt:YAK1:YPD:Cocktail


title: May16_Cell_17


title: May16_Cell_16


title: May16_Cell_15


title: May16_Cell_27


title: 29yd:YPD:YAK1:YPD:Cocktail


title: May16_Cell_14


title: May16_Cell_13


title: 29yc:YPD:YAK1:YPD:None


title: 29r:Rapamycin:YAK1:YPD:Cocktail


title: May16_Cell_12


title: 29g:Glucose_Dropout:YAK1:YPD:Cocktail


title: 29a:Azetidine:YAK1:YPD:Cocktail


title: 24c:SDC:TPK123:SDC:None


title: 29m:Menadione:YAK1:YPD:Cocktail


title: 24s:Salt:TPK123:YPD:Cocktail


title: 24t:Tunicamycin:TPK123:YPD:Cocktail


title: 24r:Rapamycin:TPK123:YPD:Cocktail


title: 24yd:YPD:TPK123:YPD:Cocktail


title: 24m:Menadione:TPK123:YPD:Cocktail


title: Mar27_x_x_161_Cell_94

value: normal


title: 24h:Heatshock:TPK123:YPD:Cocktail

value: YPD


title: May16_Cell_1


title: May16_Cell_10


title: May16_Cell_11


title: Mar27_x_x_161_Cell_95


title: Mar27_x_x_161_Cell_93


title: Mar27_x_x_161_Cell_90


title: Mar27_x_x_161_Cell_89


title: Mar27_x_x_161_Cell_92


title: 29f:Fluconazole:YAK1:YPD:Cocktail

value: Cocktail


title: Mar27_x_x_161_Cell_87


title: 24a:Azetidine:TPK123:YPD:Cocktail


title: 29h:Heatshock:YAK1:YPD:Cocktail


title: 23c:SDC:TOR2:SDC:None


title: Mar27_x_x_161_Cell_86


title: 23d:SDC:TOR2:SDC:Cocktail


title: 24f:Fluconazole:TPK123:YPD:Cocktail


title: Mar27_x_x_161_Cell_85


title: Mar27_x_x_161_Cell_83


title: Mar27_x_x_161_Cell_88


title: Mar27_x_x_161_Cell_84


title: 24yc:YPD:TPK123:YPD:None


title: Mar27_x_x_161_Cell_82


title: 23yd:YPD:TOR2:YPD:Cocktail


title: 23r:Rapamycin:TOR2:YPD:Cocktail


title: 23yc:YPD:TOR2:YPD:None


title: Mar27_x_x_161_Cell_91


title: 23m:Menadione:TOR2:YPD:Cocktail

value: Menadione


title: 23g:Glucose_Dropout:TOR2:YPD:Cocktail


title: 23a:Azetidine:TOR2:YPD:Cocktail


title: Mar27_x_x_161_Cell_79


title: Mar27_x_x_161_Cell_77


title: 23h:Heatshock:TOR2:YPD:Cocktail


title: Mar27_x_x_161_Cell_80


title: Mar27_x_x_161_Cell_78


title: Mar27_x_x_161_Cell_76


title: Mar27_x_x_161_Cell_75


title: 23t:Tunicamycin:TOR2:YPD:Cocktail


title: 22d:SDC:STE11:SDC:Cocktail

value: SDC


title: 22t:Tunicamycin:STE11:YPD:Cocktail

value: Tunicamycin


title: 22s:Salt:STE11:YPD:Cocktail


title: Mar27_x_x_161_Cell_74


title: Mar27_x_x_161_Cell_73


title: 22r:Rapamycin:STE11:YPD:Cocktail


title: Mar27_x_x_161_Cell_72


title: Mar27_x_x_161_Cell_71


title: 22yd:YPD:STE11:YPD:Cocktail


title: 22yc:YPD:STE11:YPD:None


title: 22m:Menadione:STE11:YPD:Cocktail


title: Mar27_x_x_161_Cell_69


title: Mar27_x_x_161_Cell_81


title: 23f:Fluconazole:TOR2:YPD:Cocktail


title: Mar27_x_x_161_Cell_70


title: 22c:SDC:STE11:SDC:None


title: Mar27_x_x_161_Cell_68


title: Mar27_x_x_161_Cell_96


title: Mar27_x_x_161_Cell_66


title: Mar27_x_x_161_Cell_64


title: 22f:Fluconazole:STE11:YPD:Cocktail


title: Mar27_x_x_161_Cell_65


title: 22h:Heatshock:STE11:YPD:Cocktail


title: 22g:Glucose_Dropout:STE11:YPD:Cocktail


title: Mar27_x_x_161_Cell_63


title: Mar27_x_x_160_Cell_9


title: Mar27_x_x_160_Cell_8


title: Mar27_x_x_160_Cell_7


title: 21yd:YPD:SSN3:YPD:Cocktail


title: 21t:Tunicamycin:SSN3:YPD:Cocktail

value: 5 ug/ml


title: 21d:SDC:SSN3:SDC:Cocktail


title: 21r:Rapamycin:SSN3:YPD:Cocktail

value: Rapamycin


title: Mar27_x_x_160_Cell_62


title: Mar27_x_x_160_Cell_61


title: 21yc:YPD:SSN3:YPD:None


title: Mar27_x_x_160_Cell_60


title: 21m:Menadione:SSN3:YPD:Cocktail


title: 21f:Fluconazole:SSN3:YPD:Cocktail


title: 22a:Azetidine:STE11:YPD:Cocktail


title: 21c:SDC:SSN3:SDC:None


title: Mar27_x_x_160_Cell_59


title: 21h:Heatshock:SSN3:YPD:Cocktail


title: Mar27_x_x_160_Cell_58


title: Mar27_x_x_160_Cell_56


title: 21a:Azetidine:SSN3:YPD:Cocktail


title: Mar27_x_x_160_Cell_55


title: 20c:SDC:SNF1:SDC:None


title: Mar27_x_x_160_Cell_57


title: 20t:Tunicamycin:SNF1:YPD:Cocktail


title: 20d:SDC:SNF1:SDC:Cocktail


title: 20s:Salt:SNF1:YPD:Cocktail


title: 21s:Salt:SSN3:YPD:Cocktail


title: Mar27_x_x_160_Cell_53


title: 20r:Rapamycin:SNF1:YPD:Cocktail

value: 1 ug/ml


title: 20yd:YPD:SNF1:YPD:Cocktail


title: 20m:Menadione:SNF1:YPD:Cocktail


title: Mar27_x_x_160_Cell_51


title: Mar27_x_x_160_Cell_52


title: Mar27_x_x_160_Cell_50


title: Mar27_x_x_160_Cell_6


title: 20yc:YPD:SNF1:YPD:None


title: 20h:Heatshock:SNF1:YPD:Cocktail


title: Mar27_x_x_160_Cell_49


title: 20g:Glucose_Dropout:SNF1:YPD:Cocktail


title: Mar27_x_x_160_Cell_48


title: Mar27_x_x_160_Cell_54


title: 20f:Fluconazole:SNF1:YPD:Cocktail


title: Mar27_x_x_161_Cell_67


title: 19c:SDC:SLT2:SDC:None


title: 20a:Azetidine:SNF1:YPD:Cocktail


title: Mar27_x_x_160_Cell_47


title: Mar27_x_x_160_Cell_45


title: Mar27_x_x_160_Cell_42


title: Mar27_x_x_160_Cell_46


title: 19d:SDC:SLT2:SDC:Cocktail


title: 19t:Tunicamycin:SLT2:YPD:Cocktail


title: 19yd:YPD:SLT2:YPD:Cocktail


title: Mar27_x_x_160_Cell_5


title: 19s:Salt:SLT2:YPD:Cocktail

value: Salt


title: Mar27_x_x_160_Cell_44


title: Mar27_x_x_160_Cell_4


title: 19r:Rapamycin:SLT2:YPD:Cocktail


title: Mar27_x_x_160_Cell_40


title: 19g:Glucose_Dropout:SLT2:YPD:Cocktail

value: YPsorbitol (2.02%)


title: 19m:Menadione:SLT2:YPD:Cocktail


title: 19f:Fluconazole:SLT2:YPD:Cocktail


title: 18c:SDC:SCH9:SDC:None


title: 19h:Heatshock:SLT2:YPD:Cocktail

value: Heatshock


title: Mar27_x_x_160_Cell_41


title: Mar27_x_x_160_Cell_34


title: Mar27_x_x_160_Cell_35


title: Mar27_x_x_160_Cell_33


title: 19a:Azetidine:SLT2:YPD:Cocktail


title: 18r:Rapamycin:SCH9:YPD:Cocktail


title: 18t:Tunicamycin:SCH9:YPD:Cocktail


title: 18yd:YPD:SCH9:YPD:Cocktail


title: Mar27_x_x_160_Cell_32


title: Mar27_x_x_160_Cell_31


title: Mar27_x_x_160_Cell_43


title: 19yc:YPD:SLT2:YPD:None


title: 18yc:YPD:SCH9:YPD:None


title: Mar27_x_x_160_Cell_3


title: 18m:Menadione:SCH9:YPD:Cocktail


title: 18h:Heatshock:SCH9:YPD:Cocktail

value: 39 Degrees


title: Mar27_x_x_160_Cell_29


title: Mar27_x_x_160_Cell_30


title: Mar27_x_x_160_Cell_36


title: Mar27_x_x_160_Cell_28


title: 18a:Azetidine:SCH9:YPD:Cocktail


title: 17d:SDC:RIM15:SDC:Cocktail


title: 18f:Fluconazole:SCH9:YPD:Cocktail


title: Mar27_x_x_160_Cell_39


title: Mar27_x_x_160_Cell_26


title: Mar27_x_x_160_Cell_25


title: 17t:Tunicamycin:RIM15:YPD:Cocktail


title: 17s:Salt:RIM15:YPD:Cocktail


title: Mar27_x_x_160_Cell_23


title: 17r:Rapamycin:RIM15:YPD:Cocktail


title: Mar27_x_x_160_Cell_24


title: 17yd:YPD:RIM15:YPD:Cocktail


title: Mar27_x_x_160_Cell_22


title: 17yc:YPD:RIM15:YPD:None


title: Mar27_x_x_160_Cell_2


title: 17h:Heatshock:RIM15:YPD:Cocktail


title: 17m:Menadione:RIM15:YPD:Cocktail


title: Mar27_x_x_160_Cell_20


title: Mar27_x_x_160_Cell_21


title: Mar27_x_x_160_Cell_19


title: 17g:Glucose_Dropout:RIM15:YPD:Cocktail


title: 17f:Fluconazole:RIM15:YPD:Cocktail


title: Mar27_x_x_160_Cell_18


title: Mar27_x_x_160_Cell_17


title: Mar27_x_x_160_Cell_27


title: Mar27_x_x_160_Cell_15


title: 17a:Azetidine:RIM15:YPD:Cocktail


title: 16c:SDC:RIM11:SDC:None


title: Mar27_x_x_160_Cell_16


title: 16s:Salt:RIM11:YPD:Cocktail


title: Mar27_x_x_160_Cell_13


title: Mar27_x_x_160_Cell_12


title: 16yc:YPD:RIM11:YPD:None


title: Mar27_x_x_160_Cell_37


title: 16r:Rapamycin:RIM11:YPD:Cocktail


title: 16yd:YPD:RIM11:YPD:Cocktail


title: Mar27_x_x_160_Cell_10


title: 16m:Menadione:RIM11:YPD:Cocktail


title: 16h:Heatshock:RIM11:YPD:Cocktail


title: 16g:Glucose_Dropout:RIM11:YPD:Cocktail


title: 16f:Fluconazole:RIM11:YPD:Cocktail


title: 16a:Azetidine:RIM11:YPD:Cocktail


title: 17c:SDC:RIM15:SDC:None


title: Mar21_Cell_44

value: ActiveEOE


title: Mar21_Cell_46


title: 16t:Tunicamycin:RIM11:YPD:Cocktail


title: Mar21_Cell_45


title: Mar21_Cell_43


title: Mar27_x_x_160_Cell_14


title: 15t:Tunicamycin:PKC1:YPD:Cocktail


title: 15c:SDC:PKC1:SDC:None


title: 15s:Salt:PKC1:YPD:Cocktail


title: 15r:Rapamycin:PKC1:YPD:Cocktail


title: Mar21_Cell_41


title: Mar21_Cell_42


title: 15yc:YPD:PKC1:YPD:None


title: Mar21_Cell_39


title: 15m:Menadione:PKC1:YPD:Cocktail


title: Mar27_x_x_160_Cell_1


title: Mar21_Cell_37


title: Mar21_Cell_38


title: Mar27_x_x_160_Cell_11


title: Mar21_Cell_36


title: 15h:Heatshock:PKC1:YPD:Cocktail


title: Mar21_Cell_35


title: Mar21_Cell_34


title: Mar21_Cell_40


title: 15g:Glucose_Dropout:PKC1:YPD:Cocktail


title: Mar21_Cell_33


title: Mar21_Cell_32


title: Mar21_Cell_31


title: 15a:Azetidine:PKC1:YPD:Cocktail

value: Azetidine


title: Mar21_Cell_28


title: Mar21_Cell_30


title: 14s:Salt:PHO85:YPD:Cocktail


title: 14c:SDC:PHO85:SDC:None


title: Mar21_Cell_27


title: 14yd:YPD:PHO85:YPD:Cocktail


title: Mar21_Cell_29


title: 14r:Rapamycin:PHO85:YPD:Cocktail


title: 14t:Tunicamycin:PHO85:YPD:Cocktail


title: 15yd:YPD:PKC1:YPD:Cocktail


title: Mar21_Cell_26


title: Mar21_Cell_24


title: 14m:Menadione:PHO85:YPD:Cocktail


title: Mar21_Cell_25


title: Mar21_Cell_23


title: 15f:Fluconazole:PKC1:YPD:Cocktail

value: Fluconazole


title: 14h:Heatshock:PHO85:YPD:Cocktail


title: Mar27_x_x_160_Cell_38


title: Mar21_Cell_22


title: 14f:Fluconazole:PHO85:YPD:Cocktail

value: 250 ug/ml


title: 14a:Azetidine:PHO85:YPD:Cocktail


title: Mar21_Cell_21


title: 14d:SDC:PHO85:SDC:Cocktail


title: 13d:SDC:PBS2:SDC:Cocktail


title: 13c:SDC:PBS2:SDC:None


title: Mar13_Cell_96


title: 13t:Tunicamycin:PBS2:YPD:Cocktail


title: Mar13_Cell_95


title: 13s:Salt:PBS2:YPD:Cocktail


title: 13r:Rapamycin:PBS2:YPD:Cocktail


title: Mar13_Cell_94


title: Mar13_Cell_93

value: Low Del


title: Mar13_Cell_92


title: 13m:Menadione:PBS2:YPD:Cocktail

value: YPD


title: 14yc:YPD:PHO85:YPD:None


title: Mar13_Cell_90


title: 13h:Heatshock:PBS2:YPD:Cocktail

value: Cocktail


title: 13yd:YPD:PBS2:YPD:Cocktail


title: 13yc:YPD:PBS2:YPD:None


title: Mar13_Cell_88


title: 13g:Glucose_Dropout:PBS2:YPD:Cocktail


title: Mar13_Cell_89


title: 13f:Fluconazole:PBS2:YPD:Cocktail


title: Mar13_Cell_86


title: Mar13_Cell_87


title: Mar13_Cell_85


title: 12d:SDC:MRK1:SDC:Cocktail


title: Mar13_Cell_84


title: 13a:Azetidine:PBS2:YPD:Cocktail


title: Mar13_Cell_82


title: Mar13_Cell_83


title: Mar13_Cell_91


title: 12t:Tunicamycin:MRK1:YPD:Cocktail


title: Mar13_Cell_81


title: 12yd:YPD:MRK1:YPD:Cocktail


title: 12s:Salt:MRK1:YPD:Cocktail


title: Mar13_Cell_80


title: 12f:Fluconazole:MRK1:YPD:Cocktail


title: 12h:Heatshock:MRK1:YPD:Cocktail


title: 12r:Rapamycin:MRK1:YPD:Cocktail


title: Mar13_Cell_79


title: Mar13_Cell_76


title: Mar13_Cell_77


title: 12a:Azetidine:MRK1:YPD:Cocktail


title: 12m:Menadione:MRK1:YPD:Cocktail

value: Menadione


title: 12yc:YPD:MRK1:YPD:None


title: Mar13_Cell_75


title: 11t:Tunicamycin:KSS1:YPD:Cocktail


title: Mar13_Cell_73


title: 11s:Salt:KSS1:YPD:Cocktail


title: 11d:SDC:KSS1:SDC:Cocktail

value: SDC


title: Mar13_Cell_72


title: 11r:Rapamycin:KSS1:YPD:Cocktail


title: 11yd:YPD:KSS1:YPD:Cocktail


title: Mar13_Cell_71


title: Mar13_Cell_70


title: 11m:Menadione:KSS1:YPD:Cocktail


title: Mar13_Cell_69


title: Mar13_Cell_68


title: 11f:Fluconazole:KSS1:YPD:Cocktail


title: Mar13_Cell_66


title: Mar13_Cell_67


title: 10t:Tunicamycin:KSP1:YPD:Cocktail

value: Tunicamycin


title: 11a:Azetidine:KSS1:YPD:Cocktail


title: 10s:Salt:KSP1:YPD:Cocktail


title: 11g:Glucose_Dropout:KSS1:YPD:Cocktail


title: 10c:SDC:KSP1:SDC:None


title: Mar13_Cell_74


title: Mar13_Cell_65


title: Mar13_Cell_60


title: 10yc:YPD:KSP1:YPD:None


title: 10yd:YPD:KSP1:YPD:Cocktail


title: 10m:Menadione:KSP1:YPD:Cocktail


title: Mar13_Cell_64


title: Mar13_Cell_58


title: 10g:Glucose_Dropout:KSP1:YPD:Cocktail


title: Mar13_Cell_59


title: Mar13_Cell_55


title: Mar13_Cell_57


title: Mar13_Cell_56


title: 11h:Heatshock:KSS1:YPD:Cocktail


title: 10h:Heatshock:KSP1:YPD:Cocktail


title: 9d:SDC:KIN1:SDC:Cocktail


title: 10a:Azetidine:KSP1:YPD:Cocktail


title: Mar13_Cell_63


title: 10f:Fluconazole:KSP1:YPD:Cocktail


title: Mar13_Cell_78


title: Mar13_Cell_54


title: Mar13_Cell_53


title: 10r:Rapamycin:KSP1:YPD:Cocktail


title: Jun6_Cell_94


title: 9c:SDC:KIN1:SDC:None


title: 9r:Rapamycin:KIN1:YPD:Cocktail


title: 9yd:YPD:KIN1:YPD:Cocktail


title: Jun6_Cell_93


title: Mar13_Cell_52


title: Jun6_Cell_96


title: Jun6_Cell_91


title: Jun6_Cell_95


title: 9yc:YPD:KIN1:YPD:None


title: Jun6_Cell_90


title: 9f:Fluconazole:KIN1:YPD:Cocktail


title: Mar13_Cell_61


title: Jun6_Cell_88


title: 9m:Menadione:KIN1:YPD:Cocktail


title: 9t:Tunicamycin:KIN1:YPD:Cocktail

value: 5 ug/ml


title: Jun6_Cell_86


title: 8t:Tunicamycin:IRE1:YPD:Cocktail


title: Jun6_Cell_87


title: 8s:Salt:IRE1:YPD:Cocktail


title: 8r:Rapamycin:IRE1:YPD:Cocktail

value: Rapamycin


title: Jun6_Cell_84


title: 9a:Azetidine:KIN1:YPD:Cocktail


title: 8yd:YPD:IRE1:YPD:Cocktail


title: Jun6_Cell_85


title: Jun6_Cell_92


title: Jun6_Cell_83


title: 8yc:YPD:IRE1:YPD:None


title: Jun6_Cell_82


title: 9h:Heatshock:KIN1:YPD:Cocktail


title: Jun6_Cell_89


title: 9g:Glucose_Dropout:KIN1:YPD:Cocktail


title: Jun6_Cell_80


title: Jun6_Cell_81


title: 8f:Fluconazole:IRE1:YPD:Cocktail


title: 8g:Glucose_Dropout:IRE1:YPD:Cocktail


title: 8h:Heatshock:IRE1:YPD:Cocktail


title: 8m:Menadione:IRE1:YPD:Cocktail


title: 8a:Azetidine:IRE1:YPD:Cocktail


title: Jun6_Cell_78


title: HTB.R342W.3

city: St. Louis

first: Govindaswamy

last: Chinnadurai

state: MO

address: 1100 South Grand Blvd

department: Molecular Microbiology and Immunology

institute: Saint Louis University

data_processing:
Sequencing was performed on an Ion Torrent Proton.
Reads were aligned to the hg19 human genome sequence using the TMAP aligner map4 algorithm. Soft-clipping at both 5’ and 3’ ends of the reads was permitted during alignment with a minimum seed length of 20 nt.
The nucleotide coverage for all non-redundant exons was calculated and normalized to total exon coverage using custom scripts in R. Expression values are total normalized nucleotide exon coverage per gene.
Fold changes in gene expression, p values and q values were calculated using custom R scripts and Microsoft Excel. Expressed genes were defined as those with at least 900 nucleotides of average normalized coverage in at least one of the four groups or a p value less than or equal to 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet of average nucleotide exon coverage per expressed gene in each group with fold change in expression and statistics

source_name: HTB17_mutant R342W

growth_protocol: HTB17 cells overexpressing wt CtBP1 or R342W were grown in 150 mm dishes in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
The cells were washed with PBS and RNA was isolated using TRIzol reagent (Invitrogen).
Ribosomal RNA was depleted from total RNA and libraries were constructed using the Eukaryotic RiboMinus and Ion Total RNA-seq v2 kits (Life Technologies, Thermofisher) according to the manufacturer’s directions.

tag: cell line

value: glioblastoma cell line

tag: genotype/variation

value: mutant R342W


title: 7c:SDC:HOG1:SDC:None


title: Jun6_Cell_77

tag: disease

tag: cell isolation batch


title: 7d:SDC:HOG1:SDC:Cocktail


title: HTB.R342W.1


title: HTB.R342W.2


title: 7t:Tunicamycin:HOG1:YPD:Cocktail


title: 7r:Rapamycin:HOG1:YPD:Cocktail

value: 1 ug/ml


title: Jun6_Cell_76

tag: cluster


title: 7s:Salt:HOG1:YPD:Cocktail

value: Salt


title: Jun6_Cell_79


title: HTB.CtBP.3

description: CtBP.ave

source_name: HTB17_wild type CtBP

value: wild type CtBP


title: 7yc:YPD:HOG1:YPD:None


title: Jun6_Cell_75

value: ActiveEOE


title: 7yd:YPD:HOG1:YPD:Cocktail


title: 7m:Menadione:HOG1:YPD:Cocktail


title: HTB.CtBP.2

description: CtBP.ave


title: Jun6_Cell_74


title: HTB.CtBP.1

description: CtBP.ave


title: 7h:Heatshock:HOG1:YPD:Cocktail

value: Heatshock

value: 39 Degrees


title: 7f:Fluconazole:HOG1:YPD:Cocktail

value: Fluconazole

value: 250 ug/ml


title: Jun6_Cell_73


title: Jun6_Cell_72


title: 6d:SDC:FUS3:SDC:Cocktail


title: Jun6_Cell_71


title: 6s:Salt:FUS3:YPD:Cocktail

value: YPD


title: 6t:Tunicamycin:FUS3:YPD:Cocktail

value: Cocktail


title: 6r:Rapamycin:FUS3:YPD:Cocktail


title: 6yd:YPD:FUS3:YPD:Cocktail


title: 6yc:YPD:FUS3:YPD:None


title: Jun6_Cell_68


title: 7g:Glucose_Dropout:HOG1:YPD:Cocktail

value: YPsorbitol (2.02%)


title: 6f:Fluconazole:FUS3:YPD:Cocktail


title: Jun6_Cell_67


title: 5d:SDC:CTK1:SDC:Cocktail

value: SDC


title: Jun6_Cell_70


title: 7a:Azetidine:HOG1:YPD:Cocktail

value: Azetidine


title: 5c:SDC:CTK1:SDC:None


title: 6g:Glucose_Dropout:FUS3:YPD:Cocktail


title: 5t:Tunicamycin:CTK1:YPD:Cocktail

value: Tunicamycin

value: 5 ug/ml


title: Jun6_Cell_65


title: 6m:Menadione:FUS3:YPD:Cocktail

value: Menadione


title: 5s:Salt:CTK1:YPD:Cocktail


title: 6h:Heatshock:FUS3:YPD:Cocktail


title: 5r:Rapamycin:CTK1:YPD:Cocktail

value: Rapamycin


title: Jagged1 treated hPDLs cells 4

type: RNA

city: BANGKOK

first: KANOKPORN

last: HANSAMUIT

address: HENRY DUNANT

country: Thailand

institute: CHULALONGKORN UNIVERSITY

description: Gene expression data from Jagged1 treated hPDLs cells from sample 4

hyb_protocol: Ten μg of target was added on the gene chip array. Hybridization was performed for 16 h at 45 ̊C.

scan_protocol: Scanning was done after hybridization with the laser set to 635 nm at fixed PMT setting and 10 mm. resolution.

data_processing: Relative performance of related samples was examined using Expression console and transcriptome analysis console (TAC) software.

label: Biotin

source_name: Jagged1 treated hPDLs cells

label_protocol: Genechip one-cycle target labeling (Affymatrix Inc., Santa Clara, CA, USA) was used for RNA array hybridization. Five g of RNA was converted to cDNA and then purified by phenol-chloroform-isoamylalcohol and ethanol precipitation. RNA target was quantified by absorbance at 260 nmafter labeling.

growth_protocol: Cell explant was performed for cell isolation protocol. The isolated cells were maintained in Dulbecco’s Modified Eagle’s Medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine (Invitrogen, Carlsbad, CA, USA), 100 Units/ml Penicillin (Invitrogen), 100 μg/ml Streptomycin (Invitrogen), and 5 μg/ml Amphotericin B (Invitrogen) (normal growth media) at 37°C in a humidified 5% CO2 atmosphere. Culture medium was changed every

extract_protocol: Total RNA was collected using RNeasy kit (Qiagen, USA).

treatment_protocol: Notch ligand, Jagged1 (R&D systems, USA), was indirectly immobilized on 24 well plate according to previous publications (Osathanon T, 2013). Briefly, tissue culture surfaces were incubated with recombinant protein G at concentration of 50 g/mL for 16 h. After washing, surfaces were then incubated with bovine serum albumin (10 mg/mL) for 2 h and Jagged1/Fc (10 nM) for 2 h, respectively. Human IgG Fc fragment was employed in the control condition.

tag: tissue

value: periodontal ligament cells


title: Jagged1 treated hPDLs cells 2

description: Gene expression data from Jagged1 treated hPDLs cells from sample 2

tag: treatment

value: bovine serum albumin (10 mg/mL) for 2 h and Jagged1/Fc (10 nM) for 2 h


title: hPDLs cells control 4

description: Gene expression data from hPDLs cells from sample 4 (control4)

source_name: hPDLs cells from

value: Human IgG Fc fragment


title: Jagged1 treated hPDLs cells 5

description: Gene expression data from Jagged1 treated hPDLs cells from sample 5


title: Jagged1 treated hPDLs cells 1

description: Gene expression data from Jagged1 treated hPDLs cells from sample 1


title: hPDLs cells control 5

description: Gene expression data from hPDLs cells from sample 5 (control5)

source_name: hPDLs cells


title: hPDLs cells control 3

description: Gene expression data from hPDLs cells from sample 3 (control3)


title: Jagged1 treated hPDLs cells 3

description: Gene expression data from Jagged1 treated hPDLs cells from sample 3


title: Jun6_Cell_69

value: ActiveEOE


title: 6a:Azetidine:FUS3:YPD:Cocktail


title: Jun6_Cell_64


title: 5m:Menadione:CTK1:YPD:Cocktail


title: Jun6_Cell_66


title: 5yc:YPD:CTK1:YPD:None


title: Jun6_Cell_63


title: 5h:Heatshock:CTK1:YPD:Cocktail

value: Heatshock


title: 5g:Glucose_Dropout:CTK1:YPD:Cocktail


title: hPDLs cells control 2

description: Gene expression data from hPDLs cells from sample 2 (control2)


title: Jun6_Cell_62


title: 5f:Fluconazole:CTK1:YPD:Cocktail


title: Jun6_Cell_61


title: pp4r3a-2_rep1_sRNA

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

country: China

institute: Fudan University

data_processing:
Base-calling was performed by Bioinformatic core @UCR
Raw reads were trimmed by cutadapt 1.9 using defaut parameters, and size-selected for 18-42 nt reads
Trimmed reads were mapped to the Arabidopsis genome using ShortStack v3.4 with parameters "--ranmax 50 --bowtie_m 1000"
Mapped reads were counted by a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools/)
Genome_build: Araport11
Supplementary_files_format_and_content: WIG files containing raw read coveage in RPM aross the genome

organism: Arabidopsis thaliana

growth_protocol: 12-day-old seedlings grown on ½ Murashige and Skoog (MS) plates under 16h light/8h dark cycle

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
To isolate small RNAs from total RNA, 50 µg of total RNA from each sample was resolved on 15% urea-PAGE gel, and the 18–30-nt region was excised from the gel. Small RNAs were recovered by soaking the smashed gel in 0.3M NaCl overnight, followed by ethanol precipitation. Small RNA libraries were constructed following instructions from the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (E7300)

tag: ecotype background

value: 12-day-old seedlings


title: pp4r3a-2_rep2_sRNA


title: pp4r3a-2_rep3_sRNA


title: hPDLs cells control 1

description: Gene expression data from hPDLs cells from sample 1 (control1)


title: 3d:SDC:CDC7:SDC:Cocktail


title: 3t:Tunicamycin:CDC7:YPD:Cocktail


title: Jun6_Cell_60


title: pp4r3a-1_rep2_sRNA


title: 3r:Rapamycin:CDC7:YPD:Cocktail

value: 1 ug/ml


title: pp4r3a-1_rep1_sRNA


title: pp4r3a-1_rep3_sRNA


title: 3c:SDC:CDC7:SDC:None


title: 3yc:YPD:CDC7:YPD:None


title: Jun6_Cell_59


title: Col0_rep3_sRNA

source_name: wild type_seedling

value: wild type


title: 3m:Menadione:CDC7:YPD:Cocktail

value: YPD


title: Col0_rep2_sRNA


title: 3yd:YPD:CDC7:YPD:Cocktail

value: Cocktail


title: 3s:Salt:CDC7:YPD:Cocktail

value: Salt


title: 3h:Heatshock:CDC7:YPD:Cocktail

value: 39 Degrees


title: 3g:Glucose_Dropout:CDC7:YPD:Cocktail

value: YPsorbitol (2.02%)


title: Jun6_Cell_57


title: Jun6_Cell_56


title: 3f:Fluconazole:CDC7:YPD:Cocktail

value: Fluconazole

value: 250 ug/ml


title: 5a:Azetidine:CTK1:YPD:Cocktail

value: Azetidine


title: 10d:SDC:KSP1:SDC:Cocktail

value: SDC


title: Col0_rep1_sRNA


title: Mar13_Cell_62


title: 2d:SDC:CDC5:SDC:Cocktail


title: 3a:Azetidine:CDC7:YPD:Cocktail


title: Jun6_Cell_55


title: Jun6_Cell_54


title: Jun6_Cell_58


title: 2t:Tunicamycin:CDC5:YPD:Cocktail

value: Tunicamycin

value: 5 ug/ml


title: 2r:Rapamycin:CDC5:YPD:Cocktail

value: Rapamycin


title: Jun6_Cell_52

value: ActiveEOE


title: 2yc:YPD:CDC5:YPD:None


title: 2m:Menadione:CDC5:YPD:Cocktail

value: Menadione


title: pp4r3a-2_rep2_RNA

data_processing:
Base-calling was performed by Bioinformatic core @UCR
Quality-filtered raw reads were mapped to the Araport11 genome using STAR, with parameters "--outSAMmultNmax 1   --outFilterMultimapNmax 50   --outFilterMismatchNoverLmax 0.1   --alignIntronMax 5000"
Mapped reads were counted by a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools/)
Genome_build: Araport11
Supplementary_files_format_and_content: Tab-deliminated txt containing raw read counts from exon and intron for each gene

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies, USA, 15596018)
Polyadenylated RNA was isolated from total RNA extracted from 12-day-old seedlings using the Magnetic mRNA Isolation Kit (New England Biolabs). RNA-seq libraries were prepared using NEBNext® mRNA Library Prep Reagent Set for Illumina (New England Biolabs)

value: 12-day-old seedlings


title: pp4r3a-2_rep1_RNA


title: 2a:Azetidine:CDC5:YPD:Cocktail


title: pp4r3a-1_rep2_RNA


title: Jun6_Cell_51


title: 4c:SDC:CDC15:SDC:None


title: pp4r3a-2_rep3_RNA


title: Jun6_Cell_48


title: 4t:Tunicamycin:CDC15:YPD:Cocktail


title: 2s:Salt:CDC5:YPD:Cocktail


title: 4s:Salt:CDC15:YPD:Cocktail


title: pp4r3a-1_rep1_RNA


title: Col0_rep3_RNA


title: pp4r3a-1_rep3_RNA


title: Jun6_Cell_47


title: Jun6_Cell_49


title: 4r:Rapamycin:CDC15:YPD:Cocktail

value: 1 ug/ml


title: 2yd:YPD:CDC5:YPD:Cocktail


title: Jun6_Cell_53


title: 2h:Heatshock:CDC5:YPD:Cocktail

value: Heatshock


title: Col0_rep2_RNA

value: wild type


title: 4yc:YPD:CDC15:YPD:None

value: YPD


title: 4m:Menadione:CDC15:YPD:Cocktail

value: Cocktail


title: 2f:Fluconazole:CDC5:YPD:Cocktail


title: 4g:Glucose_Dropout:CDC15:YPD:Cocktail


title: Jan30_Cell_75

value: Remission


title: 4f:Fluconazole:CDC15:YPD:Cocktail


title: sci-ATAC-seq

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
scitools align: hg19 default parameters
scitools callpeak: (macs2 - default parameters)
scitools count
scitools tfidf then scitools LSI
scitools tsne
Genome_build: GRCh37
Supplementary_files_format_and_content: counts matrix

source_name: HCC1143 TNBC Cell Line

extract_protocol:
Nuclei isolation using NIB (PMC6145927)
single-cell combinatorial indexing ATAC-seq (PMC6145927)

treatment_protocol: Treatment for 72 hours with MEK, PI3K, BET, combination, or vehicle (DMSO) (PMC6145927)

value: MEK (72h, 1 uM trametinib), PI3K (72h, 1 uM BEZ235), BET (72h, 1 uM JQ1), or DMSO (72h)


title: 1c:SDC:ATG1:SDC:None


title: 4h:Heatshock:CDC15:YPD:Cocktail

value: 39 Degrees


title: 4a:Azetidine:CDC15:YPD:Cocktail


title: Jan30_Cell_74


title: 1t:Tunicamycin:ATG1:YPD:Cocktail


title: 1s:Salt:ATG1:YPD:Cocktail

value: Salt


title: Jan30_Cell_73


title: 1r:Rapamycin:ATG1:YPD:Cocktail


title: mATAC-seq_DKO_R2

city: Ithaca

first: Roman

last: Spektor

state: New York

address: 618 Tower Rd, Vet Research Tower, Room T2 007

institute: Cornell University

description: methyl-ATAC-seq on DKO

library_source: genomic

data_processing:
Trimming for mATAC-seq was performed using Fastp -q 20 -l 20 -a CTGTCTCTTATACACATCT. methyl-ATAC-Seq:  Trimmed fastq files were aligned using Bismark v0.19.0 to hg19 using the following settings: --score_min L,0,-0.6 --ambig_bam.  Bisulfite reads to be used for MethylKit were filtered for non-conversion using Bismark’s filter_non_conversion and deduplicated using deduplicate_bismark.  Methylation was extracted using Bismark’s methylation extractor --gzip --bedgraph --counts --ignore 9 --ignore_3prime 9.  Reads used for peak calling and ATAC-seq visualization were deduplicated using deduplicate_bismark without filtering for non-conversion. mATAC-seq bigwigs were made using Deeptools bamCoverage --binSize 1 --normalizeUsing RPKM --ignoreForNormalization chrM.
Genome_build: hg19
Supplementary_files_format_and_content: bw for all samples, bedGraph and cov files also for mATAC-seq samples

molecule: genomic DNA

source_name: Human Colorectal Tumor

growth_protocol: Cultured cells (#28 HCT116 Parental, #30 DNMT1 KO, #38 3b KO, and  #343 DKO) were procured from the GRCF at Johns Hopkins and cultured in McCoy’s Modified 5A Medium containing 10% heat-inactivated FBS and 1X Penn/Strep (Gibco #15140122).   Cells for each experiment were grown apart for at least 2 passages before library preparation.

extract_protocol: methyl-ATAC-seq: Cell lysis was performed identically to Omni-ATAC-seq. Cells were trypsinized and subsequently inactivated in cell culture media. Following inactivation, cells were pelleted and resuspended in cold PBS (without Ca++ and Mg++).  Cells were stained with Trypan Blue and counted on a hemocytometer.  Lysis and tagmentation was performed exactly as described in [PMID: 28846090] with modifications to inactivation and size selection.  Briefly, 250,000 cells were lysed on ice for 3 minutes in ice-cold 50uL Lysis Buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.01% Digitonin in DEPC H2O), resuspended in 1mL ice-cold RBS-Wash (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20) and pelleted cold at 500g for 10min. Tagmentation was performed in 1X Tagmentation Buffer (10mM Tris pH 7.4, 5mM MgCl2, 10% DMF, 33% PBS, 0.1% Tween-20, 0.01% Digitonin) using 700nM Tn5 Transposase assembled using pre-annealed methylated-MedsA/B for 30 minutes at 37C. Inactivation and size-selection was performed identically to our modified Omni-ATAC-seq protocol. Tagmentation was inactivated with the addition of 5 volumes SDS Lysis Buffer (100mM Tris pH 7.4, 50mM NaCl, 10mM EDTA, 0.5% SDS in DEPC H2O) and 100ug Proteinase K (Invitrogen #25530049) for 30 minutes at 55C followed by Isopropanol Precipitation using GlycoBlue (Invitrogen #AM9516) as a carrier.  DNA was size selected using Ampure XP beads (0.5X – 1.8X). Tagmented DNA was End-Repaired for 30min at 37C (5U Klenow Exo- (NEB #M2012S), 1X NEB Buffer 2, and 0.5mM/ea dATP, dGTP, dTTP, and 5mCdCTP (NEB #N0365S)).  End repair was cleaned using a Ampure XP (Beckman Coulter # A63880) 1.8X cleanup.  5% of the product was kept for quality control PCR. Bisulfite conversion was performed using EZ DNA Methylation-Lightning (Zymo #D5030T) following the manufacturer’s protocol. PCR was immediately performed using PfuTurbo Cx (Agilent # 600410) (94C 2min, 13 cycles of: [98C 10sec, 65C 30sec, 72C 30sec], 72C 5min) followed by a final 1.8X Ampure XP cleanup.

value: DKO (DNMT1, DNMT3B double knockout)

tag: passages


title: 5yd:YPD:CTK1:YPD:Cocktail

tag: strain background


title: 1yd:YPD:ATG1:YPD:Cocktail

tag: media


title: 1yc:YPD:ATG1:YPD:None

tag: stress


title: Jan30_Cell_72


title: Jun6_Cell_46


title: Col0_rep1_RNA


title: Jun6_Cell_45


title: 1h:Heatshock:ATG1:YPD:Cocktail

tag: perturbation


title: Jan30_Cell_71


title: mATAC-seq_HCT116_R1

description: methyl-ATAC-seq on HCT116

value: wildtype


title: mATAC-seq_HCT116_R2

description: methyl-ATAC-seq on HCT116


title: 2c:SDC:CDC5:SDC:None

value: SDC

tag: kinase inhibitor


title: Omni-ATAC-seq_DKO_R2

description: Omni-ATAC-seq on DKO

data_processing: Trimming for Omni-ATAC-seq was performed using Fastp -q 20 -l 20 -a CTGTCTCTTATACACATCT.  Omni-ATAC-seq:  Trimmed fastq files were aligned using BWA-mem to hg19.  Reads were deduplicated using Picard MarkDuplicates. bigwigs were made using Deeptools bamCoverage --binSize 1 --normalizeUsing RPKM --ignoreForNormalization chrM.

extract_protocol: Omni-ATAC-seq: Cells were trypsinized and subsequently inactivated in cell culture media. Following inactivation, cells were pelleted and resuspended in cold PBS (without Ca++ and Mg++).  Cells were stained with Trypan Blue and counted on a hemocytometer.  Lysis and tagmentation was performed exactly as described in [PMID: 28846090] with modifications to inactivation and size selection.  Briefly, 100,000 cells were lysed on ice for 3 minutes in ice-cold 50uL Lysis Buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.01% Digitonin in DEPC H2O), resuspended in 1mL ice-cold RBS-Wash (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween20) and pelleted cold at 500g for 10min.  Tagmentation was performed in 1X Tagmentation Buffer (10mM Tris pH 7.4, 5mM MgCl2, 10% DMF, 33% PBS, 0.1% Tween-20, 0.01% Digitonin) using 100nM Tn5 Transposase for 30 minutes at 37C.  Tagmentation was inactivated with the addition of 5 volumes SDS Lysis Buffer (100mM Tris pH 7.4, 50mM NaCl, 10mM EDTA, 0.5% SDS in DEPC H2O) and 100ug Proteinase K (Invitrogen #25530049) for 30 minutes at 55C followed by Isopropanol Precipitation using GlycoBlue (Invitrogen #AM9516) as a carrier.  DNA was size selected using Ampure XP beads (0.5X – 1.8X). PCR was performed for using Q5 DNA polymerase (NEB #M0491S) with 1X GC buffer (72C 5min, 98C 30sec, 11 cycles of: [98C 10sec, 65C 30sec, 72C 30sec], 72C 5min) followed by a final 1.8X Ampure XP cleanup.


title: 1g:Glucose_Dropout:ATG1:YPD:Cocktail

value: YPsorbitol (2.02%)


title: mATAC-seq_DKO_R1

description: methyl-ATAC-seq on DKO


title: 27d:SDC:WT3:SDC:Cocktail

value: WT


title: Jan30_Cell_69


title: Omni-ATAC-seq_HCT116_R2

description: Omni-ATAC-seq on HCT116


title: 28c:SDC:WT4:SDC:None


title: 1a:Azetidine:ATG1:YPD:Cocktail

value: Azetidine


title: Omni-ATAC-seq_HCT116_R1

description: Omni-ATAC-seq on HCT116


title: Jan30_Cell_68


title: Jan30_Cell_67


title: 27c:SDC:WT3:SDC:None


title: 25c:SDC:WT1:SDC:None


title: 1m:Menadione:ATG1:YPD:Cocktail

value: Menadione


title: YFP_nls_C: nuclear YFP-HA, replicate C

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Read Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and Cutadapt 1.7.1. Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.13 and ShortRead 1.16.3. With Bowtie2 2.2.4 we identified and removed reads that align to the spiked-in PhiX.
Alignment: The preprocessed reads were aligned with Tophat v2.0.13 to the reference genome of Homo sapiens (GRCh37.73).  Default Tophat parameter settings were used, except for ‘min-intron-length=50’, ‘max-intron-length=500,000’, ‘no-coverage-search’ and ‘read-realign-edit-dist=3’. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: The number of reads in the alignments that overlap with gene features were counted with HTSeq-count v0.6.1p1 with parameters 'm=union', 'stranded=reverse', 'a=0', 't=exon' and 'i=gene id'. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor.
Identifying differential gene expression: With the EdgeR 3.8.6 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts (Robinson et al, 2007). We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate.
Genome_build: GRCh37
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are Ensembl IDs.

source_name: Flp-In T-Rex-293 cells

growth_protocol: The Flp-In T-Rex-293 cell line (Life Technologies) was used as a host to generate tetracycline inducible expression cell lines. Cells were co-transfected with 0.3µg pcDNA5/FRT/TO plasmid (Life Technologies) expressing the respective gene of interest and 2.7 µg pOG44 plasmid (Life Technologies) expressing the Flp recombinase. Stable integration of the pcDNA5/FRT/TO expression vector was selected using 100 µg/ml Hygromycin B (InvivoGen). Selection for the pcDNA6/TR plasmid expressing the Tet-repressor was maintained using 15 µg/ml Blasticidin. Since Flp-In cells contain a single integrated FRT site, polyclonal selection of isogenic cell lines was performed. Stable cell lines were maintained in growth medium containing 15 µg/ml Blasticidin (Gibco) and 10 µg/ml Hygromycin B (Invivogen).

extract_protocol:
5 million cells per condition were lysed and homogenized using Trizol reagent (Ambion, Life Technologies) and subsequent phase separation was performed using Chloroform (Sigma) following centrifugation according to the Trizol reagent protocol. Total RNA was isolated using the PureLink RNA Mini Kit (Ambion, Life Technologies) according to the manufacturers’ user manual. In brief, the aqueous layer containing the RNA was mixed with 70% (v/v) ethanol and bound to an RNaesy column (Ambion, Life Technologies). Genomic DNA was removed by on-column DNAse treatment using PureLink DNAse (Life Technologies). Subsequently, the RNA was washed and then eluted in non-DEPC treated nuclease free water and stored in aliquots at –80 °C until further processing.
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2ug of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version Rev E, October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NextSeq 500 instrument (High Output, 75 bp, Single Reads, v2).

treatment_protocol: Expression of DSCAM-ICD-YFP-HA, DSCAML1-ICD-YFP-HA, YFP-HA-NLS or YFP-HA-CYT was induced with 1 µg/ml Tetracycline (Sigma) and cells were lysed and RNA was extracted after 24 hours.

value: Flp-In T-Rex-293

tag: stable genomic integration

tag: inducible expression

value: stable cell line with Tetracycline inducible expression of transgene

value: enhanced YFP with  Human influenza hemagglutinin (HA) tag


title: Jan30_Cell_66


title: 26d:SDC:WT2:SDC:Cocktail

tag: genotype


title: 25d:SDC:WT1:SDC:Cocktail


title: 28t:Tunicamycin:WT4:YPD:Cocktail

value: Tunicamycin

value: 5 ug/ml


title: YFP_nls_B: nuclear YFP-HA, replicate B

tag: cell line

value: enhanced YFP with Human influenza hemagglutinin (HA) tag


title: 1f:Fluconazole:ATG1:YPD:Cocktail

value: YPD

value: Fluconazole

value: 250 ug/ml

value: Cocktail


title: Jan30_Cell_65

value: Remission


title: YFP_nls_A: nuclear YFP-HA, replicate A

tag: genotype/variation


title: 26t:Tunicamycin:WT2:YPD:Cocktail


title: Jan30_Cell_70

tag: disease


title: 25t:Tunicamycin:WT1:YPD:Cocktail


title: Jan30_Cell_64

tag: cell isolation batch


title: 27t:Tunicamycin:WT3:YPD:Cocktail


title: 26c:SDC:WT2:SDC:None


title: Jan30_Cell_63

tag: cluster


title: 10k:Tunicamycin:WT2:YPD:None


title: YFP_cyt_B: cytoplasmic YFP-HA, replicate B

value: SV40 NLS fused to enhanced YFP with Human influenza hemagglutinin (HA) tag


title: 2k:Tunicamycin:WT1:YPD:None


title: 26k:Tunicamycin:WT4:YPD:None


title: YFP_cyt_C: cytoplasmic YFP-HA, replicate C


title: YFP_cyt_A: cytoplasmic YFP-HA, replicate A


title: Jan30_Cell_61


title: 28s:Salt:WT4:YPD:Cocktail

value: Salt


title: 27s:Salt:WT3:YPD:Cocktail


title: Jan30_Cell_62


title: 7C_DSL1_ICD: DSCAML1-ICD-YFP-HA, replicate C

value: mouse DSCAML1 cytoplasmic domain, aa 1613-2053,  fused to enhanced YFP with Human influenza hemagglutinin (HA) tag at C-terminus


title: Jan30_Cell_60


title: 26s:Salt:WT2:YPD:Cocktail

value: WT


title: 25s:Salt:WT1:YPD:Cocktail


title: 25k:Salt:WT4:YPD:None


title: 7B_DSL1_ICD: DSCAML1-ICD-YFP-HA, replicate B


title: Jan30_Cell_59


title: 17k:Salt:WT3:YPD:None


title: 7A_DSL1_ICD: DSCAML1-ICD-YFP-HA, replicate A


title: 1k:Salt:WT1:YPD:None


title: 18k:Tunicamycin:WT3:YPD:None


title: 3C_DS_ICD: DSCAM-ICD-YFP-HA, replicate C

value: mouse DSCAM cytoplasmic domain, aa 1616-2013, fused to enhanced YFP with Human influenza hemagglutinin (HA) tag at C-terminus


title: 28r:Rapamycin:WT4:YPD:Cocktail

value: Rapamycin

value: 1 ug/ml


title: 27r:Rapamycin:WT3:YPD:Cocktail


title: Jan30_Cell_57


title: 3B_DS_ICD: DSCAM-ICD-YFP-HA, replicate B

value: Flp-In T-Rex-293

value: stable cell line with Tetracycline inducible expression of transgene


title: Jan30_Cell_58


title: 26r:Rapamycin:WT2:YPD:Cocktail


title: Jan30_Cell_56


title: 25r:Rapamycin:WT1:YPD:Cocktail


title: 3A_DS_ICD: DSCAM-ICD-YFP-HA, replicate A


title: 2g:Glucose_Dropout:CDC5:YPD:Cocktail

value: YPsorbitol (2.02%)


title: 19k:Rapamycin:WT3:YPD:None


title: Jan30_Cell_55


title: 11k:Rapamycin:WT2:YPD:None


title: Jan30_Cell_54


title: 3k:Rapamycin:WT1:YPD:None


title: 28yd:YPD:WT4:YPD:Cocktail


title: Omni-ATAC-seq_DKO_R1

description: Omni-ATAC-seq on DKO

value: DKO (DNMT1, DNMT3B double knockout)


title: 27k:Rapamycin:WT4:YPD:None


title: 26yd:YPD:WT2:YPD:Cocktail


title: Jan30_Cell_52


title: 9k:Salt:WT2:YPD:None


title: 25yd:YPD:WT1:YPD:Cocktail


title: 27yd:YPD:WT3:YPD:Cocktail


title: 28yc:YPD:WT4:YPD:None


title: 27yc:YPD:WT3:YPD:None


title: 26yc:YPD:WT2:YPD:None


title: Jan30_Cell_53


title: 25yc:YPD:WT1:YPD:None


title: Jan30_Cell_50


title: Jan30_Cell_49


title: 12k:Menadione:WT2:YPD:None

value: Menadione


title: Jan30_Cell_48


title: 20k:Menadione:WT3:YPD:None

value: YPD


title: 28m:Menadione:WT4:YPD:Cocktail


title: 4k:Menadione:WT1:YPD:None


title: Jan30_Cell_47


title: 27m:Menadione:WT3:YPD:Cocktail


title: Jan30_Cell_45


title: Jan30_Cell_46


title: 31k:Heatshock:WT4:YPD:None

value: Heatshock

value: 39 Degrees


title: 23k:Heatshock:WT3:YPD:None


title: 15k:Heatshock:WT2:YPD:None


title: 26m:Menadione:WT2:YPD:Cocktail

value: Cocktail


title: 25m:Menadione:WT1:YPD:Cocktail


title: Jan30_Cell_44

value: Remission


title: 7k:Heatshock:WT1:YPD:None


title: Jan30_Cell_51


title: Jan30_Cell_43


title: 27h:Heatshock:WT3:YPD:Cocktail


title: 26h:Heatshock:WT2:YPD:Cocktail


title: 28k:Menadione:WT4:YPD:None


title: 25h:Heatshock:WT1:YPD:Cocktail


title: 32k:Glucose_Dropout:WT4:YPD:None


title: Jan30_Cell_41


title: 24k:Glucose_Dropout:WT3:YPD:None


title: Jan30_Cell_42


title: 16k:Glucose_Dropout:WT2:YPD:None


title: Jan30_Cell_40


title: 8k:Glucose_Dropout:WT1:YPD:None


title: 28g:Glucose_Dropout:WT4:YPD:Cocktail


title: 26g:Glucose_Dropout:WT2:YPD:Cocktail


title: Jan30_Cell_38


title: 25g:Glucose_Dropout:WT1:YPD:Cocktail


title: 29k:Fluconazole:WT4:YPD:None

value: Fluconazole

value: 250 ug/ml


title: 21k:Fluconazole:WT3:YPD:None


title: Jan30_Cell_36


title: 13k:Fluconazole:WT2:YPD:None


title: 28h:Heatshock:WT4:YPD:Cocktail


title: 5k:Fluconazole:WT1:YPD:None


title: Jan30_Cell_37


title: 28f:Fluconazole:WT4:YPD:Cocktail


title: 27f:Fluconazole:WT3:YPD:Cocktail


title: Jan30_Cell_34


title: 25f:Fluconazole:WT1:YPD:Cocktail


title: Jan30_Cell_35


title: 28a:Azetidine:WT4:YPD:Cocktail

value: Azetidine


title: 26f:Fluconazole:WT2:YPD:Cocktail

value: WT


title: 27a:Azetidine:WT3:YPD:Cocktail


title: Jun6_Cell_50

value: ActiveEOE


title: Jan30_Cell_32


title: 27g:Glucose_Dropout:WT3:YPD:Cocktail


title: 30k:Azetidine:WT4:YPD:None


title: Jan30_Cell_39


title: Jan30_Cell_33


title: 26a:Azetidine:WT2:YPD:Cocktail


title: Jan30_Cell_31


title: 14k:Azetidine:WT2:YPD:None


title: 22k:Azetidine:WT3:YPD:None


title: Jan30_Cell_30


title: 6k:Azetidine:WT1:YPD:None


title: WT5_16S rRNA Seq

city: Nanjing City

first: Xingyin

last: Liu

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

description:
Analyzed by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China)
processed data file:
OTUS_Majorbio.txt
Majorbio_OTUs_assignment_and_abundance.txt

data_processing:
Raw fastq files were quality-filtered by Trimmomatic and merged by FLASH according to the following criteria: (i) The reads were truncated at any site receiving an average quality score <20 over a 50 bp sliding window. (ii) Sequences whose overlap being longer than 10 bp were merged according to their overlap with mismatch no more than 2 bp. (iii)Sequences of each sample were separated according to barcodes (exactly matching) and Primers (allowing 2 nucleotide mismatching), and reads containing ambiguous bases were removed.
Operational taxonomic units (OTUs) were subtract to negative controls to prevent any potential contaminant 16S reads. clustered with 97% similarity cutoff using UPARSE?version 7.1 http://drive5.com/uparse/) with a novel ?greedy? algorithm that performs chimera filtering and OTU clustering simultaneously.
The taxonomy of each 16S rRNA gene sequence was analyzed by RDP Classifier algorithm (http://rdp.cme.msu.edu/) against the Silva (SSU123) 16S rRNA database using confidence threshold of 70%.
To subtracted potential contaminates existed in kit and water, only genera OTU with an average relative abundance of greater or equal to 10^-4 and existed in at least 10% subjects were considered in the analyses.

organism: Drosophila melanogaster

source_name: Gut

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle

extract_protocol:
Total genome DNA from 30 adult fly midguts was extracted using the kit (Tiangen, Beijing, China). DNA concentration and purity was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific). The V3-V4 hypervariable regions of the bacteria 16S rRNA gene were amplified with primers 338F (5’- ACTCCTACGGGAGGCAGCAG-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) by thermocycler PCR system (GeneAmp 9700, ABI, USA). The PCR reactions including water and regents as negative controlswere conducted using the following program: 3 min of denaturation at 95 °C, 27 cycles of 30 s at 95 °C, 30s for annealing at 55 °C, and 45s for elongation at 72 °C, and a final extension at 72 °C for 10 min. PCR reactions were performed in triplicate 20 μL mixture containing 4 μL of 5 × FastPfu Buffer, 2 μL of 2.5 mM dNTPs, 0.8 μL of each primer (5 μM), 0.4 μL of FastPfu Polymerase and 10 ng of template DNA. The resulted PCR products were extracted from a 2% agarose gel and further purified using the AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA) and quantified using QuantiFluor™-ST (Promega, USA) according to the manufacturer’s instruction.
Purified amplicons were pooled in equimolar and paired-end sequenced (2 × 300) on an Illumina MiSeq platform (Illumina, San Diego,USA).

tag: tissue

value: intestine

tag: strain

tag: Sex

value: female

tag: fly number


title: Jan30_Cell_29

source_name: esophagus


title: WT4_16S rRNA Seq


title: WT3_16S rRNA Seq


title: WT1_16S rRNA Seq


title: KL5_16S rRNA Seq


title: WT2_16S rRNA Seq


title: 25a:Azetidine:WT1:YPD:Cocktail

tag: strain background


title: healthy lymphnodes pool(37)

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

country: Italy

institute: University of Firenze

hyb_protocol: Hybridization was performed on human whole genome 44,000 (Agilent-014850) oligonucleotide microarrays using reagents and protocols provided by the manufacturer (Agilent Technologies, Manual Part Number G4140-90042) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: healthy lymphnodes pool

label_protocol: cDNA synthesis and Cy3 labeling were performed with 500 ng of total RNA by Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was isolated by Trizol reagent according to the manufacturer’s protocol (Invitrogen S.R.L, Italy). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). High quality quantified RNA was purified on silica gel columns using the RNeasy MinElute Cleanup kit (QIAGEN S.p.A., Italy).

tag: gender

value: mix

tag: age (years)


title: KL4_16S rRNA Seq


title: Jan30_Cell_26


title: Jan30_Cell_27


title: Jan30_Cell_25


title: KL2_16S rRNA Seq


title: Jan30_Cell_28


title: FL-g3rel(38)

source_name: follicular lymphoma biopsy

value: F

tag: grade

value: FL III A

tag: Stage

value: IA

tag: response

value: complete remission

tag: time to relapse

tag: os (months)


title: DLBCL(30)

source_name: DLBCL biopsy

value: DLBCL

value: IIIA

value: partial remission


title: KL3_16S rRNA Seq


title: Jan30_Cell_24


title: KL1_16S rRNA Seq


title: Jan30_Cell_22


title: Jan30_Cell_21


title: Jan30_Cell_19


title: DLBCL(14)

value: IVA


title: Jan30_Cell_18

value: Remission


title: Jan30_Cell_20


title: FL-g2rel(26)

value: M

value: FL II


title: FL-g2rel(23)


title: FL-g3rel(21)


title: FL-g2(28)


title: FL-g2(19)


title: FL-g1rel(18)

value: FL I


title: mla6_pool

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description:
hv_pool2
Hordeum vulgare L. (Barley)
Blumeria graminis f. sp. hordei (Bgh)
Small RNA-Seq
Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at pooled time points: 0, 16, 20, 24, 32, and 48 HAI.

data_processing:
Library strategy: PARE-seq
The 50 base pair single-end reads obtained from Illumina Hi-Seq 2500 were quality filtered and adapters were trimmed using Trimmomatic version 0.33 (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170). Trimmed PARE read data, along with predicted miRNAs, and either the barley or the Blumeria transcriptomes were processed with both the CleaveLand (Addo-Quaye et al., 2009. Bioinformatics 25(1): 130–131. DOI: 10.1093/bioinformatics/btn604) and sPARTA (Kakrana et al., 2014. Nucleic Acids Res. 42(18): e139. DOI: 10.1093/nar/gku693) programs.
Genome_build: Barley (Mascher et al., 2017. Nature 544: 427–433. DOI: 10.1038/nature22043) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu et al., 2010. Science 330 (6010): 1543-1546. DOI: 10.1126/science.1194573).
Supplementary_files_format_and_content: *.collapsed_v2.csv: Comma-separated PARE count files.

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: CI 16151 and its derived mutant barley lines were maintained via single seed descent. Genotypes were grown in separate trays (19.5 x 27.5-cm) in a climate-controlled greenhouse using a split plot design. Each tray consisted of six rows of 16 seedlings, with rows randomly assigned to one of six harvest timepoints (0, 16, 20, 24, 32, and 48 HAI).

extract_protocol:
Total RNA was isolated from 0.5 g of each seedling pool using a hot (60°C) phenol / guanidine thiocyanate method (Caldo et al., 2004. Plant Cell 16: 2514-2528. DOI: 10.1105/tpc.104.023382).
PARE DNA-sequencing (PARE-seq) libraries were prepared by the Meyers group at the Danforth Center (St. Louis, MO, USA) using the protocol described in [Zhai et al., 2014. Methods 67(1): 84-90. DOI:10.1016/j.ymeth.2013.06.025] and were subjected to single-end sequencing (50-bp reads) using the Illumina Hi-Seq2500 Sequencing System. The five libraries were barcoded separately and run on a single flow cell lane.

treatment_protocol: Seven days after sowing, seedling trays were inoculated at 16:00 with a high density of Bgh isolate 5874 (AVRa1, AVRa6, vira8, AVRa12, vira13, AVRLa) and positioned randomly in a controlled growth chamber (18°C, 8 h darkness, 16 h light). Rows of seedlings were harvested at the assigned time points, pooled, and immediately placed into liquid nitrogen. The entire procedure was replicated three times in successive weeks resulting in 90 experimental units (5 genotypes x 6 timepoints x 3 replications). Following RNA extraction, all 6 timepoints (0, 16, 20 24, 32, and 48 hours after inoculation with Bgh 5874) were pooled for each of the 5 genotypes.

tag: plant genotype

tag: fungal isolate

value: Bgh isolate 5874

value: Barley infected first leaf

tag: timepoint


title: mla6 + bln1_pool

description:
hv_pool5
Hordeum vulgare L. (Barley)
Blumeria graminis f. sp. hordei (Bgh)
Small RNA-Seq
Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at pooled time points: 0, 16, 20, 24, 32, and 48 HAI.


title: rar3_pool

description:
hv_pool3
Hordeum vulgare L. (Barley)
Blumeria graminis f. sp. hordei (Bgh)
Small RNA-Seq
Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at pooled time points: 0, 16, 20, 24, 32, and 48 HAI.


title: bln1_pool

description:
hv_pool4
Hordeum vulgare L. (Barley)
Blumeria graminis f. sp. hordei (Bgh)
Small RNA-Seq
Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at pooled time points: 0, 16, 20, 24, 32, and 48 HAI.


title: DRB_treated_WDR43_FLAG_ChIP-seq

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
ChIP DNA
DRB_WDR43-FLAG-ChIP-seq_peaks.bed

data_processing:
alignment: bowtie2
peak calling: MACS
genome build: mm9
Supplementary_files_format_and_content: bedgraph or bed files for the output by MACS

source_name: mES cells

growth_protocol: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by NEBNEXT  ChIP-seq library preparation kit or  NEBNEXT Ultra RNA-seq library preparation kit  RNA-seq library preparation kit

tag: cell type

value: mES cells

tag: treatment

value: DRB

tag: genotype/variation

value: Fbio-tagged WDR43

tag: antibody

value: FLAG, Sigma F1804


title: FL-g2rel(13)

value: IVB


title: FL-g3(36)

value: FL III A


title: mla6_bln1_t48_rep1

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 48 HAI

data_processing:
The 50 base pair single-end reads obtained from Illumina Hi-Seq 2500 were quality filtered and adapters were trimmed using Trimmomatic version 0.33 (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170).  Reads were compared with the Rfam database using the Infernal program version 1.1.2 (Nawrocki and Eddy, 2013. Bioinformatics 29 (22): 2933-2935. DOI: 10.1093/bioinformatics/btt509) and used to filter tRNAs, rRNAs, snoRNAs and snRNAs from the data. The reads were also filtered using the Triticeae Repeat Sequence Database (Wicker et al., 2008. BMC Genomics 9: 518. DOI: 10.1186/1471-2164-9-518) to remove any known triticeae-specific repeat sequences.
For each of the 90 samples, read count estimation was done using RSEM (Li and Dewey, 2011. BMC Bioinformatics 12: 323. DOI: 10.1186/1471-2105-12-323) with Trimmomatic (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170) trimmed reads as input.
Genome_build: Barley (Mascher et al., 2017. Nature 544: 427–433. DOI: 10.1038/nature22043) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu et al., 2010. Science 330 (6010): 1543-1546. DOI: 10.1126/science.1194573).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew in respective csv files

extract_protocol:
Total RNA was isolated from 0.5 g of each pool using a hot (60˚C) phenol / guanidine thiocyanate method (Caldo et al., 2004. Plant Cell 16: 2514-2528. DOI: 10.1105/tpc.104.023382).
Small RNA-sequencing (small RNA-seq) libraries were prepared by the Iowa State University DNA Facility (Ames, Iowa, USA) using the Illumina TruSeq small RNA library preparation kit and were subjected to single-end sequencing (100-bp reads) using the Illumina Hi-Seq 2500 Sequencing System. A split-split-plot design was used to run the 90 samples on three Hi-Seq 2500 flow cells. Each replication was run on a separate flow cell with each plant genotype randomly assigned to each lane and 6 barcodes randomly assigned to the 6 time points within each genotype (lane).

treatment_protocol: Seven days after sowing, seedling trays were inoculated at 16:00 with a high density of Bgh isolate 5874 (AVRa1, AVRa6, vira8, AVRa12, vira13, AVRLa) and positioned randomly in a controlled growth chamber (18°C, 8 h darkness, 16 h light). Rows of seedlings were harvested at the assigned time points, pooled, and immediately placed into liquid nitrogen. The entire procedure was replicated three times in successive weeks resulting in 90 experimental units (5 genotypes x 6 timepoints x 3 replications).

tag: tissue

value: Barley infected first leaf (PO:0007094)

value: 48 HAI

tag: replication

value: Rep 1


title: Jan30_Cell_23

data_processing:
Basecalling was performed with Illumina's bcl2fastq v2.15.0
Identifying information was removed from the fastqs with desnp v1.0 (manuscript in preparation)
kallisto v0.42.5 was used to quantify transcripts from two different models: Gencode v26 and the UCSC knownGenes table (Dec 2014).  Parameters: --bias
Genome_build: GRCh38
Supplementary_files_format_and_content: Abundance.tsv files from kallisto: tab-separated, containing abundance estimates in TPM

extract_protocol:
Single cells were isolated on the Fluidigm C1 system using the 7-10 uM capture chip and manually examined to remove empty chambers and chambers with multiple cells
Libraries were constructed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1 system (CloneTech)

tag: disease

tag: cell isolation batch

tag: cluster


title: DMSO_WDR43_FLAG_ChIP

description:
ChIP DNA
DMSO_WDR43-FLAG-ChIP-seq_peaks.bed

value: DMSO


title: ActD_WDR43_FLAG_ChIP

description:
ChIP DNA
ActD_WDR43-FLAG-ChIP-seq_peaks.bed

value: ActD


title: mla6_bln1_t32_rep3

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 32 HAI

value: 32 HAI

value: Rep 3


title: WT_pool

description:
hv_pool1
Hordeum vulgare L. (Barley)
Blumeria graminis f. sp. hordei (Bgh)
Small RNA-Seq
Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at pooled time points: 0, 16, 20, 24, 32, and 48 HAI.


title: FL-g3(1)

tag: gender

value: M

tag: age (years)

tag: grade

value: II

value: complete remission


title: FL-g1(12)

value: FL I

tag: Stage

value: IIIA

tag: response

tag: time to relapse


title: mla6_bln1_t48_rep2

tag: plant genotype

tag: fungal isolate

value: Bgh isolate 5874

value: Rep 2


title: mla6_bln1_t32_rep1

tag: timepoint


title: mla6_bln1_t48_rep3


title: mla6_bln1_t24_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 24 HAI

value: 24 HAI


title: mla6_bln1_t20_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 20 HAI

value: 20 HAI


title: NHO7

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: disease

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1,65µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44k using Agilent's recommended hybridization chamber.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9,1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction.

data_processing: the signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median

source_name: Heterotopic ossification mesenchymal stromal cell

label_protocol: 1µg of total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technologies) following manufacturer's protocol.

growth_protocol: HO explants were seeded in α-MEM supplemented with 10% FCS (foetal calf serum) and 1% antibiotics at 37°C in 5% CO2. Explants were removed after one to two weeks when sprouting adherent cells were in sufficient number.

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer Platform (Agilent Technologies)

treatment_protocol: Adherent cells were trypsinized at sub-confluence and amplified during 2 passages

tag: condition

value: disease


title: mla6_bln1_t24_rep3

value: Barley infected first leaf (PO:0007094)


title: mla6_bln1_t20_rep1


title: mla6_bln1_t16_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 16 HAI

value: 16 HAI


title: mla6_bln1_t16_rep3


title: mla6_bln1_t20_rep3


title: mla6_bln1_t16_rep1

value: Rep 1


title: mla6_bln1_t0_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 0 HAI

value: 0 HAI


title: mla6_bln1_t0_rep3


title: AP2-G-DD ap2-g mutant 84 hpi

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description: Three AP2-G motifs in ap2-g promoter mutated (GTAC → GATC)

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: AP2-G-DD ap2-g mutant +Shld1

growth_protocol: Parasites were cultured at 37°C in the presence of 6% oxygen and 5% carbon dioxide, in RPMI 1640 media supplemented with hypoxanthine, 0.5% Albumax II (Invitrogen), and 2.5 nM WR99210.

extract_protocol: Starting at 30 hpi, samples were harvested in Trizol for total RNA extraction for the next 66 hours.

treatment_protocol: For all lines, 0.5 μM Shld1 was added starting at 24 hpi to stabilize the AP2-G-DD protein.

tag: strain

value: AP2-G-DD ap2-g mutant

tag: hpi

tag: treatment

source_name: 3D7 Mixed Stage Reference Pool + 50% cDNA from samples

value: 3D7 + AP2-G-DD


title: AP2-G-DD ap2-g mutant 90 hpi

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: AP2-G-DD ap2-g mutant 66 hpi


title: NHO4

description: disease


title: AP2-G-DD ap2-g mutant 60 hpi


title: mla6_bln1_t24_rep1

tag: tissue

tag: replication


title: AP2-G-DD ap2-g mutant 72 hpi


title: NHO5

description: disease


title: mla6_bln1_t32_rep2

value: 32 HAI


title: mla6_bln1_t0_rep1


title: control8

description: no disease

source_name: bone marrow mesenchymal stromal cell from healthy donor

value: no disease


title: control9

description: no disease


title: NHO3

description: disease


title: NHO6

description: disease


title: NHO2

description: disease


title: control7

description: no disease


title: AP2-G-DD ap2-g mutant 78 hpi


title: bln1_t32_rep2

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 32 HAI


title: bln1_t48_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 48 HAI

value: 48 HAI

value: Rep 3


title: bln1_t48_rep2


title: bln1_t32_rep1


title: AP2-G-DD ap2-g mutant 48 hpi


title: AP2-G-DD ap2-g mutant 54 hpi


title: AP2-G-DD ap2-g mutant 42 hpi


title: AP2-G-DD ap2-g mutant 36 hpi


title: control6

description: no disease


title: control5

description: no disease


title: bln1_t24_rep1

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 24 HAI


title: NHO1

description: disease


title: AP2-G-DD ap2-g mutant 30 hpi


title: bln1_t48_rep1


title: bln1_t20_rep2

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 20 HAI


title: bln1_t20_rep3


title: bln1_t24_rep2


title: RNA_Lam_rep2

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

description: cDNA

data_processing:
RNA-seq reads were mapped to the D. melanogaster reference genome (version dm3) using HISAT v2.1.0 with option --max-intronlen 50,000. Reads with low mapping quality were removed using SAMtools with option -q 30.
Gene expression was quantified with StringTie for the reference annotation version r5.12.
Genome_build: dm3
Supplementary_files_format_and_content: RNA-seq processed data files are non-normalized read counts per gene. One processed data file is supplied for each replicate. The files are in a plain text format (tab-delimited).

source_name: cultured cells

growth_protocol: Drosophila melanogaster S2 cell line (from the collection of IMG RAS) was grown at 25°C in Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 50 units/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol:
Total RNA was isolated from two biological replicates of Lam-KD or control S2 cells using Trizol reagent (Invitrogen), and contaminating DNA was removed by DNase I treatment. RNA quality was assessed using capillary electrophoresis with a Bioanalyzer 2100 (Agilent). Poly(A)+ RNA was extracted from total RNA using oligo(dT) magnetic beads (Thermo Fisher Scientific).
For library preparation NEBNext Ultra II RNA library preparation kit (New England Biolabs) was used following manufacturer’s instructions.  After preparation, libraries were quantified using a Qubit fluorometer and quantitative PCR.

treatment_protocol: dsRNAs against lacZ or lamin Dm0 for RNAi treatment of S2 cells were prepared as previously described (Shevelyov et al. 2009). dsRNAs against LBR were prepared by the same way using Drosophila genome DNA as a template for PCR amplification and primers provided in the Supplementary Table 1. Treatment of cells with dsRNA was performed during five days using a previously described protocol (Clemens et al. 2000).

tag: cell line

tag: developmental stage

value: late stage embryo

tag: cell type

value: macrophage-like

tag: library strategy

value: RNA-seq


title: bln1_t20_rep1

value: Bgh isolate 5874


title: AP2-G-DD 90 hpi

description: Parental line

source_name: AP2-G-DD +Shld1


title: control3

description: no disease


title: bln1_t16_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 16 HAI


title: bln1_t24_rep3

value: 24 HAI


title: bln1_t16_rep2

value: Rep 2


title: bln1_t0_rep1

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 0 HAI


title: bln1_t16_rep1