title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM H2O2 rep2

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.H2O2.rep2

data_processing:
Raw reads were aligned to genome (ATCC 42720) with gsnap (2018-02-05) spliced alignment
sam to bam conversion with picardtools (2.14.1)
bam to read counts using "featureCounts" from subread (1.6.0)
CPM file generated from DESeq2
Genome_build: candida_lusitaniae_ATCC42720_w_CBS_6936_MT (MT contamination fixed and MT genome assembled)
Supplementary_files_format_and_content: tab-delimited text file of read counts per feature and Experiment
Supplementary_files_format_and_content: csv-delimited text files of CPM normalized counts for each Experiment

organism: Clavispora lusitaniae

source_name: Exponential phase yeast cultures

growth_protocol: Overnight cultures grown in YPD at 30 C were back diluted into 5 ml YPD and grown at 37 C to mid-exponential phase on a roller drum, diluted into pre-warmed medium then grown, at 37 C, to mid-exponential phase again before 30 minutes treatment.

extract_protocol:
RNA was harvested from snap-frozen pellets (using liquid nitrogen) using the MasterPure Yeast RNA Purification Kit (Epicentre)
Libraries were prepared using the Kapa mRNA HyperPrep Library  Kit (Roche) following standard Illumina protocols

treatment_protocol: 30 minutes treatment with vehicle (water), 0.5 mM diamide, or 0.5 mM hydrogen peroxide

tag: strain

tag: genotype

value: mrr1delta +MRR1-Y813C+P1174P(t)


title: L0416-411

status: Public on Feb 25 2021

type: SRA

city: University of Helsinki

first: Aapo

last: Kahilainen

address: P.O. Box 65

department: Research Centre for Ecological Change

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
Sequenced reads were first trimmed for adaptor sequence using Trimmomatic.
To verify the family structure, the trimmed sequence reads were mapped against an existing Melitaea cinxia genome by Ahola et al. (Nature Communications 2014) using STAR, and the SNPs called using the software package SAMtools. The genetic distances between samples and clustering based on neighbour-joining trees were then determined using the R packages “ape” (version 5.1) and “adegenet” (version 2.1.1). One sample (sample name S29, title L0416-218) was identified as not belonging to the family it was assigned to originally and it was removed from further analyses.
To build one complete and diverse de novo transcriptome, two transcriptomes were built using both the Trinity (v2.6.5) and Velvet/Oases pipelines. The two transcriptomes were then combined using EvidentialGene to yield a single transcriptome of 69 182 putative transcripts. The combined transcriptome was then mapped against the genome of M. cinxia (Ahola et al., Nature Communications, 2014) using GMAP (v. 2018-07-04) to identify transcripts that exhibited any probability to map to the mitochondrial genome (29 transcripts in total).
Read counts of transcripts in the de novo transcriptome were obtained using RSEM (v. 1.3.0) with parameters --paired-end --strandedness reverse. In this process bowtie was used as the aligner with parameters --seed-length 25 -n 2 -e 99999999 -m 200 -I 1 -X 1000.
After obtaining a matrix of raw read counts, transcripts with > 1 counts-per-million in a minimum of four samples were kept, the 29 mitochondrial genome mapping transcripts were discarded, and the remaining raw read counts normalized according to TMM normalization as implemented in in the Bioconductor R-package edgeR (Robinson et al. Bioinformatics 2010).
Genome_build: De novo transcriptome
Supplementary_files_format_and_content: De novo transcriptome, fasta sequence for each transcript.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every transcript and every sample.
Supplementary_files_format_and_content: Matrix table with TMM-normalized transcript counts for a filtered set of transcripts and every sample.

molecule: polyA RNA

organism: Melitaea cinxia

source_name: full organism

growth_protocol: Melitaea cinxia larvae reared in 28 deg. Celsius day temperature (08:00-20:00) and 15 deg. Celsius night temperature (20:00-08:00). Larvae fed daily with ad libitum Plantago lanceoalta.

extract_protocol:
Larvae were frozen in liquid nitrogen at 4th larval instar and stored at -80 deg. Celsius until extraction. The frozen larvae were subsequently homogenized in dry ice in their entirety, followed by RNA and DNA extraction following a TRIzol-chloroform purification protocol.
RNA libraries were prepared by using Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: In addition to a control treatment, in which the larvae were fed with well watered Plantago lanceolata (40 ml water per day), the larvae experienced three different treatments with feeding on water limited P. lanceolata (20ml water per day). In these three treatments the larvae were fed with water limited P. lanceolata at different stages during pre-diapause development: (1) at late pre-diapause development during 3rd and 4th larval instars ("late water limitation"), (2) at early pre-diapause development during 1st and 2nd larval instars ("early water limitation"), and (3) throughout their pre-diapause development from the 1st to the 5th larval instar ("constant water limitation").

tag: full-sib family

tag: egg clutch

tag: treatment

value: constant water limitation


title: S232_20200114180155_5

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

data_processing:
trimming with bbduk
alignment with star 2.6.0a
Expression quantification with htseq-count 0.9.1
Genome_build: cellRanger pre-build hg38 Ensembl Assembly 93
Supplementary_files_format_and_content: tab-delimited text files include avarege CPM values for each patient

molecule: total RNA

organism: Homo sapiens

source_name: CUP cells

growth_protocol: CUP stem-like cells were isolated and grown in ultra-low attachment flasks in DMEM/F12 supplemented with N2 (Gibco), BSA 0.5%, L-Glutamine 2mM, Pen/strep

extract_protocol:
Cell pellets of growing spheres were lysed in Triazol and RNA was extracted with RNeasy Micro Kit (Qiagen); FFPE tissue slices were  extracted with Maxwell® RSC RNA FFPE Kit (promega)
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Illumina NovaSeq 6000 with a read length of 100 bp

tag: cell type

value: Cancers of Unknown Primary cells

tag: patient

tag: type

value: Cell


title: S232_20200114180155_4


title: h+ rpb1-CTD-(ALT-S5A)29::NatMX [ALT-S5A-2]

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description:
control used: GSM5012302
DESeq2_ALT_S5A_vs_markWT.xlsx

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: h+ rpb1-CTD-(ALT-S5A)29::NatMX

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

tag: genotype/variation

value: h+ rpb1-CTD-(ALT-S5A)29::NatMX

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: L0416-401

value: late water limitation


title: S232_20200114180155_3


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM H2O2 rep1

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.H2O2.rep1


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM H2O2 rep3

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.H2O2.rep3


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM H2O2 rep3

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.H2O2.rep3

value: mrr1delta +MRR1-Y813C


title: S232_20200114180155_2


title: h+ rpb1-CTD-(ALT-S5A)29::NatMX [ALT-S5A-1]


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM H2O2 rep2

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.H2O2.rep2


title: L0416-386

value: early water limitation


title: L0416-389


title: h+ rpb1-CTD-(ALT-P3A)29::NatMX [ALT-P3A-3]

description:
control used: GSM5012302
DESeq2_ALT_P3A_vs_markWT.xlsx

source_name: h+ rpb1-CTD-(ALT-P3A)29::NatMX

value: h+ rpb1-CTD-(ALT-P3A)29::NatMX


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM H2O2 rep1

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.H2O2.rep1


title: S232_20200114180155_1


title: h+ rpb1-CTD-(ALT-S5A)29::NatMX [ALT-S5A-3]


title: L0416-382


title: h+ rpb1-CTD-(ALT-P3A)29::NatMX [ALT-P3A-1]


title: S232_20191127150431_14

source_name: Colorectal cancer stem-like cells (Colorectosphere)

value: Metastatic Colorectal Cancer Primary cells


title: L0416-378


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM H2O2 rep3

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.H2O2.rep3

value: mrr1delta +MRR1-L1191H+Q1197*


title: S232_20191127150431_13


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM H2O2 rep2

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.H2O2.rep2


title: L0416-377


title: h+ rpb1-CTD-(S2A-S7A)29::NatMX [S2A-S7A-3]

description:
control used: GSM4880425; GSM4880426; GSM4880427
S2A_S7A_v_markWT_DESeq2.xlsx

source_name: h+ rpb1-CTD-(S2A-S7A)29::NatMX

value: h+ rpb1-CTD-(S2A-S7A)29::NatMX


title: L0416-404


title: h+ rpb1-CTD-(S2A-S7A)29::NatMX [S2A-S7A-2]


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM H2O2 rep1

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.H2O2.rep1


title: L0416-374

value: control


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM H2O2 rep3

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.H2O2.rep3

value: mrr1delta +MRR1-ancestral


title: h+ rpb1-CTD-(S2A-S7A)29::NatMX [S2A-S7A-1]


title: L0416-372


title: h+ rpb1-CTD-(ALT-P3A)29::NatMX [ALT-P3A-2]


title: h+ rpb1-CTD-S2A29::NatMX [S2A-3]

description:
control used: GSM4880425; GSM4880426; GSM4880427
S2A_v_markWT_DESeq2.xlsx

source_name: h+ rpb1-CTD-S2A29::NatMX

value: h+ rpb1-CTD-S2A29::NatMX


title: S232_20191127150431_10

source_name: CUP stem-like cells (Agnosphere)


title: L0416-366


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM H2O2 rep1

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.H2O2.rep1


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM H2O2 rep2

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.H2O2.rep2


title: L0416-348


title: L0416-347


title: h+ rpb1-CTD-S2A29::NatMX [S2A-1]


title: h+ rpb1-CTD-S2A29::NatMX [S2A-2]


title: h+ rpb1-CTD-Y1F29::NatMX [Y1F-3]

description:
control used: GSM4880425; GSM4880426; GSM4880427
Y1F_v_markWT_DESeq2.xlsx

source_name: h+ rpb1-CTD-Y1F29::NatMX

value: h+ rpb1-CTD-Y1F29::NatMX


title: Strain U04 mrr1Δ 0.5 mM H2O2 rep3

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.H2O2.rep3


title: L0416-332


title: Strain U04 mrr1Δ 0.5 mM H2O2 rep1

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.H2O2.rep1


title: L0416-346


title: Strain U04 mrr1Δ 0.5 mM H2O2 rep2

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.H2O2.rep2


title: Strain U04 0.5 mM H2O2 rep3

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.H2O2.rep3

value: wildtype


title: S232_20191127150431_9

value: Cancers of Unknown Primary cells


title: h+ rpb1-CTD-Y1F29::NatMX [Y1F-2]


title: S232_20191127150431_12

value: Cell


title: S232_20191127150431_7

source_name: Melanoma Stem-like cells (Melanmosphere)

value: Metastatic Melanoma Primary cells


title: S232_20191127150431_5


title: h+ rpb1-CTD-Y1F29::NatMX [Y1F-1]

value: log phase culture, YES medium


title: S232_20191127150431_11


title: L0416-331


title: Strain U04 0.5 mM H2O2 rep2

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.H2O2.rep2


title: CB_2018_10_25_20


title: S232_20191127150431_8


title: CB_2018_10_25_19


title: L0416-327


title: L0416-325


title: CB_2018_10_25_18


title: Strain U04 0.5 mM H2O2 rep1

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.H2O2.rep1


title: CB_2018_10_25_17


title: S232_20191127150431_6


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM diamide rep2

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.dia.rep2

value: mrr1delta +MRR1-Y813C+P1174P(t)

value: 0.5 mM diamide


title: L0416-324


title: L0416-319


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM diamide rep3

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.dia.rep3


title: CB_2018_10_25_15


title: L0416-309

value: late water limitation


title: WT 2 [re-analysis]

description: This is duplicated sample record of GSM1264157 for the convenient retrieval of the complete raw data from SRA

source_name: S. pombe cells

growth_protocol: Two biological replicates of the WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A cultures were grown in YES (yeast extracts plus supplements) media at 30°C till they reached OD600 0.4 -0.7.

extract_protocol:
Cells were harvested and RNA was isolated using the Qiagen RNeasy kit. RNA quality was assessed on a Bioanalyzer instrument (Agilent) and 1µg of total RNA was used to prepare polyA+ RNA using the Illumina TruSeq RNA sample kit .
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded total RNA Sample Prep Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled (8 samples per lane) for paired-end sequencing performed using an Illumina HiSeq 2000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

value: rpb1CTD-WT 1-18

tag: genetic markers

value: h- ade6 ura4-D18 leu1–32


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) 0.5 mM diamide rep1

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.dia.rep1


title: L0416-307


title: WT 1 [re-analysis]

description: This is duplicated sample record of GSM1264149 for the convenient retrieval of the complete raw data from SRA


title: h+ rpb1-CTD-WT18::NatMX [rpb1_18_plus_1]

description:
control used: GSM5012302
rpb1_18_v_markWT_DESeq2.xlsx

source_name: h+ rpb1-CTD-WT18::NatMX

value: h+ rpb1-CTD-WT18::NatMX

value: vegetative growth


title: L0416-295

value: early water limitation


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM diamide rep3

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.dia.rep3

value: mrr1delta +MRR1-Y813C


title: CB_2018_10_25_14


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM diamide rep2

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.dia.rep2


title: CB_2018_10_25_13


title: Strain U04 mrr1Δ +MRR1-Y813C 0.5 mM diamide rep1

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.dia.rep1


title: CB_2018_10_25_16


title: h+ rpb1-CTD-WT18::NatMX [rpb1_18_plus_2]


title: CB_2018_10_25_12


title: L0416-290


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM diamide rep3

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.dia.rep3

value: mrr1delta +MRR1-L1191H+Q1197*


title: L0416-289


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM diamide rep2

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.dia.rep2


title: CB_2018_10_25_11


title: L0416-283


title: CB_2018_10_25_10


title: L0416-279


title: CB_2018_10_25_9


title: CB_2018_10_25_8


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM diamide rep2

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.dia.rep2

value: mrr1delta +MRR1-ancestral


title: cog7,msh2_35gen_vs_350gen_R3.txt

type: RNA

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to microarrays in 8x15k format, made by Agilent (Design ID: 016322) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from technical replicates (dye swap) were averaged.

organism: Saccharomyces cerevisiae

source_name: cells from continuous culture

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: Continuous cultures of W303 Saccharomyces cerevisiae wold type strain and its derivatives were conducted at a dilution rate of 0.17–0.18 volumes per hour, and the culture was continued for up to 350 generations at a constant temperature of 30 °C. Cell samples were collected after 35 generations and then after 200 or 350 generations, depending on strain cultured. Cells were sedimented by centrifugation, flash-frozen in LN2 and kept at –80oC.

extract_protocol: Total RNA was prepared from deeply frozen yeast cell pellet samples using the hot acidic phenol procedure.

tag: growth period

value: 35 generations

value: 350 generations


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM diamide rep3

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.dia.rep3


title: L0416-269

value: constant water limitation


title: L0416-266


title: CB_2018_10_25_6

value: Cancers of Unknown Primary cells

value: Cell


title: L0416-268


title: L0416-260


title: CB_2018_10_25_7


title: cog7,msh2_35gen_vs_350gen_R2.txt


title: nup133,msh2_35gen_vs_350gen_R2.txt


title: nup133,msh2_35gen_vs_350gen_R3.txt


title: Strain U04 mrr1Δ 0.5 mM diamide rep3

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.dia.rep3


title: Strain U04 mrr1Δ +MRR1-ancestral 0.5 mM diamide rep1

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.dia.rep1


title: L0416-259


title: msh2_35gen_vs_350gen_R3.txt


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* 0.5 mM diamide rep1

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.dia.rep1


title: msh2_35gen_vs_350gen_R2.txt


title: cog7,msh2_35gen_vs_350gen_R1.txt


title: CB_2018_10_25_4

value: Metastatic Colorectal Cancer Primary cells


title: Strain U04 mrr1Δ 0.5 mM diamide rep1

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.dia.rep1


title: CB_2018_10_25_5


title: msh2_35gen_vs_350gen_R1.txt


title: L0416-258


title: nup133_35gen_vs_200gen_R1.txt

value: 200 generations


title: cog7_35gen_vs_200gen_R3.txt


title: CB_2018_10_25_2


title: Strain U04 0.5 mM diamide rep1

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.dia.rep1

value: wildtype

value: 0.5 mM diamide


title: Strain U04 mrr1Δ 0.5 mM diamide rep2

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.dia.rep2


title: CB_2018_10_25_3


title: Cytotrophoblast_control_Input-2

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

library_source: genomic

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using MACS2 v2.1.1 with -q 0.05 and --broad.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalization and 100 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig tracks; peak files (BroadPeak)

molecule: genomic DNA

source_name: Cytotrophoblast

growth_protocol: Cytotrophoblast cells were isolated from term human placentas (n = 2) using an adaptation of the method developed by Kliman et al. (Endocrinology, 1986), as described in Desforges et al (Adv Exp Med Biol, 2015). Isolated cells were plated in culture medium (Dulbecco's modified Eagle's medium and Ham's F‐12 1:1, 10% heat inactivated fetal calf serum, 0.6% glutamine and the antibiotics 1% gentamicin, 0.2% penicillin and 0.2% streptomycin) onto 35 mm culture dishes, at a density of 2.5 × 10^6, and were maintained in primary culture at 37°C in a humidified incubator (95% air–5% CO2).

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 mins, followed by chromatin extraction and sonication. Immunoprecipitation was performed with 10 µg of chromatin for 2.5 µg of anti-H3K27ac or H3K4me3 antibody. DNA was purified using the GeneJET PCR purification kit (Thermo Fisher).
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.

treatment_protocol: At 66 hours of culture, matched cell samples had control media or 25(OH)D added to a final concentration of 20 μM and were cultured for a period of 24 hours before collection at 90 hours.

value: Cytotrophoblast

value: Control

tag: chip antibody


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) control rep3

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.ctl.rep3

value: mrr1delta +MRR1-Y813C+P1174P(t)

value: vehicle (water)


title: Cytotrophoblast_vitD_Input-2


title: L0416-226


title: L0416-228


title: nup133_35gen_vs_200gen_R3.txt


title: L0416-227


title: L0416-256

value: early water limitation


title: nup133_35gen_vs_200gen_R2.txt


title: L0416-224


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) control rep2

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.ctl.rep2


title: Cytotrophoblast_vitD_H3K4me3-2

value: anti-H3K4me3 (Diagenode C15410003)


title: Strain U04 mrr1Δ +MRR1-Y813C+P1171P(t) control rep1

description:
U04 mrr1Δ +MRR1-Y813C+P1174P(t)
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.Y8P1.ctl.rep1


title: CB_2018_10_25_1


title: cog7_35gen_vs_200gen_R1.txt


title: L0416-219


title: Strain U04 mrr1Δ +MRR1-Y813C control rep3

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.ctl.rep3

value: mrr1delta +MRR1-Y813C


title: Cytotrophoblast_control_H3K4me3-2


title: cog7_35gen_vs_200gen_R2.txt


title: Strain U04 0.5 mM diamide rep2

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.dia.rep2


title: WT_35gen_vs_200gen_R3


title: Cytotrophoblast_vitD_H3K27ac-2

value: anti-H3K27ac (Diagenode C15410196)


title: L0416-218


title: L0416-192

value: late water limitation


title: Cytotrophoblast_control_H3K27ac-2


title: GMTMS-iCMs

city: Beijing

first: Yang

last: Zhao

address: No. 5 Yiheyuan Road Haidian District

country: China

institute: Peking University

data_processing:
Quality control. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts (Novogene). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level. eatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: mm9
Supplementary_files_format_and_content: text files include gene counts or FPKM values  for each Sample

organism: Mus musculus

source_name: induced cardiomyocytes from MICFs

growth_protocol: MICFs were isolated from Myh6-mCherry mice with MI surgery for 5 days and plated into 10 cm dishes. Viruses were added to the culture medium 48h post plating. Twenty-four hours later, the viral medium was replaced with conditional medium mainly containing DMEM/M199 (4:1) supplemented with 10% FBS, 10% KSR, 1% NEAA, 1% Glutamax, 1% PS. Doxycycline (1 μg/ml) was also added to the iCM-inducing medium, which was changed every 3 days.

extract_protocol:
Total RNA was extracted from cells according to the manufacturer’s protocol (TransGene, ET111).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four weeks after viral transduction, reprogrammed cells were dissociated with incubation in enzymes. First, with 0.25% Trypsin /EDTA at 37 °C for 5-7 min, cells together with a large amount of ECMs were removed from the plate. Then, collagenases I/II/IV (2 mg/ml) were added to the well and incubated at 37 °C for 30-40 min. By passing through 40 µm cell strainers, dissociated cells were sorted by Aria3 (BD).

value: induced cardiomyocytes


title: L0416-216

value: constant water limitation


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* control rep3

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.ctl.rep3

value: mrr1delta +MRR1-L1191H+Q1197*


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* control rep2

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.ctl.rep2


title: L0416-190


title: Strain U04 mrr1Δ +MRR1-Y813C control rep1

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.ctl.rep1


title: L0416-186


title: MICFs

source_name: cardiac fibroblasts from adult injured mice (MICFs)

value: cardiac fibroblasts


title: Strain U04 mrr1Δ +MRR1-L1191H+Q1197* control rep1

description:
U04 mrr1Δ +MRR1-L1191H+Q1197*
Fluconazole-sensitive, low Mrr1 activity, premature stop codon
U04.L1Q1.ctl.rep1

source_name: Exponential phase yeast cultures


title: WT_35gen_vs_200gen_R1

value: 35 generations


title: DU145-Vector-rep3

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Gene expression of Prostate cancer

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: DU145 Cell Line

growth_protocol: All cells were cultured in their paired medium and incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from prostate  cancer cells (including DU145-TFEB and DU145-Vector) were isolated by  using a RNeasy mini kit (Qiagen, Germany) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: DU145 cell line were transfected with TFEB-overexpression lentivirus or blank ventor lentivirus as control group.

tag: cell line

tag: tfeb

value: Vector Control

tag: cancer type

value: Prostate Cancer


title: DU145-Vector-rep1

description: Gene expression of Prostate cancer


title: DU145-Vector-rep2

description: Gene expression of Prostate cancer


title: L0416-183

source_name: full organism


title: DU145-TFEB-rep3

description: Gene expression of Prostate cancer

value: Overexpression


title: Strain U04 mrr1Δ +MRR1-Y813C control rep2

description:
U04 mrr1Δ +MRR1-Y813C
Fluconazole-resistant, constitutive Mrr1 activity
U04.Y813C.ctl.rep2

tag: strain

tag: genotype


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR3 DNA

city: North Chicago

first: Gustavo

middle: Javier

last: Martinez

state: United States

address: 3333 Green Bay Rd Department of Microbiology and Immunology

department: Center for Cancer Cell Biology, Immunology and Infection

institute: Rosalind Franklin University

description: ATAC-seq using Nextera DNA library preparation

data_processing:
For RNA seq, STAR(v2.6.1)  were used for alignment, DUST scores were calculated with PRINSEQ Lite and low-complexity reads (DUST > 4) were removed from the BAM files. The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the featureCounts (v 1.6.5) using the default option along with a minimum quality cut off (Phred > 10). After removing absent features (zero counts in all samples), the raw counts were then imported to R/Bioconductor package DESeq2 (v 1.24.0) to identify differentially expressed genes among samples.
For ATAC seq, bowtie(-p 15 -m 1 –best - strata -X 2000 -S --fr --chunkmbs 1024) were used for the alignment, duplicate reads (identified by picard MarkDuplicates), mitochondria DNA, Y chromosome DNA and fragments larger than 100bp were excluded by samtools. Coordinates of reads were then shifted (plus strand +4, minus strain −5). Fragments were used to call peak summits with MACS2 with  parameters "--nomodel -q 0.01 --keep-dup all --call-summits". The summits for each peak from all replicates were expanded to regions with a uniform size of 500 bp. We excluded regions that intersected ENCODE blacklisted regions for mm10. We identified the Tn5 insertion site by isolating the first 9bp of each read and computed the number of transposase insertions per peak for each replicate with bedtools coverage (version 2.16.2). Raw ATAC-seq counts in each peak for all replicates of all samples were normalized between replicates with size factors computed with DESeq2 to differential coverage. Pairwise contrasts were performed with DESeq2 and differentially accessible regions were filtered based on a false discovery rate (p adj) value of less than 0.05 and -0.5> Log2fc >0.5. All bedgraph files of ATAC-seq or ChIP-seq are normalized by multiplying counts to a scaling factor calculated by 109/ accumulation-factor (accumulation-factor calculation: awk ‘{sum+=(($3-$2)∗$4)} END {print sum}’).
Genome_build: mm10
Supplementary_files_format_and_content: Text file table of RNA- and ATAC-seq differential expression table using EdgeR or DEseq2

source_name: P14 Thy1.1 Thy1.2 cells from d4 LCMV infected mice

extract_protocol:
For RNA-seq, cells were directly resuspended with lysis buffer from SMART-seq v4 Ultra Low Input RNA kit. For ATAC-seq, nuclei were isolated and resuspended in 1X TD buffer with Tn5 transposase.
For RNA-seq, cDNA obtained from the SMART-seq v4 Ultra Low Input RNA kit protocol and libraries generated with barcoded primers using Nextera DNA library preparation kit.  For ATAC-seq, tagmented genomic DNA was amplified with barcoded primers with KAPA HiFi real-time library amplification kit .

treatment_protocol: Splenocytes were harvested from d4 or d8 post-LCMV infection, stained for Thy1.1 and/or Thy1.2 and cells purifed by FACS. Cells were washed twice with cold 1X PBS prior to extraction protocol.

value: CD8+ T cells (P14 TCR transgenic)

tag: experimental treatment

value: LCMV d4 infected animals


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR2 DNA


title: Strain U04 mrr1Δ +MRR1-ancestral control rep3

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.ctl.rep3

value: mrr1delta +MRR1-ancestral

tag: treatment


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR1 DNA

tag: cell type


title: L0416-182

tag: full-sib family

tag: egg clutch


title: DU145-TFEB-rep2

description: Gene expression of Prostate cancer


title: GMTMM-iCMs


title: Strain U04 mrr1Δ +MRR1-ancestral control rep2

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.ctl.rep2

value: vehicle (water)


title: P14 Thy1.1 WT_BR3 DNA

source_name: P14 Thy1.1 cells from d4 LCMV infected mice


title: DU145-TFEB-rep1

description: Gene expression of Prostate cancer


title: WT_35gen_vs_200gen_R2

value: 200 generations


title: P14 Thy1.1 WT_BR2 DNA


title: L0416-113

value: early water limitation


title: Strain U04 mrr1Δ control rep3

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.ctl.rep3


title: P14 Thy1.1 WT_BR1 DNA


title: REC-1 cells, G8

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
The Cell Ranger software (version 3.0.1) offered by 10x Genomics was used to analyze the data.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis

source_name: Mantle cell lymphoma cells

growth_protocol: 3 x 10e6 REC-1 cells grew for 48 h in 5 ml RPMI1640 medium (supplemented with 10% heat-inactivated fetal bovine serum and 2 mmol/l L-Glutamine)

extract_protocol:
Cells were harvested and were washed with phosphate-buffered saline (PBS), stained with propidium iodide (2 µg/ml), and 30,000 cells were sorted by FACS (ARIA III, BD Biosciences, San Jose, CA, US) to exclude possible cell debris, apoptotic cells, and doublets. After counting of the cells using trypan blue staining, they were loaded into the 10x Genomics Chromium (10x Genomics, Pleasanton, CA, US).
To generate the libraries, the Chromium Single Cell 3’ Kit v2 Chemistry was applied and all steps were performed following the standard 10x Genomics protocol. For the quantification of the libraries a QubitTM 3.0 Fluometer (Thermo Fisher) was utilized and a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies, Waldbronn, Germany) was used for quality check. The reads were sequenced to a length of 50 bp in paired-end format on a S1 flowcell with a Novaseq 6000 (Ilumina, San Diego, CA, US).
scRNA-Seq

treatment_protocol: Ibrutinib (Selleck Chemicals, Absource Diagnostics, Munich, Germany), dissolved in DMSO,  was added to the 48 h sample at seeding and after 42 h to the 6 h sample reaching a final concentration of 400 nM, Ctr was untreated.

value: B cells

value: 400 nM ibrutinib for 48 h


title: Strain U04 mrr1Δ control rep2

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.ctl.rep2


title: L0416-086

value: control


title: Strain U04 mrr1Δ control rep1

description:
U04 mrr1Δ
MRR1 null, intermediate fluconazole resistance
U04mrr1.ctl.rep1

value: wildtype


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR2 RNA

description: processed with Ultra low SMARTER kit followed by Nextera DNA


title: L0416-084


title: REC-1 cells, G6

value: untreated


title: REC-1 cells, F4


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR1 RNA


title: Strain U04 control rep2

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.ctl.rep2


title: P14 Thy1.1 WT_BR3 RNA


title: L0416-047

value: late water limitation


title: Strain U04 control rep3

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.ctl.rep3


title: REC-1 cells, F2


title: Strain U04 control rep1

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.ctl.rep1


title: L0416-117


title: Strain U04 mrr1Δ +MRR1-ancestral control rep1

description:
U04 mrr1Δ +MRR1-ancestral
Fluconazole-sensitive, low Mrr1 activity
U04.anc.ctl.rep1


title: P14 Thy1.1 WT_BR2 RNA


title: Fo47 culture R2

city: Xi'an

first: Li

last: Guo

state: Shaanxi

address: 28 Xianning West Road

institute: Xi'an Jiao Tong University

description: 3 days in potato dextrose broth

data_processing:
Illumina Casava1.7 software used for basecalling.
DATA FILTERING: java -jar trimmomatic-0.32.jar PE -phred33 control_a.fq control_b.fq control_aPaired.fq control_aUnpaired.fq control_bPaired.fq control_bUnpaired.fq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36
Mapping using Tophat and bowtie
Transcript assembly using Cufflinks
Differential gene expression called using Cuffdiff
Genome_build: Arabidopsis thaliana TAIR10, Fusarium oxysporum 5176 genome, F. oxysporum 47 genome

organism: Fusarium oxysporum

source_name: Fungal mycelium

growth_protocol: Arabidopsis thaliana Col-0 seeds (ARBC Ohio State University) were germinated on autoclaved MetroMix360® potting mix and allowed to grow in growth chamber with a photoperiod of 14-hour light and 10-hour dark at 24 C.

extract_protocol:
Total RNAs were extracted from leaves of healthy and infected basil plants using Trizol reagent (Thermo Fisher Scientific, MA) following manufacturer’s protocol. After removal of genomic DNA by DNase I (New England Biolabs, MA) treatment, RNA samples were quantified using NanoDrop 1000 (Thermo Fisher Scientific, MA) and assessed for integrity using Agilent Bioanalyzer 2100 (Agilent, MA).
Library construction was conducted using Illumina TruSeq mRNA library preparation kit (Illumina, CA)

treatment_protocol: For F. oxysporum infection, Arabidopsis plants of 14 days old were root-dipped for 30 seconds in 1x106 spores/ml fungal spore suspension of FO5176 or FO47 and sterile dH2O for control. Inoculated plants were planted in autoclaved potting mix and incubated in 28C growth chamber of the same photoperiod as above.


title: SC3

city: Fuzhou

first: Jing-Hao

last: Huang

state: Fujian

address: Wusi Road

department: Pomological Institute

institute: Fujian Academy of Agricultural Sciences

description: Control treatments

data_processing:
The raw reads obtained from high-throughput sequencing were subjected to the Illumina pipeline filter for removement of adapter dimers, junk and low-complexity sequences, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Clean reads were subjected to BLAST searches against miRBase 21 (http://www.mirbase.org/) to identify known miRNAs.
The remaining non-annotated sequences of 18-30 nucleotides (nt) in length were mapped to the Citrus clementina genome (JGI version 1.0, http://www.phytozome.org/clementine.php) with the MTide program (http://bis.zju.edu.cn/MTide) to identify novel miRNAs.
Both the fold-change and P-value of each miRNA identified in each library were calculated using DESeq software, and the P-value was then adjusted to the false discovery rate (FDR) according to the Benjamini Hochberg Method. A 1.5-fold cut-off was set for determination of up- and down-regulated miRNAs, in addition to a FDR of less than 1.
Target genes of miRNAs obtained were predicted using TargetFinder.

organism: Citrus maxima

source_name: 10 uM H3BO3 for 15 weeks

growth_protocol: 11-week-old Citrus sinensis and C. grandis seedlings were sand cultured in ceramic pots, grown in a greenhouse under natural photoperiod and environmental temperature.

extract_protocol:
Root total RNA was extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Approximately 1 μg of mixed total RNA from five replicates was used to prepare a small RNA (sRNA) library with the TruSeq Small RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s protocol. The sRNA libraries were gel-purifid in 6% PAGE gels, and their concentration was then diluted to 2 ng/μl. The insert size of the sRNA libraries was tested with an Agilent 2100 bioanalyser. Aftr accurate quantifiation via qRT-PCR, single-end sequencing was performed on an Illumina HiSeq 2500.

treatment_protocol: Plants were irrigated with Hogland’s nutrient solution containing 10 (control) or 400 (B-toxic) μM H3BO3 every other day for 15 weeks

tag: tissue

value: Root tips


title: L0416-112


title: P14 Thy1.1 WT_BR1 RNA


title: REC-1 cells, G7

value: 400 nM ibrutinib for 6 h


title: P14 Thy1.1 Thy1.2 Kdm6b KO_BR3 RNA


title: Fo47 culture R1

description: 3 days in potato dextrose broth


title: SC2

description: Control treatments


title: L0416-083


title: REC-1 cells, F3


title: P14 shKdm6b_BR4 RNA

source_name: P14 Thy1.1 Ametrine+ cells from d8 LCMV infected mice

value: LCMV d8 infected animals


title: L0416-037

value: constant water limitation


title: Fo5176 culture R1

description: 3 days in potato dextrose broth


title: L0416-034


title: SB3

description: long-term Boron toxic treatments

source_name: 400 uM H3BO3 for 15 weeks


title: P14 shKdm6b_BR3 RNA


title: P14 shKdm6b_BR1 RNA


title: SB2

description: long-term Boron toxic treatments


title: L0416-046


title: L0416-032


title: SB1

description: long-term Boron toxic treatments


title: IHFB2 rep1

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
DL1 with ihfB-2 mutation
IHFB2_rep1

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the GCF_000007985.2/ASM798v2 genome assembly using smalt
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Genome_build: GCF_000007985.2
Supplementary_files_format_and_content: tab-delimited text file include the differential expression results of DESeq2and raw and normalized counts  for each sample.

organism: Geobacter sulfurreducens

source_name: IHFB2 rep1

growth_protocol: The cells were grown anaerobically at 30 oC in NBAF medium, supplemented with acetate and fumarate, and collected during the exponential growth phase (OD600= 0.3)

extract_protocol:
For each biological sample, total RNA samples were extracted using the RNeasy mini kit (Qiagen), then they were examined with an Agilent 2100 Bioanalyzer and quantified using NanoDrop 200c (Thermo Scientific).
Illumina sequencing was performed at the UUSMD (UNAM, Mexico). After removing residual DNA using DNase I (ThermoScientific) and ribosomal RNA with Terminator 5´-Phosphate-dependent exonuclease (Epicentre), the mRNA-enriched RNA was chemically fragmented to 150~200 bp. Based on these cleaved RNA fragments, cDNA was synthesized using a random hexamer primer and reverse transcriptase. After end reparation and ligation of adaptors, the products were amplified by PCR, further purified, and used to create the final cDNA library. Libraries were sequenced on an Illumina Genome Analyzer IIx.

treatment_protocol: RNA Later (Ambion) was added to cultures before harvesting cells


title: IHFB2 rep2

description:
DL1 with ihfB-2 mutation
IHFB2_rep2

source_name: IHFB2 rep2


title: P14 shCD4_BR4 RNA


title: L0416-041


title: P14 shCD4_BR3 RNA


title: IHFA1 rep2

description:
DL1 with ihfA-1 mutation
IHFA1_rep2

source_name: IHFA1 rep2


title: L0416-031


title: QGY-7703_PRMT7_sh2

first: Haitao

last: Chen

address: 1838 North Guangzhou Ave

institute: Southern medical university

data_processing:
FastQC v0.11.8 software was used for quality control of the RNA-seq data, and nucleotides with sequencing quality smaller than 20 were trimmed off.
RNA-seq reads were mapped to hg19 genome by tophat2 v2.1.1 software.
mRNA abundance and gene expression change were evaluated by Cufflinks v2.2.1 and Cuffdiff v2.2.1, respectively.
The functional enrichment of the differentially expressed genes was analyzed through the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression text files (FPKM)

growth_protocol: QGY-7703 cell line was cultured in DMEM medium supplemented with 10% FBS at 37 °C incubator with 5% CO2.

extract_protocol:
Total RNA were extracted with TRIzol reagent (Sigma) according to the manufacturer’s instruction.
RNA-seq library was constructed according to KAPA HyperPrep Kits’ instruction (Roche, KK8504).

treatment_protocol: The PRTM7 shRNA vector or the control vector plus VSVG and gag/pol encoding plasmids were transfected into the 293T cells, respectively. 24 h and 48 h later, the virus supernatant was harvested to infect QGY-7703 cells, respectively. Finally, the medium was replaced with fresh DMEM medium supplemented with puromycin (final concentration was 2.5 μg/ml) to screen stably transformed cells after the second infection.

value: hepatocellular carcinoma (HCC)

value: PRMT7 knockdown


title: L0416-013


title: IHFA1 rep1

description:
DL1 with ihfA-1 mutation
IHFA1_rep1

source_name: IHFA1 rep1


title: SC1

description: Control treatments


title: QGY-7703_PRMT7_sh1


title: P14 shCD4_BR2 RNA

value: CD8+ T cells (P14 TCR transgenic)


title: L0416-012


title: P14 shKdm6b_BR2 RNA


title: Fo5176 culture R2

description: 3 days in potato dextrose broth


title: L0416-033


title: DL1 rep2

source_name: DL1 rep2

value: WT


title: P14 shCD4_BR1 RNA


title: DL1 rep1


title: L0416-011


title: QGY-7703_control


title: 60_RCa14_A5

status: Public on Feb 24 2021

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
RNA-seq data were aligned to the MacaM v7.8 assembly of the Indian rhesus macaque genome ( available at https://www.unmc.edu/rhesusgenechip/index.htm ) Alignment was performed using STAR v2.4.0g1 using the annotation as a splice junction reference. Transcripts were annotated using the MacaM v7.8.2 annotation.
Transcript abundance was estimated using htseq-count v0.6.1p1
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: blood

extract_protocol:
Total RNA was prepared using QIAGEN Paxgene RNA kits. Globin transcripts were depleted using Ambion GlobinClear solution.
500-1000 ng of Globin depleted RNA was used for library preparation. Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq™ mRNA stranded kit as per manufacturer’s instructions.

value: blood

tag: subject

tag: timepoint

value: Phase II D7

tag: group

value: Single


title: 58_RLu13_A5


title: 57_RBp13_A5


title: 59_RQi14_A5


title: 56_RGy13_A5


title: 55_RSg14_A5

value: Double


title: 54_RFe14_A5


title: 51_RJh14_A5


title: 52_RJi13_A5


title: 50_RTa14_A5


title: 53_RUk13_A5


title: 48_RHp13_A5


title: 49_REc14_A5


title: 44_RQi14_A5

value: Phase II D0


title: 47_RYn14_A5


title: 45_RCa14_A5


title: 46_RFf14_A5


title: 42_RBp13_A5


title: 43_RLu13_A5


title: 39_RFe14_A5


title: 40_RSg14_A5


title: 37_RJi13_A5


title: 35_RTa14_A5


title: 34_REc14_A5


title: 33_RHp13_A5


title: 38_RUk13_A5


title: 36_RJh14_A5


title: 32_RYn14_A5


title: 31_RFf14_A5


title: 27_RBp13_A4

value: Phase I D10


title: 25_RSg14_A3


title: 24_RFe14_A3


title: 23_RUk13_A3


title: 22_RJi13_A3


title: 21_RJh14_A3


title: 20_RTa14_A3


title: 19_REc14_A3


title: 18_RHp13_A3


title: 15_RCa14_A2

value: Phase I D0


title: 16_RFf14_A3


title: 17_RYn14_A3


title: 14_RQi14_A2


title: 10_RSg14_A1


title: 13_RLu13_A2


title: 11_RGy13_A2


title: 8_RUk13_A1


title: 12_RBp13_A2


title: 30_RCa14_A4


title: 29_RQi14_A4


title: 5_RTa14_A1


title: 4_REc14_A1


title: 26_RGy13_A4


title: 6_RJh14_A1


title: 28_RLu13_A4


title: 9_RFe14_A1


title: 2_RYn14_A1


title: 3_RHp13_A1


title: 1_RFf14_A1


title: 41_RGy13_A5


title: 7_RJi13_A1


title: 298_Wang_ChIPGFP_BWX3655_rep2

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: xerD-mgfp mut3 (spec)

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1 independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al. 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature. Staphylococcus aureus strains were derived from HG003 (Herbert et al. 2010, PMID: 20212089). Cells were grown in tryptic soy broth (TSB) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al., 2013, PMID: 24158908; Wang et al. 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-PrC, or anti-His antibodies according to previous publication (Graham et al. 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina HiSeq2500, Nextseq550, or MiSeq sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

tag: protocol

value: CH, 37degree C

value: xerD-mgfp mut3 (spec)

tag: antibody

value: ChIP using anti-GFP antibodies


title: 299_Wang_ChIPGFP_BWX3898

description: xerD (Y277F)-mgfp mut3 (spec)

value: xerD (Y277F)-mgfp mut3 (spec)


title: 400_Wang_ChIPPrC_BWX3970

description: xerD-prC (spec)

value: xerD-prC (spec)

value: ChIP using anti-PrC antibodies


title: 424_Wang_WGS_BWX4162

description:
XDS∆5 no a.b.: ∆XDS1 (1717kb) (loxP no a.b.), ∆XDS2 (1912kb) (loxP no a.b.), ∆XDS3 (1989kb) (loxP no a.b.), ∆XDS4 (2033kb) (loxP no a.b.), ∆XDS5 (2597kb) (loxP no a.b.)
Whole genome sequencing sample

treatment_protocol: Cells were growing in CH medium at 37˚C, collected and processed for whole genome sequencing

value: XDS<delta>5 no a.b.:<delta>XDS1 (1717kb) (loxP no a.b.), <delta>XDS2 (1912kb) (loxP no a.b.), <delta>XDS3 (1989kb) (loxP no a.b.), <delta>XDS4 (2033kb) (loxP no a.b.), <delta>XDS5 (2597kb) (loxP no a.b.)


title: 423_Wang_WGS_BWX3510

description:
∆dif (loxP-kan-loxP)
Whole genome sequencing sample

value: <delta>dif (loxP-kan-loxP)


title: 425_Wang_WGS_BWX4215

description:
∆xerD (loxP-erm-loxP)
Whole genome sequencing sample

value: <delta>xerD (loxP-erm-loxP)


title: 422_Wang_WGS_BWX3450

description:
∆xerC (loxP-erm-loxP)
Whole genome sequencing sample

value: <delta>xerC (loxP-erm-loxP)


title: 411_Wang_input_BWX3381_rep2

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP)

value: parS<delta>9 no a.b., -117degree parS (loxP-kan-loxP)

value: none, input


title: 412_Wang_input_BWX3655_rep2

description: xerD-mgfp mut3 (spec)


title: 293_Wang_HiC_BWX4162

description: XDS∆5 no a.b.: ∆XDS1 (1717kb) (loxP no a.b.), ∆XDS2 (1912kb) (loxP no a.b.), ∆XDS3 (1989kb) (loxP no a.b.), ∆XDS4 (2033kb) (loxP no a.b.), ∆XDS5 (2597kb) (loxP no a.b.)

data_processing:
Library strategy: Hi-C
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1 independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle: mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

tag: restriction enzyme

value: HindIII


title: 295_Wang_HiC_BWX4215

description: ∆xerD (loxP-erm-loxP)


title: 291_Wang_HiC_BWX4006

description: parS∆9 no a.b., -1˚ parS no a.b., -19˚ (XDS)12 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -1degree parS no a.b., -19degree (XDS)12 (loxP-spec-loxP)


title: 292_Wang_HiC_BWX4037

description: parS∆9 no a.b., -1˚ parS no a.b., +26˚ (XDS)12 (loxP no a.b.), -19˚ (XDS)12 (loxP no a.b.)

value: parS<delta>9 no a.b., -1degree parS no a.b., +26degree (XDS)12 (loxP no a.b.), -19degree (XDS)12 (loxP no a.b.)


title: 294_Wang_HiC_BWX4168

description: parS∆9 no a.b., -80˚ (XDS)12 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -80degree (XDS)12 (loxP-spec-loxP)


title: Strain U04 0.5 mM diamide rep3

description:
U04
Fluconazole-resistant, constitutive Mrr1 activity
U04.dia.rep3

data_processing:
Raw reads were aligned to genome (ATCC 42720) with gsnap (2018-02-05) spliced alignment
sam to bam conversion with picardtools (2.14.1)
bam to read counts using "featureCounts" from subread (1.6.0)
CPM file generated from DESeq2
Genome_build: candida_lusitaniae_ATCC42720_w_CBS_6936_MT (MT contamination fixed and MT genome assembled)
Supplementary_files_format_and_content: tab-delimited text file of read counts per feature and Experiment
Supplementary_files_format_and_content: csv-delimited text files of CPM normalized counts for each Experiment

source_name: Exponential phase yeast cultures

extract_protocol:
RNA was harvested from snap-frozen pellets (using liquid nitrogen) using the MasterPure Yeast RNA Purification Kit (Epicentre)
Libraries were prepared using the Kapa mRNA HyperPrep Library  Kit (Roche) following standard Illumina protocols

value: wildtype

value: 0.5 mM diamide


title: 287_Wang_HiC_BWX3870

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -80˚ (XDS)12 (loxP-spec-loxP)

value: CH, 37degree C

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -80degree (XDS)12 (loxP-spec-loxP)


title: 290_Wang_HiC_BWX3910

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -109˚ (XDS)12 (loxP-kan-loxP), xerD(Y277F) (loxP-cat-loxP)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -109degree (XDS)12 (loxP-kan-loxP), xerD(Y277F) (loxP-cat-loxP)


title: 289_Wang_HiC_BWX3903

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), ycgO::tetR-cfp (phleo), -109˚ tetO48 (cat)

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), ycgO::tetR-cfp (phleo), -109degree tetO48 (cat)


title: 286_Wang_HiC_BWX3510

description: ∆dif (loxP-kan-loxP)


title: 296_Wang_HiC_BWX5141_xyl60m

description: parS∆9 no a.b., -94˚ parS (loxP no a.b.), -80˚ (XDS)12 (loxP-spec-loxP), lacA::PxylA Ec sspB (loxP-erm-loxP), smc-ssrA (loxP-kan-loxP)

treatment_protocol: Cells were growing in CH medium at 37˚C, xylose was added to 0.5% final concentration for 60min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 0.5% xylose for 60 min

value: parS<delta>9 no a.b., -94degree parS (loxP no a.b.), -80degree (XDS)12 (loxP-spec-loxP), lacA::PxylA Ec sspB (loxP-erm-loxP), smc-ssrA (loxP-kan-loxP)


title: 288_Wang_HiC_BWX3872

description: parS∆9 no a.b., -59˚ parS loxP-kan-loxP), -109˚ (XDS)12 (loxP-spec-loxP)

value: parS<delta>9 no a.b., -59degree parS loxP-kan-loxP), -109degree (XDS)12 (loxP-spec-loxP)


title: 426_Wang_WGS_PY79

description:
wild-type
Whole genome sequencing sample

value: wild-type


title: 285_Wang_HiC_BWX3474_rep2

description: parS∆9 no a.b., -117˚ parS (loxP-kan-loxP), ∆xerD (loxP-erm-loxP)

value: parS<delta>9 no a.b., -117degree parS (loxP-kan-loxP), <delta>xerD (loxP-erm-loxP)


title: 297_Wang_HiC_BWX5142_xyl60m

description: parS∆9 no a.b., -80˚ (XDS)12 (loxP-spec-loxP), lacA::PxylA Ec sspB (loxP-erm-loxP), smc-ssrA (loxP-kan-loxP)

value: parS<delta>9 no a.b., -80degree (XDS)12 (loxP-spec-loxP), lacA::PxylA Ec sspB (loxP-erm-loxP), smc-ssrA (loxP-kan-loxP)


title: 284_Wang_HiC_BWX3474


title: 283_Wang_HiC_BWX3381_rep2

value: parS<delta>9 no a.b., -117degree parS (loxP-kan-loxP)


title: 274_Wang_input_BWX4962

description: parS∆9 no a.b., XDS∆5 no a.b., -117˚ parS (loxP-kan-loxP),

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1)  independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature. Staphylococcus aureus strains were derived from HG003 (Herbert et al 2010, PMID: 20212089). Cells were grown in tryptic soy broth (TSB) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, or anti-His antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina HiSeq2500, Nextseq550, or MiSeq sequencing platforms. Illumina Truseq indexes were used.

value: parSdelta9 no a.b., XDSdelta5 no a.b., -117degree parS (loxP-kan-loxP),

value: none, input


title: LysM replicate 4

city: Houston

first: Nathaniel

middle: Karl

last: Berg

state: Texas

address: 6431 Fannin Street, MSB 5.026

institute: University of Texas Health Science Center at Houston

data_processing:
Integrated Nextseq 550 base calling
Bases with quality scores < 20 and adapter sequences were removed from raw data with Cutadapt (v1.15), followed by alignment of clean RNA-seq reads to GRCm38 with STAR (v2.5.3a)
Gene abundance was counted by HTseq-count uniquely-mapped reads number with default parameter using GencodeM15. Genes with > 5 reads in at least one sample were included for differential expression analysis by DESeq2 software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene values for each sample, log2FC (Netrin1loxp/loxp LysM Cre vs. LysM Cre), and adjusted P values

source_name: BAL Cells

extract_protocol:
Cell pellet RNA was harvested using Trizol reagent. libraries were prepared with KAPA mRNA Hyper Prep Kit (KK8581, Roche Holding AG, Switzerland)
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with intratracheal LPS and then BAL cells were collected 3-days later using 3 washes with ice cold PBS. Neutrophils were depleted from the BAL samples using antibody-mediated isolation. The resulting cells were pelleted.

value: BAL Cells

value: LysM Cre

value: Three days post LPS challenge


title: LysM replicate 3


title: Netrin1loxp/loxp LysM Cre replicate 3

value: Netrin1loxp/loxp LysM Cre


title: Netrin1loxp/loxp LysM Cre replicate 2


title: LysM replicate 1


title: Netrin1loxp/loxp LysM Cre replicate 1


title: LysM replicate 2


title: 234_Wang_HiC_BWX4055_1mMIPTG_20min

description: parS∆9 no a.b., -1 ̊ parS no a.b., +26˚  12x XDS (loxP no a.b.), -19˚  12x XDS (loxP no a.b.), yvbJ::Pspank (optRBS) xerD (cat), ∆xerD (loxP-erm-loxP)

data_processing:
Library strategy: HiC-Seq
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.     For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) or Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence: NC_007795.1)  independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) genomes was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) and Staphylococcus aureus (NCTC8325) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1; NC_007795.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: matrix.txt files: 10kb bins of B. subtilis genome; normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files: genome position; reads; number of reads at each genome position

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 20min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 1mM IPTG for 20 min

value: parSdelta9 no a.b., -1degree parS no a.b., +26degree  12x XDS (loxP no a.b.), -19degree  12x XDS (loxP no a.b.), yvbJ::Pspank (optRBS) xerD (cat), deltaxerD (loxP-erm-loxP)

value: HindIII


title: 235_Wang_HiC_BWX4055_1mMIPTG_25min

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 25 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 1mM IPTG for 25 min


title: 252_Wang_ChIPSMC_BWX4962

value: CH, 37degree C

value: ChIP using anti-SMC antibodies


title: C3H/HeJ AA mice - Tofa #2

first: Zhenpeng

last: Dai

state: NY

address: 1150 St. Nicholas Ave

department: Dermatology

institute: Columbia University

description:
DZ23
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

data_processing:
Pooled and sequenced on an Illumina HiSeq 4000 Output run to generate 16-23 million 75-bp paired-end reads per sample at GENEWIZ (South Plainfield, NJ, GENEWIZ). The FASTQ files were aligned to the mouse reference genome (mm10) with Subread aligner (Rsubread_1.28.1, R version: 3.4.4, Platform: x86_64-pc-linux-gnu (64-bit)). Raw counts were generated using the same package, Subread aligner (Rsubread_1.28.1, R version: 3.4.4, Platform: x86_64-pc-linux-gnu (64-bit)).
Differential expression (DE) analysis was performed using DESeq2 package (v1.18.1) of R. DE was defined using a significance of FDR<0.05 comparing each treated cohort to the vehicle-treated cohort. Unsupervised hierarchical clustering and gene adjacency matrices were generated using Multiple Experiment Viewer (MeV).
To visualize the difference in expression in the ALADIN genes, the z-score normalized hit counts of the ALADIN genes were inputs for clustering.
Clustering results in this study were done naïve to the treatment status of each sample, and unblinded at the end.
iPathwayGuide (https://www.advaitabio.com) and ClusterProfiler package (v3.6.0) of R was used for the pathway analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx: Excel file includes raw counts.
Supplementary_files_format_and_content: processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx: Excel file includes abundance measurements.

source_name: skin biopsies

extract_protocol:
Total cellular RNA was extracted using RNeasy Plus Micro Kit (catalog 74034, QIAGEN) from skin homogenates of indicated JAKi treated mice or control. RNA quality and quantity were determined using an Agilent BioAnalyzer (Agilent Technologies).
Libraries were constructed, pooled and sequenced on an Illumina HiSeq Mid Output run to generate 16-23 million 75-bp paired-end reads per sample at GENEWIZ (South Plainfield, NJ, GENEWIZ).

treatment_protocol: The JAK inhibitors were first dissolved in a small volume of DMSO (catalog D12345, Thermo Scientific) and further were diluted with polyethylene glycol 300 (catalog 202371, MilliporeSigma). For topical treatment, C3H/HeJ AA mice were topically treated with 2% (w/w) various JAKis in Aquaphor (Aquaphor) twice daily, or vehicle control.

value: C3H/HeJ AA

value: skin

value: Tofa


title: 232_Wang_HiC_BWX4055_1mMIPTG_10min

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 1mM IPTG for 10 min


title: 230_Wang_HiC_BWX4004

description: parS∆9 no a.b., -1 ̊ parS no a.b., +26˚  12x XDS (loxP-kan-loxP)

value: parSdelta9 no a.b., -1degree parS no a.b., +26degree  12x XDS (loxP-kan-loxP)


title: 231_Wang_HiC_BWX4055_0IPTG


title: C3H/HeJ AA mice - RUXO #2

description:
DZ20
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: RUXO


title: C3H/HeJ AA mice - RUXO #1

description:
DZ19
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - Tofa #1

description:
DZ22
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK3i #3

description:
DZ18
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK3i #1

description:
DZ16
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK3i #2

description:
DZ17
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: 228_Wang_HiC_BWX3908

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-kan-loxP), ∆xerD (loxP-erm-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerD (loxP-erm-loxP)


title: C3H/HeJ AA mice - RUXO #3

description:
DZ21
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: 227_Wang_HiC_BWX3906

description: parS∆9 (loxP-spec-loxP), -94˚ parS (loxP no a.b.), -109˚ 12x XDS (loxP-kan-loxP), ∆xerC (loxP-erm-loxP)

value: parSdelta9 (loxP-spec-loxP), -94degree parS (loxP no a.b.), -109degree 12x XDS (loxP-kan-loxP), deltaxerC (loxP-erm-loxP)


title: 238_Wang_HiC_SaWX013

description: HG003, geh (40˚)::pWX726 (BsXDS12 loxP-kan-loxP)

organism: Staphylococcus aureus

source_name: Staphylococcus aureus HG003

treatment_protocol: Cells were growing in TSB medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: TSB, 37degree C

value: HG003, geh (40degree)::pWX726 (BsXDS12 loxP-kan-loxP)


title: 237_Wang_HiC_aTP742

description: HG003 ΔparB (loxP-kan-loxP)

value: HG003 {delta}parB (loxP-kan-loxP)


title: C3H/HeJ AA mice - JAK2i #3

description:
DZ15
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - Tofa #3

description:
DZ24
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: 236_Wang_HiC_HG003

description: S. aureus subsp. aureus NCTC8325 with rsbU and tcaR repaired


title: 233_Wang_HiC_BWX4055_1mMIPTG_15min

treatment_protocol: Cells were growing in CH medium at 37˚C, IPTG was added to 1mM final concentration for 15 min, fixed by 3% formaldehyde for 30min at room temperature

value: CH, 37degree C, 1mM IPTG for 15 min


title: C3H/HeJ AA mice - JAK2i #2

description:
DZ14
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK2i #1

description:
DZ13
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK1i #2

description:
DZ11
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK1i #1

description:
DZ10
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - JAK1i #3

description:
DZ12
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - Control #3

description:
DZ09
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: untreated


title: C3H/HeJ AA mice - Control #1

description:
DZ07
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - Control #2

description:
DZ08
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx


title: C3H/HeJ AA mice - Tofa pretreatment

description:
DZ06
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: Tofa pretreatment


title: C3H/HeJ AA mice - RUXO pretreatment

description:
DZ05
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: RUXO pretreatment


title: Vero 48h Input 2

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description:
monkey_counts.txt
V2_in_2

data_processing:
Adapters were trimmed using fastp.
Trimmed reads were first aligned to a file of known repetitive sequences. These reads were discarded.
Remaining reads were then aligned to the SARS-CoV-2 genome
Remaining reads were then aligned to the host genome (human or monkey)
Counts were quantified using featureCounts
Genome_build: hg38 or ChlSab1.1
Supplementary_files_format_and_content: filtered counts matrix

organism: Chlorocebus sabaeus

source_name: VeroE6 cells

growth_protocol: Cell lines were cultured using standard media and passaging conditions.

extract_protocol:
Sample proteins were digested and RNA was extracted via commercial spin column (Zymo).
TAKARA Bio SMART-Seq library prep kit was used to prepare RNA-seq libraries
Paired end RNA sequencing

treatment_protocol: Cells were either not infected with SARS-CoV-2, or infected for 24 or 48 hours. In each of these conditions, bulk RNA seq was performed (input) and also RNA-seq after crosslinking and pulldown for the SARS-CoV-2 viral RNA.

tag: cell line

tag: infection duration

value: SARS-CoV-2 infection, 48h

tag: pulldown

value: No


title: Vero 48h Input 3

description:
monkey_counts.txt
V2_in_3


title: Vero 24h Input 2

description:
monkey_counts.txt
V1_in_2

value: SARS-CoV-2 infection, 24h


title: Vero 48h Input 1

description:
monkey_counts.txt
V2_in_1


title: Vero 24h IP 2

description:
monkey_counts.txt
V1_ip_2

value: Yes


title: Vero 24h Input 3

description:
monkey_counts.txt
V1_in_3


title: Vero 48h IP 2

description:
monkey_counts.txt
V2_ip_2


title: C3H/HeJ AA mice - JAK2i pretreatment

description:
DZ03
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

tag: strain

value: C3H/HeJ AA

value: skin

value: JAK2i pretreatment


title: Vero 24h Input 1

description:
monkey_counts.txt
V1_in_1


title: C3H/HeJ AA mice - JAK1i pretreatment

description:
DZ02
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: JAK1i pretreatment


title: Vero 48h IP 1

description:
monkey_counts.txt
V2_ip_1


title: Vero 48h IP 3

description:
monkey_counts.txt
V2_ip_3


title: Vero 24h IP 3

description:
monkey_counts.txt
V1_ip_3


title: Vero 24h IP 1

description:
monkey_counts.txt
V1_ip_1


title: Vero Mock IP 3

description:
monkey_counts.txt
VM_ip_3


title: C3H/HeJ AA mice - Control pretreatment

description:
DZ01
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: Control pretreatment


title: Vero Mock Input 3

description:
monkey_counts.txt
VM_in_3


title: Vero Mock IP 2

description:
monkey_counts.txt
VM_ip_2


title: Vero Mock IP 1

description:
monkey_counts.txt
VM_ip_1


title: C3H/HeJ AA mice - JAK3i pretreatment

description:
DZ04
processed_data-Raw_gene_counts_JAKi_AA-mice.xlsx
processed_data-ALADIN_CTL_signature_genes-JAKi_AA-mice.xlsx

value: JAK3i pretreatment


title: Vero Mock Input 1

description:
monkey_counts.txt
VM_in_1


title: Vero Mock Input 2

description:
monkey_counts.txt
VM_in_2


title: N2a KO Torin1 Ribo-seq rep3

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
15_S14_L005
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt
processed data file: TE_ctrl_Torin1_vs_KO_Torin1.txt

data_processing:
all fastq files were adaptor stripped using cutadapt. Only trimmed reads were retained, with a minimum length of 15 and a quality cutoff of 2 (parameters: -a CTGTAGGCACCATCAAT -- trimmed-only --minimum-length = 15 --quality-cutoff = 2
reads were mapped, using default parameters, with HISAT2 (Kim et al., 2015), using their pre-prepared UCSC mm10 genome and index
Only primary alignments were retained and reads were removed if they mapped to rRNA, tRNA and pseudogenes according to mm10 RepeatMasker definitions from UCSC. A full set of transcript and CDS sequences for Ensembl release 84 was then established. Only canonical transcripts [defined by mm10 knownCanonical table, downloaded from UCSC] were retained with their corresponding CDS. Reads were then mapped to the canonical transcriptome with bowtie2 (Langmead and Salzberg, 2012) using default parameters
Counts were made by aggregating any reads overlapping with the CDS and RPKMs were then generated through normalising by CDS length and total counts for the sample
For Riboseq data; The P-site position of each read was predicted by riboWaltz (Lauria et al., 2018) and confirmed by inspection. Counts were made by aggregating P-sites overlapping with the CDS and P-sites Per Kilobase Million (PPKMs) were then generated through normalising by CDS length and total counts for the sample
For Riboseq data; Transcripts were only kept in the analysis if they had a CPM > 1 in all triplicates for either at least one of the conditions in the pairwise comparison. For further analysis transcripts were filtered if their CDS length was not a multiple of three and if they did not begin with a standard start codon (Lawrence et al., 2000) and end with a standard stop codon (UAG, UGA, UAA).
Differential expression was finally performed pairwise between Ctrl or KO triplicates in the presence of Torin1 or Vehicle using edgeR (Robinson et al., 2010) on default settings
TE was assessed using RiboDiff (Zhong et al) with default parameters with the same Ribo-Seq and RNA-Seq samples as input, using the same expression pre-filters as the edgeR differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: EdgeR files, tab delimited. Normalised  gene abundance for each replicate and differential expression
Supplementary_files_format_and_content: RiboDiffOuput files, tab delimited

source_name: Neuro-2a_eIF4E3 KO_Torin1 2hrs

growth_protocol: DMEM high glucose, no pyruvate, 10% FBS, 1% PEN/STREP, humidified athmosphere at 5% CO2 37 °C

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent as described by the manufacturer.
For Ribo-seq, cells were lysed in polysome lysis buffer as described in Weiss et al 2021.
For RNA-seq, libraries were prepared following Illumina Truseq Stranded mRNA kit.
For Ribo-seq, homemade protocol was adapted from Ingolia et al 2012 and is available at Weiss et al 2021.

treatment_protocol: Cells were seeded 48 hours before treatment. Each replicate correspond to a different passage of the cells. Treatment was performed by adding 250 nM Torin1 in DMSO or an equivalent volume of vehicle (DMSO) for 2 hours at 37 °C

value: Neuroblastoma cell line

tag: genotype

value: eIF4E3 KO

value: Torin1 2hrs


title: N2a KO vehicle Ribo-seq rep2

description:
24_S11_L004
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt

source_name: Neuro-2a_eIF4E3 KO_DMSO 2hrs

value: DMSO 2hrs


title: N2a KO Torin1 Ribo-seq rep1

description:
12_S6_L003
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt
processed data file: TE_ctrl_Torin1_vs_KO_Torin1.txt


title: N2a KO vehicle Ribo-seq rep1

description:
22_S7_L003
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a KO Torin1 Ribo-seq rep2

description:
14_S10_L004
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt
processed data file: TE_ctrl_Torin1_vs_KO_Torin1.txt


title: N2a ctrl Torin1 Ribo-seq rep3

description:
35_S16_L005
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt
processed data file: TE_ctrl_vehicle_vs_KO_vehicle.txt

source_name: Neuro-2a_WT_Torin1 2hrs

value: WT


title: N2a ctrl Torin1 Ribo-seq rep2

description:
34_S12_L004
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt
processed data file: TE_ctrl_vehicle_vs_KO_vehicle.txt


title: N2a ctrl vehicle Ribo-seq rep1

description:
42_S9_L003
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt

source_name: Neuro-2a_WT_DMSO 2hrs


title: N2a KO Torin1 RNA-seq rep3

description:
T3d_S42_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a ctrl vehicle Ribo-seq rep2

description:
44_S13_L004
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a KO Torin1 RNA-seq rep2

description:
T2d_S40_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a KO Torin1 RNA-seq rep1

description:
T1d_S36_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a ctrl vehicle Ribo-seq rep3

description:
45_S17_L005
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl Torin1 Ribo-seq rep1

description:
32_S8_L003
processed data file: Riboseq_ctrl_vehicle_vs_ctrl_Torin1.txt
processed data file: TE_ctrl_vehicle_vs_KO_vehicle.txt


title: N2a KO vehicle Ribo-seq rep3

description:
25_S15_L005
processed data file: Riboseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a KO vehicle RNA-seq rep3

description:
T3c_S43_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt


title: N2a KO vehicle RNA-seq rep2

description:
T2c_S39_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt


title: TLG004_1406853_PD1_low_Tumor_Treg_rep4

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: sgRNA transduced OT-I cells

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: Treg cells from the MC38 colon adenocarcinoma-bearing mice

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Tregs were sorted from lymph node/tumor from the B16 melanoma tumor and MC38 colon adenocarcinoma, and Tregs were sorted from pheripheral lymph node from WT mice.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: background strain

value: Foxp3-YFP+ cells

tag: cell population

value: tumor infiltrating Treg

tag: tissue source

value: MC38 colon adenocarcinoma

tag: cell markers

value: PD1 low


title: THG004_1406849_PD1_high_Tumor_Treg_rep4

description: sgRNA transduced OT-I cells

tag: cell type

value: PD1 high


title: TLG003_1406852_PD1_low_Tumor_Treg_rep3

description: sgRNA transduced OT-I cells


title: N2a KO vehicle RNA-seq rep1

description:
T1c_S35_L005
processed data file: RNAseq_KO_vehicle_vs_KO_Torin1.txt

tag: treatment


title: SAL142_1888479_Fasn KO_Tumor Treg_rep3

description: sgRNA transduced OT-I cells

source_name: Treg cells from the B16 melanoma-bearing mice

value: B16 melanoma tumor

value: Fasn KO


title: THG002_1406847_PD1_high_Tumor_Treg_rep2

description: sgRNA transduced OT-I cells


title: TLG001_1406850_PD1_low_Tumor_Treg_rep1

description: sgRNA transduced OT-I cells


title: TLG002_1406851_PD1_low_Tumor_Treg_rep2

description: sgRNA transduced OT-I cells


title: THG003_1406848_PD1_high_Tumor_Treg_rep3

description: sgRNA transduced OT-I cells


title: N2a ctrl vehicle RNA-seq rep3

description:
T3a_S41_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl vehicle RNA-seq rep2

description:
T2a_S37_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl Torin1 RNA-seq rep1

description:
T1b_S34_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl vehicle RNA-seq rep1

description:
T1a_S33_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl Torin1 RNA-seq rep2

description:
T2b_S38_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: N2a ctrl Torin1 RNA-seq rep3

description:
T3b_S44_L005
processed data file: RNAseq_ctrl_vehicle_vs_ctrl_Torin1.txt


title: SAL141_1888478_Fasn KO_Tumor Treg_rep2

description: sgRNA transduced OT-I cells


title: Spleen Treg cells in EAE

data_processing:
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

source_name: Treg cells isolated from spleen in the experimental autoimmune encephalomyelitis (EAE) mouse model

growth_protocol: Wild-type Foxp3 YFP-Cre mice were immunized subcutaneously at four injection sites with a total of 200  ul of emulsified incomplete Freund s adjuvant supplemented with 1 mg Mycobacterium tuberculosis strain H37Ra (Difco) (complete Freund's adjuvant; CFA) and 200 ug myelin oligodendrocyte glycoprotein (amino acids 35 55; MOG35 55), and received i.p. injections of 200 ng pertussis toxin (PTX; List Biological Laboratories) at the time of immunization and 48 h later

extract_protocol:
Foxp3-YFP+ Treg cells were isolated from the spleen and CNS (spinal cord and brain) of Foxp3 YFP-Cre mice at the peak of EAE (day 15) after MOG immunization
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: YFP-Foxp3+ Treg cells


title: SAL137_1888474_WT_Tumor Treg_rep2

description: sgRNA transduced OT-I cells


title: CNS Treg cells in EAE

source_name: Treg cells isolated from CNS in the experimental autoimmune encephalomyelitis (EAE) mouse model


title: SAL140_1888477_Fasn KO_Tumor Treg_rep1

description: sgRNA transduced OT-I cells


title: Scap Treg-specific deletion2

source_name: CD45+ immune cells in mice bearing B16 tumours

growth_protocol: Mice were injected subcutaneously with 2 × 10^5 B16-F10 melanoma cells in the right flank

extract_protocol:
CD45+ immune cells were sorted from B16 tumors on day 19 and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: CD45+ immune cells


title: SAL138_1888475_WT_Tumor Treg_rep3

description: sgRNA transduced OT-I cells


title: wild-type2


title: Scap Treg-specific deletion1


title: wild-type1


title: SAL136_1888473_WT_Tumor Treg_rep1

description: sgRNA transduced OT-I cells


title: SAL123_1876265_Scap KO_Tumor Treg_rep1

description: sgRNA transduced OT-I cells

value: Scap KO


title: THG001_1406846_PD1_high_Tumor_Treg_rep1

description: sgRNA transduced OT-I cells


title: SAL119_1876261_WT_Tumor Treg_rep1

description: sgRNA transduced OT-I cells


title: SAL120_1876262_WT_Tumor Treg_rep2

description: sgRNA transduced OT-I cells