title: Leaves, dEPS_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample200


title: Leaves, DEpS_mock_2h, Rep2

status: Public on May 09 2023

type: SRA

city: Saint Paul

first: You

last: Lu

state: MN

address: 1500 Gortner Avenue

department: Department of Plant and Microbial Biology

country: USA

institute: University of Minnesota, Twin Cities

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample202

library_source: transcriptomic

data_processing:
quality filter (during lane de-multiplexing): reads with any undetermined bases (N) in the barcode were removed
barcode trimming: internal barcodes were trimmed off of sequence reads
artifacts filtering: reads that resemble seqeuncing artifacts were removed using the artifacts filter in the fastx toolkit
read mapping: reads were mapped to TAIR10 transcripts using bowtie version bowtie-0.12.8
counting mapped reads: reads mapping to the forward strand of transcript(s) from a single gene were tallied (raw counts)
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts for reads mapped to TAIR10 genes

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown under a 12hr photoperiod in a controlled environment at 22°C and 75% relative humidity.

extract_protocol:
Total RNA extraction
Stranded mRNA Tag-Seq libraries were prepared as previously described, Rallapalli et al. BMC Genomics. 2014;15:341. doi: 10.1186/1471-2164-15-341

treatment_protocol: 3 leaves (leaf stages 7-9) of a single plant of each genotype from 31-32 days-old plants were syringe-inoculated with a 50 μM solution of estradiol or water (mock), and harvested at the indicated time after treatment. Leaves of plants from the same genotype and time point sampling in four independent experiments were pooled into a single biological replicate.

tag: genotype

tag: treatment

value: mock

tag: timepoint

value: 2 h


title: Leaves, DePS_mock_2h, Rep2

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample201


title: Leaves, DEPS_mock_2h, Rep2

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample199


title: Leaves, Deps_mock_0h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample195

value: 0 h


title: Leaves, GUS_mock_0h, Rep2

description:
Leaves from mock-treated Col-0/pER-GUS plants at 0 h, 2nd repeat
sample198


title: Leaves, deps_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample196


title: Leaves, dePs_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample193


title: Leaves, rr_mock_0h, Rep2

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample197


title: Leaves, DEps_mock_0h, Rep2

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample191


title: Leaves, depS_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample192


title: Leaves, DePs_mock_0h, Rep2

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample190


title: Leaves, deps_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample214


title: Leaves, DepS_mock_0h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample189


title: Leaves, dePS_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample186


title: Leaves, dEpS_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample187


title: Leaves, dEPs_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample188


title: Leaves, DEPs_mock_0h, Rep2

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample185


title: Leaves, DePS_mock_0h, Rep2

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample183


title: Leaves, DEpS_mock_0h, Rep2

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample184


title: Leaves, dEPS_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample182


title: Leaves, GUS_Ed_6h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 6 h, 1st repeat
sample180

value: 50 μM Ed

value: 6 h


title: Leaves, rr_Ed_6h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample179


title: Leaves, DEPS_mock_0h, Rep2

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample181


title: Leaves, dEps_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample176


title: Leaves, Deps_ETI_6h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample177


title: Leaves, deps_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample178


title: Leaves, depS_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample174


title: Leaves, dEps_mock_0h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample194


title: Leaves, DePs_ETI_6h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample172


title: Leaves, DepS_ETI_6h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample171


title: Leaves, dEpS_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample169


title: Leaves, dePS_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample168


title: Leaves, dePs_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample175


title: Leaves, DEpS_ETI_6h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample166


title: Leaves, DePS_ETI_6h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 6 h, 1st repeat
sample165


title: Leaves, DEPS_ETI_6h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 6 h, 1st repeat
sample163


title: Leaves, DEPs_ETI_6h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample167


title: Leaves, GUS_Ed_5h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 5 h, 1st repeat
sample162

value: 5 h


title: Leaves, dEPS_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample164


title: Leaves, rr_Ed_5h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample161


title: Leaves, deps_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample160


title: Leaves, dePs_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample157


title: Leaves, dEps_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample158


title: Leaves, depS_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample156


title: Leaves, Deps_ETI_5h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample159


title: Leaves, dEpS_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample151


title: Leaves, dEPs_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample152


title: Leaves, DepS_ETI_5h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample153


title: Leaves, DEps_ETI_5h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample155


title: Leaves, DEPs_ETI_5h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample149


title: Leaves, DEps_ETI_6h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample173


title: Leaves, dePS_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample150


title: Leaves, dEPS_ETI_5h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample146


title: Leaves, DEPS_ETI_5h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 5 h, 1st repeat
sample145


title: Leaves, dEPs_ETI_6h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 6 h, 1st repeat
sample170


title: Leaves, GUS_Ed_4h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 4 h, 1st repeat
sample144

value: 4 h


title: Leaves, rr_Ed_4h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample143


title: Leaves, dEps_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample140


title: Leaves, dePs_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample139


title: Leaves, Deps_ETI_4h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample141


title: Leaves, deps_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample142


title: Leaves, DePs_ETI_4h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample136


title: Leaves, DEps_ETI_4h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample137


title: Leaves, DepS_ETI_4h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample135


title: Leaves, dEPs_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample134


title: Leaves, dePS_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample132


title: Leaves, dEpS_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample133


title: Leaves, DePs_ETI_5h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample154


title: Leaves, DEpS_ETI_4h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample130


title: Leaves, DePS_ETI_4h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample129


title: Leaves, dEPS_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample128


title: Leaves, DEPs_ETI_4h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 4 h, 1st repeat
sample131


title: Leaves, DEpS_ETI_5h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample148


title: Leaves, DEPS_ETI_4h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 4 h, 1st repeat
sample127


title: Leaves, rr_Ed_3h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample125

value: 3 h


title: Leaves, GUS_Ed_3h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 3 h, 1st repeat
sample126


title: Leaves, DePS_ETI_5h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample147


title: Leaves, dePs_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample121


title: Leaves, deps_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample124


title: Leaves, Deps_ETI_3h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample123


title: Leaves, dEps_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample122


title: Leaves, DepS_ETI_3h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample117


title: Leaves, DePs_ETI_3h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample118


title: Leaves, dEPs_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample116


title: Leaves, depS_ETI_4h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 1st repeat
sample138


title: Leaves, depS_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample120


title: Leaves, DEps_ETI_3h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample119


title: Leaves, dePS_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample114


title: Leaves, dEpS_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample115


title: Leaves, dEPS_ETI_3h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample110


title: Leaves, DEPS_ETI_3h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 3 h, 1st repeat
sample109


title: Leaves, GUS_Ed_2h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 2 h, 1st repeat
sample108


title: Leaves, Deps_ETI_2h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample105


title: Leaves, rr_Ed_2h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample107


title: Leaves, DePS_ETI_3h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample111


title: Leaves, dePs_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample103


title: Leaves, dEps_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample104


title: Leaves, depS_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample102


title: Leaves, DEps_ETI_2h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample101


title: Leaves, DePs_ETI_2h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample100


title: Leaves, dePS_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample096


title: Leaves, dEPs_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample098


title: Leaves, dEpS_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample097


title: Leaves, DEPs_ETI_2h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample095


title: Leaves, DePS_ETI_2h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample093


title: Leaves, DEpS_ETI_3h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 3 h, 1st repeat
sample112


title: Leaves, DEPs_ETI_3h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 3 h, 1st repeat
sample113


title: Leaves, dEPS_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample092


title: Leaves, deps_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample088

value: 1 h


title: Leaves, GUS_Ed_1h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 1 h, 1st repeat
sample090


title: Leaves, rr_Ed_1h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample089


title: Leaves, Deps_ETI_1h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample087


title: Leaves, dEps_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample086


title: Leaves, dePs_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample085


title: Leaves, depS_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample084


title: Leaves, deps_ETI_2h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample106


title: Leaves, DEps_ETI_1h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample083


title: Leaves, DepS_ETI_1h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample081


title: Leaves, dEPs_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample080


title: Leaves, DEpS_ETI_1h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample076


title: Leaves, DePS_ETI_1h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample075


title: Leaves, DEpS_ETI_2h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample094


title: Leaves, dEpS_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample079


title: Leaves, DEPs_ETI_1h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample077


title: Leaves, rr_Ed_0h, Rep1

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample071


title: Leaves, DepS_ETI_2h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample099


title: Leaves, deps_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample070


title: Leaves, GUS_Ed_0h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 0 h, 1st repeat
sample072


title: Leaves, dEPS_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample074


title: Leaves, DEPS_ETI_1h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 1 h, 1st repeat
sample073


title: Leaves, dePs_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample067


title: Leaves, DEPS_ETI_2h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 2 h, 1st repeat
sample091


title: Leaves, Deps_ETI_0h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample069


title: Leaves, dEPs_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample062


title: Leaves, DepS_ETI_0h, Rep1

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample063


title: Leaves, depS_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample066


title: Leaves, DePs_ETI_0h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample064


title: Leaves, DePs_ETI_1h, Rep1

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 1st repeat
sample082


title: Leaves, DEps_ETI_0h, Rep1

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample065


title: Leaves, dEpS_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample061


title: Leaves, dePS_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample060


title: Leaves, DePS_ETI_0h, Rep1

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample057


title: Leaves, dePS_ETI_1h, Rep1

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 1 h, 1st repeat
sample078


title: Leaves, GUS_mock_5h, Rep1

description:
Leaves from mock-treated Col-0/pER-GUS plants at 5 h, 1st repeat
sample054


title: Leaves, dEPS_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample056


title: Leaves, DEPS_ETI_0h, Rep1

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 0 h, 1st repeat
sample055


title: Leaves, dePs_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample049


title: Leaves, dEps_ETI_0h, Rep1

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample068


title: Leaves, Deps_mock_5h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample051


title: Leaves, dEPs_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample044


title: Leaves, dEpS_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample043


title: Leaves, DEps_mock_5h, Rep1

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample047


title: Leaves, depS_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample048


title: Leaves, DepS_mock_5h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample045


title: Leaves, dePS_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample042


title: Leaves, DEpS_mock_5h, Rep1

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample040


title: Leaves, DePS_mock_5h, Rep1

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample039


title: Leaves, dEPS_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample038


title: Leaves, DEPS_mock_5h, Rep1

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 5 h, 1st repeat
sample037


title: Leaves, DEPs_mock_5h, Rep1

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample041


title: Leaves, rr_mock_2h, Rep1

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample035


title: Leaves, GUS_mock_2h, Rep1

description:
Leaves from mock-treated Col-0/pER-GUS plants at 2 h, 1st repeat
sample036


title: Leaves, DEPs_ETI_0h, Rep1

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample059


title: Leaves, Deps_mock_2h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample033


title: Leaves, deps_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample034


title: Leaves, DEpS_ETI_0h, Rep1

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample058


title: Leaves, deps_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample052


title: Leaves, depS_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample030


title: Leaves, dePs_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample031


title: Leaves, DEps_mock_2h, Rep1

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample029


title: Leaves, rr_mock_5h, Rep1

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 1st repeat
sample053


title: Leaves, DePs_mock_5h, Rep1

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample046


title: Leaves, dEpS_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample025


title: Leaves, dePS_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample024


title: Leaves, dEPs_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample026


title: Leaves, DepS_mock_2h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample027


title: Leaves, dEps_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample032


title: Leaves, DePS_mock_2h, Rep1

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample021


title: Leaves, dEps_mock_5h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 1st repeat
sample050


title: Leaves, DEPS_mock_2h, Rep1

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 2 h, 1st repeat
sample019


title: Leaves, DEpS_mock_2h, Rep1

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 2 h, 1st repeat
sample022


title: Leaves, GUS_mock_0h, Rep1

description:
Leaves from mock-treated Col-0/pER-GUS plants at 0 h, 1st repeat
sample018


title: Leaves, deps_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample016


title: Leaves, dEPS_mock_2h, Rep1

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample020


title: Leaves, dEps_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample014


title: Leaves, dePs_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample013


title: Leaves, Deps_mock_0h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample015


title: Leaves, DePs_mock_2h, Rep1

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample028


title: Leaves, DEps_mock_0h, Rep1

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample011


title: Leaves, DePs_mock_0h, Rep1

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample010


title: Leaves, dEpS_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample007


title: Leaves, dEPs_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample008


title: Leaves, dePS_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample006


title: Leaves, depS_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample012


title: Leaves, DEpS_mock_0h, Rep1

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample004


title: Leaves, DePS_mock_0h, Rep1

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample003


title: Leaves, DEPs_mock_0h, Rep1

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample005


title: Leaves, DepS_mock_0h, Rep1

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample009


title: Leaves, dEPS_mock_0h, Rep1

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 0 h, 1st repeat
sample002


title: Leaves, DEPs_mock_2h, Rep1

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 2 h, 1st repeat
sample023


title: Leaves, DEPS_mock_0h, Rep1

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 0 h, 1st repeat
sample001


title: HaCaT cells, KO Clone 4, rep1

city: Nicosia

first: Katerina

last: Strati

state: Nicosia

address: 1 Panepistimiou Avenue - Aglantzia

department: Biological Sciences

country: Cyprus

institute: University of Cyprus

library_source: genomic

data_processing:
Trimmed for adapter sequences and poor quality bases using Trimmomatic v.0.38
Alignment using Bowtie2 v.2.2.6. against GRCh38
MACS2 2.1.2 was used for peak calling to identify open chromatin regions.
Assembly: GRCh38
Supplementary files format and content: Peaks table, Column 1: Chromosome, Column 2: Start position, Column 3: End position, Column 4: Peak ID, Column 5: Peak score , Column 6: Strand, Column 7: signalValue, Region fold enrichment, Column 8: -log10(pvalue), Column 9: -log10(qvalue), Column 10: Point-source for the peak. 0-based offset from peak start position.

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Minelute PCR Purification Kit (Qiagen, 28004)
NEBNext Ultra II RNA Library Prep Kit for Illumina
Tagmented DNA was barcoded with Nextera Index Kit v2 (Illumina, FC-131-2001)

treatment_protocol: Live cell samples were thawed, washed, and treated with DNAse I (LifeTech, EN0521). After cell lysis and cytosol removal, nuclei were treated with Tn5 enzyme (Illumina, 20034197)

tag: tissue

value: Skin

tag: cell line

value: HaCaT immortalized keratinocyte cell line from male adult human skin (CLS, 300493)

tag: cell type

value: OCT4 knockout


title: HaCaT cells, KO Clone 4, rep2


title: Leaves, rr_mock_0h, Rep1

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 1st repeat
sample017


title: HaCaT cells, Control, rep1

value: WT


title: sample 5, cardiac pericytes C1, treated with Spike [C1_S_S5]

city: Bristol

first: Elisa

last: Avolio

address: Upper Maudlin Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

data_processing:
RNA-Seq was carried out on an Illumina HiSeq platform, with a 2x75bp configuration, ~20M reads per sample.
RNA-sequencing reads were mapped using the STAR alignment tool (version 2.5.4b).
Differential expression analysis was performed using the Bioconductor package EdgeR, which implements a generalized linear model based on a negative binomial test model for RNA-Seq in R.
P values were corrected for multiple testing using BH FDR. A cut-off of FDR ≤0.1 was applied to select differentially expressed genes
Assembly: Homo sapiens GRCh38 reference genome available on ENSEMBL
Supplementary files format and content: Count.txt

source_name: Heart

growth_protocol: Pericytes were extracted from human hearts and expanded in vitro using ECGM-2 medium (PromoCell) as described in Avolio et al 2022 - doi: 10.1172/JCI152308

extract_protocol:
Total RNA was extracted using ice-cold Qiazol
RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-Seq was carried out on an Illumina HiSeq platform, with a 2x75bp configuration, ~20M reads

treatment_protocol: Pericytes were exposed for 48 hours either to a recombinant Spike protein (S1+S2 domains, 1 microgram/mL, produced as described in Avolio et al. 2021 - doi: 10.1042/CS20210735) or PBS vehicle, in the absence of FBS and growth factors

value: Heart

value: primary cells

value: cardiac pericytes

value: Spike protein


title: sample 1, cardiac pericytes A1, treated with Spike [A1_S_S1]


title: sample 6, cardiac pericytes C1, treated with vehicle [C1_V_S6]

value: PBS vehicle


title: sample 2, cardiac pericytes A1, treated with vehicle [A1_V_S2]


title: sample 4, cardiac pericytes B1, treated with vehicle [B1_V_S4]


title: HBEC YAP rep2

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

description: ChIP-seq data from control human bronchial epithelial cells, using YAP antibody.

data_processing:
The ChIP-seq fastq files were aligned to the build version hg19 of the human genome using Bowtie2 with the default parameters. Reads that were unmapped, not primary alignment or with MAPQ score lower than 30 were removed. Duplicated reads were marked by Picard and were discarded from the alignments and the resulting SAM files were converted to BAM format with samtools. Peak-calling was performed for each individual replicate against the IgG control ChIP-seq consistently using the narrow-peak mode from Model-based Analysis for ChIP-Seq (MACS2) at a p-value cutoff of 0.05 with nomodel option and extsize of 150. Additionally, peaks were filter by summit fold-chagne > 2. Peaks within the blacklisted regions (hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/) were removed. Overlapped peaks between replicates were then identified using the findOverlapsOfPeaks function from the ChIPpeakAnno R package and were used for downstream analysis.
Assembly: hg19

source_name: Human Bronchial Epithelial Cells

growth_protocol: HBECs for ChIP were cultured in Pneumocult EX Plus media and cross-linked in 1mM EGS in PBS for 30min followed by a 1% formaldehyde treatment for 10 min. Fixation was subsequently neutralized with 0.125M glycine in PBS.

extract_protocol:
Immunoprecipitated complexes were collected by Protein A/G Magnetic beads (Pierce, 8802). Samples were washed with low salt buffer (20mM Tris, 140mM NaCl, 1mM EDTA, 0.1% NaDeoxycholate, 0.1% SDS, 1% Triton X-100), followed by a high salt buffer (20mM Tris, 500mM NaCl, 1mM EDTA, 0.5% NaDeoxycholate, 1% Triton X-100), and a LiCl buffer (20mM Tris, 1mM EDTA, 0.1% NaDeoxycholate, 1% Triton X-100, 250mM LiCl). Chromatin was de-crosslinked overnight at 65C and purified using the Qiaquick PCR purification kit (Qiagen, 28104).
For ChIP-seq, the purified DNA was ligated to specific adaptors and sequenced using DNB-seq, performed by BGI, to a depth of 40 million reads.

treatment_protocol: Harvested chromatin was isolated as single samples from each patient line, sonicated using the Bioruptor UCD- 200 and the incubated with the following antibodies at 4 °C overnight: Rabbit anti-Yap (Abcam,  Cat# ab52771, 3ug), Rabbit anti-TEAD (AvivaSysBio, Cat# ARP38276, 1ug), and Mouse anti-P63 (Biocare # CM163, 5ug).

tag: chip antibody

value: YAP


title: sample 3, cardiac pericytes B1, treated with Spike [B1_S_S3]


title: Q, 36h, 2

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
All the high-quality reads were merged together, and de novo assembled using Trinity to build a reference genome for L. racemosa. Reads of each sample were aligned to the constructed reference genome via hisat2 program
Gene counts were obtained using featureCounts.
Supplementary files format and content: One csv file containing raw count values for each sample

organism: Laguncularia racemosa

source_name: leaf

growth_protocol: Mature seeds were picked in Sanya Qingmei harbor natural mangrove reserve and Putian mangrove distribution area in Fujian province. After soaked in distilled water for 7 days, those seeds were planted into plastic basin (diameter × height =10 cm × 15 cm) with the medium of red soil (50%), sandy soil (40%), and nutrient soil (10%). The cultural condition was kept as follow: temperature 30/28℃ (day/night), illumination time 16: 8h (light: dark), illumination intensity 400 mol m-2 s-1, and constant humidity 85%.

extract_protocol:
Total RNAs was extracted from the leaves of each plant using TRIzol.
Illumina libraries were prepared following manufacturer’s instruction

treatment_protocol: About eight weeks from the germination day, the seedlings can be found six leaves or 12 cm high and then treated by freezing temperature (0℃) stress. The first three groups were treated with 0℃ for 0h, 3h, and 12h, respectively. Seedlings from the last group were treated by 0℃ for 12h and then were recovered in 30/28℃ (day/night) for one day.

value: leaf

tag: age

value: 8 weeks

value: wt

value: control 36h


title: Q, 36h, 3


title: Q, 12h, 3

value: control 12h


title: HBEC Input rep1 (control for YAP and TP63)

description: ChIP-seq data from control human bronchial epithelial cells, using IgG control.

value: Input Control


title: Q, 36h, 1


title: HBEC YAP rep1


title: Q, 3h, 2

value: control 3h


title: Q, 12h, 1


title: Q, 12h, 2


title: Q, 3h, 3


title: HaCaT cells, Control, rep2

value: Skin


title: Q, 0h, 3

value: control 0h


title: P, 36h, 1

value: freezing temperature 12h with 24h recovery


title: Q, 0h, 2


title: Q, 3h, 1


title: Q, 0h, 1


title: P, 12h, 3

value: freezing temperature 12h


title: HBEC TP63 rep2

description: ChIP-seq data from human bronchial epithelial cells treated, using TP63 antibody.


title: P, 12h, 2


title: P, 12h, 1


title: P, 36h, 2


title: HBEC TP63 rep1


title: P, 0h, 2

value: freezing temperature 0h


title: P, 3h, 2

value: freezing temperature 3h


title: P, 0h, 1


title: P, 0h, 3


title: KO_M2

city: ithaca

first: Luye

last: An

address: 618 tower road

department: biomedical sciences

institute: cornell university

data_processing:
Raw data were aligned to geneome using package STAR with default parameters
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include reads per gene

organism: Mus musculus

source_name: Tumor tissue

extract_protocol:
Fresh tumor tissues were homogenized and stained with antibodies. F4/80+ macrophages were sorted using FACS ARIA and direclty isolated into TrizolLS and subjected to RNA extraction
50ng of total RNA was used for initial prep. mRNA was enriched using Poly A enrichment method. Library was prepared using NEBNext Ultra II directional RNA library prep kit

treatment_protocol: Braf/Mek inhibitors were administered daily until tissue collection

value: Tumor tissue

value: Ccr2 KO (Ccr2RFP/RFP)

tag: Sex

value: Male

value: Braf/Mek inhibitors

tag: disease state

value: resistant/rebound


title: KO_M3


title: KO_M1


title: WT_M5

value: Control (Ccr2RFP/+)


title: WT_M4


title: KO_M5


title: KO_M4


title: WT_M3


title: WT_M2


title: 7 hpf rRNA-deplete clutch G Triptolide

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

institute: University of Pittsburgh

data_processing:
RNA-seq reads were trimmed of trailing Ns and adapter sequence using Trim Galore v0.6.6 with Cutadapt v1.15 (Martin, 2011). For gene-level quantification, RNA-seq reads were pseudo-aligned to the Hsym 1.0 protein-coding transcriptome (Hydractinia Genome Project, 2023) using kallisto v0.46.1 (Bray et al., 2016) in paired rf-stranded mode. For differential expression analysis, counts were rounded to integers for DESeq2 v4.0.3 (Love et al., 2014) on poly(A)+ samples and rRNA-depleted samples separately, discarding genes that had < 10 reads in any one sample.
Assembly: Hsym v1.0
Supplementary files format and content: Tab-delimited kallisto gene read counts

organism: Hydractinia symbiolongicarpus

source_name: Whole embryo

growth_protocol: Fertilization was performed by mixing gametes in artificial sea water at 20º C, washing after 15 minutes, then transferring to a 23º C incubator at 30 minutes post fertilization

extract_protocol:
Frozen embryos in 1.5 ml eppendorf tubes were homogenized with a pestle in 500 µl of TRIzol (Invitrogen #15596026) (note that for later timepoints 24-72 h.p.f., some particulates remained after pestling). 100µl chloroform was added, vortexed for 15 sec, then centrifuged at 13,000 RPM at 4ºC for 15 minutes. The aqueous phase plus 340 µl of isopropanol and 1 µl of GlycoBlue (Invitrogen #AM9515) were added to a new tube and precipitated overnight at -20º C. To pellet, tubes were centrifuged at 13,000 RPM at 4º C for 30 minutes, supernatant removed, 500 µl of cold 75% ethanol added, and centrifuged at 13,000 RPM at 4º C for 15 minutes. Ethanol was drawn off with a P200, then P10 pipet and tubes left to air dry in a fume hood for 10 minutes.
rRNA depletion was performed as per Phelps et al NAR 2021 using custom generated nuclear and mitochondrial rRNA antisense oligos. poly(A) selection was performed using NEB-Next Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L). Strand-specific RNA-seq libraries were constructed using the NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with the following parameters: 12-35 ng of rRNA-depleted or poly(A)+ selected RNA was fragmented at 94º C for 15 minutes in first-strand buffer, then subjected to half-reaction volume library prep with 5-fold dilution of adapters and 9 cycles of PCR amplification; Sera-Mag Select beads were used for cleanup steps (Cytiva 29343045).

value: Whole embryo

value: Wild type

tag: developmental stage

value: 7 hpf

value: Triptolide 20 uM


title: WT_M1


title: 7 hpf rRNA-deplete clutch D Triptolide


title: P, 3h, 3

value: leaf

value: 8 weeks

value: wt


title: 7 hpf rRNA-deplete clutch B


title: 7 hpf rRNA-deplete clutch D DMSO

value: DMSO 0.5%


title: 7 hpf rRNA-deplete clutch G DMSO


title: 6 hpf rRNA-deplete clutch B

value: 6 hpf


title: 4 hpf rRNA-deplete clutch C

value: 4 hpf


title: 4 hpf rRNA-deplete clutch A


title: 5 hpf rRNA-deplete clutch B

value: 5 hpf


title: 3 hpf rRNA-deplete clutch C

value: 3 hpf


title: 2 hpf rRNA-deplete clutch C

value: 2 hpf


title: 3 hpf rRNA-deplete clutch A


title: 2 hpf rRNA-deplete clutch A


title: S6-Pdtd

city: La Jolla

first: Mark

last: Onaitis

state: California

address: 855 Health Sciences Dr

department: Surgery

institute: University of California San Diego

data_processing:
FastQC was used for quality control of sequencing reads
Cutadapt was used for trimming reads and removing adaptors
Reads were then aligned to mouse reference genome, GRCm38 using Hisat2
Total reads are counted by FeatureCounts
Differential gene-expression analysis was perfomed using DEseq2
Assembly: GRCm38
Supplementary files format and content: Combined count file, .txt

source_name: Lung

extract_protocol:
RNA was extracted from sorted Type I, Type II and double positive population using RNeasy mini kit
RNA-seq libraries were prepared from total RNA using TruSeq Stranded kit (illumina) as per the manufacture's protocol.

value: Lung

value: Alveolar epithelial cells

value: Tamoxifen


title: 1 hpf rRNA-deplete clutch A

value: 1 hpf


title: S5-Tdtm


title: 30 mpf rRNA-deplete clutch A

value: Whole embryo

value: 30 mpf


title: S4-PdPn


title: Unfert egg rRNA-deplete clutch D

value: Wild type

value: Unfertilized egg


title: S3-Pdtd


title: Unfert egg rRNA-deplete clutch C


title: S1-PdPn


title: Unfert egg rRNA-deplete clutch A


title: 7 hpf polyA clutch D Triptolide

molecule: polyA RNA

value: 7 hpf

value: Triptolide 20 uM


title: 7 hpf polyA clutch G Triptolide


title: S2-Tdtm


title: 7 hpf polyA clutch G DMSO


title: 7 hpf polyA clutch D DMSO


title: 17_UK1uM_m2

city: Amsterdam

first: Anne

last: ten Hove

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Amsterdam UMC

description:
murine organoids treated with UK14,304 1uM for 4d
Geneid; "Chr"; "Start"; "End"; "Strand"; "Length"; "X.media.ssd1.ayliyim.bam.11_NE1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.12_NE1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.13_NE1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.14_NE1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.15_NE1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.16_UK1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.17_UK1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.18_UK1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.19_UK1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.1_Ctrl_HCl_m1.bam";  "X.media.ssd1.ayliyim.bam.20_UK1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.2_Ctrl_HCl_m2.bam"; "X.media.ssd1.ayliyim.bam.3_Ctrl_HCl_m3.bam"; "X.media.ssd1.ayliyim.bam.4_Ctrl_HCl_m4.bam"; "X.media.ssd1.ayliyim.bam.6_Ctrl_DMSO_m1.bam"; "X.media.ssd1.ayliyim.bam.7_Ctrl_DMSO_m2.bam"; "X.media.ssd1.ayliyim.bam.8_Ctrl_DMSO_m3.bam"; "X.media.ssd1.ayliyim.bam.9_Ctrl_DMSO_m4.bam"

data_processing:
cDNA preparation for sequencing was done using the HiSeq4000 in a 50 bp single-ended fashion with a depth of 40 M reads per sample.
Raw reads were checked for quality with FastQC (v0.11.8) and MultiQC (v1.7).
Mapping was done with STAR (v2.7.3) against mouse genome GRCm38.
Post-alignment processing was done using SAMtools (v1.9), whereupon reads were counted using featureCounts in the Subread package (v.1.6.4).
Assembly: GRCm38
Supplementary files format and content: Tab-delimited tekst files include counts for all samples.

source_name: small intestine

extract_protocol:
Total RNA was isolated from samples using Bioline ISOLATE II RNA Mini Kit. RNA quality was assured using the TapeStation 4200 (Agilent). Samples with an RNA  183 integrity number (RNA) >8 were used for further analyses.
Libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche).

value: small intestine

value: organoids

value: WT


title: 19_UK1uM_m4


title: 18_UK1uM_m3


title: 72 hpf polyA clutch F

value: 72 hpf


title: 72 hpf polyA clutch E


title: 48 hpf polyA clutch F

value: 48 hpf


title: 14_NE1uM_m4

description:
murine organoids treated with norepinephrine 1uM for 4d
Geneid; "Chr"; "Start"; "End"; "Strand"; "Length"; "X.media.ssd1.ayliyim.bam.11_NE1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.12_NE1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.13_NE1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.14_NE1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.15_NE1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.16_UK1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.17_UK1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.18_UK1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.19_UK1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.1_Ctrl_HCl_m1.bam";  "X.media.ssd1.ayliyim.bam.20_UK1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.2_Ctrl_HCl_m2.bam"; "X.media.ssd1.ayliyim.bam.3_Ctrl_HCl_m3.bam"; "X.media.ssd1.ayliyim.bam.4_Ctrl_HCl_m4.bam"; "X.media.ssd1.ayliyim.bam.6_Ctrl_DMSO_m1.bam"; "X.media.ssd1.ayliyim.bam.7_Ctrl_DMSO_m2.bam"; "X.media.ssd1.ayliyim.bam.8_Ctrl_DMSO_m3.bam"; "X.media.ssd1.ayliyim.bam.9_Ctrl_DMSO_m4.bam"

value: norepinephrine 1uM


title: 15_NE1uM_m5


title: 20_UK1uM_m5


title: 16_UK1uM_m1


title: 24 hpf polyA clutch E

value: 24 hpf


title: 7 hpf polyA clutch D


title: 24 hpf polyA clutch F


title: 12_NE1uM_m2


title: 11_NE1uM_m1


title: 9_Ctrl_DMSO_m4

description:
murine organoids treated with DMSO for 4d
Geneid; "Chr"; "Start"; "End"; "Strand"; "Length"; "X.media.ssd1.ayliyim.bam.11_NE1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.12_NE1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.13_NE1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.14_NE1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.15_NE1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.16_UK1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.17_UK1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.18_UK1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.19_UK1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.1_Ctrl_HCl_m1.bam";  "X.media.ssd1.ayliyim.bam.20_UK1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.2_Ctrl_HCl_m2.bam"; "X.media.ssd1.ayliyim.bam.3_Ctrl_HCl_m3.bam"; "X.media.ssd1.ayliyim.bam.4_Ctrl_HCl_m4.bam"; "X.media.ssd1.ayliyim.bam.6_Ctrl_DMSO_m1.bam"; "X.media.ssd1.ayliyim.bam.7_Ctrl_DMSO_m2.bam"; "X.media.ssd1.ayliyim.bam.8_Ctrl_DMSO_m3.bam"; "X.media.ssd1.ayliyim.bam.9_Ctrl_DMSO_m4.bam"

value: DMSO


title: 8_Ctrl_DMSO_m3


title: 7 hpf polyA clutch B


title: 6_Ctrl_DMSO_m1


title: 7_Ctrl_DMSO_m2


title: 4_Ctrl_HCl_m4

description:
murine organoids treated with HCl for 4d
Geneid; "Chr"; "Start"; "End"; "Strand"; "Length"; "X.media.ssd1.ayliyim.bam.11_NE1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.12_NE1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.13_NE1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.14_NE1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.15_NE1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.16_UK1uM_m1.bam"; "X.media.ssd1.ayliyim.bam.17_UK1uM_m2.bam"; "X.media.ssd1.ayliyim.bam.18_UK1uM_m3.bam"; "X.media.ssd1.ayliyim.bam.19_UK1uM_m4.bam"; "X.media.ssd1.ayliyim.bam.1_Ctrl_HCl_m1.bam";  "X.media.ssd1.ayliyim.bam.20_UK1uM_m5.bam"; "X.media.ssd1.ayliyim.bam.2_Ctrl_HCl_m2.bam"; "X.media.ssd1.ayliyim.bam.3_Ctrl_HCl_m3.bam"; "X.media.ssd1.ayliyim.bam.4_Ctrl_HCl_m4.bam"; "X.media.ssd1.ayliyim.bam.6_Ctrl_DMSO_m1.bam"; "X.media.ssd1.ayliyim.bam.7_Ctrl_DMSO_m2.bam"; "X.media.ssd1.ayliyim.bam.8_Ctrl_DMSO_m3.bam"; "X.media.ssd1.ayliyim.bam.9_Ctrl_DMSO_m4.bam"

value: HCl


title: 13_NE1uM_m3


title: 4 hpf polyA clutch A

value: 4 hpf


title: 4 hpf polyA clutch C


title: 3_Ctrl_HCl_m3


title: 5 hpf polyA clutch B

value: 5 hpf


title: 2_Ctrl_HCl_m2


title: 3 hpf polyA clutch C

value: Whole embryo

value: 3 hpf


title: 6 hpf polyA clutch B

value: Wild type

value: 6 hpf


title: 48 hpf polyA clutch E


title: 3 hpf polyA clutch A


title: 2 hpf polyA clutch C

value: 2 hpf


title: 1_Ctrl_HCl_m1


title: 1 hpf polyA clutch A

value: 1 hpf


title: 30 mpf polyA clutch A

value: 30 mpf


title: shPlekho1 GC-Tfh cells_day 14_rep2

city: Birmingham

first: Fangming

last: Zhu

state: AL

address: 845 19th Street South

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Low quality reads and sequencing adapters were removed using Trim Galore! (v.0.4.4).
Trimmed reads were aligned to the mouse genome mm10 and quantified using Salmon (0.14.1).
Further analyses were performed with R software (v.4.0.3).
Raw read counts were normalized using the Bioconductor package DESeq2 (v.1.28.1).
Assembly: Mus Musculus genome (version mm10)
Supplementary files format and content: Comma-Separated Values File with FPKM of indicated sample.

source_name: PR8-OVA flu infected ex vivo OT-II T cells

extract_protocol:
Cells were sorted directly into TRIzol-LS Reagent (Invitrogen) and RNA was isolated using miRNeasy Micro Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mediastinal lymph node

tag: knockdown

value: PR8-OVA flu infection day 14


title: shPlekho1 GC-Tfh cells_day 14_rep1


title: shCD9 GC-Tfh cells_day 14_rep2


title: shCD9 GC-Tfh cells_day 14_rep1


title: 2 hpf polyA clutch A


title: Unfert egg polyA clutch C

value: Unfertilized egg


title: Unfert egg polyA clutch D


title: Unfert egg polyA clutch A


title: 1 hpf polyA pilot expt


title: BRO7F-019_Baseline_WTS

city: Seoul

first: Yeon Hee

last: Park

address: 81 Ilwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: paired-end sequence reads

data_processing:
After trimming poor quality bases from the FASTQ files, reads were aligned to the human reference genome (hg19) with STAR v2.5.2b.
Alignment quality was verified with SAMTOOLS (v 0.1.19).
Estimated gene expression was calculated in terms of Transcripts Per Million (TPM) using RSEM v1.3.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for for every gene and every sample

source_name: breast tissue of breast cancer patients

extract_protocol:
Total RNA from fresh-frozen tumor tissues was extracted with an RNeasy Mini Kit (Qiagen) and from FFPE tissues using ReliaPrep™ FFPE Total RNA Miniprep System (Promega) according to the manufacturer’s instructions.
Seqeuncing libraries were prepared using the TruSeq RNA Access Library Prep Kit (Illumina, Inc.) using standard Illumina protocols.

value: breast

tag: gender

value: female

value: breast cancer

tag: time

value: Baseline


title: BRO7F-019_PD_WTS

description: paired-end sequence reads

value: PD


title: BRO7F-017_PD_WTS

description: paired-end sequence reads


title: BRO7F-017_Baseline_WTS

description: paired-end sequence reads


title: BRO7F-016_Baseline_WTS

description: paired-end sequence reads


title: 1 hpf unselected pilot expt


title: BRO7F-016_PD_WTS

description: paired-end sequence reads


title: BRO7F-015_PD_WTS

description: paired-end sequence reads


title: sample 175 [9_2_10]

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

description:
9_2_10_CTGTGTTG-AGCTCCTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

data_processing:
fastq files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
NOTE: Samples 1-96 are READ 1 ALIGNS TO ANTISENSE STRAND while 97-177 are READ 1 ALIGNS TO SENSE STRAND. This is just how the adaptors are made for such a big experiment. Because featureCounts requires strand orientation, I have noted on each counts file whether the "forward" and "reverse" command was used (prefix "f_" or "r_", respectively). If you realign and forget to do this, you will find that you get an excellent alignment to the genome but very few reads will be called as genes. This is totally artificial, so make sure you are sensitive to read orientation OR use a method that doesn't require strandedness information (e.g. Salmon).
Genome_build: HAv3.1
Supplementary_files_format_and_content: featureCounts output files

organism: Apis mellifera

source_name: St.Isabel1_soldier_whole brain

growth_protocol: Honey bees were flash frozen in liquid nitrogen and stored at -80C until processing

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and assessed on a Nanodrop, Qubit, and Bioanalyzer
The libraries were quantitated by qPCR and sequenced on one lane for 151 cycles from each end of the fragments on a NovaSeq 6000  using a NovaSeq S4 reagent kit. Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming). Adaptor sequence in read1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index). Adaptor sequence in read2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNAGATCTCGGTGGTCGCCGTATCAT.

treatment_protocol: Frozen honey bee heads were freeze dried (~52 minutes) and dissected in a dry ice/ethanol bath.

tag: caste

value: worker

tag: group

value: soldier

tag: colony location

tag: colony latitude

tag: colony longitude

value: whole brain


title: sample 177 [11_2_10]

description:
11_2_10_CGTATTCG-AGTCGACA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas1_soldier_whole brain

tag: tissue


title: sample 176 [10_4_10]

description:
10_4_10_AACGACGT-CGGATTGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel2_forager_whole brain

value: forager


title: BRO7F-015_Baseline_WTS

description: paired-end sequence reads


title: BRO7F-014_PD_WTS

description: paired-end sequence reads


title: BRO7F-014_Baseline_WTS

description: paired-end sequence reads


title: sample 174 [7_4_13]

description:
7_4_13_TGATACGC-ACTCGTTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Comerio_forager_whole brain

value: Comerio


title: BRO7F-008_PD_WTS

description: paired-end sequence reads


title: sample 173 [11_4_12]

description:
11_4_12_TAACGAGG-CGAGACTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas1_forager_whole brain


title: sample 172 [6_4_10]

description:
6_4_10_TTCGCAGT-TGATCGGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Ponce2_forager_whole brain


title: BRO7F-002_PD_WTS

description: paired-end sequence reads


title: BRO7F-006_Baseline_WTS

description: paired-end sequence reads


title: sample 171 [6_2_9]

description:
6_2_9_CCGATGTA-CCAAGTTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Ponce2_soldier_whole brain


title: sample 169 [1_4_9]

description:
1_4_9_AGCGGAAT-AGTGCAGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas1_forager_whole brain


title: BRO7F-002_Baseline_WTS

description: paired-end sequence reads


title: sample 170 [2_2_9]

description:
2_2_9_GTGAGCTT-TTGATCCG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas2_soldier_whole brain


title: sample 168 [12_2_9]

description:
12_2_9_GTACTCTC-TACCAGGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas2_soldier_whole brain


title: sample 167 [10_4_8]

description:
10_4_8_TCAAGGAC-GACGAATG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: BRO7F-001_Baseline_WTS

description: paired-end sequence reads


title: sample 165 [9_2_8]

description:
9_2_8_GCTGACTA-GAGATGTC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 163 [6_4_9]

description:
6_4_9_ACACGGTT-TCGAACCA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: VP64_pDNA

city: Cambridge

first: John

last: Doench

state: MA

address: 75 Ames St

department: Genetic Perturbation Platform

institute: Broad Institute

description: pDNA for Cas12a CRISPRa secondary screen with VP64 activator in MelJuso cells, selumetinib screen

data_processing:
Raw read counts were retrieved from sequencing data using PoolQ version 3.2.9-3.2.11
Assembly: NCBI GRCh38 primary assembly
Supplementary files format and content: counts-secondary_library_cas12a_crispra_MELJUSO_v2.txt is contains the raw readcount of the samples. single_guide_oligo.csv contains all single guide constructs. dual_guide_oligo.csv contains all dual guide constricts. union_triple_guide_oligo.csv contains trio guide constructs target the union of resistant hits (Z-score > 2) and sensitized hit (Z-score < -2) across VP64 and p65 for untreated and selumetinib modifiers in the primary screen. shuffle_triple_guide_oligo.csv contains all possible shuffled of trio guide constructs target the overlapping hits between vp64 and p65 in the Selumetinib resistant, Selumetinib sensitize, viability resistant, and viability sensitize in the primary screen.

source_name: MelJuSo

extract_protocol:
Genomic DNA (gDNA) was isolated using the KingFisher Flex Purification System with the Mag-Bind® Blood & Tissue DNA HDQ Kit (Omega Bio-Tek). The gDNA concentrations were quantitated by Qubit.For PCR amplification, gDNA was divided into 100 μL reactions such that each well had at most 10 μg of gDNA. Plasmid DNA (pDNA) was also included at a maximum of 100 pg per well. Per 96-well plate, a master mix consisted of 150 μL DNA Polymerase (Titanium Taq; Takara), 1 mL of 10x buffer, 800 μL of dNTPs (Takara), 50 μL of P5 stagger primer mix (stock at 100 μM concentration), 500 μL of DMSO (if used), and water to bring the final volume to 4 mL. Each well consisted of 50 μL gDNA and water, 40 μL PCR master mix, and 10 μL of a uniquely barcoded P7 primer (stock at 5 μM concentration). PCR cycling conditions were as follows: (1) 95°C for 1 minute; (2) 94°C for 30 seconds; (3) 52.5°C for 30 seconds; (4) 72°C for 30 seconds; (5) go to (2), x 27; (6) 72°C for 10 minutes. PCR primers were synthesized at Integrated DNA Technologies (IDT). PCR products were purified with Agencourt AMPure XP SPRI beads according to manufacturer’s instructions (Beckman Coulter, A63880), using a 1:1 ratio of beads to PCR product. Samples were sequenced on a HiSeq2500 HighOutput (Illumina) with a 5% spike-in of PhiX, using a custom oligo (oligo sequence: CTTGTGGAAAGGACGAAACACCGGT AATTTCTACTCTTGTAGAT).
Oligonucleotide pools were synthesized by Genscript. BsmBI recognition sites were appended to each guide sequence along with the appropriate overhang sequences (bold italic) for cloning into the guide expression vectors, as well as primer sites to allow differential amplification of subsets from the same synthesis pool. The final oligonucleotide sequence was thus: 5′-[forward primer]CGTCTCAAGAT[guide RNA]TTTTTTGAATCGAGACG[reverse primer]. Primers were used to amplify individual subpools using 25 μL 2x NEBnext PCR master mix (New England Biolabs), 2 μL of oligonucleotide pool (~40 ng), 5 μL of primer mix at a final concentration of 0.5 μM, and 18 μL water. PCR cycling conditions: (1) 98°C for 30 seconds; (2) 53°C for 30 seconds; (3) 72°C for 30 seconds; (4) go to (1), x 24. The resulting amplicons were PCR-purified (Qiagen) and cloned into the library vector via Golden Gate cloning with Esp3I (Fisher Scientific) and T7 ligase (Epizyme); the library vector was pre-digested with BsmBI (New England Biolabs). The ligation product was isopropanol precipitated and electroporated into Stbl4 electrocompetent cells (Invitrogen) and grown at 30 °C for 16 h on agar with 100 μg/mL carbenicillin. Colonies were scraped and plasmid DNA (pDNA) was prepared (HiSpeed Plasmid Maxi, Qiagen). To confirm library representation and distribution, the pDNA was sequenced.

tag: cell line

value: MelJuSo

tag: replicate

value: pDNA

tag: drugarm

value: Selumetinib

tag: activator


title: sample 166 [10_2_9]

description:
10_2_9_GTGCTTAC-AGGAGGAA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel2_soldier_whole brain


title: BRO7F-013_Baseline_WTS

description: paired-end sequence reads


title: sample 159 [6_4_8]

description:
6_4_8_CTCCTAGA-TGTGAAGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: MELJUSO_VP64_RepB_Selumetinib_D21

description: Cas12a CRISPRa secondary screen with VP64 activator in MelJuso cells, selumetinib screen, repB

value: B


title: sample 161 [1_2_8]

description:
1_2_8_TGACTTCG-GTCCTAAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas1_soldier_whole brain


title: MELJUSO_VP64_RepA_Selumetinib_D21

description: Cas12a CRISPRa secondary screen with VP64 activator in MelJuso cells, selumetinib screen, repA

value: A


title: p65_pDNA

description: pDNA for Cas12a CRISPRa secondary screen with p65 activator in MelJuso cells, dropout screen

value: Dropout


title: sample 160 [10_2_8]

description:
10_2_8_GAGCTTGT-ATTCGAGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: MELJUSO_p65_RepB_Selumetinib_D21

description: Cas12a CRISPRa secondary screen with p65 activator in MelJuso cells, selumetinib screen, repB


title: MELJUSO_VP64_RepB_Dropout_D21

description: Cas12a CRISPRa secondary screen with VP64 activator in MelJuso cells, dropout screen, repB


title: MELJUSO_VP64_RepA_Dropout_D21

description: Cas12a CRISPRa secondary screen with VP64 activator in MelJuso cells, dropout screen, repA


title: MELJUSO_p65_RepB_Dropout_D21

description: Cas12a CRISPRa secondary screen with p65 activator in MelJuso cells, dropout screen, repB


title: MELJUSO_p65_RepA_Selumetinib_D21

description: Cas12a CRISPRa secondary screen with p65 activator in MelJuso cells, selumetinib screen, repA


title: MELJUSO_p65_RepA_Dropout_D21

description: Cas12a CRISPRa secondary screen with p65 activator in MelJuso cells, dropout screen, repA


title: sample 155 [11_2_6]

description:
11_2_6_CTACTTGG-CTGGAGTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 157 [4_4_8]

description:
4_4_8_TAGACGTG-TTGGTGAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Penuelas2_forager_whole brain


title: sample 156 [12_4_6]

description:
12_4_6_ATGGCGAA-CGATAGAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas2_forager_whole brain


title: sample 164 [7_2_9]

description:
7_2_9_AATACGCG-CTATCGCA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Comerio_soldier_whole brain


title: sample 152 [12_4_10]

description:
12_4_10_TGTTCGAG-GAGATACG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 153 [6_4_7]

description:
6_4_7_CTTGGATG-GATAGCGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 154 [10_2_7]

description:
10_2_7_CACGTTGT-TGAGGTGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL090, Lg, CD8, TEM

city: New York

first: Thomas

last: Connors

state: New York

address: 3595 Broadway CHN 10-24

institute: Columbia University Medical Center

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for each Sample
Supplementary files format and content: comma-delimited CSV file combined for all Samples

source_name: Lung

extract_protocol:
Total RNA was extracted from cells sorted in RLT lysis buffer (Qiagen) using RNeasy Plus Micro Kit (Qiagen, Germantown, MD, USA). RNA was quantified using Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA).
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation.

treatment_protocol: Sorted CD69hi effector memory T cells

value: Lung

value: primary

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

tag: donor age_years


title: HDL090, MLN, CD8, TEM

source_name: Gut Lymph Node

value: Gut Lymph Node


title: HDL090, LLN, CD8, TEM

source_name: Lung Lymph Node

value: Lung Lymph Node


title: sample 151 [11_4_13]

description:
11_4_13_AGCAAGCA-GTCTCCTT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

value: worker


title: HDL090, LLN, CD4, TEM


title: sample 162 [1_4_8]

description:
1_4_8_TGGATCAC-ACCAATGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 150 [10_2_11]

description:
10_2_11_GTTGCGAT-CACAAGTC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

value: soldier


title: sample 149 [9_4_11]

description:
9_4_11_AACGTGGA-TACATCGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel1_forager_whole brain

value: whole brain


title: HDL090, MLN, CD4, TEM


title: sample 158 [6_2_7]

description:
6_2_7_CCGGAATT-CATTCGGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 148 [7_2_11]

description:
7_2_11_GTCCTTCT-CTGACACA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL090, Jej, CD4, TEM

source_name: Jejunum

value: Jejunum


title: HDL090, Ile, CD4, TEM

source_name: Ileum

value: Ileum


title: HDL090, Jej, CD8, TEM


title: HDL090, Ile, CD8, TEM


title: HDL081, LLN, CD8, TEM


title: sample 144 [2_4_11]

description:
2_4_11_CAGGAGAT-ACCTAAGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas2_forager_whole brain

value: forager


title: HDL081, MLN, CD8, TEM


title: sample 147 [6_2_10]

description:
6_2_10_ACAGACCT-CAACCTAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Ponce2_soldier_whole brain


title: sample 143 [2_2_10]

description:
2_2_10_TAGGTAGG-AGTCTGTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL081, Lg, CD8, TEM


title: HDL081, LLN, CD4, TEM


title: sample 142 [1_4_10]

description:
1_4_10_AGTCGCTT-AGGTTCGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas1_forager_whole brain


title: sample 141 [1_2_10]

description:
1_2_10_CGTTGAGT-GACTATGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL081, MLN, CD4, TEM


title: HDL081, Lg, CD4, TEM


title: HDL090, Lg, CD4, TEM


title: sample 139 [12_2_10]

description:
12_2_10_TCGTCTCA-TGTGCGTT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL081, Jej, CD4, TEM


title: sample 138 [11_2_9]

description:
11_2_9_CTGAAGCT-CTCAGAGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas1_soldier_whole brain


title: HDL081, Ile, CD8, TEM


title: HDL081, Jej, CD8, TEM


title: sample 140 [12_4_9]

description:
12_4_9_TTCCTGTG-TTCAGGAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 137 [10_4_9]

description:
10_4_9_ATTGCGTG-GCCATAAC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel2_forager_whole brain


title: sample 146 [4_4_11]

description:
4_4_11_TGTTGTGG-AAGGACAC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL081, Ile, CD4, TEM


title: sample 145 [4_2_12]

description:
4_2_12_CATCGTGA-TGCAGGTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Penuelas2_soldier_whole brain


title: HDL078, MLN, CD8, TEM


title: sample 136 [10_2_10]

description:
10_2_10_CCAAGACT-TTACCGAG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel2_soldier_whole brain


title: sample 135 [9_4_10]

description:
9_4_10_GCTGTAAG-GCTCTGTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 134 [9_2_9]

description:
9_2_9_GAGTGGTT-CGTTATGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel1_soldier_whole brain


title: HDL078, Lg, CD4, TEM


title: HDL078, Lg, CD8, TEM


title: sample 133 [7_4_12]

description:
7_4_12_AGCTTGAG-GTCTGATC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Comerio_forager_whole brain

value: Comerio


title: sample 132 [7_2_10]

description:
7_2_10_ACGACAGA-TAGTTGCG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 131 [4_4_10]

description:
4_4_10_TGACGCAT-CCTACTGA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Penuelas2_forager_whole brain


title: HDL078, LLN, CD8, TEM


title: HDL078, Jej, CD4, TEM


title: HDL078, LLN, CD4, TEM


title: HDL078, Jej, CD8, TEM


title: HDL078, Ile, CD8, TEM


title: HDL078, Ile, CD4, TEM


title: sample 130 [4_2_11]

description:
4_2_11_TCGCATTG-CTTGCTGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 128 [1_2_9]

description:
1_2_9_CGAAGAAC-GACTTAGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas1_soldier_whole brain


title: sample 127 [12_4_8]

description:
12_4_8_CCGTATCT-CGTACGAA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas2_forager_whole brain


title: HDL074, MLN, CD8, TEM

source_name: Gut Lymph Node


title: sample 124 [9_4_9]

description:
9_4_9_GTGGTGTT-CTTACAGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL074, MLN, CD4, TEM


title: HDL074, LLN, CD8, TEM

source_name: Lung Lymph Node


title: HDL078, MLN, CD4, TEM


title: sample 126 [11_4_11]

description:
11_4_11_AGTGTTGG-CGTCAATG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas1_forager_whole brain


title: sample 121 [4_4_9]

description:
4_4_9_TCAACTGG-CAGAATCG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL074, Lg, CD8, TEM

source_name: Lung


title: HDL074, LLN, CD4, TEM


title: HDL074, Lg, CD4, TEM


title: sample 120 [4_2_10]

description:
4_2_10_AGTTGGCT-ATGGTTGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 122 [6_2_8]

description:
6_2_8_CTGCACTT-GAACGCTT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 129 [2_4_10]

description:
2_4_10_CGTGATCA-TGCCATTC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 123 [7_4_11]

description:
7_4_11_TGCGAACT-TACGGTTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 119 [2_4_8]

description:
2_4_8_CAGGTTAG-GCTGGATT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 118 [2_2_8]

description:
2_2_8_ACACCAGT-GATGCACT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas2_soldier_whole brain


title: sample 117 [12_4_7]

description:
12_4_7_GTGTCTGA-CCGACTAT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 116 [12_2_8]

description:
12_2_8_AGTTACGG-TTGGTCTC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas2_soldier_whole brain


title: sample 125 [11_2_8]

description:
11_2_8_TGAACCTG-GAAGAGGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 115 [11_4_10]

description:
11_4_10_ATCTCGCT-GCCTTGTT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL073, MLN, CD8, TEM


title: HDL073, MLN, CD4, TEM


title: HDL074, Jej, CD4, TEM

source_name: Jejunum


title: HDL074, Ile, CD8, TEM

source_name: Ileum


title: HDL074, Ile, CD4, TEM


title: HDL073, LLN, CD4, TEM


title: HDL073, Lg, CD8, TEM


title: HDL073, LLN, CD8, TEM


title: sample 114 [11_2_7]

description:
11_2_7_GAAGGTTC-GATACTGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Patillas1_soldier_whole brain


title: sample 113 [9_4_8]

description:
9_4_8_TCCAATCG-GTCAGTTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel1_forager_whole brain


title: sample 110 [7_2_8]

description:
7_2_8_CAACGGAT-TAAGTGGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Comerio_soldier_whole brain


title: HDL074, Jej, CD8, TEM


title: HDL073, Jej, CD4, TEM


title: sample 109 [4_2_9]

description:
4_2_9_TGACTGAC-CAGTTCTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Penuelas2_soldier_whole brain


title: sample 108 [2_4_7]

description:
2_4_7_TAGAGCTC-AGGCTTCT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas2_forager_whole brain


title: sample 107 [2_2_7]

description:
2_2_7_TCCGTGAA-GAATCGTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL073, Ile, CD4, TEM


title: sample 106 [1_4_7]

description:
1_4_7_CTCGATAC-ACCAGCTT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Salinas1_forager_whole brain


title: HDL071, MLN, CD8, TEM


title: sample 105 [1_2_7]

description:
1_2_7_CTTACCTG-CTCATTGC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL071, MLN, CD4, TEM


title: sample 112 [9_2_7]

description:
9_2_7_CGGTCATA-GTAGAGCA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel1_soldier_whole brain


title: sample 103 [11_4_9]

description:
11_4_9_CCTCAGTT-GTATGCTG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 111 [7_4_10]

description:
7_4_10_TGGCTATC-ACGTGATG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Comerio_forager_whole brain


title: HDL073, Lg, CD4, TEM


title: HDL071, LLN, CD4, TEM


title: HDL071, Lg, CD8, TEM


title: HDL071, Lg, CD4, TEM


title: sample 100 [9_2_6]

description:
9_2_6_TGTACCGT-TCTCTAGG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 99 [7_4_7]

description:
7_4_7_CTCATCAG-CGCTAGTA_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL071, Jej, CD4, TEM


title: sample 98 [7_2_7]

description:
7_2_7_AGTCTCAC-AATGGACG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL071, Ile, CD8, TEM


title: HDL073, Jej, CD8, TEM


title: HDL071, Jej, CD8, TEM


title: sample 97 [6_2_6]

description:
6_2_6_GCCTATCA-CGACCATT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Ponce2_soldier_whole brain


title: HDL073, Ile, CD8, TEM


title: HDL071, Ile, CD4, TEM


title: sample 96 [4_4_7]

description:
4_4_7_CTAGCGCT-GTGTAGAC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: Penuelas2_forager_whole brain


title: HDL069, MLN, CD8, TEM

source_name: Gut Lymph Node


title: sample 104 [12_2_7]

description:
12_2_7_TCCTACCT-TGGAGAGT_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: sample 94 [2_4_6]

description:
2_4_6_CGTCTGCG-TTCACAAT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.


title: sample 95 [4_2_8]

description:
4_2_8_TCGATATC-ACACGAGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.


title: HDL069, LLN, CD8, TEM

source_name: Lung Lymph Node


title: HDL069, MLN, CD4, TEM


title: HDL071, LLN, CD8, TEM


title: sample 93 [2_2_6]

description:
2_2_6_TACTCATA-CCTGTGGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.


title: sample 92 [1_4_6]

description:
1_4_6_ACGCACCT-GGTGAAGG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.


title: sample 102 [10_4_7]

description:
10_4_7_TCACAGCA-AATGCCTC_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.

source_name: St.Isabel2_forager_whole brain


title: sample 101 [9_4_7]

description:
9_4_7_AAGTCGAG-ACATTGCG_L003
Read 1 aligns to the SENSE strand and Read 2 aligns to the ANTISENSE strand.


title: HDL069, LLN, CD4, TEM


title: HDL069, Lg, CD8, TEM

source_name: Lung


title: HDL069, Lg, CD4, TEM


title: HDL069, Jej, CD8, TEM


title: sample 91 [1_2_6]

description:
1_2_6_GTATGTTC-AACAGGAA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_soldier_whole brain


title: sample 89 [12_2_5]

description:
12_2_5_TATCGCAC-CTTAGTGT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_soldier_whole brain


title: sample 90 [12_4_5]

description:
12_4_5_CGCTATGT-TCCGACAC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas2_forager_whole brain


title: sample 88 [11_4_7]

description:
11_4_7_TCTGTTGG-TCGAATGG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_forager_whole brain


title: HDL069, Jej, CD4, TEM

source_name: Jejunum


title: HDL069, Ile, CD8, TEM

source_name: Ileum


title: HDL069, Ile, CD4, TEM


title: sample 87 [11_2_5]

description:
11_2_5_CTCACCAA-CTAGGCAA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Patillas1_soldier_whole brain


title: BY4742 eIF4E-AID strain, 1 hour DMSO, rnaseq, biol rep 1

city: Berkeley

first: Paige

middle: D

last: Diamond

state: CA

address: Barker Hall

department: MCB

institute: University of California - Berkeley

data_processing:
Ribosome profiling reads were first trimmed using Cutadapt to remove adapter sequences.
Reads from ribosome profiling were processed as detailed in (McGlincy and Ingolia 2017). Ribosome profiling and RNA-seq reads were aligned using STAR (Dobin et al. 2013) to the S288C reference genome R64.1.
Assembly: R64-sacCer3
Supplementary files format and content: Tab-delimited text file containing raw, unnormalized read counts for each sample.

organism: Saccharomyces cerevisiae

growth_protocol: Cells were treated with 500 µM indole-3-acetic acid (IAA) (Sigma-Aldrich #12886) or DMSO for either 1 or 8 hours and grown at 30C  to mid-log phase (typically 150 mL cultures at OD600 0.6 – 1.0) in YPD.

extract_protocol:
30ug of RNA for ribosome profiling was harvested by TRIzol extraction; 1ug of RNA for RNA-seq was harvested by phenol-chloroform extraction.
Ribosome profiling was conducted as detailed in (McGlincy and Ingolia 2017) for 1-hour eIF4E depletion samples and corresponding DMSO controls. Adjustments were made to (McGlincy and Ingolia 2017) for the 8-hour eIF4E depletion samples and their corresponding DMSO control samples as follows. Reverse transcription was performed with primer PD1131. rRNA depletion was achieved via subtractive hybridization was performed using complementary oligos PD1043-1046 as described in (Ingolia et al. 2012 p. 20). Circularization was performed with CircLigase I (Epicentre #CL4111K) instead of CircLigase II, following the manufacturer’s protocol recommendations.   Total RNA for RNA-sequencing was isolated from cell lysates using acid phenol extraction (Ares 2012). For 1-hour eIF4E depletion samples and corresponding DMSO controls, poly(A) enrichment was performed using DynabeadsTM oligo(dT)25 (Thermo Scientific #61002) according to the manufacturer instructions. For 8-hour eIF4E depletion samples and corresponding DMSO controls, rRNA depletion was performed using QIAseq FastSelect -rRNA yeast kit (Qiagen #334215) according to the manufacturer instructions. All libraries were generated with NEBNext Ultra II Directional RNA library prep kit (NEB #E7760).

tag: time point

tag: agent

value: DMSO


title: BY4742 eIF4E-AID strain, 1 hour IAA, ribo profiling, biol rep 2

value: 500microM IAA


title: sample 86 [10_4_5]

description:
10_4_5_GAACCGCG-TGACCTTA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.


title: HDL047, MLN, CD8, TEM


title: BY4742 eIF4E-AID strain, 1 hour DMSO, ribo profiling, biol rep 2


title: BY4742 eIF4E-AID strain, 1 hour DMSO, ribo profiling, biol rep 1


title: HDL047, MLN, CD4, TEM


title: HDL047, LLN, CD8, TEM


title: LY-364747 2

city: Shanghai

first: Xiuliang

last: Cui

state: Shanghai

address: Changhai Road 225

institute: Second Military Medicine University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the mouse-reference assembly mm10 using STAR (v2.4.2a).
We calculated differential expression P-values using DESeq2.
Assembly: mm10
Supplementary files format and content: gene_counts_mat.txt: Tab-delimited text file containing raw counts.

source_name: mouse embryonic fibroblast

growth_protocol: 0.5x10^6 P3-P5 MEFs were plated onto 6 cm cell culture dishes and cultured in DMEM supplemented with 10% FBS, 100 units/ml penicillin, and 100 μg/ml streptomycin (Gibco) at 37°C with 5% CO2 for 2 hours for attachment.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After 2 hours, molecule was added to the culture medium at dosages of 10 μM to treat the MEFs. The culture medium was changed every 3 days while the molecule was continuing treated the MEFs.

value: mouse embryonic fibroblast

value: mouse hepatic-like cells


title: CHIR-99021 2


title: CHIR-99021 1


title: BY4742 eIF4E-AID strain, 1 hour IAA, ribo profiling, biol rep 1


title: HDL047, LLN, CD4, TEM


title: BY4742 eIF4E-AID strain, 1 hour DMSO, rnaseq, biol rep 2


title: BY4742 eIF4E-AID strain, 1 hour IAA, rnaseq, biol rep 2


title: sample 84 [9_4_5]

description:
9_4_5_TCATCCTT-AGCGAGCT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_forager_whole brain


title: sample 83 [9_2_5]

description:
9_2_5_CTGCTTCC-GATAGATC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel1_soldier_whole brain


title: Carbidopa 2

value: Carbidopa


title: Carbidopa 1


title: LY-364747 1


title: sample 82 [7_4_6]

description:
7_4_6_GGTCACGA-GTATTATG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_forager_whole brain


title: HDL047, Lg, CD8, TEM

value: Lung

value: primary


title: BY4742 eIF4E-AID strain, 1 hour IAA, rnaseq, biol rep 1


title: MEF 2

value: WT

value: Control


title: sample 80 [6_4_5]

description:
6_4_5_GTGAATAT-TCTCATTC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_forager_whole brain


title: sample 85 [10_2_6]

description:
10_2_6_AGGTTATA-CAGTTCCG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: St.Isabel2_soldier_whole brain


title: MEF 1


title: HDL047, Lg, CD4, TEM

value: T cell


title: Mouse 6

city: Los Angeles

first: Olujimi

last: Ajijola

address: 100 Medical Plaza

department: Cardiovascular Center

institute: UCLA

description:
Mouse-1-3
10x Genomics
Chromium single cell

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1. scRNAseq analysis was done in Seurat (R) and Scanpy (python).
Assembly: mm10
Supplementary files format and content: neuron.dge.csv: Digital gene expression matrix.
Supplementary files format and content: neuron.metadata.csv: Cell type metadata containing the neuronal sub types.

source_name: Stellate ganglia

extract_protocol:
Bilateral stellate ganglia in C57BL/6 mice were identified, isolated, and collected in artificial cerebrospinal fluid (ACSF; Figure 1A). Next, 16 left and right stellate ganglia combined were incubated for an hour at 37°C in a digestion solution prepared with 500 μl TrypLE Express (ThermoFisher Scientific, Waltham, Massachusetts), 2000 μl Papain solution (Worthington Biochemical Corporation, Lakewood, New Jersey; 25 units/mL in ACSF), 100 μl Collagenase-Dispase (Millipore Sigma, Burlington, Massachusetts; 20 mg/mL in ACSF) and 270 μl DNase I (Worthington Biochemical Corporation, Lakewood, New Jersey; 200 units/mL in ACSF). After an hour, the cells were carefully triturated with fire-blown Pasteur pipettes every thirty minutes. Following the second trituration, 100 μl fresh Collagenase-Dispase (20 mg/mL in ACSF) was added to the solution and cells were incubated for another hour at 37°C, triturating every thirty minutes. Next, the suspension was filtered through a 40 um filter (ThermoFisher Scientific, Waltham, Massachusetts) and ACSF was added to halt enzymatic digestion. The suspension was spun down at 100g for four minutes at room temperature, and the pellet collected and resuspended in 500 μL ACSF and 500 μL supplemented Neurobasal-A medium (ThermoFisher Scientific, Waltham, Massachusetts; 250 μL B27, 250 μL Penicillin-streptomycin, 31.3 μL L-Glutamine). The cell suspension was transferred onto a density gradient (Millipore Sigma, Burlington, Massachusetts) and centrifuged at 100g for 10 minutes at room temperature. The supernatant was carefully removed until the solution was concentrated to 500 μL. Single cell RNA sequencing used microfluidic capture-based encapsulation, barcoding, and library preparation (10x Genomics Chromium scRNAseq system (10x Genomics, Pleasanton, California)). Cells were loaded into a Chromium Chip B along with partitioning oil, reverse transcription reagents, and a mix of hydrogel beads containing 3,500,000 unique 10X Barcodes. Paired end sequencing was performed on a Novaseq S4 system, using the v3 Illumina platform. Coverage depth was 20K per cell, and the read length was 2x50. Analysis including demultiplexing, reference-based mapping (GRCm38.98), and UMI identification, was performed according to the 10X Cell Ranger pipeline. We modified the reference by adding in the sequences for GFP to detect their transcripts in cells.
Chromium Single Cell Gene Expression Protocol V3 enables library preparation of hundreds to thousands of individual cells (500-10000 cells per sample) for 3’ digital gene expression profiling analysis simultaneously. Cells are loaded into a Chromium Chip B along with partitioning oil, reverse transcription reagents, and a mix of hydrogel beads containing 3,500,000 unique 10X Barcodes. After a 8 min run on the 10X Genomics Chromium Controller an emulsion is formed as the cells and reagents are passed through the microfluidic channels of the Chip. A fraction (1-10%) of the droplets within the emulsion will include a single cell in addition to a gel bead which releases its contents to deliver oligo(dT) primers containing a unique 10X Cell Barcode that is used to index the 3’ end of cDNA molecules during reverse transcription. Libraries are generated and sequenced starting from cDNA and 10X Barcodes enable the assignment of transcripts to individual cells during Illumina sequence analysis.

value: Neuron

value: Stellate ganglia

tag: strain

tag: age

value: 8-10 weeks


title: Mouse 8

description:
Mouse-1-7
10x Genomics
Chromium single cell


title: sample 79 [6_2_5]

description:
6_2_5_ACAGGCGC-CTCTGCCT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Ponce2_soldier_whole brain

tag: caste

value: worker

tag: group

value: soldier

value: whole brain


title: HDL047, Jej, CD8, TEM

value: Jejunum


title: HDL047, Jej, CD4, TEM


title: Mouse 4

description:
Mouse-2-4
10x Genomics
Chromium single cell


title: Mouse 5

description:
Mouse-2-6
10x Genomics
Chromium single cell


title: Mouse 3

description:
Mouse-2-3
10x Genomics
Chromium single cell


title: Mouse 1

description:
Mouse-2-1
10x Genomics
Chromium single cell


title: sample 77 [4_2_7]

description:
4_2_7_TGCGAGAC-CATTGTTG_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_soldier_whole brain

tag: colony location

tag: colony latitude


title: sample 78 [4_4_6]

description:
4_4_6_CATAGAGT-TGCCACCA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Penuelas2_forager_whole brain

value: forager

tag: colony longitude

tag: tissue


title: HDL047, Ile, CD8, TEM

value: Ileum

tag: cell line


title: sample 76 [2_4_5]

description:
2_4_5_GACGTCTT-GGTTCACC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_forager_whole brain


title: HDL046, LLN, CD8, TEM

source_name: Lung Lymph Node

value: Lung Lymph Node


title: HDL047, Ile, CD4, TEM


title: HDL046, LLN, CD4, TEM


title: sample 81 [7_2_5]

description:
7_2_5_AACTGTAG-ACGCCGCA_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Comerio_soldier_whole brain

value: Comerio


title: Mouse 7

description:
Mouse-1-6
10x Genomics
Chromium single cell


title: E16.5 forebrain, Littermate pair 1, Zfp661 KO

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

description: 10X genomics

data_processing:
Raw fastq reads were mapped onto the mouse genome (mm10), and gene-cell matrices were generated using the count function in Cell Ranger (v7.0.0). High-quality cells were selected based on the following criteria: cells with 2000-40000 Unique Molecular Identifiers (UMIs) and 1000-6500 genes detected, and with the percentage of UMIs from mitochondrial genes no greater than 10%. The gene-cell matrices were updated by selecting high-quality cells and excluding mitochondrial genes using the reanalysis function in Cell Ranger.
Cell types were assigned by projection onto a reference map for E16.5 mouse forebrains (La Manno et al. 2021) using Seurat (v4.3.0) with the first 30 dimensions of PCA selected.
Assembly: mm10
Supplementary files format and content: tar of 10X gene-cell matrices (.tar), tab-delimited text files for cell type annotation of individual cells (.txt).

source_name: forebrain

extract_protocol:
Embryonic forebrains were isolated and dissociated into single-cell suspension using the Papain Dissociation System (Worthington LK003150) by incubating at 37°C for 45 min. The cell suspension was passed through cellTrics Cell Strainers (20 μm) to remove cell debris and clumps. The suspension was then subjected to a discontinuous density gradient centrifugation using the Papain Dissociation System at 70 g for 6 min to further remove remaining debris and membrane fragments. The cells were collected, resuspended in 0.04% BSA/PBS solution, and washed twice using 0.04% BSA/PBS solution.
The samples were barcoded using the 10x Chromium Controller by targeting for 2000 recovered cells per sample. Single-cell 5’ RNA-seq libraries were constructed using Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (10x, PN-1000265) following the manufacturer’s protocol (10x, CG000331 Rev D). The resulting libraries were sequenced using NovaSeq 6000 (sequencing configuration: read 1: 28 bp; i7 index: 10 bp; i5 index: 10 bp; read 2: 150 bp).

value: mouse embryonic brain

value: forebrain

value: mixture of C57BL/6J and B6D2F1/J

value: Zfp661 KO

tag: developmental stage


title: E16.5 forebrain, Littermate pair 2, WT

description: 10X genomics

value: WT


title: E16.5 forebrain, Littermate pair 2, Zfp661 KO

description: 10X genomics


title: sample 74 [1_4_5]

description:
1_4_5_TGGCCGGT-TAGAGCGC_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas1_forager_whole brain


title: sample 75 [2_2_5]

description:
2_2_5_AGTACTCC-AACCTGTT_L003
Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

source_name: Salinas2_soldier_whole brain


title: HDL046, Lg, CD8, TEM

source_name: Lung

value: Lung

value: primary

value: T cell


title: E16.5 forebrain, Littermate pair 1, WT

description: 10X genomics


title: HiC, ZFP661OE replicate 2, library 2

description: Arima-HiC

data_processing:
Mouse genome (mm10) fragments were generated using the “digest_genome” tool in HiC-Pro utilities (Servant, Varoquaux et al. 2015) with restriction motifs “GATC” and “G^ANTC”. Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. HiC-Pro pipelines (v2.11.4) were then used with above genome fragments and the parameter “LIGATION_SITE = GATCGATC, GANTGATC, GANTANTC, GATCANTC” to generate valid interaction pairs and contact maps.
Pooled valid interaction pairs in EV control were used as input, and chromatin loops were detected from both 5 kb-resolution and 10 kb-resolution Hi-C maps using HiCCUPS in Juicer (v1.6) with the following parameters: “-r 5000,10000 -k KR -f .1,.1 -p 4,2 -i 7,5 -t 0.02,1.5,1.75,2 -d 20000,20000 --ignore-sparsity”. The loop anchors from 5 kb maps (where the length of anchors equaled 5 kb) were extended to 10 kb by extending 2.5 kb on each side.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for valid interaction pairs (.allValidPairs.gz), hic file (.hic) and bedpe file for hiccups loops (.bedpe).

source_name: R1 mESCs

growth_protocol: Cells were cultured in a 37 °C humidified incubator with 5% CO2.

extract_protocol:
Cells were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min.
Cells with approximately 4 μg of DNA were used as input to generate proximally ligated DNA using the Arima-HiC kit (Arima, A510008) according to the manufacturer’s protocol (Arima, A160134 v01). Briefly, crosslinked cells were digested using the Arima restriction enzyme cocktail, the 5’ overhangs were filled in and labeled with a biotinylated nucleotide, and the spatially proximal ends were ligated. The proximally ligated DNAs were purified and sonicated using the Covaris ME220 (8 microTube-130 AFA fiber strip V2: duration 42s, peak power 70w, duty factor 20%, cycle per burst 1000#). Then, size selection was performed on the resulting DNA Fragments (for size ranging from 200 to 600 bp). 2 μg of the resulting DNA fragments were used as input, and fragments labelled with biotin were bound to beads to construct Hi-C libraries using the KAPA HyperPrep Kit (Roche, KK8502) following the protocol provided by Arima (A160139 v00).

value: R1 mESCs

value: mouse embryonic stem cells

value: ZFP661-3HA OE


title: HiC, ZFP661OE replicate 2, library 1

description: Arima-HiC


title: HiC, ZFP661OE replicate 1, library 1

description: Arima-HiC