title: HFWL7BBXY_1_IDT_DUI_NXT_350


title: HFWL7BBXY_1_IDT_DUI_NXT_126

status: Public on Oct 25 2020

type: SRA

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: transcriptomic

data_processing:
Smart-seq2 and SMARTer sequencing data were aligned with TopHat2 version 2.1.1 (Kim et al., 2013)
GRCm38 (mm10) mouse genome reference was used for alignment and gene annotation from UCSC.
Read counts for genes were calculated using velocyto version 0.17 (La Manno et al., 2018) and the cell-gene count matrix obtained was used for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CSV file containing the raw read counts matrix of all the samples from the experiment calculated using the tool velocyto.

molecule: total RNA

organism: Mus musculus

source_name: Thymocytes

extract_protocol:
For replicate 1, full-length single-cell RNA-seq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. Thymocytes were sorted into 96-well plates containing the lysis buffer (0.2% Triton-100, 1U/µl RNase inhibitor)Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems) and IS PCR primer (IDT), with 25 cycles of amplification. For replicate 2, full-length single-cell RNA-seq libraries were prepared using the SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing (Takara Bio). All reactions were downscaled to one quarter of the original protocol and performed following thermal cycling manufacturer’s conditions. Thymocytes were sorted into 96-well plates containing 2.5 µl of the Reaction buffer (1x Lysis Buffer, RNase Inhibitor 1U/µl). Reverse transcription was performed using 2.5 µl of the RT MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio). cDNA was amplified using 8 µl of the PCR MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio) with 25 cycles of amplification.
Replicate 1 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq2000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes. Replicate 2 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with double indexed Nextera PCR primers (IDT). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE100) reads with library indexes corresponding to cell barcodes.

tag: replicate

tag: genotype

value: MHCII KO

tag: cell type

value: Thymocytes

tag: strain

tag: cell population

tag: protocol

value: SMARTer


title: HFWL7BBXY_2_IDT_DUI_NXT_266


title: HFWL7BBXY_2_IDT_DUI_NXT_30


title: HFWL7BBXY_1_IDT_DUI_NXT_296


title: HFWL7BBXY_1_IDT_DUI_NXT_168

value: TCRhiDP


title: HFWL7BBXY_3_IDT_DUI_NXT_120


title: HFWL7BBXY_1_IDT_DUI_NXT_159

value: WT


title: HFWL7BBXY_1_IDT_DUI_NXT_66


title: HFWL7BBXY_2_IDT_DUI_NXT_221


title: HFWL7BBXY_2_IDT_DUI_NXT_363


title: HFWL7BBXY_3_IDT_DUI_NXT_293


title: HFWL7BBXY_2_IDT_DUI_NXT_193


title: HFWL7BBXY_2_IDT_DUI_NXT_103


title: HFWL7BBXY_1_IDT_DUI_NXT_305


title: HFWL7BBXY_3_IDT_DUI_NXT_349


title: HFWL7BBXY_2_IDT_DUI_NXT_189


title: HFWL7BBXY_3_IDT_DUI_NXT_263


title: HFWL7BBXY_1_IDT_DUI_NXT_119


title: HFWL7BBXY_2_IDT_DUI_NXT_205


title: HFWL7BBXY_1_IDT_DUI_NXT_43


title: HFWL7BBXY_2_IDT_DUI_NXT_289


title: HFWL7BBXY_1_IDT_DUI_NXT_273


title: HFWL7BBXY_1_IDT_DUI_NXT_169


title: HFWL7BBXY_3_IDT_DUI_NXT_78


title: HFWL7BBXY_3_IDT_DUI_NXT_33


title: HFWL7BBXY_2_IDT_DUI_NXT_89


title: HFWL7BBXY_1_IDT_DUI_NXT_247


title: HFWL7BBXY_3_IDT_DUI_NXT_37


title: HFWL7BBXY_3_IDT_DUI_NXT_341


title: HFWL7BBXY_2_IDT_DUI_NXT_43


title: HFWL7BBXY_1_IDT_DUI_NXT_255


title: HFWL7BBXY_1_IDT_DUI_NXT_13


title: HFWL7BBXY_1_IDT_DUI_NXT_355


title: HFWL7BBXY_2_IDT_DUI_NXT_13


title: HFWL7BBXY_1_IDT_DUI_NXT_37


title: HFWL7BBXY_2_IDT_DUI_NXT_319


title: HFWL7BBXY_3_IDT_DUI_NXT_297


title: HFWL7BBXY_3_IDT_DUI_NXT_275


title: HFWL7BBXY_2_IDT_DUI_NXT_273


title: HFWL7BBXY_1_IDT_DUI_NXT_179


title: HFWL7BBXY_3_IDT_DUI_NXT_239


title: HFWL7BBXY_3_IDT_DUI_NXT_363


title: HFWL7BBXY_1_IDT_DUI_NXT_195


title: HFWL7BBXY_3_IDT_DUI_NXT_167


title: HFWL7BBXY_2_IDT_DUI_NXT_315


title: HFWL7BBXY_2_IDT_DUI_NXT_47


title: HFWL7BBXY_3_IDT_DUI_NXT_177


title: HFWL7BBXY_3_IDT_DUI_NXT_137


title: HFWL7BBXY_2_IDT_DUI_NXT_181


title: HFWL7BBXY_3_IDT_DUI_NXT_181


title: HFWL7BBXY_1_IDT_DUI_NXT_201


title: HFWL7BBXY_1_IDT_DUI_NXT_351


title: HFWL7BBXY_3_IDT_DUI_NXT_253


title: HFWL7BBXY_1_IDT_DUI_NXT_197


title: HFWL7BBXY_3_IDT_DUI_NXT_89


title: HFWL7BBXY_2_IDT_DUI_NXT_91


title: HFWL7BBXY_2_IDT_DUI_NXT_373


title: HFWL7BBXY_3_IDT_DUI_NXT_111


title: HFWL7BBXY_2_IDT_DUI_NXT_87


title: HFWL7BBXY_2_IDT_DUI_NXT_131


title: HFWL7BBXY_2_IDT_DUI_NXT_61


title: HFWL7BBXY_2_IDT_DUI_NXT_309


title: HFWL7BBXY_2_IDT_DUI_NXT_365


title: HFWL7BBXY_1_IDT_DUI_NXT_11


title: HFWL7BBXY_1_IDT_DUI_NXT_55


title: HFWL7BBXY_1_IDT_DUI_NXT_73


title: HFWL7BBXY_3_IDT_DUI_NXT_185


title: HFWL7BBXY_3_IDT_DUI_NXT_157


title: HFWL7BBXY_2_IDT_DUI_NXT_235


title: HFWL7BBXY_1_IDT_DUI_NXT_151


title: HFWL7BBXY_2_IDT_DUI_NXT_109


title: HFWL7BBXY_2_IDT_DUI_NXT_379


title: HFWL7BBXY_3_IDT_DUI_NXT_117


title: HFWL7BBXY_1_IDT_DUI_NXT_383


title: HFWL7BBXY_2_IDT_DUI_NXT_261


title: HFWL7BBXY_3_IDT_DUI_NXT_321


title: HFWL7BBXY_1_IDT_DUI_NXT_131


title: HFWL7BBXY_3_IDT_DUI_NXT_217


title: HFWL7BBXY_1_IDT_DUI_NXT_185


title: HFWL7BBXY_3_IDT_DUI_NXT_133


title: HFWL7BBXY_3_IDT_DUI_NXT_105


title: HFWL7BBXY_2_IDT_DUI_NXT_321


title: HFWL7BBXY_2_IDT_DUI_NXT_237


title: HFWL7BBXY_2_IDT_DUI_NXT_251


title: HFWL7BBXY_2_IDT_DUI_NXT_311


title: HFWL7BBXY_2_IDT_DUI_NXT_115


title: HFWL7BBXY_3_IDT_DUI_NXT_323


title: HFWL7BBXY_2_IDT_DUI_NXT_285


title: HFWL7BBXY_3_IDT_DUI_NXT_365


title: HFWL7BBXY_3_IDT_DUI_NXT_43


title: HFWL7BBXY_1_IDT_DUI_NXT_307


title: HFWL7BBXY_1_IDT_DUI_NXT_215


title: HFWL7BBXY_3_IDT_DUI_NXT_25


title: HFWL7BBXY_3_IDT_DUI_NXT_231


title: HFWL7BBXY_2_IDT_DUI_NXT_163


title: HFWL7BBXY_2_IDT_DUI_NXT_323


title: HFWL7BBXY_1_IDT_DUI_NXT_59


title: HFWL7BBXY_1_IDT_DUI_NXT_5


title: HFWL7BBXY_1_IDT_DUI_NXT_347


title: HFWL7BBXY_3_IDT_DUI_NXT_203


title: HFWL7BBXY_2_IDT_DUI_NXT_171


title: HFWL7BBXY_3_IDT_DUI_NXT_361


title: HFWL7BBXY_3_IDT_DUI_NXT_335


title: HFWL7BBXY_1_IDT_DUI_NXT_175


title: HFWL7BBXY_1_IDT_DUI_NXT_1


title: HFWL7BBXY_3_IDT_DUI_NXT_259


title: HFWL7BBXY_3_IDT_DUI_NXT_145


title: HFWL7BBXY_2_IDT_DUI_NXT_255


title: HFWL7BBXY_1_IDT_DUI_NXT_177


title: HFWL7BBXY_1_IDT_DUI_NXT_371


title: HFWL7BBXY_1_IDT_DUI_NXT_339


title: HFWL7BBXY_3_IDT_DUI_NXT_115


title: HFWL7BBXY_3_IDT_DUI_NXT_313


title: HUVEC 5312 rep2

type: RNA

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

description:
replicate 2
Sample 32

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Raw data was processed using lumi package of R. Background correction and quantile normalization was done using default parameter settings of lumiExpresso function. Variance stabilization transform was added to lumiExpresso for variance stabilizing. Detection Pvalue was used to filter the probes not expressed in all samples of a cell type

label: biotin

organism: Homo sapiens

source_name: Human umbilical vein endothelial cells

label_protocol: Illumina

growth_protocol: Commercial endothelial cells from ScienCell Research

extract_protocol: ScienCell, Qiagen Kit.

treatment_protocol: No treatment

tag: gender

value: Male

tag: developmental stage

value: fetal


title: HUVEC 5312 rep1

description:
replicate 1
Sample 31


title: HUVEC 10297 rep2

description:
replicate 2
Sample 30


title: HPMEC 11844 rep1

description:
replicate 1
Sample 27

source_name: Human pulmonary microvascular endothelial cells


title: HUVEC 10297 rep1

description:
replicate 1
Sample 29


title: HPAEC 11925 rep2

description:
replicate 2
Sample 20

source_name: Human pulmonary arterial endothelial cells


title: HPMEC 11415 rep2

description:
replicate 2
Sample 26


title: HPMEC 11415 rep1

description:
replicate 1
Sample 25


title: HPMEC 10298 rep1

description:
replicate 1
Sample 23


title: HPMEC 10298 rep2

description:
replicate 2
Sample 24


title: HPAEC 9134 rep1

description:
replicate 1
Sample 21


title: HFWL7BBXY_1_IDT_DUI_NXT_271


title: HFWL7BBXY_2_IDT_DUI_NXT_73


title: HPAEC 11925 rep1

description:
replicate 1
Sample 19


title: HPAEC 10321 rep2

description:
replicate 2
Sample 18


title: HPAEC 9134 rep2

description:
replicate 2
Sample 22


title: HCMEC 11926 rep2

description:
replicate 2
Sample 16

source_name: Human cardiac microvascular endothelial cells


title: HPMEC 11844 rep2

description:
replicate 2
Sample 28


title: HPAEC 10321 rep1

description:
replicate 1
Sample 17


title: HFWL7BBXY_1_IDT_DUI_NXT_103


title: HFWL7BBXY_1_IDT_DUI_NXT_243


title: HCMEC 11926 rep1

description:
replicate 1
Sample 15


title: HFWL7BBXY_2_IDT_DUI_NXT_49


title: HFWL7BBXY_1_IDT_DUI_NXT_7


title: HFWL7BBXY_3_IDT_DUI_NXT_269


title: HFWL7BBXY_1_IDT_DUI_NXT_75


title: HCMEC 10319 rep2

description:
replicate 2
Sample 14


title: HFWL7BBXY_2_IDT_DUI_NXT_245


title: HFWL7BBXY_3_IDT_DUI_NXT_189


title: HFWL7BBXY_1_IDT_DUI_NXT_379


title: HFWL7BBXY_3_IDT_DUI_NXT_163


title: HFWL7BBXY_3_IDT_DUI_NXT_3


title: HFWL7BBXY_2_IDT_DUI_NXT_17


title: HFWL7BBXY_1_IDT_DUI_NXT_139


title: HCMEC 10299 rep2

description:
replicate 2
Sample 12


title: LSECs fetal 11605 rep2

description:
replicate 2
Sample 10

source_name: Human hepatic sinusoidal endothelail cells


title: HFWL7BBXY_3_IDT_DUI_NXT_191


title: LSECs fetal 11359 rep1

description:
replicate 1
Sample 7


title: LSECs fetal 11605 rep1

description:
replicate 1
Sample 9


title: HCMEC 10319 rep1

description:
replicate 1
Sample 13


title: LSECs adult 200565 rep2

description:
replicate 2
Sample 4

value: adult


title: LSECs fetal 11359 rep2

description:
replicate 2
Sample 8


title: LSECs fetal 10691 rep1

description:
replicate 1
Sample 5


title: HFWL7BBXY_2_IDT_DUI_NXT_119


title: LSECs fetal 10691 rep2

description:
replicate 2
Sample 6


title: HCMEC 10299 rep1

description:
replicate 1
Sample 11


title: HFWL7BBXY_3_IDT_DUI_NXT_273


title: HFWL7BBXY_3_IDT_DUI_NXT_327


title: HFWL7BBXY_1_IDT_DUI_NXT_29


title: LSECs adult 200565 rep1

description:
replicate 1
Sample 3


title: HFWL7BBXY_3_IDT_DUI_NXT_333


title: HFWL7BBXY_3_IDT_DUI_NXT_69


title: LSECs adult 200356 rep2

description:
replicate 2
Sample 2


title: P2274_N704_S505


title: P2279_N727_S507


title: P2222_N706_S517


title: LSECs adult 200356 rep1

description:
replicate 1
Sample 1


title: P2279_N720_S506


title: LSEC fetal 11359 [methylation]

type: genomic

description:
11359
Sample 4.Beta

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data was processed using minfi package in R. SWAN method was used for normalization. Average beta values were used for analysis.

label: cy3, cy5

molecule: genomic DNA

source_name: LSEC fetal

label_protocol: standard Illumina protocol

extract_protocol: Qiagen Kit

value: Human hepatic sinusoidal endothelial cells


title: P2277_N722_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_59


title: HFWL7BBXY_1_IDT_DUI_NXT_279


title: HFWL7BBXY_2_IDT_DUI_NXT_217


title: P2276_N704_S520


title: HFWL7BBXY_3_IDT_DUI_NXT_97


title: P2275_N721_S502


title: LSEC fetal 10691 [methylation]

description:
10691
Sample 3.Beta


title: P2280_N711_S515


title: HFWL7BBXY_2_IDT_DUI_NXT_127


title: HFWL7BBXY_3_IDT_DUI_NXT_369


title: P2276_N706_S522


title: P2274_N701_S511


title: HFWL7BBXY_2_IDT_DUI_NXT_259


title: P2279_N727_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_77


title: HFWL7BBXY_2_IDT_DUI_NXT_39


title: P2222_N705_S508


title: P2220_N711_S503


title: P2277_N716_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_61


title: P2277_N726_S513


title: P2275_N721_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_263


title: HFWL7BBXY_2_IDT_DUI_NXT_355


title: HFWL7BBXY_1_IDT_DUI_NXT_335


title: LSEC adult 200356 [methylation]

description:
200356
Sample 1.Beta

source_name: LSEC adult


title: HFWL7BBXY_2_IDT_DUI_NXT_331


title: P2275_N722_S507


title: P2277_N718_S520


title: P2274_N712_S511


title: LSEC adult 200565 [methylation]

description:
200565
Sample 2.Beta


title: HFWL7BBXY_1_IDT_DUI_NXT_221


title: P2277_N726_S517


title: LSEC fetal 11605 [methylation]

description:
11605
Sample 5.Beta


title: HFWL7BBXY_2_IDT_DUI_NXT_67


title: P2276_N711_S520


title: HFWL7BBXY_2_IDT_DUI_NXT_141


title: HFWL7BBXY_2_IDT_DUI_NXT_155


title: P2277_N727_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_19


title: P2276_N701_S513


title: P2275_N722_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_179


title: P2221_N712_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_353


title: HFWL7BBXY_1_IDT_DUI_NXT_97


title: P2276_N711_S517


title: P2222_N701_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_39


title: HFWL7BBXY_1_IDT_DUI_NXT_183


title: HFWL7BBXY_1_IDT_DUI_NXT_313


title: P2221_N707_S502


title: P2276_N711_S516


title: HFWL7BBXY_1_IDT_DUI_NXT_129


title: HFWL7BBXY_2_IDT_DUI_NXT_145


title: P2276_N712_S518


title: P2221_N709_S504


title: HFWL7BBXY_1_IDT_DUI_NXT_237


title: HFWL7BBXY_2_IDT_DUI_NXT_359


title: P2274_N705_S503


title: P2278_N714_S502


title: P2222_N702_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_265


title: HFWL7BBXY_3_IDT_DUI_NXT_19


title: HFWL7BBXY_1_IDT_DUI_NXT_117


title: P2277_N721_S520


title: HFWL7BBXY_3_IDT_DUI_NXT_67


title: P2222_N709_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_127


title: P2275_N723_S502


title: P2276_N707_S518


title: HFWL7BBXY_2_IDT_DUI_NXT_121


title: P2275_N720_S505


title: P2274_N701_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_9


title: HFWL7BBXY_1_IDT_DUI_NXT_23


title: HFWL7BBXY_1_IDT_DUI_NXT_85


title: HFWL7BBXY_2_IDT_DUI_NXT_337


title: P2275_N721_S508


title: P2222_N707_S517


title: P2279_N716_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_197


title: HFWL7BBXY_2_IDT_DUI_NXT_143


title: P2275_N719_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_257


title: P2275_N716_S503


title: P2275_N722_S511


title: HFWL7BBXY_2_IDT_DUI_NXT_377


title: HFWL7BBXY_2_IDT_DUI_NXT_287


title: P2274_N704_S511


title: HFWL7BBXY_3_IDT_DUI_NXT_11


title: HFWL7BBXY_1_IDT_DUI_NXT_241


title: P2279_N716_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_359


title: HFWL7BBXY_3_IDT_DUI_NXT_131


title: P2275_N726_S505


title: HFWL7BBXY_3_IDT_DUI_NXT_199


title: P2275_N722_S503


title: P2276_N705_S518


title: P2277_N722_S517


title: P2279_N723_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_211


title: P2274_N707_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_329


title: HFWL7BBXY_1_IDT_DUI_NXT_233


title: P2277_N718_S516


title: P2222_N708_S504


title: P2277_N727_S516


title: HFWL7BBXY_3_IDT_DUI_NXT_71


title: HFWL7BBXY_3_IDT_DUI_NXT_187


title: HFWL7BBXY_1_IDT_DUI_NXT_123


title: P2222_N710_S506


title: P2279_N724_S502


title: P2279_N716_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_51


title: P2277_N718_S515


title: P2277_N718_S522


title: P2277_N718_S517


title: HFWL7BBXY_1_IDT_DUI_NXT_317


title: HFWL7BBXY_3_IDT_DUI_NXT_93


title: P2280_N711_S516


title: HFWL7BBXY_1_IDT_DUI_NXT_155


title: P2222_N704_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_159


title: HFWL7BBXY_2_IDT_DUI_NXT_125


title: P2274_N707_S505


title: P2221_N708_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_375


title: P2277_N721_S515


title: P2275_N724_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_229


title: P2277_N716_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_293


title: P2276_N701_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_187


title: P2279_N723_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_283


title: HFWL7BBXY_2_IDT_DUI_NXT_215


title: HFWL7BBXY_3_IDT_DUI_NXT_261


title: P2222_N708_S503


title: P2279_N719_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_113


title: P2277_N722_S516


title: HFWL7BBXY_1_IDT_DUI_NXT_109


title: HFWL7BBXY_2_IDT_DUI_NXT_29


title: HFWL7BBXY_2_IDT_DUI_NXT_231


title: P2274_N705_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_157


title: P2279_N722_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_99


title: HFWL7BBXY_2_IDT_DUI_NXT_333


title: HFWL7BBXY_2_IDT_DUI_NXT_133


title: P2221_N708_S504


title: P2276_N711_S522


title: P2277_N716_S520


title: P2276_N710_S520


title: P2280_N710_S513


title: HFWL7BBXY_1_IDT_DUI_NXT_113


title: P2221_N708_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_103


title: HFWL7BBXY_3_IDT_DUI_NXT_35


title: P2277_N718_S521


title: HFWL7BBXY_1_IDT_DUI_NXT_181


title: P2276_N703_S518


title: P2220_N707_S502


title: HFWL7BBXY_1_IDT_DUI_NXT_345


title: P2276_N711_S518


title: HFWL7BBXY_2_IDT_DUI_NXT_263


title: HFWL7BBXY_2_IDT_DUI_NXT_33


title: P2277_N724_S521


title: P2276_N712_S515


title: HFWL7BBXY_1_IDT_DUI_NXT_285


title: HFWL7BBXY_2_IDT_DUI_NXT_295


title: HFWL7BBXY_1_IDT_DUI_NXT_89


title: P2220_N712_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_209


title: P2277_N720_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_207


title: HFWL7BBXY_2_IDT_DUI_NXT_317


title: P2274_N710_S510


title: HFWL7BBXY_1_IDT_DUI_NXT_235


title: HFWL7BBXY_1_IDT_DUI_NXT_35


title: HFWL7BBXY_2_IDT_DUI_NXT_339


title: HFWL7BBXY_3_IDT_DUI_NXT_23


title: P2276_N712_S522


title: P2274_N706_S506


title: P2274_N703_S507


title: HFWL7BBXY_3_IDT_DUI_NXT_245


title: HFWL7BBXY_2_IDT_DUI_NXT_225


title: HFWL7BBXY_1_IDT_DUI_NXT_205


title: P2222_N710_S517


title: P2276_N706_S518


title: P2277_N726_S522


title: HFWL7BBXY_3_IDT_DUI_NXT_277


title: HFWL7BBXY_3_IDT_DUI_NXT_339


title: P2280_N715_S515


title: P2275_N727_S507


title: P2280_N707_S517


title: HFWL7BBXY_1_IDT_DUI_NXT_219


title: P2277_N724_S513


title: P2277_N724_S518


title: HFWL7BBXY_3_IDT_DUI_NXT_81


title: P2278_N711_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_351


title: HFWL7BBXY_1_IDT_DUI_NXT_287


title: P2279_N721_S507


title: P2275_N726_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_319


title: P2275_N720_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_123


title: P2276_N711_S521


title: HFWL7BBXY_3_IDT_DUI_NXT_79


title: HFWL7BBXY_2_IDT_DUI_NXT_69


title: P2276_N701_S515


title: P2279_N722_S505


title: P2275_N722_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_299


title: P2275_N718_S510


title: HFWL7BBXY_1_IDT_DUI_NXT_381


title: HFWL7BBXY_3_IDT_DUI_NXT_307


title: P2222_N709_S503


title: P2277_N716_S515


title: HFWL7BBXY_3_IDT_DUI_NXT_135


title: P2279_N719_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_303


title: P2222_N701_S507


title: P2277_N721_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_79


title: P2279_N726_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_63


title: P2277_N716_S513


title: HFWL7BBXY_3_IDT_DUI_NXT_13


title: P2280_N707_S515


title: HFWL7BBXY_1_IDT_DUI_NXT_207


title: P2275_N718_S502


title: P2274_N702_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_35


title: HFWL7BBXY_2_IDT_DUI_NXT_105


title: HFWL7BBXY_1_IDT_DUI_NXT_21


title: HFWL7BBXY_3_IDT_DUI_NXT_21


title: P2275_N727_S502


title: P2277_N724_S522


title: P2277_N722_S513


title: HFWL7BBXY_1_IDT_DUI_NXT_47


title: P2274_N712_S505


title: P2279_N724_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_195


title: HFWL7BBXY_1_IDT_DUI_NXT_187


title: P2276_N702_S515


title: P2279_N724_S506


title: P2274_N710_S505


title: HFWL7BBXY_1_IDT_DUI_NXT_17


title: HFWL7BBXY_2_IDT_DUI_NXT_201


title: P2275_N719_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_229


title: P2274_N711_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_45


title: HFWL7BBXY_2_IDT_DUI_NXT_85


title: P2275_N723_S510


title: P2276_N704_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_129


title: P2221_N707_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_63


title: HFWL7BBXY_1_IDT_DUI_NXT_161


title: HFWL7BBXY_2_IDT_DUI_NXT_207


title: HFWL7BBXY_3_IDT_DUI_NXT_325


title: P2275_N721_S510


title: P2222_N710_S505


title: HFWL7BBXY_3_IDT_DUI_NXT_125


title: HFWL7BBXY_2_IDT_DUI_NXT_161


title: HFWL7BBXY_2_IDT_DUI_NXT_53


title: P2274_N711_S510


title: P2276_N711_S515


title: HFWL7BBXY_2_IDT_DUI_NXT_37


title: HFWL7BBXY_2_IDT_DUI_NXT_357


title: HFWL7BBXY_1_IDT_DUI_NXT_295


title: HFWL7BBXY_1_IDT_DUI_NXT_259


title: P2277_N716_S521


title: P2276_N701_S518


title: P2276_N710_S517


title: HFWL7BBXY_1_IDT_DUI_NXT_337


title: P2221_N709_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_185


title: HFWL7BBXY_3_IDT_DUI_NXT_355


title: P2275_N722_S505


title: P2279_N724_S507


title: P2222_N704_S508


title: P2275_N720_S507


title: P2222_N703_S504


title: P2276_N707_S515


title: HFWL7BBXY_2_IDT_DUI_NXT_265


title: HFWL7BBXY_1_IDT_DUI_NXT_341


title: P2222_N705_S502


title: P2276_N701_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_269


title: HFWL7BBXY_2_IDT_DUI_NXT_173


title: HFWL7BBXY_1_IDT_DUI_NXT_25


title: P2278_N707_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_171


title: P2274_N705_S511


title: P2222_N701_S503


title: P2274_N706_S507


title: HFWL7BBXY_3_IDT_DUI_NXT_183


title: HFWL7BBXY_2_IDT_DUI_NXT_93


title: HFWL7BBXY_2_IDT_DUI_NXT_275


title: P2279_N718_S511


title: P2279_N719_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_7


title: HFWL7BBXY_3_IDT_DUI_NXT_169


title: P2278_N712_S503


title: P2222_N707_S503


title: P2279_N721_S503


title: HFWL7BBXY_2_IDT_DUI_NXT_81


title: HFWL7BBXY_1_IDT_DUI_NXT_31


title: P2278_N712_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_15


title: HFWL7BBXY_1_IDT_DUI_NXT_69


title: HFWL7BBXY_3_IDT_DUI_NXT_53


title: P2220_N710_S504


title: P2222_N704_S506


title: P2277_N722_S520


title: HFWL7BBXY_3_IDT_DUI_NXT_77


title: P2222_N705_S503


title: P2279_N722_S503


title: RNA-mock-24H-2

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

country: China

institute: China Agricultural Universtiy

description: mRNA_expression_profile_MOCK-infected.txt

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) and ASFV (MK333180.1) genome by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 20, fold-changed (FC) ≧ 2 and p-value < 0.05.
For small RNA-seq, sequencing adapters (AGATCGGAAGAGCACACGTCT) was removed by using cutadpt1.18. Reads were mapped to pig genome by using Bowtie2.2.5. The unmapped reads were collected and then mapped to ASFV genome. A brief annotation of PAMs encoded small RNAs were performed by using unitas_1.7.0. FeatureCount_1.6.4 was used for quantifying abundance of each miRNA. RPM values were calculated to measure the expression levels of each miRNA. Differential expression analysis of miRNAs was performed by DESeq2_1.22.2. Differentially expressed miRNAs were filtered by the following parameters: fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples. Tab-delimited text file includes reads_count for each small RNA-seq samples.

organism: Sus scrofa

source_name: 24 h mock control, PAMs collected from 4-week-old SPF pigs

growth_protocol: Porcine alveolar macrophages (PAMs) were collected from 4-week-old SPF pigs as previously described. PAMs were maintained in RPMI1640 medium supplemented with 10% FBS at 37°C with 5% CO2.

extract_protocol:
The RNA was extracted from the infected cells at 0-, 6-, 12- and 24-hpi.
For strand specific RNA-seq, depletion of ribosomal RNA (rRNA) and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit. For small RNA-seq, small RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit.

treatment_protocol: Cells were infected with ASFV Chinese isolates (Pig/HLJ/18) at a multiplicity of infection (MOI) of 1 and incubated for 1 h at 37°C. The infected cells were then cultured at 37°C with fresh RPMI 1640 medium supplemented with 10% FBS.

tag: condition

value: Specific pathogen free (SPF)

tag: age

value: porcine alveolar macrophages

tag: infection

value: No infection

tag: time

value: 24 hours post infection

tag: fraction

value: total RNAs


title: RNA-mock-24H-3


title: P2277_N727_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_1


title: RNA-mock-24H-1


title: RNA-mock-12H-3

source_name: 12 h mock control, PAMs collected from 4-week-old SPF pigs

value: 12 hours post infection


title: P2222_N706_S504


title: HFWL7BBXY_2_IDT_DUI_NXT_271


title: HFWL7BBXY_1_IDT_DUI_NXT_227


title: P2276_N702_S521


title: P2220_N710_S502


title: RNA-mock-12H-2


title: P2274_N707_S506


title: P2275_N720_S506


title: RNA-mock-12H-1


title: P2279_N721_S505


title: P2222_N704_S504


title: RNA-mock-6H-3

source_name: 6 h mock control, PAMs collected from 4-week-old SPF pigs

value: 6 hours post infection


title: P2279_N721_S506


title: P2220_N708_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_241


title: HFWL7BBXY_2_IDT_DUI_NXT_257


title: P2279_N719_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_45


title: P2275_N724_S505


title: RNA-mock-6H-2


title: RNA-mock-6H-1


title: P2277_N722_S522


title: P2275_N723_S505


title: P2221_N707_S504


title: HFWL7BBXY_3_IDT_DUI_NXT_295


title: HFWL7BBXY_1_IDT_DUI_NXT_211


title: P2277_N726_S520


title: HFWL7BBXY_1_IDT_DUI_NXT_171


title: HFWL7BBXY_1_IDT_DUI_NXT_111


title: HFWL7BBXY_3_IDT_DUI_NXT_205


title: P2222_N702_S517


title: P2276_N703_S520


title: HFWL7BBXY_2_IDT_DUI_NXT_303


title: ModA2 OFF 2

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq  2.20.0.422 pipeline
bowtie aligner (2.3.2) was used to map reads to the 723 genomic DNA sequence; accession number CP007472
edgeR version 3.18.1 was used to perform differential expression analysis.
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA2 ON vs modA2 OFF

organism: Haemophilus influenzae

source_name: isolates

growth_protocol: mid-log cultures in supplemented BHI (sBHI; containing haemin and NAD)

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

tag: sample type

value: ModA2 OFF

tag: expression

value: methyltransferase absent


title: ModA2 OFF 1


title: ModA2 OFF 3


title: ModA2 ON 3

value: ModA2 ON

value: methyltransferase present


title: P2220_N712_S502

value: Thymocytes

value: TCRhiDP


title: P2277_N720_S518

value: WT


title: HFWL7BBXY_2_IDT_DUI_NXT_349

value: SMARTer


title: P2277_N723_S515


title: P2220_N709_S517


title: ModA2 ON 2


title: P2221_N708_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_139


title: ModA2 ON 1


title: HFWL7BBXY_2_IDT_DUI_NXT_351


title: P2279_N721_S508


title: P2276_N707_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_249


title: P2274_N702_S511


title: P2277_N721_S521


title: P2275_N726_S502


title: P2276_N705_S520


title: ChIP-seq_SCC1_2_days_washout

city: Oxford

first: Wojciech

last: Siwek

state: Oxfordshire

address: Department of Biochemistry, South Parks Road

department: Biochemistry

institute: Oxford University

library_source: genomic

data_processing:
Mapping was performed with bowtie2 software version 2.3.4.3 in default mode.
Genome_build: hg38
Supplementary_files_format_and_content: Coverage bigwig files were generated using bamCompare software against the input sequencing by subtraction, with 50bp bin size and read count scaling.

source_name: HeLa cells

growth_protocol: Cell lines were grown at 37°C, 5% CO2 in DMEM containing glucose, glutamine and pyruvate (Gibco, 41966-029) supplemented with 10% newborn calf serum (Gibco, 16010-159) and 1% Penicillin-Streptomycin (Gibco, 15140-122).

extract_protocol:
Beads were re-suspended in 30μL of ChIPmentation reaction buffer (10 mM Tris-HCl pH 8.0; 5mM MgCl2; 1μL TDE1 (Tn5 enzyme) (Nextera DNA Library Prep Kit, Illumina)). In parallel 1μL of input was diluted in 29μL of ChIPmentation reaction buffer. The samples were incubated in 37° C for 10 minutes followed by washing twice in ice-cold LiCl Buffer and TE Buffer. Next, the beads were suspended in 200µl of Elution Buffer (50mM Tris-HCl pH 7.5; 1% SDS; 10mM EDTA; protease inhibitors (Roche)). In parallel the input reaction was mixed with 170μL of the Elution Buffer. All samples were incubated at 65°C overnight for decrosslinking followed by treatment with PureLink RNaseA (Thermo Fisher Scientific) and Proteinase K. The DNA was purified with MinElute PCR Purification Kit (Qiagen) (10μL elution).
For preparation of sequencing libraries the purified DNA was amplified using Q5 Hot start DNA polymerase using indexing primers described in (Buenrostro et al., 2013). Initial amplification was performed: 98°C 30 seconds; [98°C 10 seconds; 63°C 30 seconds; 72°C 1 minute]x 5 cycles followed by library quantification with qPCR: 95°C 3 minutes; [95°C 10 seconds; 58°C 30 seconds; 72°C 1 minute] and additional PCR amplification (conditions as for the initial 5 cycles). The required number of additional cycles was calculated from the qPCR data by determining the number of cycles to reach 50% of the maximum signal. After library amplification and indexing, DNA was purified and size selected with AMPure XP magnetic beads (Beckman Coulter) according to manufacturer’s protocol. After purification the libraries concentration was determined by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) according to manufacturer’s protocol. The fragment size was estimated by DNA ScreenTape (Agilent) and the final library quality was measured with KAPA Library quantification kit (Roche) according to manufacturer’s protocol. For sequencing, multiplexed libraries were diluted to 2nM concentration (calculated based the on the KAPA Library quantification kit).

treatment_protocol: The ChIPmentation procedure was adopted from (Schmidl et al., 2015). In brief, 12*107 naïve, stimulated with IFNγ (Merck) for 24h or primed HeLa cells (2 and 7 days after interferon gamma washout) were collected by centrifugation for 5 minutes at 500g. Next, the cells were re-suspended in 25 mL of medium supplemented with 1% formaldehyde and incubated for 10 minutes in room temperature. Cross-linking was quenched by addition of 25mL of 125mM glycine in PBS. Cells were harvested by centrifugation, washed two times with 10mL of cold PBS, frozen in liquid nitrogen and kept in -80°C. To fragment chromatin, cell pellets were re-suspended in Lysis Buffer (50mM Tris-HCl pH 7.5; 1% SDS; 10mM EDTA; protease inhibitors (Roche)) and sonicated with Qsonica Q800R2; 107 cells in 0.3mL of buffer per 0.5mL tube with the following conditions: time – 5 minutes, pulse – 30 seconds ON/OFF, amplitude – 75%. The resulting material was tested for proper sonication by fragment analysis confirming DNA size between 500 and 4000bp. Chromatin samples were aliquoted at 5*106 cells per tube and frozen in -80°C. For a single immunoprecipitation, 25μL of protein A or G Dynabeads beads (Thermo Fisher Scientific) were washed twice with ChIP Dilution Buffer (20mM Tris-HCl pH 7.5; 0.1% SDS; 1% Triton X-100; 150mM NaCl; 2mM EDTA; protease inhibitors (Roche)). In parallel, the sample was diluted with ChIP Dilution Buffer up to 2mL and clarified at 12000g for 10 minutes in 4°C. Input DNA was collected from the supernatant (10µL). Samples were incubated with the beads and a given antibody over night at 4°C with rotation. Beads were washed at 4°C as follows: twice with Low Salt Wash Buffer (50mM Tris-HCl pH 7.5; 150mM NaCl; 1mM EDTA; 1% TritonX-100; 0.1% Na-Deoxycholate; protease inhibitors (Roche)); twice with High Salt Wash Buffer (50mM Tris-HCl pH 7.5; 500mM NaCl; 1mM EDTA; 1% TritonX-100; 0.1% Na-Deoxycholate; protease inhibitors (Roche)); twice with LiCl Wash Buffer (10mM Tris-HCl pH 7.5; 0.5% NP-40; 0.5% Na-Deoxycholate; 250mM LiCl; 1mM EDTA; protease inhibitors (Roche)); twice with TE Buffer (10mM Tris-HCl pH 7.5; 1mM EDTA; protease inhibitors (Roche)) and finally twice with 10mM Tris-HCl pH 7.5.

tag: treatment

value: cells 2 days after interferon gamma washout

tag: chip antibody

value: SCC1 (Abcam, ab992)

tag: tell line

value: HeLa


title: ChIP-seq_SCC1_7_days_washout

value: cells 7 days after interferon gamma washout


title: HFWL7BBXY_2_IDT_DUI_NXT_21

tag: replicate

tag: genotype


title: P2280_N715_S516

tag: cell type

tag: strain


title: ChIP-seq_SCC1_priming

value: cells induced with interferon gamma for 24h


title: P2276_N702_S516

tag: cell population

tag: protocol


title: P2280_N712_S517


title: P2222_N706_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_75


title: ChIP-seq_SCC1_naive

value: naïve cells


title: P2279_N726_S506


title: P2275_N720_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_329


title: RNA-seq_SCC1-AID_TIR1+_IAA+_reinduction_rep3

description:
RNA-seq_SCC1-AID_DESeq2_normalized_counts.tab
RNA-seq_SCC1-AID_TIR1+_reinduction_DESeq2_IAA+_vs_IAA-.tab

data_processing:
Mapping was performed with bwa-mem software version 0.7.17.1 in Simple Illumina mode.
Gene counts were estimated with htseq count software version 0.9.1. Parameters: union mode, feature type exon, ID Attribute gene_id.
DESeq2 version 2.11.40.6 was used to estimate the differential expression between samples.
Genome_build: hg38
Supplementary_files_format_and_content: normalized counts,  Differential expression files were generated using DESeq2.

molecule: polyA RNA

extract_protocol:
Three biological replicates of naïve, priming, primed, reinduced and induced cells were processed for RNA isolation using the TRIzol Reagent. Qubit RNA BR Assay Kit (Thermo Fisher Scientific) was used for quantification and RNA ScreenTape (Agilent) for accessing RNA integrity.
RNA was used for polyA positive library preparation with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) according to the manufacturer's protocol. Sequencing was performed on the NovaSeq6000 System (Illumina) with 150bp read length in paired end mode.

treatment_protocol: TIR1 positive and negative cells were treated or not with auxin for 3h followed by treatment with IFN gamma (Merck) or mock medium for 16h. Cells were then washed three times with PBS and trypsinized (Gibco) to remove residual INFγ and cleave the extracellular domains of plasma membrane proteins, including the INFγ receptor, to stop residual signaling. Part of the culture treated with interferon was processed for RNA isloation. Fresh medium was added to the other cultures and cells were allowed to proliferate for 48h. Next IFNγ was added or not to the primed and naïve cells. After 24h cells were washed, trypsinized, centrifuged 500g for 5 minutes and the pellets were processed for downstream analysis.

tag: cell line

tag: genetic perturbation

value: cohesin component SCC1 translationally fused to the AID degron

value: Cells positive for the osTIR1 E3 ligase

tag: treatment with iaa during priming phase

value: YES

tag: treatment with interferon gamma

value: cells reinduced with interferon gamma for 24h


title: RNA-seq_SCC1-AID_TIR1+_IAA+_reinduction_rep2


title: P2276_N706_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_361


title: RNA-seq_SCC1-AID_TIR1+_IAA+_reinduction_rep1


title: P2222_N708_S505


title: P2280_N712_S515


title: P2274_N704_S502


title: RNA-seq_SCC1-AID_TIR1+_IAA+_primed_rep3

description:
RNA-seq_SCC1-AID_DESeq2_normalized_counts.tab
RNA-seq_SCC1-AID_TIR1+_primed_DESeq2_IAA+_vs_IAA-.tab

value: cells 48h after interferon gamma washout


title: P2274_N712_S510


title: P2220_N709_S503


title: P2222_N709_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_77


title: P2222_N704_S505


title: HFWL7BBXY_3_IDT_DUI_NXT_139


title: P2275_N720_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_65


title: P2274_N706_S510


title: RNA-seq_SCC1-AID_TIR1+_IAA+_primed_rep1


title: P2279_N722_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_87


title: P2275_N719_S503


title: RNA-seq_SCC1-AID_TIR1+_IAA+_priming_rep3

description:
RNA-seq_SCC1-AID_DESeq2_normalized_counts.tab
RNA-seq_SCC1-AID_TIR1+_priming_DESeq2_IAA+_vs_IAA-.tab

value: cells induced with interferon gamma for 16h


title: RNA-seq_SCC1-AID_TIR1+_IAA+_priming_rep2


title: P2277_N719_S521


title: P2222_N706_S503


title: P2279_N719_S511


title: HFWL7BBXY_1_IDT_DUI_NXT_9


title: RNA-seq_SCC1-AID_TIR1+_IAA+_priming_rep1


title: P2221_N712_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_55


title: RNA-seq_SCC1-AID_TIR1+_IAA-_induction_rep3

description: RNA-seq_SCC1-AID_DESeq2_normalized_counts.tab

value: NO


title: P2222_N702_S507

value: Thymocytes


title: P2274_N710_S503


title: HFWL7BBXY_2_IDT_DUI_NXT_243


title: HFWL7BBXY_3_IDT_DUI_NXT_123


title: RNA-seq_SCC1-AID_TIR1+_IAA-_induction_rep2


title: P2278_N711_S505

value: TCRhiDP


title: HFWL7BBXY_3_IDT_DUI_NXT_221

value: WT


title: P2274_N707_S508


title: RNA-seq_SCC1-AID_TIR1+_IAA+_primed_rep2


title: P2222_N705_S517


title: RNA-seq_SCC1-AID_TIR1+_IAA-_induction_rep1


title: P2222_N701_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_247

value: SMARTer


title: P2222_N703_S502


title: P2277_N723_S517


title: HFWL7BBXY_1_IDT_DUI_NXT_213


title: P2279_N723_S506


title: P2276_N702_S517


title: HFWL7BBXY_1_IDT_DUI_NXT_53


title: HFWL7BBXY_3_IDT_DUI_NXT_159


title: RNA-seq_SCC1-AID_TIR1+_IAA-_reinduction_rep1


title: P2222_N707_S508


title: P2277_N720_S513


title: HFWL7BBXY_2_IDT_DUI_NXT_213


title: P2279_N720_S510


title: P2279_N723_S511


title: RNA-seq_SCC1-AID_TIR1+_IAA-_primed_rep3


title: HFWL7BBXY_2_IDT_DUI_NXT_223


title: P2275_N721_S506


title: RNA-seq_SCC1-AID_TIR1+_IAA-_primed_rep2


title: P2279_N724_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_335


title: RNA-seq_SCC1-AID_TIR1+_IAA-_reinduction_rep3


title: P2221_N707_S503


title: RNA-seq_SCC1-AID_TIR1+_IAA-_primed_rep1


title: HFWL7BBXY_2_IDT_DUI_NXT_135


title: RNA-seq_SCC1-AID_TIR1+_IAA-_priming_rep3


title: P2275_N716_S506


title: RNA-seq_SCC1-AID_TIR1+_IAA-_reinduction_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_233


title: RNA-seq_SCC1-AID_TIR1+_IAA-_priming_rep2


title: RNA-seq_SCC1-AID_TIR1+_IAA-_priming_rep1


title: P2220_N712_S517


title: P2274_N706_S505


title: RNA-seq_SCC1-AID_TIR1+_IAA-_naive_rep3

value: naive cells


title: P2221_N710_S504


title: P2276_N703_S522


title: HFWL7BBXY_3_IDT_DUI_NXT_219


title: HFWL7BBXY_3_IDT_DUI_NXT_197


title: P2276_N704_S522


title: P2278_N712_S502


title: HFWL7BBXY_1_IDT_DUI_NXT_133


title: P2222_N701_S504


title: P2276_N712_S513


title: P2278_N711_S503


title: RNA-seq_SCC1-AID_TIR1+_IAA-_naive_rep2


title: RNA-seq_SCC1-AID_TIR1+_IAA-_naive_rep1


title: P2276_N712_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_153


title: RNA-seq_SCC1-AID_TIR1-_IAA+_reinduction_rep3


title: P2278_N710_S506


title: P2277_N721_S518


title: P2279_N726_S511


title: P2280_N710_S516


title: P2276_N701_S522


title: HFWL7BBXY_2_IDT_DUI_NXT_71


title: RNA-seq_SCC1-AID_TIR1-_IAA+_reinduction_rep2

value: Cells negative for the osTIR1 E3 ligase


title: P2277_N723_S518


title: P2279_N718_S507


title: HFWL7BBXY_3_IDT_DUI_NXT_201


title: P2277_N723_S516


title: P2274_N710_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_193


title: P2277_N716_S522


title: RNA-seq_SCC1-AID_TIR1-_IAA+_primed_rep3

value: HeLa


title: P2277_N720_S521


title: HFWL7BBXY_2_IDT_DUI_NXT_183


title: P2275_N722_S508


title: RNA-seq_SCC1-AID_TIR1-_IAA+_primed_rep2


title: P2278_N714_S506


title: HFWL7BBXY_1_IDT_DUI_NXT_245


title: RNA-seq_SCC1-AID_TIR1-_IAA+_primed_rep1


title: P2278_N711_S502


title: HFWL7BBXY_1_IDT_DUI_NXT_15


title: P2279_N727_S511


title: P2275_N721_S511


title: P2276_N702_S513


title: HFWL7BBXY_3_IDT_DUI_NXT_279


title: P2277_N719_S516


title: HFWL7BBXY_3_IDT_DUI_NXT_175


title: RNA-seq_SCC1-AID_TIR1-_IAA+_priming_rep3


title: RNA-seq_SCC1-AID_TIR1-_IAA+_priming_rep1


title: P2280_N707_S516


title: RNA-seq_SCC1-AID_TIR1-_IAA+_priming_rep2


title: P2275_N718_S507


title: P2276_N707_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_175


title: RNA-seq_SCC1-AID_TIR1-_IAA+_reinduction_rep1


title: HFWL7BBXY_3_IDT_DUI_NXT_85


title: P2276_N710_S521


title: HFWL7BBXY_1_IDT_DUI_NXT_135


title: RNA-seq_SCC1-AID_TIR1-_IAA-_induction_rep3


title: P2222_N710_S503


title: P2275_N716_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_27


title: P2274_N706_S511


title: RNA-seq_SCC1-AID_TIR1-_IAA-_induction_rep1


title: RNA-seq_SCC1-AID_TIR1-_IAA-_reinduction_rep3


title: P2222_N706_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_125


title: P2277_N724_S515


title: P2274_N702_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_11


title: HFWL7BBXY_3_IDT_DUI_NXT_257


title: P2274_N701_S508


title: P2279_N719_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_229


title: RNA-seq_SCC1-AID_TIR1-_IAA-_reinduction_rep1


title: RNA-seq_SCC1-AID_TIR1-_IAA-_reinduction_rep2


title: P2280_N711_S517


title: P2274_N706_S503


title: P2279_N720_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_277


title: RNA-seq_SCC1-AID_TIR1-_IAA-_primed_rep3


title: P2276_N704_S516


title: RNA-seq_SCC1-AID_TIR1-_IAA-_induction_rep2


title: RNA-seq_SCC1-AID_TIR1-_IAA-_primed_rep1


title: P2275_N726_S503


title: P2220_N708_S517


title: P2278_N710_S503


title: P2280_N714_S515


title: HFWL7BBXY_3_IDT_DUI_NXT_303


title: P2274_N705_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_57


title: P2274_N707_S507


title: RNA-seq_SCC1-AID_TIR1-_IAA-_priming_rep3


title: P2220_N711_S502


title: P2276_N705_S515


title: RNA-seq_SCC1-AID_TIR1-_IAA-_priming_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_325


title: P2276_N710_S516


title: RNA-seq_SCC1-AID_TIR1-_IAA-_priming_rep1


title: HFWL7BBXY_2_IDT_DUI_NXT_57


title: P2277_N727_S520


title: P2277_N720_S516


title: HFWL7BBXY_3_IDT_DUI_NXT_267


title: RNA-seq_SCC1-AID_TIR1-_IAA-_primed_rep2


title: RNA-seq_SCC1-AID_TIR1-_IAA-_naive_rep2


title: P2221_N710_S502


title: P2276_N704_S517


title: P2275_N716_S502


title: HFWL7BBXY_1_IDT_DUI_NXT_191


title: P2277_N723_S522


title: RNA-seq_SCC1-AID_TIR1-_IAA-_naive_rep1


title: HFWL7BBXY_3_IDT_DUI_NXT_1


title: HFWL7BBXY_2_IDT_DUI_NXT_191


title: HFWL7BBXY_2_IDT_DUI_NXT_367


title: P2275_N727_S511


title: RNA-seq_reinduction_rep3

data_processing:
Mapping was performed with bwa-mem software version 0.7.17.1 in Simple Illumina mode.
Gene counts were estimated with htseq count software version 0.9.1. Parameters: union mode, feature type exon, ID Attribute gene_id.
DESeq2 version 2.11.40.6 was used to estimate the differential expression between samples.
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression files were generated using DESeq2.

extract_protocol:
Three biological replicates of naïve, priming, primed and reinduced cells were processed for RNA isolation using the TRIzol Reagent. Qubit RNA BR Assay Kit (Thermo Fisher Scientific) was used for quantification and RNA ScreenTape (Agilent) for accessing RNA integrity.
Isolated RNA was used for polyA positive library preparation with the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), according to the manufacturer's protocol. Sequencing was performed on the NextSeq 500 System with the NextSeq 500/550 Kit (Illumina) with 85bp read length in single end mode.

treatment_protocol: Cells were cultured and split into two parallel cultures. One was mock treated with medium and the other with IFNγ (Merck) for 24h. Cells were then washed three times with PBS and trypsinized (Gibco) to remove residual INFγ and cleave the extracellular domains of plasma membrane proteins, including the INFγ receptor, to stop residual signaling. Fresh medium was added and cells were allowed to proliferate for 48h. Next IFNγ was added or not to the primed and naïve cells. After 24h cells were washed, trypsinized, centrifuged 500g for 5 minutes and the pellets were processed for downstream analysis.


title: P2275_N724_S503


title: P2221_N710_S503


title: P2278_N714_S503


title: P2276_N705_S516


title: RNA-seq_reinduction_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_41


title: RNA-seq_SCC1-AID_TIR1-_IAA-_naive_rep3


title: RNA-seq_reinduction_rep1


title: P2220_N709_S502


title: P2274_N707_S502


title: P2276_N704_S518


title: HFWL7BBXY_3_IDT_DUI_NXT_107


title: RNA-seq_primed_rep3


title: HFWL7BBXY_1_IDT_DUI_NXT_67


title: HFWL7BBXY_2_IDT_DUI_NXT_329


title: RNA-seq_primed_rep2


title: RNA-seq_primed_rep1


title: P2274_N712_S502


title: P2279_N718_S506


title: P2222_N704_S507


title: P2276_N712_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_249


title: P2274_N705_S506


title: RNA-seq_priming_rep3


title: HFWL7BBXY_2_IDT_DUI_NXT_97


title: P2280_N715_S517


title: P2222_N709_S517


title: RNA-seq_priming_rep2


title: HFWL7BBXY_3_IDT_DUI_NXT_49


title: P2222_N701_S517


title: P2222_N707_S502


title: P2277_N719_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_305


title: P2275_N719_S505


title: RNA-seq_naive_rep3


title: RNA-seq_priming_rep1


title: P2274_N704_S510


title: HFWL7BBXY_3_IDT_DUI_NXT_31


title: RNA-seq_naive_rep2


title: P2275_N724_S510


title: HFWL7BBXY_1_IDT_DUI_NXT_137


title: P2220_N710_S503


title: P2277_N718_S518


title: RNA-seq_naive_rep1


title: P2222_N705_S504


title: P2277_N719_S515


title: P2278_N710_S502


title: P2275_N724_S507


title: HFWL7BBXY_3_IDT_DUI_NXT_147


title: HFWL7BBXY_1_IDT_DUI_NXT_323


title: input

treatment_protocol: The ChIPmentation procedure was adopted from (Schmidl et al., 2015). In brief, 12*107 naive, stimulated with IFNγ (Merck) for 24h or primed HeLa cells (2 and 7 days after interferon gamma washout) were collected by centrifugation for 5 minutes at 500g. Next, the cells were re-suspended in 25 mL of medium supplemented with 1% formaldehyde and incubated for 10 minutes in room temperature. Cross-linking was quenched by addition of 25mL of 125mM glycine in PBS. Cells were harvested by centrifugation, washed two times with 10mL of cold PBS, frozen in liquid nitrogen and kept in -80°C. To fragment chromatin, cell pellets were re-suspended in Lysis Buffer (50mM Tris-HCl pH 7.5; 1% SDS; 10mM EDTA; protease inhibitors (Roche)) and sonicated with Qsonica Q800R2; 107 cells in 0.3mL of buffer per 0.5mL tube with the following conditions: time – 5 minutes, pulse – 30 seconds ON/OFF, amplitude – 75%. The resulting material was tested for proper sonication by fragment analysis confirming DNA size between 500 and 4000bp. Chromatin samples were aliquoted at 5*106 cells per tube and frozen in -80°C. For a single immunoprecipitation, 25μL of protein A or G Dynabeads beads (Thermo Fisher Scientific) were washed twice with ChIP Dilution Buffer (20mM Tris-HCl pH 7.5; 0.1% SDS; 1% Triton X-100; 150mM NaCl; 2mM EDTA; protease inhibitors (Roche)). In parallel, the sample was diluted with ChIP Dilution Buffer up to 2mL and clarified at 12000g for 10 minutes in 4°C. Input DNA was collected from the supernatant (10µL). Samples were incubated with the beads and a given antibody over night at 4°C with rotation. Beads were washed at 4°C as follows: twice with Low Salt Wash Buffer (50mM Tris-HCl pH 7.5; 150mM NaCl; 1mM EDTA; 1% TritonX-100; 0.1% Na-Deoxycholate; protease inhibitors (Roche)); twice with High Salt Wash Buffer (50mM Tris-HCl pH 7.5; 500mM NaCl; 1mM EDTA; 1% TritonX-100; 0.1% Na-Deoxycholate; protease inhibitors (Roche)); twice with LiCl Wash Buffer (10mM Tris-HCl pH 7.5; 0.5% NP-40; 0.5% Na-Deoxycholate; 250mM LiCl; 1mM EDTA; protease inhibitors (Roche)); twice with TE Buffer (10mM Tris-HCl pH 7.5; 1mM EDTA; protease inhibitors (Roche)) and finally twice with 10mM Tris-HCl pH 7.5.

value: input


title: P2275_N723_S503


title: P2274_N704_S508


title: P2279_N716_S511


title: HFWL7BBXY_3_IDT_DUI_NXT_331


title: HFWL7BBXY_3_IDT_DUI_NXT_65


title: ChIP-seq_H3K4me2_2_days_washout

value: cells 2 days after interferon gamma washout

value: H3K4me2 (Abcam, ab32356)


title: ChIP-seq_H3K4me2_7_days_washout

value: cells 7 days after interferon gamma washout


title: HFWL7BBXY_2_IDT_DUI_NXT_31


title: P2279_N720_S508


title: ChIP-seq_H3K4me2_priming

value: cells induced with interferon gamma for 24h


title: ChIP-seq_H3K4me2_naive


title: P2276_N703_S521


title: P2274_N704_S507


title: P2222_N706_S505


title: P2274_N703_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_195


title: ChIP-seq_H3K79me2_7_days_washout

value: H3K79me2 (Abcam, ab3594)


title: P2275_N721_S507


title: P2276_N710_S522


title: HFWL7BBXY_1_IDT_DUI_NXT_153


title: P2276_N706_S516


title: ChIP-seq_H3K79me2_2_days_washout


title: P2279_N723_S507


title: ChIP-seq_H3K79me2_priming


title: HFWL7BBXY_1_IDT_DUI_NXT_311


title: P2274_N702_S506


title: P2220_N711_S504


title: ChIP-seq_H3K79me2_naive


title: P2221_N710_S517


title: P2275_N723_S511


title: HFWL7BBXY_1_IDT_DUI_NXT_147


title: P2274_N703_S508


title: ChIP-seq_H3K36me3_2_days_washout

value: H3K36me3 (Abcam, ab9050)


title: P2275_N720_S510


title: P2220_N710_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_301


title: HFWL7BBXY_2_IDT_DUI_NXT_281


title: ChIP-seq_H3K36me3_priming


title: P2275_N716_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_167


title: ChIP-seq_H3K36me3_7_days_washout


title: P2221_N709_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_289


title: P2275_N721_S505


title: P2279_N727_S508


title: ChIP-seq_H3K36me_naive


title: HFWL7BBXY_1_IDT_DUI_NXT_173


title: P2222_N703_S505


title: P2279_N726_S505


title: P2274_N701_S510


title: ChIP-seq_H3K27ac_7_days_washout

value: H3K27ac (Abcam, ab4729)


title: HFWL7BBXY_2_IDT_DUI_NXT_239


title: P2274_N705_S502


title: P2278_N707_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_203


title: P2276_N710_S515


title: ChIP-seq_H3K27ac_2_days_washout


title: ChIP-seq_H3K27ac_priming


title: P2276_N707_S521


title: P2280_N711_S513


title: P2221_N711_S503


title: P2279_N727_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_41


title: ChIP-seq_H3K27ac_naive


title: HFWL7BBXY_1_IDT_DUI_NXT_87


title: P2277_N727_S515


title: P2277_N723_S520


title: ChIP-seq_H33-HA_7_days_washout

value: HA (Merck, 12CA5)


title: HFWL7BBXY_1_IDT_DUI_NXT_163


title: ChIP-seq_H33-HA_2_days_washout


title: P2277_N719_S522


title: P2278_N712_S505


title: HFWL7BBXY_2_IDT_DUI_NXT_199


title: ChIP-seq_H33-HA_priming


title: HFWL7BBXY_2_IDT_DUI_NXT_211


title: P2280_N714_S516


title: ChIP-seq_H33-HA_naive


title: HFWL7BBXY_1_IDT_DUI_NXT_157


title: ChIP-seq_PolII_7_days_washout

value: RNA PolII (Abcam, ab817)


title: P2279_N716_S506

value: Thymocytes


title: P2275_N726_S510


title: P2280_N710_S515

value: TCRhiDP


title: HFWL7BBXY_2_IDT_DUI_NXT_111

value: WT


title: HFWL7BBXY_3_IDT_DUI_NXT_243

value: SMARTer


title: ChIP-seq_PolII_2_days_washout


title: ChIP-seq_PolII_priming


title: P2275_N722_S502


title: P2222_N709_S505


title: P2274_N702_S507


title: ChIP-seq_PolII_naive

value: naive cells


title: P2276_N706_S513


title: HFWL7BBXY_2_IDT_DUI_NXT_227


title: P2277_N721_S522


title: P2277_N726_S521


title: HFWL7BBXY_3_IDT_DUI_NXT_235


title: P2279_N716_S507


title: ATAC_input

extract_protocol:
Cells were re-suspended in 50µL of ATAC lysis buffer (10mM Tris-HCl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.01% Igepal CA-630) and centrifuged immediately for 10 minutes at 500 g at 4 °C. The cell pellets were re-suspended in 50µL tagmentation reaction buffer (25µL 2× TD buffer, 22.5 µl dH2O, and 2.5µL TDE1 (Tn5 enzyme) (Nextera DNA Library Prep Kit, Illumina)) and incubated in 37°C for 30 minutes. DNA was purified with MinElute PCR Purification Kit (Qiagen) (10μL elution).
For preparation of sequencing libraries the purified DNA was amplified using Q5 Hot start DNA polymerase using indexing primers described in (Buenrostro et al., 2013). Initial amplification was performed: 98°C 30 seconds; [98°C 10 seconds; 63°C 30 seconds; 72°C 1 minute]x 5 cycles followed by library quantification with qPCR: 95°C 3 minutes; [95°C 10 seconds; 58°C 30 seconds; 72°C 1 minute] and additional PCR amplification (conditions as for the initial 5 cycles). The required number of additional cycles was calculated from the qPCR data by determining the number of cycles to reach 50% of the maximum signal. After library amplification and indexing, DNA was purified and size selected with AMPure XP magnetic beads (Beckman Coulter) according to manufacturer’s protocol. After purification the libraries concentration was determined by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) according to manufacturer’s protocol. The fragment size was estimated by DNA ScreenTape (Agilent) and the final library quality was measured with KAPA Library quantification kit (Roche) according to manufacturer’s protocol. For sequencing, multiplexed libraries were diluted to 2nM concentration (calculated based the on the KAPA Library quantification kit).

treatment_protocol: The ATAC-seq procedure was adopted from (Chen et al., 2016). In brief, 5*104 naïve, stimulated with IFNγ (Merck) for 24h or primed HeLa cells (2 and 7 days after interferon gamma washout) were collected by centrifugation for 5 minutes at 500g.


title: P2280_N710_S517


title: P2275_N719_S506


title: ATAC-seq_7_days_washout


title: HFWL7BBXY_1_IDT_DUI_NXT_81


title: P2222_N704_S502


title: P2278_N715_S502


title: P2275_N723_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_293


title: ATAC-seq_2_days_washout


title: ATAC-seq_priming


title: P2222_N705_S507


title: P2274_N712_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_143


title: P2277_N724_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_241


title: P2279_N718_S502


title: TCRhighCD8SP_rep2

data_processing:
100bp pair-end reads, obtained by Illumina HiSeq 2500, were mapped to Mus musculus mm9 genome by the TopHat software (TopHat v2.1.0, Bowtie v2.2.6.0, TopHat setting was '-N 0 -g 1 -x 1').
Read counts for genes were calculated using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: CSV with gene-based read counts from HTSeq

extract_protocol:
Mechanical dissociation of fresh thymus tissue. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, 74134).
Sequencing libraries for RNA-seq were prepared using the Illumina TruSeq Stranded total RNA Kit (RS-122-2201).

tag: celltype

value: wild type


title: ATAC-seq_naive

value: HeLa


title: HFWL7BBXY_1_IDT_DUI_NXT_165


title: P2222_N705_S506


title: TCRhighCD8SP_rep1


title: HFWL7BBXY_1_IDT_DUI_NXT_41


title: P2222_N710_S504


title: P2279_N718_S510


title: P2277_N722_S515


title: CD69-CD4SP_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_283


title: P2274_N706_S502


title: HFWL7BBXY_3_IDT_DUI_NXT_343


title: P2276_N706_S520


title: P2275_N716_S511


title: P2280_N714_S513


title: CD69-CD4SP_rep1


title: P2277_N722_S518


title: HFWL7BBXY_2_IDT_DUI_NXT_165


title: P2274_N702_S508


title: P2279_N726_S510


title: HFWL7BBXY_1_IDT_DUI_NXT_199


title: CD69+CD4SP_rep1


title: P2276_N707_S520


title: P2222_N702_S503


title: P2276_N702_S518


title: HFWL7BBXY_2_IDT_DUI_NXT_219


title: HFWL7BBXY_3_IDT_DUI_NXT_317


title: CD69+CD4+CD8low_rep2


title: P2276_N710_S513


title: P2279_N722_S506


title: P2278_N715_S505


title: P2279_N726_S507


title: CD69+CD4+CD8low_rep1


title: HFWL7BBXY_3_IDT_DUI_NXT_29


title: HFWL7BBXY_3_IDT_DUI_NXT_209


title: P2222_N702_S505


title: CD69+DP_rep1


title: P2275_N718_S505


title: P2274_N701_S503


title: CD69+CD4SP_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_101


title: CD69-DP_rep3


title: HFWL7BBXY_3_IDT_DUI_NXT_173


title: P2279_N726_S508


title: P2279_N721_S502


title: CD69-DP_rep1


title: HFWL7BBXY_1_IDT_DUI_NXT_301


title: P2222_N704_S503


title: P2274_N705_S507


title: P2277_N720_S515


title: P2276_N705_S522


title: HFWL7BBXY_1_IDT_DUI_NXT_217


title: CD69+DP_rep2


title: HFWL7BBXY_3_IDT_DUI_NXT_165


title: P2222_N709_S504


title: P2278_N707_S503


title: P2279_N721_S511


title: HFWL7BBXY_1_IDT_DUI_NXT_261


title: P2274_N710_S502


title: FL-E95-WT-Mm9-Rep2-PolyA-RNAseq-L11519

city: Berlin

first: Lila

last: Allou

address: 63-73 Ihnestrasse

department: FG Development and Disease

institute: Max Planck Institute For Molecular Genetics

data_processing:
Paired-end RNA-seq reads were mapped using the STAR mapper (splice junctions based on RefSeq; options: --alignIntronMin 20 –alignIntronMax 500000 – outFilterMismatchNmax 10).
Uniquely mapped paired-end reads were subsequently used for expression analysis using the Cufflinks package (version 2.2.1; default settings)
In a first step, transcripts of each sample were assembled using Cufflinks provided with reference gene annotations from ensembl. The resulting assemblies were then merged using Cuffmerge.
Genome_build: Mm9
Supplementary_files_format_and_content: BigWig

source_name: Forelimb

extract_protocol:
Total RNAs were extracted using the Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.
Samples were poly-A enriched and sequenced using Illumina technology following standard protocols.

treatment_protocol: Limbs from E9.5 mouse embryos were dissected in PBS, snap frozen and stored at -80° C.

value: Wild type

tag: embryonic stage


title: P2278_N715_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_361


title: P2221_N711_S517


title: FL-E95-GFP-3xpA-Mm9-Rep1-PolyA-RNAseq-L15593

value: Mutant (GFP+Stop Cassette Insertion)


title: P2274_N703_S503


title: FL-E95-GFP-3xpA-Mm9-Rep2-PolyA-RNAseq-L15594


title: HFWL7BBXY_1_IDT_DUI_NXT_325


title: P2276_N712_S520


title: FL-E95-3xpA-Mm9-Rep2-PolyA-RNAseq-L15856

value: Mutant (Stop Cassette Insertion)


title: P2274_N702_S502


title: P2277_N727_S522


title: P2279_N727_S505


title: CD69-DP_rep2


title: HFWL7BBXY_2_IDT_DUI_NXT_9


title: P2222_N703_S517


title: P2274_N703_S511


title: HFWL7BBXY_1_IDT_DUI_NXT_121


title: P2276_N711_S513


title: FLHL-E115-G4WT-Mm9-Rep1-H3K4me3-ChIP-L1776

data_processing:
Single-end ChIP-seq reads were mapped with bowtie (v2.2.6).
Filtered for mapping quality MAPQ ≥ 10.
Duplicates were removed using samtools rmdup (v1.8).
For generating coverage tracks, reads were extended to 300 bp (H3K27ac, H3K4me1, and H3K4me3) or 200 bp (CTCF and Rad21) and scaled to r.p.m. (106 per number of unique reads) using bedtools genomecov v2.27.1
Genome_build: Mm9

source_name: Forelimb Hindlimb

extract_protocol:
ChIP experiments were performed following the protocol described in (Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations. Ibrahim et al.,Genome Research 2013).
Snap frozen samples were first digested and chromatin was sonicated with a Diagenode Bioruptor (45 cycles- 30 sec pulse, 30 sec pause, HI power). 25-35 ug of chromatin was used in each immunoprecipitation with 1ug of the following specific antibodies: anti-H3K4me3, Millipore, cat. No. 07-473; anti-H3K4me1, Diagenode, cat. No. C15410037; anti-H3K27ac, Diagenode, cat. No. C15410174; anti-CTCF, Active Motif, cat. No. 61311; anti-Rad21, abcam, cat.No. ab992. Libraries were prepared using the Nextera adaptors and sequenced.

treatment_protocol: Limbs from E9.5 or E11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 1% PFA, snap frozen, and stored at -80 °C.


title: FLHL-E115-G4WT-Mm9-Rep2-H3K4me3-ChIP-L6989


title: FLHL-E115-G4WT-Mm9-Rep2-H3K4me1-ChIP-L14892


title: HFWL7BBXY_1_IDT_DUI_NXT_61


title: P2277_N723_S513


title: HFWL7BBXY_2_IDT_DUI_NXT_369


title: P2279_N720_S505


title: P2222_N708_S502


title: FLHL-E115-G4WT-Mm9-Rep1-H3K4me1-ChIP-L14891


title: P2277_N726_S515


title: P2220_N707_S503


title: P2222_N702_S504


title: HFWL7BBXY_1_IDT_DUI_NXT_19


title: P2276_N707_S522


title: HFWL7BBXY_1_IDT_DUI_NXT_223


title: P2274_N704_S506


title: P2277_N718_S513


title: P2222_N701_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_23


title: P2279_N723_S505


title: mpimg_L19378_E9-5FL3xpA-Rep3-cHiC

description:
mpimg_L19377_L19378_E9-5FL3xpA_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
mpimg_L19377_L19378_E9-5FL3xpA_Rep2_Rep3_merged.hicup.MAPQ30.Raw_10kb-cHiC.WashU.txt

data_processing:
Library strategy: capture HiC
Raw sequencing reads were processed with the HiCUP pipeline v0.6.1 (no size selection, Nofill: 1, Format: Sanger) using Bowtie2 v2.3.4.1 for mapping short reads. Replicates were then merged by combining their bam files.
Juicer tools v1.7.6 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
As an additional filtering step, read-pairs with genomic distances ≤ 10 kb were removed. Afterwards, cHi-C maps were generated with the Juicer tools ‘pre’ command using a custom chrom.sizes file containing only the length of the genomic region of interest (4.75 Mb) and requesting a MAPQ≥30.
Genome_build: Mm9

extract_protocol:
The capture HiC protocol was performed as decribed in (Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016).
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipiated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).

treatment_protocol: Limbs, forebrains, and midhindbrains from E9.5 or E10.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.

tag: tissue

value: Forelimb


title: mpimg_L19081-1_E9-5-MHB-Rep3-cHiC

description:
mpimg_L19079_L19080_L19081_E9-5-MHB-Rep1_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
mpimg_L19079_L19080_L19081_E9-5-MHB-Rep1_Rep2_Rep3_merged.hicup.MAPQ30.Raw_10kb-cHiC.WashU.txt

source_name: Midhindbrain Boundary

value: Midhindbrain Boundary


title: HFWL7BBXY_3_IDT_DUI_NXT_17


title: P2274_N710_S508


title: P2277_N721_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_193


title: mpimg_L19080-1_E9-5-MHB-Rep2-cHiC


title: P2276_N703_S513


title: P2274_N712_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_367


title: P2221_N711_S502


title: P2275_N718_S506


title: mpimg_L19078-1_E9-5-FB-Rep3-cHiC

description:
mpimg_L19076_L19077_L19078_E9-5-FB-Rep1_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
mpimg_L19076_L19077_L19078_E9-5-FB-Rep1_Rep2_Rep3_merged.hicup.MAPQ30.Raw_10kb-cHiC.WashU.txt

source_name: Forebrain

value: Forebrain


title: mpimg_L19377_E9-5FL3xpA-Rep2-cHiC


title: P2276_N701_S516

source_name: Thymocytes


title: mpimg_L19077-1_E9-5-FB-Rep2-cHiC


title: FL-E95-3xpA-Mm9-Rep1-PolyA-RNAseq-L15855


title: mpimg_L19076-1_E9-5-FB-Rep1-cHiC


title: HFWL7BBXY_1_IDT_DUI_NXT_107


title: P2274_N707_S510


title: P2220_N708_S504


title: HFWL7BBXY_1_IDT_DUI_NXT_51


title: P2279_N727_S506


title: P2277_N727_S518


title: mpimg_L12978-1_CD1FLE9-5-cHiC

description:
mpimg_L12976_L12977_L12978_CD1FLE9-5_Rep1_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
mpimg_L12976_L12977_L12978_CD1FLE9-5_Rep1_Rep2_Rep3_merged.hicup.MAPQ30.Raw_10kb-cHiC.WashU.txt


title: HFWL7BBXY_2_IDT_DUI_NXT_107


title: P2279_N716_S510


title: mpimg_L12977-1_CD1FLE9-5-cHiC


title: mpimg_L19079-1_E9-5-MHB-Rep1-cHiC


title: P2277_N723_S521


title: mpimg_L12976-1_CD1FLE9-5-cHiC


title: HFWL7BBXY_1_IDT_DUI_NXT_45


title: P2278_N714_S505


title: P2279_N718_S503


title: P2220_N711_S517


title: HFWL7BBXY_3_IDT_DUI_NXT_59


title: P2277_N724_S520


title: Virtual4C_FL-E95-WT-Mm9-Rep3-cHiC-L12978

description:
FL-E95-WT-Mm9-MergedRep1Rep2Rep3-Virtual4C_En1_promoter.3kb_norm.bedgraph
FL-E95-WT-Mm9-MergedRep1Rep2Rep3-Virtual4C_En1_promoter.5kb_norm.bedgraph

data_processing:
Library strategy: capture HiC
Raw sequencing reads were processed with the HiCUP pipeline v0.6.1 (no size selection, Nofill: 1, Format: Sanger) using Bowtie2 v2.3.4.1 for mapping short reads. Replicates were then merged by combining their bam files.
Virtual 4C-like profiles were generated from mapped, filtered and deduplicated cHiC read pairs obtained from the HiCUP pipeline.
A read pair was considered in a profile, when it had a MAPQ≥30 and one read mapped to the defined viewpoint region while the other one mapped outside of it. Out of these pairs, reads mapping outside of the viewpoint region were counted per restriction fragment and binned to a 1kb grid. The count value of restriction fragments spanning more than one bin was distributed proportionally to the corresponding bins.
The profiles were smoothed by averaging over five bins and scaled individually by the factor 103 / counts within the enriched region. For the computation of the scaling factor, the viewpoint region and a margin ±3 or 5 kb around it were excluded.
The processing was performed with custom Java code using htsjdk v.2.12.0 (https://samtools.github.io/htsjdk/).
Genome_build: Mm9

treatment_protocol: Limbs from E9.5 or E10.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.


title: HFWL7BBXY_1_IDT_DUI_NXT_269


title: P2222_N709_S502


title: P2279_N720_S503


title: HFWL7BBXY_1_IDT_DUI_NXT_189


title: Virtual4C_FL-E95-WT-Mm9-Rep1-cHiC-L12976


title: P2276_N706_S515


title: P2279_N723_S510


title: HFWL7BBXY_2_IDT_DUI_NXT_267


title: P2278_N715_S506


title: P2276_N712_S521


title: HFWL7BBXY_1_IDT_DUI_NXT_373


description: mESCs-WT-Mm9-Rep1-DamID-merge-LamB1-L14085__vs__mESCs-WT-Mm9-Rep1-DamID-merge-Dam-L14080.bw

data_processing:
Library strategy: DamID-seq
Raw reads from DamID-seq  experiments were mapped using the alignment tool BWA mem.
Mapped reads were RPKM normalized.
A log2 foldchange between the Dam-Lamin B1 transduced samples and the respective Dam only-encoding samples was calculated for every DpnII restriction enzyme site ('GATC')
Genome_build: Mm9
Supplementary_files_format_and_content: BigWig

source_name: Mouse embryonic stem cells

growth_protocol: G4 embryonic stem cells (mESCs) were seeded on CD1 mouse embryonic fibrobalst (MEF) feeders and cultured under standard ESC culture conditions.

extract_protocol:
DNA adenine methytransferase identification experiments were performed as described in (The Application of DamID to Identify Peripheral Gene Sequences in Differentiated and Primary Cells. Robson et al., Methods Mol Biol 2016)
mESCs and cultured cells isolated from mouse hindlimb buds at E11.5 (HLCCs) were both separately transduced with Dam-Lamin B1- and Dam only-encoding lentiviruses over 24h. At 72 hr post-transduction, genomic DNA was extracted from trypsinized mESCs and HLCCs and processed into libraries for next generation sequencing (NGS).

treatment_protocol: Limbs from E11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin and a primary cell culture was derived.

value: Mouse embryonic stem cells

value: Stem cells

tag: transduced with

value: Dam-Lamin B1


title: P2280_N712_S516


title: HFWL7BBXY_1_IDT_DUI_NXT_239


title: P2277_N719_S520


title: HFWL7BBXY_1_IDT_DUI_NXT_289


description: HLLCs-E115-WT-Mm9-Rep1-DamID-merge-LamB1-L15037__vs__HLLCs-E115-WT-Mm9-Rep1-DamID-merge-Dam-L15038.bw

source_name: Hindlimb

value: Hindlimb

value: Dam


title: P2274_N704_S503

value: Thymocytes


title: HFWL7BBXY_3_IDT_DUI_NXT_315

value: WT


title: HLLCs-E115-WT-Mm9-Rep1-DamID-merge-LamB1-L15037


title: P2222_N708_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_167

value: TCRhiDP

value: SMARTer


title: P2277_N720_S520


title: P2280_N707_S513


title: P2274_N706_S508


title: FLHL-E115-WT-Mm9-Rep2-Rad21-ChIP-L17113

data_processing:
Single-end ChIP-seq reads were mapped with bowtie (v2.2.6).
Filtered for mapping quality MAPQ ≥ 10.
Duplicates were removed using samtools rmdup (v1.8).
For generating coverage tracks, reads were extended to 300 bp (H3K27ac, H3K4me1, and H3K4me3) or 200 bp (CTCF and Rad21) and scaled to r.p.m. (106 per number of unique reads) using bedtools genomecov v2.27.1
Genome_build: Mm9
Supplementary_files_format_and_content: BigWig

value: Forelimb Hindlimb


title: P2274_N702_S503


title: HFWL7BBXY_2_IDT_DUI_NXT_169


title: P2275_N718_S503


title: FLHL-E115-WT-Mm9-Rep2-CTCF-ChIP-L17109


title: P2279_N722_S502


title: P2275_N727_S506


title: Virtual4C_FL-E95-WT-Mm9-Rep2-cHiC-L12977


title: mESCs-WT-Mm9-Rep1-DamID-merge-Dam-L14080


title: P2222_N708_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_83


title: P2279_N727_S502


title: FLHL-E115-WT-Mm9-Rep2-2-H3K27ac-ChIP-L16619


title: P2277_N724_S517


title: HFWL7BBXY_2_IDT_DUI_NXT_117


title: FLHL-E115-WT-Mm9-Rep2-1-H3K27ac-ChIP-L16619


title: HFWL7BBXY_2_IDT_DUI_NXT_5


title: P2279_N719_S508


title: P2279_N718_S505


title: FLHL-E115-WT-Mm9-Rep1-Rad21-ChIP-L17112


title: HFWL7BBXY_2_IDT_DUI_NXT_55


title: P2276_N702_S522


title: HFWL7BBXY_3_IDT_DUI_NXT_225


title: FLHL-E115-WT-Mm9-Rep1-H3K27ac-ChIP-L16618


title: P2274_N701_S507


title: P2274_N703_S505


title: HFWL7BBXY_3_IDT_DUI_NXT_299


title: FLHL-E115-WT-Mm9-Rep1-CTCFT-ChIP-L17108


title: P2274_N701_S505


title: P2276_N703_S517


title: P2276_N703_S516


title: HFWL7BBXY_2_IDT_DUI_NXT_65


title: FLHL-E115-Del27-Mm9-Rep2-H3K4me3-ChIP-L14890

description: FLHL-E115-Del27-Mm9-Merge-H3K4me3-ChIP.bw

value: Mutant (27 kb deletion)


title: P2280_N715_S513


title: P2277_N726_S518


title: HFWL7BBXY_3_IDT_DUI_NXT_213


title: FLHL-E115-Del27-Mm9-Rep1-H3K4me3-ChIP-L14447


title: P2279_N726_S502


title: P2277_N726_S516


title: HFWL7BBXY_3_IDT_DUI_NXT_305


title: P2276_N703_S515


title: FLHL-E115-3xpA-Mm9-Rep2-Rad21-ChIP-L17115


title: FLHL-E115-3xpA-Mm9-Rep2-H3K4me3-ChIP-L15853

description: FLHL-E115-3xpA-Mm9-Merge-H3K4me3-ChIP.bw


title: HFWL7BBXY_1_IDT_DUI_NXT_57


title: P2222_N710_S502


title: P2222_N708_S517


title: P2275_N724_S502


title: HFWL7BBXY_2_IDT_DUI_NXT_253


title: FLHL-E115-3xpA-Mm9-Rep2-H3K4me1-ChIP-L15851

description: FLHL-E115-3xpA-Mm9-Merge-H3K4me1-ChIP.bw


title: P2276_N710_S518


title: P2220_N707_S517


title: P2277_N719_S518


title: P2274_N705_S510


title: FLHL-E115-3xpA-Mm9-Rep2-CTCF-ChIP-L17111


title: P2275_N724_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_353


title: FLHL-E115-3xpA-Mm9-Rep2-2-H3K27ac-ChIP-L16623

description: FLHL-E115-3xpA-Mm9-Merge-H3K27ac-ChIP.bw


title: P2274_N710_S511


title: P2276_N707_S513


title: FLHL-E115-3xpA-Mm9-Rep2-1-H3K27ac-ChIP-L16623


title: P2222_N707_S507


title: FLHL-E115-3xpA-Mm9-Rep1-Rad21-ChIP-L17114


title: P2220_N708_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_119


title: P2279_N722_S510


title: FLHL-E115-3xpA-Mm9-Rep1-H3K4me3-ChIP-L15852


title: HFWL7BBXY_2_IDT_DUI_NXT_151


title: FLHL-E115-3xpA-Mm9-Rep1-H3K4me1-ChIP-L15850


title: P2275_N716_S510


title: HFWL7BBXY_3_IDT_DUI_NXT_91


title: HFWL7BBXY_2_IDT_DUI_NXT_99


title: P2222_N707_S505


title: P2275_N723_S507


title: HFWL7BBXY_2_IDT_DUI_NXT_177


title: P2279_N724_S503


title: P2222_N701_S505


title: P2221_N709_S503


title: HFWL7BBXY_3_IDT_DUI_NXT_129


title: HFWL7BBXY_3_IDT_DUI_NXT_113


title: P2274_N711_S508


title: P2222_N706_S508


title: HFWL7BBXY_3_IDT_DUI_NXT_83


title: P2275_N719_S502


title: P2275_N726_S506


title: HFWL7BBXY_2_IDT_DUI_NXT_27


title: P2222_N710_S507


title: FL-E95-WT-Mm9-Rep2-1-H3K27ac-ChIP-L16551

value: Wild type


title: P2274_N711_S507


title: P2220_N712_S504


title: HFWL7BBXY_3_IDT_DUI_NXT_291


title: P2279_N716_S508


title: FL-E95-WT-Mm9-Rep2-2-H3K27ac-ChIP-L16551


title: P2221_N711_S504


title: HFWL7BBXY_1_IDT_DUI_NXT_95


title: P2275_N718_S511


title: FLHL-E115-3xpA-Mm9-Rep1-CTCF-ChIP-L17110


title: FLHL-E115-3xpA-Mm9-Rep1-2-H3K27ac-ChIP-L16622


title: FL-E95-WT-Mm9-Rep1-2-H3K27ac-ChIP-L16550


title: HFWL7BBXY_2_IDT_DUI_NXT_279


title: P2279_N721_S510


title: P2221_N712_S517


title: P2276_N702_S520


title: FL-E95-WT-Mm9-Rep1-2-H3K4me3-ChIP-L14203


title: FLHL-E115-3xpA-Mm9-Rep1-1-H3K27ac-ChIP-L16622


title: FL-E95-WT-Mm9-Rep2-H3K4me3-ChIP-L15854


title: FL-E95-WT-Mm9-Rep1-1-H3K27ac-ChIP-L16550


title: HFWL7BBXY_3_IDT_DUI_NXT_141


title: P2221_N712_S504


title: P2275_N718_S508


title: FL-E95-WT-Mm9-Rep1-1-H3K4me3-ChIP-L14203


title: P2222_N703_S508


title: HFWL7BBXY_2_IDT_DUI_NXT_347


title: P2275_N727_S503


title: P2274_N707_S511


title: Brain-E95-WT-Mm9-Rep2-2-H3K27ac-ChIP-L16553

source_name: Brain

value: Brain


title: HFWL7BBXY_2_IDT_DUI_NXT_371


title: P2280_N712_S513


title: HFWL7BBXY_1_IDT_DUI_NXT_363


title: P2279_N724_S511


title: Brain-E95-WT-Mm9-Rep2-2-H3K4me3-ChIP-L16555


title: Htt+Sis1_rep3

city: Martinsried

first: Courtney

middle: Lee

last: Klaips

address: Am Klopferspitz 18

department: Department of Cellular Biochemistry

institute: Max Planck Institute for Biochemistry

data_processing:
Illumina CASAVA version 1.8 software used for basecalling
Clean reads were obtained by removing reads containing adapter sequence, poly-N, and low quality reads
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
HTSeq v0.6.1 was used to count the read numbers mapped to each gene.
Expression levels were calculted using the FPKM (expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) method as per Trapnell, Cole, et al., 2010.
Genome_build: Ensembl release 81 Saccharomyces cerevisiae
Supplementary_files_format_and_content: Excel table including FPKM values for genes and samples
Supplementary_files_format_and_content: Excel table with raw gene counts for genes and samples

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: S. cerevisiae expressing either empty vector controls or combinations of Sis1 and Htt97Q were grown under inducing conditions at 30C for ~21 h before harvesting. Cell pellets were harvested, flash frozen and sent to Novogene for processing.

extract_protocol:
mRNA was purified from 1 ug total RNA extracts using poly-T oligo-attached magnetic beads.
Sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina. Index codes were added and clustering was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina). Library preparations were subjected to Illumina paired-end sequencing.

tag: plasmid expression

value: Htt97Q and Sis1


title: HFWL7BBXY_1_IDT_DUI_NXT_115


title: HFWL7BBXY_1_IDT_DUI_NXT_315


title: Htt+Sis1_rep2


title: P2274_N711_S511


title: HFWL7BBXY_3_IDT_DUI_NXT_161


title: Htt+Sis1_rep1


title: P2279_N724_S505


title: Brain-E95-WT-Mm9-Rep1-H3K4me3-ChIP-L16554


title: HFWL7BBXY_2_IDT_DUI_NXT_7


title: Htt_rep3


title: P2276_N704_S515


title: Brain-E95-WT-Mm9-Rep1-2-H3K27ac-ChIP-L16552


title: Htt_rep2


title: HFWL7BBXY_3_IDT_DUI_NXT_233


title: P2222_N703_S503


title: Htt_rep1


title: P2279_N720_S507


title: HFWL7BBXY_1_IDT_DUI_NXT_251


title: Brain-E95-WT-Mm9-Rep1-1-H3K27ac-ChIP-L16552


title: FLHL-E115-WT-Mm9-Rep2-ATAC-L17221

data_processing:
Paired-end ATAC-seq reads were trimmed to 30 bp to allow fragments with close-by transposition events (<50 bp) to map.
Trimmed reads were mapped with Bowtie2 (v2.2.6).
Duplicate fragments were removed using Picard RemoveDuplicates (https://broadinstitute.github.io/picard/).
Coverage tracks (bigWig) were generated with deepTools2 for properly mapped read pairs (FLAG 0 × 2) with mapping quality ≥20.
Genome_build: Mm9

extract_protocol:
Transposition reactions were performed using the Nextera Tn5 Transposase Kit (Nextera Kit, Illumina) according to the manufacturer's guidelines.
The limb cells were first lysed. Following this, the transposition reaction was performed on the lysed cells followed by a purification step. Libraries were prepared using the Nextera adaptors and sequenced.

treatment_protocol: Limbs from E11.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 1% PFA and were directly processed to assess chromatin accessibility.

value: Wild Type


title: Sis1_rep2


title: Brain-E95-WT-Mm9-Rep2-1-H3K27ac-ChIP-L16553


title: FLHL-E115-WT-Mm9-Rep1-ATAC-L17220


title: P2278_N710_S505

data_processing:
Smart-seq2 and SMARTer sequencing data were aligned with TopHat2 version 2.1.1 (Kim et al., 2013)
GRCm38 (mm10) mouse genome reference was used for alignment and gene annotation from UCSC.
Read counts for genes were calculated using velocyto version 0.17 (La Manno et al., 2018) and the cell-gene count matrix obtained was used for downstream analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CSV file containing the raw read counts matrix of all the samples from the experiment calculated using the tool velocyto.


title: Sis1_rep3


title: HFWL7BBXY_3_IDT_DUI_NXT_309


title: Brain-E95-WT-Mm9-Rep2-1-H3K4me3-ChIP-L16555


title: Sis1_rep1


title: HFWL7BBXY_2_IDT_DUI_NXT_137


title: FLHL-E115-3xpA-Mm9-Rep2-ATAC-L17219

value: Mutant (Stop Cassette Insertion)


title: P2276_N704_S513


title: HFWL7BBXY_1_IDT_DUI_NXT_141


title: P2274_N710_S506


title: FLHL-E115-3xpA-Mm9-Rep1-ATAC-L17218


title: P2276_N701_S520


title: P2222_N702_S508


title: FL-E95-WT-Mm9-Rep1-PolyA-RNAseq-L10170

value: Forelimb


title: HFWL7BBXY_3_IDT_DUI_NXT_149


title: WT_rep2

value: empty vector


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 12 hours (duplicate)

city: New York

first: Zheng

last: Xu

state: New York

address: 630W 168th Street

department: Pathology

country: USA

institute: Columbia University

data_processing:
Reads were mapped and fpkm was evaluated using TopHat (version 2.1.0) with maximun 4 mistches and 10 multiple hits.
Genome_build: Reference human genome, NCBI/build 37.2
Supplementary_files_format_and_content: comma separated file containing fpkm value.

source_name: Cultured Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 Medium supplemented with 10% FBS, 2 mM L-glutamine and 50 mg/L gentamicin sulfate

extract_protocol:
RNA were extacted from 18 samples using the Rneasy Mini Kit (Qiagen)
Libraries were prepared from the total RNA sampleswith Illumina's TruSeq RNA prep kit, using poly-A pull-down to enrich for mRNAs

treatment_protocol: Jurkat cells were treated with three different concentrations of ILT3.Fc (0ug/ml, 12.5ug/ml and 25ug/ml) for three different times (6h, 12h and 24h). Each sample was duplicated.

value: Jurkat

tag: treatment

value: 25µg/ml of ILT3.Fc for 12 hours


title: WT_rep1


title: P2275_N727_S508

extract_protocol:
For replicate 1, full-length single-cell RNA-seq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. Thymocytes were sorted into 96-well plates containing the lysis buffer (0.2% Triton-100, 1U/µl RNase inhibitor)Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kapa Biosystems) and IS PCR primer (IDT), with 25 cycles of amplification. For replicate 2, full-length single-cell RNA-seq libraries were prepared using the SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing (Takara Bio). All reactions were downscaled to one quarter of the original protocol and performed following thermal cycling manufacturer’s conditions. Thymocytes were sorted into 96-well plates containing 2.5 µl of the Reaction buffer (1x Lysis Buffer, RNase Inhibitor 1U/µl). Reverse transcription was performed using 2.5 µl of the RT MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio). cDNA was amplified using 8 µl of the PCR MasterMix (SMART-Seq v5 Ultra Low Input RNA Kit for Sequencing, Takara Bio) with 25 cycles of amplification.
Replicate 1 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq2000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE75) reads with library indexes corresponding to cell barcodes. Replicate 2 followed purification of amplified cDNA with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with double indexed Nextera PCR primers (IDT). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end (PE100) reads with library indexes corresponding to cell barcodes.


title: HFWL7BBXY_1_IDT_DUI_NXT_203


title: P2275_N726_S508


title: HFWL7BBXY_1_IDT_DUI_NXT_281


title: HFWL7BBXY_2_IDT_DUI_NXT_95


title: D3: Mutant (w[1118]; Gpdh1[12]/[14]; Ldh[16]/[17])

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

data_processing:
Samples were demultiplexed with bcl2fastq v2.20.0.422
Adapters and low quality sequences were removed with cutadapt v1.12 using the options "-m 30 -q 30"
Read with fewer than 30 high quality bases were excluded from further analysis
Reads were mapped against dmel r6.21 using hisat2 version 2.1.0 with the parameters "--no-unal"
Mapped reads were assigned to genes using the FlyBase dmel annotation 6.21 with htseq-count 0.9.0
Genome_build: dmel r6.21
Supplementary_files_format_and_content: tab-delimited text files including gene counts for each sample

organism: Drosophila melanogaster

source_name: mid-L3 larvae

growth_protocol: Drosophila eggs were collected on molasses egg caps with yeast paste an maintained at 25ºC for 60 hours.

extract_protocol:
Larvae were collected as described in Li, H., Tennessen, J. M. Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry (GC-MS)-based Metabolomics. J. Vis. Exp. (136), e57847, doi:10.3791/57847 (2018). RNA was extracted using a Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mid-L3 larvae


title: P2277_N719_S513


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 12 hours


title: HFWL7BBXY_3_IDT_DUI_NXT_379


title: D2: Mutant (w[1118]; Gpdh1[12]/[14]; Ldh[16]/[17])


title: P2220_N709_S504


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 12 hours

value: 12.5µg/ml of ILT3.Fc for 12 hours


title: D1: Mutant (w[1118]; Gpdh1[12]/[14]; Ldh[16]/[17])


title: WT_rep3


title: HFWL7BBXY_1_IDT_DUI_NXT_79

value: Thymocytes


title: Jurkat cells treated with 0µg/ml of ILT3.Fc for 12 hours

value: 0µg/ml of ILT3.Fc for 12 hours


title: C3: Control (w[1118]; Gpdh1[12]/+; Ldh[16]/+)


title: P2276_N705_S513

value: WT


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 6 hours (duplicate)

value: 25µg/ml of ILT3.Fc for 6 hours


title: P2274_N703_S506


title: HFWL7BBXY_3_IDT_DUI_NXT_283

value: SMARTer


title: HFWL7BBXY_2_IDT_DUI_NXT_83

value: TCRhiDP


title: C2: Control (w[1118]; Gpdh1[12]/+; Ldh[16]/+)


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 6 hours (duplicate)

value: 12.5µg/ml of ILT3.Fc for 6 hours


title: C1: Control (w[1118]; Gpdh1[12]/+; Ldh[16]/+)


title: HFWL7BBXY_2_IDT_DUI_NXT_147


title: HFWL7BBXY_2_IDT_DUI_NXT_297


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 12 hours (duplicate)


title: B3: Mutant (w[1118]; Gpdh1[12]/[14])


title: P2277_N721_S513


title: P2278_N707_S502


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 6 hours


title: B2: Mutant (w[1118]; Gpdh1[12]/[14])


title: HFWL7BBXY_3_IDT_DUI_NXT_179


title: B1: Mutant (w[1118]; Gpdh1[12]/[14])


title: HFWL7BBXY_1_IDT_DUI_NXT_349


title: P2279_N719_S502


title: A3: Control (w[1118]; Gpdh1[12]/+)


title: Jurkat cells treated with 0µg/ml of ILT3.Fc for 6 hours

value: 0µg/ml of ILT3.Fc for 6 hours


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 24 hours (duplicate)

value: 25µg/ml of ILT3.Fc for 24 hours


title: A2: Control (w[1118]; Gpdh1[12]/+)


title: P2274_N712_S503


title: P2220_N707_S504


title: A1: Control (w[1118]; Gpdh1[12]/+)


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 24 hours (duplicate)

value: 12.5µg/ml of ILT3.Fc for 24 hours


title: sRNA-mock-24H-2

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) and ASFV (MK333180.1) genome by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 20, fold-changed (FC) ≧ 2 and p-value < 0.05.
For small RNA-seq, sequencing adapters (AGATCGGAAGAGCACACGTCT) was removed by using cutadpt1.18. Reads were mapped to pig genome by using Bowtie2.2.5. The unmapped reads were collected and then mapped to ASFV genome. A brief annotation of PAMs encoded small RNAs were performed by using unitas_1.7.0. FeatureCount_1.6.4 was used for quantifying abundance of each miRNA. RPM values were calculated to measure the expression levels of each miRNA. Differential expression analysis of miRNAs was performed by DESeq2_1.22.2. Differentially expressed miRNAs were filtered by the following parameters: fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples. Tab-delimited text file includes reads_count for each small RNA-seq samples.

tag: condition

value: Specific pathogen free (SPF)

tag: age

value: porcine alveolar macrophages

tag: infection

value: No infection

tag: time

value: 24 hours post infection

tag: fraction

value: small RNAs


title: Jurkat cells treated with 0µg/ml of ILT3.Fc for 24 hours (duplicate)

value: Jurkat

value: 0µg/ml of ILT3.Fc for 24 hours


title: Jurkat cells treated with 0µg/ml of ILT3.Fc for 6 hours (duplicate)


title: sRNA-mock-24H-1

tag: cell type


title: sRNA-mock-24H-3


title: P2279_N723_S502

tag: replicate

tag: genotype

value: Thymocytes

tag: strain

tag: cell population

tag: protocol


title: P2274_N712_S508


title: sRNA-mock-12H-2

value: 12 hours post infection


title: P2222_N705_S505

value: WT


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 24 hours

tag: cell line


title: Jurkat cells treated with 12.5µg/ml of ILT3.Fc for 6 hours


title: Jurkat cells treated with 25µg/ml of ILT3.Fc for 24 hours


title: P2276_N705_S521


title: P2274_N711_S502


title: sRNA-mock-12H-1


title: Jurkat cells treated with 0µg/ml of ILT3.Fc for 24 hours


title: P2222_N707_S504


title: P2222_N710_S508


title: sRNA-mock-6H-3

value: 6 hours post infection


title: sRNA-mock-12H-3


title: sRNA-mock-6H-2


title: P2280_N714_S517


title: P2275_N719_S510


title: P2277_N720_S522


title: P2275_N716_S505


title: mAST-VM C

city: Seoul

first: Jae-Jin

last: Song

address: 222, Wangsimni-ro

department: Hanyang Biomedical Research Institute

country: South Korea

institute: Hanyang university

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were mapped to mouse genome (mm9) using STAR program.
Read counts were calculated using HTSeq program.
The differential expression analysis was performed using DESeq and FPKM(Fragments Per Kilobase Of Exon Per Million Fragments Mapped)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reat counts and FPKM for each sample

source_name: Ventral midbrain

growth_protocol: Astrocytes were isolated from mouse or rat VMs or cortices (Ctx) on postnatal day 5–7 and cultured in astro-medium

extract_protocol:
Total RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) through the RNA isolation protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Astrocyte progenitor cells

value: Nurr1+Foxa2-expressing lentiviruses

value: Ventral midbrain

tag: developmental stage

value: postnatal day 5

tag: passages

value: ICR


title: sRNA-mock-6H-1

extract_protocol:
The RNA was extracted from the infected cells at 0-, 6-, 12- and 24-hpi.
For strand specific RNA-seq, depletion of ribosomal RNA (rRNA) and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit. For small RNA-seq, small RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit.


title: mAST-VM NF

tag: transduced with

value: mock virus (control)

tag: tissue


title: Sputum_Healthy_8

city: Großhansdorf

first: Espen

middle: E

last: Groth

address: Wöhrendamm 80

department: Department of Pulmonology

institute: LungenClinic Grosshansdorf

hyb_protocol: A total of 1650 ng of labeled cRNA per sample was hybridized to Agilent Human GE 4x44k v2 arrays according to the manufacturer's instructions.

scan_protocol: Hybridized arrays were scanned using an Agilent SureScan scanner system (resolution 5 µm, default protocol).

data_processing: Scan images were analyzed with the Agilent Feature Extraction Software (version 11.5.1, default parameters, protocol GE1_1105_Oct12). Output txt files were imported into the R/Bioconductor programming environment applying functions from the limma package (version 3.42.2). Background correction was performed on median foreground signals (substracting the median background and setting post-subtraction negative intensities equal to half the minimum of the positive corrected intensities of each array). Subsequently, quantile normalization and log2-transformation were performed. Control probes as well as probes flagged as IsNotUniform, IsSaturated or IsPopOutlier by the default Agilent Feature Extraction software algorithm were removed from the dataset. Following further exclusion of probes that were not flagged as IsFound and IsPosSig in at least 50% of biological replicates in any one disease condition, probe summarization was performed for downstream probe-level analysis.

source_name: Healthy sputum sample

label_protocol: RNA was processed using the Low Input Quick Amp labelling Kit (Agilent, Cy3, following manufacturer's standard protocols), followed by purification via Qiagen RNeasy columns. Dye incorporation and RNA yield were measured on an NanoDrop 6000 spectrophotometer (Thermo Fisher).

extract_protocol: Depending on the method of fixation/preservation, sputum samples were: 1) thawed and directly supplied to nucleic acid extraction, or: 2) sputum cells were extracted from paraffin bocks (by cutting thick slices with a microtome using alcohol- and heat-sterilized blades) and deparaffinized by incubation with xylene and ethanol, followed by a drying step using a vacuum centrifuge. Extraction of nucleic acids was performed using the AllPrep Micro Kit (Qiagen) following the manufacturer's standard instructions. Nucleic acid yield was measured using a NanoDrop spectrophotometer (Thermo Fisher). Total RNA integrity was assessed with an Agilent BioAnalyzer and RNA 6000 Nano Kit. Samples with RIN < 3 were excluded from further processing.

treatment_protocol: Induced sputum samples were obtained following inhalation of nebulized saline. Following manual separation from saliva and contaminants, sputum plugs were incubated with Sputolysin (DTT, Calbiochem), followed by suspension in PBS, filtration through nylon meshes and centrifugation (with removal of supernatant). Purified sputum cell pellets were resuspended in BSA/PBS and aliquots were taken for preparation of cytospin slides. The latter were subsequently stained (Giemsa) und subjected to differential cell counting. Remaining sputum cell suspensions were again pelleted by centrifugation and, depending on the method of fixation/preservation applied, 1) resuspended in RLT lysis buffer and subsequently stored at -80°C, or, 2) preserved with HOPE medium and later casted into a paraffin block (as commonly performed in routine pathology protocols) with subsequent storage at 4°C.

tag: disease group

value: HC

tag: fixation/preservation technique

value: RLT

tag: age (years)

tag: gender

value: m

tag: inhalative corticosteroid dose (daily fluticasone equivalent µg)

tag: cumulative packyears

tag: diff cell count

value: alveolar macrophages (%):80.375

value: neutrophils (%):16.5

value: eosinophils (%):0

value: lymphocytes (%):1.625

value: ciliated cells (%):0.75

value: monocytes (%):0

value: squamous cells (%):0.75

tag: rna integrity number (rin)


title: Sputum_Healthy_9

value: alveolar macrophages (%):66.25

value: neutrophils (%):28

value: eosinophils (%):0.25

value: lymphocytes (%):2.5

value: ciliated cells (%):1

value: squamous cells (%):2


title: mAST-VM

tag: cell type

value: Astrocyte progenitor cells

value: Ventral midbrain

value: postnatal day 5

value: ICR


title: MG-Haloperidol-D6

city: Davis

first: Russell

last: Hovey

state: CA

address: 1 Shields Ave

department: Animal Science

institute: University of California Davis

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol treatment for 5 days

hyb_protocol: Amplified biotinylated-cRNA was hybridized to Affymetrix GeneChip Porcine Genome Arrays for 16 h at 45oC. Genechips were washed and stained in the GeneChip® Fluidics Station 450 with Streptavidin-conjugated to phycoerythrin, then biotin-coupled polyclonal anti-streptavidin antibody and streptavidin-phycoerythrin again.

scan_protocol: GeneChips were scanned using Affymetrix Genechip scanner

data_processing: The data were RMA-normalized and transformed using log to the base 2. Data were filtered to remove probesets that were not expressed in at least 2 samples in at least one treatment group

source_name: Pig mammary gland, ovariectomized, haloperidol treated

label_protocol: 1ug total RNA was reverse transcribed to double stranded cDNA using reverse transcriptase (Superscript II) and oligo-dT priming.  Following double-stranded cDNA preparation, biotinylated-cRNA was synthesized by in vitro transcription (Enzo Life Sciences BioArray).

growth_protocol: Female peripurbertal yucatan miniature swine (5 months old) were housed in groups with free access to water and maintained on a diet of Pig and Sow pellets provided twice daily.

extract_protocol: TrReagent extraction of total RNA was performed according to the manufacturer's instructions. Dnase treatment of the total RNA was performed using the Zymo Research DNA-free RNA kit. An agilent was used to verify RNA quantity and quality.

treatment_protocol: On Day 1, 32 females were ovariectomized and 4 females underwent an operation that left the ovaries intact. The next day bromocriptine treatment was started on the 32 ovariectomized animals, while the sham animals received saline.  After 8 days of bromocriptine, animals (n=4) were assigned either bromocriptine, haloperidol, bromocriptine+estrogen, bromocriptine+progesterone, bromocriptine+estrogen+progesterone, haloperidol+estrogen, haloperidol+progesterone or haloperidol+estrogen+progesterone for 5 days (day 9 - day 14).  Pigs were injected with BrDU 24 hours before euthanasia to label proliferating cells.

tag: status

value: ovariectomized

tag: treatment

value: haloperidol

value: Mammary gland


title: MG-Estrogen+Prog-D5

description: Mammary gland gene expression from pigs given bromocriptine for 8 days, then bromocriptine+estrogen+progesterone for 5 days

source_name: Pig mammary gland, ovariectomized, bromocriptine+estrogen+progesterone treated

value: bromocriptine+estrogen+progesterone


title: MG-Hal+Estrogen-D7

description: Mammary gland gene expression from pigs given bromocriptine treatment for 8 days then haloperidol+estrogen treatment for 5 days

source_name: Pig mammary gland, ovariectomized, haloperidol+estrogen treated

value: haloperidol+estrogen


title: MG-Estrogen-D3

description: Mammary gland gene expression from pigs given bromocriptine for 8 days, then bromocriptine+estrogen for 5 days

source_name: Pig mammary gland, ovariectomized, bromocriptine+estrogen treated

value: bromocriptine+estrogen