title: set2 TES seq 0h replicate 3

description:
TES seq
CHI114A88_S27_L003

source_name: set2 TES seq 0h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: set2 TES seq 0h replicate 2

status: Public on Dec 15 2020

type: SRA

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
TES seq
CHI114A87_S26_L003

library_source: transcriptomic

data_processing:
library strategy: TES-Seq
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 2 --alignIntronMax 1” (i.e. not allowing introns) was used to align TES-seq reads to the SK1 genome assembly (plus three spike-in sequences). The alignments with mapping quality of >=10 were kept for further analysis.
For the TES-seq data, the reads kept were those with soft-clipping at the 3’ end (size of soft-clipping part <=10) and with at least two consecutive non-templated As in the soft-clipping part. Insertions/deletions were also not allowed.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10".  The 3’-most nucleotide of aligned reads were extracted to generate the genome-wide tracks of TSSs.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the TES BedGraph tracks across the genome, for both forward and reverse strands.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in regular YPD  (2.0% (wt/vol) glucose) and grown to exponential phase (OD600 < 2.0) at 30°C and 300 rpm. Approximately 0.05 OD of exponentially growing yeast were inoculated into new flasks containing reduced glucose YPD (1.0% (wt/vol) glucose). After 16-18 hours, cells were then pelleted, washed with sterile miliQ water, and re-suspended in supplemented sporulation (SPO) media at an OD600 of 2.5.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol:chloroform:isoamyl alcohol (25:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
To obtain libraries representing the 3’ ends of polyadenylated transcripts, at least 1 μg was used for 3’ end sequencing. RNA fragments were mixed with 2.5 μM GsuI20TVN primer (/5BiotinTEG/ GAGCTAGTTCTGGAGTTTTTTTTTTTTTTTTTTTTVN), 0.5 mM 5-Methylcytosine-dNTPs (D1030, Zymo Research) and 0.5 μl RNasin Plus. Reaction mixtures were denatured at 65°C for 5 minutes and held at 50°C without allowing to cool. SuperScript IV, reaction buffer and 0.4 μg of Actinomycin D were added to the hot reaction mixtures and reverse transcription was performed at 50°C for 10 minutes, 80°C for 10 minutes and held at 4°C. Samples were cleaned with 1.8x volume HighPrep beads and biotinylated RNA:DNA hybrids were captured on MyOne Streptavidin C1 Dynabeads. After capture, streptavidin beads were washed once with 1x NEbuffer 2 (B7002S, NEB), re-suspended in water and subjected to second strand synthesis. The 50 μl second strand synthesis reaction consisted of 20 μl re-suspended streptavidin beads, 1X NEbuffer 2, 250 μM dNTPs, 26 μM NAD+ (B9007S), 2.5 units RNase H, 10 units E.coli DNA ligase (M0205S), and 15 units DNA polymerase I (M0209S). Second strand synthesis reactions were conducted at 16°C for 2.5 hours on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After reaction, beads were washed once with 1x binding and washing buffer (5.0 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1.0 M NaCl) and once with buffer B (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 0.1 mg/ml BSA). Washed beads were re-suspended in 18 μl buffer B and digested with 10 units of GsuI (ER0461, ThermoFisher Scientific) at 30°C for 1 hour on a thermomixer (1400 rpm for 15 seconds, rest for 2 minutes). After digestion, the DNA fragments in the supernatant were extracted with Phenol/chloroform and precipitated at -20°C overnight in ethanol with 0.3 M sodium acetate and 1 μl linear acrylamide. Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Gel purified libraries were quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.

treatment_protocol: For the regular WT time course, 50 μM CuSO4 was added after 2h in SPO and 1 μM β-estradiol was added after 6h in SPO for synchronous sporulation. For the mutant samples and their controls,  50 μM CuSO4 was added after 2h in SPO. Additionally after 2h in SPO, all cells with the SPT16-AID allele were treated with 3-indole-acetic acid (3-IAA, Sigma-Aldrich I3750) to a final concentration of 500 μM from a 1 M stock dissolved in DMSO.

tag: strain/background

tag: treatment

value: no treatment


title: set3 TES seq 0h replicate 1

description:
TES seq
CHI114A89_S28_L003

source_name: set3 TES seq 0h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: 67_1_10

type: genomic

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

institute: King's College London

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

hyb_protocol: Samples were processed according to the Illumina Infinium Methylation EPIC BeadChip protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium MethylationEPIC BeadChip using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions. Normalized betas using dasen function

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: buccal swab at age 10

label_protocol: 500 ng DNA was sodium bisulphite treatedas amplified using the EZ-96 DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s standard protocol

extract_protocol: genomic DNA was extracted and purified from buccal and blood samples using standardised protocols.

tag: familyid

tag: twinid

tag: gender

value: Female

tag: tissue

value: Buccal

tag: age

value: Age 10

tag: disease state

value: Exposed

tag: smokingpackyears

tag: category


title: 67_1_18C

source_name: buccal swab at age 18

value: Age 18


title: set2 set3 TES seq 0h replicate 3

description:
TES seq
CHI114A85_S64_L006

source_name: set2 set3 TES seq 0h

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: 66_2_18B

description:
comments: This sample matched with  66_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

value: Male

value: Blood


title: set2 TES seq 0h replicate 1

description:
TES seq
CHI114A86_S25_L003


title: 66_2_18C


title: set2 set3 TES seq 0h replicate 2

description:
TES seq
CHI114A84_S63_L006


title: set2 set3 TES seq 0h replicate 1

description:
TES seq
CHI114A83_S62_L006


title: Wild-type control TES seq 0h replicate 3

description:
TES seq
CHI114A82_S61_L006

source_name: Wild-type control TES seq 0h

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: Wild-type control TES seq 0h replicate 2

description:
TES seq
CHI114A81_S42_L004


title: 66_1_18C

value: Notexposed


title: 66_1_5

source_name: buccal swab at age 5

value: Age 5


title: Wild-type control TES seq 0h replicate 1

description:
TES seq
CHI114A80_S41_L004


title: Wild-type TES seq 0h replicate 2

description:
TES seq
CHI114A46_S24_L003

source_name: Wild-type TES seq 0h


title: 65_2_5


title: Wild-type TES seq 0h replicate 3

description:
TES seq
CHI114A57_S31_L004


title: 66_2_5


title: 68_1_18B

description:
comments: This sample matched with  68_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TES seq 0h replicate 1

description:
TES seq
CHI114A35_S18_L002


title: 65_2_18C


title: Wild-type TSS seq 0h no decapping control

description:
TSS seq
CHI114A23_S47_L006

data_processing:
library strategy: TSS (Transcription Start Sites (TSS)-Seq
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
The custom 5’ adapter sequence specific to the protocol was removed by re-running cutadapt with the parameters “-g CACTCTGAGCAATACC -O 16 --minimum-length=20”, and only the reads containing the adapter sequence were used for further analysis.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 2 --alignIntronMax 1” (i.e. not allowing introns) was used to align TSS-seq reads to the SK1 genome assembly (plus three spike-in sequences). The alignments with mapping quality of >=10 were kept for further analysis.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10".  The 5’-most nucleotide of aligned reads were extracted to generate the genome-wide tracks of TSSs.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the TSS BedGraph tracks across the genome, for both forward and reverse strands.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both sense and antisense coverage. See data processing step for more details.

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol:chloroform:isoamyl alcohol (25:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
To obtain libraries representing the 5’ ends of polyadenylated and capped transcripts, approximately 5 µg of poly(A)+-RNA together with in-vitro spike ins were first subjected to zinc-mediated fragmentation (Ambion) at 70 °C. The reaction was cleaned up using Qiagen min-elute columns to isolate RNA fragments with mode length of ~200 nt. These fragments were then incubated with shrimp alkaline phosphatase at 37 °C to remove the 5’ phosphate groups of non-capped fragments followed by acid-phenol/chloroform extraction and ethanol precipitation. With the exception of a non-decapping control sample, dephosphorylated fragments were next treated with Cap-Clip™ acid pyrophosphatase (CellScript) to remove the 5’-terminal caps from fragments representing the bona fide 5’ ends of transcripts. After another round of acid-phenol/chloroform extraction and ethanol precipitation, all samples were treated with T4 RNA ligase 1, high concentration (NEB) to introduce a custom adapter sequence to the 5’ un-capped ends of fragments. Excess adapters were removed via a column clean up step. First strand cDNA synthesis was performed using Superscript IV (ThermoFisher) and second strand synthesis was performed using a KAPA HiFi HotStart ReadyMix (KAPA Biosystems). Double-stranded cDNA was quantified by Qubit (Life Technologies) and used as input for library preparation using a KAPA Hyper Prep kit (KAPA Biosystems) and KAPA Single-indexed adapters (KAPA Biosystems). Amplified libraries were cleaned and purified by gel extraction. Libraries quantified by Qubit and were sequenced on the Illumina HiSeq 4000 platform with 75-base single-end reads.


title: 66_2_10


title: 65_2_10


title: 65_2_18B

description:
comments: This sample matched with  65_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 65_1_18C


title: Wild-type TSS seq 8h replicate 3

description:
TSS seq
CHI114A31_S49_L006

source_name: Wild-type TSS seq 8h

value: 50 μM CuSO4 (2h), 1 μM β-estradiol (6h)


title: Wild-type TSS seq 9h replicate 3

description:
TSS seq
CHI114A32_S50_L006

source_name: Wild-type TSS seq 9h


title: 65_1_18B

description:
comments: This sample matched with  65_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 65_1_10


title: Wild-type TSS seq 8h replicate 2

description:
TSS seq
CHI114A19_S43_L005


title: Wild-type TSS seq 8h replicate 1

description:
TSS seq
CHI114A8_S38_L005


title: Wild-type TSS seq 9h replicate 1

description:
TSS seq
CHI114A9_S39_L005


title: Wild-type TSS seq 7h NDT80 uninduced replicate 3

description:
TSS seq
CHI114A34_S52_L006

source_name: Wild-type TSS seq 7h NDT80 uninduced

value: 50 μM CuSO4 (2h)


title: 64_2_18C


title: Wild-type TSS seq 7h NDT80 uninduced replicate 2

description:
TSS seq
CHI114A22_S46_L006


title: 66_1_18B

description:
comments: This sample matched with  66_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TSS seq 7h NDT80 uninduced replicate 1

description:
TSS seq
CHI114A11_S41_L005


title: Wild-type TSS seq 7h replicate 3

description:
TSS seq
CHI114A30_S48_L006

source_name: Wild-type TSS seq 7h


title: 64_2_18B

description:
comments: This sample matched with  64_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 64_2_10


title: 64_1_5


title: 64_1_18C


title: 64_1_18B

description:
comments: This sample matched with  64_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TSS seq 9h replicate 2

description:
TSS seq
CHI114A20_S44_L005


title: Wild-type TSS seq 7h replicate 1

description:
TSS seq
CHI114A7_S37_L005


title: SPT16-AID control TSS seq 6h replicate 3

description:
TSS seq
CHI114A151_S62_L008

source_name: SPT16-AID control TSS seq 6h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative

value: 50 μM CuSO4 (2h), 500 μM indole-3-acetic acid (2h)


title: Wild-type TSS seq 7h replicate 2

description:
TSS seq
CHI114A18_S42_L005


title: SPT16-AID control TSS seq 6h replicate 2

description:
TSS seq
CHI114A150_S61_L008


title: 64_1_10


title: SPT16-AID control TSS seq 6h replicate 1

description:
TSS seq
CHI114A149_S60_L008


title: 63_2_5


title: 63_2_18B

description:
comments: This sample matched with  63_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 64_2_5


title: SPT16-AID, OsTIR TSS seq 6h replicate 3

description:
TSS seq
CHI114A145_S42_L006

source_name: SPT16-AID, OsTIR TSS seq 6h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: 63_2_10


title: SPT16-AID, OsTIR TSS seq 6h replicate 1

description:
TSS seq
CHI114A143_S40_L006


title: set3 TSS seq 6h replicate 3

description:
TSS seq
CHI114A103_S34_L003

source_name: set3 TSS seq 6h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: 63_1_18C

value: Female


title: set3 TSS seq 6h replicate 2

description:
TSS seq
CHI114A102_S33_L003


title: 63_1_18B

description:
comments: This sample matched with  63_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 63_1_10

value: Buccal


title: 62_2_18B

description:
comments: This sample matched with  62_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 62_2_5


title: set2 TSS seq 6h replicate 3

description:
TSS seq
CHI114A100_S31_L003

source_name: set2 TSS seq 6h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: 62_2_18C


title: set2 set3 TSS seq 6h replicate 3

description:
TSS seq
CHI114A97_S70_L006

source_name: set2 set3 TSS seq 6h


title: set2 TSS seq 6h replicate 2

description:
TSS seq
CHI114A111_S20_L002


title: set2 TSS seq 6h replicate 1

description:
TSS seq
CHI114A98_S29_L003


title: 62_2_10

value: Age 10


title: 63_2_18C

value: Age 18

value: Exposed


title: 62_1_18C

value: Male


title: set2 set3 TSS seq 6h replicate 2

description:
TSS seq
CHI114A96_S69_L006

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: set2 set3 TSS seq 6h replicate 1

description:
TSS seq
CHI114A95_S68_L006


title: 62_1_5


title: SPT16-AID, OsTIR TSS seq 6h replicate 2

description:
TSS seq
CHI114A144_S41_L006


title: Wild-type control TSS seq 6h replicate 3

description:
TSS seq
CHI114A94_S67_L006

source_name: Wild-type control TSS seq 6h

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: 62_1_10

source_name: buccal swab at age 10

value: Notexposed


title: Wild-type control TSS seq 6h replicate 2

description:
TSS seq
CHI114A93_S66_L006


title: 63_1_5

value: Age 5


title: Wild-type control TSS seq 6h replicate 1

description:
TSS seq
CHI114A92_S65_L006


title: set3 TSS seq 6h replicate 1

description:
TSS seq
CHI114A101_S32_L003


title: Wild-type TSS seq 6h replicate 3

description:
TSS seq
CHI114A29_S17_L002

source_name: Wild-type TSS seq 6h


title: 61_2_5


title: 61_2_18C

source_name: buccal swab at age 18


title: 61_2_18B

description:
comments: This sample matched with  61_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

value: Blood


title: Wild-type TSS seq 6h replicate 1

description:
TSS seq
CHI114A6_S27_L003

value: 50 μM CuSO4 (2h)


title: 61_2_10


title: 61_1_5


title: 61_1_18C


title: Wild-type TSS seq 60 min RTG replicate 1

description:
TSS seq
CHI114A122_S4_L001

source_name: Wild-type TSS seq 60 min RTG

value: 50 μM CuSO4 (2h), shift from SPO to YPD (6h)


title: Wild-type TSS seq 60 min RTG replicate 3

description:
TSS seq
CHI114A124_S6_L001


title: Wild-type TSS seq 5h replicate 3

description:
TSS seq
CHI114A28_S16_L002

source_name: Wild-type TSS seq 5h


title: 62_1_18B

description:
comments: This sample matched with  62_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TSS seq 5h replicate 2

description:
TSS seq
CHI114A16_S10_L002


title: 60_2_18C


title: 60_2_5

source_name: buccal swab at age 5


title: 61_1_10


title: Wild-type TSS seq 5h replicate 1

description:
TSS seq
CHI114A5_S5_L001


title: Wild-type TSS seq 6h replicate 2

description:
TSS seq
CHI114A17_S11_L002


title: Wild-type TSS seq 4h replicate 3

description:
TSS seq
CHI114A27_S15_L002

source_name: Wild-type TSS seq 4h


title: Wild-type TSS seq 4h replicate 1

description:
TSS seq
CHI114A4_S4_L001


title: 60_2_18B

description:
comments: This sample matched with  60_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TSS seq 4h replicate 2

description:
TSS seq
CHI114A15_S9_L002


title: 60_1_5


title: 60_1_18B

description:
comments: This sample matched with  60_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 60_1_18C


title: Wild-type TSS seq 3h IME1 uninduced replicate 1

description:
TSS seq
CHI114A10_S40_L005

source_name: Wild-type TSS seq 3h IME1 uninduced

value: no treatment


title: Wild-type TSS seq 3h IME1 uninduced replicate 3

description:
TSS seq
CHI114A33_S51_L006


title: Wild-type TSS seq 3h replicate 3

description:
TSS seq
CHI114A26_S14_L002

source_name: Wild-type TSS seq 3h


title: Wild-type TSS seq 60 min RTG replicate 2

description:
TSS seq
CHI114A123_S5_L001


title: Wild-type TSS seq 3h IME1 uninduced replicate 2

description:
TSS seq
CHI114A21_S45_L005


title: 60_1_10


title: Wild-type TSS seq 3h replicate 2

description:
TSS seq
CHI114A14_S8_L001


title: 61_1_18B

description:
comments: This sample matched with  61_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 59_2_18B

description:
comments: This sample matched with  59_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 59_2_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: 60_2_10


title: Wild-type TSS seq 30 min RTG replicate 3

description:
TSS seq
CHI114A121_S58_L005

source_name: Wild-type TSS seq 30 min RTG


title: 59_2_18C


title: 59_1_5


title: 59_1_18C


title: 59_1_18B

description:
comments: This sample matched with  59_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 59_1_10


title: Wild-type TSS seq 2h replicate 2

description:
TSS seq
CHI114A13_S7_L001

source_name: Wild-type TSS seq 2h


title: Wild-type TSS seq 3h replicate 1

description:
TSS seq
CHI114A3_S3_L001


title: Wild-type TSS seq 30 min RTG replicate 2

description:
TSS seq
CHI114A120_S57_L005


title: 58_2_5


title: Wild-type TSS seq 2h replicate 3

description:
TSS seq
CHI114A25_S13_L002


title: 59_2_10


title: Wild-type TSS seq 2h replicate 1

description:
TSS seq
CHI114A2_S2_L001


title: Wild-type TSS seq 15 min RTG replicate 3

description:
TSS seq
CHI114A118_S55_L005

source_name: Wild-type TSS seq 15 min RTG


title: Wild-type TSS seq 15 min RTG replicate 2

description:
TSS seq
CHI114A117_S72_L006


title: Wild-type TSS seq 30 min RTG replicate 1

description:
TSS seq
CHI114A119_S56_L005


title: 58_2_10


title: Wild-type TSS seq 15 min RTG replicate 1

description:
TSS seq
CHI114A116_S71_L006


title: 58_2_18B

description:
comments: This sample matched with  58_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type TSS seq 120 min RTG replicate 2

description:
TSS seq
CHI114A126_S35_L003

source_name: Wild-type TSS seq 120 min RTG


title: Wild-type TSS seq 120 min RTG replicate 3

description:
TSS seq
CHI114A127_S36_L003


title: Wild-type TSS seq 120 min RTG replicate 1

description:
TSS seq
CHI114A125_S7_L001


title: 58_1_18C


title: 58_1_18B

description:
comments: This sample matched with  58_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 58_1_5


title: 58_1_10


title: SPT16-AID control TSS seq 0h replicate 2

description:
TSS seq
CHI114A147_S58_L007

source_name: SPT16-AID control TSS seq 0h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative


title: 57_2_5


title: 58_2_18C


title: SPT16-AID control TSS seq 0h replicate 1

description:
TSS seq
CHI114A146_S57_L007


title: 57_2_18C


title: 57_2_18B

description:
comments: NA
genomic DNA from blood sample
betas_normalised.csv


title: 57_2_10


title: 57_1_18C


title: 57_1_5


title: 57_1_18B


title: set3 TSS seq 0h replicate 2

description:
TSS seq
CHI114A78_S17_L002

source_name: set3 TSS seq 0h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: set3 TSS seq 0h replicate 3

description:
TSS seq
CHI114A79_S1_L001


title: 56_2_5


title: SPT16-AID, OsTIR TSS seq 0h replicate 1

description:
TSS seq
CHI114A140_S37_L006

source_name: SPT16-AID, OsTIR TSS seq 0h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: set2 TSS seq 0h replicate 3

description:
TSS seq
CHI114A76_S15_L002

source_name: set2 TSS seq 0h


title: set2 TSS seq 0h replicate 1

description:
TSS seq
CHI114A74_S13_L002


title: 56_2_18C

value: Buccal


title: set3 TSS seq 0h replicate 1

description:
TSS seq
CHI114A77_S16_L002


title: set2 TSS seq 0h replicate 2

description:
TSS seq
CHI114A75_S14_L002

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: 57_1_10

source_name: buccal swab at age 10

value: Age 10


title: set2 set3 TSS seq 0h replicate 3

description:
TSS seq
CHI114A73_S40_L004

source_name: set2 set3 TSS seq 0h


title: SPT16-AID control TSS seq 0h replicate 3

description:
TSS seq
CHI114A148_S59_L008


title: 56_2_18B

description:
comments: This sample matched with  56_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

value: Age 18


title: set2 set3 TSS seq 0h replicate 2

description:
TSS seq
CHI114A72_S39_L004


title: 56_1_5


title: set2 set3 TSS seq 0h replicate 1

description:
TSS seq
CHI114A71_S38_L004


title: SPT16-AID, OsTIR TSS seq 0h replicate 2

description:
TSS seq
CHI114A141_S38_L006


title: Wild-type control TSS seq 0h replicate 3

description:
TSS seq
CHI114A70_S37_L004

source_name: Wild-type control TSS seq 0h


title: 56_1_18C

source_name: buccal swab at age 18


title: 56_1_10


title: Wild-type control TSS seq 0h replicate 1

description:
TSS seq
CHI114A68_S49_L005


title: 55_2_5

source_name: buccal swab at age 5

value: Female

value: Exposed


title: 56_1_18B

description:
comments: This sample matched with  56_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male


title: 65_1_5


title: Wild-type control TSS seq 0h replicate 2

description:
TSS seq
CHI114A69_S50_L005

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: 55_2_18C


title: Wild-type TSS seq 0h replicate 2

description:
TSS seq
CHI114A12_S6_L001

source_name: Wild-type TSS seq 0h


title: Wild-type mRNA seq 9h replicate 3

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin 2011) with parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --minimum-length=20”.
STAR (version 2.5.2) (Dobin et al. 2013) with parameters “--alignIntronMin 3 --alignIntronMax 5000” was used to perform the read mapping to the S. cerevisiae SK1 genome assembly from Keeney lab. Alignments with mapping quality of <10 or soft/hard-clipping were filtered.
Alignments from forward strand and reverse strand were separated by using  "samtools view -b -f 0x10" and "samtools view -b -F 0x10" to split the alignments.
The tool “bedtools genomecov” (Quinlan and Hall 2010) was used to generate the RNA-seq BedGraph tracks across the genome, for both forward and reverse strands.
BedGraph files were converted to bigWig using the tool bedGraphToBigWig from UCSC (Kent et al., 2010).
Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Genome-wide bigWig files for both forward and reverse strands. See data processing step for more details.

source_name: Wild-type mRNA seq 9h

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using hot acid phenol:chloroform:isoamyl alcohol (25:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in RNAse-free sterile water.
At least 2 μg of total RNA was treated with DNAse and purified on column (Macherey-Nagel). At least 400 ng of purified total RNA was used as the inputs for the KAPA mRNA Hyper Prep kit (KK8580, Roche). Libraries were prepared according to manufacturer’s instructions. After bead based clean up, libraries were sequenced on an Illumina HiSeq 4000 to an equivalent of 75 bases single-end reads, at a depth of approximately 20 million reads per library.

value: 50 μM CuSO4 (2h), 1 μM β-estradiol (6h)


title: 55_1_5

value: Age 5

value: Notexposed


title: 55_2_18B

description:
comments: This sample matched with  55_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: SPT16-AID, OsTIR TSS seq 0h replicate 3

description:
TSS seq
CHI114A142_S39_L006


title: 56_2_10


title: 55_1_18B

description:
comments: This sample matched with  55_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 55_2_10


title: Wild-type mRNA seq 8h replicate 3

source_name: Wild-type mRNA seq 8h


title: Wild-type mRNA seq 9h replicate 1


title: Wild-type mRNA seq 9h replicate 2


title: 55_1_18C


title: Wild-type TSS seq 0h replicate 1

description:
TSS seq
CHI114A1_S1_L001


title: 55_1_10


title: Wild-type mRNA seq 8h replicate 2


title: 54_2_5


title: Wild-type mRNA seq 8h replicate 1


title: Wild-type mRNA seq 7h NDT80 uninduced replicate 3

source_name: Wild-type mRNA seq 7h NDT80 uninduced

value: 50 μM CuSO4 (2h)


title: Wild-type mRNA seq 7h NDT80 uninduced replicate 2


title: 54_2_18C


title: 66_1_10


title: Wild-type TSS seq 0h replicate 3

description:
TSS seq
CHI114A24_S12_L002

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) Sk1 derivative

value: no treatment


title: 54_2_18B

description:
comments: This sample matched with  54_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 54_2_10


title: Wild-type mRNA seq 7h NDT80 uninduced replicate 1


title: 54_1_5


title: Wild-type mRNA seq 7h replicate 3

source_name: Wild-type mRNA seq 7h


title: 54_1_18C


title: Wild-type mRNA seq 7h replicate 1


title: 54_1_10


title: 54_1_18B

description:
comments: This sample matched with  54_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: SPT16-AID control mRNA seq 6h replicate 2

source_name: SPT16-AID control mRNA seq 6h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative

value: 50 μM CuSO4 (2h), 500 μM indole-3-acetic acid (2h)


title: SPT16-AID control mRNA seq 6h replicate 1


title: 53_2_18C

value: Buccal


title: 53_2_10


title: SPT16-AID control mRNA seq 6h replicate 3


title: 53_2_18B

description:
comments: This sample matched with  53_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: set3 mRNA seq 6h replicate 3

source_name: set3 mRNA seq 6h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: 53_1_18C


title: 53_1_5


title: SPT16-AID, OsTIR mRNA seq 6h replicate 2

source_name: SPT16-AID, OsTIR mRNA seq 6h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: set3 mRNA seq 6h replicate 2


title: set3 mRNA seq 6h replicate 1


title: 52_2_5


title: 52_2_18C

value: Age 18


title: set2 mRNA seq 6h replicate 2

source_name: set2 mRNA seq 6h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative


title: set2 mRNA seq 6h replicate 3


title: 53_1_10

value: Age 10


title: 52_2_18B

description:
comments: This sample matched with  52_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: set2 mRNA seq 6h replicate 1


title: 52_2_10


title: 53_2_5

value: Male


title: Wild-type mRNA seq 7h replicate 2

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative

value: 50 μM CuSO4 (2h), 1 μM β-estradiol (6h)


title: set2 set3 mRNA seq 6h replicate 2

source_name: set2 set3 mRNA seq 6h

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: set2 set3 mRNA seq 6h replicate 1


title: SPT16-AID, OsTIR mRNA seq 6h replicate 1


title: 52_1_10

value: Notexposed


title: 52_1_18C


title: 52_1_18B

description:
comments: This sample matched with  52_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: SPT16-AID, OsTIR mRNA seq 6h replicate 3


title: Wild-type control mRNA seq 6h replicate 3

source_name: Wild-type control mRNA seq 6h

value: 50 μM CuSO4 (2h)


title: 51_2_5

value: Age 5

value: Exposed


title: 51_2_18C


title: Wild-type control mRNA seq 6h replicate 2


title: Wild-type mRNA seq 6h replicate 3

source_name: Wild-type mRNA seq 6h


title: 53_1_18B

description:
comments: This sample matched with  53_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type mRNA seq 6h replicate 2


title: Wild-type mRNA seq 6h replicate 1


title: 51_2_18B

description:
comments: This sample matched with  51_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type mRNA seq 60 min RTG replicate 3

source_name: Wild-type mRNA seq 60 min RTG

value: 50 μM CuSO4 (2h), shift from SPO to YPD (6h)


title: 51_1_18C

value: Buccal


title: 51_1_5


title: 51_1_18B

description:
comments: This sample matched with  51_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18


title: set2 set3 mRNA seq 6h replicate 3


title: Wild-type mRNA seq 60 min RTG replicate 2


title: Wild-type mRNA seq 60 min RTG replicate 1


title: 51_1_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

source_name: buccal swab at age 10


title: Wild-type mRNA seq 5h replicate 3

source_name: Wild-type mRNA seq 5h


title: 52_1_5

source_name: buccal swab at age 5


title: Wild-type mRNA seq 5h replicate 2


title: Wild-type control mRNA seq 6h replicate 1


title: Wild-type mRNA seq 5h replicate 1


title: 50_2_5


title: 50_2_18B

description:
comments: This sample matched with  50_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 50_2_18C

source_name: buccal swab at age 18


title: Wild-type mRNA seq 4h replicate 1

source_name: Wild-type mRNA seq 4h


title: Wild-type mRNA seq 4h replicate 3


title: 50_2_10


title: 50_1_18C


title: 50_1_18B

description:
comments: This sample matched with  50_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type mRNA seq 3h IME1 uninduced replicate 1

source_name: Wild-type mRNA seq 3h IME1 uninduced

value: no treatment


title: 51_2_10


title: 50_1_10


title: Wild-type mRNA seq 3h IME1 uninduced replicate 2


title: Wild-type mRNA seq 3h IME1 uninduced replicate 3


title: 50_1_5


title: 49_2_5


title: Wild-type mRNA seq 3h replicate 3

source_name: Wild-type mRNA seq 3h


title: 49_2_18C


title: Wild-type mRNA seq 3h replicate 1


title: 49_2_18B

description:
comments: This sample matched with  49_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 49_2_10


title: Wild-type mRNA seq 3h replicate 2


title: 49_1_5


title: Wild-type mRNA seq 30 min RTG replicate 3

source_name: Wild-type mRNA seq 30 min RTG


title: 49_1_18C


title: 49_1_18B

description:
comments: This sample matched with  49_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type mRNA seq 4h replicate 2


title: Wild-type mRNA seq 30 min RTG replicate 1


title: 48_2_5


title: Wild-type mRNA seq 2h replicate 3

source_name: Wild-type mRNA seq 2h


title: Wild-type mRNA seq 2h replicate 2


title: 49_1_10


title: Wild-type mRNA seq 2h replicate 1


title: Wild-type mRNA seq 15 min RTG replicate 3

source_name: Wild-type mRNA seq 15 min RTG


title: 48_2_18C


title: Wild-type mRNA seq 15 min RTG replicate 2


title: 48_2_18B

description:
comments: This sample matched with  48_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Wild-type mRNA seq 15 min RTG replicate 1


title: 48_1_5


title: 48_2_10


title: Wild-type mRNA seq 120 min RTG replicate 2

source_name: Wild-type mRNA seq 120 min RTG


title: 48_1_18B

description:
comments: This sample matched with  48_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 48_1_18C


title: Wild-type mRNA seq 120 min RTG replicate 3


title: 48_1_10


title: Wild-type mRNA seq 120 min RTG replicate 1


title: SPT16-AID control mRNA seq 0h replicate 2

source_name: SPT16-AID control mRNA seq 0h

value: FW6109 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6) SK1 derivative


title: Wild-type mRNA seq 30 min RTG replicate 2


title: 47_2_5


title: SPT16-AID control mRNA seq 0h replicate 3


title: SPT16-AID control mRNA seq 0h replicate 1


title: 47_2_18C

value: Age 18


title: SPT16-AID, OsTIR mRNA seq 0h replicate 2

source_name: SPT16-AID, OsTIR mRNA seq 0h

value: FW6083 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, SPT16::SPT16-3V5-AID::KanMX6, his3::pCUP-OsTIR::His3MX) SK1 derivative


title: 47_2_10

value: Age 10


title: SPT16-AID, OsTIR mRNA seq 0h replicate 3


title: SPT16-AID, OsTIR mRNA seq 0h replicate 1


title: 47_2_18B

description:
comments: This sample matched with  47_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Female


title: set3 mRNA seq 0h replicate 3

source_name: set3 mRNA seq 0h

value: FW5770 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set3::His3MX) SK1 derivative


title: 47_1_18C


title: 14dpi animal #2, lung sample for bulk RNA-seq

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-lung-2

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the MesAur 1.0 version of the Mesocricetus auratus genome using standard parameter, using the Refseq gtf file downloaded from ENSEMBL, with the following adjustments to extend 3' UTR lengthes:
cat ../MesAur/Mesocricetus_auratus.MesAur1.0.99.gtf | perl -ane 'print if (!($F[2] =~ m/five_prime_utr/ || $F[2] =~ m/gene/ || $F[2] =~ m/three_prime_utr/ || $F[2] =~ m/transcript/))' | bedtools sort -i /dev/stdin > ma1_genes.gtf
cat ma1_genes.gtf | perl -ane 'print if ($F[6] eq "+")' > ma1_genes_plus.gtf
cat ma1_genes.gtf | perl -ane 'print if ($F[6] eq "-")' > ma1_genes_minus.gtf
cat ma1_genes_plus.gtf | perl -ne 'm/transcript_id \"([^\"]*)\"/; print "$1\n";' | sort -u > transcripts_plus.txt
cat ma1_genes_minus.gtf | perl -ne 'm/transcript_id \"([^\"]*)\"/; print "$1\n";' | sort -u > transcripts_minus.txt
samtools faidx genome-ma1.fa
for t in `cat transcripts_plus.txt`; do grep $t ma1_genes_plus.gtf > temp_plus.gtf; chr=`cut -f 1 temp_plus.gtf | head -1`; l=`grep -P "^$chr\t" genome-ma1.fa.fai | cut -f 2`; export l; s=`tac temp_plus.gtf | grep -P "\texon\t" | head -1`; r=`tac temp_plus.gtf | grep -P "\texon\t" | head -1 | perl -F'\t' -ane '$l=$ENV{"l"}; $F[4]+=1000; if ($F[4] > $l-1) {$F[4] = $l-1} print(join("\t", @F));'`; export s; export r; cat temp_plus.gtf | perl -ne 'chomp; chomp $s; chomp $r; $s=$ENV{"s"}; $r=$ENV{"r"}; if ($_ eq $s) {print "$r\n"} else {print "$_\n"}'; done > ma1_genes_longer_plus.gtf
for t in `cat transcripts_minus.txt`; do grep $t ma1_genes_minus.gtf > temp_minus.gtf; s=`cat temp_minus.gtf | grep -P "\texon\t" | head -1`; r=`cat temp_minus.gtf | grep -P "\texon\t" | head -1 | perl -F'\t' -ane '$F[3]-=1000; if ($F[3] < 1) {$F[3] = 1} print(join("\t", @F));'`; export s; export r; cat temp_minus.gtf | perl -ne 'chomp; chomp $s; chomp $r; $s=$ENV{"s"}; $r=$ENV{"r"}; if ($_ eq $s) {print "$r\n"} else {print "$_\n"}'; done > ma1_genes_longer_minus.gtf
cat ma1_genes_longer_plus.gtf ma1_genes_longer_minus.gtf | bedtools sort -i /dev/stdin > ma1_genes_longer.gtf
The 3'-UTR of the Ifit2 gene was in addition manually extended for 1000 nt
Reads were then quantified using quasR (Gaidatzis et al, 2015)
For SARS-CoV-2 alignements, GenBank entry MN908947 was used
For single-cell RNA-sequencing data, fastq files were processed using a merged MesAur/SARS-CoV-2 genome by applying CellRanger 3.1.0 with standard parameters
Genome_build: MesAur 1.0
Genome_build: SARS-CoV-2 MN908947
Supplementary_files_format_and_content: ma1_genes_longer.gtf
readcounts_ma.tsv
h5 matrix

organism: Mesocricetus auratus

source_name: Syrian gold hamster

growth_protocol:
Clinical evaluation of hamsters included twice-daily monitoring and weighting. Animals with >15 % body weight loss for over 48 h were euthanized in accordance with the animal use protocol. Naïve hamsters (n = 3) and hamsters at time points 2, 3, 5 and 14 days post infection (dpi) (n = 3, each) were selected randomly.
Euthanasia prior analysis occurred by exsanguination under anesthesia as previously described  (Osterrieder et al. 2020). 1 mL peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial for bulk RNA and proteomics analysis.

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
For isolation of cells from whole blood, 250 µL blood were lysed in red blood cell lysis buffer (BioLegend), washed and centrifuged according to the manufacturer’s instructions. Resulting RBC-free pellets were resuspended in low-BSA buffer (1× PBS, 0.04 % BSA), filtered with 40 µm FloMi filters (Merck) suitable for volumes below 500 µL and counted microscopically by hemocytometer in trypan blue.
For isolation of single cells lobus caudalis of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA), filtered with 40 µm FloMi filters (Merck) suitable for low volumes and quantified microscopically in trypan blue.
For Lung RNA Bulk Sequencing the lobus medialis of the right lung lobe was removed carefully and stored in RNA Later Solution for a maximum of 24 hours at 4°C (Thermofisher). Lung Tissue was homogenized using the TissueLyser II system (Qiagen) and the homogenate stored in Trizol reagent.
For WBC RNA Bulk Sequencing, white blood cells were isolated as described for scSeq followed by lysis in Trizol reagent.
RNA was extracted using the DirectZol kit (Zymo research)
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits (New England Biolabs, 10xGenomics), see column "library construction protocol" in the SAMPLES section.

treatment_protocol: At 10–12 weeks of age hamsters were infected intranasally as previously described (Osterrieder et al. 2020). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 intranasally under anesthesia.

tag: sars-cov-2 infection

value: yes

tag: sampling timepoint

value: lung

tag: adapter sequence

value: GATCGGAAGAGCACACGT


title: 14dpi animal #3, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-WBC-3

value: blood


title: set3 mRNA seq 0h replicate 2


title: 14dpi animal #3, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-lung-3


title: 47_1_10

value: Notexposed


title: 5dpi animal #2, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d5-WBC-2


title: 47_1_18B

description:
comments: This sample matched with  47_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: 14dpi animal #1, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-lung-1


title: set2 mRNA seq 0h replicate 3

source_name: set2 mRNA seq 0h

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) Sk1 derivative


title: 46_2_5

value: Age 5

value: Exposed


title: set3 mRNA seq 0h replicate 1


title: 5dpi animal #1, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d5-lung-1


title: 46_2_18C

value: Buccal


title: 5dpi animal #3, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d5-lung-3


title: 5dpi animal #2, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d5-lung-2


title: 47_1_5

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: 3dpi animal #3, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-WBC-3


title: 3dpi animal #2, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-WBC-2


title: set2 mRNA seq 0h replicate 2

value: FW5767 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-GAL4(848).ER::URA3, set2::His3MX) SK1 derivative

value: no treatment


title: 14dpi animal #2, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-WBC-2


title: 3dpi animal #1, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-WBC-1


title: set2 set3 mRNA seq 0h replicate 3

source_name: set2 set3 mRNA seq 0h

value: FW2912 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3, set3::His3MX, set2::His3MX; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3, set3::His3MX, set2::His3MX) SK1 derivative


title: 3dpi animal #3, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-lung-3


title: 46_2_18B

description:
comments: This sample matched with  46_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18

value: Age 18


title: 14dpi animal #1, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d14-WBC-1


title: 46_2_10

source_name: buccal swab at age 10

value: Age 10


title: 46_1_5

source_name: buccal swab at age 5

value: Female


title: set2 mRNA seq 0h replicate 1


title: set2 set3 mRNA seq 0h replicate 2


title: 5dpi animal #1, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d5-WBC-1


title: 3dpi animal #1, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-lung-1


title: 3dpi animal #2, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d3-lung-2


title: set2 set3 mRNA seq 0h replicate 1


title: 46_1_18C

source_name: buccal swab at age 18


title: Wild-type control mRNA seq 0h replicate 3

source_name: Wild-type control mRNA seq 0h

value: FW2795 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG,  irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1-  GAL4(848).ER::URA3; MATα, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, irt1::pCUP-3HA-IME1::HphMX , ndt80::pGAL-NDT80::TRP1, ura3::pGPD1- GAL4(848).ER::URA3) SK1 derivative


title: 2dpi animal #2, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-WBC-2

value: yes


title: 46_1_18B

description:
comments: This sample matched with  46_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 2dpi animal #2, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-lung-2

value: lung


title: 46_1_10


title: 2dpi animal #3, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-WBC-3

value: GATCGGAAGAGCACACGT


title: Wild-type control mRNA seq 0h replicate 1


title: 2dpi animal #1, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-lung-1


title: 45_2_5


title: Uninfected animal #3, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-WBC-3

value: no

value: blood


title: 2dpi animal #3, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-lung-3


title: Uninfected animal #2, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-WBC-2


title: Uninfected animal #3, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-lung-3


title: Wild-type mRNA seq 0h replicate 3

source_name: Wild-type mRNA seq 0h


title: Uninfected animal #2, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-lung-2


title: Uninfected animal #1, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-WBC-1


title: Wild-type mRNA seq 0h replicate 2


title: Wild-type control mRNA seq 0h replicate 2


title: Uninfected animal #1, lung sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d0-lung-1


title: Wild-type mRNA seq 0h replicate 1


title: 2dpi animal #1, blood sample for bulk RNA-seq

description:
ma1_genes_longer.gtf
readcounts_ma.tsv
ma-d2-WBC-1


title: 45_2_18B

description:
comments: This sample matched with  45_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: CFC-5dpc-2: Select 5dpc BCWD_Sham CFControl BiologicalRep2

city: Hagerman

first: Jacob

middle: W.

last: Bledsoe

state: Idaho

address: 3059F National Fish Hatchery Road

department: Aquaculture Research Institute

country: USA

institute: University of Idaho

data_processing:
Base calling was performed using Illumina NextSeq Control Software v4.0.1.41 and RTA v2.11.3. Demultiplexing was conducted using Local Run Manager v2.4.0.2385.
Raw reads were screened for quality prior to quantifying transcript abundance on raw data.
A reference transcriptome index was built from all transcripts available from the NCBI Omyk_1.0 assembly (GCF_002163495.1) and was made decoy-aware using genome assembly.
Transcript quantification was conducted with Salmon v.1.2.1 using a selective alignment approach with GC bias correction (default paramters with the exception of -l ISR --gcBias).
For gene level analyses, transcripts were summarized to the gene level using the Omyk_1.0 GCF_002163495.1 GFF annotation file as the reference.
Genome_build: GCF_002163495.1
Supplementary_files_format_and_content: Tab-delimited files containing quant.sf output from Salmon v.1.2.1 listing the length, effective length, transcripts per million (TPM) and number of reads for each transcript.

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: intestine

growth_protocol: All-female cohorts of a selected strain of rainbow trout (Select), and a common commercial strain (Commercial) were reared together starting from eggs. At 65 days post hatch, fish from each strain were stocked separately into four 150L tanks each, supplied with flow-through SPF-dechlorinated water. Fish were stocked at a density of 45 fish per tank. A commercial trout starter diet was offered to satitation over the duration of the experiment.

extract_protocol:
Whole intestines were isolated from trout at the time of sampling and stored in 1 mL of Qiazol (Qiagen) at -80C. Samples were thawed and homogenized on a TissueLyser (Qiagen). Total RNA was purified using a RNeasy 96 kit (Qiagen) with on-column DNase I treatment.
For each pooled sample, 800 ng of input RNA was used to isolate mRNA using the NEBNext Poly(A) Magnetic mRNA Isolation module (NEB; Ipswich, MA, Cat# E7490). The mRNA template was used to generate stranded, unique dual indexed libraries with the Ultra II Direction RNA Library Prep Kit (NEB, Cat#E7760). Sequencing was done on an Illumina NextSeq500 using a 150-cycle (2 x 75) v2.5 HIgh Output kit.

treatment_protocol: For both strains of trout, three tanks of fish were experimentally infected with Flavobacterium psychrophilum (CSF 259-93) by intramuscular injection and one control tank was mock challenged by sham injection. Disease challenge lasted 21 days. Sampling was conducted at 45 days post challenge (dpc) (Early Infection) and 21 dpc (Late/Recovered Infection). Two pools of RNA isolated from two fish intestines each per tank were used for RNAseq library preparation. Due to high mortality in the commercial trout strain, samples were only collected from one infected tank of commercial trout at the 21 dpc time point.

tag: strain

value: Select

tag: Sex

value: female

tag: days post infection

tag: tank

value: CFControl

tag: stage of infection

value: Early

value: intestine


title: CF2-5dpc-2: Select 5dpc BCWD CF2 BiologicalRep2

value: BCWD


title: CF3-5dpc-1: Select 5dpc BCWD CF3 BiologicalRep1


title: 45_2_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Buccal

value: Exposed


title: shOGT_1

city: hangzhou

first: Junchen

last: Chen

state: zhejiang

address: zhejiang university, kaixuan road

country: China

institute: zhejiang university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated and used to quantify gene-expression level.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: adult neural stem cells

extract_protocol:
Total RNA was extracted from aNSCs using TRIzol reagent and was purified with chloroform following the manufacturer’s protocol.
All samples used for the cDNA library was assessed by NanoDrop 2000, and the RNA integrity value (RIN) was determined with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).

tag: cell type

value: adult neural stem cells

value: 8 weeks

tag: treatment

value: lentivirus infection co-expressing shRNA against mouse Ogt


title: 45_1_5

tag: familyid

tag: twinid

value: Female

value: Age 5

value: Notexposed


title: CF3-5dpc-2: Select 5dpc BCWD CF3 BiologicalRep2

tag: tissue


title: 45_1_18C

tag: gender

tag: age

value: Age 18


title: CF1-5dpc-1: Select 5dpc BCWD CF1 BiologicalRep1

tag: disease state


title: 45_2_18C

tag: smokingpackyears

tag: category


title: 45_1_18B

description:
comments: This sample matched with  45_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: TFC-5dpc-2: Commercial 5dpc BCWD_Sham TFControl BiologicalRep2

value: Commercial

value: TFControl


title: 45_1_10

value: Age 10


title: ctrl_1

value: lentivirus infection co-expressing scramble shRNA


title: TFC-5dpc-1: Commercial 5dpc BCWD_Sham TFControl BiologicalRep1

value: female


title: TF3-5dpc-1: Commercial 5dpc BCWD TF3 BiologicalRep1

value: Early


title: TF3-5dpc-2: Commercial 5dpc BCWD TF3 BiologicalRep2

value: intestine


title: TF2-5dpc-2: Commercial 5dpc BCWD TF2 BiologicalRep2

value: BCWD


title: 44_2_5

value: Male

value: Buccal


title: CFC-5dpc-1: Select 5dpc BCWD_Sham CFControl BiologicalRep1

value: Select

value: CFControl


title: TF2-5dpc-1: Commercial 5dpc BCWD TF2 BiologicalRep1


title: Citeseq mouse GBM: KO4_ADT

city: Brussels

first: Daliya

last: Kancheva

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

description:
KO4_Citeseq_ISC08_ADT
processed data file:
Citeseq_Mouse.GBM.KO4_WT4.filtered.RNA.feature.bc.matrix.csv
Citeseq_Mouse.GBM.KO4_WT4.filtered.ADT.feature.bc.matrix.csv
annot.Citeseq_Mouse.GBM.KO4_WT4.csv

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
The output count matrices of Cell Ranger count were then aggregated using Cellranger aggr
Genome_build: mm10 (mouse) / GRCh38 (human)
Supplementary_files_format_and_content: comma-delimited text files including raw counts for the aggregated samples (output Cellranger aggr) and annotation metadata with information per cell

source_name: glioblastoma

extract_protocol:
All methods listed in Antunes et al. Single-cell multi-omic profiling of glioblastoma-associated myeloid cells across species and disease stage reveals macrophage competition and functional specialization. Nature Neuroscience. 2020.
All methods listed in Antunes et al. Single-cell multi-omic profiling of glioblastoma-associated myeloid cells across species and disease stage reveals macrophage competition and functional specialization. Nature Neuroscience. 2020.

tag: strain background

tag: genotype

value: CCR2 knockout

value: glioblastoma tissue

value: Grade IV glioblastoma

tag: platform

value: 10x Genomics

tag: number of cells


title: TF1-5dpc-2: Commercial 5dpc BCWD TF1 BiologicalRep2

tag: strain

tag: Sex

tag: days post infection


title: TF1-5dpc-1: Commercial 5dpc BCWD TF1 BiologicalRep1

tag: tank

tag: stage of infection


title: shOGT_2

tag: cell type

value: adult neural stem cells

value: 8 weeks

tag: treatment

value: lentivirus infection co-expressing shRNA against mouse Ogt


title: Citeseq mouse GBM: WT4_cDNA

description:
WT4_Citeseq_ISC09_cDNA
processed data file:
Citeseq_Mouse.GBM.KO4_WT4.filtered.RNA.feature.bc.matrix.csv
Citeseq_Mouse.GBM.KO4_WT4.filtered.ADT.feature.bc.matrix.csv
annot.Citeseq_Mouse.GBM.KO4_WT4.csv

value: WT

tag: tissue


title: CF2-5dpc-1: Select 5dpc BCWD CF2 BiologicalRep1


title: 44_2_18C

tag: familyid

tag: twinid

tag: gender

value: Age 18

value: Exposed


title: 44_2_18B

description:
comments: This sample matched with  44_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood

tag: age

tag: disease state

tag: smokingpackyears


title: CF1-5dpc-2: Select 5dpc BCWD CF1 BiologicalRep2

value: female

value: Early

value: intestine


title: Citeseq mouse GBM: WT4_ADT

description:
WT4_Citeseq_ISC09_ADT
processed data file:
Citeseq_Mouse.GBM.KO4_WT4.filtered.RNA.feature.bc.matrix.csv
Citeseq_Mouse.GBM.KO4_WT4.filtered.ADT.feature.bc.matrix.csv
annot.Citeseq_Mouse.GBM.KO4_WT4.csv

tag: strain background

tag: genotype


title: 44_2_10

value: Male

value: Buccal

value: Age 10

tag: category


title: ctrl_2

tag: strain

value: lentivirus infection co-expressing scramble shRNA


title: CF3-21dpc-2: Select 21dpc BCWD CF3 BiologicalRep2

value: Select

tag: Sex

value: Late

value: BCWD


title: CF3-21dpc-1: Select 21dpc BCWD CF3 BiologicalRep1

tag: days post infection


title: CFC-21dpc-1: Select 21dpc BCWD_Sham CFControl BiologicalRep1

tag: tank

value: CFControl


title: Citeseq mouse GBM: KO4_cDNA

description:
KO4_Citeseq_ISC08_cDNA
processed data file:
Citeseq_Mouse.GBM.KO4_WT4.filtered.RNA.feature.bc.matrix.csv
Citeseq_Mouse.GBM.KO4_WT4.filtered.ADT.feature.bc.matrix.csv
annot.Citeseq_Mouse.GBM.KO4_WT4.csv

value: CCR2 knockout

value: glioblastoma tissue

value: Grade IV glioblastoma

tag: platform

value: 10x Genomics

tag: number of cells


title: CF2-21dpc-2: Select 21dpc BCWD CF2 BiologicalRep2

tag: stage of infection


title: Bulk_Brain_H3K4me3_rep2

city: New York

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
CZ618
processed data file: Paired-Tag_bigwigs.tar.gz

library_source: genomic

data_processing:
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13rd base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.
Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.6.0a) for RNA or bowtie2 for DNA. Mapped DNA reads of H3K4me1, H3K27ac and H3K27me3 were further filtered by mapping quality (MAPK>10). Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

source_name: Mouse frontal cortex and hippocampus

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, 16000044) and 1% penicillin-streptomycin (Thermo Fisher Scientific, 10378016) at 37 °C with 5% CO2.

extract_protocol: Libraries were constructed by Paired-tag workflow. First, permeabilized nuclei are incubated with antibodies targeting specific histone modifications (or other DNA binding proteins) to target the binding of protein A-fused Tn5 to chromatin. Tagmentation reaction and reverse transcription (RT) are then sequentially performed. Specifically, reactions are carried out in 12 different wells, each with a well-specific DNA barcode included in the transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy is used to introduce the 2nd and 3rd rounds of DNA barcodes to the nuclei, by sequentially attaching well-specific DNA barcodes to the 5’-end of both chromatin DNA fragments and cDNA from RT in 96-well plates. Finally, the barcoded nuclei are divided into sub-libraries and lysed, the chromatin DNA and cDNA are purified and used to prepare for sequencing libraries with an improved “amplify-and-split” strategy. For the RNA part, Tn5 transposases bound to the 2nd sequencing adaptor are used. For the DNA part, the fragment sizes of DNA from targeted tagmentation are shorter than those of cDNA from RT, which would result in lower library yields if Tn5 tagmentation is used to add the 2nd adaptor. Thus, to maximize efficiency, we used a type IIS endonuclease to create a nick and the 2nd sequencing adaptor is then introduced by ligation.

treatment_protocol: To prepare nuclei, HeLa S3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific, 10010-23) and counted using BioRad TC20 cell counter. The cells were then resuspended in cold Nuclei Permeabilization Buffer 1 (NPB1: 10 mM Tris-HCl pH 7.4 [Sigma, T4661], 10 mM NaCl [Sigma, S7653], 3 mM MgCl2 [Sigma, 63069], 1X Protease Inhibitor [Roche, 05056489001], 0.5 U/µL RNase OUT [Invitrogen, 10777-019] and 0.5 U/µL SUPERase Inhibitor [Invitrogen, AM2694]) with 0.1% IGEPAL CA-630 (Sigma, I8896) and centrifuged for 10 min at 1,000 g, 4 °C and proceed to Paired-tag experiments.

tag: tissue

value: Mouse frontal cortex and hippocampus

tag: chip antibody


title: CF2-21dpc-1: Select 21dpc BCWD CF2 BiologicalRep1


title: Bulk_Brain_H3K4me3_rep1

description:
CZ617
processed data file: Paired-Tag_bigwigs.tar.gz


title: 44_1_5

tag: familyid

tag: twinid

value: Age 5

value: Exposed


title: CF1-21dpc-2: Select 21dpc BCWD CF1 BiologicalRep2

value: female


title: CF1-21dpc-1: Select 21dpc BCWD CF1 BiologicalRep1

value: intestine


title: sc_Paired_seq_Brain_sub_library_RNA#06

description:
CZ612
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: TFC-21dpc-1: Commercial 21dpc BCWD_Sham TFControl BiologicalRep1

value: Commercial

value: TFControl


title: 44_1_18B

description:
comments: This sample matched with  44_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: gender

value: Male

value: Blood

tag: age

value: Age 18


title: TFC-21dpc-2: Commercial 21dpc BCWD_Sham TFControl BiologicalRep2

value: Late

tag: disease state


title: TF1-21dpc-2: Commercial 21dpc BCWD TF1 BiologicalRep2

value: BCWD


title: CFC-21dpc-2: Select 21dpc BCWD_Sham CFControl BiologicalRep2

value: Select

value: CFControl


title: TF1-21dpc-1: Commercial 21dpc BCWD TF1 BiologicalRep1


title: 44_1_10

value: Buccal

value: Age 10

tag: smokingpackyears


title: sc_Paired_seq_Brain_sub_library_RNA#05

description:
CZ611
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Select 4dpc IHNV_Sham CIControl BiologicalRep2

source_name: Select 4dpc IHNV_Sham CIControl_intestine

growth_protocol: All-female cohorts of a selected strain of rainbow trout (Select), and a common commercial strain (Commercial) were reared together starting from eggs. At 65 days post hatch, fish from each strain were stocked separately into four 150L tanks each, supplied with flow-through SPF-dechlorinated water. Fish were stocked at a density of 45 fish per tank. A  commercial trout starter diet was offered to satitation over the duration of the experiment.

treatment_protocol: For both strains of trout, three tanks of fish were experimentally infected with IHNv (CSF 220-90) by static bath and one tank was mock challenged by static bath (Sham). Disease challenge lasted 20 days. Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two pools of RNA isolated from two fish intestines each per tank were used for RNAseq library preparation.

value: CIControl

value: Early


title: Select 4dpc IHNV_Sham CIControl BiologicalRep1


title: Select 4dpc IHNV CI3 BiologicalRep2

source_name: Select 4dpc IHNV CI3_intestine

value: IHNV


title: Select 4dpc IHNV CI3 BiologicalRep1


title: 43_2_5

value: Age 5

value: Notexposed


title: sc_Paired_seq_Brain_sub_library_RNA#04

description:
CZ610
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz

value: Mouse frontal cortex and hippocampus


title: sc_Paired_seq_Brain_sub_library_DNA#05

description:
CZ603
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: 43_2_18C


title: 44_1_18C

value: Exposed


title: Select 4dpc IHNV CI2 BiologicalRep1

source_name: Select 4dpc IHNV CI2_intestine

value: intestine


title: Select 4dpc IHNV CI2 BiologicalRep2


title: 43_2_18B

description:
comments: This sample matched with  43_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Male


title: Select 4dpc IHNV CI1 BiologicalRep2

source_name: Select 4dpc IHNV CI1_intestine


title: 43_1_5


title: sc_Paired_seq_Brain_sub_library_DNA#04

description:
CZ602
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: 43_2_10


title: sc_Paired_seq_Brain_sub_library_RNA#03

description:
CZ609
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Commercial 4dpc IHNV_Sham TIControl BiologicalRep2

source_name: Commercial 4dpc IHNV_Sham TIControl_intestine

value: Commercial

value: TIControl


title: sc_Paired_seq_Brain_sub_library_DNA#03

description:
CZ601
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: Commercial 4dpc IHNV TI3 BiologicalRep2

source_name: Commercial 4dpc IHNV TI3_intestine


title: 43_1_18C

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv

value: Age 18


title: Commercial 4dpc IHNV_Sham TIControl BiologicalRep1


title: sc_Paired_seq_Brain_sub_library_DNA#06

description:
CZ604
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: sc_Paired_seq_Brain_sub_library_RNA#02

description:
CZ608
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: 43_1_18B

description:
comments: This sample matched with  43_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: Commercial 4dpc IHNV TI3 BiologicalRep1


title: Commercial 4dpc IHNV TI2 BiologicalRep2

source_name: Commercial 4dpc IHNV TI2_intestine


title: Commercial 4dpc IHNV TI2 BiologicalRep1


title: sc_Paired_seq_Brain_sub_library_DNA#02

description:
CZ600
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: 43_1_10


title: Commercial 4dpc IHNV TI1 BiologicalRep1

source_name: Commercial 4dpc IHNV TI1_intestine


title: 42_2_5


title: 42_2_18C


title: Select 20dpc IHNV_Sham CIControl BiologicalRep2

source_name: Select 20dpc IHNV_Sham CIControl_intestine

value: Select

value: Late


title: Commercial 4dpc IHNV TI1 BiologicalRep2


title: Select 20dpc IHNV_Sham CIControl BiologicalRep1


title: sc_Paired_seq_Brain_sub_library_DNA#01

description:
CZ599
processed data file: Paired-seq_DNA_filtered_matrix.tar.gz


title: Select 20dpc IHNV CI3 BiologicalRep2

source_name: Select 20dpc IHNV CI3_intestine


title: Select 4dpc IHNV CI1 BiologicalRep1


title: Select 20dpc IHNV CI2 BiologicalRep2

source_name: Select 20dpc IHNV CI2_intestine


title: Select 20dpc IHNV CI3 BiologicalRep1


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#08

description:
CZ588
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: 42_2_10

source_name: buccal swab at age 10

value: Buccal


title: Select 20dpc IHNV CI2 BiologicalRep1


title: Select 20dpc IHNV CI1 BiologicalRep2

source_name: Select 20dpc IHNV CI1_intestine


title: Select 20dpc IHNV CI1 BiologicalRep1


title: 42_1_5

source_name: buccal swab at age 5


title: Commercial 20dpc IHNV_Sham TIControl BiologicalRep2

source_name: Commercial 20dpc IHNV_Sham TIControl_intestine


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#07

description:
CZ595
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#07

description:
CZ587
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: Commercial 20dpc IHNV_Sham TIControl BiologicalRep1


title: Commercial 20dpc IHNV TI3 BiologicalRep1

source_name: Commercial 20dpc IHNV TI3_intestine


title: 42_1_18C

source_name: buccal swab at age 18


title: Commercial 20dpc IHNV TI2 BiologicalRep2

source_name: Commercial 20dpc IHNV TI2_intestine


title: 42_1_18B

description:
comments: This sample matched with  42_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

source_name: whole blood at age 18


title: Commercial 20dpc IHNV TI2 BiologicalRep1


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#06

description:
CZ594
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz

source_name: Mouse frontal cortex and hippocampus


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#06

description:
CZ586
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: 41_2_5

value: Female


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#05

description:
CZ593
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#08

description:
CZ596
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Commercial 20dpc IHNV TI1 BiologicalRep2

source_name: Commercial 20dpc IHNV TI1_intestine


title: 42_1_10

value: Age 10


title: Select Strain 65dph Biological Rep5

source_name: Select 65 days post hatch, intestine

growth_protocol: All-female cohorts of a selected strain of rainbow trout (ARS-KO), and a common commercial strain (Commercial) were reared together  from eggs. Upon hatching, fry were stocked into separate flow-through raceways (15°C spring water) at equal densities. Fish were fed a commercial trout starter diet for the duration of the experiment.

extract_protocol:
Whole intestines were isolated from trout fry and stored in 1 mL of Qiazol (Qiagen) at -80C. Samples were thawed and homogenized on a TissueLyser (Qiagen). Total RNA was purified using a RNeasy 96 kit (Qiagen) with on-column DNase I treatment.
For each sample, 800 ng of input RNA was used to isolate mRNA using the NEBNext Poly(A) Magnetic mRNA Isolation module (NEB; Ipswich, MA, Cat# E7490). The mRNA template was used to generate stranded, unique dual indexed libraries with the Ultra II Direction RNA Library Prep Kit (NEB, Cat#E7760). Sequencing was done on an Illumina NextSeq500 using a 150-cycle (2 x 75) v2.5 HIgh Output kit.

treatment_protocol: Samples were collected at 20 days post hatch and 65 days post hatch from the two trout strains to evaluate effects of development and host genetics.

value: female

tag: developmental stage

value: 65 days post hatch


title: Select Strain 65dph Biological Rep3


title: Select Strain 65dph Biological Rep4


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#05

description:
CZ585
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: 42_2_18B

description:
comments: This sample matched with  42_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

tag: category


title: Select Strain 65dph Biological Rep2

tag: strain


title: 41_2_18C


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#04

description:
CZ592
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Commercial 20dpc IHNV TI1 BiologicalRep1

value: IHNV


title: Commercial Strain 65dph Biological Rep5

source_name: Commercial 65 days post hatch, intestine

tag: Sex


title: 41_2_18B

description:
comments: This sample matched with  41_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Select Strain 65dph Biological Rep1


title: Commercial 20dpc IHNV TI3 BiologicalRep2

tag: days post infection


title: sc_Paired_seq_Brain_sub_library_RNA#01

description:
CZ607
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#04

description:
CZ584
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: Commercial Strain 65dph Biological Rep4


title: 41_2_10

description:
comments: NA
genomic DNA from buccal samples
betas_normalised.csv


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#03

description:
CZ591
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: 41_1_5

value: Age 5

value: Notexposed


title: Commercial Strain 65dph Biological Rep3


title: Select Strain 20dph Biological Rep5

source_name: Select 20 days post hatch, intestine

value: 20 days post hatch


title: Commercial Strain 65dph Biological Rep1

value: intestine


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#03

description:
CZ583
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz

value: Mouse frontal cortex and hippocampus


title: 41_1_18C


title: Select Strain 20dph Biological Rep4


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#02

description:
CZ590
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Select Strain 20dph Biological Rep2


title: 41_1_18B

description:
comments: This sample matched with  41_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#02

description:
CZ582
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: Select Strain 20dph Biological Rep3


title: 41_1_10


title: Select Strain 20dph Biological Rep1


title: Commercial Strain 20dph Biological Rep5

source_name: Commercial 20 days post hatch, intestine

value: Commercial


title: sc_Paired_tag_Brain_H3K4me3_sub_library_RNA#01

description:
CZ589
processed data file: Paired-Tag_RNA_filtered_matrix.tar.gz


title: Commercial Strain 20dph Biological Rep4


title: Commercial Strain 20dph Biological Rep3


title: sc_Paired_tag_Brain_H3K4me3_sub_library_DNA#01

description:
CZ581
processed data file: Paired-Tag_H3K4me3_DNA_filtered_matrix.tar.gz


title: 40_2_5


title: 40_2_18C


title: 40_2_18B

description:
comments: This sample matched with  40_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: Commercial Strain 65dph Biological Rep2


title: Forelimb bud at embryonic day E12.5

city: Montreal

first: Marie

last: Kmita

state: QC

address: 110 Pine Avenue

country: Canada

institute: IRCM (Institut de Recherches Cliniques de Montréal)

description: Forelimb bud at embryonic day E12.5

data_processing:
sample demultiplexing using Cell Ranger Single-Cell Software Suite version3.0.1
Sequencing reads were aligned on a custom genome on which sequences of IRES-venus, tdTomato, Cre et eGFP were added to Mus_musculus.GRCm38.93. Genome. using Cell Ranger Single-Cell Software Suite version3.0.1
filtering using Cell Ranger Single-Cell Software Suite version3.0.1
barcode counting using Cell Ranger Single-Cell Software Suite version3.0.1
UMI counting using Cell Ranger Single-Cell Software Suite version3.0.1
Genome_build: Sequencing reads were aligned on a custom genome on which sequences of IRES-venus, tdTomato, Cre et eGFP were added to Mus_musculus.GRCm38.93. Genome.
Supplementary_files_format_and_content: datasets created from the out files generated by the cellranger count function (Cell Ranger Single-Cell Software Suite version3.0.1) using Read10X function from Seurat R package v3.1

source_name: Forelimb bud

extract_protocol:
Dissection of forelimb buds from Hoxa13:Cre/+;mT-mG embryos were performed at E10.5, E11.5 and E12.5. Forelimbs were dissected in cold 1XPBS, after centrifugation at 300 rcf for 5 min at 4 °C the forelimbs were incubated in dissociation buffer (450 μl of 0.25% Trypsine/EDTA (GIBCO), 50 μl 10% bovine serum albumin (BSA), 1 μl DNAseI (NEB)) for 10 min at 37 °C. After incubation limb cells were gently mixed by pipetting up and down 10–15 times until they were dissociated, then 10% final fetal bovine serum (FBS) was added. Dissociated cells were filtered using a cell strainer (40 μm Nylon, BD Falcon), counted in order to determine the final volume in which to resuspend the cells and assessed for cell viability using 0.4% Trypan blue. After centrifugation at 300 rcf for 7 min at 4 °C the resulting pellet of cells was resuspended in the appropriate volume of 1XPBS, 0.04% BSA in order to have a 1500 cells/μl. Before being processed dissociated cells were counted one more time and assessed for cell viability using 0.4% Trypan blue.
The single cell preparation was processed using Chromium Single Cell 3' Reagent Kits v3 (10X Genomics, Pleasanton, CA) following the manufacturer recommendation. Briefly, forelimb cells were partitioned into gel beads in emulsion for cell lysis, barcoding with oligo-dT primers and reverse transcription in order to produce barcoded, full-length cDNA from poly-adenylated mRNA. cDNA library was amplified, fragmented and size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer.
10X Chromium Single Cell 3`. Libraries were sequenced on NovaSeq 6000 with 100 bp paired-end reads.

tag: genotype

value: Forelimb bud

value: embryonic day E12.5


title: Commercial Strain 20dph Biological Rep1


title: Commercial Strain 20dph Biological Rep2


title: Forelimb bud at embryonic day E11.5

description: Forelimb bud at embryonic day E11.5

value: embryonic day E11.5


title: Mct8Slco1c1 KO J5str_MOATP5

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Mct8Slco1c1 KO

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads quality was evaluated from FastQC.
Reference Genome was indexed from Bowtie (Langmead B et al. 2009) and sequence reads were aligned using TopHat (Trapnell C et al. 2009). Mapping data quality was evaluated from Qualimap (Garcia-Alcalde F et al. 2012)
We quantified reads to specific genes and transcripts using the Python module HT-SEQ (Anders S et al. 2015).
RNA-Seq data were normalized using Trimmed Mean of M values (Robinson MD and A Oshlack 2010) from EdgeR.
Genome_build: Mouse sequenced genome GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include TMM values for each sample.

source_name: striatum

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Quiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
500 ng of total RNA were used with the TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) to construct index-tagged cDNA libraries. Libraries were quantified using a Quant-iT™ dsDNA HS assay with the Q-bit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequence-by-synthesis single reads of 75 base length using the TruSeq SBS Kit v5 (Illumina) were generated on the Genome Analyzer IIx following the standard RNA sequencing protocol. Reads were further processed using the CASAVA package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: striatum

value: Mct8Slco1c1 KO


title: Mct8Slco1c1 KO J7str_MOATP7

description: Mct8Slco1c1 KO


title: 40_2_10

value: Buccal


title: Mct8Slco1c1 KO J6str_MOATP6

description: Mct8Slco1c1 KO


title: Mct8Slco1c1 KO J4str_MOATP4

description: Mct8Slco1c1 KO


title: Mct8Slco1c1 KO J3str_MOATP3

description: Mct8Slco1c1 KO


title: 40_1_5

value: Female

value: Exposed


title: Mct8Slco1c1 KO J1str_MOATP1

description: Mct8Slco1c1 KO


title: Mct8Slco1c1 KO J2str_MOATP2

description: Mct8Slco1c1 KO


title: 40_1_18C

value: Age 18


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#12

data_processing:
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13rd base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.
Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.6.0a) for RNA or bowtie2 for DNA. Mapped DNA reads of H3K4me1, H3K27ac and H3K27me3 were further filtered by mapping quality (MAPK>10). Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

extract_protocol:
Single-cell suspension were prepared from douncing of the frozen tissues, in Doucing Buffer with Protease/RNase Inhibitor cocktail (DBI: 0.25 M sucrose [Sigma, S7903], 25 mM KCl [Sigma, P9333], 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT [Sigma, D9779], 1X Protease Inhibitor, 0.5 U/µL RNase OUT and 0.5 U/µL SUPERase Inhibitor) supplemented with 0.1% Triton-X 100 (Sigma T9284). The cell suspension was then filtered by 30 µm Cell-Tric (Sysmex) and spun-down for 10 min, 1,000 g at 4 °C. After washing the cell pellets with DBI and spun-down again, NIB with 0.2% IGEPAL CA-630 were added to resuspend the nuclei pellets and rotate for 10 min at 4 °C. The nuclei were counted by BioRad TC20 cell counter and proceed to Paired-tag experiments immediately.
Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: specifically, reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified and subjected to an optimized “amplify-and-split” strategy based on that we previously developed, to give rise DNA and RNA libraries for sequencing


title: WT (Mct8Slco1c1 ko) I6str_WTa6

description: WT (Mct8Slco1c1 ko)

value: WT (Mct8Slco1c1 ko)


title: 40_1_18B

description:
comments: This sample matched with  40_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Blood


title: WT (Mct8Slco1c1 ko) I5str_WTa5

description: WT (Mct8Slco1c1 ko)


title: WT (Mct8Slco1c1 ko) I2str_WTa2

description: WT (Mct8Slco1c1 ko)


title: WT (Mct8Slco1c1 ko) I4str_WTa4

description: WT (Mct8Slco1c1 ko)


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#11


title: 40_1_10

value: Age 10


title: WT (Mct8Slco1c1 ko) I1str_WTa1

description: WT (Mct8Slco1c1 ko)


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#10


title: WT (Mct8Slco1c1 ko) I3str_Wta3

description: WT (Mct8Slco1c1 ko)


title: 39_2_18C

value: Notexposed


title: Mct8Dio2 KO H7str_MD7

description: Mct8Dio2 KO

value: Mct8Dio2 KO


title: Forelimb bud at embryonic day E10.5

description: Forelimb bud at embryonic day E10.5

value: embryonic day E10.5


title: Mct8Dio2 KO H5str_MD5

description: Mct8Dio2 KO


title: Mct8Dio2 KO H4str_MD4

description: Mct8Dio2 KO


title: 39_1_5

value: Age 5


title: WT (Mct8Slco1c1 ko) I7str_WTa7

description: WT (Mct8Slco1c1 ko)


title: Mct8Dio2 KO H3str_MD3

description: Mct8Dio2 KO


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#09


title: Mct8Dio2 KO H2str_MD2

description: Mct8Dio2 KO


title: Mct8Dio2 KO H1str_MD1

description: Mct8Dio2 KO


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#12


title: 39_2_18B

description:
comments: This sample matched with  39_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: WT-MMI G7str_WTH7

description: WT-MMI

value: WT-SH


title: 39_2_10


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#08


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#11


title: WT-MMI G6str_WTH6

description: WT-MMI


title: 39_2_5


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#08


title: Mct8Dio2 KO H6str_MD6

description: Mct8Dio2 KO


title: WT-MMI G5str_WTH5

description: WT-MMI


title: WT-MMI G4str_WTH4

description: WT-MMI


title: 39_1_18B

description:
comments: This sample matched with  39_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: WT-MMI G3str_WTH3

description: WT-MMI


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#10


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#07


title: WT-MMI G1str_WTH1

description: WT-MMI


title: 39_1_10


title: 38_2_5

value: Male


title: WT-MMI G2str_WTH2

description: WT-MMI


title: WT F7str_WT9

description: WT

value: WT


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#07


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#09


title: WT F6str_WT8

description: WT


title: WT F5str_WT7

description: WT


title: 38_2_18B

description:
comments: This sample matched with  38_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#06


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#06


title: WT F2str_WT3

description: WT


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#05


title: WT F4str_WT6

description: WT


title: WT F3str_WT4

description: WT


title: 38_2_18C


title: Mct8Slco1c1 KO E7CTX_MOATP7

description: Mct8Slco1c1 KO

source_name: cerebral cortex

value: cerebral cortex


title: WT F1str_WT1

description: WT

value: striatum


title: 39_1_18C


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#05


title: 38_2_10

source_name: buccal swab at age 10


title: Mct8Slco1c1 KO E6CTX_MOATP6

description: Mct8Slco1c1 KO

value: Mct8Slco1c1 KO


title: 38_1_18C

value: Buccal


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#04


title: 38_1_5


title: Mct8Slco1c1 KO E3CTX_MOATP3

description: Mct8Slco1c1 KO


title: 38_1_10


title: Mct8Slco1c1 KO E2CTX_MOATP2

description: Mct8Slco1c1 KO


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#04


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#03


title: WT (Mct8Slco1c1 ko) D6CTX_WTa6

description: WT (Mct8Slco1c1 ko)


title: WT (Mct8Slco1c1 ko) D7CTX_WTa7

description: WT (Mct8Slco1c1 ko)


title: 38_1_18B

description:
comments: This sample matched with  38_1_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv


title: 37_2_5

value: Female


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#03


title: WT (Mct8Slco1c1 ko) D3CTX_Wta3

description: WT (Mct8Slco1c1 ko)


title: 37_2_18C

value: Exposed


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_DNA#02


title: WT (Mct8Slco1c1 ko) D4CTX_WTa4

description: WT (Mct8Slco1c1 ko)


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#02


title: WT (Mct8Slco1c1 ko) D5CTX_WTa5

description: WT (Mct8Slco1c1 ko)


title: WT (Mct8Slco1c1 ko) D2CTX_WTa2

description: WT (Mct8Slco1c1 ko)


title: sc_Paired_tag_Brain_H3K27me3_H3K9me3_sub_library_RNA#01


title: Mct8Dio2 KO C7CTX_MD7

description: Mct8Dio2 KO


title: Mct8Slco1c1 KO E4CTX_MOATP4

description: Mct8Slco1c1 KO


title: Mct8Dio2 KO C6CTX_MD6

description: Mct8Dio2 KO


title: Mct8Slco1c1 KO E5CTX_MOATP5

description: Mct8Slco1c1 KO


title: WT (Mct8Slco1c1 ko) D1CTX_WTa1

description: WT (Mct8Slco1c1 ko)


title: 37_2_10


title: Mct8Dio2 KO C4CTX_MD4

description: Mct8Dio2 KO


title: Mct8Dio2 KO C3CTX_MD3

description: Mct8Dio2 KO


title: Mct8Dio2 KO C5CTX_MD5

description: Mct8Dio2 KO


title: 37_1_5


title: 37_2_18B

description:
comments: This sample matched with  37_2_450K in the EPICvs450K comparison analysis
genomic DNA from blood sample
betas_normalised.csv

value: Age 18


title: 37_1_18C


title: Mct8Dio2 KO C2CTX_MD2

description: Mct8Dio2 KO


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#16


title: Mct8Dio2 KO C1CTX_MD1

description: Mct8Dio2 KO


title: WT-MMI B6CTX_WTH6

description: WT-MMI


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#15


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#16


title: WT-MMI B7CTX_WTH7

description: WT-MMI


title: Mct8Slco1c1 KO E1CTX_MOATP1

description: Mct8Slco1c1 KO


title: 37_1_10


title: WT-MMI B4CTX_WTH4

description: WT-MMI


title: WT-MMI B3CTX_WTH3

description: WT-MMI


title: 36_2_5


title: WT-MMI B5CTX_WTH5

description: WT-MMI


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_RNA#14


title: WT-MMI B1CTX_WTH1

description: WT-MMI


title: sc_Paired_tag_Brain_H3K4me1_H3K27ac_sub_library_DNA#15


title: WT A7CTX_WT9

description: WT


title: 36_2_18C